Relevant bibliographies by topics / Protein; Ligands

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Protein; Ligands'

Author: Grafiati
Published: 4 June 2021
Last updated: 16 February 2022

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Journal articles on the topic "Protein; Ligands"

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Karasev, Dmitry, Boris Sobolev, Alexey Lagunin, Dmitry Filimonov, and Vladimir Poroikov. "Prediction of Protein–ligand Interaction Based on Sequence Similarity and Ligand Structural Features." International Journal of Molecular Sciences 21, no. 21 (October 31, 2020): 8152. http://dx.doi.org/10.3390/ijms21218152.

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Computationally predicting the interaction of proteins and ligands presents three main directions: the search of new target proteins for ligands, the search of new ligands for targets, and predicting the interaction of new proteins and new ligands. We proposed an approach providing the fuzzy classification of protein sequences based on the ligand structural features to analyze the latter most complicated case. We tested our approach on five protein groups, which represented promised targets for drug-like ligands and differed in functional peculiarities. The training sets were built with the original procedure overcoming the data ambiguity. Our study showed the effective prediction of new targets for ligands with an average accuracy of 0.96. The prediction of new ligands for targets displayed the average accuracy 0.95; accuracy estimates were close to our previous results, comparable in accuracy to those of other methods or exceeded them. Using the fuzzy coefficients reflecting the target-to-ligand specificity, we provided predicting interactions for new proteins and new ligands; the obtained accuracy values from 0.89 to 0.99 were acceptable for such a sophisticated task. The protein kinase family case demonstrated the ability to account for subtle features of proteins and ligands required for the specificity of protein–ligand interaction.
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Southern, Craig, Jennifer M. Cook, Zaynab Neetoo-Isseljee, Debra L. Taylor, Catherine A. Kettleborough, Andy Merritt, Daniel L. Bassoni, et al. "Screening β-Arrestin Recruitment for the Identification of Natural Ligands for Orphan G-Protein–Coupled Receptors." Journal of Biomolecular Screening 18, no. 5 (February 8, 2013): 599–609. http://dx.doi.org/10.1177/1087057113475480.

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A variety of G-protein–coupled receptor (GPCR) screening technologies have successfully partnered a number of GPCRs with their cognate ligands. GPCR-mediated β-arrestin recruitment is now recognized as a distinct intracellular signaling pathway, and ligand-receptor interactions may show a bias toward β-arrestin over classical GPCR signaling pathways. We hypothesized that the failure to identify native ligands for the remaining orphan GPCRs may be a consequence of biased β-arrestin signaling. To investigate this, we assembled 10 500 candidate ligands and screened 82 GPCRs using PathHunter β-arrestin recruitment technology. High-quality screening assays were validated by the inclusion of liganded receptors and the detection and confirmation of these established ligand-receptor pairings. We describe a candidate endogenous orphan GPCR ligand and a number of novel surrogate ligands. However, for the majority of orphan receptors studied, measurement of β-arrestin recruitment did not lead to the identification of cognate ligands from our screening sets. β-Arrestin recruitment represents a robust GPCR screening technology, and ligand-biased signaling is emerging as a therapeutically exploitable feature of GPCR biology. The identification of cognate ligands for the orphan GPCRs and the extent to which receptors may exist to preferentially signal through β-arrestin in response to their native ligand remain to be determined.
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Finkina, Ekaterina I., Daria N. Melnikova, Ivan V. Bogdanov, Natalia S. Matveevskaya, Anastasia A. Ignatova, Ilia Y. Toropygin, and Tatiana V. Ovchinnikova. "Impact of Different Lipid Ligands on the Stability and IgE-Binding Capacity of the Lentil Allergen Len c 3." Biomolecules 10, no. 12 (December 13, 2020): 1668. http://dx.doi.org/10.3390/biom10121668.

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Previously, we isolated the lentil allergen Len c 3, belonging to the class of lipid transfer proteins, cross-reacting with the major peach allergen Pru p 3 and binding lipid ligands. In this work, the allergenic capacity of Len c 3 and effects of different lipid ligands on the protein stability and IgE-binding capacity were investigated. Impacts of pH and heat treating on ligand binding with Len c 3 were also studied. It was shown that the recombinant Len c 3 (rLen c 3) IgE-binding capacity is sensitive to heating and simulating of gastroduodenal digestion. While being heated or digested, the protein showed a considerably lower capacity to bind specific IgE in sera of allergic patients. The presence of lipid ligands increased the thermostability and resistance of rLen c 3 to digestion, but the level of these effects was dependent upon the ligand’s nature. The anionic lysolipid LPPG showed the most pronounced protective effect which correlated well with experimental data on ligand binding. Thus, the Len c 3 stability and allergenic capacity can be retained in the conditions of food heat cooking and gastroduodenal digestion due to the presence of certain lipid ligands.
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Raingeval, Claire, and Isabelle Krimm. "NMR investigation of protein–ligand interactions for G-protein coupled receptors." Future Medicinal Chemistry 11, no. 14 (July 2019): 1811–25. http://dx.doi.org/10.4155/fmc-2018-0312.

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In this review, we report NMR studies of ligand–GPCR interactions, including both ligand-observed and protein-observed NMR experiments. Published studies exemplify how NMR can be used as a powerful tool to design novel GPCR ligands and investigate the ligand-induced conformational changes of GPCRs. The strength of NMR also lies in its capability to explore the diverse signaling pathways and probe the allosteric modulation of these highly dynamic receptors. By offering unique opportunities for the identification, structural and functional characterization of GPCR ligands, NMR will likely play a major role for the generation of novel molecules both as new tools for the understanding of the GPCR function and as therapeutic compounds for a large diversity of pathologies.
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Hutchens, T. W., and J. O. Porath. "Protein recognition of immobilized ligands: promotion of selective adsorption." Clinical Chemistry 33, no. 9 (September 1, 1987): 1502–8. http://dx.doi.org/10.1093/clinchem/33.9.1502.

