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Journal articles on the topic 'Protein binding'

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Published: 4 June 2021

Last updated: 1 August 2024

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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 (July 22, 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 requirements account for the fact that PTB acts both as a suppressor of splicing and an activator of translation. In the latter case, the role of PTB in translation has been studied extensively and it appears that this protein is required for an alternative form of translation initiation that is mediated by a large RNA structural element termed an IRES (internal ribosome entry site) that allows the synthesis of picornaviral proteins and cellular proteins that function to control cell growth and cell death. In the present review, we discuss how PTB regulates these disparate processes.

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2

Viswanathan, Raji, Eduardo Fajardo, Gabriel Steinberg, Matthew Haller, and Andras Fiser. "Protein—protein binding supersites." PLOS Computational Biology 15, no. 1 (January 7, 2019): e1006704. http://dx.doi.org/10.1371/journal.pcbi.1006704.

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3

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 (July 2002): 571–74. http://dx.doi.org/10.1093/protein/15.7.571.

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4

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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5

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 (February 1, 2005): 65–70. http://dx.doi.org/10.1093/protein/gzi006.

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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

Lipovsek, D. "Adnectins: engineered target-binding protein therapeutics." Protein Engineering Design and Selection 24, no. 1-2 (November 10, 2010): 3–9. http://dx.doi.org/10.1093/protein/gzq097.

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8

Hisatomi, Osamu, Mari Kotoura, Daisuke Kitano, Tatsushi Goto, Akiyuki Hasegawa, Eiri Ono, and Fumio Tokunaga. "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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9

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 (April 1992): 8140–45. http://dx.doi.org/10.1016/s0021-9258(18)42418-0.

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10

Fischer, B. E., U. Schlokat, M. Himmelspach, and F. Dorner. "Binding of hirudin to meizothrombin." Protein Engineering Design and Selection 11, no. 8 (August 1, 1998): 715–21. http://dx.doi.org/10.1093/protein/11.8.715.

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11

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

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12

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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13

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 (November 1, 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, DLG and ZO-1 proteins), PH (pleckstrin homology) and FF (a domain with two conserved phenylalanines) domains. Here we demonstrate, using peptides, that the arrayed domains retain their binding integrity. Furthermore, we show that the protein-domain chip can ‘fish’ proteins out of a total cell lysate; these domain-bound proteins can then be detected on the chip with a specific antibody, thus producing an interaction map for a cellular protein of interest. Using this approach we have confirmed the domain-binding profile of the signalling molecule Sam68 (Src-associated during mitosis 68), and have identified a new binding profile for the core small nuclear ribonucleoprotein SmB′. This protein-domain chip not only identifies potential binding partners for proteins, but also promises to recognize qualitative differences in protein ligands (caused by post-translational modification), thus getting at the heart of signal transduction pathways.

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14

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 (July 2, 1991): 6380–86. http://dx.doi.org/10.1021/bi00240a005.

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15

Sear, Richard P. "Specific protein–protein binding in many-component mixtures of proteins." Physical Biology 1, no. 2 (April 29, 2004): 53–60. http://dx.doi.org/10.1088/1478-3967/1/2/001.

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16

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 (March 1, 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 free TM2 in a competition assay. The 10-kD protein-binding site was mapped to the region spanning residues 39-107 on TM2 by using several COOH-terminal and NH2-terminal truncation mutants of TM2. The 10-kD protein was isolated from an extract of NIH 3T3 cells transformed by v-Ha-ras by affinity chromatography on a GST/TM2 truncation mutant followed by SDS-PAGE and electroelution. Partial amino acid sequence analysis of the purified 10-kD protein, two-dimensional polyacrylamide gel analysis and a binding experiment revealed that the 10-kD protein was identical to a calcium-binding protein derived from mRNA named pEL98 or 18A2 that is homologous to S100 protein. Immunoblot analysis of the distribution of the 10-kD protein in Triton-soluble and -insoluble fractions of NIH 3T3 cells revealed that some of the 10-kD protein was associated with the Triton-insoluble cytoskeletal residue in a Ca(2+)-dependent manner. Furthermore, immunofluorescent staining of NIH 3T3 cells showed that some of the 10-kD protein colocalized with nonmuscle TMs in microfilament bundles. These results suggest that some of the pEL98 protein interacts with microfilament-associated nonmuscle TMs in NIH 3T3 cells.

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17

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

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18

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 (October 31, 2011): 695–703. http://dx.doi.org/10.1177/0148607111413901.

