Journal articles on the topic 'Substrats interactifs'
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1
Chen, Xiaobo, Jiayue Chen, Bing Yan, Wei Zhang, Luke W. Guddat, Xiang Liu, and Zihe Rao. "Structural basis for the broad substrate specificity of two acyl-CoA dehydrogenases FadE5 from mycobacteria." Proceedings of the National Academy of Sciences 117, no. 28 (June 29, 2020): 16324–32. http://dx.doi.org/10.1073/pnas.2002835117.
Abstract:
FadE, an acyl-CoA dehydrogenase, introduces unsaturation to carbon chains in lipid metabolism pathways. Here, we report that FadE5 fromMycobacterium tuberculosis(MtbFadE5) andMycobacterium smegmatis(MsFadE5) play roles in drug resistance and exhibit broad specificity for linear acyl-CoA substrates but have a preference for those with long carbon chains. Here, the structures ofMsFadE5 andMtbFadE5, in the presence and absence of substrates, have been determined. These reveal the molecular basis for the broad substrate specificity of these enzymes. FadE5 interacts with the CoA region of the substrate through a large number of hydrogen bonds and an unusual π–π stacking interaction, allowing these enzymes to accept both short- and long-chain substrates. Residues in the substrate binding cavity reorient their side chains to accommodate substrates of various lengths. Longer carbon-chain substrates make more numerous hydrophobic interactions with the enzyme compared with the shorter-chain substrates, resulting in a preference for this type of substrate.
2
Kim, Ikjin, Kaixia Mi, and Hai Rao. "Multiple Interactions of Rad23 Suggest a Mechanism for Ubiquitylated Substrate Delivery Important in Proteolysis." Molecular Biology of the Cell 15, no. 7 (July 2004): 3357–65. http://dx.doi.org/10.1091/mbc.e03-11-0835.
Abstract:
The mechanism underlying the delivery of ubiquitylated substrates to the proteasome is poorly understood. Rad23 is a putative adaptor molecule for this process because it interacts with ubiquitin chains through its ubiquitin-associated motifs (UBA) and with the proteasome through a ubiquitin-like element (UBL). Here, we demonstrate that the UBL motif of Rad23 also binds Ufd2, an E4 enzyme essential for ubiquitin chain assembly onto its substrates. Mutations in the UBL of Rad23 alter its interactions with Ufd2 and the proteasome, and impair its function in the UFD proteolytic pathway. Furthermore, Ufd2 and the proteasome subunit Rpn1 compete for the binding of Rad23, suggesting that Rad23 forms separate complexes with them. Importantly, we also find that the ability of other UBL/UBA proteins to associate with Ufd2 correlates with their differential involvement in the UFD pathway, suggesting that UBL-mediated interactions may contribute to the substrate specificity of these adaptors. We propose that the UBL motif, a protein-protein interaction module, may be used to facilitate coupling between substrate ubiquitylation and delivery, and to ensure the orderly handoff of the substrate from the ubiquitylation machinery to the proteasome.
3
Lim, Jia Jia, Youngjin Lee, Tue Tu Ly, Jung Youn Kang, Jung-Gyu Lee, Jun Yop An, Hyung-Seop Youn, et al. "Structural insights into the interaction of p97 N-terminus domain and VBM in rhomboid protease, RHBDL4." Biochemical Journal 473, no. 18 (September 12, 2016): 2863–80. http://dx.doi.org/10.1042/bcj20160237.
Abstract:
RHBDL4 is an active rhomboid that specifically recognizes and cleaves atypical, positively charged transmembrane endoplasmic reticulum-associated degradation (ERAD) substrates. Interaction of valosin-containing protein (p97/VCP) and RHBDL4 is crucial to retrotranslocate polyubiquitinated substrates for ERAD pathway. Here, we report the first complex structure of VCP-binding motif (VBM) with p97 N-terminal domain (p97N) at 1.88 Å resolution. Consistent with p97 adaptor proteins including p47-ubiquitin regulatory X (UBX), gp78-VCP-interacting motif (VIM), OTU1-UBX-like element, and FAF1-UBX, RHBDL4 VBM also binds at the interface between the two lobes of p97N. Notably, the RF residues in VBM are involved in the interaction with p97N, showing a similar interaction pattern with that of FPR signature motif in the UBX domain, although the directionality is opposite. Comparison of VBM interaction with VIM of gp78, another α-helical motif that interacts with p97N, revealed that the helix direction is inversed. Nevertheless, the conserved arginine residues in both motifs participate in the majority of the interface via extensive hydrogen bonds and ionic interactions with p97N. We identified novel VBM-binding mode to p97N that involves a combination of two types of p97–cofactor specificities observed in the UBX and VIM interactions. This highlights the induced fit model of p97N interdomain cleft upon cofactor binding to form stable p97–cofactor complexes. Our mutational and biochemical analyses in defining the specific interaction between VBM and p97N have elucidated the importance of the highly conserved VBM, applicable to other VBM-containing proteins. We also showed that RHBDL4, ubiquitins, and p97 co-operate for efficient substrate dislocation.
4
Cavitt, T. Brian, and Niyati Pathak. "Modeling Bacterial Attachment Mechanisms on Superhydrophobic and Superhydrophilic Substrates." Pharmaceuticals 14, no. 10 (September 26, 2021): 977. http://dx.doi.org/10.3390/ph14100977.
Abstract:
Superhydrophilic and superhydrophobic substrates are widely known to inhibit the attachment of a variety of motile and/or nonmotile bacteria. However, the thermodynamics of attachment are complex. Surface energy measurements alone do not address the complexities of colloidal (i.e., bacterial) dispersions but do affirm that polar (acid-base) interactions (ΔGAB) are often more significant than nonpolar (Lifshitz-van der Waals) interactions (ΔGLW). Classical DLVO theory alone also fails to address all colloidal interactions present in bacterial dispersions such as ΔGAB and Born repulsion (ΔGBorn) yet accounts for the significant electrostatic double layer repulsion (ΔGEL). We purpose to model both motile (e.g., P. aeruginosa and E. coli) and nonmotile (e.g., S. aureus and S. epidermidis) bacterial attachment to both superhydrophilic and superhydrophobic substrates via surface energies and extended DLVO theory corrected for bacterial geometries. We used extended DLVO theory and surface energy analyses to characterize the following Gibbs interaction energies for the bacteria with superhydrophobic and superhydrophilic substrates: ΔGLW, ΔGAB, ΔGEL, and ΔGBorn. The combination of the aforementioned interactions yields the total Gibbs interaction energy (ΔGtot) of each bacterium with each substrate. Analysis of the interaction energies with respect to the distance of approach yielded an equilibrium distance (deq) that seems to be independent of both bacterial species and substrate. Utilizing both deq and Gibbs interaction energies, substrates could be designed to inhibit bacterial attachment.
5
Tsang, Yik Pui, Antonio Jesús López Quiñones, Letícia Salvador Vieira, and Joanne Wang. "Interaction of ALK Inhibitors with Polyspecific Organic Cation Transporters and the Impact of Substrate-Dependent Inhibition on the Prediction of Drug–Drug Interactions." Pharmaceutics 15, no. 9 (September 13, 2023): 2312. http://dx.doi.org/10.3390/pharmaceutics15092312.
Abstract:
Small molecules targeting aberrant anaplastic lymphoma kinase (ALK) are active against ALK-positive non-small-cell lung cancers and neuroblastoma. Several targeted tyrosine kinase inhibitors (TKIs) have been shown to interact with polyspecific organic cation transporters (pOCTs), raising concerns about potential drug–drug interactions (DDIs). The purpose of this study was to assess the interaction of ALK inhibitors with pOCTs and the impact of substrate-dependent inhibition on the prediction of DDIs. Inhibition assays were conducted in transporter-overexpressing cells using meta-iodobenzylguanidine (mIBG), metformin, or 1-methyl-4-phenylpyridinium (MPP+) as the substrate. The half-maximal inhibitory concentrations (IC50) of brigatinib and crizotinib for the substrates tested were used to predict their potential for in vivo transporter mediated DDIs. Here, we show that the inhibition potencies of brigatinib and crizotinib on pOCTs are isoform- and substrate-dependent. Human OCT3 (hOCT3) and multidrug and toxin extrusion protein 1 (hMATE1) were highly sensitive to inhibition by brigatinib and crizotinib for all three tested substrates. Apart from hMATE1, substrate-dependent inhibition was observed for all other transporters with varying degrees of dependency; hOCT1 inhibition showed the greatest substrate dependency, with differences in IC50 values of up to 22-fold across the tested substrates, followed by hOCT2 and hMATE2-K, with differences in IC50 values of up to 16- and 12-fold, respectively. Conversely, hOCT3 inhibition only showed a moderate substrate dependency (IC50 variance < 4.8). Among the substrates used, metformin was consistently shown to be the most sensitive substrate, followed by mIBG and MPP+. Pre-incubation of ALK inhibitors had little impact on their potencies toward hOCT2 and hMATE1. Our results underscore the complexity of the interactions between substrates and the inhibitors of pOCTs and have important implications for the clinical use of ALK inhibitors and their DDI predictions.
6
Rittmann, B. E. "Microbiological Detoxification of Hazardous Organic Contaminants: The Crucial Role of Substrate Interactions." Water Science and Technology 25, no. 11 (June 1, 1992): 403–10. http://dx.doi.org/10.2166/wst.1992.0319.
Abstract:
Microbiological detoxification of hazardous organic pollutants is highly promising, but its reliable implementation requires a sophisticated understanding of several different substrate types and how they interact. This paper carefully defines the substrate types and explains how their interactions affect the bacteria's electron and energy flows, information flow, and degradative activity. For example, primary substrates, which are essential for growth and maintenance of the bacteria, also interact with degradation of specific hazardous pollutants by being inducers, inhibitors, and direct or indirect cosubstrates. The target contaminants, which often are secondary substrates, also have the interactive roles of self-inhibitor, inhibitor of primary-substrate utilization, inducer, and a part of an aggregate primary substrate.
