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Journal articles on the topic 'Protein binding'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Sawicka, Kirsty, Martin Bushell, Keith A. Spriggs, and Anne E. Willis. "Polypyrimidine-tract-binding protein: a multifunctional RNA-binding protein." Biochemical Society Transactions 36, no. 4 (2008): 641–47. http://dx.doi.org/10.1042/bst0360641.

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PTB (polypyrimidine-tract-binding protein) is a ubiquitous RNA-binding protein. It was originally identified as a protein with a role in splicing but it is now known to function in a large number of diverse cellular processes including polyadenylation, mRNA stability and translation initiation. Specificity of PTB function is achieved by a combination of changes in the cellular localization of this protein (its ability to shuttle from the nucleus to the cytoplasm is tightly controlled) and its interaction with additional proteins. These differences in location and trans-acting factor requiremen

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2

Anil, Kumar Tomar, Saraswat Mayank, Singh Sooch Balwinder, Singh Sarman, P. Singh Tej, and Yadav Savita. "Prediction of Heparin binding sites on Human Serum Albumin, Matrix Metalloproteinase-2 and DNA Topoisomerase1." International Journal of BioSciences and Technology (IJBST) ISSN: 0974-3987 3, no. 1 (2010): 21–26. https://doi.org/10.5281/zenodo.1438292.

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<strong>ABSTRACT:</strong> Heparin binds a wide range of proteins of different structure as well as functions and play crucial roles in a number of biological processes. Human seminal plasma consists of many heparin binding proteins (HBPs). HBPs play crucial role in modulation of capacitation through heparin and have been correlated with fertility in many species. Very little scientific information is available about the binding modes of heparin and HBPs. There is not any well defined binding space, characterized by some consensus sequence over protein except that binding region always do cons

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3

Viswanathan, Raji, Eduardo Fajardo, Gabriel Steinberg, Matthew Haller, and Andras Fiser. "Protein—protein binding supersites." PLOS Computational Biology 15, no. 1 (2019): e1006704. http://dx.doi.org/10.1371/journal.pcbi.1006704.

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4

Wilkins, Anna L., Yiming Ye, Wei Yang, Hsiau-Wei Lee, Zhi-ren Liu, and Jenny J. Yang. "Metal-binding studies for a de novo designed calcium-binding protein." Protein Engineering, Design and Selection 15, no. 7 (2002): 571–74. http://dx.doi.org/10.1093/protein/15.7.571.

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5

NAKANO, Akihiko. "Protein Secretion and GTP-binding Proteins." Seibutsu Butsuri 31, no. 2 (1991): 53–57. http://dx.doi.org/10.2142/biophys.31.53.

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6

Rodilla-Sala, E., G. C. Lunazzi, W. Stremmel, and C. Tiribelli. "BSP-bilirubin binding protein, fatty acid binding protein and bilitranslocase are immunological distinct proteins." Journal of Hepatology 11 (January 1990): S53. http://dx.doi.org/10.1016/0168-8278(90)91545-8.

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7

Guo, Ting, Yanxin Shi, and Zhirong Sun. "A novel statistical ligand-binding site predictor: application to ATP-binding sites." Protein Engineering, Design and Selection 18, no. 2 (2005): 65–70. http://dx.doi.org/10.1093/protein/gzi006.

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8

ESPEJO, Alexsandra, Jocelyn CÔTÉ, Andrzej BEDNAREK, Stephane RICHARD, and Mark T. BEDFORD. "A protein-domain microarray identifies novel protein–protein interactions." Biochemical Journal 367, no. 3 (2002): 697–702. http://dx.doi.org/10.1042/bj20020860.

