Journal articles: 'Ionic and molecular recognition'

1

Liu, Zhilian, Lin Jiang, Zhi Liang, and Yunhua Gao. "Photo-switchable molecular devices based on metal-ionic recognition." Tetrahedron Letters 46, no. 5 (January 2005): 885–87. http://dx.doi.org/10.1016/j.tetlet.2004.11.164.

Full text

APA, Harvard, Vancouver, ISO, and other styles

2

Jha, Kshitij C., Hua Liu, Michael R. Bockstaller, and Hendrik Heinz. "Facet Recognition and Molecular Ordering of Ionic Liquids on Metal Surfaces." Journal of Physical Chemistry C 117, no. 49 (November 27, 2013): 25969–81. http://dx.doi.org/10.1021/jp4032404.

Full text

APA, Harvard, Vancouver, ISO, and other styles

3

Machado, Isabel, Veli Cengiz Özalp, Elixabete Rezabal, and Thomas Schäfer. "DNA Aptamers are Functional Molecular Recognition Sensors in Protic Ionic Liquids." Chemistry - A European Journal 20, no. 37 (July 25, 2014): 11820–25. http://dx.doi.org/10.1002/chem.201403354.

Full text

APA, Harvard, Vancouver, ISO, and other styles

4

Ta, Daniel D., and Sergei V. Dzyuba. "Squaraine-Based Optical Sensors: Designer Toolbox for Exploring Ionic and Molecular Recognitions." Chemosensors 9, no. 11 (October 25, 2021): 302. http://dx.doi.org/10.3390/chemosensors9110302.

Full text

Abstract:

Small molecule-based chromogenic and fluorogenic probes play an indispensable role in many sensing applications. Ideal optical chemosensors should provide selectivity and sensitivity towards a variety of analytes. Synthetic accessibility and attractive photophysical properties have made squaraine dyes an enticing platform for the development of chemosensors. This review highlights the versatility of modular assemblies of squaraine-based chemosensors and chemodosimeters that take advantage of the availability of various structurally and functionally diverse recognition motifs, as well as utilizing additional recognition capabilities due to the unique structural features of the squaraine ring.

APA, Harvard, Vancouver, ISO, and other styles

5

Faul, Charl F. J., Philipp Krattiger, Bernd M. Smarsly, and Helma Wennemers. "Ionic self-assembled molecular receptor-based liquid crystals with tripeptide recognition capabilities." Journal of Materials Chemistry 18, no. 25 (2008): 2962. http://dx.doi.org/10.1039/b802690d.

Full text

APA, Harvard, Vancouver, ISO, and other styles

6

Rebek, J., and D. Nemeth. "Molecular recognition: ionic and aromatic stacking interactions bind complementary functional groups in a molecular cleft." Journal of the American Chemical Society 108, no. 18 (September 1986): 5637–38. http://dx.doi.org/10.1021/ja00278a052.

Full text

APA, Harvard, Vancouver, ISO, and other styles

7

Tlili, Amal, Ghada Attia, Sohayb Khaoulani, Zouhour Mazouz, Chouki Zerrouki, Nourdin Yaakoubi, Ali Othmane, and Najla Fourati. "Contribution to the Understanding of the Interaction between a Polydopamine Molecular Imprint and a Protein Model: Ionic Strength and pH Effect Investigation." Sensors 21, no. 2 (January 17, 2021): 619. http://dx.doi.org/10.3390/s21020619.

Full text

Abstract:

Several studies were devoted to the design of molecularly imprinted polymer (MIP)-based sensors for the detection of a given protein. Here, we bring elements that could contribute to the understanding of the interaction mechanism involved in the recognition of a protein by an imprint. For this purpose, a polydopamine (PDA)-MIP was designed for bovine serum albumin (BSA) recognition. Prior to BSA grafting, the gold surfaces were functionalized with mixed self-assembled monolayers of (MUDA)/(MHOH) (1/9, v/v). The MIP was then elaborated by dopamine electropolymerization and further extraction of BSA templates by incubating the electrode in proteinase K solution. Three complementary techniques, electrochemistry, zetametry, and Fourier-transform infrared spectrometry, were used to investigate pH and ionic strength effects on a MIP’s design and the further recognition process of the analytes by the imprints. Several MIPs were thus designed in acidic, neutral, and basic media and at various ionic strength values. Results indicate that the most appropriate conditions, to achieve a successful MIPs, were an ionic strength of 167 mM and a pH of 7.4. Sensitivity and dissociation constant of the designed sensor were of order of (3.36 ± 0.13) µA·cm−2·mg−1·mL and (8.56 ± 6.09) × 10−11 mg/mL, respectively.

APA, Harvard, Vancouver, ISO, and other styles

8

SUGAWARA, Masao, Kazunori ODASHIMA, and Yoshio UMEZAWA. "Novel approaches to molecular recognition of ionic and neutral species by using membranes." membrane 15, no. 3 (1990): 112–20. http://dx.doi.org/10.5360/membrane.15.112.

Full text

APA, Harvard, Vancouver, ISO, and other styles

9

Xu, Limin, Lingxiang Jiang, Markus Drechsler, Yu Sun, Zhirong Liu, Jianbin Huang, Ben Zhong Tang, Zhibo Li, Martien A. Cohen Stuart, and Yun Yan. "Self-Assembly of Ultralong Polyion Nanoladders Facilitated by Ionic Recognition and Molecular Stiffness." Journal of the American Chemical Society 136, no. 5 (January 23, 2014): 1942–47. http://dx.doi.org/10.1021/ja410443n.

Full text

APA, Harvard, Vancouver, ISO, and other styles

10

Gómez-González, Borja, Luis García-Río, Nuno Basílio, Juan C. Mejuto, and Jesus Simal-Gandara. "Molecular Recognition by Pillar[5]arenes: Evidence for Simultaneous Electrostatic and Hydrophobic Interactions." Pharmaceutics 14, no. 1 (December 28, 2021): 60. http://dx.doi.org/10.3390/pharmaceutics14010060.

Full text

Abstract:

The formation of inclusion complexes between alkylsulfonate guests and a cationic pillar[5]arene receptor in water was investigated by NMR and ITC techniques. The results show the formation of host-guest complexes stabilized by electrostatic interactions and hydrophobic effects with binding constants of up to 107 M−1 for the guest with higher hydrophobic character. Structurally, the alkyl chain of the guest is included in the hydrophobic aromatic cavity of the macrocycle while the sulfonate groups are held in the multicationic portal by ionic interactions.

APA, Harvard, Vancouver, ISO, and other styles

11

D’Amelio, Nicola, Benjamin Tanielian, Mourad Sadqi, Pilar López-Navajas, and Victor Muñoz. "Cognate DNA Recognition by Engrailed Homeodomain Involves a Conformational Change Controlled via an Electrostatic-Spring-Loaded Latch." International Journal of Molecular Sciences 23, no. 5 (February 22, 2022): 2412. http://dx.doi.org/10.3390/ijms23052412.