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Abstract We are using simple immobilized ligands to evaluate the biochemistry and mechanisms of selective, high-affinity, protein adsorption events. Several specific means have recently been developed to more selectively utilize the favorable entropy changes associated with the displacement of protein-bound water during the formation and stabilization of protein-ligand recognition events. For protein and peptide immobilization these include, besides hydrophobic interaction, for example, metal ion, pi-electron-mediated, and thiophilic interactions. This latter type of protein-ligand recognition process represents a previously unrecognized interaction mechanism of considerable selectivity, affinity, and utility. Specific examples of the above-mentioned principles and protein fractionations include (a) thiophilic adsorption of immunoglobulins to achieve immunoglobulin-free serum for in vitro production and purification of monoclonal antibodies and (b) urea-induced binding of estrogen-receptor proteins to immobilized DNA. The interaction mechanisms are discussed in terms of the molecular architecture of protein surfaces. We present possibilities for the further utilization of these immobilized ligands and their associated proteins in the areas of clinical biochemistry and immunology.
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Mary, Sophie, Jean-Alain Fehrentz, Marjorie Damian, Pascal Verdié, Jean Martinez, Jacky Marie, and Jean-Louis Banères. "How ligands and signalling proteins affect G-protein-coupled receptors' conformational landscape." Biochemical Society Transactions 41, no. 1 (January 29, 2013): 144–47. http://dx.doi.org/10.1042/bst20120267.

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The dynamic character of GPCRs (G-protein-coupled receptors) is essential to their function. However, the details of how ligands and signalling proteins stabilize a receptor conformation to trigger the activation of a given signalling pathway remain largely unexplored. Multiple data, including recent results obtained with the purified ghrelin receptor, suggest a model where ligand efficacy and functional selectivity are directly related to different receptor conformations. Importantly, distinct effector proteins (G-proteins and arrestins) as well as ligands are likely to affect the conformational landscape of GPCRs in different manners, as we show with the isolated ghrelin receptor. Such modulation of the GPCR conformational landscape by pharmacologically distinct ligands and effector proteins has major implications for the design of new drugs that activate specific signalling pathways.
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Galano-Frutos, Juan J., M. Carmen Morón, and Javier Sancho. "The mechanism of water/ion exchange at a protein surface: a weakly bound chloride in Helicobacter pylori apoflavodoxin." Physical Chemistry Chemical Physics 17, no. 43 (2015): 28635–46. http://dx.doi.org/10.1039/c5cp04504e.

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Ferreira de Freitas, Renato, and Matthieu Schapira. "A systematic analysis of atomic protein–ligand interactions in the PDB." MedChemComm 8, no. 10 (2017): 1970–81. http://dx.doi.org/10.1039/c7md00381a.

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We compiled a list of 11 016 unique structures of small-molecule ligands bound to proteins representing 750 873 protein–ligand atomic interactions, and analyzed the frequency, geometry and the impact of each interaction type. The most frequent ligand–protein atom pairs can be clustered into seven interaction types.
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Mehta, Simpi, and Seema R. Pathak. "INSILICO DRUG DESIGN AND MOLECULAR DOCKING STUDIES OF NOVEL COUMARIN DERIVATIVES AS ANTI-CANCER AGENTS." Asian Journal of Pharmaceutical and Clinical Research 10, no. 4 (April 1, 2017): 335. http://dx.doi.org/10.22159/ajpcr.2017.v10i4.16826.

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Objective: Cancer is the major worldwide problem. It arises due to uncontrolled growth of cells. In the present study a series of novel coumarin derivatives were designed and computationallyoptimized to investigate the interaction between designed ligands and 10 pdb files of five selected proteins. The objective here was to analyse in silico anticancerous activity of designed ligands to reduce cost and time for getting novel anticancerous drug with minimum side effects.Methods: Docking studies were performed to find outmaximum interaction between designed ligands and selected five proteins using Schrondinger software Maestro. Capecitabin has been used as reference compound. Structures of selected proteins were downloaded from protein data bank.Results: All the designed ligands showed mild to excellent binding with proteins.Most of the ligands exhibited better interaction compared to reference compoundcapacitabin with all pdb files. Some of designed ligands amongst (1-7) showed excellent docking score with all pdb files(2v5z, 2v60, 2v61) ofAmine oxidase. Conclusion: All the designed ligands were docked with ten pdb files of five different proteins and it was found that out of seven designed ligand, ligand 4 showed best binding (docking score -10.139 ) with pdb 2v5z of protein Amine oxidase. Docked ligand cavity of ligand 4 showed important hydrophobic/non polar residues such asIle199,Ile316,Trp119,Phe168,Ile198,Cys172,Tyr188,Tyr398,Tyr435,Phe343,Tyr60,Leu328,Leu171 and showed pi-pi interaction with Tyr326.Further wet lab studies are continued in our laboratory to confirm and find out efficiency and activity of target compounds.Keywords: Docking, Mono Amine Oxidase, Coumarin derivatives, Anticancerous activity, binding energy, Ramachandran Plot, Hydrophobic residue.
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GORETZKI, Lothar, and Barbara M. MUELLER. "Low-density-lipoprotein-receptor-related protein (LRP) interacts with a GTP-binding protein." Biochemical Journal 336, no. 2 (December 1, 1998): 381–86. http://dx.doi.org/10.1042/bj3360381.