7
Roche, Sandra, Kasper Pedersen, Grainne Dunne, Denis Collins, Aoife Devery, John Crown, Martin Clynes, and Robert O'Connor. "Pharmacological interactions of TKIs with the P-gp drug transport protein." Journal of Clinical Oncology 30, no. 15_suppl (May 20, 2012): 2536. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.2536.
Abstract:
2536 Background: Tyrosine Kinase Inhibitors (TKIs) can interact with drug transport proteins. P-gp is a transporter with two important roles in cancer drug therapy. If overexpressed in tumour cells it can cause drug resistance. However, P-gp, expressed in tissues as part of normal drug clearance mechanisms, is also involved in termination of drug action. Hence, TKI-mediated interactions with P-gp have significant therapeutic consequences. Methods: P-gp over-expressing cancer cell lines were used to determine the inhibitor or substrate status of tyrosine kinase inhibitors (erlotinib, gefitinib, lapatinib, dasatinb, neratinib, afatinib and pazopanib). Cell proliferation assays in combination with a potent P-gp inhibitor, or P-gp substrate were also employed. Findings were augmented using LC-MS-based quantitation of cellular levels of target drugs. Results: We summarise our findings of four distinct interactions with P-gp among various TKIs. Some agents have little interaction at conventional doses; others can act as P-gp inhibitors without being substrates; substrates without being inhibitors or substrates which also prevent the actions of the transporter.Eachof the investigated TKIs has a distinct relationship with P-gp. As examples, lapatinib is an inhibitor but not a substrate, dasatinib is a substrate but not an inhibitor, while pazopanib has little interaction with P-gp. Other agents also have an effect on or are affected by P-gp to varying amounts with some of these interactions likely to be suprapharmacological. Conclusions: P-gp protein has important roles both in resistance and drug toxicology, hence, a clear understanding of the interaction of emerging drugs with this transporter is vital. Agents which are inhibitors of P-gp may have applications in drug resistance circumvention but may also greatly exacerbate the toxicity of concurrently administered P-gp substrate cytotoxics; conversely the activity of P-gp substrate TKIs may be reduced by tumour overexpression of the transporter. Hence in vitro screening of TKI-transporter interactions may identify putative TKI resistance mechanisms, help guide the development of combination schedule trials and/or reducing unwanted treatment side effects.
8
Courtade, Gaston, Reinhard Wimmer, Åsmund K. Røhr, Marita Preims, Alfons K. G. Felice, Maria Dimarogona, Gustav Vaaje-Kolstad, et al. "Interactions of a fungal lytic polysaccharide monooxygenase with β-glucan substrates and cellobiose dehydrogenase." Proceedings of the National Academy of Sciences 113, no. 21 (May 5, 2016): 5922–27. http://dx.doi.org/10.1073/pnas.1602566113.
Abstract:
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that catalyze oxidative cleavage of glycosidic bonds using molecular oxygen and an external electron donor. We have used NMR and isothermal titration calorimetry (ITC) to study the interactions of a broad-specificity fungal LPMO, NcLPMO9C, with various substrates and with cellobiose dehydrogenase (CDH), a known natural supplier of electrons. The NMR studies revealed interactions with cellohexaose that center around the copper site. NMR studies with xyloglucans, i.e., branched β-glucans, showed an extended binding surface compared with cellohexaose, whereas ITC experiments showed slightly higher affinity and a different thermodynamic signature of binding. The ITC data also showed that although the copper ion alone hardly contributes to affinity, substrate binding is enhanced for metal-loaded enzymes that are supplied with cyanide, a mimic of O2−. Studies with CDH and its isolated heme b cytochrome domain unambiguously showed that the cytochrome domain of CDH interacts with the copper site of the LPMO and that substrate binding precludes interaction with CDH. Apart from providing insights into enzyme–substrate interactions in LPMOs, the present observations shed new light on possible mechanisms for electron supply during LPMO action.
9
Jabaiah, Abeer M., Jennifer A. Getz, Witold A. Witkowski, Jeanne A. Hardy, and Patrick S. Daugherty. "Identifi cation of protease exosite-interacting peptides that enhance substrate cleavage kinetics." Biological Chemistry 393, no. 9 (September 1, 2012): 933–41. http://dx.doi.org/10.1515/hsz-2012-0162.
Abstract:
Abstract Many peptidases are thought to require non-active site interaction surfaces, or exosites, to recognize and cleave physiological substrates with high specifi city and catalytic effi ciency. However, the existence and function of protease exosites remain obscure owing to a lack of effective methods to identify and characterize exosite-interacting substrates. To address this need, we modifi ed the cellular libraries of peptide substrates (CLiPS) methodology to enable the discovery of exosite-interacting peptide ligands. Invariant cleavage motifs recognized by the active sites of thrombin and caspase-7 were displayed on the outer surface of bacteria adjacent to a candidate exosite-interacting peptide. Exosite peptide libraries were then screened for ligands that accelerate cleavage of the active site recognition motif using two-color fl ow cytometry. Exosite CLiPS (eCLiPS) identifi ed exosite-binding peptides for thrombin that were highly similar to a critical exosite interaction motif in the thrombin substrate, proteaseactivated receptor 1. Protease activity probes incorporating exosite-binding peptides were cleaved ten-fold faster than substrates without exosite ligands, increasing their sensitivity to thrombin activity in vitro. For comparison, screening with caspase-7 yielded peptides that modestly enhanced (two-fold) substrate cleavage rates. The eCLiPS method provides a new tool to profi le the ligand specifi city of protease exosites and to develop improved substrates.
10
FAGHIHI, SHAHAB, HOJATOLLAH VALI, and MARYAM TABRIZIAN. "EFFECTS OF CRYSTAL SIZE AND ORIENTATION OF SUBSTRATES ON CELL ADHESION: IMPLICATION FOR MEDICAL IMPLANTS." International Journal of Modern Physics B 22, no. 18n19 (July 30, 2008): 3069–81. http://dx.doi.org/10.1142/s0217979208047936.
Abstract:
The aim of this study is to investigate the effect of atomic structure of polycrystalline materials on cell-substrate interactions. Samples are prepared from rods and sheets of Ti -6 Al -4 V substrates with predominately two distinct crystallographic orientations as well as nano-structured and annealed titanium fabricated through high-pressure torsion and heat treatment processes. The degree of preosteoblast attachment and rate of growth, which are regulated through the activity and interaction of proteins present in the extracellular matrix, are notably increased on the nano-structured titanium and substrate having predominant [Formula: see text] orientation. The improved cell activity is attributed to the nano-structured feature of these substrates consisting of ultra-fine crystals (< 50 nm) and specific atomic order of [Formula: see text] substrate which provide higher degree of surface wettability. These findings demonstrate the advantages of nano-structured titanium over the conventional and coated titanium implants, as both mechanical properties and cellular response are improved. Furthermore, crystal orientation of the substrates can influence cell responses and, therefore, substrate engineering can be used to improve and control cell-substrate interactions.
11
Jaya, Nomalie, Victor Garcia, and Elizabeth Vierling. "Substrate binding site flexibility of the small heat shock protein molecular chaperones." Proceedings of the National Academy of Sciences 106, no. 37 (August 26, 2009): 15604–9. http://dx.doi.org/10.1073/pnas.0902177106.
Abstract:
Small heat shock proteins (sHSPs) serve as a first line of defense against stress-induced cell damage by binding and maintaining denaturing proteins in a folding-competent state. In contrast to the well-defined substrate binding regions of ATP-dependent chaperones, interactions between sHSPs and substrates are poorly understood. Defining substrate-binding sites of sHSPs is key to understanding their cellular functions and to harnessing their aggregation-prevention properties for controlling damage due to stress and disease. We incorporated a photoactivatable cross-linker at 32 positions throughout a well-characterized sHSP, dodecameric PsHsp18.1 from pea, and identified direct interaction sites between sHSPs and substrates. Model substrates firefly luciferase and malate dehydrogenase form strong contacts with multiple residues in the sHSP N-terminal arm, demonstrating the importance of this flexible and evolutionary variable region in substrate binding. Within the conserved α-crystallin domain both substrates also bind the β-strand (β7) where mutations in human homologs result in inherited disease. Notably, these binding sites are poorly accessible in the sHSP atomic structure, consistent with major structural rearrangements being required for substrate binding. Detectable differences in the pattern of cross-linking intensity of the two substrates and the fact that substrates make contacts throughout the sHSP indicate that there is not a discrete substrate binding surface. Our results support a model in which the intrinsically-disordered N-terminal arm can present diverse geometries of interaction sites, which is likely critical for the ability of sHSPs to protect efficiently many different substrates.
12
Bolduc, David M., Daniel R. Montagna, Yongli Gu, Dennis J. Selkoe, and Michael S. Wolfe. "Nicastrin functions to sterically hinder γ-secretase–substrate interactions driven by substrate transmembrane domain." Proceedings of the National Academy of Sciences 113, no. 5 (December 22, 2015): E509—E518. http://dx.doi.org/10.1073/pnas.1512952113.
Abstract:
γ-Secretase is an intramembrane-cleaving protease that processes many type-I integral membrane proteins within the lipid bilayer, an event preceded by shedding of most of the substrate’s ectodomain by α- or β-secretases. The mechanism by which γ-secretase selectively recognizes and recruits ectodomain-shed substrates for catalysis remains unclear. In contrast to previous reports that substrate is actively recruited for catalysis when its remaining short ectodomain interacts with the nicastrin component of γ-secretase, we find that substrate ectodomain is entirely dispensable for cleavage. Instead, γ-secretase–substrate binding is driven by an apparent tight-binding interaction derived from substrate transmembrane domain, a mechanism in stark contrast to rhomboid—another family of intramembrane-cleaving proteases. Disruption of the nicastrin fold allows for more efficient cleavage of substrates retaining longer ectodomains, indicating that nicastrin actively excludes larger substrates through steric hindrance, thus serving as a molecular gatekeeper for substrate binding and catalysis.