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19

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

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20

Kimura, Hitomi, Robert Noiva, Takemitsu Mizunaga, Kiyoshi Yamauchi, Ryuya Horiuchi, Sheue-Yann Cheng, and William J. Lennarz. "Thyroid hormone binding protein contains glycosylation site binding protein activity." Biochemical and Biophysical Research Communications 170, no. 3 (August 1990): 1319–24. http://dx.doi.org/10.1016/0006-291x(90)90538-x.

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21

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

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22

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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23

Day, Austin L., Per Greisen, Lindsey Doyle, Alberto Schena, Nephi Stella, Kai Johnsson, David Baker, and Barry Stoddard. "Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold." Protein Engineering, Design and Selection 31, no. 10 (October 1, 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 enhanced 25-D3 binding affinity and crystallographic analyses. The deviation in specificity is due in part to unexpected altertion of its conformation, corresponding to a significant change of the orientation of an α-helix and an equally large movement of a loop, both of which flank the designed ligand-binding pocket. Those changes led to engineered protein constructs that exhibit significantly more contacts and complementarity towards the 25-D3 ligand than the initial designed protein had been predicted to form towards its intended THC ligand. Molecular dynamics simulations imply that the initial computationally designed mutations may contribute to the movement of the helix. These analyses collectively indicate that accurate prediction and control of backbone dynamics conformation, through a combination of improved conformational sampling and/or de novo structure design, represents a key area of further development for the design and optimization of engineered ligand-binding proteins.

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24

Tsonis, P. A., and P. F. Goetinck. "Homology of cellular vitamin A-binding protein with DNA-binding proteins." Biochemical Journal 249, no. 3 (February 1, 1988): 933–34. http://dx.doi.org/10.1042/bj2490933.

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25

Du, Gehua, and Glenn D. Prestwich. "Protein Structure Encodes the Ligand Binding Specificity in Pheromone Binding Proteins." Biochemistry 34, no. 27 (July 11, 1995): 8726–32. http://dx.doi.org/10.1021/bi00027a023.

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26

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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27

Siggers, Trevor, and Raluca Gordân. "Protein–DNA binding: complexities and multi-protein codes." Nucleic Acids Research 42, no. 4 (November 16, 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 recognition codes. We discuss the impact of new high-throughput technologies for the characterization of protein–DNA binding, and how these technologies are uncovering new complexities in protein–DNA recognition. Finally, we review the concept of multi-protein recognition codes in which new DNA-binding specificities are achieved by the assembly of multi-protein complexes.

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28

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 (February 1996): 20–30. http://dx.doi.org/10.1006/jmbi.1996.0065.

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29

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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30

Zhu, H., J. Anchin, K. Ramnarayan, J. Zheng, T. Kawai, S. Mong, and M. E. Wolff. "Analysis of high-affinity binding determinants in the receptor binding epitope of basic fibroblast growth factor." Protein Engineering Design and Selection 10, no. 4 (April 1, 1997): 417–21. http://dx.doi.org/10.1093/protein/10.4.417.

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31

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 (November 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 TBP only through the non-T/E1A domain. Consistent with this observation, we found that a mutation within the Leu-X-Cys-X-Glu motif of RBP2 resulted in loss of ability to precipitate p107, while RB- and TBP-binding activities were retained. We located the non-T/E1A binding site of RBP2 on a 15-kDa fragment that is independent from the Leu-X-Cys-X-Glu motif and encodes binding activity for RB and TBP but does not interact with p107. Despite the presence of a non-T/E1A binding site, however, recombinant RBP2 retained the ability to preferentially precipitate active hypophosphorylated RB from whole-cell lysates. In addition, we found that cotransfection of RBP2 can reverse in vivo RB-mediated suppression of E2F activity. These findings confirm the differential binding specificities of the related RB, p107, and TBP proteins and support the presence of multifunctional domains on the nuclear RBP2 product which may allow complex interactions with the cellular transcription machinery.

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32

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 (November 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 TBP only through the non-T/E1A domain. Consistent with this observation, we found that a mutation within the Leu-X-Cys-X-Glu motif of RBP2 resulted in loss of ability to precipitate p107, while RB- and TBP-binding activities were retained. We located the non-T/E1A binding site of RBP2 on a 15-kDa fragment that is independent from the Leu-X-Cys-X-Glu motif and encodes binding activity for RB and TBP but does not interact with p107. Despite the presence of a non-T/E1A binding site, however, recombinant RBP2 retained the ability to preferentially precipitate active hypophosphorylated RB from whole-cell lysates. In addition, we found that cotransfection of RBP2 can reverse in vivo RB-mediated suppression of E2F activity. These findings confirm the differential binding specificities of the related RB, p107, and TBP proteins and support the presence of multifunctional domains on the nuclear RBP2 product which may allow complex interactions with the cellular transcription machinery.