Full text

Abstract:

Transcription factors must scan genomic DNA, recognize the cognate sequence of their control element(s), and bind tightly to them. The DNA recognition process is primarily carried out by their DNA binding domains (DBD), which interact with the cognate site with high affinity and more weakly with any other DNA sequence. DBDs are generally thought to bind to their cognate DNA without changing conformation (lock-and-key). Here, we used nuclear magnetic resonance and circular dichroism to investigate the interplay between DNA recognition and DBD conformation in the engrailed homeodomain (enHD), as a model case for the homeodomain family of eukaryotic DBDs. We found that the conformational ensemble of enHD is rather flexible and becomes gradually more disordered as ionic strength decreases following a Debye–Hückel’s dependence. Our analysis indicates that enHD’s response to ionic strength is mediated by a built-in electrostatic spring-loaded latch that operates as a conformational transducer. We also found that, at moderate ionic strengths, enHD changes conformation upon binding to cognate DNA. This change is of larger amplitude and somewhat orthogonal to the response to ionic strength. As a consequence, very high ionic strengths (e.g., 700 mM) block the electrostatic-spring-loaded latch and binding to cognate DNA becomes lock-and-key. However, the interplay between enHD conformation and cognate DNA binding is robust across a range of ionic strengths (i.e., 45 to 300 mM) that covers the physiologically-relevant conditions. Therefore, our results demonstrate the presence of a mechanism for the conformational control of cognate DNA recognition on a eukaryotic DBD. This mechanism can function as a signal transducer that locks the DBD in place upon encountering the cognate site during active DNA scanning. The electrostatic-spring-loaded latch of enHD can also enable the fine control of DNA recognition in response to transient changes in local ionic strength induced by variate physiological processes.

APA, Harvard, Vancouver, ISO, and other styles

12

Mamardashvili, Galina, Nugzar Mamardashvili, and Oscar Koifman. "Macrocyclic Receptors for Identification and Selective Binding of Substrates of Different Nature." Molecules 26, no. 17 (August 31, 2021): 5292. http://dx.doi.org/10.3390/molecules26175292.

Full text

Abstract:

Molecular recognition of host/guest molecules represents the basis of many biological processes and phenomena. Enzymatic catalysis and inhibition, immunological response, reproduction of genetic information, biological regulatory functions, the effects of drugs, and ion transfer—all these processes include the stage of structure recognition during complexation. The goal of this review is to solicit and publish the latest advances in the design and sensing and binding abilities of porphyrin-based heterotopic receptors with well-defined geometries, the recognition ability of which is realized due to ionic, H-bridge, charge transfer, hydrophobic, and hydrophilic interactions. The dissection of the considered low-energy processes at the molecular scale expands our capabilities in the development of effective systems for controlled recognition, selective delivery, and prolonged release of substrates of different natures (including drugs) to their sites of functioning.

APA, Harvard, Vancouver, ISO, and other styles

13

Zhao, Zhongliang, Caihong Zhu, Qianping Guo, Yan Cai, Xuesong Zhu, and Bin Li. "Preparation of lysozyme-imprinted nanoparticles on polydopamine-modified titanium dioxide using ionic liquid as a stabilizer." RSC Advances 9, no. 26 (2019): 14974–81. http://dx.doi.org/10.1039/c9ra00941h.

Full text

APA, Harvard, Vancouver, ISO, and other styles

14

Milman, Boris L., and Zeev B. Alfassi. "Detection and Identification of Cations and Anions of Ionic Liquids by Means of Electrospray Ionization Mass Spectrometry and Tandem Mass Spectrometry." European Journal of Mass Spectrometry 11, no. 1 (February 2005): 35–42. http://dx.doi.org/10.1255/ejms.663.

Full text

Abstract:

Electrospray ionization (ESI) and collision-induced dissociation (CID) spectra of nine ionic liquids have been measured. The main fragmentations of most of these ionic liquid cations were due to the loss of a butene molecule. In contrast to tetraalkylammonium ions, CID spectra of aromatic cations may represent insufficient information for unambiguous identification due to their only partial fragmentation. CID spectra of ionic liquid anions, however, allowed their reliable recognition, since isomers/isobars of such inorganic species are rare. Detection limits of cations and anions in a mixture of different ionic liquids seemed to depend on their surface activity as determined by the hydrophobicity of these species.

APA, Harvard, Vancouver, ISO, and other styles

15

Hosseini, Mir Wais, Dimitris Tsiourvas, Jean-Marc Planeix, Zili Sideratou, Nicolas Thomas, and Constantinos M. Paleos. "Molecular Networks Forming Crystalline and Liquid Crystalline Phases by Combined Hydrogen-Bonding and Ionic Interactions." Collection of Czechoslovak Chemical Communications 69, no. 5 (2004): 1161–68. http://dx.doi.org/10.1135/cccc20041161.

Full text

Abstract:

Molecular recognition of cyclic bisamidinium dication with a series of 4-alkoxybenzoates afforded materials exhibiting lamellar crystalline structures at low temperatures and highly ordered smectic phases at higher temperatures. The liquid crystalline behaviour was investigated by differential scanning calorimetry, polarized optical microscopy and established by X-ray diffraction. Combined hydrogen-bonding and ionic interactions resulted in supramolecular networks which have sufficient stability to maintain their structure at high temperatures following the melting of the long alkyl chains.

APA, Harvard, Vancouver, ISO, and other styles

16

Soda, Kunitsugu, Keiichi Kakuyama, and Yoichiro Miki. "Non-random ionic-charge distribution responsible for the structural stability and molecular recognition of proteins." Biosystems 43, no. 3 (August 1997): 199–204. http://dx.doi.org/10.1016/s0303-2647(97)00038-5.

Full text

APA, Harvard, Vancouver, ISO, and other styles

17

Tominaga, Yuichi, Takuya Kubo, Kunimitsu Kaya, and Ken Hosoya. "Effective Recognition on the Surface of a Polymer Prepared by Molecular Imprinting Using Ionic Complex." Macromolecules 42, no. 8 (April 28, 2009): 2911–15. http://dx.doi.org/10.1021/ma802880z.

Full text

APA, Harvard, Vancouver, ISO, and other styles

18

González, Laura, Belén Altava, Michael Bolte, M. Isabel Burguete, Eduardo García-Verdugo, and Santiago V. Luis. "Synthesis of Chiral Room Temperature Ionic Liquids from Amino Acids - Application in Chiral Molecular Recognition." European Journal of Organic Chemistry 2012, no. 26 (July 26, 2012): 4996–5009. http://dx.doi.org/10.1002/ejoc.201200607.

Full text

APA, Harvard, Vancouver, ISO, and other styles

19

Garcia-Rio, Luis, Nuno Basílio, and Vitor Francisco. "Counterion effect on sulfonatocalix[n]arene recognition." Pure and Applied Chemistry 92, no. 1 (January 28, 2020): 25–37. http://dx.doi.org/10.1515/pac-2019-0305.