13
Hadjicharalambous, Andreas, Alex J. Whale, Geylani Can, J. Mark Skehel, Jonathan M. Houseley, and Philip Zegerman. "Checkpoint kinase interaction with DNA polymerase alpha regulates replication progression during stress." Wellcome Open Research 8 (July 26, 2023): 327. http://dx.doi.org/10.12688/wellcomeopenres.19617.1.
Abstract:
Background: In eukaryotes, replication stress activates a checkpoint response, which facilitates genome duplication by stabilising the replisome. How the checkpoint kinases regulate the replisome remains poorly understood. The aim of this study is to identify new targets of checkpoint kinases within the replisome during replication stress. Methods: Here we use an unbiased biotin proximity-ligation approach in Saccharomyces cerevisiae to identify new interactors and substrates of the checkpoint kinase Rad53 in vivo. Results: From this screen, we identified the replication initiation factor Sld7 as a Rad53 substrate, and Pol1, the catalytic subunit of polymerase a, as a Rad53-interactor. We showed that CDK phosphorylation of Pol1 mediates its interaction with Rad53. Combined with other interactions between Rad53 and the replisome, this Rad53-Pol1 interaction is important for viability and replisome progression during replication stress. Conclusions: Together, we explain how the interactions of Rad53 with the replisome are controlled by both replication stress and the cell cycle, and why these interactions might be important for coordinating the stabilisation of both the leading and lagging strand machineries.
14
Zhong, Xiaoyan, Yuxian Shen, Petek Ballar, Andria Apostolou, Reuven Agami, and Shengyun Fang. "AAA ATPase p97/Valosin-containing Protein Interacts with gp78, a Ubiquitin Ligase for Endoplasmic Reticulum-associated Degradation." Journal of Biological Chemistry 279, no. 44 (August 24, 2004): 45676–84. http://dx.doi.org/10.1074/jbc.m409034200.
Abstract:
Endoplasmic reticulum-associated degradation (ERAD) is a protein quality control mechanism that eliminates unwanted proteins from the endoplasmic reticulum (ER) through a ubiquitin-dependent proteasomal degradation pathway. gp78 is a previously described ER membrane-anchored ubiquitin ligase (E3) involved in ubiquitination of ER proteins. AAA ATPase (ATPase associated with various cellular activities) p97/valosin-containing protein (VCP) subsequently dislodges the ubiquitinated proteins from the ER and chaperones them to the cytosol, where they undergo proteasomal degradation. We now report that gp78 physically interacts with p97/VCP and enhances p97/VCP-polyubiquitin association. The enhanced association correlates with decreases in ER stress-induced accumulation of polyubiquitinated proteins. This effect is abolished when the p97/VCP-interacting domain of gp78 is removed. Further, using ERAD substrate CD3δ, gp78 consistently enhances p97/VCP-CD3δ binding and facilitates CD3δ degradation. Moreover, inhibition of endogenous gp78 expression by RNA interference markedly increases the levels of total polyubiquitinated proteins, including CD3δ, and abrogates VCP-CD3δ interactions. The gp78 mutant with deletion of its p97/VCP-interacting domain fails to increase CD3δ degradation and leads to accumulation of polyubiquitinated CD3δ, suggesting a failure in delivering ubiquitinated CD3δ for degradation. These data suggest that gp78-p97/VCP interaction may represent one way of coupling ubiquitination with retrotranslocation and degradation of ERAD substrates.
15
Fritz, Jutta, Alexander Strehblow, Andreas Taschner, Sandy Schopoff, Pawel Pasierbek, and Michael F. Jantsch. "RNA-Regulated Interaction of Transportin-1 and Exportin-5 with the Double-Stranded RNA-Binding Domain Regulates Nucleocytoplasmic Shuttling of ADAR1." Molecular and Cellular Biology 29, no. 6 (January 5, 2009): 1487–97. http://dx.doi.org/10.1128/mcb.01519-08.
Abstract:
ABSTRACT Double-stranded RNA (dsRNA)-binding proteins interact with substrate RNAs via dsRNA-binding domains (dsRBDs). Several proteins harboring these domains exhibit nucleocytoplasmic shuttling and possibly remain associated with their substrate RNAs bound in the nucleus during nuclear export. In the human RNA-editing enzyme ADAR1-c, the nuclear localization signal overlaps the third dsRBD, while the corresponding import factor is unknown. The protein also lacks a clear nuclear export signal but shuttles between the nucleus and the cytoplasm. Here we identify transportin-1 as the import receptor for ADAR1. Interestingly, dsRNA binding interferes with transportin-1 binding. At the same time, each of the dsRBDs in ADAR1 interacts with the export factor exportin-5. RNA binding stimulates this interaction but is not a prerequisite. Thus, our data demonstrate a role for some dsRBDs as RNA-sensitive nucleocytoplasmic transport signals. dsRBD3 in ADAR1 can mediate nuclear import, while interaction of all dsRBDs might control nuclear export. This finding may have implications for other proteins containing dsRBDs and suggests a selective nuclear export mechanism for substrates interacting with these proteins.
16
Kolo, K., and Ph Claeys. "In vitro formation of Ca-oxalates and the mineral glushinskite by fungal interaction with carbonate substrates and seawater." Biogeosciences Discussions 2, no. 2 (April 15, 2005): 451–97. http://dx.doi.org/10.5194/bgd-2-451-2005.
Abstract:
Abstract. This study investigates the in vitro formation of Ca-oxalates and glushinskite through fungal interaction with carbonate substrates and seawater. In the first experiment, thin-sections prepared from dolomitic rock samples of Terwagne Formation (Carboniferous, Viséan, northern France) served as substrates. The thin sections placed in Petri dishes were exposed to fungi grown from naturally existing airborne spores. In the second experiment, fungal growth and mineral formation was monitored using only standard seawater (SSW) as substrate. Fungal growth media consisted of a high protein/carbohydrates and sugar diet with demineralised water for irrigation. Fungal growth process reached completion under uncontrolled laboratory conditions. The fungal interaction and attack on the carbonate substrates resulted in the formation of Ca-oxalates (weddellite CaC2O4·2(H2O), whewellite (CaC2O4·(H2O)) and glushinskite MgC2O4·2(H2O) associated with the destruction of the original substrate and its replacement by the new minerals. The seawater substrate resulted also in the formation of glushinskite and Ca-oxalates. Both of Ca and Mg were mobilized from the experimental substrates by fungi. The newly formed minerals and textural changes caused by fungal attack on the carbonate substrate were investigated using light and scanning electron microscopy (SEM-EDX), x-ray diffraction (XRD) and Raman spectroscopy. The results document the role of microorganisms in biomineralization, neo-mineral formation and sediment diagenesis. They also reveal the capacity of living fungi to interact with liquid substrates and precipitate new minerals. This work is the first report on the in vitro formation of the mineral glushinskite through fungal-carbonate and sea water substrates interactions processes.
17
Zhang, Yuan-Wei, Sotiria Tavoulari, Steffen Sinning, Antoniya A. Aleksandrova, Lucy R. Forrest, and Gary Rudnick. "Structural elements required for coupling ion and substrate transport in the neurotransmitter transporter homolog LeuT." Proceedings of the National Academy of Sciences 115, no. 38 (September 4, 2018): E8854—E8862. http://dx.doi.org/10.1073/pnas.1716870115.
Abstract:
The coupled transport of ions and substrates allows transporters to accumulate substrates using the energy of transmembrane ion gradients and electrical potentials. During transport, conformational changes that switch accessibility of substrate and ion binding sites from one side of the membrane to the other must be controlled so as to prevent uncoupled movement of ions or substrates. In the neurotransmitter:sodium symporter (NSS) family, Na+stabilizes the transporter in an outward-open state, thus decreasing the likelihood of uncoupled Na+transport. Substrate binding, in a step essential for coupled transport, must overcome the effect of Na+, allowing intracellular substrate and Na+release from an inward-open state. However, the specific elements of the protein that mediate this conformational response to substrate binding are unknown. Previously, we showed that in the prokaryotic NSS transporter LeuT, the effect of Na+on conformation requires the Na2 site, where it influences conformation by fostering interaction between two domains of the protein. Here, we used cysteine accessibility to measure conformational changes of LeuT inEscherichia colimembranes. We identified a conserved tyrosine residue in the substrate binding site required for substrate to convert LeuT to inward-open states by establishing an interaction between the two transporter domains. We further identify additional required interactions between the two transporter domains in the extracellular pathway. Together with our previous work on the conformational effect of Na+, these results identify mechanistic components underlying ion–substrate coupling in NSS transporters.
18
Shrestha, Rashmi, and Chittaranjan Das. "Crystal structure of the Thr316Ala mutant of a yeast JAMM deubiquitinase: implication of active-site loop dynamics in catalysis." Acta Crystallographica Section F Structural Biology Communications 77, no. 6 (May 24, 2021): 163–70. http://dx.doi.org/10.1107/s2053230x21005124.
Abstract:
AMSH, an endosome-associated deubiquitinase (DUB) with a high specificity for Lys63-linked polyubiquitin chains, plays an important role in endosomal–lysosomal sorting and down-regulation of cell-surface receptors. AMSH belongs to the JAMM family of DUBs that contain two insertion segments, Ins-1 and Ins-2, in the catalytic domain relative to the JAMM core found in the archaebacterial AfJAMM. Structural analyses of the AMSH homologs human AMSH-LP and fission yeast Sst2 reveal a flap-like structure formed by Ins-2 near the active site that appears to open and close during its catalytic cycle. A conserved phenylalanine residue of the flap interacts with a conserved aspartate residue of the Ins-1 β-turn to form a closed `lid' over the active site in the substrate-bound state. Analyses of these two residues (Phe403 and Asp315) in Sst2 showed that their interaction plays an important role in controlling the flexibility of Ins-2. The Lys63-linked diubiquitin substrate-bound form of Sst2 showed that the conserved phenylalanine also interacts with Thr316 of Ins-1, which is substituted by tyrosine in other AMSH orthologs. Although Thr316 makes no direct interaction with the substrate, its mutation to alanine resulted in a significant loss of activity. In order to understand the contribution of Thr316 to catalysis, the crystal structure of this mutant was determined. In spite of the effect of the mutation on catalytic activity, the structure of the Sst2 Thr316Ala mutant did not reveal significant changes in either the overall structure or the active-site arrangement relative to the wild type. The Phe403–Thr316 van der Waals interaction is impaired by the Thr316Ala mutation, abrogating the adoption of the closed active-site conformation required for catalysis. Since van der Waals interactions with phenylalanine are conserved across substrate-bound forms of AMSH-LP and Sst2, these interactions may be critical for loop immobilization and the positioning of the isopeptide bond of Lys63-linked polyubiquitin-chain substrates.
