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Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins. Molecules 2021; 26:molecules26030634. [PMID: 33530506 PMCID: PMC7865441 DOI: 10.3390/molecules26030634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/18/2021] [Accepted: 01/23/2021] [Indexed: 01/10/2023] Open
Abstract
The α and polyproline II (PPII) basins are the two most populated regions of the Ramachandran map when constructed from the protein coil library, a widely used denatured state model built from the segments of irregular structure found in the Protein Data Bank. This indicates the α and PPII conformations are dominant components of the ensembles of denatured structures that exist in solution for biological proteins, an observation supported in part by structural studies of short, and thus unfolded, peptides. Although intrinsic conformational propensities have been determined experimentally for the common amino acids in short peptides, and estimated from surveys of the protein coil library, the ability of these intrinsic conformational propensities to quantitatively reproduce structural behavior in intrinsically disordered proteins (IDPs), an increasingly important class of proteins in cell function, has thus far proven elusive to establish. Recently, we demonstrated that the sequence dependence of the mean hydrodynamic size of IDPs in water and the impact of heat on the coil dimensions, provide access to both the sequence dependence and thermodynamic energies that are associated with biases for the α and PPII backbone conformations. Here, we compare results from peptide-based studies of intrinsic conformational propensities and surveys of the protein coil library to those of the sequence-based analysis of heat effects on IDP hydrodynamic size, showing that a common structural and thermodynamic description of the protein denatured state is obtained.
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Bhatt VS, Zeng D, Krieger I, Sacchettini JC, Cho JH. Binding Mechanism of the N-Terminal SH3 Domain of CrkII and Proline-Rich Motifs in cAbl. Biophys J 2017; 110:2630-2641. [PMID: 27332121 DOI: 10.1016/j.bpj.2016.05.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/29/2016] [Accepted: 05/04/2016] [Indexed: 12/14/2022] Open
Abstract
The N-terminal Src homology 3 (nSH3) domain of a signaling adaptor protein, CT-10 regulator of kinase II (CrkII), recognizes proline-rich motifs (PRMs) of binding partners, such as cAbl kinase. The interaction between CrkII and cAbl kinase is involved in the regulation of cell spreading, microbial pathogenesis, and cancer metastasis. Here, we report the detailed biophysical characterizations of the interactions between the nSH3 domain of CrkII and PRMs in cAbl. We identified that the nSH3 domain of CrkII binds to three PRMs in cAbl with virtually identical affinities. Structural studies, by using x-ray crystallography and NMR spectroscopy, revealed that the binding modes of all three nSH3:PRM complexes are highly similar to each other. Van 't Hoff analysis revealed that nSH3:PRM interaction is associated with favorable enthalpy and unfavorable entropy change. The combination of experimentally determined thermodynamic parameters, structure-based calculations, and (15)N NMR relaxation analysis highlights the energetic contribution of conformational entropy change upon the complex formation, and water molecules structured in the binding interface of the nSH3:PRM complex. Understanding the molecular basis of nSH3:PRM interaction will provide, to our knowledge, new insights for the rational design of small molecules targeting the interaction between CrkII and cAbl.
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Affiliation(s)
- Veer S Bhatt
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Danyun Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Inna Krieger
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Jae-Hyun Cho
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas.
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Zhou Q, Sun X, Xia X, Fan Z, Luo Z, Zhao S, Shakhnovich E, Liang H. Exploring the Mutational Robustness of Nucleic Acids by Searching Genotype Neighborhoods in Sequence Space. J Phys Chem Lett 2017; 8:407-414. [PMID: 28045264 DOI: 10.1021/acs.jpclett.6b02769] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
To assess the mutational robustness of nucleic acids, many genome- and protein-level studies have been performed, where nucleic acids are treated as genetic information carriers and transferrers. However, the molecular mechanisms through which mutations alter the structural, dynamic, and functional properties of nucleic acids are poorly understood. Here we performed a SELEX in silico study to investigate the fitness distribution of the l-Arm-binding aptamer genotype neighborhoods. Two novel functional genotype neighborhoods were isolated and experimentally verified to have comparable fitness as the wild-type. The experimental aptamer fitness landscape suggests the mutational robustness is strongly influenced by the local base environment and ligand-binding mode, whereas bases distant from the binding pocket provide potential evolutionary pathways to approach the global fitness maximum. Our work provides an example of successful application of SELEX in silico to optimize an aptamer and demonstrates the strong sensitivity of mutational robustness to the site of genetic variation.