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The low-density-lipoprotein-receptor-related protein (LRP) binds and internalizes numerous ligands, including lipoproteins, proteinase–inhibitor complexes and others. We have shown previously that LRP-mediated ligand internalization is dependent on cAMP-dependent protein kinase (PKA) activity. Here, we investigated whether ligation of LRP increases the intracellular cAMP level and PKA activity via a stimulatory GTP-binding protein. Treatment of LRP-expressing cell lines with the LRP ligands lactoferrin or urokinase-type plasminogen activator caused a significant elevation in cAMP and stimulated PKA activity in a dose-dependent manner. Addition of the 39 kDa receptor-associated protein (RAP), an antagonist for ligand interactions with LRP, blocked the lactoferrin-induced increase in PKA activity, demonstrating a requirement for ligand binding to LRP. Incubation of cell membrane fractions with lactoferrin increased GTPase activity in a time- and dose-dependent manner, and treatment with LRP ligands suppressed cholera-toxin-mediated ADP-ribosylation of the Gsα subunit of a heterotrimeric G-protein. Affinity precipitation of LRP with RAP resulted in co-precipitation of two isoforms of Gsα from detergent extracts. We thus conclude that LRP is a signalling receptor that associates directly with a stimulatory heterotrimeric G-protein and activates a downstream PKA-dependent pathway.
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Dissertations / Theses on the topic "Protein; Ligands"

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Almeida, T. B. "Identification and optimisation of ligands to target protein-protein interactions : EB1-SxIP proteins." Thesis, University of Liverpool, 2016. http://livrepository.liverpool.ac.uk/3004877/.

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End binding protein 1 (EB1) is a key element in the complex network of protein-protein interactions at microtubule growing ends which has a fundamental role in microtubule polymerisation. EB1 regulates the microtubule dynamic behaviour, through protein recruitment, and has been associated with several disease states, such as cancer and neuronal diseases. Diverse EB1 binding partners are recognised through a conserved SxIP motif within an intrinsically disordered region enriched with basic, serine and proline residues. Crystal structure of EB1 in complex with a peptide containing the SxIP motif demonstrated that the isoleucine-proline dipeptide is bound into a well‐defined cavity of EB1 that may be suitable for small molecule targeting. The research described herein reports the use of a multidisciplinary approach for the discovery of the first small molecule scaffold to target the EB1 recruiting domain. This approach included virtual screening (structure and ligand based design) and multiparameter compound selection. Solution NMR structures of the C-terminal domain of EB1 in the free form and in complex with the small molecule are also reported. A key finding from these structures is that the hydrophobic binding pocket reported to be essential for recruiting SxIP proteins is not pre-formed but highly dynamic in solution. This brings new insights to the protein recruitment mechanism regulated by EB1 and for the identification of new small molecule inhibitors for the EB1-SxIP protein interactions. The interaction of short length peptides containing the SxIP motif with EB1 was characterised through the use of solution NMR and ITC methods. The contributions for the binding of the SxIP motif and neighbouring residues to EB1 were quantified in terms of binding energy. A structural model shows that the binding pocket of EB1 is largely extended when in complex. This research describes not only the first chemical scaffold that targets EB1, it details important structural features of the interaction of this protein with SxIP containing peptides. This structural information provides fundamental understanding of this interaction that can be exploited in the future to discover higher affinity ligands.
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Hassan, Hani Mutlak Abdullah. "Chemical Synthesis of Protein Ligands." Thesis, University of Manchester, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.501975.

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Larsson, Emma. "Calcium-dependent affinity ligands for protein purification." Thesis, KTH, Skolan för kemi, bioteknologi och hälsa (CBH), 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-278695.

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The rapid growth of the biopharmaceutical industry has led to increasing demands on the protein production process. An important aspect is the yield of functional protein, which can be greatly affected by the choice of downstream purification. Purification based on acidic elution can be an issue for pH-sensitive proteins, since dramatic changes in pH can lead to protein aggregation and loss of function. The harsh, acidic elution conditions used in conventional purification of antibodies by Protein A affinity chromatography can thus be problematic. To address this, a calcium-dependent protein domain, called ZCa, has previously been developed for mild purification of antibodies, with elution close to physiological pH. Presented here are engineered variants of ZCa with novel affinity towards other biotherapeutics, which could also benefit from mild purification. Phage display selection, using a ZCa-based library, was applied to isolate promising ZCa-based binders against antigen-binding fragments, tissue plasminogen activator, and granulocyte colony stimulating factor, yet to be characterized. Additionally, three ZCa-based variants from a previous selection, with affinity for single-chain variable fragments (scFvs), have been identified and characterized. In a purification setup, they were shown to elute the scFv protein at neutral pH in a calcium-dependent manner. The reported results demonstrate that novel affinity can be introduced to the ZCa domain, while maintaining the calcium-dependent behavior that enables gentle purification. This offers a strategy for broadening the range of proteins that can be purified under mild conditions, with the benefit of reducing protein aggregation and thus increasing the yield of functional protein.
Den snabba tillväxten inom bioläkemedelsindustrin har lett till ökade krav på processen för proteinproduktion. En viktig aspekt är utbytet av funktionellt protein, där valet av reningsmetod kan ha stor påverkan. Proteinrening med syraeluering kan utgöra ett problem för pH-känsliga proteiner, då stora förändringar i pH kan leda till aggregering och försämrad funktionalitet. Det låga pH som används för eluering i den traditionella reningen av antikroppar med Protein A-baserad affinitetskromatografi kan därmed vara problematiskt. Som ett svar på detta har en kalciumberoende proteindomän, vid namn ZCa, tidigare utvecklats för mild rening av antikroppar med eluering nära fysiologiskt pH. I det här arbetet presenteras nya varianter av ZCa som modifierats för att binda till andra bioläkemedel, vilka också skulle kunna gynnas av mild proteinrening. Fagdisplay av ett ZCa-baserat bibliotek har applicerats för att isolera lovande ZCa-baserade bindare mot antikroppsfragment (Fab), vävnadsplasminogenaktivator och granulocytkolonistimulerande faktor, vilka ännu inte karaktäriserats. Utöver detta identifierades och karaktäriserades tre ZCa-baserade varianter från en tidigare selektion, med affinitet för enkelkedjiga antikroppsfragment (scFv). Då dessa varianter utvärderades för rening visade alla på kalciumberoende eluering av scFv vid neutralt pH. Det här demonstrerar att ny affinitet kan introduceras till ZCa-domänen, där det kalciumberoende beteende som möjliggör mild proteinrening bevaras. Detta erbjuder en strategi för att utöka antalet proteiner som kan renas under milda kalciumberoende förhållanden, vilket med fördel kan minska aggregering och därmed öka utbytet av funktionellt protein.
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Street, Ian Philip. "Protein - carbohydrate interactions in glycogen phosphorylase." Thesis, University of British Columbia, 1985. http://hdl.handle.net/2429/25049.