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Protein domains mediate protein—protein interactions through binding to short peptide motifs in their corresponding ligands. These peptide recognition modules are critical for the assembly of multiprotein complexes. We have arrayed glutathione S-transferase (GST) fusion proteins, with a focus on protein interaction domains, on to nitrocellulose-coated glass slides to generate a protein-domain chip. Arrayed protein-interacting modules included WW (a domain with two conserved tryptophans), SH3 (Src homology 3), SH2, 14.3.3, FHA (forkhead-associated), PDZ (a domain originally identified in PSD-95

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9

Lipovsek, D. "Adnectins: engineered target-binding protein therapeutics." Protein Engineering Design and Selection 24, no. 1-2 (2010): 3–9. http://dx.doi.org/10.1093/protein/gzq097.

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10

Siggers, Trevor, and Raluca Gordân. "Protein–DNA binding: complexities and multi-protein codes." Nucleic Acids Research 42, no. 4 (2013): 2099–111. http://dx.doi.org/10.1093/nar/gkt1112.

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Abstract Binding of proteins to particular DNA sites across the genome is a primary determinant of specificity in genome maintenance and gene regulation. DNA-binding specificity is encoded at multiple levels, from the detailed biophysical interactions between proteins and DNA, to the assembly of multi-protein complexes. At each level, variation in the mechanisms used to achieve specificity has led to difficulties in constructing and applying simple models of DNA binding. We review the complexities in protein–DNA binding found at multiple levels and discuss how they confound the idea of simple

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11

Nelson, R. M., and G. L. Long. "Binding of protein S to C4b-binding protein. Mutagenesis of protein S." Journal of Biological Chemistry 267, no. 12 (1992): 8140–45. http://dx.doi.org/10.1016/s0021-9258(18)42418-0.

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12

Fischer, B. E., U. Schlokat, M. Himmelspach, and F. Dorner. "Binding of hirudin to meizothrombin." Protein Engineering Design and Selection 11, no. 8 (1998): 715–21. http://dx.doi.org/10.1093/protein/11.8.715.

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13

Ma, Buyong, Sandeep Kumar, Chung-Jung Tsai, and Ruth Nussinov. "Folding funnels and binding mechanisms." Protein Engineering, Design and Selection 12, no. 9 (1999): 713–20. http://dx.doi.org/10.1093/protein/12.9.713.

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14

Jarvis, Jacqueline A., Sharon L. A. Munro, and David J. Craik. "Homology model of thyroxine binding globulin and elucidation of the thyroid hormone binding site." "Protein Engineering, Design and Selection" 5, no. 1 (1992): 61–67. http://dx.doi.org/10.1093/protein/5.1.61.

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15

Keller, Rob C. A. "Identification of Possible Lipid Binding Regions in Food Proteins and Peptides and Additional In Silico Analysis." Food Biophysics 13, no. 2 (2018): 139–46. https://doi.org/10.1007/s11483-018-9519-6.

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The results of the search for potential helical lipid binding regions in a number of well-known food proteins is described. All selected food proteins have either well-described or strong indications of protein-lipid interaction features. The results are obtained with the aid of a number of selected bioinformatics tools. The identified potential lipid binding regions either correspond nicely with regions demonstrated experimentally or can be identified as novel lipid binding regions. The results are discussed in relation to earlier found experimental results and if relevant are discussed in me

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16

Day, Austin L., Per Greisen, Lindsey Doyle, et al. "Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold." Protein Engineering, Design and Selection 31, no. 10 (2018): 375–87. http://dx.doi.org/10.1093/protein/gzy031.

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Abstract Attempts to create novel ligand-binding proteins often focus on formation of a binding pocket with shape complementarity against the desired ligand (particularly for compounds that lack distinct polar moieties). Although designed proteins often exhibit binding of the desired ligand, in some cases they display unintended recognition behavior. One such designed protein, that was originally intended to bind tetrahydrocannabinol (THC), was found instead to display binding of 25-hydroxy-cholecalciferol (25-D3) and was subjected to biochemical characterization, further selections for enhanc

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17

Takenaga, K., Y. Nakamura, S. Sakiyama, Y. Hasegawa, K. Sato, and H. Endo. "Binding of pEL98 protein, an S100-related calcium-binding protein, to nonmuscle tropomyosin." Journal of Cell Biology 124, no. 5 (1994): 757–68. http://dx.doi.org/10.1083/jcb.124.5.757.