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Affiliation(s)
- Qingtong Zhou
- iHuman Institute, ShanghaiTech University , Shanghai 201210, China
| | - Xianbao Sun
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Xiaole Xia
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi, Jiangsu 214122, China
| | - Zhou Fan
- iHuman Institute, ShanghaiTech University , Shanghai 201210, China
- Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 200031, China
- University of Chinese Academy of Sciences , Beijing 100049, China
- School of Life Science and Technology, ShanghaiTech University , Shanghai 201210, China
| | - Zhaofeng Luo
- School of Life Science, University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University , Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University , Shanghai 201210, China
| | - Eugene Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China , Hefei, Anhui 230026, China
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Uversky VN, Dunker AK. The case for intrinsically disordered proteins playing contributory roles in molecular recognition without a stable 3D structure. F1000 BIOLOGY REPORTS 2013; 5:1. [PMID: 23361308 PMCID: PMC3542772 DOI: 10.3410/b5-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The classical 'lock-and-key' and 'induced-fit' mechanisms for binding both originated in attempts to explain features of enzyme catalysis. For both of these mechanisms and for their recent refinements, enzyme catalysis requires exquisite spatial and electronic complementarity between the substrate and the catalyst. Thus, binding models derived from models originally based on catalysis will be highly biased towards mechanisms that utilize structural complementarity. If mere binding without catalysis is the endpoint, then the structural requirements for the interaction become much more relaxed. Recent observations on specific examples suggest that this relaxation can reach an extreme lack of specific 3D structure, leading to molecular recognition with biological consequences that depend not only upon structural and electrostatic complementarity between the binding partners but also upon kinetic, entropic, and generalized electrostatic effects. In addition to this discussion of binding without fixed structure, examples in which unstructured regions carry out important biological functions not involving molecular recognition will also be discussed. Finally, we discuss whether 'intrinsically disordered protein' (IDP) represents a useful new concept.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, University of South Florida Tampa, FL 33612, USA ; Institute for Biological Instrumentation, Russian Academy of Sciences 142290 Pushchino, Moscow Region, Russia
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Schrank TP, Wrabl JO, Hilser VJ. Conformational heterogeneity within the LID domain mediates substrate binding to Escherichia coli adenylate kinase: function follows fluctuations. Top Curr Chem (Cham) 2013; 337:95-121. [PMID: 23543318 DOI: 10.1007/128_2012_410] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteins exist as dynamic ensembles of molecules, implying that protein amino acid sequences evolved to code for both the ground state structure as well as the entire energy landscape of excited states. Accumulating theoretical and experimental evidence suggests that enzymes use such conformational fluctuations to facilitate allosteric processes important for substrate binding and possibly catalysis. This phenomenon can be clearly demonstrated in Escherichia coli adenylate kinase, where experimentally observed local unfolding of the LID subdomain, as opposed to a more commonly postulated rigid-body opening motion, is related to substrate binding. Because "entropy promoting" glycine mutations designed to increase specifically the local unfolding of the LID domain also affect substrate binding, changes in the excited energy landscape effectively tune the function of this enzyme without changing the ground state structure or the catalytic site. Thus, additional thermodynamic information, above and beyond the single folded structure of an enzyme-substrate complex, is likely required for a full and quantitative understanding of how enzymes work.
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Affiliation(s)
- Travis P Schrank
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77555-1068, USA,
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Dadarlat VM, Gorenstein LA, Post CB. Prediction of protein relative enthalpic stability from molecular dynamics simulations of the folded and unfolded states. Biophys J 2012; 103:1762-73. [PMID: 23083720 DOI: 10.1016/j.bpj.2012.08.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 08/01/2012] [Accepted: 08/17/2012] [Indexed: 11/18/2022] Open
Abstract
For proteins of known structure, the relative enthalpic stability with respect to wild-type, ΔΔH(U), can be estimated by direct computation of the folded and unfolded state energies. We propose a model by which the change in stability upon mutation can be predicted from all-atom molecular dynamics simulations for the folded state and a peptide-based model for the unfolded state. The unfolding enthalpies are expressed in terms of environmental and hydration-solvent reorganization contributions that readily allow a residue-specific analysis of ΔΔH(U). The method is applied to estimate the relative enthalpic stability of variants with buried charged groups in T4 lysozyme. The predicted relative stabilities are in good agreement with experimental data. Environmental factors are observed to contribute more than hydration to the overall ΔΔH(U). The residue-specific analysis finds that the effects of burying charge are both localized and long-range. The enthalpy for hydration-solvent reorganization varies considerably among different amino-acid types, but because the variant folded state structures are similar to those of the wild-type, the hydration-solvent reorganization contribution to ΔΔH(U) is localized at the mutation site, in contrast to environmental contributions. Overall, mutation of apolar and polar amino acids to charged amino acids are destabilizing, but the reasons are complex and differ from site to site.