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It has long been observed that some organo-fluorine compounds exhibit enhanced biological activity over their non-fluorinated precursors, however reasons for these unusual properties still remain poorly understood. An explanation which has been widely used relates to the ability of the C-F fragment of the analog to participate in hydrogen-bonding interactions with its protein receptor. For this reason, fluorinated carbohydrates have been used as hydrogen-bonding probes with a number of proteins. Thus there exists a need for a systematic investigation into the hydrogen-bonding ability of the C-F fragment, and the enzyme glycogen phosphorylase provides an excellent subject for such a study. The glucopyranose binding site in the inactive (T-state) conformation of the enzyme has been well characterised and high resolution crystallographic data is available. Thus by comparison of kinetic and crystallographic data for the natural effectors and the fluorinated substrate analogs considerable insight into the hydrogen bonding ability of the C-F fragment and the nature of carbohydrate-protein interactions should be gained. Little is known about the active (R-state) conformation of the enzyme and about the T-state to R-state transition. Use of fluorinated analogs of the enzymes natural substrate, glucose-l-phosphate, could also shed light on these questions. With these aims in mind, all of the isomeric mono-fluorinated derivatives of glucose and glucose-l-phosphate have been synthesised. Some deoxy and difluorinated analogs of glucose and mannose have also been prepared. Kinetic results obtained using the analogs of glucose indicate that the 3 and 6 positions of the sugar participate in strong hydrogen-bonding interactions with the protein while the other positions are only involved in relatively weak interactions. These results agree well with recent X-ray crystallographic data. None of the analogs of glucose-l-phosphate exhibited any substrate activity. The 2-deoxyfluoro analog had a similar affinity to glucose-1-phosphate and therefore probably binds in the same mode. The lack of substrate activity in this case can be explained by the destabi1isation of the putative oxo-carbonium ion intermediate at C(l), by the adjacent fluorine substituent. The other analogs of glucose-l-phosphate showed lower affinity for the enzyme. The similar inhibition constants obtained for these compounds suggested a binding mode in which the glucopyranose ring contributes little to the overall binding energy. This has led to the proposal of a molecular mechanism for the T-state to R-state transition.
Science, Faculty of
Chemistry, Department of
Graduate
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Linhult, Martin. "Protein engineering to explore and improve affinity ligands." Doctoral thesis, KTH, Biotechnology, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3632.

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In order to produce predictable and robust systems forprotein purification and detection, well characterized, small,folded domains descending from bacterial receptors have beenused. These bacterial receptors, staphylococcal protein A (SPA)and streptococcal protein G (SPG), possess high affinity to IgGand / or HSA. They are composed of repetitive units in whicheach one binds the ligand independently. The domains foldindependently and are very stable. Since the domains also havewellknown three-dimensional structures and do not containcysteine residues, they are very suitable as frameworks forfurther protein engineering.

Streptococcal protein G (SPG) is a multidomain proteinpresent on the cell surface ofStreptococcus. X-ray crystallography has been used todetermine the binding site of the Ig-binding domain. In thisthesis the region responsible for the HSA affinity of ABD3 hasbeen determined by directed mutagenesis followed by functionaland structural analysis. The analysis shows that the HSAbindinginvolves residues mainly in the second α-helix.

Most protein-based affinity chromatography media are verysensitive towards alkaline treatment, which is the preferredmethod for regeneration and removal of contaminants from thepurification devices in industrial applications. Here, aprotein engineering strategy has been used to improve thetolerance to alkaline conditions of different domains fromprotein G, ABD3 and C2. Amino acids known to be susceptibletowards high pH were substituted for less alkali susceptibleresidues. The new, engineered variants of C2 and ABD shownhigher stability towards alkaline pH. Also, very important forthe potential use as affinity ligands, these mutated variantsretained the secondary structure and the affinity to HSA andIgG, respectively. Moreover, dimerization was performed toinvestigate whether a higher binding capacity could be obtainedby multivalency. For ABD, binding studies showed that divalentligands coupled using non-directed chemistry demonstrated anincreased molar binding capacity compared to monovalentligands. In contrast, equal molar binding capacities wereobserved for both types of ligands when using a directed ligandcoupling chemistry involving the introduction and recruitmentof a unique C-terminal cysteine residue.