19
Pfefferkorn, Hermann W., and Karlfried Fuchs. "A field classification of fossil plant substrate interactions." Neues Jahrbuch für Geologie und Paläontologie - Abhandlungen 183, no. 1-3 (December 20, 1991): 17–36. http://dx.doi.org/10.1127/njgpa/183/1991/17.
20
Goldman, Samuel, Ria Das, Kevin K. Yang, and Connor W. Coley. "Machine learning modeling of family wide enzyme-substrate specificity screens." PLOS Computational Biology 18, no. 2 (February 10, 2022): e1009853. http://dx.doi.org/10.1371/journal.pcbi.1009853.
Abstract:
Biocatalysis is a promising approach to sustainably synthesize pharmaceuticals, complex natural products, and commodity chemicals at scale. However, the adoption of biocatalysis is limited by our ability to select enzymes that will catalyze their natural chemical transformation on non-natural substrates. While machine learning and in silico directed evolution are well-posed for this predictive modeling challenge, efforts to date have primarily aimed to increase activity against a single known substrate, rather than to identify enzymes capable of acting on new substrates of interest. To address this need, we curate 6 different high-quality enzyme family screens from the literature that each measure multiple enzymes against multiple substrates. We compare machine learning-based compound-protein interaction (CPI) modeling approaches from the literature used for predicting drug-target interactions. Surprisingly, comparing these interaction-based models against collections of independent (single task) enzyme-only or substrate-only models reveals that current CPI approaches are incapable of learning interactions between compounds and proteins in the current family level data regime. We further validate this observation by demonstrating that our no-interaction baseline can outperform CPI-based models from the literature used to guide the discovery of kinase inhibitors. Given the high performance of non-interaction based models, we introduce a new structure-based strategy for pooling residue representations across a protein sequence. Altogether, this work motivates a principled path forward in order to build and evaluate meaningful predictive models for biocatalysis and other drug discovery applications.
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Zhao, Shiji, Fanglue Ni, Tianyin Qiu, Jacob T. Wolff, Shiou-Chuan Tsai, and Ray Luo. "Molecular Basis for Polyketide Ketoreductase–Substrate Interactions." International Journal of Molecular Sciences 21, no. 20 (October 13, 2020): 7562. http://dx.doi.org/10.3390/ijms21207562.
Abstract:
Polyketides are a large class of structurally and functionally diverse natural products with important bioactivities. Many polyketides are synthesized by reducing type II polyketide synthases (PKSs), containing transiently interacting standalone enzymes. During synthesis, ketoreductase (KR) catalyzes regiospecific carbonyl to hydroxyl reduction, determining the product outcome, yet little is known about what drives specific KR–substrate interactions. In this study, computational approaches were used to explore KR–substrate interactions based on previously solved apo and mimic cocrystal structures. We found five key factors guiding KR–substrate binding. First, two major substrate binding motifs were identified. Second, substrate length is the key determinant of substrate binding position. Third, two key residues in chain length specificity were confirmed. Fourth, phosphorylation of substrates is critical for binding. Finally, packing/hydrophobic effects primarily determine the binding stability. The molecular bases revealed here will help further engineering of type II PKSs and directed biosynthesis of new polyketides.
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Gnoth, Kathrin, Joachim Wolfgang Bär, Fred Rosche, Jens-Ulrich Rahfeld, and Hans-Ulrich Demuth. "Contribution of amino acids in the active site of dipeptidyl peptidase 4 to the catalytic action of the enzyme." PLOS ONE 19, no. 4 (April 16, 2024): e0289239. http://dx.doi.org/10.1371/journal.pone.0289239.
Abstract:
Dipeptidyl peptidase 4 (DP4)/CD26 regulates the biological function of various peptide hormones by releasing dipeptides from their N-terminus. The enzyme is a prominent target for the treatment of type-2 diabetes and various DP4 inhibitors have been developed in recent years, but their efficacy and side effects are still an issue. Many available crystal structures of the enzyme give a static picture about enzyme-ligand interactions, but the influence of amino acids in the active centre on binding and single catalysis steps can only be judged by mutagenesis studies. In order to elucidate their contribution to inhibitor binding and substrate catalysis, especially in discriminating the P1 amino acid of substrates, the amino acids R125, N710, E205 and E206 were investigated by mutagenesis studies. Our studies demonstrated, that N710 is essential for the catalysis of dipeptide substrates. We found that R125 is not important for dipeptide binding but interacts in the P1`position of the peptide backbone. In contrast to dipeptide substrates both amino acids play an essential role in the binding and arrangement of long natural substrates, particularly if lacking proline in the P1 position. Thus, it can be assumed that the amino acids R125 and N710 are important in the DP4 catalysed substrate hydrolysis by interacting with the peptide backbone of substrates up- and downstream of the cleavage site. Furthermore, we confirmed the important role of the amino acids E205 and E206. However, NP Y, displaying proline in P1 position, is still processed without the participation of E205 or E206.
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Kang, Ming-Hsi, and Bruce W. Banfield. "Pseudorabies Virus Tegument Protein Us2 Recruits the Mitogen-Activated Protein Kinase Extracellular-Regulated Kinase (ERK) to Membranes through Interaction with the ERK Common Docking Domain." Journal of Virology 84, no. 17 (June 16, 2010): 8398–408. http://dx.doi.org/10.1128/jvi.00794-10.
Abstract:
ABSTRACT The pseudorabies virus (PRV) Us2 protein binds to the extracellular-regulated kinase (ERK) and inhibits the activation of ERK nuclear targets by sequestering cytoplasmic ERK on cellular membranes. Utilizing a series of Us2 truncations, we determined that the minimal portion of Us2 required for interaction with ERK is contained within its amino-terminal 214 amino acids. The loss of the ability of Us2 to bind to ERK in coimmunoprecipitation experiments was accompanied by a failure of Us2 to form oligomers, raising the possibility that higher-order Us2 structures are required for ERK interaction. To map the Us2 interaction site on ERK, we introduced mutations into the region of ERK that interacts with the ERK kinase, MEK, or into the common docking (CD) domain that mediates interactions with many ERK substrates. ERK carrying mutations within the MEK binding region maintained the ability to bind Us2, whereas ERK carrying mutations within the CD domain did not. Furthermore, the ERK CD domain was required for the Us2-mediated recruitment of ERK to membranes. Taken together, these findings suggest that Us2 regulates ERK activity by spatially restricting ERK localization and also by interfering with select ERK-substrate interactions.
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Ngoei, Kevin R. W., Bruno Catimel, Nicole Church, Daisy S. Lio, Con Dogovski, Matthew A. Perugini, Paul M. Watt, Heung-Chin Cheng, Dominic C. H. Ng, and Marie A. Bogoyevitch. "Characterization of a novel JNK (c-Jun N-terminal kinase) inhibitory peptide." Biochemical Journal 434, no. 3 (February 24, 2011): 399–413. http://dx.doi.org/10.1042/bj20101244.
Abstract:
An improved understanding of the roles of protein kinases in intracellular signalling and disease progression has driven significant advances in protein kinase inhibitor discovery. Peptide inhibitors that target the kinase protein substrate-binding site have continued to attract attention. In the present paper, we describe a novel JNK (c-Jun N-terminal kinase) inhibitory peptide PYC71N, which inhibits JNK activity in vitro towards a range of recombinant protein substrates including the transcription factors c-Jun, ATF2 (activating trancription factor 2) and Elk1, and the microtubule regulatory protein DCX (doublecortin). Analysis of cell culture studies confirmed the actions of a cell-permeable version of PYC71 to inhibit c-Jun phosphorylation during acute hyperosmotic stress. The analysis of the in vitro data for the kinetics of this inhibition indicated a substrate–inhibitor complex-mediated inhibition of JNK by PYC71N. Alanine-scanning replacement studies revealed the importance of two residues (PYC71N Phe9 or Phe11 within an FXF motif) for JNK inhibition. The importance of these residues was confirmed through interaction studies showing that each change decreased interaction of the peptide with c-Jun. Furthermore, PYC71N interacted with both non-phosphorylated (inactive) JNK1 and the substrate c-Jun, but did not recognize active JNK1. In contrast, a previously characterized JNK-inhibitory peptide TIJIP [truncated inhibitory region of JIP (JNK-interacting protein)], showed stronger interaction with active JNK1. Competition binding analysis confirmed that PYC71N inhibited the interaction of c-Jun with JNK1. Taken together, the results of the present study define novel properties of the PYC71N peptide as well as differences from the characterized TIJIP, and highlight the value of these peptides to probe the biochemistry of JNK-mediated substrate interactions and phosphorylation.
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Wang, S. F., W. K. Fong, W. Wang, K. K. Leung, and C. Surya. "Growth of SnS van der Waals Epitaxies on Layered Substrates." MRS Proceedings 1493 (2013): 213–17. http://dx.doi.org/10.1557/opl.2013.234.
Abstract:
ABSTRACTIn this paper we present systematic investigations on the growth of SnS van der Waals epitaxies (vdWEs) on different substrates, including crystalline and layered substrates, by molecular beam epitaxy (MBE). Experimental growth of SnS on conventional 3D substrates, such as GaAs, indicates strong interaction between the SnS layer and the substrate resulting in poor crystallinity in general. Substantial improvement in the film crystallinity can be obtained when the deposition is made on layered substrates, with saturated surface bonds, as observed in SnS films deposited on mica and crystalline substrates with a graphene buffer layer. Crystal size as large as one micron and rocking curve FWHM of 0.118° was observed despite the large lattice mismatches. This represents significant improvement over the reported value of ∼3°. Several symmetric growth orientations are observed for films grown on mica substrates. The results indicate that weak vdW interactions between the saturated bonds of the substrate surface and the SnS unit layer which is an important factor for achieving high quality epitaxy layered materials.