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The cDNA coding for mouse fibroblast tropomyosin isoform 2 (TM2) was placed into a bacterial expression vector to produce a fusion protein containing glutathione-S-transferase (GST) and TM2 (GST/TM2). Glutathione-Sepharose beads bearing GST/TM2 were incubated with [35S]methionine-labeled NIH 3T3 cell extracts and the materials bound to the fusion proteins were analyzed to identify proteins that interact with TM2. A protein of 10 kD was found to bind to GST/TM2, but not to GST. The binding of the 10-kD protein to GST/TM2 was dependent on the presence of Ca2+ and inhibited by molar excess of fre

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18

Noy, Noa, and William S. Blaner. "Interactions of retinol with binding proteins: studies with rat cellular retinol-binding protein and with rat retinol-binding protein." Biochemistry 30, no. 26 (1991): 6380–86. http://dx.doi.org/10.1021/bi00240a005.

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19

Hisatomi, Osamu, Mari Kotoura, Daisuke Kitano, et al. "1P210 DNA-binding proteins expressed in regenerating newt retina(7. Nucleic acid binding protein,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S199. http://dx.doi.org/10.2142/biophys.46.s199_2.

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20

Knudtson, K. L., M. Boes, A. Sandra, B. L. Dake, B. A. Booth, and R. S. Bar. "Distribution of Chimeric IGF Binding Protein (IGFBP)-3 and IGFBP-4 in the Rat Heart: Importance of C-Terminal Basic Region." Endocrinology 142, no. 9 (2001): 3749–55. http://dx.doi.org/10.1210/endo.142.9.8353.

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Abstract IGF binding proteins-3 and -4, whether given in the perfused rat heart or given iv in the intact animal, cross the microvascular endothelium of the heart and distribute in subendothelial tissues. IGF binding protein-3, like IGF-I/II, localizes in cardiac muscle, with lesser concentrations in CT elements. In contrast, IGFBP-4 preferentially localizes in CT. In this study, chimeric IGF binding proteins were prepared in which a basic 20-amino-acid C-terminal region of IGF binding protein-3 was switched with the homologous region of IGF binding protein-4, and vice-versa, to create IGF bin

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21

Bertina, R. M., A. van Wijngaarden, J. Reinalda-Poot, S. R. Poort, and V. J. J. Bom. "Determination of Plasma Protein S - The Protein Cofactor of Activated Protein C." Thrombosis and Haemostasis 53, no. 02 (1985): 268–72. http://dx.doi.org/10.1055/s-0038-1661291.

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SummaryProtein S, an important cofactor of activated protein C, and C4b-binding protein were purified from human plasma. Specific antibodies against the purified proteins were raised in rabbits and used for the development of immunologic assays for these proteins in plasma: an immunoradiometric assay for protein S (which measures both free protein S and protein S complexed with C4b-binding protein) and an electroimmunoassay for C4b- binding protein. Ranges for the concentrations of these proteins were established in healthy volunteers and patients using oral anticoagulant therapy. A slight dec

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22

Sear, Richard P. "Specific protein–protein binding in many-component mixtures of proteins." Physical Biology 1, no. 2 (2004): 53–60. http://dx.doi.org/10.1088/1478-3967/1/2/001.

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23

Zhang, Jian, Zhiqiang Ma, and Lukasz Kurgan. "Comprehensive review and empirical analysis of hallmarks of DNA-, RNA- and protein-binding residues in protein chains." Briefings in Bioinformatics 20, no. 4 (2017): 1250–68. http://dx.doi.org/10.1093/bib/bbx168.