The staphylococcal protein A-derived domain Z is also a wellknown and thoroughly characterized fusion partner widely usedin affinity chromatography systems. This domain is consideredto be relatively tolerant towards alkaline conditions.Nevertheless, it is desirable to further improve the stabilityin order to enable an SPA-based affinity medium to withstandeven longer exposure to the harsh conditions associated withcleaning in place (CIP) procedures. For this purpose adifferent protein engineering strategy was employed. Smallchanges in stability due to the mutations would be difficult toassess. Hence, in order to enable detection of improvementsregarding the alkaline resistance of the Z domain, a by-passmutagenesis strategy was utilized, where a mutated structurallydestabilized variant, Z(F30A) was used as a surrogateframework. All eight asparagines in the domain were exchangedone-by-one. The residues were all shown to have differentimpact on the alkaline tolerance of the domain. By exchangingasparagine 23 for a threonine we were able to remarkablyincrease the stability of the Z(F30A)-domain towards alkalineconditions. Also, when grafting the N23T mutation to the Zscaffold we were able to detect an increased tolerance towardsalkaline treatment compared to the native Z molecule. In allcases, the most sensitive asparagines were found to be locatedin the loops region.

In summary, the work presented in this thesis shows theusefulness of protein engineering strategies, both to explorethe importance of different amino acids regarding stability andfunctionality and to improve the characteristics of aprotein.

Keywords:binding, affinity, human serum albumin (HSA),albumin-binding domain (ABD), affinity chromatography,deamidation, protein A, stabilization, Z-domain, capacity,protein G, cleaning-in-place (CIP), protein engineering, C2receptor.

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Georgiou, Charis. "Rational design of isoform specific ligands." Thesis, University of Edinburgh, 2017. http://hdl.handle.net/1842/28713.

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Cyclophilins (Cyp) are proteins that catalyze the interconversion of trans/cis isomers of proline belonging to the peptidyl-prolyl isomerases family (PPIase). In addition to their PPIase activity, Cyps have diverse biological roles and have been implicated in a number of different diseases such as HIV-1 and HCV. Although several Cyp inhibitors have been reported in the literature, none are able to inhibit with high specificity various Cyp isoforms. To facilitate the development of isoform-specific Cyp ligands, we have pursued detailed studies of Cyp dynamics and ligand binding thermodynamics using molecular simulations, biophysical assays and protein X-ray crystallography. Research efforts were focussed on the identification of novel Cyp inhibitors using X-ray crystallographic studies and Surface Plasmon Resonance (SPR) experiments on fragments from an in-house bespoke library of small compounds. These biophysical studies revealed a number of fragments that are able to bind to diverse Cyp isoforms with high micromolar – low millimolar activity. To further examine the binding of these fragments to cyclophilins, identify interactions with the proteins and explain specificity trends from SPR and X-ray results, molecular dynamics (MD) simulations and free energy calculations were pursued. Models of apo and holo Cyps in complex with fragments that we had experimentally tested were set up using the Amber, AmberTools and FESetup software. Free energy calculations were performed using the thermodynamic integration (TI) technique with the Sire/OpenMM software. The results were analysed with custom scripts. Correlations between computed and measured binding energies, and calculated and observed binding modes were analysed to help develop guidelines for the development of isoform specific cyclophilin ligands. A detailed comparison of the merits and drawbacks of the experimental and computational techniques used in this work has also been made, and strategies for effective combination of the methodologies in structure-based projects are outlined.
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Duraj-Thatte, Anna. "Fluorescent GFP chromophores as potential ligands for various nuclear receptors." Diss., Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/44764.

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Nuclear receptors are ligand activated transcription factors, where upon binding with small molecule ligands, these proteins are involved in the regulation of gene expression. To date there are approximately 48 human nuclear receptors known, involved in multiple biological and cellular processes, ranging from differentiation to maintenance of homeostasis. Due to their critical role in transcriptional regulation, these receptors are implicated in several diseases. Currently, 13% of prescribed drugs in the market are NR ligands for diseases such as cancer, diabetes and osteoporosis. In addition to drug discovery, the mechanism of function, mobility and trafficking of these receptors is poorly understood. Gaining insight into the relationship between the function and /or dysfunction of these receptors and their mobility will aid in a better understanding of the role of these receptors. The green fluorescent protein (GFP) has revolutionized molecular biology by providing the ability to monitor protein function and structure via fluorescence. The fluorescence contribution from this biological marker is the chromophore, formed from the polypeptide backbone of three amino acid residues, buried inside 11-stranded â-barrel protein. Synthesis of GFP derivatives of is based on the structure of the arylmethyleneimidazolidinone (AMI), creating a molecule that is only weakly fluorescent. Characterizing these AMI derivatives for other proteins can provide a powerful visualization tool for analysis of protein function and structure. This development could provide a very powerful method for protein analysis in vitro and in vivo. Development of such fluorescent ligands will prove beneficial for the nuclear receptors. In this work, libraries of AMIs derviatives were synthesized by manipulating various R groups around the core structure, and tested for their ability to serve as nuclear receptor ligands with the ability to fluoresce upon binding. The fluorogens are developed for steroidal and non-steroidal receptors, two general classes of nuclear receptors. Specific AMIs were designed and developed for steroid receptor estrogen receptor á (ERá). These ligands are showed to activate the receptor with an EC50 of value 3 ìM and the 10-fold activation with AMI 1 and AMI 2 in comparison to the 21-fold activation observed with natural ERá ligand, 17â-estradiol. These novel ligands were not able to display the fluorescence upon binding the receptor. However, fluorescence localized in nucleus was observed in case of another AMI derivative, AMI 10, which does not activate the receptor. Such ligands open new avenues for developing fluorescent probes for ERá that do not involve fluorescent conjugates attached to a known ERá ligand core. AMIs were also characterized for non-steroidal receptors,specifically the pregnane x receptor (PXR) and retinoic acid receptor á (RARá). To date, fluorogens which turn fluorescence upon binding and activate the receptor have not been developed for these receptors. With respect to PXR, several AMI derivatives were discovered to bind and activate this receptor with a fold-activation better than the known agonist, rifampicin. The best characterized AMI derivative, AMI 4, activates the receptor with an EC50 of value 6.3 ìM and the 154-fold activation in comparison to the 90-fold activation and an EC50 value of 1.3 ìM seen with rifamipicin. This ligand is not only able to activate PXR but also displays fluorescence upon binding to the receptor. The fluroscence pattern was observed around the nucleus. Besides AMI 4, 16 other AMI derivatives are identified that activate PXR with different activation profiles. Thus, a novel class of PXR ligands with fluorescence ability has been developed. The AMI derivatives able to bind and activate RAR, also displayed activation profiles that were comparable to the wild-type ligand, all trans retinoic acid. These ligands activated the receptor with an EC50 value of 220 nM with AMI 109 in comparison to an EC50 value of 0.8 nM with the natural ligand for RARá. When these ligands were tested for fluorescence in yeast, the yeast were able to fluoresce only in the presence of the receptor and the AMI derivative, indicating that these agonists also have the ability to fluoresce.
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Tosch, Paul. "Investigations of ephrin ligands during development." Title page, abstract and table of contents only, 2002. http://web4.library.adelaide.edu.au/theses/09PH/09pht713.pdf.