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ACUÑA, SERGIO M., MARIA A. SANCHEZ, and PEDRO G. TOLEDO. "SURFACE FORCES AND ADHESION BETWEEN ELECTROLYTIC COPPER CATHODE SURFACES AND MICROSPHERE SURFACES OF GLASS AND POLYSTYRENE IN AQUEOUS ELECTROLYTE SOLUTIONS." International Journal of Nanoscience 03, no. 04n05 (August 2004): 499–510. http://dx.doi.org/10.1142/s0219581x04002309.
Abstract:
Surface forces and adhesion between electrolytic copper cathode surfaces and sphere surfaces of glass and polystyrene were measured with an atomic force microscope (AFM) in water and in aqueous medium containing 104, 10-3 and 10-2 M sodium chloride at ambient temperature. Two types of copper surfaces were considered, oxidized and just-polished. Copper surfaces are submicroscopically rough and so at "contact", a film of intervening fluid separates substrate from probe. At close proximity, the interaction of the copper surfaces with either of the two probes is repulsive and such that extending and retracting force curves are essentially hysteresis-free. At higher separations, extending force curves for any probe-substrate combination were markedly repulsive and DLVO type. The higher the electrolyte concentration, the lower the range of the repulsive force. The system polystyrene-polished substrate displayed contact jumps for the higher electrolyte concentrations considered here, thus suggesting true adhesion between the surfaces. Strong and extremely long-ranged adhesive behavior were measured for the interaction between glass probes and oxidized copper substrates in low salt concentration solutions; at the origin are submicroscopic bubbles or cavities trapped between the surfaces and stabilized by the chemical heterogeneity of the interacting surfaces. A long-ranged, although weak, attractive interaction between polystyrene probes and just-polished copper substrates in aqueous salt solution belongs to the interacting surfaces although the intensity and range seems enhanced by the formation of bubbles.
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Sarver, Jeffrey G., Wieslaw A. Klis, James P. Byers, and Paul W. Erhardt. "Microplate Screening of the Differential Effects of Test Agents on Hoechst 33342, Rhodamine 123, and Rhodamine 6G Accumulation in Breast Cancer Cells that Overexpress P-Glycoprotein." Journal of Biomolecular Screening 7, no. 1 (February 2002): 29–34. http://dx.doi.org/10.1177/108705710200700105.
Abstract:
A microplate screening method has been developed to evaluate the effects of test agents on the accumulation of the fluorescent P-glycoprotein (Pgp) substrates Hoechst 33342, rhodamine 123, and rhodamine 6G in multidrug-resistant (MDR) breast cancer cells that overexpress Pgp. All three substrates exhibit substantially higher accumulation in MCF7 non-MDR cells versus NCI/ADR-RES MDR cells, while incubation with 50 μM reserpine significantly reduces or eliminates these differences. Rhodamine 123 shows the lowest substrate accumulation efficiency in non-MDR cells relative to the substrate incubation level. The effects of several chemosensitizing agents and a series of paclitaxel analogs on the accumulation of each fluorescent substrate suggest that there are distinct differences in the substrate interaction profiles exhibited by these different agents. The described methods may be useful in Pgp-related research in the areas of cancer MDR, oral drug absorption, the blood-brain barrier, renal/hepatic transport processes, and drug-drug interactions.
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Chen, Jiayao, Jing Li, Lirong Xu, Wei Hong, Yuzhao Yang, and Xudong Chen. "The Glass-Transition Temperature of Supported PMMA Thin Films with Hydrogen Bond/Plasmonic Interface." Polymers 11, no. 4 (April 2, 2019): 601. http://dx.doi.org/10.3390/polym11040601.
Abstract:
The interfacial effect is one of the significant factors in the glass-transition temperature (Tg) of the polymeric thin film system, competing against the free surface effect. Herein, the Tgs of poly (methyl methacrylate) (PMMA) films with different thicknesses and substrates are studied by fluorescence measurements, focusing on the influence of interfacial effects on the Tgs. The strong interaction between PMMA and quartz substrate leads to increased Tgs with the decreased thickness of the film. The plasmonic silver substrate causes enhanced fluorescence intensity near the interface, resulting in the delayed reduction of the Tgs with the increasing film thickness. Moreover, as a proof of the interface-dependent Tgs, hydrogen bonds of PMMA/quartz and molecules orientation of PMMA/silver are explored by the Raman spectroscopy, and the interfacial interaction energy is calculated by the molecular dynamics simulation. In this study, we probe the inter-relationship between the interfacial interactions arising from the different substrates and the Tg behavior of polymer thin films.
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Zakaria, Yusdar, Cut Intan Novita, and Samadi Samadi. "Efektivitas Fermentasi dengan Sumber Substrat yang Berbeda Terhadap Kualitas Jerami Padi." Jurnal Agripet 13, no. 1 (April 1, 2013): 22–25. http://dx.doi.org/10.17969/agripet.v13i1.548.
Abstract:
Effectivity of fermentation with different substrates source on rice straw qualityABSTRACT. The research on effectivity of fermentation with different substrates source on rice straw quality has been conducted at Animal Husbandry Field Laboratory, University of Syiah Kuala. The objective of study is to learn rice straw fermented quality as animal feed with addition of different substrat. Complete Randomize Design with factorial pattern consist of two factors which were A = storage time with 2 level ( a1 = one month; a2 = two month) and B = substrate sources (b1 = Coccoa skin fruit, b2 = rice bean and b3 = sagoo). Variables observed were protein level, crude fiber and ash level. The statistical analisis show that there is no significant effect of treatment on protein level, crude fiber and ash. There is no interaction between source of substrates and storage time. These results revealed that all substrates source (coccoa skin fruit, rice bran and sagoo) could used as an energy for starter in rice straw fermented.
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Lee, Kyeong-Ryoon, Ji-Eun Chang, Jongmin Yoon, Hyojeong Jin, and Yoon-Jee Chae. "Findings on In Vitro Transporter-Mediated Drug Interactions and Their Follow-Up Actions for Labeling: Analysis of Drugs Approved by US FDA between 2017 and 2021." Pharmaceutics 14, no. 10 (September 29, 2022): 2078. http://dx.doi.org/10.3390/pharmaceutics14102078.
Abstract:
Understanding possible follow-up actions on in vitro findings helps determine the necessity of labeling for drug interactions. We analyzed information for in vitro findings on transporter-mediated interactions of drugs approved by the U.S. Food and Drug Administration’s Center for Drug Evaluation and Research for the last five years (i.e., 2017–2021) and their follow-up actions for labeling. Higher R values than the pre-defined cut-off were observed with 3.7–39.1% inhibitor drugs in a simple prediction. Among these drugs, 16–41.7% were labeled with their potential drug interactions, while results of supporting studies or scientific rationales were submitted for the other drugs leading to no interaction labeling. In vitro transporter substrates were reported with 1.7–67.6% of drugs. The interaction labels for these substrate drugs were observed in up to 40% of drugs, while the other drugs were not labeled on the drug interactions with claims for their low interaction potential, evidenced by clinical studies or scientific rationales. The systematic and comprehensive analysis in this study will provide insight into the management of in vitro findings for transporter substrate or inhibitor drugs.
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OLIVEIRA JUNIOR, VALDIR MOURA DE, THAYS SOUSA LOPES, JOÃO VALDENOR PEREIRA FILHO, JAILDO RIBEIRO BARBOSA, ROBERT WILLIAM FERREIRA SOARES, and CARMEM CRISTINA MARECO DE SOUSA PEREIRA. "CRESCIMENTO VEGETATIVO DA MORINGA EM DISTINTOS REGIMES DE IRRIGAÇÃO ASSOCIADOS A COMPOSIÇÕES DE DIFERENTES SUBSTRATOS." IRRIGA 1, no. 4 (December 23, 2021): 646–52. http://dx.doi.org/10.15809/irriga.2021v1n4p646-652.