Full text

Abstract:

AbstractSulfonatocalixarenes, like other ionic receptors, possess counterions that can affect the molecular recognition process. In the present review it is shown that the competitive effect of the alkaline cations frequently used as counterions determines not only the magnitude of the external guest association constant, but also the stoichiometry of the complexes. Experimental evidences are shown about the interaction of the counterions with sulfonatocalixarene, allowing to quantify its association equilibrium constants. The counterions recognition will be a competitive process that must be taken into account when investigating the interaction of calixarenes with an external guests. When the external guest is a neutral molecule it will be possible to form ternary complexes where the counterion shows a competitive and cooperative effect. By increasing the size of the receptor, sulfonatocalix[6] and sulfonatocalix[8]arene, the complexity of the system is increased due to the formation of counterion complexes with stoichiometries 1:1 and 1:2. In the presence of an external guest, the formation of heteroternary complexes with 1:1:1 stoichiometries including a counterion and an organic cation will be possible.

APA, Harvard, Vancouver, ISO, and other styles

20

Porteu, Fl, S. Palacin, A. Ruaudel-Teixier, and A. Barraud. "Synthesis of an ionic network by molecular recognition between two porphyrins at the air-water interface." Thin Solid Films 210-211 (April 1992): 769–72. http://dx.doi.org/10.1016/0040-6090(92)90399-v.

Full text

APA, Harvard, Vancouver, ISO, and other styles

21

Chaumont, Alain, and Georges Wipff. "Halide anion solvation and recognition by a macrotricyclic tetraammonium host in an ionic liquid: a molecular dynamics study." New Journal of Chemistry 30, no. 4 (2006): 537. http://dx.doi.org/10.1039/b518109g.

Full text

APA, Harvard, Vancouver, ISO, and other styles

22

Sedghamiz, Tahereh, and Maryam Bahrami. "Chiral ionic liquid interface as a chiral selector for recognition of propranolol enantiomers: A molecular dynamics simulations study." Journal of Molecular Liquids 292 (October 2019): 111441. http://dx.doi.org/10.1016/j.molliq.2019.111441.

Full text

APA, Harvard, Vancouver, ISO, and other styles

23

Ma, Wanwan, Yena An, and Kyung Ho Row. "Preparation and evaluation of a green solvent-based molecularly imprinted monolithic column for the recognition of proteins by high-performance liquid chromatography." Analyst 144, no. 21 (2019): 6327–33. http://dx.doi.org/10.1039/c9an01259a.

Full text

APA, Harvard, Vancouver, ISO, and other styles

24

Fan, Jie-Ping, Wen-Ya Dong, Xue-Hong Zhang, Jia-Xin Yu, Cong-Bo Huang, Li-Juan Deng, Hui-Ping Chen, and Hai-Long Peng. "Preparation and Characterization of Protein Molecularly Imprinted Poly (Ionic Liquid)/Calcium Alginate Composite Cryogel Membrane with High Mechanical Strength for the Separation of Bovine Serum Albumin." Molecules 27, no. 21 (October 27, 2022): 7304. http://dx.doi.org/10.3390/molecules27217304.

Full text

Abstract:

In order to improve the mechanical strength and imprinting efficiency, a novel bovine serum albumin (BSA) molecularly imprinted poly(ionic liquid)/calcium alginate composite cryogel membrane (MICM) was prepared. The results of the tensile test indicated that the MICM had excellent mechanical strength which could reach up to 90.00 KPa, 30.30 times higher than the poly (ionic liquid) membrane without calcium alginate; the elongation of it could reach up to 93.70%, 8.28 times higher than the poly (ionic liquid) membrane without calcium alginate. The MICM had a very high welling ratio of 1026.56% and macropore porosity of 62.29%, which can provide effective mass transport of proteins. More remarkably, it had a very high adsorption capacity of 485.87 mg g−1 at 20 °C and 0.66 mg mL−1 of the initial concentration of BSA. Moreover, MICM also had good selective and competitive recognition toward BSA, exhibiting potential utility in protein separation. This work can provide a potential method to prepare the protein-imprinted cryogel membrane with both high mechanical strength and imprinting efficiency.

APA, Harvard, Vancouver, ISO, and other styles

25

McBean, G. J., and J. Flynn. "Molecular mechanisms of cystine transport." Biochemical Society Transactions 29, no. 6 (November 1, 2001): 717–22. http://dx.doi.org/10.1042/bst0290717.

Full text

Abstract:

The transport of l-cystine into cells of the mammalian brain is an essential step in the supply of cysteine for synthesis of the antioxidant glutathione. Uptake of lcystine in rat brain synaptosomes occurs by three mechanisms that are distinguishable on the basis of their ionic dependence, kinetics of transport and specificity of inhibitors. Almost 90°% of lcystine transport is by a low-affinity, sodium-dependent mechanism (Km = 473 ± 146 μM), that is mediated by the XAG-family of glutamate transporters. Both lglutamate (IC50 = 9.1 ± 0.4 μM) and lcysteine sulphinate (IC50 = 16.4 ± 3.6 μM) are non-competitive inhibitors of sodium-dependent l[14C]cystine transport, whereas ltrans-pyrrolidine-2,4-dicarboxylic acid (IC50 = 5.6 ± 2.0 μM), lserine-O-sulphate (IC50 = 13.2 ± 5.4 μM), kainate (IC50 = 215 ± 78 μM) and lcysteine (IC50 = 363 ± 63 μM) are competitive inhibitors. lCystine has no effect on the sodium-dependent uptake of D-[3H]aspartate. These results suggest that lcystine binds to a site that is different from the lglutamate recognition site on XAG-glutamate transporters. In rat brain slices, sodium-dependent transport of both lglutamate and lcystine is necessary for maintaining glutathione levels. Uptake of lcystine is sensitive to inhibition by an increased extracellular concentration of lglutamate, which has important implications for understanding conditions that may initiate oxidative stress.

APA, Harvard, Vancouver, ISO, and other styles

26

D’Urso, Alessandro, Jung Kyu Choi, Murtaza Shabbir-Hussain, Fidelis N. Ngwa, Maria I. Lambousis, Roberto Purrello, and Milan Balaz. "Recognition of left-handed Z-DNA of short unmodified oligonucleotides under physiological ionic strength conditions." Biochemical and Biophysical Research Communications 397, no. 2 (June 2010): 329–32. http://dx.doi.org/10.1016/j.bbrc.2010.05.119.

Full text

APA, Harvard, Vancouver, ISO, and other styles

27

Drouet, Christophe, Christian Rey, Christèle Combes, Sophie Cazalbou, Stephanie Sarda, and David Grossin. "Nanocrystalline Apatites: A Versatile Functionalizable Platform for Biomedical Applications for Bone Engineering… and beyond." Key Engineering Materials 696 (May 2016): 14–22. http://dx.doi.org/10.4028/www.scientific.net/kem.696.14.