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Abstract Proteins interact with a variety of molecules including proteins and nucleic acids. We review a comprehensive collection of over 50 studies that analyze and/or predict these interactions. While majority of these studies address either solely protein–DNA or protein–RNA binding, only a few have a wider scope that covers both protein–protein and protein–nucleic acid binding. Our analysis reveals that binding residues are typically characterized with three hallmarks: relative solvent accessibility (RSA), evolutionary conservation and propensity of amino acids (AAs) for binding. Motivated

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24

Ozheriedov, D. S., and P. A. Karpov. "Structural profile of ligand-based inhibition of bacterial FtsZ." Faktori eksperimental'noi evolucii organizmiv 32 (September 1, 2023): 142–47. http://dx.doi.org/10.7124/feeo.v32.1551.

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Aim. The idea of the study was to compare and generalize RCSB Protein Data Bank and ChEMBL data in order to establish the structural and biological relationship of experimentaly proved effectors of FtsZ with binding sites. Methods. Literature and database search. Comparison of protein and ligand structures. Protein structure modeling, MD, structural superimposition, etc. Results. The experimental protein-ligand complexes structures of bacterial FtsZ were revised. The structural superimposition of experinental PDB and full-atomic AlphaFold2 models of bacterial FtsZs confirmed their significant

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25

Sani, B. P., A. Vaid, J. C. Comley, and J. A. Montgomery. "Novel retinoid-binding proteins from filarial parasites." Biochemical Journal 232, no. 2 (1985): 577–83. http://dx.doi.org/10.1042/bj2320577.

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The present study deals with the discovery and partial characterization of specific binding proteins for retinol and retinoic acid from filarial parasites (worms of the superfamily Filarioidea), including those from two species of Onchocerca. These binding proteins, which are distinct in their physicochemical properties and in the mode of ligand interactions from the host-tissue retinoid-binding proteins, may be involved in the mediation of the putative biological roles of retinoids in the control of parasitic growth, differentiation and reproduction. Parasite retinol-binding protein and retin

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26

MOHAN, ABHILASH, SHARMILA ANISHETTY, and PENNATHUR GAUTAM. "GLOBAL METAL-ION BINDING PROTEIN FINGERPRINT: A METHOD TO IDENTIFY MOTIF-LESS METAL-ION BINDING PROTEINS." Journal of Bioinformatics and Computational Biology 08, no. 04 (2010): 717–26. http://dx.doi.org/10.1142/s0219720010004884.

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Metal-ion binding proteins play a vital role in biological processes. Identifying putative metal-ion binding proteins is through knowledge-based methods. These involve the identification of specific motifs that characterize a specific class of metal-ion binding protein. Metal-ion binding motifs have been identified for the common metal ions. A robust global fingerprint that is useful in identifying a metal-ion binding protein from a non-metal-ion binding protein has not been devised. Such a method will help in identifying novel metal-ion binding proteins and proteins that do not possess a cano

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27

Turner, M. W. "Mannose binding protein." Biochemical Society Transactions 22, no. 1 (1994): 88–94. http://dx.doi.org/10.1042/bst0220088.

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28

Kraft, Robert, David N. Herndon, Gabriela A. Kulp, Gabriel A. Mecott, Heiko Trentzsch, and Marc G. Jeschke. "Retinol Binding Protein." Journal of Parenteral and Enteral Nutrition 35, no. 6 (2011): 695–703. http://dx.doi.org/10.1177/0148607111413901.

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29

Taylor, Frederick R., and Andrew A. Kandutsch. "Oxysterol binding protein." Chemistry and Physics of Lipids 38, no. 1-2 (1985): 187–94. http://dx.doi.org/10.1016/0009-3084(85)90066-0.

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30

Kimura, Hitomi, Robert Noiva, Takemitsu Mizunaga, et al. "Thyroid hormone binding protein contains glycosylation site binding protein activity." Biochemical and Biophysical Research Communications 170, no. 3 (1990): 1319–24. http://dx.doi.org/10.1016/0006-291x(90)90538-x.

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31

Neely, E. Kirk, Stephen D. Smith, and Ron G. Rosenfeld. "Human leukemic T and B lymphoblasts produce insulin-like growth factor binding proteins 2 and 4." Acta Endocrinologica 124, no. 6 (1991): 707–14. http://dx.doi.org/10.1530/acta.0.1240707.