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"May 2002." Addendum inside back cover. Bibliography: p. 139-157. Aims to isolate ephrin ligands from Drosophila melanogaster and analyse their involvement in Drosophila deveopment. Also investigates the potential of ephrin B-1 as a causative gene in the human condition Aicardi's syndrome.
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Robinson, Daniel D. "Applications of pattern recognition and pattern analysis to molecule design." Thesis, University of Oxford, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.343465.

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Boussert, Stéphanie Van Dorsselaer Alain Giralt Ernest. "Structural studies of proteins and protein complexes by mass spectrometry and atomic force microscopy." Strasbourg : Université Louis Pasteur, 2008. http://eprints-scd-ulp.u-strasbg.fr:8080/977/01/BOUSSERT_Stephanie_2008.pdf.

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Books on the topic "Protein; Ligands"

1

Neve, Kim A., ed. Functional Selectivity of G Protein-Coupled Receptor Ligands. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-335-0.

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Roterman, Irena, and Leszek Konieczny, eds. Self-Assembled Molecules – New Kind of Protein Ligands. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-65639-7.

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Siegfried, Schwarz. Molecules of life & mutations: Understanding diseases by understanding proteins. Basel: Karger, 2002.

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Schwarz, Siegfried. Molecules of life & mutations: Understanding diseases by understanding proteins. Basel: Karger, 2002.

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Schwarz, Siegfried. Molecules of life & mutations: Understanding diseases by understanding proteins. Basel: Karger, 2002.

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Protein-ligand interactions: Methods and applications. 2nd ed. New York: Humana Press, 2013.

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Johnson, Michael L., Jo M. Holt, and Gary K. Ackers. Biothermodynamics. Amsterdam [Netherlands]: Elsevier/Academic Press, 2011.

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Easterfield, Howard James. Analogues of phosphotyrosine: New components of ligands for protein tyrosine kinase enzymes. Birmingham: University of Birmingham, 1999.

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Hernandez, Marta. The study of ligand binding specificities of the lipid binding proteins: Recombinant human a-tocopherol transport protein (a-ttp), supernatant protein factor (spf) and S. cerevisiae Sec 14p for vitamin e (rrr-a-tocopherol) and other hydrophobic ligands. St. Catharines, Ont: Brock University, Dept. of Biotechnology, 2003.

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Nava, Phillip J. Synthesis of fluorescent analogues of a-tocopherol as ligands for the human a-tocopherol transfer protein (a-TTP). St. Catharines, Ont: Brock University, Centre for Biotechnology, 2006.

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Book chapters on the topic "Protein; Ligands"

1

Wang, Jianpeng. "Protein Ligands Engineering." In Springer Theses, 27–45. Berlin, Heidelberg: Springer Berlin Heidelberg, 2016. http://dx.doi.org/10.1007/978-3-662-53399-4_3.

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Dobrodziej, Jennifer, Hanqing Dong, Kurt Zimmermann, and Christopher M. Hickey. "Evaluating Ligands for Ubiquitin Ligases Using Affinity Beads." In Targeted Protein Degradation, 59–75. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1665-9_4.

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Pitt, William R., Mark D. Calmiano, Boris Kroeplien, Richard D. Taylor, James P. Turner, and Michael A. King. "Structure-Based Virtual Screening for Novel Ligands." In Protein-Ligand Interactions, 501–19. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-398-5_19.

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Kay, Brian K., Michael D. Scholle, and Fred J. Stevens. "EH Domains and Their Ligands." In Modular Protein Domains, 279–90. Weinheim, FRG: Wiley-VCH Verlag GmbH & Co. KGaA, 2005. http://dx.doi.org/10.1002/3527603611.ch14.

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Ciulli, Alessio. "Biophysical Screening for the Discovery of Small-Molecule Ligands." In Protein-Ligand Interactions, 357–88. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-398-5_13.

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Rybarska, Joanna, Barbara Piekarska, Barbara Stopa, Grzegorz Zemanek, Leszek Konieczny, and Irena Roterman. "Supramolecular Systems as Protein Ligands." In Self-Assembled Molecules – New Kind of Protein Ligands, 1–20. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-65639-7_1.