Full text

Abstract:

This contribution gathers various examples illustrating the fact that nanocrystalline apatites represent a genuine multi-functionalizable platform for a wide range of biomedical applications. It is indeed possible to convey additional functionalities to the already appealing properties of biomimetic apatites, via appropriate ionic substitutions and/or through controlled molecular adsorptions. In link with bone regeneration, we depict here examples of enhanced osteoconduction/induction and of the addition of antibacterial features to bone implants. But we also point out the promise of apatite-based colloidal nanoparticles in other domains not related to bone, such as nanomedicine (cell diagnosis/therapy), which we address by conferring luminescence properties and by adding cell recognition abilities.

APA, Harvard, Vancouver, ISO, and other styles

28

Ustinova, Kseniya, Zora Novakova, Makoto Saito, Marat Meleshin, Jana Mikesova, Zsofia Kutil, Petra Baranova, et al. "The disordered N-terminus of HDAC6 is a microtubule-binding domain critical for efficient tubulin deacetylation." Journal of Biological Chemistry 295, no. 9 (January 17, 2020): 2614–28. http://dx.doi.org/10.1074/jbc.ra119.011243.

Full text

Abstract:

Histone deacetylase 6 (HDAC6) is a multidomain cytosolic enzyme having tubulin deacetylase activity that has been unequivocally assigned to the second of the tandem catalytic domains. However, virtually no information exists on the contribution of other HDAC6 domains on tubulin recognition. Here, using recombinant protein expression, site-directed mutagenesis, fluorimetric and biochemical assays, microscale thermophoresis, and total internal reflection fluorescence microscopy, we identified the N-terminal, disordered region of HDAC6 as a microtubule-binding domain and functionally characterized it to the single-molecule level. We show that the microtubule-binding motif spans two positively charged patches comprising residues Lys-32 to Lys-58. We found that HDAC6-microtubule interactions are entirely independent of the catalytic domains and are mediated by ionic interactions with the negatively charged microtubule surface. Importantly, a crosstalk between the microtubule-binding domain and the deacetylase domain was critical for recognition and efficient deacetylation of free tubulin dimers both in vitro and in vivo. Overall, our results reveal that recognition of substrates by HDAC6 is more complex than previously appreciated and that domains outside the tandem catalytic core are essential for proficient substrate deacetylation.

APA, Harvard, Vancouver, ISO, and other styles

29

Shamovsky, Igor L., Gregory M. Ross, Richard J. Riopelle, and Donald F. Weaver. "Molecular modelling studies of a nerve growth factor receptor." Canadian Journal of Chemistry 76, no. 10 (October 1, 1998): 1389–401. http://dx.doi.org/10.1139/v98-183.

Full text

Abstract:

Using computer simulations, a geometry for the receptor binding site for nerve growth factor (NGF) has been proposed. Variable basis Monte Carlo simulated annealing calculations have been used to ascertain the structures of the complexes of four fully active NGF analogues with the second leucine-rich motif (LRM-2) of trkA, a putative binding site for NGF. The previously suggested bioactive conformation of the amino and carboxyl termini of NGF docks favourably with the receptor defined by the LRM-2 of trkA: only minor conformational changes take place in the NGF analogues upon docking. Extensive intermolecular van der Waals contacts arise from the geometric fit of the NGF binding domain to the LRM-2. Within this receptor environment, five distinct binding areas reveal a highly selective multiple-point NGF-trkA recognition based on hydrophobic, ionic, hydrogen bonding, and van der Waals interactions. Binding specificity is determined primarily by residues Lys100, Asp109, and Phe113 of trkA which bind to conserved NGF residues Asp16, Arg114, Lys115, and Phe7. An explicit atom-level model of the high-affinity NGF receptor is thus developed.Key words: NGF, trkA, leucine-rich motif, protein docking, Alzheimer's disease.

APA, Harvard, Vancouver, ISO, and other styles

30

Ciobanu, Marius, and Carmen-Simona Jordan. "Viologen capped by nucleobase—building blocks for functional materials: synthesis and structure–properties relationship." Journal of Materials Science 56, no. 35 (October 11, 2021): 19425–38. http://dx.doi.org/10.1007/s10853-021-06554-1.

Full text

Abstract:

AbstractThe current study presents a new class of functional derivatives (1–3) consisting of a dicationic viologen (4,4’-bipyridinium unit) (V2+) capped by nucleobases thymine (NB1), adenine (NB2), thymine/adenine (NB1, NB2), and ion-paired with amphiphilic anion 3,4,5-tris(dodecyloxy)benzene sulfonate (DOBS−). The target of our work focuses on the design and synthesis of molecular building blocks in which three different functionalities are combined: chromophore (V2+ unit), molecular recognition (NB unit), and thermotropic liquid crystal (DOBS unit). The resulted materials exhibit liquid crystalline properties at ambient temperature with significant particularities-induced by nucleobases in the mesogen structure. Structure–properties relationship study focuses on providing knowledge about (1) how the thermotropic, redox properties, thermochromism, or ionic conductive properties are influenced by the presence of purinic or pyrimidinic nucleobases, and (2) how effective is their ability to self-assembly by hydrogen bonding in nonpolar solvents. The presence of nucleobases has been proved to have a substantial impact on electron transfer rate during the reduction of viologen moieties by intermolecular aggregation. Ionic conductivity and thermochromic properties of derivatives 1–3 were investigated and compared to a non-containing nucleobase analog methyl viologen with 3,4,5-tris(dodecyloxy)benzene sulfonate anion (MV) as reference. Graphical abstract

APA, Harvard, Vancouver, ISO, and other styles

31

Henderson, J. Nathan, Agnieszka M. Kuriata, Raimund Fromme, Michael E. Salvucci, and Rebekka M. Wachter. "Atomic Resolution X-ray Structure of the Substrate Recognition Domain of Higher Plant Ribulose-bisphosphate Carboxylase/Oxygenase (Rubisco) Activase." Journal of Biological Chemistry 286, no. 41 (August 31, 2011): 35683–88. http://dx.doi.org/10.1074/jbc.c111.289595.

Full text

Abstract:

The rapid release of tight-binding inhibitors from dead-end ribulose-bisphosphate carboxylase/oxygenase (Rubisco) complexes requires the activity of Rubisco activase, an AAA+ ATPase that utilizes chemo-mechanical energy to catalyze the reactivation of Rubisco. Activase is thought to play a central role in coordinating the rate of CO2 fixation with the light reactions of photosynthesis. Here, we present a 1.9 Å crystal structure of the C-domain core of creosote activase. The fold consists of a canonical four-helix bundle, from which a paddle-like extension protrudes that entails a nine-turn helix lined by an irregularly structured peptide strand. The residues Lys-313 and Val-316 involved in the species-specific recognition of Rubisco are located near the tip of the paddle. An ionic bond between Lys-313 and Glu-309 appears to stabilize the glycine-rich end of the helix. Structural superpositions onto the distant homolog FtsH imply that the paddles extend away from the hexameric toroid in a fan-like fashion, such that the hydrophobic sides of each blade bearing Trp-302 are facing inward and the polar sides bearing Lys-313 and Val-316 are facing outward. Therefore, we speculate that upon binding, the activase paddles embrace the Rubisco cylinder by placing their hydrophobic patches near the partner protein. This model suggests that conformational adjustments at the remote end of the paddle may relate to selectivity in recognition, rather than specific ionic contacts involving Lys-313. Additionally, the superpositions predict that the catalytically critical Arg-293 does not interact with the bound nucleotide. Hypothetical ring-ring stacking and peptide threading models for Rubisco reactivation are briefly discussed.