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Abstract. The production of insulin-like growth factors and insulin-like growth factor binding proteins by twelve human leukemic lymphoblast cell lines was evaluated by radioimmunoassay, affinity cross-linking, ligand blot, and immunoprecipitation of conditioned media. In all cell lines, detectable IGF-I and IGF-II levels were <0.1 μg/l and <0.3 μg/l, respectively. IGF binding proteins were identified in 6/12 of the lymphoblast cell lines studied. A pair of IGF binding proteins at 31 and 33 kD, immunoprecipitated with an antibody recognizing IGF binding protein 2 but not by an IGF bindin

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32

Mazen, Alice, Gérard Gradwohl, and Gilbert de Murcia. "Zinc-binding proteins detected by protein blotting." Analytical Biochemistry 172, no. 1 (1988): 39–42. http://dx.doi.org/10.1016/0003-2697(88)90408-3.

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33

Tsonis, P. A., and P. F. Goetinck. "Homology of cellular vitamin A-binding protein with DNA-binding proteins." Biochemical Journal 249, no. 3 (1988): 933–34. http://dx.doi.org/10.1042/bj2490933.

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34

Du, Gehua, and Glenn D. Prestwich. "Protein Structure Encodes the Ligand Binding Specificity in Pheromone Binding Proteins." Biochemistry 34, no. 27 (1995): 8726–32. http://dx.doi.org/10.1021/bi00027a023.

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35

Kühn, Uwe, and Tomas Pieler. "XenopusPoly(A) Binding Protein: Functional Domains in RNA Binding and Protein – Protein Interaction." Journal of Molecular Biology 256, no. 1 (1996): 20–30. http://dx.doi.org/10.1006/jmbi.1996.0065.

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36

Rupal, Hemantkumar Desai, and Rao Chunduri Jayaprada. "Immuno-compatibility assessment of phytal-proteins of Zingiber zerumbet and serum gamma globulins of rheumatoid arthritis disease subjects." GSC Biological and Pharmaceutical Sciences 23, no. 1 (2023): 168–73. https://doi.org/10.5281/zenodo.7925188.

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Phytal proteins are of great importance as they exhibit unique characteristics as immune modulators. <em>Zingiber zerumbet</em> family plants are used in various ways, including as food, beverages, and ornaments. The metabolites and extracts of these plants indicated an anti-viral, anti-cancer, anti-diabetic, and anti-inflammatory therapeutic characteristics features. Rheumatoid arthritis (RA) is an auto-immune condition that causes joint inflammation and malformations. The up- and down-regulation of certain rheumatoid arthritis proteins result in serious side effects. Ayurveda and o

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37

Kelly, L. E. "Purification and properties of a 23 kDa Ca2+-binding protein from Drosophila melanogaster." Biochemical Journal 271, no. 3 (1990): 661–66. http://dx.doi.org/10.1042/bj2710661.

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Recent reports have shown that there exists in mammalian brain a number of heat-stable Ca2(+)-binding proteins that are distinct from calmodulin [McDonald & Walsh (1985) Biochem. J. 232, 559-567]. We have attempted to characterize equivalent Ca2(+)-binding proteins from Drosophila. Affigel-phenothiazine chromatography, which can be used to purify calmodulin and other Ca2(+)-binding proteins, allowed the identification of a possible heat-stable 23 kDa Ca2(+)-binding protein. A purification procedure for this protein has been devised. Purified 23 kDa protein shows characteristics typical of

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38

Gonick, Harvey C. "Lead-Binding Proteins: A Review." Journal of Toxicology 2011 (2011): 1–10. http://dx.doi.org/10.1155/2011/686050.