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33

MacDonald, P. N., and D. E. Ong. "Binding specificities of cellular retinol-binding protein and cellular retinol-binding protein, type II." Journal of Biological Chemistry 262, no. 22 (August 1987): 10550–56. http://dx.doi.org/10.1016/s0021-9258(18)60997-4.

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34

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 decrease in protein S antigen was observed in patients with liver disease (0.78 ± 0.25 U/ml); no significant decrease in protein S was observed in patients with DIC (0.95 ± 0.25 U/ml).Criteria were developed for the laboratory diagnosis of an isolated protein S deficiency

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35

Chang, Chia-Ching, and P. C. Huang. "Semi-empirical simulation of Zn/Cd binding site preference in the metal binding domains of mammalian metallothionein." "Protein Engineering, Design and Selection" 9, no. 12 (1996): 1165–72. http://dx.doi.org/10.1093/protein/9.12.1165.

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36

Dey, Raja, P. Roychowdhury, and C. Mukherjee. "Homology modelling of the ligand-binding domain of glucocorticoid receptor: binding site interactions with cortisol and corticosterone." Protein Engineering, Design and Selection 14, no. 8 (August 2001): 565–71. http://dx.doi.org/10.1093/protein/14.8.565.

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37

Williamson, Mike P. "Protein Binding: A Fuzzy Concept." Life 13, no. 4 (March 23, 2023): 855. http://dx.doi.org/10.3390/life13040855.

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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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38

Zeitlinger, Markus A., Hartmut Derendorf, Johan W. Mouton, Otto Cars, William A. Craig, David Andes, and Ursula Theuretzbacher. "Protein Binding: Do We Ever Learn?" Antimicrobial Agents and Chemotherapy 55, no. 7 (May 2, 2011): 3067–74. http://dx.doi.org/10.1128/aac.01433-10.

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ABSTRACTAlthough the influence of protein binding (PB) on antibacterial activity has been reported for many antibiotics and over many years, there is currently no standardization for pharmacodynamic models that account for the impact of protein binding of antimicrobial agentsin vitro. This might explain the somewhat contradictory results obtained from different studies. Simplein vitromodels which compare the MIC obtained in protein-free standard medium versus a protein-rich medium are prone to methodological pitfalls and may lead to flawed conclusions. Withinin vitrotest systems, a range of test conditions, including source of protein, concentration of the tested antibiotic, temperature, pH, electrolytes, and supplements may influence the impact of protein binding. As new antibiotics with a high degree of protein binding are in clinical development, attention and action directed toward the optimization and standardization of testing the impact of protein binding on the activity of antibioticsin vitrobecome even more urgent. In addition, the quantitative relationship between the effects of protein bindingin vitroandin vivoneeds to be established, since the physiological conditions differ. General recommendations for testing the impact of protein bindingin vitroare suggested.

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39

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 (December 15, 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 by drawbacks of the prior studies, we perform a large-scale analysis to quantify and contrast the three hallmarks for residues that bind DNA-, RNA-, protein- and (for the first time) multi-ligand-binding residues that interact with DNA and proteins, and with RNA and proteins. Results generated on a well-annotated data set of over 23 000 proteins show that conservation of binding residues is higher for nucleic acid- than protein-binding residues. Multi-ligand-binding residues are more conserved and have higher RSA than single-ligand-binding residues. We empirically show that each hallmark discriminates between binding and nonbinding residues, even predicted RSA, and that combining them improves discriminatory power for each of the five types of interactions. Linear scoring functions that combine these hallmarks offer good predictive performance of residue-level propensity for binding and provide intuitive interpretation of predictions. Better understanding of these residue-level interactions will facilitate development of methods that accurately predict binding in the exponentially growing databases of protein sequences.

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40

Sun, Zhaoxi, Yu N. Yan, Maoyou Yang, and John Z. H. Zhang. "Interaction entropy for protein-protein binding." Journal of Chemical Physics 146, no. 12 (March 28, 2017): 124124. http://dx.doi.org/10.1063/1.4978893.