APA, Harvard, Vancouver, ISO, and other styles

32

Xiang, Haiyan, Mijun Peng, Hui Li, Sheng Peng, and Shuyun Shi. "High-capacity hollow porous dummy molecular imprinted polymers using ionic liquid as functional monomer for selective recognition of salicylic acid." Journal of Pharmaceutical and Biomedical Analysis 133 (January 2017): 75–81. http://dx.doi.org/10.1016/j.jpba.2016.11.007.

Full text

APA, Harvard, Vancouver, ISO, and other styles

33

Ponzi, Aurora, Marin Sapunar, Nadja Došlić, and Piero Decleva. "Discrimination of Excited States of Acetylacetone through Theoretical Molecular-Frame Photoelectron Angular Distributions." Molecules 27, no. 6 (March 10, 2022): 1811. http://dx.doi.org/10.3390/molecules27061811.

Full text

Abstract:

Photoelectron angular distribution (PAD) in the laboratory frame for randomly oriented molecules is typically described by a single anisotropy parameter, the so-called asymmetry parameter. However, especially from a theoretical perspective, it is more natural to consider molecular photoionization by using a molecular frame. The molecular frame PADs (MFPADs) may be used to extract information about the electronic structure of the system studied. In the last decade, significant experimental efforts have been directed to MFPAD measurements. MFPADs are highly characterizing signatures of the final ionic states. In particular, they are very sensitive to the nature of the final state, which is embodied in the corresponding Dyson orbital. In our previous work on acetylacetone, a prototype system for studying intra-molecular hydrogen bond interactions, we followed the dynamics of the excited states involved in the photoexcitation–deexcitation process of this molecule. It remains to be explored the possibility of discriminating between different excited states through the MFPAD profiles. The calculation of MFPADs to differentiate excited states can pave the way to the possibility of a clear discrimination for all the cases where the recognition of excited states is otherwise intricate.

APA, Harvard, Vancouver, ISO, and other styles

34

Flieger, Jolanta, Joanna Feder-Kubis, and Małgorzata Tatarczak-Michalewska. "Chiral Ionic Liquids: Structural Diversity, Properties and Applications in Selected Separation Techniques." International Journal of Molecular Sciences 21, no. 12 (June 15, 2020): 4253. http://dx.doi.org/10.3390/ijms21124253.

Full text

Abstract:

Ionic liquids (ILs) are chemical compounds composed of ions with melting points below 100 °C exhibiting a design feature. ILs are commonly used as the so-called green solvents, reagents or highly efficient catalysts in varied chemical processes. The huge application potential of ionic liquids (IL) justifies the growing interest in these compounds. In the last decade, increasing attention has been devoted to the development of new methods in the synthesis of stable chiral ionic liquids (CILs) and their application in various separation techniques. The beginnings of the successful use of CILs to separate enantiomers date back to the 1990 s. Most chiral ILs are based on chiral cations or chiral anions. There is also a limited number of CILs possessing both a chiral cation and a chiral anion. Due to the high molecular diversity of both ions, of which at least one has a chiral center, we have the possibility to design a large variety of optically active structures, thus expanding the range of CIL applications. Research utilizing chiral ionic liquids only recently has become more popular. However, it is the area that still has great potential for future development. This review aimed to describe the diversity of structures, properties and examples of applications of chiral ionic liquids as new chiral solid materials and chiral components of the anisotropic environment, providing chiral recognition of enantiomeric analytes, which is useful in liquid chromatography, countercurrent chromatography and other various CIL-based extraction techniques including aqueous biphasic (ABS) extraction systems, solid–liquid two-phase systems, liquid–liquid extraction systems with hydrophilic CILs, liquid–liquid extraction systems with hydrophobic CILs, solid-phase extraction and induced-precipitation techniques developed in the recent years. The growing demand for pure enantiomers in the pharmaceutical and food industries sparks further development in the field of extraction and separation systems modified with CILs highlighting them as affordable and environmentally friendly both chiral selectors and solvents.

APA, Harvard, Vancouver, ISO, and other styles

35

Latif, Usman, Serpil Can, Hermann F. Sussitz, and Franz L. Dickert. "Molecular Imprinted Based Quartz Crystal Microbalance Sensors for Bacteria and Spores." Chemosensors 8, no. 3 (August 4, 2020): 64. http://dx.doi.org/10.3390/chemosensors8030064.

Full text

Abstract:

A molecular imprinting strategy was combined with mass-sensitive transducers to generate robust and reliable biomimetic sensor systems for the detection of bioparticles. The patterning of polymers with bioanalytes enabled us to detect Escherichia coli (E. coli) bacteria with quartz crystal microbalance (QCM). The QCM sensor results were compared with direct Atomic Force Microscopy (AFM) measurements—bacteria cells adhering to the sensor coatings were counted. The recognition sites generated by Bacillus subtilis (B. subtilis) spores could successfully and reversibly recognize the template analyte and ensured rapid sensing. Cross sensitive measurements clearly showed the advantage of the molecular imprinting strategy, by which spores of Bacillus species (subtilis and thuringiensis) could easily be differentiated and selectively detected. The growth of B. subtilis from its spores was observed at 42 °C in appropriate nutrient solution of glucose and ammonium sulfate over a period of 15 h. Moreover, the growth of B. subtilis bacteria from its respective spores was studied by increasing the glucose concentration until saturation effect of the sensor. The polymeric sensor coatings were patterned to fix the B. subtilis in order to investigate osmotic effects according to a frequency response of 400 Hz by altering the ionic strength of 0.1 M.

APA, Harvard, Vancouver, ISO, and other styles

36

Zhao, Xiubo, Fang Pan, Luis Garcia-Gancedo, Andrew J. Flewitt, Gregory M. Ashley, Jikui Luo, and Jian R. Lu. "Interfacial recognition of human prostate-specific antigen by immobilized monoclonal antibody: effects of solution conditions and surface chemistry." Journal of The Royal Society Interface 9, no. 75 (May 2, 2012): 2457–67. http://dx.doi.org/10.1098/rsif.2012.0148.