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Lead-binding proteins are a series of low molecular weight proteins, analogous to metallothionein, which segregate lead in a nontoxic form in several organs (kidney, brain, lung, liver, erythrocyte). Whether the lead-binding proteins in every organ are identical or different remains to be determined. In the erythrocyte, delta-aminolevulinic acid dehydratase (ALAD) isoforms have commanded the greatest attention as proteins and enzymes that are both inhibitable and inducible by lead. ALAD-2, although it binds lead to a greater degree than ALAD-1, appears to bind lead in a less toxic form. What m

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39

Kurumatani, Natsumi, Hiroyuki Monji, and Takenao Ohkawa. "Binding Site Extraction by Similar Subgraphs Mining from Protein Molecular Surfaces and Its Application to Protein Classification." International Journal on Artificial Intelligence Tools 23, no. 03 (2014): 1460007. http://dx.doi.org/10.1142/s0218213014600070.

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Most proteins express their functions by binding with other proteins or molecular compounds (ligands). Since the characteristics of the local portion involved in binding (binding site) often determine the function of the protein, clarifying the location of the binding site of the protein helps analyze the function of proteins. Binding sites that bind to similar ligands often have common surface structures (surface motifs). Extracting the surface motifs among several proteins with similar functions improves binding site prediction. We propose a method that predicts binding sites by extracting t

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40

Graeff, Moritz, and Stephan Wenkel. "Regulation of protein function by interfering protein species." BioMolecular Concepts 3, no. 1 (2012): 71–78. http://dx.doi.org/10.1515/bmc.2011.053.

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AbstractMost proteins do not function alone but act in protein complexes. For several transcriptional regulators, it is known that they have to homo- or heterodimerize prior to DNA binding. These protein interactions occur through defined protein-protein-interaction (PPI) domains. More than two decades ago, inhibitor of DNA binding (ID), a small protein containing a single helix-loop-helix (HLH) motif was identified. ID is able to interact with the larger DNA-binding basic helix-loop-helix (bHLH) transcription factors, but due to the lack of the basic domain required for DNA binding, ID traps

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41

Kim, Y. W., G. A. Otterson, R. A. Kratzke, A. B. Coxon, and F. J. Kaye. "Differential specificity for binding of retinoblastoma binding protein 2 to RB, p107, and TATA-binding protein." Molecular and Cellular Biology 14, no. 11 (1994): 7256–64. http://dx.doi.org/10.1128/mcb.14.11.7256-7264.1994.

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The growth suppressor activities of the RB and p107 products are believed to be mediated by the reversible binding of a heterogeneous family of cellular proteins to a conserved T/E1A pocket domain that is present within both proteins. To study the functional role of these interactions, we examined the properties of cellular retinoblastoma binding protein 2 (RBP2) binding to RB, p107, and the related TATA-binding protein (TBP) product. We observed that although RBP2 bound exclusively to the T/E1A pocket of p107, it could interact with RB through independent T/E1A and non-T/E1A domains and with

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42

Kim, Y. W., G. A. Otterson, R. A. Kratzke, A. B. Coxon, and F. J. Kaye. "Differential specificity for binding of retinoblastoma binding protein 2 to RB, p107, and TATA-binding protein." Molecular and Cellular Biology 14, no. 11 (1994): 7256–64. http://dx.doi.org/10.1128/mcb.14.11.7256.

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The growth suppressor activities of the RB and p107 products are believed to be mediated by the reversible binding of a heterogeneous family of cellular proteins to a conserved T/E1A pocket domain that is present within both proteins. To study the functional role of these interactions, we examined the properties of cellular retinoblastoma binding protein 2 (RBP2) binding to RB, p107, and the related TATA-binding protein (TBP) product. We observed that although RBP2 bound exclusively to the T/E1A pocket of p107, it could interact with RB through independent T/E1A and non-T/E1A domains and with

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43

Bitencourt-Ferreira, Gabriela, and Walter Filgueira de Azevedo Junior. "Electrostatic Potential Energy in Protein-Drug Complexes." Current Medicinal Chemistry 28, no. 24 (2021): 4954–71. http://dx.doi.org/10.2174/0929867328666210201150842.