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Christianson, D. W., and W. N. Lipscomb. "Reaction Coordinate Approach to the Binding of Ligands to Carboxypeptidase A." In Protein Structure and Protein Engineering, 65–74. Berlin, Heidelberg: Springer Berlin Heidelberg, 1988. http://dx.doi.org/10.1007/978-3-642-74173-9_8.

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Sathish, Jean Gerard, and Reginald James Matthews. "SHP-1 twelve years on: structure, ligands, substrates and biological roles." In Protein Phosphatases, 301–31. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-540-40035-6_15.

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Sousa, Isabel T., and M. Ângela Taipa. "Biomimetic Affinity Ligands for Protein Purification." In Methods in Molecular Biology, 231–62. Totowa, NJ: Humana Press, 2014. http://dx.doi.org/10.1007/978-1-62703-977-2_20.

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Sousa, Isabel T., and M. Ângela Taipa. "Biomimetic Affinity Ligands for Protein Purification." In Methods in Molecular Biology, 167–99. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0775-6_14.

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Conference papers on the topic "Protein; Ligands"

1

Timkin, Pavel, E. Timofeev, A. Chupalov, and Evgeniy Borodin. "ANALYSIS AND SELECTION OF LIGANDS FOR TRPM8 USING HARD DOCKING AND MACHINE LEARNING." In XIV International Scientific Conference "System Analysis in Medicine". Far Eastern Scientific Center of Physiology and Pathology of Respiration, 2020. http://dx.doi.org/10.12737/conferencearticle_5fe01d9b233509.17835494.

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In this work, using the in-silico experiment modeling method, the receptor and its ligands were docked in order to obtain the data necessary to study the possibility of using machine learning and hard intermolecular docking methods to predict potential ligands for various receptors. The protein TRPM8 was chosen, which is a member of the TRP superfamily of proteins and its classic agonist menthol as a ligand. It is known that menthol is able to bind to tyrosine 745 of the B chain. To carry out all the manipulations, we used the Autodock software and a special set of graphic tools designed to work with in silico models of chemicals. As a result of all the manipulations, the menthol conformations were obtained that can bind to the active center of the TRPM8 receptor.
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Howl, John. "Chimeric ligands for G-protein-coupled receptors." In VIth Conference Biologically Active Peptides. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 1999. http://dx.doi.org/10.1135/css199903009.

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ERGUNER, BEKIR, MASAHIRO HATTORI, SUSUMU GOTO, and MINORU KANEHISA. "CHARACTERIZING COMMON SUBSTRUCTURES OF LIGANDS FOR GPCR PROTEIN SUBFAMILIES." In Proceedings of the 10th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2010). IMPERIAL COLLEGE PRESS, 2010. http://dx.doi.org/10.1142/9781848166585_0003.

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Cuppoletti, John. "Composite Synthetic Membranes Containing Native and Engineered Transport Proteins." In ASME 2008 Conference on Smart Materials, Adaptive Structures and Intelligent Systems. ASMEDC, 2008. http://dx.doi.org/10.1115/smasis2008-449.

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Our membrane transport protein laboratory has worked with material scientists, computational chemists and electrical and mechanical engineers to design bioactuators and sensing devices. The group has demonstrated that it is possible to produce materials composed native and engineered biological transport proteins in a variety of synthetic porous and solid materials. Biological transport proteins found in nature include pumps, which use energy to produce gradients of solutes, ion channels, which dissipate ion gradients, and a variety of carriers which can either transport substances down gradients or couple the uphill movement of substances to the dissipation of gradients. More than one type of protein can be reconstituted into the membranes to allow coupling of processes such as forming concentration gradients with ion pumps and dissipating them with an ion channel. Similarly, ion pumps can provide ion gradients to allow the co-transport of another substance. These systems are relevant to bioactuation. An example of a bioactuator that has recently been developed in the laboratory was based on a sucrose-proton exchanger coupled to a proton pump driven by ATP. When coupled together, the net reaction across the synthetic membrane was ATP driven sucrose transport across a flexible membrane across a closed space. As sucrose was transported, net flow of water occurred, causing pressure and deformation of the membrane. Transporters are regulated in nature. These proteins are sensitive to voltage, pH, sensitivity to a large variety of ligands and they can be modified to gain or lose these responses. Examples of sensors include ligand gated ion channels reconstituted on solid and permeable supports. Such sensors have value as high throughput screening devices for drug screening. Other sensors that have been developed in the laboratory include sensors for membrane active bacterial products such as the anthrax pore protein. These materials can be self assembled or manufactured by simple techniques, allowing the components to be stored in a stable form for years before (self) assembly on demand. The components can be modified at the atomic level, and are composed of nanostructures. Ranges of sizes of structures using these components range from the microscopic to macroscopic scale. The transport proteins can be obtained from natural sources or can be produced by recombinant methods from the genomes of all kingdoms including archea, bacteria and eukaryotes. For example, the laboratory is currently studying an ion channel from a thermophile from deep sea vents which has a growth optimum of 90 degrees centigrade, and has membrane transport proteins with very high temperature stability. The transport proteins can also be genetically modified to produce new properties such as activation by different ligands or transport of new substances such as therapeutic agents. The structures of many of these proteins are known, allowing computational chemists to help understand and predict the transport processes and to guide the engineering of new properties for the transport proteins and the composite membranes. Supported by DARPA and USARMY MURI Award and AFOSR.
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Timmons, Sheila, and Jack Hawiger. "REGULATION OF PLATELET RECEPTORS FOR FIBRINOGEN AND VON WILLEBRAND FACTOR BY PROTEIN KINASE." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644674.