Abstract:
CRESCIMENTO VEGETATIVO DA MORINGA EM DISTINTOS REGIMES DE IRRIGAÇÃO ASSOCIADOS A COMPOSIÇÕES DE DIFERENTES SUBSTRATOS VALDIR MOURA DE OLIVEIRA JUNIOR1; THAYS SOUSA LOPES1; JOÃO VALDENOR PEREIRA FILHO1; JAILDO RIBEIRO BARBOSA1; ROBERT WILLIAM FERREIRA SOARES1; CARMEM CRISTINA MARECO DE SOUSA PEREIRA2 1Centro Integrado de Ensino Superior, Universidade Estadual do Piauí (UESPI), Rua Almir Benvindo, s/n, bairro Aeroporto, 64860-000, Uruçuí, Piauí, Brasil. valdirjunior@aluno.uespi.br; thayslopes@aluno.uespi.br; joaovaldenor@urc.uespi.br; jaildobarbosa@aluno.uespi.br; robertsoares@aluno.uespi.br 2 Departamento de Engenharia Agrícola, Universidade Federal Rural de Pernambuco (UFRPE), Rua Dom Manuel de Medeiros, s/n - Dois Irmãos, 52171-900, Recife, Pernambuco, Brasil. crismareco@hotmail.com 1 RESUMO A moringa possui ampla adaptabilidade e se condiciona, com muita facilidade, ao clima e solo do Nordeste brasileiro. Ainda são escassas as informações sobre a produção de mudas desta espécie sob composições de substratos associados a regimes de irrigação. Desta forma, o objetivo desse trabalho foi caracterizar o comportamento vegetativo de plantas de moringa submetidas a distintas composições de substratos e regimes de irrigação. O experimento foi realizado em ambiente telado, no período de setembro a outubro de 2020, na área experimental da Universidade Estadual do Piauí, Uruçuí. Adotou-se um delineamento experimental em esquema fatorial, sendo, o primeiro fator, dois regimes de irrigação (50 e 100% da ETo) e o segundo fator, cinco substratos (SB1 = latossolo vermelho; SB2 = substrato comercial; SB3 = solo + esterco; SB4 = solo + cinza vegetal; SB5 = solo + borra de café), com 5 repetições. Aos 45 dias após a semeadura (DAS) foram avaliadas a altura de plantas e o diâmetro do caule. Os parâmetros de crescimento inicial da cultura da moringa foram afetados significativamente pela interação (regimes de irrigação x substratos), sendo os melhores resultados obtidos, na maioria dos substratos utilizados, com a aplicação do regime hídrico de 100% da ETo. Palavras-chave: Moringa oleifera Lam, produção de mudas, déficit hídrico. OLIVEIRA JUNIOR, V. M.; LOPES, T. S.; PEREIRA FILHO, J. V.; BARBOSA, J. R.; SOARES, R. W. F.; PEREIRA, C. C. M. S. VEGETATION GROWTH OF MORINGA IN DIFFERENT IRRIGATION REGIMES ASSOCIATED WITH COMPOSITIONS OF DIFFERENT SUBSTRATES 2 ABSTRACT Moringa has wide adaptability and is very easily conditioned to the climate and soil of northeastern Brazil. Information on the production of seedlings of this species under compositions of substrates associated with irrigation regimes is still scarce. Thus, this work aimed to characterize the vegetative behavior of moringa plants submitted to different compositions of substrates and irrigation regimes. The experiment was carried out in a screened environment, from September to October 2020, in the experimental area of the State University of Piauí, Uruçuí. An experimental design was adopted in a factorial scheme, the first factor being two irrigation regimes (50 and 100% of ETo) and the second factor, five substrates (SB1 = red oxisol; SB2 = commercial substrate; SB3 = soil + manure; SB4 = soil + vegetable ash; SB5 = soil + coffee grounds), with 5 repetitions. At 45 days after sowing (DAS), plant height and stem diameter was evaluated. The initial growth parameters of the moringa crop were significantly affected by the interaction (irrigation regimes x substrates), with the best results obtained, in most of the substrates used, with the application of the water regime of 100% of ETo. Keywords: Moringa oleifera Lam, seedling production, water deficit.
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Bersani, Massimo, Bruno Morten, Maria Prudenziati, and Alessandro Gualtieri. "Interactions between lead oxide and ceramic substrates for thick film technology." Journal of Materials Research 12, no. 2 (February 1997): 501–8. http://dx.doi.org/10.1557/jmr.1997.0072.
Abstract:
This paper deals with the mechanisms and kinetics of interactions between screen printed and fired PbO layers and ceramic substrates: alumina and beryllia. The interaction with alumina occurs via two main processes: (i) a reaction between PbO and Al2O3 grains, which induces the formation of a crystalline phase, Pb2Al2O5; and (ii) an interdiffusion process involving Pb and the intergranular amorphous phase in the ceramic substrate. This latter process results in a compositional change of the intergranular phase at considerable depths inside the ceramic substrate, as well as in the formation of a high lead glass layer on the substrate surface. Since PbO is not completely reacted, the Pb penetration in the ceramic is diffusion limited (penetration depth , where td is the reaction time) with an activation energy of 1.20 ± 0.05 eV. The ceramic microstructure significantly affects the interaction processes.
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Chen, Li, and Kiran Madura. "Rad23 Promotes the Targeting of Proteolytic Substrates to the Proteasome." Molecular and Cellular Biology 22, no. 13 (July 1, 2002): 4902–13. http://dx.doi.org/10.1128/mcb.22.13.4902-4913.2002.
Abstract:
ABSTRACT Rad23 contains a ubiquitin-like domain (UbLR23) that interacts with catalytically active proteasomes and two ubiquitin (Ub)-associated (UBA) sequences that bind Ub. The UBA domains can bind Ub in vitro, although the significance of this interaction in vivo is poorly understood. Rad23 can interfere with the assembly of multi-Ub chains in vitro, and high-level expression caused stabilization of proteolytic substrates in vivo. We report here that Rad23 interacts with ubiquitinated cellular proteins through the synergistic action of its UBA domains. Rad23 plays an overlapping role with Rpn10, a proteasome-associated multi-Ub chain binding protein. Mutations in the UBA domains prevent efficient interaction with ubiquitinated proteins and result in poor suppression of the growth and proteolytic defects of a rad23Δ rpn10Δ mutant. High-level expression of Rad23 revealed, for the first time, an interaction between ubiquitinated proteins and the proteasome. This increase was not observed in rpn10Δ mutants, suggesting that Rpn10 participates in the recognition of proteolytic substrates that are delivered by Rad23. Overexpression of UbLR23 caused stabilization of a model substrate, indicating that an unregulated UbLR23-proteasome interaction can interfere with the efficient delivery of proteolytic substrates by Rad23. Because the suppression of a rad23Δ rpn10Δ mutant phenotype required both UbLR23 and UBA domains, our findings support the hypothesis that Rad23 encodes a novel regulatory factor that translocates ubiquitinated substrates to the proteasome.
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Johnson, Jill L., and Elizabeth A. Craig. "An Essential Role for the Substrate-Binding Region of Hsp40s in Saccharomyces cerevisiae." Journal of Cell Biology 152, no. 4 (February 19, 2001): 851–56. http://dx.doi.org/10.1083/jcb.152.4.851.
Abstract:
In addition to regulating the ATPase cycle of Hsp70, a second critical role of Hsp40s has been proposed based on in vitro studies: binding to denatured protein substrates, followed by their presentation to Hsp70 for folding. However, the biological importance of this model is challenged by the fact that deletion of the substrate-binding domain of either of the two major Hsp40s of the yeast cytosol, Ydj1 and Sis1, leads to no severe defects, as long as regions necessary for Hsp70 interaction are retained. As an in vivo test of this model, requirements for viability were examined in a strain having deletions of both Hsp40 genes. Despite limited sequence similarity, the substrate-binding domain of either Sis1 or Ydj1 allowed cell growth, indicating they share overlapping essential functions. Furthermore, the substrate-binding domain must function in cis with a functional Hsp70-interacting domain. We conclude that the ability of cytosolic Hsp40s to bind unfolded protein substrates is an essential function in vivo.
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Azzahra, Annisyaban Fatiha, Regaputra Satria Janitra, Wahyu Widayat, Farhan Azhwin Maulana, Safri Ishmayana, and Muhammad Yusuf. "Analisis Interaksi ?-Amilase Bacillus licheniformis (BLA) dan Mutannya (MTBLA) dengan Maltoheptaosa pada Suhu Tinggi menggunakan Metode In Silico." Jurnal Sains dan Kesehatan 5, no. 6 (December 31, 2023): 972–84. http://dx.doi.org/10.25026/jsk.v5i6.2013.
Abstract:
?-Amylase is an enzyme that hydrolyzes starch into oligosaccharides used in the food and health industry sector. Hydrolysis products such as maltopentose can be a high-nutrition source for patients with kidney failure and calorie deficit. Therefore, increasing the thermostability of enzymes needs to be done to meet industrial criteria. In this study, we studied the effect of the Bacillus licheniformis ?-amylase (BLA) mutation on its activity at 298 and 373 K in silico through enzyme-substrate interaction analysis. Maltoheptaose was used as a model substrate. At 373 K, the Asn190Phe mutation plays a direct role in forming interactions with the substrate while the Gln264Ser mutation does not play a direct role. At 298 K the Asn265Tyr mutation plays a direct role in the enzyme-substrate interaction. In this study, we found a relationship between enzyme-substrate interaction and activity, the most determining factor being the interaction with the catalytic residue. At 298 K, the total interaction of the mutant BLA (MTBLA)-maltoheptaose was slightly stronger than that of BLA-maltoheptaose. However, the interaction of maltoheptaose with catalytic residues in BLA is stronger than in MTBLA. This is in agreement with the previous experiment at 298 K. A similar pattern is found at 373 K. Thereby, MTBLA activity at 373 K is also not more improved than BLA. Keywords: ?-Amylase, activity, thermostability, Bacillus licheniformis, In silico Abstrak ?-Amilase merupakan enzim yang menghidrolisis pati menjadi oligosakarida yang digunakan di sektor industri makanan dan kesehatan. Produk hidrolisis seperti maltopentosa dapat menjadi sumber makanan tinggi nutrisi untuk pasien gagal ginjal dan defisit kalori. Oleh sebab itu, peningkatan termostabilitas enzim perlu dilakukan untuk memenuhi kriteria industri. Pada penelitian ini kami mempelajari pengaruh mutasi ?-amilase Bacillus licheniformis (BLA) terhadap aktivitasnya pada suhu 298 dan 373 K secara in silico melalui analisis interaksi enzim-substrat. Maltoheptaosa digunakan sebagai model substrat. Pada suhu 373 K, mutasi Asn190Phe berperan langsung membentuk interaksi dengan substrat sedangkan mutasi Gln264Ser tidak berperan langsung. Pada suhu 298 K mutasi Asn265Tyr berperan langsung terhadap interaksi enzim-substrat. Pada penelitian ini, kami menemukan hubungan antara interaksi enzim-substrat terhadap aktivitas, faktor yang paling menentukan adalah interaksinya dengan residu katalitik. Pada suhu 298 K, total interaksi mutan BLA (MTBLA)-maltoheptaosa sedikit lebih kuat dibandingkan BLA-maltoheptaosa. Namun, interaksi maltoheptaosa dengan residu katalitik pada BLA lebih kuat daripada MTBLA. Hal ini bersesuaian dengan eksperimen sebelumnya pada suhu 298 K. Pola yang mirip terlihat pada 373 K, sehingga aktivitas MTBLA pada suhu 373 K juga tidak lebih baik daripada BLA. Kata Kunci: ?-Amilase, aktivitas, termostabilitas, Bacillus licheniformis, In silico
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Gour-Salin, B. J., P. Lachance, M. C. Magny, C. Plouffe, R. Ménard, and A. C. Storer. "E64 [trans-epoxysuccinyl-l-leucylamido-(4-guanidino)butane] analogues as inhibitors of cysteine proteinases: investigation of S2 subsite interactions." Biochemical Journal 299, no. 2 (April 15, 1994): 389–92. http://dx.doi.org/10.1042/bj2990389.