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Affiliation(s)
- Voichita M Dadarlat
- Markey Center for Structural Biology, Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana, USA
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Yeh LCC, Falcon WE, Garces A, Lee JC, Lee JC. A host-guest relationship in bone morphogenetic protein receptor-II defines specificity in ligand-receptor recognition. Biochemistry 2012; 51:6968-80. [PMID: 22894880 DOI: 10.1021/bi3003023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the most intriguing questions confronting the bone morphogenetic protein family is the mechanism of ligand recognition, because there are more ligands than receptors. Crystal structures of two type II receptors, ActR-II and BMPR-II, are essentially identical, and a loop structure (A-loop) has been suggested to play a role in determining ligand specificity. A solution biophysical study showed mutations of several A-loop residues in these two receptors exert different ligand binding effects. Thus, the issues of mechanism of ligand recognition and specificity remain unresolved. We examined effects of mutations of residues Y40, G47, and S107 in BMPR-II. These residues are not identified as being in contact with the ligand in the BMP-7-BMPR-II complex but are found mutated in genetic diseases. They are likely to be useful in identifying their roles in differentiating the various BMP ligands. Spectroscopic probing revealed little mutation-induced structural change in BMPR-II. Ligand binding studies revealed that Y40 plays a significant role in differentiating three distinct ligands; G47 and S107 affect ligand binding to a lesser extent. The role of the A-loop in ActR-II or BMPR-II is dependent on the host sequence of the receptor extracellular domain (ECD) in which it is embedded, suggesting a host-guest relationship between the A-loop and the rest of the ECD. Computational analysis demonstrated a long-range connectivity between Y40, G47, and S107 and other locations in BMPR-II. An integration of these results on functional energetics and protein structures clearly demonstrates, for the first time, an intradomain communication network within BMPR-II.
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Affiliation(s)
- Lee-Chuan C Yeh
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
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8
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Interfacial water molecules in SH3 interactions: Getting the full picture on polyproline recognition by protein-protein interaction domains. FEBS Lett 2012; 586:2619-30. [DOI: 10.1016/j.febslet.2012.04.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 04/27/2012] [Accepted: 04/30/2012] [Indexed: 01/16/2023]
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Wang Y, Shen JK, Schroeder SJ. Nucleotide Dynamics at the A-Site Cleft in the Peptidyltransferase Center of H. marismortui 50S Ribosomal Subunits. J Phys Chem Lett 2012; 3:1007-1010. [PMID: 26286564 DOI: 10.1021/jz3001882] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Resistance mutations to antibiotics targeting rRNA can be far from the drug-binding site. Crystallography studies revealed that the antibiotic resistance mutation G2482A (G2447A in E. coli ) in Haloarcula marismortui 50S ribosomes does not directly contact the drug or introduce changes to the ribosomal structure except for losing a potassium ion coordinated to a base triple at the drug-binding site. Using molecular dynamics simulations, we tested hypotheses regarding the effects of the G2482A mutation and ion coordination on the conformational dynamics of the 50S ribosome. Simulations show that the mutation enhances conformational fluctuation at the antibiotic binding site, weakens the hydrogen-bonding network, and increases flexibility at the 50S peptidyl transferase center (PTC). Our data supports the view that distant mutations can perturb the dynamic network in the ribosomal PTC, thereby raising the entropic cost of antibiotic binding. These results underscore the importance of considering conformational dynamics in rational drug design.