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41

Day, Eric S., Shaun M. Cote, and Adrian Whitty. "Binding Efficiency of Protein–Protein Complexes." Biochemistry 51, no. 45 (November 2012): 9124–36. http://dx.doi.org/10.1021/bi301039t.

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42

Moreira, Irina S., Pedro A. Fernandes, and Maria J. Ramos. "Backbone Importance for Protein−Protein Binding." Journal of Chemical Theory and Computation 3, no. 3 (April 4, 2007): 885–93. http://dx.doi.org/10.1021/ct6003824.

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43

Liang, Shide, Lan Xiao, Fenglou Mao, Lin Jiang, Yuzhen Han, and Luhua Lai. "Grafting of protein-protein binding sites." Chinese Science Bulletin 45, no. 18 (September 2000): 1707–12. http://dx.doi.org/10.1007/bf02898992.

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44

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 (November 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 strong experimental structural information, we investigated the underlying binding mechanism and the resulting local and global surface plasticity in the binding interfaces of distinct antibody-antigen complexes. In all studied allergen-antibody complexes, we clearly observe that experimentally suggested epitopes reveal less plasticity, while non-epitope regions show high surface plasticity. Surprisingly, the paratope shows higher conformational diversity reflected in substantially higher surface plasticity, compared to the epitope. This work allows a visualization and characterization of antibody-antigen interfaces and might have strong implications for antibody-antigen docking and in the area of epitope prediction.

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45

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 may be of greater significance is that a low molecular weight lead-binding protein, approximately 10 kDa, appears in the erythrocyte once blood lead exceeds 39 μg/dL and eventually surpasses the lead-binding capacity of ALAD. In brain and kidney of environmentally exposed humans and animals, a cytoplasmic lead-binding protein has been identified as thymosinβ4, a 5 kDa protein. In kidney, but not brain, another lead-binding protein has been identified as acyl-CoA binding protein, a 9 kDa protein. Each of these proteins, when coincubated with liver ALAD and titrated with lead, diminishes the inhibition of ALAD by lead, verifying their ability to segregate lead in a nontoxic form.

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46

Scheife, Richard T. "Protein Binding: What Does it Mean?" DICP 23, no. 7-8 (July 1989): S27—S31. http://dx.doi.org/10.1177/106002808902300706.

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Protein binding can enhance or detract from a drug's performance. As a general rule, agents that are minimally protein bound penetrate tissue better than those that are highly bound, but they are excreted much faster. Among drugs that are less than 80–85 percent protein bound, differences appear to be of slight clinical importance. Agents that are highly protein bound may, however, differ markedly from those that are minimally bound in terms of tissue penetration and half-life. Drugs may bind to a wide variety of plasma proteins, including albumin. If the percentage of protein-bound drug is greater when measured in human blood than in a simple albumin solution, the clinician should suspect that the agent may be bound in vivo to one of these “minority” plasma proteins. The concentration of several plasma proteins can be altered by many factors, including stress, surgery, liver or kidney dysfunction, and pregnancy. In such circumstances, free drug concentrations are a more accurate index of clinical effect than are total concentrations. Formulary committees must grasp the clinical significance of qualitative and quantitative differences in protein binding when evaluating competing agents.

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Qiu, Jiajun, Michael Bernhofer, Michael Heinzinger, Sofie Kemper, Tomas Norambuena, Francisco Melo, and Burkhard Rost. "ProNA2020 predicts protein–DNA, protein–RNA, and protein–protein binding proteins and residues from sequence." Journal of Molecular Biology 432, no. 7 (March 2020): 2428–43. http://dx.doi.org/10.1016/j.jmb.2020.02.026.

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48

Bach, L. "Insulin-Like Growth Factor Binding Protein-6: The “Forgotten” Binding Protein?" Hormone and Metabolic Research 31, no. 02/03 (January 1999): 226–34. http://dx.doi.org/10.1055/s-2007-978723.

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49

Yuan, Ming, Lena Mogemark, and Maria Fällman. "Fyn binding protein, Fyb, interacts with mammalian actin binding protein, mAbp1." FEBS Letters 579, no. 11 (March 25, 2005): 2339–47. http://dx.doi.org/10.1016/j.febslet.2005.03.031.

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50

Hillarp, A., and B. Dahlbäck. "Novel subunit in C4b-binding protein required for protein S binding." Journal of Biological Chemistry 263, no. 25 (September 1988): 12759–64. http://dx.doi.org/10.1016/s0021-9258(18)37818-9.

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