Full text

Abstract:

The specific recognition between monoclonal antibody (anti-human prostate-specific antigen, anti-hPSA) and its antigen (human prostate-specific antigen, hPSA) has promising applications in prostate cancer diagnostics and other biosensor applications. However, because of steric constraints associated with interfacial packing and molecular orientations, the binding efficiency is often very low. In this study, spectroscopic ellipsometry and neutron reflection have been used to investigate how solution pH, salt concentration and surface chemistry affect antibody adsorption and subsequent antigen binding. The adsorbed amount of antibody was found to vary with pH and the maximum adsorption occurred between pH 5 and 6, close to the isoelectric point of the antibody. By contrast, the highest antigen binding efficiency occurred close to the neutral pH. Increasing the ionic strength reduced antibody adsorbed amount at the silica–water interface but had little effect on antigen binding. Further studies of antibody adsorption on hydrophobic C8 (octyltrimethoxysilane) surface and chemical attachment of antibody on (3-mercaptopropyl)trimethoxysilane/4-maleimidobutyric acid N -hydroxysuccinimide ester-modified surface have also been undertaken. It was found that on all surfaces studied, the antibody predominantly adopted the ‘flat on’ orientation, and antigen-binding capabilities were comparable. The results indicate that antibody immobilization via appropriate physical adsorption can replace elaborate interfacial molecular engineering involving complex covalent attachments.

APA, Harvard, Vancouver, ISO, and other styles

37

Sun, Yang, Weishi Xue, Jianfeng Zhao, Qianqian Bao, Kailiang Zhang, Yupeng Liu, and Hua Li. "Direct Electrochemistry of Glucose Dehydrogenase-Functionalized Polymers on a Modified Glassy Carbon Electrode and Its Molecular Recognition of Glucose." International Journal of Molecular Sciences 24, no. 7 (March 24, 2023): 6152. http://dx.doi.org/10.3390/ijms24076152.

Full text

Abstract:

A glucose biosensor was layer-by-layer assembled on a modified glassy carbon electrode (GCE) from a nanocomposite of NAD(P)+-dependent glucose dehydrogenase, aminated polyethylene glycol (mPEG), carboxylic acid-functionalized multi-wall carbon nanotubes (fMWCNTs), and ionic liquid (IL) composite functional polymers. The electrochemical electrode was denoted as NF/IL/GDH/mPEG-fMWCNTs/GCE. The composite polymer membranes were characterized by cyclic voltammetry, ultraviolet-visible spectrophotometry, electrochemical impedance spectroscopy, scanning electron microscopy, and transmission electron microscopy. The cyclic voltammogram of the modified electrode had a pair of well-defined quasi-reversible redox peaks with a formal potential of −61 mV (vs. Ag/AgCl) at a scan rate of 0.05 V s−1. The heterogeneous electron transfer constant (ks) of GDH on the composite functional polymer-modified GCE was 6.5 s−1. The biosensor could sensitively recognize and detect glucose linearly from 0.8 to 100 µM with a detection limit down to 0.46 μM (S/N = 3) and a sensitivity of 29.1 nA μM−1. The apparent Michaelis–Menten constant (Kmapp) of the modified electrode was 0.21 mM. The constructed electrochemical sensor was compared with the high-performance liquid chromatography method for the determination of glucose in commercially available glucose injections. The results demonstrated that the sensor was highly accurate and could be used for the rapid and quantitative determination of glucose concentration.

APA, Harvard, Vancouver, ISO, and other styles

38

Gryl, Marlena. "Charge density and optical properties of multicomponent crystals containing active pharmaceutical ingredients or their analogues." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 71, no. 4 (July 24, 2015): 392–405. http://dx.doi.org/10.1107/s2052520615013505.

Full text

Abstract:

Active pharmaceutical ingredients (APIs), through their favourable donor/acceptor spatial distribution and synthon formation flexibility, are attractive building blocks in modern materials crystallography. The optical properties of a crystal strongly depend on two factors,i.e.the spatial distribution of molecules in the crystal structure and the electronic properties of molecular building blocks (dipole moments, polarizabilities, hyperpolarizabilities). Although the latter are easy to predict throughab initiocalculations, the former are not. Only a combination of experimental and theoretical charge density studies together with prediction and measurement of optical properties enable full analysis of the obtained functional material in terms of its usefulness in practical applications. This article presents design strategies of optical materials based on selected pharmaceutical molecules. Factors that contribute to molecular recognition in the four selected polar/chiral crystal phases (derived through charge density and Hirshfeld surfaces analysis) have been determined. Theoretically predicted optical properties of the molecular/ionic building blocks as well as bulk effects have been confirmed experimentally. This research is a first step in the design of novel optical materials based on push–pull molecules and APIs.

APA, Harvard, Vancouver, ISO, and other styles

39

Nardella, Caterina, Angelo Toto, Daniele Santorelli, Livia Pagano, Awa Diop, Valeria Pennacchietti, Paola Pietrangeli, Lucia Marcocci, Francesca Malagrinò, and Stefano Gianni. "Folding and Binding Mechanisms of the SH2 Domain from Crkl." Biomolecules 12, no. 8 (July 22, 2022): 1014. http://dx.doi.org/10.3390/biom12081014.

Full text

Abstract:

SH2 domains are structural modules specialized in the recognition and binding of target sequences containing a phosphorylated tyrosine residue. They are mostly incorporated in the 3D structure of scaffolding proteins that represent fundamental regulators of several signaling pathways. Among those, Crkl plays key roles in cell physiology by mediating signals from a wide range of stimuli, and its overexpression is associated with several types of cancers. In myeloid cells expressing the oncogene BCR/ABL, one interactor of Crkl-SH2 is the focal adhesion protein Paxillin, and this interaction is crucial in leukemic transformation. In this work, we analyze both the folding pathway of Crkl-SH2 and its binding reaction with a peptide mimicking Paxillin, under different ionic strength and pH conditions, by using means of fluorescence spectroscopy. From a folding perspective, we demonstrate the presence of an intermediate along the reaction. Moreover, we underline the importance of the electrostatic interactions in the early event of recognition, occurring between the phosphorylated tyrosine of the Paxillin peptide and the charge residues of Crkl-SH2. Finally, we highlight a pivotal role of a highly conserved histidine residue in the stabilization of the binding complex. The experimental results are discussed in light of previous works on other SH2 domains.

APA, Harvard, Vancouver, ISO, and other styles

40

Liu, Lingyu, Xudong Zhu, Yanbo Zeng, Hailong Wang, Yixia Lu, Jian Zhang, Zhengzhi Yin, Zhidong Chen, Yiwen Yang, and Lei Li. "An Electrochemical Sensor for Diphenylamine Detection Based on Reduced Graphene Oxide/Fe3O4-Molecularly Imprinted Polymer with 1,4-Butanediyl-3,3’-bis-l-vinylimidazolium Dihexafluorophosphate Ionic Liquid as Cross-Linker." Polymers 10, no. 12 (December 1, 2018): 1329. http://dx.doi.org/10.3390/polym10121329.