Abstract:
A number of epoxysuccinyl amino acid benzyl esters (HO-Eps-AA-OBzl) and benzyl amides (HO-Eps-AA-NHBzl) (where AA represents amino acid) were synthesized as analogues of E64, a naturally occurring inhibitor of cysteine proteinases. These inhibitors were designed to evaluate if selectivity for cathepsin B could be achieved by varying the amino acid on the basis of known substrate specificity. Contrary to the situation with substrates, it was found that variation of the amino acid in the E64 analogues does not lead to major changes in the kinetic parameter kinac./Ki and that the specificity of these analogues does not parallel that observed for substrates. This is particularly true in the case of the benzyl ester derivatives where the deviation from substrate-like behaviour is more important than with the benzyl amide derivatives. The results suggest that the amide proton of the benzyl amide group in HO-Eps-AA-NHBzl interacts in the S2 subsite in both cathepsin B and papain and contributes to increase the potency of these inhibitors. The kinetic data also suggest that differences in the orientation of the C alpha-C beta bond of the side chain in the S2 subsite of the enzyme might explain the differences between substrate and E64 analogue specificities. This hypothesis is supported by the fact that the order of inactivation rates with chloromethane inhibitors (which are believed to be good models of enzyme-substrate interactions) is indeed very similar to that observed with the corresponding amidomethylcoumarin substrates. In conclusion, the information available from S2-P2 interactions with substrates cannot be used to enhance the selectivity of the E64 analogues in a rational manner.
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Tang, Jordan, and Gerald Koelsch. "A Possible Function of the Flaps of Aspartic Proteases: The Capture of Substrate Side Chains Determines the Specificity of Cleavage Positions." Protein & Peptide Letters 2, no. 1 (August 1995): 257–65. http://dx.doi.org/10.2174/092986652904220523163110.
Abstract:
Abstract: A major function is proposed for the flaps of aspartic proteases. In a free enzyme with opep. flaps, the conserved flap residues, Tyr75 in eukaryotic aspartic proteases and Ile50 in HIV protease, 'capture' side chains of substrates by hydrophobic interaction, which results in placing the interacting substrate side chains in the S1 or S1' pocket for hydrolysis. This mechanism is highly efficient in determining the specificity of cleavage sites.
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Amimoto, Ikumi, Rino Watanabe, and Yoshiaki Hirano. "Cell Behavior on Peptide-Immobilized Substrate with Cell Aggregation Inducing Property." Processes 10, no. 9 (September 5, 2022): 1779. http://dx.doi.org/10.3390/pr10091779.
Abstract:
Cell aggregates have been applied in various fields such as regenerative medicine and drug toxicity testing. We have shown that H-(Lys-Pro)12-OH (KP24), a repeating sequence of lysine (Lys) and proline (Pro), induces uniformly sized cell aggregates simply by its presence in cell suspension. In this study, we considered that this peptide could be applied to a three-dimensional culture substrate that can induce uniform cell aggregates by immobilizing it on the substrate. Therefore, mouse fibroblasts (L929) were seeded on KP24-immobilized glass substrates and cell behavior was observed. We also seeded human-derived cells, namely, human mesenchymal stem cells (hMSC), on KP24-immobilized substrates and characterized their cell assemblies. Furthermore, KP24 was chemically immobilized on the substrate surface, which allowed us to trace the mechanism of KP24–cell interaction. As a mechanism analysis of the cell aggregation ability of KP24, we investigated whether KP24 interacts with the cell surface without being incorporated into the cell.
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Ostrowska, Natalia, Michael Feig, and Joanna Trylska. "Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease." PLOS Computational Biology 19, no. 4 (April 25, 2023): e1011054. http://dx.doi.org/10.1371/journal.pcbi.1011054.
Abstract:
Biochemical processes in cells, including enzyme-catalyzed reactions, occur in crowded conditions with various background macromolecules occupying up to 40% of cytoplasm’s volume. Viral enzymes in the host cell also encounter such crowded conditions as they often function at the endoplasmic reticulum membranes. We focus on an enzyme encoded by the hepatitis C virus, the NS3/4A protease, which is crucial for viral replication. We have previously found experimentally that synthetic crowders, polyethylene glycol (PEG) and branched polysucrose (Ficoll), differently affect the kinetic parameters of peptide hydrolysis catalyzed by NS3/4A. To gain understanding of the reasons for such behavior, we perform atomistic molecular dynamics simulations of NS3/4A in the presence of either PEG or Ficoll crowders and with and without the peptide substrates. We find that both crowder types make nanosecond long contacts with the protease and slow down its diffusion. However, they also affect the enzyme structural dynamics; crowders induce functionally relevant helical structures in the disordered parts of the protease cofactor, NS4A, with the PEG effect being more pronounced. Overall, PEG interactions with NS3/4A are slightly stronger but Ficoll forms more hydrogen bonds with NS3. The crowders also interact with substrates; we find that the substrate diffusion is reduced much more in the presence of PEG than Ficoll. However, contrary to NS3, the substrate interacts more strongly with Ficoll than with PEG crowders, with the substrate diffusion being similar to crowder diffusion. Importantly, crowders also affect the substrate-enzyme interactions. We observe that both PEG and Ficoll enhance the presence of substrates near the active site, especially near catalytic H57 but Ficoll crowders increase substrate binding more than PEG molecules.
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Tramonte, Rafael Prandini, Nicolli Cristina Osório, Flávio Henrique Ragonha, Gisele Daiane Pinha, Liliana Rodrigues, and Roger Paulo Mormul. "Periphyton consumption by an invasive snail species is greater in simplified than in complex habitats." Canadian Journal of Zoology 97, no. 1 (January 2019): 13–21. http://dx.doi.org/10.1139/cjz-2017-0359.
Abstract:
Habitat complexity may stabilize consumer–resource interactions and reduce the probability of invasion in aquatic habitats. We tested the hypotheses that (i) higher habitat complexity reduces resource consumption independently of grazer species, but that (ii) invasive grazers have a greater influence on decreasing resources independently of habitat complexity. We performed an experiment using artificial substrates to simulate different complexity levels. We evaluated Melanoides tuberculata (O.F. Müller, 1774) and Aylacostoma chloroticum Hylton Scott, 1954 consumption of specific algal groups and the interaction between habitat complexity and grazer species. Moreover, we evaluated grazer activity on the different substrates during the experiment. The results support only the first hypothesis and indicate lower resource consumption on complex substrates compared with simpler substrates. Additionally, the effect of the grazing of the invasive species on taxon richness was greater in simplified than in complex habitats. The grazing activity on the substrate suggests a relationship between resource exploitation and habitat complexity in which the invasive grazing species visited the simple habitat less frequently. However, the effects of invasive grazers on food resources were higher on the simple substrate. The effects of grazing activity on food resources depend on the interaction between habitat complexity and grazer species. In this way, the introduction of an invasive species may have negative impacts on the structure and function of periphytic communities, mainly in simplified aquatic ecosystems.
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BIONDI, Ricardo M., and Angel R. NEBREDA. "Signalling specificity of Ser/Thr protein kinases through docking-site-mediated interactions." Biochemical Journal 372, no. 1 (May 15, 2003): 1–13. http://dx.doi.org/10.1042/bj20021641.
Abstract:
Signal transduction pathways use protein kinases for the modification of protein function by phosphorylation. A major question in the field is how protein kinases achieve the specificity required to regulate multiple cellular functions. Here we review recent studies that illuminate the mechanisms used by three families of Ser/Thr protein kinases to achieve substrate specificity. These kinases rely on direct docking interactions with substrates, using sites distinct from the phospho-acceptor sequences. Docking interactions also contribute to the specificity and regulation of protein kinase activities. Mitogen-activated protein kinase (MAPK) family members can associate with and phosphorylate specific substrates by virtue of minor variations in their docking sequences. Interestingly, the same MAPK docking pocket that binds substrates also binds docking sequences of positive and negative MAPK regulators. In the case of glycogen synthase kinase 3 (GSK3), the presence of a phosphate-binding site allows docking of previously phosphorylated (primed) substrates; this docking site is also required for the mechanism of GSK3 inhibition by phosphorylation. In contrast, non-primed substrates interact with a different region of GSK3. Phosphoinositide-dependent protein kinase-1 (PDK1) contains a hydrophobic pocket that interacts with a hydrophobic motif present in all known substrates, enabling their efficient phosphorylation. Binding of the substrate hydrophobic motifs to the pocket in the kinase domain activates PDK1 and other members of the AGC family of protein kinases. Finally, the analysis of protein kinase structures indicates that the sites used for docking substrates can also bind N- and C-terminal extensions to the kinase catalytic core and participate in the regulation of its activity.
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MANNSFELD, STEFAN C. B., and TORSTEN FRITZ. "ADVANCED MODELLING OF EPITAXIAL ORDERING OF ORGANIC LAYERS ON CRYSTALLINE SURFACES." Modern Physics Letters B 20, no. 11 (May 10, 2006): 585–605. http://dx.doi.org/10.1142/s0217984906011189.
Abstract:
A fine balance between weak molecule-molecule interactions and usually only weakly laterally varying molecule-substrate interactions governs the physical structure of organic-inorganic and organic-organic heteroepitaxial thin films. Therefore, it is important to investigate the energetics of realistically large overlayer domains. So far, Potential calculations for large domains of organic overlayers on crystalline substrates were computationally demanding due to the vast number of atoms to be considered. Here, we present a technique which for the first time enables the calculation of both the molecule-substrate interaction potential and the molecule-molecule interaction potential for large molecular domains (up to several thousands of rather large molecules) by utilizing potential energy grid files. This technique does not only allow the investigation of the substrate influence but also full Monte-Carlo based structural optimizations, if applied to 2D crystalline overlayers. Furthermore, it provides an estimate for the energetic gain combined with the differently aligned overlayer domains. In several examples we will discuss the usefulness of this method. As a general result, we will provide evidence that energetically favorable lattice structures in OMBE systems are not restricted to commensurate unit cells or coincident super cells.