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Positive and negative regulation of platelet receptors for adhesive proteins, fibrinogen (F) and von Willebrand Factor (vWF) determines whether binding of these ligands will or will not take place. We have shown previously that ADP stimulates and cyclic AMP inhibits binding of F and vWF to human platelets. Now we show that positive regulation of F and vWF binding to platelets via the glycoprotein 11b/1111a complex is dependent on platelet Protein Kinase C, a calcium- and phospholipid-dependent enzyme. A potent activator of Protein Kinase C, phorbol-12-myristoyl-13-acetate (PMA) induced saturable and specific binding of F and vWF which was inhibited by synthetic peptides, gamma chain .dodecapeptide (gamma 400-411) and RGDS. The phosphorylation of 47kDa protein (P47), a marker of Protein Kinase C activation in platelets, preceded binding of F and vWF induced with PMA as well as with ADP and thrombin. Sphingosine, an inhibitor of Protein Kinase C, blocked binding of F and vWF to platelets stimulated with PMA, ADP, and thrombin. Inhibition of binding was concentration-dependent and it was accompanied by inhibition of platelet aggregation. Thus, stimulation of Protein Kinase C is required for exposure of platelet receptors for adhesive proteins whereas inhibition of Protein Kinase C prevents receptorexposure. Protein Kinase C fulfills the role of an intraplatelet signal transducer, regulating receptors for adhesive proteins, and constitutes a target for pharmacologic modulation of the adhesive interactions of platelets.
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Tobysheva, P. D., L. A. Khamidullina, I. S. Puzyrev, and A. V. Pestov. "Biological activity of complexes based on polycarbonyl ligands: assessment of the mode of action using molecular docking." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.249.

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Herre, Jurgen, Hans Gronlund, Heather Brookes, Ben Murton, Niyi Opaleye, Edwin Chilvers, Bart Lambrecht, et al. "Allergens As Immuno-Modulatory Proteins: The Cat Dander Protein FelD1 Enhances Toll-Like Receptor Activation By Lipid Ligands." In American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California. American Thoracic Society, 2012. http://dx.doi.org/10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a1415.

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Zhu, X. D., Y. Y. Fei, J. P. Landry, and Y. S. Sun. "Label-Free Screening Small Molecule Compounds for Protein Ligands with Optically Detected Microarrays." In Bio-Optics: Design and Application. Washington, D.C.: OSA, 2011. http://dx.doi.org/10.1364/boda.2011.bmc7.

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Zhu, X. D., Y. Y. Fei, J. P. Landry, and Y. S. Sun. "Screening Small Molecule Compounds for Protein Ligands with Label-Free, Optically Detected Microarrays." In Biomedical Optics. Washington, D.C.: OSA, 2010. http://dx.doi.org/10.1364/biomed.2010.btud13.

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Lee, Hae-Jeong, Marvi A. Matos, Lisa Pakstis, Marcus T. Cicerone, and Joy P. Dunkers. "Quantitation of Laminin Adsorbed Onto Polydimethylsiloxane Surfaces Using Various Treatment Protocols." In ASME 2008 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2008. http://dx.doi.org/10.1115/sbc2008-192785.

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There is considerable interest in how cells respond to mechanical stimuli, from the ligands used to transmit the stimulus to the signaling pathways initiated and the proteins expressed upon phenotype change [1]. Previous work focused on the evaluation of the quality of the extracellular matrix (ECM) coating and cell proliferation [2]. Our focus is the characterization of a flexible polymeric substrate, treated with ECM, used to induce tensile strain on cells. In this work, we expand our physical characterization of the protein modified polydimethylsiloxane (PDMS) surface by quantifying the coverage of laminin on PDMS, plasma-treated PDMS, and PDMS treated with plasma and aminopropyltrimethoxysilane (APTMS) (Silane_70 protocol) using X-ray reflectivity.
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Reports on the topic "Protein; Ligands"

1

Lehnert, B., and D. Allen. Targeted in vitro evolution of protein ligands. Office of Scientific and Technical Information (OSTI), November 2000. http://dx.doi.org/10.2172/767437.

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Zhou, Xia-Ying. Effects of ancillary ligands on selectivity of protein labeling with platinum(II) chloro complexes. Office of Scientific and Technical Information (OSTI), February 1990. http://dx.doi.org/10.2172/6941351.

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Shin, Seung-Uon. Antibody-NKG2D Ligand (Rae-1Beta) Fusion Protein for Breast Cancer Therapy. Fort Belvoir, VA: Defense Technical Information Center, August 2005. http://dx.doi.org/10.21236/ada446435.

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Bartsch, Richard A. New Proton-Ionizable, Calixarene-Based Ligands for Selective Metal Ion Separations. Office of Scientific and Technical Information (OSTI), June 2012. http://dx.doi.org/10.2172/1041406.

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Montal, Mauricio. Channel Protein Engineering: A Novel Approach towards the Molecular Dissection Determinants in Ligand-Regulated Channels. Fort Belvoir, VA: Defense Technical Information Center, February 1990. http://dx.doi.org/10.21236/ada219134.

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Dmitriev, Igor P., and Elena A. Kashentseva. Targeting of Adenovirus Vectors to Breast Cancer Mediated by Soluble Receptor-Ligand Fusion Proteins. Fort Belvoir, VA: Defense Technical Information Center, June 2002. http://dx.doi.org/10.21236/ada407364.

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Trewhella, J. The role of low frequency collective modes in biological function: Ligand binding and cooperativity in calcium-binding proteins. Office of Scientific and Technical Information (OSTI), November 2000. http://dx.doi.org/10.2172/768788.

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