Full text

Abstract:

In this paper, we report a new composite of reduced graphene oxide/Fe3O4-ionic liquid based molecularly imprinted polymer (RGO/Fe3O4-IL-MIP) fabricated for diphenylamine (DPA) detection. RGO/Fe3O4-IL-MIP was prepared with RGO/Fe3O4 as supporter, ionic liquid 1-vinyl-3-butylimidazolium hexafluorophosphate ([VC4mim][PF6]) as functional monomer, ionic liquid 1,4-butanediyl-3,3’-bis-l-vinylimidazolium dihexafluorophosphate ([V2C4(mim)2][(PF6)2]) as cross-linker, and diphenylamine (DPA) as template molecule. Fourier transform infrared spectroscopy, thermal gravimetric analysis, scanning electron microscopy, and vibrating sample magnetometer were employed to characterize the RGO/Fe3O4-IL-MIP composite. RGO/Fe3O4-IL-MIP was then drop-cast onto a glassy carbon electrode to construct an electrochemical sensor for DPA. The differential pulse voltammetry (DPV) peak current response for 20 μM DPA of RGO/Fe3O4-IL-MIP modified glassy carbon electrode (GCE) was 3.24 and 1.68 times that of RGO/Fe3O4-IL-NIP and RGO/Fe3O4-EGDMA-MIP modified GCEs, respectively, indicating the advantage of RGO/Fe3O4-IL-MIP based on ionic liquid (IL) as a cross-linker. The RGO/Fe3O4-IL-MIP sensor demonstrated good recognition for DPA. Under the optimized conditions, the RGO/Fe3O4-IL-MIP sensor exhibited a DPA detection limit of 0.05 μM (S/N = 3) with a linear range of 0.1–30 μM. Moreover, the new RGO/Fe3O4-IL-MIP based sensor detected DPA in real samples with satisfactory results.

APA, Harvard, Vancouver, ISO, and other styles

41

Dragomir, Isabela S., Alina Asandei, Irina Schiopu, Ioana C. Bucataru, Loredana Mereuta, and Tudor Luchian. "The Nanopore-Tweezing-Based, Targeted Detection of Nucleobases on Short Functionalized Peptide Nucleic Acid Sequences." Polymers 13, no. 8 (April 9, 2021): 1210. http://dx.doi.org/10.3390/polym13081210.

Full text

Abstract:

The implication of nanopores as versatile components in dedicated biosensors, nanoreactors, or miniaturized sequencers has considerably advanced single-molecule investigative science in a wide range of disciplines, ranging from molecular medicine and nanoscale chemistry to biophysics and ecology. Here, we employed the nanopore tweezing technique to capture amino acid-functionalized peptide nucleic acids (PNAs) with α-hemolysin-based nanopores and correlated the ensuing stochastic fluctuations of the ionic current through the nanopore with the composition and order of bases in the PNAs primary structure. We demonstrated that while the system enables the detection of distinct bases on homopolymeric PNA or triplet bases on heteropolymeric strands, it also reveals rich insights into the conformational dynamics of the entrapped PNA within the nanopore, relevant for perfecting the recognition capability of single-molecule sequencing.

APA, Harvard, Vancouver, ISO, and other styles

42

Shepard, Caroline P., Raymond G. Emehiser, Saswata Karmakar, and Patrick J. Hrdlicka. "Factors Impacting Invader-Mediated Recognition of Double-Stranded DNA." Molecules 28, no. 1 (December 23, 2022): 127. http://dx.doi.org/10.3390/molecules28010127.

Full text

Abstract:

The development of chemically modified oligonucleotides enabling robust, sequence-unrestricted recognition of complementary chromosomal DNA regions has been an aspirational goal for scientists for many decades. While several groove-binding or strand-invading probes have been developed towards this end, most enable recognition of DNA only under limited conditions (e.g., homopurine or short mixed-sequence targets, low ionic strength, fully modified probe strands). Invader probes, i.e., DNA duplexes modified with +1 interstrand zippers of intercalator-functionalized nucleotides, are predisposed to recognize DNA targets due to their labile nature and high affinity towards complementary DNA. Here, we set out to gain further insight into the design parameters that impact the thermal denaturation properties and binding affinities of Invader probes. Towards this end, ten Invader probes were designed, and their biophysical properties and binding to model DNA hairpins and chromosomal DNA targets were studied. A Spearman’s rank-order correlation analysis of various parameters was then performed. Densely modified Invader probes were found to result in efficient recognition of chromosomal DNA targets with excellent binding specificity in the context of denaturing or non-denaturing fluorescence in situ hybridization (FISH) experiments. The insight gained from the initial phase of this study informed subsequent probe optimization, which yielded constructs displaying improved recognition of chromosomal DNA targets. The findings from this study will facilitate the design of efficient Invader probes for applications in the life sciences.

APA, Harvard, Vancouver, ISO, and other styles

43

Kaur, Nirmaljeet, and Harish Kumar Chopra. "Synthesis and applications of carbohydrate based chiral ionic liquids as chiral recognition agents and organocatalysts." Journal of Molecular Liquids 298 (January 2020): 111994. http://dx.doi.org/10.1016/j.molliq.2019.111994.

Full text

APA, Harvard, Vancouver, ISO, and other styles

44

Yu, Raymond B., and Joselito P. Quirino. "Chiral Selectors in Capillary Electrophoresis: Trends During 2017–2018." Molecules 24, no. 6 (March 21, 2019): 1135. http://dx.doi.org/10.3390/molecules24061135.

Full text

Abstract:

Chiral separation is an important process in the chemical and pharmaceutical industries. From the analytical chemistry perspective, chiral separation is required for assessing the fit-for-purpose and the safety of chemical products. Capillary electrophoresis, in the electrokinetic chromatography mode is an established analytical technique for chiral separations. A water-soluble chiral selector is typically used. This review therefore examines the use of various chiral selectors in electrokinetic chromatography during 2017–2018. The chiral selectors were both low and high (macromolecules) molecular mass molecules as well as molecular aggregates (supramolecules). There were 58 papers found by search in Scopus, indicating continuous and active activity in this research area. The macromolecules were sugar-, amino acid-, and nucleic acid-based polymers. The supramolecules were bile salt micelles. The low molecular mass selectors were mainly ionic liquids and complexes with a central ion. A majority of the papers were on the use or preparation of sugar-based macromolecules, e.g., native or derivatised cyclodextrins. Studies to explain chiral recognition of macromolecular and supramolecular chiral selectors were mainly done by molecular modelling and nuclear magnetic resonance spectroscopy. Demonstrations were predominantly on drug analysis for the separation of racemates.

APA, Harvard, Vancouver, ISO, and other styles

45

Stickney, Leigh M., Janet S. Hankins, Xin Miao, and George A. Mackie. "Function of the Conserved S1 and KH Domains in Polynucleotide Phosphorylase." Journal of Bacteriology 187, no. 21 (November 1, 2005): 7214–21. http://dx.doi.org/10.1128/jb.187.21.7214-7221.2005.