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Acheson, A., J. L. Sunshine, and U. Rutishauser. "NCAM polysialic acid can regulate both cell-cell and cell-substrate interactions." Journal of Cell Biology 114, no. 1 (July 1, 1991): 143–53. http://dx.doi.org/10.1083/jcb.114.1.143.
Abstract:
We have proposed previously that the polysialic acid (PSA) moiety of NCAM can influence membrane-membrane apposition, and thereby serve as a selective regulator of a variety of contact-dependent cell interactions. In this study, cell and tissue culture models are used to obtain direct evidence that the presence of PSA on the surface membrane can affect both cell-cell and cell-substrate interactions. Using a neuroblastoma/sensory neuron cell hybrid, it was found that removal of PSA with a specific neuraminidase (endo-N) augments cell-cell aggregation mediated by the L1 cell adhesion molecule as well as cell attachment to a variety of tissue culture substrates. In studies of embryonic spinal cord axon bundling, which involves both cell-cell and cell-substrate interactions, the pronounced defasciculation produced by removal of PSA is most easily explained by an increase in cell-substrate interaction. The fact that in both studies NCAM's intrinsic adhesion function was found not to be an important variable further illustrates that regulation of the cell surface by PSA can extend beyond binding mediated by the NCAM polypeptide.
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Matsui, Toshiaki, Hiroaki Tsujimoto, Hiroki Muroyama, and Koichi Eguchi. "Interfacial Interaction Between Ni and Oxide in SOFC Anodes." ECS Meeting Abstracts MA2023-01, no. 54 (August 28, 2023): 37. http://dx.doi.org/10.1149/ma2023-015437mtgabs.
Abstract:
The interfacial properties of Ni/oxide were quantitatively evaluated by determining the contact angle of nickel particles on oxide substrates at the operating temperature of solid oxide fuel cells (SOFCs). Nickel was coated on 8 mol% Y2O3-ZrO2 (YSZ), 10 mol% Sc2O3-1 mol% CeO2-ZrO2 (ScSZ), and Ce0.9Gd0.1O2-δ (GDC) disks by sputtering. Nickel particles were formed on the substrates by annealing these samples under reducing atmospheres. The wettability of nickel particles was found to be the worst on the YSZ substrates, indicating the lowest bond strength between Ni and YSZ. The contact angle of nickel particles for the samples heat-treated under the humidified atmosphere was smaller than that under the unhumidified atmosphere regardless of the oxide substrate. The presence of water vapor will decrease the surface tension of nickel or increase the surface tension of the oxide substrate.
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Amano, Mutsuki, Tomonari Hamaguchi, Md Hasanuzzaman Shohag, Kei Kozawa, Katsuhiro Kato, Xinjian Zhang, Yoshimitsu Yura, et al. "Kinase-interacting substrate screening is a novel method to identify kinase substrates." Journal of Cell Biology 209, no. 6 (June 22, 2015): 895–912. http://dx.doi.org/10.1083/jcb.201412008.
Abstract:
Protein kinases play pivotal roles in numerous cellular functions; however, the specific substrates of each protein kinase have not been fully elucidated. We have developed a novel method called kinase-interacting substrate screening (KISS). Using this method, 356 phosphorylation sites of 140 proteins were identified as candidate substrates for Rho-associated kinase (Rho-kinase/ROCK2), including known substrates. The KISS method was also applied to additional kinases, including PKA, MAPK1, CDK5, CaMK1, PAK7, PKN, LYN, and FYN, and a lot of candidate substrates and their phosphorylation sites were determined, most of which have not been reported previously. Among the candidate substrates for Rho-kinase, several functional clusters were identified, including the polarity-associated proteins, such as Scrib. We found that Scrib plays a crucial role in the regulation of subcellular contractility by assembling into a ternary complex with Rho-kinase and Shroom2 in a phosphorylation-dependent manner. We propose that the KISS method is a comprehensive and useful substrate screen for various kinases.
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Immovilli, Simona, Bruno Morten, Maria Prudenziati, Alessandro Gualtieri, and Massimo Bersani. "Interactions between bismuth oxide and ceramic substrates for thick film technology." Journal of Materials Research 13, no. 7 (July 1998): 1865–74. http://dx.doi.org/10.1557/jmr.1998.0265.
Abstract:
We investigated the interactions between screen printed and fired layers of Bi2O3 and ceramic substrates of alumina and beryllia. It was found that the reaction products are invariably crystalline in nature. Several transitions of Bi2O3 in its polymorphic phases were found to occur on BeO substrates, while newly formed compounds have been observed to grow on alumina substrates, i.e., Al4Bi2O9 on 99.9% Al2O3 and Bi12SiO20 on 96% Al2O3. Bismuth deeply penetrates in the ceramic interstices in all the cases. Until Bi2O3 is not completely reacted, this penetration is diffusion limited (penetration depth , where td is the reaction time) with values of the activation energy ranging from 3.7 ± 0.6 eV (BeO substrate) to 1.4 ± 0.06 eV (96% Al2O3 substrate). It is shown that these processes are notably different to those occurring in PbO/ceramic systems; moreover, they imply different adhesion phenomena of thick films on different substrates.
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Prabu-Jeyabalan, Moses, Ellen A. Nalivaika, Nancy M. King, and Celia A. Schiffer. "Viability of a Drug-Resistant Human Immunodeficiency Virus Type 1 Protease Variant: Structural Insights for Better Antiviral Therapy." Journal of Virology 77, no. 2 (January 15, 2003): 1306–15. http://dx.doi.org/10.1128/jvi.77.2.1306-1315.2003.
Abstract:
ABSTRACT Under the selective pressure of protease inhibitor therapy, patients infected with human immunodeficiency virus (HIV) often develop drug-resistant HIV strains. One of the first drug-resistant mutations to arise in the protease, particularly in patients receiving indinavir or ritonavir treatment, is V82A, which compromises the binding of these and other inhibitors but allows the virus to remain viable. To probe this drug resistance, we solved the crystal structures of three natural substrates and two commercial drugs in complex with an inactive drug-resistant mutant (D25N/V82A) HIV-1 protease. Through structural analysis and comparison of the protein-ligand interactions, we found that Val82 interacts more closely with the drugs than with the natural substrate peptides. The V82A mutation compromises these interactions with the drugs while not greatly affecting the substrate interactions, which is consistent with previously published kinetic data. Coupled with our earlier observations, these findings suggest that future inhibitor design may reduce the probability of the appearance of drug-resistant mutations by targeting residues that are essential for substrate recognition.
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Joughin, Brian A., Chengcheng Liu, Douglas A. Lauffenburger, Christopher W. V. Hogue, and Michael B. Yaffe. "Protein kinases display minimal interpositional dependence on substrate sequence: potential implications for the evolution of signalling networks." Philosophical Transactions of the Royal Society B: Biological Sciences 367, no. 1602 (September 19, 2012): 2574–83. http://dx.doi.org/10.1098/rstb.2012.0010.
Abstract:
Characterization of in vitro substrates of protein kinases by peptide library screening provides a wealth of information on the substrate specificity of kinases for amino acids at particular positions relative to the site of phosphorylation, but provides no information concerning interdependence among positions. High-throughput techniques have recently made it feasible to identify large numbers of in vivo kinase substrates. We used data from experiments on the kinases ATM/ATR and CDK1, and curated CK2 substrates to evaluate the prevalence of interactions between substrate positions within a motif and the utility of these interactions in predicting kinase substrates. Among these data, evidence of interpositional sequence dependencies is strikingly rare, and what dependency exists does little to aid in the prediction of novel kinase substrates. Significant increases in the ability of models to predict kinase–substrate specificity beyond position-independent models must come largely from inclusion of elements of biological and cellular context, rather than further analysis of substrate sequences alone. Our results suggest that, evolutionarily, kinase substrate fitness exists in a smooth energetic landscape. Taken with results from others indicating that phosphopeptide-binding domains do exhibit interpositional dependence, our data suggest that incorporation of new substrate molecules into phospho-signalling networks may be rate-limited by the evolution of suitability for binding by phosphopeptide-binding domains.
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Fadzli, Fatin Syahirah, Showkat Ahmad Bhawani, and Rania Edrees Adam Mohammad. "Microbial Fuel Cell: Recent Developments in Organic Substrate Use and Bacterial Electrode Interaction." Journal of Chemistry 2021 (June 29, 2021): 1–16. http://dx.doi.org/10.1155/2021/4570388.
Abstract:
A new bioelectrochemical approach based on metabolic activities inoculated bacteria, and the microbial fuel cell (MFC) acts as biocatalysts for the natural conversion to energy of organic substrates. Among several factors, the organic substrate is the most critical challenge in MFC, which requires long-term stability. The utilization of unstable organic substrate directly affects the MFC performance, such as low energy generation. Similarly, the interaction and effect of the electrode with organic substrate are well discussed. The electrode-bacterial interaction is also another aspect after organic substrate in order to ensure the MFC performance. The conclusion is based on this literature view; the electrode content is also a significant challenge for MFCs with organic substrates in realistic applications. The current review discusses several commercial aspects of MFCs and their potential prospects. A durable organic substrate with an efficient electron transfer medium (anode electrode) is the modern necessity for this approach.
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Ngo, Son Tung, Phuong Duy Tran-Le, Giap T. Ho, Loan Q. Le, Le Minh Bui, Bao Khanh Vu, Huong Thi Thu Phung, Hoang-Dung Nguyen, Thanh-Sang Vo, and Van V. Vu. "Interaction of carbohydrate binding module 20 with starch substrates." RSC Advances 9, no. 43 (2019): 24833–42. http://dx.doi.org/10.1039/c9ra01981b.