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Affiliation(s)
- Yuhang Wang
- †Department of Chemistry and Biochemistry, ‡School of Chemical, Biological, and Materials Engineering, and ξDepartment of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, United States
| | - Jana K Shen
- †Department of Chemistry and Biochemistry, ‡School of Chemical, Biological, and Materials Engineering, and ξDepartment of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, United States
| | - Susan J Schroeder
- †Department of Chemistry and Biochemistry, ‡School of Chemical, Biological, and Materials Engineering, and ξDepartment of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, United States
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Wrabl JO, Gu J, Liu T, Schrank TP, Whitten ST, Hilser VJ. The role of protein conformational fluctuations in allostery, function, and evolution. Biophys Chem 2011; 159:129-41. [PMID: 21684672 DOI: 10.1016/j.bpc.2011.05.020] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 05/26/2011] [Accepted: 05/26/2011] [Indexed: 11/17/2022]
Abstract
It is now well-known that proteins exist at equilibrium as ensembles of conformational states rather than as unique static structures. Here we review from an ensemble perspective important biological effects of such spontaneous fluctuations on protein allostery, function, and evolution. However, rather than present a thorough literature review on each subject, we focus instead on connecting these phenomena through the ensemble-based experimental, theoretical, and computational investigations from our laboratory over the past decade. Special emphasis is given to insights that run counter to some of the prevailing ideas that have emerged over the past 40 years of structural biology research. For instance, when proteins are viewed as conformational ensembles rather than as single structures, the commonly held notion of an allosteric pathway as an obligate series of individual structural distortions loses its meaning. Instead, allostery can result from energetic linkage between distal sites as one Boltzmann distribution of states transitions to another. Additionally, the emerging principles from this ensemble view of proteins have proven surprisingly useful in describing the role of intrinsic disorder in inter-domain communication, functional adaptation mediated by mutational control of fluctuations, and evolutionary conservation of the energetics of protein stability.
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Affiliation(s)
- James O Wrabl
- Departments of Biology and Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.
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Schrank TP, Elam WA, Li J, Hilser VJ. Strategies for the thermodynamic characterization of linked binding/local folding reactions within the native state application to the LID domain of adenylate kinase from Escherichia coli. Methods Enzymol 2011; 492:253-82. [PMID: 21333795 PMCID: PMC6585976 DOI: 10.1016/b978-0-12-381268-1.00020-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Conformational fluctuations in proteins have emerged as an important aspect of biological function, having been linked to processes ranging from molecular recognition and catalysis to allostery and signal transduction. In spite of the realization of their importance, however, the connections between fluctuations and function have largely been empirical, even when they have been quantitative. Part of the problem in understanding the role of fluctuations in function is the fact that the mere existence of fluctuations complicates the interpretation of classic mutagenesis approaches. Namely, mutagenesis, which is typically targeted to an internal position (to elicit an effect), will change the fluctuations as well as the structure of the native state. Decoupling these effects is essential to an unambiguous understanding of the role of fluctuations in function. Here, we use a mutation strategy that targets surface-exposed sites in flexible parts of the molecule for mutation to glycine. Such mutations leave the ground-state structure unaffected. As a result, we can assess the nature of the fluctuations, develop a quantitative model relating fluctuations to function (in this case, molecular recognition), and unambiguously resolve the probabilities of the fluctuating states. We show that when this approach is applied to Escherichia coli adenylate kinase (AK), unique thermodynamic and structural insights are obtained, even when classic mutagenesis approaches targeted to the same region yield ambiguous results.
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Affiliation(s)
- Travis P. Schrank
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston,Texas, USA
| | - W. Austin Elam
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jing Li
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Vincent J. Hilser
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA,Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
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Grossman M, Tworowski D, Dym O, Lee MH, Levy Y, Murphy G, Sagi I. The intrinsic protein flexibility of endogenous protease inhibitor TIMP-1 controls its binding interface and affects its function. Biochemistry 2010; 49:6184-92. [PMID: 20545310 DOI: 10.1021/bi902141x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein flexibility is thought to play key roles in numerous biological processes, including antibody affinity maturation, signal transduction, and enzyme catalysis, yet only limited information is available regarding the molecular details linking protein dynamics with function. A single point mutation at the distal site of the endogenous tissue inhibitor of metalloproteinase 1 (TIMP-1) enables this clinical target protein to tightly bind and inhibit membrane type 1 matrix metalloproteinase (MT1-MMP) by increasing only the association constant. The high-resolution X-ray structure of this complex determined at 2 A could not explain the mechanism of enhanced binding and pointed to a role for protein conformational dynamics. Molecular dynamics (MD) simulations reveal that the high-affinity TIMP-1 mutants exhibit significantly reduced binding interface flexibility and more stable hydrogen bond networks. This was accompanied by a redistribution of the ensemble of substrates to favorable binding conformations that fit the enzyme catalytic site. Apparently, the decrease in backbone flexibility led to a lower entropy cost upon formation of the complex. This work quantifies the effect of a single point mutation on the protein conformational dynamics and function of TIMP-1. Here we argue that controlling the intrinsic protein dynamics of MMP endogenous inhibitors may be utilized for rationalizing the design of selective novel protein inhibitors for this class of enzymes.
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Affiliation(s)
- Moran Grossman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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