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Background: Electrostatic interactions are one of the forces guiding the binding of molecules to proteins. The assessment of this interaction through computational approaches makes it possible to evaluate the energy of protein-drug complexes. Objective: Our purpose here is to review some the of methods used to calculate the electrostatic energy of protein-drug complexes and explore the capacity of these approaches for the generation of new computational tools for drug discovery using the abstraction of scoring function space. Method: Here we present an overview of AutoDock4 semi-empirical scor

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44

FUJII, Hiroshi. "Fatty Acid-binding Proteins: Their Structure, Function and Gene Expression." Journal of Japan Atherosclerosis Society 24, no. 7-8 (1996): 353–61. http://dx.doi.org/10.5551/jat1973.24.7-8_353.

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45

Loeffler, Hannes H., and Akio Kitao. "2P071 The Ligand-Binding Mechanism of the Glutamine Binding Protein(30. Protein function (II),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S313. http://dx.doi.org/10.2142/biophys.46.s313_3.

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46

Pastor, Nina, and Hard Weinstein. "Electrostatic analysis of DNA binding properties in lysine to leucine mutants of TATA-box binding proteins." "Protein Engineering, Design and Selection" 8, no. 6 (1995): 543–50. http://dx.doi.org/10.1093/protein/8.6.543.

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47

Zhu, H., J. Anchin, K. Ramnarayan, et al. "Analysis of high-affinity binding determinants in the receptor binding epitope of basic fibroblast growth factor." Protein Engineering Design and Selection 10, no. 4 (1997): 417–21. http://dx.doi.org/10.1093/protein/10.4.417.

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48

Fernández-Quintero, Monica L., Johannes R. Loeffler, Franz Waibl, Anna S. Kamenik, Florian Hofer, and Klaus R. Liedl. "Conformational selection of allergen-antibody complexes—surface plasticity of paratopes and epitopes." Protein Engineering, Design and Selection 32, no. 11 (2019): 513–23. http://dx.doi.org/10.1093/protein/gzaa014.

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Abstract Antibodies have the ability to bind various types of antigens and to recognize different antibody-binding sites (epitopes) of the same antigen with different binding affinities. Due to the conserved structural framework of antibodies, their specificity to antigens is mainly determined by their antigen-binding site (paratope). Therefore, characterization of epitopes in combination with describing the involved conformational changes of the paratope upon binding is crucial in understanding and predicting antibody-antigen binding. Using molecular dynamics simulations complemented with str

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49

Han, Penggang, Shangyi Liu, Xiandong Dai, Chongxu Fan, Ying Cao, and Jisheng Chen. "Identification of Glutamine Synthetase as a Contryphan-Bt Binding Protein by His-Tag Pull-Down." Protein & Peptide Letters 29, no. 1 (2022): 71–79. http://dx.doi.org/10.2174/0929866528666211213100054.

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Background: Contryphan-Bt is a D-tryptophan-containing disulfide-constrained decapeptide recently isolated from the venom of Conus betulinus. The molecular targets of contryphans are controversial, and the identification of its interacting proteins may be of great importance. Methods: His-tag pull-down assays were performed to investigate intracellular binding proteins of contryphan-Bt from rat brain lysate. Bt-Acp-[His]6, a contryphan-Bt derivative containing hexahistidine tag, was synthesized and used as the bait. As a control, Acp-[His]6 was used to exclude nonspecific bindings. Results: Gl

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Williamson, Mike P. "Protein Binding: A Fuzzy Concept." Life 13, no. 4 (2023): 855. http://dx.doi.org/10.3390/life13040855.

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Abstract:

Our understanding of protein binding interactions has matured significantly over the last few years, largely as a result of trying to make sense of the binding interactions of intrinsically disordered proteins. Here, we bring together some disparate ideas that have largely developed independently, and show that they can be linked into a coherent picture that provides insight into quantitative aspects of protein interactions, in particular that transient protein interactions are often optimised for speed, rather than tight binding.

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