Full text

Abstract:

ABSTRACT We have examined the roles of the conserved S1 and KH RNA binding motifs in the widely dispersed prokaryotic exoribonuclease polynucleotide phosphorylase (PNPase). These domains can be released from the enzyme by mild proteolysis or by truncation of the gene. Using purified recombinant enzymes, we have assessed the effects of specific deletions on RNA binding, on activity against a synthetic substrate under multiple-turnover conditions, and on the ability of truncated forms of PNPase to form a minimal RNA degradosome with RNase E and RhlB. Deletion of the S1 domain reduces the apparent activity of the enzyme by almost 70-fold under low-ionic-strength conditions and limits the enzyme to digest a single substrate molecule. Activity and product release are substantially regained at higher ionic strengths. This deletion also reduces the affinity of the enzyme for RNA, without affecting the enzyme's ability to bind to RNase E. Deletion of the KH domain produces similar, but less severe, effects, while deletion of both the S1 and KH domains accentuates the loss of activity, product release, and RNA binding but has no effect on binding to RNase E. We propose that the S1 domain, possibly arrayed with the KH domain, forms an RNA binding surface that facilitates substrate recognition and thus indirectly potentiates product release. The present data as well as prior observations can be rationalized by a two-step model for substrate binding.

APA, Harvard, Vancouver, ISO, and other styles

46

Li, Ji, Xiaoling Hu, Ping Guan, Renyuan Song, Xiangrong Zhang, Yimei Tang, Chaoli Wang, and Liwei Qian. "Preparation of core–shell structural surface molecular imprinting microspheres and recognition of l-Asparagine based on [N1111]Asn ionic liquid as template." Reactive and Functional Polymers 88 (March 2015): 8–15. http://dx.doi.org/10.1016/j.reactfunctpolym.2015.01.002.

Full text

APA, Harvard, Vancouver, ISO, and other styles

47

Ahmed, Mustapha Carab, Elena Papaleo, and Kresten Lindorff-Larsen. "How well do force fields capture the strength of salt bridges in proteins?" PeerJ 6 (June 11, 2018): e4967. http://dx.doi.org/10.7717/peerj.4967.

Full text

Abstract:

Salt bridges form between pairs of ionisable residues in close proximity and are important interactions in proteins. While salt bridges are known to be important both for protein stability, recognition and regulation, we still do not have fully accurate predictive models to assess the energetic contributions of salt bridges. Molecular dynamics simulation is one technique that may be used study the complex relationship between structure, solvation and energetics of salt bridges, but the accuracy of such simulations depends on the force field used. We have used NMR data on the B1 domain of protein G (GB1) to benchmark molecular dynamics simulations. Using enhanced sampling simulations, we calculated the free energy of forming a salt bridge for three possible lysine-carboxylate ionic interactions in GB1. The NMR experiments showed that these interactions are either not formed, or only very weakly formed, in solution. In contrast, we show that the stability of the salt bridges is overestimated, to different extents, in simulations of GB1 using seven out of eight commonly used combinations of fixed charge force fields and water models. We also find that the Amber ff15ipq force field gives rise to weaker salt bridges in good agreement with the NMR experiments. We conclude that many force fields appear to overstabilize these ionic interactions, and that further work may be needed to refine our ability to model quantitatively the stability of salt bridges through simulations. We also suggest that comparisons between NMR experiments and simulations will play a crucial role in furthering our understanding of this important interaction.

APA, Harvard, Vancouver, ISO, and other styles

48

Ding, Qingquan, Shuichi Kusano, Merna Villarejo, and Akira Ishihama. "Promoter selectivity control of Escherichia coli RNA polymerase by ionic strength: differential recognition of osmoregulated promoters by E?Dand E?Sholoenzymes." Molecular Microbiology 16, no. 4 (May 1995): 649–56. http://dx.doi.org/10.1111/j.1365-2958.1995.tb02427.x.

Full text

APA, Harvard, Vancouver, ISO, and other styles

49

Araújo, Sofia J., Erich A. Nigg, and Richard D. Wood. "Strong Functional Interactions of TFIIH with XPC and XPG in Human DNA Nucleotide Excision Repair, without a Preassembled Repairosome." Molecular and Cellular Biology 21, no. 7 (April 1, 2001): 2281–91. http://dx.doi.org/10.1128/mcb.21.7.2281-2291.2001.

Full text

Abstract:

ABSTRACT In mammalian cells, the core factors involved in the damage recognition and incision steps of DNA nucleotide excision repair are XPA, TFIIH complex, XPC-HR23B, replication protein A (RPA), XPG, and ERCC1-XPF. Many interactions between these components have been detected, using different physical methods, in human cells and for the homologous factors in Saccharomyces cerevisiae. Several human nucleotide excision repair (NER) complexes, including a high-molecular-mass repairosome complex, have been proposed. However, there have been no measurements of activity of any mammalian NER protein complex isolated under native conditions. In order to assess relative strengths of interactions between NER factors, we captured TFIIH from cell extracts with an anti-cdk7 antibody, retaining TFIIH in active form attached to magnetic beads. Coimmunoprecipitation of other NER proteins was then monitored functionally in a reconstituted repair system with purified proteins. We found that all detectable TFIIH in gently prepared human cell extracts was present in the intact nine-subunit form. There was no evidence for a repair complex that contained all of the NER components. At low ionic strength TFIIH could associate with functional amounts of each NER factor except RPA. At physiological ionic strength, TFIIH associated with significant amounts of XPC-HR23B and XPG but not other repair factors. The strongest interaction was between TFIIH and XPC-HR23B, indicating a coupled role of these proteins in early steps of repair. A panel of antibodies was used to estimate that there are on the order of 105molecules of each core NER factor per HeLa cell.

APA, Harvard, Vancouver, ISO, and other styles

50

Cheon, Na Young, Hyun-Suk Kim, Jung-Eun Yeo, Orlando D. Schärer, and Ja Yil Lee. "Single-molecule visualization reveals the damage search mechanism for the human NER protein XPC-RAD23B." Nucleic Acids Research 47, no. 16 (August 2, 2019): 8337–47. http://dx.doi.org/10.1093/nar/gkz629.

Full text

Abstract:

Abstract DNA repair is critical for maintaining genomic integrity. Finding DNA lesions initiates the entire repair process. In human nucleotide excision repair (NER), XPC-RAD23B recognizes DNA lesions and recruits downstream factors. Although previous studies revealed the molecular features of damage identification by the yeast orthologs Rad4-Rad23, the dynamic mechanisms by which human XPC-RAD23B recognizes DNA defects have remained elusive. Here, we directly visualized the motion of XPC-RAD23B on undamaged and lesion-containing DNA using high-throughput single-molecule imaging. We observed three types of one-dimensional motion of XPC-RAD23B along DNA: diffusive, immobile and constrained. We found that consecutive AT-tracks led to increase in proteins with constrained motion. The diffusion coefficient dramatically increased according to ionic strength, suggesting that XPC-RAD23B diffuses along DNA via hopping, allowing XPC-RAD23B to bypass protein obstacles during the search for DNA damage. We also examined how XPC-RAD23B identifies cyclobutane pyrimidine dimers (CPDs) during diffusion. XPC-RAD23B makes futile attempts to bind to CPDs, consistent with low CPD recognition efficiency. Moreover, XPC-RAD23B binds CPDs in biphasic states, stable for lesion recognition and transient for lesion interrogation. Taken together, our results provide new insight into how XPC-RAD23B searches for DNA lesions in billions of base pairs in human genome.

APA, Harvard, Vancouver, ISO, and other styles

Journal articles on the topic 'Ionic and molecular recognition'

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles