1
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The native state conformational heterogeneity in the energy landscape of protein folding. Biophys Chem 2022; 283:106761. [DOI: 10.1016/j.bpc.2022.106761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 11/18/2022]
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2
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Chakravorty A, Jia Z, Li L, Zhao S, Alexov E. Reproducing the Ensemble Average Polar Solvation Energy of a Protein from a Single Structure: Gaussian-Based Smooth Dielectric Function for Macromolecular Modeling. J Chem Theory Comput 2018; 14:1020-1032. [PMID: 29350933 PMCID: PMC9885857 DOI: 10.1021/acs.jctc.7b00756] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Typically, the ensemble average polar component of solvation energy (ΔGpolarsolv) of a macromolecule is computed using molecular dynamics (MD) or Monte Carlo (MC) simulations to generate conformational ensemble and then single/rigid conformation solvation energy calculation is performed on each snapshot. The primary objective of this work is to demonstrate that Poisson-Boltzmann (PB)-based approach using a Gaussian-based smooth dielectric function for macromolecular modeling previously developed by us (Li et al. J. Chem. Theory Comput. 2013, 9 (4), 2126-2136) can reproduce that ensemble average (ΔGpolarsolv) of a protein from a single structure. We show that the Gaussian-based dielectric model reproduces the ensemble average ΔGpolarsolv(⟨ΔGpolarsolv⟩) from an energy-minimized structure of a protein regardless of the minimization environment (structure minimized in vacuo, implicit or explicit waters, or crystal structure); the best case, however, is when it is paired with an in vacuo-minimized structure. In other minimization environments (implicit or explicit waters or crystal structure), the traditional two-dielectric model can still be selected with which the model produces correct solvation energies. Our observations from this work reflect how the ability to appropriately mimic the motion of residues, especially the salt bridge residues, influences a dielectric model's ability to reproduce the ensemble average value of polar solvation free energy from a single in vacuo-minimized structure.
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Affiliation(s)
- Arghya Chakravorty
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA
| | - Zhe Jia
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA
| | - Lin Li
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA
| | - Shan Zhao
- Departement of Mathematics, College of Arts and Sciences, University of Alabama, Tuscaloosa, Alabama 35487, USA
| | - Emil Alexov
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA.,Corresponding Author Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA.
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3
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Xia YL, Sun JH, Ai SM, Li Y, Du X, Sang P, Yang LQ, Fu YX, Liu SQ. Insights into the role of electrostatics in temperature adaptation: a comparative study of psychrophilic, mesophilic, and thermophilic subtilisin-like serine proteases. RSC Adv 2018; 8:29698-29713. [PMID: 35547280 PMCID: PMC9085296 DOI: 10.1039/c8ra05845h] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 08/15/2018] [Indexed: 11/21/2022] Open
Abstract
To investigate the role of electrostatics in different temperature adaptations, we performed a comparative study on subtilisin-like serine proteases from psychrophilic Vibrio sp. PA-44 (VPR), mesophilic Engyodontium album (Tritirachium album) (PRK), and thermophilic Thermus aquaticus (AQN) using multiple-replica molecular dynamics (MD) simulations combined with continuum electrostatics calculations. The results reveal that although salt bridges are not a crucial factor in determining the overall thermostability of these three proteases, they on average provide the greatest, moderate, and least electrostatic stabilization to AQN, PRK, and VPR, respectively, at the respective organism growth temperatures. Most salt bridges in AQN are effectively stabilizing and thus contribute to maintaining the overall structural stability at 343 K, while nearly half of the salt bridges in VPR interconvert between being stabilizing and being destabilizing, likely aiding in enhancing the local conformational flexibility at 283 K. The individual salt bridges, salt-bridge networks, and calcium ions contribute differentially to local stability and flexibility of these three enzyme structures, depending on their spatial distributions and electrostatic strengths. The shared negatively charged surface potential at the active center of the three enzymes may provide the active-center flexibility necessary for nucleophilic attack and proton transfer. The differences in distributions of the electro-negative, electro-positive, and electro-neutral potentials, particularly over the back surfaces of the three proteases, may modulate/affect not only protein solubility and thermostability but also structural stability and flexibility/rigidity. These results demonstrate that electrostatics contributes to both heat and cold adaptation of subtilisin-like serine proteases through fine-tuning, either globally or locally, the structural stability and conformational flexibility/rigidity, thus providing a foundation for further engineering and mutagenesis studies. Differently charged surface patches contribute to temperature adaptation of subtilisin-like serine proteases through affecting/modulating the protein solubility and thermostability and the structural flexibility/rigidity/stability.![]()
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Affiliation(s)
- Yuan-Ling Xia
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan
- Yunnan University
- Kunming
- P. R. China
| | - Jian-Hong Sun
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan
- Yunnan University
- Kunming
- P. R. China
| | - Shi-Meng Ai
- Department of Applied Mathematics
- Yunnan Agricultural University
- Kunming
- P. R. China
| | - Yi Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan
- Yunnan University
- Kunming
- P. R. China
| | - Xing Du
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan
- Yunnan University
- Kunming
- P. R. China
| | - Peng Sang
- College of Agriculture and Biological Science
- Dali University
- Dali
- P. R. China
| | - Li-Quan Yang
- College of Agriculture and Biological Science
- Dali University
- Dali
- P. R. China
| | - Yun-Xin Fu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan
- Yunnan University
- Kunming
- P. R. China
- Human Genetics Center and Division of Biostatistics
| | - Shu-Qun Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan
- Yunnan University
- Kunming
- P. R. China
- Key Laboratory for Tumor Molecular Biology of High Education in Yunnan Province
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4
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Borrel A, Camproux AC, Xhaard H. Characterization of Ionizable Groups' Environments in Proteins and Protein-Ligand Complexes through a Statistical Analysis of the Protein Data Bank. ACS OMEGA 2017; 2:7359-7374. [PMID: 31457307 PMCID: PMC6645025 DOI: 10.1021/acsomega.7b00739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 10/11/2017] [Indexed: 06/10/2023]
Abstract
We conduct a statistical analysis of the molecular environment of common ionizable functional groups in both protein-ligand complexes and inside proteins from the Protein Data Bank (PDB). In particular, we characterize the frequency, type, and density of the interacting atoms as well as the presence of a potential counterion. We found that for ligands, most guanidinium groups, half of primary and secondary amines, and one-fourth of imidazole neighbor a carboxylate group. Tertiary amines bind more rarely near carboxylate groups, which may be explained by a crowded neighborhood and hydrophobic character. In comparison to the environment seen by the ligands, inside proteins, an environment enriched in main-chain atoms is found, and the prevalence of direct charge neutralization by carboxylate groups is different. When the ionizable character of water molecules and phenolic or hydroxyl groups is accounted, considering a high-resolution dataset (less than 1.5 Å), charge neutralization could occur for well above 80% of the ligand functional groups considered, but for tertiary amines.
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Affiliation(s)
- Alexandre Borrel
- Molécules
Thérapeutiques in silico (MTi), INSERM UMRS-973, University Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex 13, France
- Faculty
of Pharmacy, Division of Pharmaceutical Chemistry and Technology, University of Helsinki, Viikinkaari 5E, P.O. Box 56, FI-00014 Helsinki, Finland
| | - Anne-Claude Camproux
- Molécules
Thérapeutiques in silico (MTi), INSERM UMRS-973, University Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex 13, France
| | - Henri Xhaard
- Faculty
of Pharmacy, Division of Pharmaceutical Chemistry and Technology, University of Helsinki, Viikinkaari 5E, P.O. Box 56, FI-00014 Helsinki, Finland
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5
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Wei G, Xi W, Nussinov R, Ma B. Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell. Chem Rev 2016; 116:6516-51. [PMID: 26807783 PMCID: PMC6407618 DOI: 10.1021/acs.chemrev.5b00562] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
All soluble proteins populate conformational ensembles that together constitute the native state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the distributions of the states on the energy landscape are determined by statistical thermodynamics; however, they are optimized to perform their biological functions. In this review we briefly describe advances in free energy landscape studies of protein conformational ensembles. Experimental (nuclear magnetic resonance, small-angle X-ray scattering, single-molecule spectroscopy, and cryo-electron microscopy) and computational (replica-exchange molecular dynamics, metadynamics, and Markov state models) approaches have made great progress in recent years. These address the challenging characterization of the highly flexible and heterogeneous protein ensembles. We focus on structural aspects of protein conformational distributions, from collective motions of single- and multi-domain proteins, intrinsically disordered proteins, to multiprotein complexes. Importantly, we highlight recent studies that illustrate functional adjustment of protein conformational ensembles in the crowded cellular environment. We center on the role of the ensemble in recognition of small- and macro-molecules (protein and RNA/DNA) and emphasize emerging concepts of protein dynamics in enzyme catalysis. Overall, protein ensembles link fundamental physicochemical principles and protein behavior and the cellular network and its regulation.
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Affiliation(s)
- Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China
| | - Wenhui Xi
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
- Sackler Inst. of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
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6
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Livesay DR, Jacobs DJ, Kanjanapangka J, Chea E, Cortez H, Garcia J, Kidd P, Marquez MP, Pande S, Yang D. Elucidating the Conformational Dependence of Calculated pKa Values. J Chem Theory Comput 2015; 2:927-38. [PMID: 26633052 DOI: 10.1021/ct600066z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The variability within calculated protein residue pKa values calculated using Poisson-Boltzmann continuum theory with respect to small conformational fluctuations is investigated. As a general rule, sites buried in the protein core have the largest pKa fluctuations but the least amount of conformational variability; conversely, sites on the protein surface generally have large conformational fluctuations but very small pKa fluctuations. These results occur because of the heterogeneous or uniform nature of the electrostatic microenvironments at the protein core or surface, respectively. Atypical surface sites with large pKa fluctuations occur at the interfaces between significant anionic and cationic potentials.
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Affiliation(s)
- Dennis R Livesay
- Department of Chemistry, Center for Macromolecular Modeling & Materials Design, and Department of Biological Sciences, California State Polytechnic University, Pomona, California, and Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina
| | - Donald J Jacobs
- Department of Chemistry, Center for Macromolecular Modeling & Materials Design, and Department of Biological Sciences, California State Polytechnic University, Pomona, California, and Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina
| | - Julie Kanjanapangka
- Department of Chemistry, Center for Macromolecular Modeling & Materials Design, and Department of Biological Sciences, California State Polytechnic University, Pomona, California, and Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina
| | - Eric Chea
- Department of Chemistry, Center for Macromolecular Modeling & Materials Design, and Department of Biological Sciences, California State Polytechnic University, Pomona, California, and Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina
| | - Hector Cortez
- Department of Chemistry, Center for Macromolecular Modeling & Materials Design, and Department of Biological Sciences, California State Polytechnic University, Pomona, California, and Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina
| | - Jorge Garcia
- Department of Chemistry, Center for Macromolecular Modeling & Materials Design, and Department of Biological Sciences, California State Polytechnic University, Pomona, California, and Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina
| | - Patrick Kidd
- Department of Chemistry, Center for Macromolecular Modeling & Materials Design, and Department of Biological Sciences, California State Polytechnic University, Pomona, California, and Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina
| | - Mario Pulido Marquez
- Department of Chemistry, Center for Macromolecular Modeling & Materials Design, and Department of Biological Sciences, California State Polytechnic University, Pomona, California, and Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina
| | - Swati Pande
- Department of Chemistry, Center for Macromolecular Modeling & Materials Design, and Department of Biological Sciences, California State Polytechnic University, Pomona, California, and Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina
| | - David Yang
- Department of Chemistry, Center for Macromolecular Modeling & Materials Design, and Department of Biological Sciences, California State Polytechnic University, Pomona, California, and Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina
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7
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Jónsdóttir LB, Ellertsson BÖ, Invernizzi G, Magnúsdóttir M, Thorbjarnardóttir SH, Papaleo E, Kristjánsson MM. The role of salt bridges on the temperature adaptation of aqualysin I, a thermostable subtilisin-like proteinase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2174-81. [DOI: 10.1016/j.bbapap.2014.08.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 08/05/2014] [Accepted: 08/20/2014] [Indexed: 11/30/2022]
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8
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Bovine α1-acid glycoprotein, a thermostable version of its human counterpart: Insights from Fourier transform infrared spectroscopy and in silico modelling. Biochimie 2014; 102:19-28. [DOI: 10.1016/j.biochi.2014.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 02/04/2014] [Indexed: 11/19/2022]
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9
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Harrison JS, Higgins CD, O'Meara MJ, Koellhoffer JF, Kuhlman BA, Lai JR. Role of electrostatic repulsion in controlling pH-dependent conformational changes of viral fusion proteins. Structure 2014; 21:1085-96. [PMID: 23823327 DOI: 10.1016/j.str.2013.05.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 05/07/2013] [Accepted: 05/13/2013] [Indexed: 11/29/2022]
Abstract
Viral fusion proteins undergo dramatic conformational transitions during membrane fusion. For viruses that enter through the endosome, these conformational rearrangements are typically pH sensitive. Here, we provide a comprehensive review of the molecular interactions that govern pH-dependent rearrangements and introduce a paradigm for electrostatic residue pairings that regulate progress through the viral fusion coordinate. Analysis of structural data demonstrates a significant role for side-chain protonation in triggering conformational change. To characterize this behavior, we identify two distinct residue pairings, which we define as Histidine-Cation (HisCat) and Anion-Anion (AniAni) interactions. These side-chain pairings destabilize a particular conformation via electrostatic repulsion through side-chain protonation. Furthermore, two energetic control mechanisms, thermodynamic and kinetic, regulate these structural transitions. This review expands on the current literature by identification of these residue clusters, discussion of data demonstrating their function, and speculation of how these residue pairings contribute to the energetic controls.
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Affiliation(s)
- Joseph S Harrison
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA.
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10
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Legg-E’Silva D, Achilonu I, Fanucchi S, Stoychev S, Fernandes M, Dirr HW. Role of Arginine 29 and Glutamic Acid 81 Interactions in the Conformational Stability of Human Chloride Intracellular Channel 1. Biochemistry 2012; 51:7854-62. [DOI: 10.1021/bi300874b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Derryn Legg-E’Silva
- Protein Structure−Function
Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050,
South Africa
| | - Ikechukwu Achilonu
- Protein Structure−Function
Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050,
South Africa
| | - Sylvia Fanucchi
- Protein Structure−Function
Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050,
South Africa
| | - Stoyan Stoychev
- Protein Structure−Function
Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050,
South Africa
| | - Manuel Fernandes
- School of
Chemistry, University of the Witwatersrand, Johannesburg 2050,
South Africa
| | - Heini W. Dirr
- Protein Structure−Function
Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050,
South Africa
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11
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Dhanasekaran V, Velmurugan D, Kanaujia SP, Sekar K. Role of invariant water molecules and water-mediated ionic interactions in D-xylose isomerase from Streptomyces rubiginosus. J Biomol Struct Dyn 2012; 31:376-84. [PMID: 22876874 DOI: 10.1080/07391102.2012.703064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The enzyme, D-xylose isomerase (D-xylose keto-isomerase; EC 5.3.1.5) is a soluble enzyme that catalyzes the conversion of the aldo-sugar D-xylose to the keto-sugar D-xylulose. A total of 27 subunits of D-xylose isomerase from Streptomyces rubiginosus were analyzed in order to identify the invariant water molecules and their water-mediated ionic interactions. A total of 70 water molecules were found to be invariant. The structural and/or functional roles of these water molecules have been discussed. These invariant water molecules and their ionic interactions may be involved in maintaining the structural stability of the enzyme D-xylose isomerase. Fifty-eight of the 70 invariant water molecules (83%) have at least one interaction with the main chain polar atom.
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Affiliation(s)
- V Dhanasekaran
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, India
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12
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Errami M, Geourjon C, Deléage G. Conservation of Amino Acids into Multiple Alignments Involved in Pairwise Interactions in Three-Dimensional Protein Structures. J Bioinform Comput Biol 2012; 1:505-520. [PMID: 15307241 DOI: 10.1142/s0219720003000228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We present an original strategy, that involves a bioinformatic software structure, in order to perform an exhaustive and objective statistical analysis of three-dimensional structures of proteins. We establish the relationship between multiple sequences alignments and various structural features of proteins. We show that amino acids implied in disulfide bonds, salt bridges and hydrophobic interactions are particularly conserved. Effects of identity, global similarity within alignments, and accessibility of interactions have been studied. Furthermore, we point out that the more variable the sequences within a multiple alignment, the more informative the multiple alignment. The results support multiple alignments usefulness for predictions of structural features.
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Affiliation(s)
- Mounir Errami
- Pôle Bioinfomatique Lyonnais-Institute de Biologie et Chimie des Protéines, Laboratoire de Bioinformatique et RMN structurales, Lyon cedex, France.
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13
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Assefa NG, Niiranen L, Willassen NP, Smalås A, Moe E. Thermal unfolding studies of cold adapted uracil-DNA N-glycosylase (UNG) from Atlantic cod (Gadus morhua). A comparative study with human UNG. Comp Biochem Physiol B Biochem Mol Biol 2012; 161:60-8. [DOI: 10.1016/j.cbpb.2011.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 09/12/2011] [Accepted: 09/13/2011] [Indexed: 10/17/2022]
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14
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Luo H, Zhang P, Robb FT. Oligomerization of an archaeal group II chaperonin is mediated by N-terminal salt bridges. Biochem Biophys Res Commun 2011; 413:389-94. [DOI: 10.1016/j.bbrc.2011.08.112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 08/23/2011] [Indexed: 11/30/2022]
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15
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Loladze VV, Makhatadze GI. Energetics of charge-charge interactions between residues adjacent in sequence. Proteins 2011; 79:3494-9. [PMID: 22072523 DOI: 10.1002/prot.23132] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 06/24/2011] [Accepted: 07/07/2011] [Indexed: 11/11/2022]
Abstract
Statistical analysis of the residue separation between a pair of ionizable side chains within 4 Å of each other was performed on a set of 1560 non-homologous PDB structures. We found that the frequency of pairs of like charges (i.e., pairs consisting of acidic residues Asp and Glu or pairs consisting of basic residues Arg and Lys) is two orders of magnitude lower than the pairs of oppositely charged residues (salt-bridges). We also found that for pairs of like charges the distribution is skewed dramatically towards short residue separation (<3). On the basis of these observations, we hypothesize that at short residue separation the repulsion between charges does not contribute much to the protein stability and the effects are largely dominated by the long range charge-charge interactions with other ionizable groups in the protein molecule. To test this hypothesis, we incorporated various pairs of charged residues at position 63 and 64 of ubiquitin and compared the stabilities of these variants. We also performed calculations of the expected changes in the charge-charge interactions. A very good correlation between experimental changes in the stability of ubiquitin variants, and changes in the energy of charge-charge interactions provides support for the hypothesis that a pair of ionizable residues next to each other in sequence modulates protein stability via long range charge-charge interactions with the rest of the protein.
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Affiliation(s)
- Vakhtang V Loladze
- Center for Biotechnology and Interdisciplinary Studies and Department of Biology, Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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16
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Yang G, Bai A, Gao L, Zhang Z, Zheng B, Feng Y. Glu88 in the non-catalytic domain of acylpeptide hydrolase plays dual roles: charge neutralization for enzymatic activity and formation of salt bridge for thermodynamic stability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1794:94-102. [PMID: 18930847 DOI: 10.1016/j.bbapap.2008.09.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 08/25/2008] [Accepted: 09/11/2008] [Indexed: 11/26/2022]
Abstract
Acylpeptide hydrolase of Aeropyrum pernix K1 is composed of a catalytic alpha/beta hydrolase domain and a non-catalytic beta-propeller domain. The Glu88 residue of the propeller domain is highly conserved in the prolyl oligopeptidase family and forms an inter-domain salt bridge with Arg526, a key residue for substrate binding. We have dissected the functions of Glu88 using site-directed mutagenesis, steady-state kinetics analyses, and molecular dynamics simulations. In E88A and E88A/R526K mutants, with a broken inter-domain salt bridge and a positive charge at position 526, catalytic activities for both a peptidase substrate and an esterase substrate were almost abolished. Analysis of the pH dependence of the mutants' reaction kinetics indicates that these mutations lead to changes in the electrostatic environment of the active site, which can be modulated by chloride ions. These findings indicate that the neutralization at position 526 is favorable for the activity of the enzyme, which is also verified by the catalytic behavior of E88A/R526V mutant. All mutants have lower thermodynamic stability than the wild-type. Therefore, Glu88 plays two major roles in the function of the enzyme: neutralizing the positive charge of Arg526, thereby increasing the enzymatic activity, and forming the Glu88-Arg526 salt bridge, thereby stabilizing the protein.
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Affiliation(s)
- Guangyu Yang
- Jilin University, Changchun 130023, People's Republic of China
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17
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Ranjani CV, Rangarajan S, Michael D, Roy S, Sekar K. Role of water molecules and ion pairs in Dps and related ferritin-like structures. Int J Biol Macromol 2008; 43:333-8. [PMID: 18674557 DOI: 10.1016/j.ijbiomac.2008.06.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Revised: 06/20/2008] [Accepted: 06/24/2008] [Indexed: 11/15/2022]
Abstract
A comparative study of water molecules and ion pairs in 11 Dps protein structures has been carried out. The invariant and common water molecules, the conserved residues interacting with them and the conserved ion pairs have been analyzed. Certain water molecules found on the interfaces between subunits are highly conserved and may be implicated in flexibility or continuing association of the subunits of the structure. It is possible that the water molecules, ion pairs and the special case of a water mediated charged network through a single water molecule are involved in maintaining the stability of the protein.
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Affiliation(s)
- C Vasuki Ranjani
- Bioinformatics Centre, 101 Raman Building, Indian Institute of Science, Bangalore 560012, India
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18
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Burendahl S, Treuter E, Nilsson L. Molecular Dynamics Simulations of Human LRH-1: The Impact of Ligand Binding in a Constitutively Active Nuclear Receptor. Biochemistry 2008; 47:5205-15. [DOI: 10.1021/bi7025084] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sofia Burendahl
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 57 Huddinge, Sweden
| | - Eckardt Treuter
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 57 Huddinge, Sweden
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 57 Huddinge, Sweden
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19
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Chu CH, Lai YJ, Huang H, Sun YJ. Kinetic and structural properties of triosephosphate isomerase from Helicobacter pylori. Proteins 2008; 71:396-406. [PMID: 17957775 DOI: 10.1002/prot.21709] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Triosephosphate isomerase (TIM) catalyzes the interconversion between dihydroxyacetone phosphate and D-glyceraldehyde-3-phosphate in the glycolysis-gluconeogenesis metabolism pathway. The Helicobacter pylori TIM gene (HpTIM) was cloned, and HpTIM was expressed and purified. The enzymatic activity of HpTIM for the substrate GAP was determined (K(m) = 3.46 +/- 0.23 mM and k(cat) = 8.8 x 10(4) min(-1)). The crystal structure of HpTIM was determined by molecular replacement at 2.3 A resolution. The overall structure of HpTIM was (beta/alpha)beta(beta/alpha)(6), which resembles the common TIM barrel fold, (beta/alpha)(8); however, a helix is missing after the second beta-strand. The conformation of loop 6 and binding of phosphate ion suggest that the determined structure of HpTIM was in the "closed" state. A highly conserved Arg-Asp salt bridge in the "DX(D/N)G" motif of most TIMs is absent in HpTIM because the sequence of this motif is "(211)SVDG(214)." To determine the significance of this salt bridge to HpTIM, four mutants, including K183S, K183A, D213Q, and D213A, were constructed and characterized. The results suggest that this conserved salt bridge is not essential for the enzymatic activity of HpTIM; however, it might contribute to the conformational stability of HpTIM.
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Affiliation(s)
- Chen-Hsi Chu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan, Republic of China
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20
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Olufsen M, Papaleo E, Smalås AO, Brandsdal BO. Ion pairs and their role in modulating stability of cold- and warm-active uracil DNA glycosylase. Proteins 2007; 71:1219-30. [DOI: 10.1002/prot.21815] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Gowri Shankar BA, Sarani R, Michael D, Mridula P, Ranjani CV, Sowmiya G, Vasundhar B, Sudha P, Jeyakanthan J, Velmurugan D, Sekar K. Ion pairs in non-redundant protein structures. J Biosci 2007; 32:693-704. [PMID: 17762142 DOI: 10.1007/s12038-007-0069-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Ion pairs contribute to several functions including the activity of catalytic triads, fusion of viral membranes, stability in thermophilic proteins and solvent-protein interactions. Furthermore, they have the ability to affect the stability of protein structures and are also a part of the forces that act to hold monomers together. This paper deals with the possible ion pair combinations and networks in 25% and 90% non-redundant protein chains. Different types of ion pairs present in various secondary structural elements are analysed. The ion pairs existing between different subunits of multisubunit protein structures are also computed and the results of various analyses are presented in detail. The protein structures used in the analysis are solved using X-ray crystallography, whose resolution is better than or equal to 1.5 A and R-factor better than or equal to 20%. This study can, therefore, be useful for analyses of many protein functions. It also provides insights into the better understanding of the architecture of protein structure.
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Affiliation(s)
- B A Gowri Shankar
- Bioinformatics Centre (Centre of Excellence in Structural Biology and Bio-computing), Indian Institute of Science, Bangalore, India
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22
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Freudenberg U, Behrens SH, Welzel PB, Müller M, Grimmer M, Salchert K, Taeger T, Schmidt K, Pompe W, Werner C. Electrostatic interactions modulate the conformation of collagen I. Biophys J 2007; 92:2108-19. [PMID: 17208984 PMCID: PMC1861768 DOI: 10.1529/biophysj.106.094284] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The pH- and electrolyte-dependent charging of collagen I fibrils was analyzed by streaming potential/streaming current experiments using the Microslit Electrokinetic Setup. Differential scanning calorimetry and circular dichroism spectroscopy were applied in similar electrolyte solutions to characterize the influence of electrostatic interactions on the conformational stability of the protein. The acid base behavior of collagen I was found to be strongly influenced by the ionic strength in KCl as well as in CaCl(2) solutions. An increase of the ionic strength with KCl from 10(-4) M to 10(-2) M shifts the isoelectric point (IEP) of the protein from pH 7.5 to 5.3. However, a similar increase of the ionic strength in CaCl(2) solutions shifts the IEP from 7.5 to above pH 9. Enhanced thermal stability with increasing ionic strength was observed by differential scanning calorimetry in both electrolyte systems. In line with this, circular dichroism spectroscopy results show an increase of the helicity with increasing ionic strength. Better screening of charged residues and the formation of salt bridges are assumed to cause the stabilization of collagen I with increasing ionic strength in both electrolyte systems. Preferential adsorption of hydroxide ions onto intrinsically uncharged sites in KCl solutions and calcium binding to negatively charged carboxylic acid moieties in CaCl(2) solutions are concluded to shift the IEP and influence the conformational stability of the protein.
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Affiliation(s)
- Uwe Freudenberg
- Leibniz Institute of Polymer Research Dresden, Max Bergmann Center of Biomaterials Dresden, Dresden, Germany
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23
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Hong H, Szabo G, Tamm LK. Electrostatic couplings in OmpA ion-channel gating suggest a mechanism for pore opening. Nat Chem Biol 2006; 2:627-35. [PMID: 17041590 DOI: 10.1038/nchembio827] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2006] [Accepted: 08/30/2006] [Indexed: 11/08/2022]
Abstract
The molecular forces that drive structural transitions between the open and closed states of channels and transporters are not well understood. The gate of the OmpA channel is formed by the central Glu52-Arg138 salt bridge, which can open to form alternate ion pairs with Lys82 and Glu128. To gain deeper insight into the channel-opening mechanism, we measured interaction energies between the relevant side chains by double-mutant cycle analysis and correlated these with the channel activities of corresponding point mutants. The closed central salt bridge has a strong interaction energy of -5.6 kcal mol(-1), which can be broken by forming the open-state salt bridge Glu52-Lys82 (DeltaDeltaG(Inter) = -3.5 kcal mol(-1)) and a weak interaction between Arg138 and Glu128 (DeltaDeltaG(Inter) = -0.6 kcal mol(-1)). A covalent disulfide bond in place of the central salt bridge completely blocks the channel. Growth assays indicate that this gating mechanism could physiologically contribute to the osmoprotection of Escherichia coli cells from environmental stress.
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Affiliation(s)
- Heedeok Hong
- Department of Molecular Physiology and Biological Physics, University of Virginia Health System, PO Box 800736, Charlottesville, Virginia 22908-0736, USA
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24
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Papaleo E, Olufsen M, De Gioia L, Brandsdal BO. Optimization of electrostatics as a strategy for cold-adaptation: a case study of cold- and warm-active elastases. J Mol Graph Model 2006; 26:93-103. [PMID: 17084098 DOI: 10.1016/j.jmgm.2006.09.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Revised: 09/26/2006] [Accepted: 09/26/2006] [Indexed: 10/24/2022]
Abstract
Adaptation to both high and low temperatures requires proteins with special properties. While organisms living at or close to the boiling point of water need to have proteins with increased stability, other properties are required at temperatures close to the freezing point of water. Indeed, it has been shown that enzymes adapted to cold environments are less resistant to heat with a concomitant increased activity as compared to their warm-active counter-parts. Several recent studies have pointed in the direction that electrostatic interactions play a central role in temperature adaptation, and in this study we investigate the role such interactions have in adaptation of elastase from Atlantic salmon and pig. Molecular dynamics (MD) simulations have been used to generate structural ensembles at 283 and 310 K of the psychrophilic and mesophilic elastase, and a total of eight 12 ns simulations have been carried out. Even though the two homologues have a highly similar three-dimensional structure, the location and number of charged amino acids are very different. Based on the simulated structures we find that very few salt-bridges are stable throughout the simulations, and provide little stabilization/destabilization of the proteins as judged by continuum electrostatic calculations. However, the mesophilic elastase is characterized by a greater number of salt-bridges as well as a putative salt-bridge network close to the catalytic site, indicating a higher rigidity of the components involved in the catalytic cycle. In addition, subtle differences are also found in the electrostatic potentials in the vicinity of the catalytic residues, which may explain the increased catalytic efficiency of the cold-adapted elastase.
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Affiliation(s)
- Elena Papaleo
- The Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø, N9037 Tromsø, Norway
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25
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Synonymous codon usage and its potential link with optimal growth temperature in prokaryotes. Gene 2006; 385:128-36. [PMID: 16989961 DOI: 10.1016/j.gene.2006.05.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Accepted: 05/29/2006] [Indexed: 12/01/2022]
Abstract
The relationship between codon usage in prokaryotes and their ability to grow at extreme temperatures has been given much attention over the past years. Previous studies have suggested that the difference in synonymous codon usage between (hyper)thermophiles and mesophiles is a consequence of a selective pressure linked to growth temperature. Here, we performed an updated analysis of the variation in synonymous codon usage with growth temperature; our study includes a large number of species from a wide taxonomic and growth temperature range. The presence of psychrophilic species in our study allowed us to test whether the same selective pressure acts on synonymous codon usage at very low growth temperature. Our results show that the synonymous codon usage for Arg (through the AGG, AGA and CGT codons) is the most discriminating factor between (hyper)thermophilic and non-thermophilic species, thus confirming previous studies. We report the unusual clustering of an Archaeal psychrophile with the thermophilic and hyperthermophilic species on the synonymous codon usage factorial map; the other psychrophiles in our study cluster with the mesophilic species. Our conclusion is that the difference in synonymous codon usage between (hyper)thermophilic and non-thermophilic species cannot be clearly attributed to a selective pressure linked to growth at high temperatures.
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26
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Saraboji K, Gromiha MM, Ponnuswamy MN. Importance of main-chain hydrophobic free energy to the stability of thermophilic proteins. Int J Biol Macromol 2005; 35:211-20. [PMID: 15811476 DOI: 10.1016/j.ijbiomac.2005.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2004] [Revised: 01/26/2005] [Accepted: 02/15/2005] [Indexed: 11/28/2022]
Abstract
Living organisms are found in the most unexpected places, including deep-sea vents at 100 degrees C and several hundred bars pressure, in hot springs. Needless to say, the proteins found in thermophilic species are much more stable than their mesophilic counterparts. There are no obvious reasons to say that one would be more stable than others. Even examination of the amino acids and comparison of structural features of thermophiles with mesophilies cannot bring satisfactory explanation for the thermal stability of such proteins. In order to bring out the hidden information behind the thermal stabilization of such proteins in terms of energy factors and their combinations, analysis were made on good resolution structures of thermophilic and their mesophilic homologous from 23 different families. From the structural coordinates, free energy contributions due to hydrophobic, electrostatic, hydrogen bonding, disulfide bonding and van der Waals interactions are computed. In this analysis, a vast majority of thermophilic proteins adopt slightly lower free energy contribution in each energy terms than its mesophilic counterparts. The major observation noted from this study is the lower hydrophobic free energy contribution due to carbon atoms and main-chain nitrogen atoms in all the thermophilic proteins. The possible combination of different free energy terms shows majority of the thermophilic proteins have lower free energy strategy than their mesophilic homologous. The derived results show that the hydrophobic free energy due to carbon and nitrogen atoms and such combinations of free energy components play a vital role in the thermostablisation of such proteins.
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Affiliation(s)
- K Saraboji
- Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600025, India
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27
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Chakravarty S, Wang L, Sanchez R. Accuracy of structure-derived properties in simple comparative models of protein structures. Nucleic Acids Res 2005; 33:244-59. [PMID: 15647507 PMCID: PMC546150 DOI: 10.1093/nar/gki162] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The accuracy of comparative models of proteins is addressed here. A set of 12 732 single-template models of sequences of known high-resolution structures was built by an automated procedure. Accuracy of several structure-derived properties, such as surface area, residue accessibility, presence of pockets, electrostatic potential and others, was determined as a function of template:target sequence identity by comparing models with their corresponding experimental structures. As expected, the average accuracy of structure-derived properties always increases with higher template:target sequence identity, but the exact shape of this relationship can differ from one property to another. A comparison of structure-derived properties measured from NMR and X-ray structures of the same protein shows that for most properties, the NMR/X-ray difference is of the same order as the error in models based on ∼40% template:target sequence identity. The exact sequence identity at which properties reach that accuracy varies between 25 and 50%, depending on the property being analyzed. A general characteristic of simple comparative models is that their surface has increased area as a consequence of being more rugged than that of experimental structures. This suggests that including solvent effects during model building or refinement could significantly improve the accuracy of surface properties in comparative models.
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Affiliation(s)
| | | | - Roberto Sanchez
- To whom correspondence should be addressed. Tel: +1 212 659 8648; Fax: +1 212 849 2456;
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28
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Kumar S, Nussinov R. Different roles of electrostatics in heat and in cold: adaptation by citrate synthase. Chembiochem 2004; 5:280-90. [PMID: 14997520 DOI: 10.1002/cbic.200300627] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Electrostatics plays a major role in heat adaptation by thermophilic proteins. Here we ask whether electrostatics similarly contributes to cold adaptation in psychrophilic proteins. We compare the sequences and structures of citrate synthases from the psychrophile Arthobacter Ds2-3R, from chicken, and from the hyperthermophile Pyrococcus furiosus. The three enzymes share similar packing, burial of nonpolar surface area, and main-chain hydrogen bonding. However, both psychrophilic and hyperthermophilic citrate synthases contain more charged residues, salt bridges, and salt-bridge networks than the mesophile. The electrostatic free-energy contributions toward protein stability by individual charged residues show greater variabilities in the psychrophilic citrate synthase than in the hyperthermophilic enzyme. The charged residues in the active-site regions of the psychrophile are more destabilizing than those in the active-site regions of the hyperthermophile. In the hyperthermophilic enzyme, salt bridges and their networks largely cluster in the active-site regions and at the dimer interface. In contrast, in the psychrophile, they are more dispersed throughout the structure. On average, salt bridges and their networks provide greater electrostatic stabilization to the thermophilic citrate synthase at 100 degrees C than to the psychrophilic enzyme at 0 degrees C. Electrostatics appears to play an important role in both heat and cold adaptation of citrate synthase. However, remarkably, the role may be different in the two types of enzyme: In the hyperthermophile, it may contribute to the integrity of both the protein dimer and the active site by possibly countering conformational disorder at high temperatures. On the other hand, in the psychrophile at low temperatures, electrostatics may contribute to enhance protein solvation and to ensure active-site flexibility.
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Affiliation(s)
- Sandeep Kumar
- Basic Research Program, SAIC-Frederick, Inc., Laboratory of Experimental and Computational Biology, NCI-Frederick, Building 469, Room 151, Frederick, MD 21702, USA
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29
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Abstract
Most positively selected mutations cause changes in metabolism, resulting in a better-adapted phenotype. But as well as acting on the information content of genes, natural selection may also act directly on nucleic acid and protein molecules. We review the evidence for direct temperature-dependent natural selection acting on genomes, transcriptomes and proteomes.
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Affiliation(s)
- Donal A Hickey
- Department of Biology, Concordia University, 7141 Sherbrooke Street, Montreal, Quebec, H4B 1R6, Canada.
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30
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Foloppe N, Nilsson L. The glutaredoxin -C-P-Y-C- motif: influence of peripheral residues. Structure 2004; 12:289-300. [PMID: 14962389 DOI: 10.1016/j.str.2004.01.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2003] [Revised: 10/16/2003] [Accepted: 10/16/2003] [Indexed: 10/22/2022]
Abstract
The variety of cellular functions performed by proteins of the thioredoxin superfamily is made possible by the wide range of redox potential associated with their active site -Cys-X-X-Cys- motif. The determinants of these differences in redox potential are of considerable interest but are not well understood. E. coli Glutaredoxin 1 (Grx1) and 3 (Grx3) are important model systems with different redox properties, despite sharing the same -Cys-Pro-Tyr-Cys- motif, very similar overall structures, and 33% sequence identity. Very long molecular dynamics simulations (0.25 micros total) and electrostatic calculations provide a revised view of the reduced Grx1 active site, which now can be reconciled with biochemical and functional data. Comparison of this new model to Grx3 uncovers differences in the structure, dynamics, and electrostatics of these active sites. The influence of peripheral residues on the properties of the -Cys-X-X-Cys- motif is illustrated specifically with the effect of a Lys to Arg substitution.
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Affiliation(s)
- Nicolas Foloppe
- Center for Structural Biochemistry, Department of Bioscience, Karolinska Institutet, S-141 57, Huddinge, Sweden
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31
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Miteva MA, Brugge JM, Rosing J, Nicolaes GAF, Villoutreix BO. Theoretical and experimental study of the D2194G mutation in the C2 domain of coagulation factor V. Biophys J 2004; 86:488-98. [PMID: 14695293 PMCID: PMC1303816 DOI: 10.1016/s0006-3495(04)74127-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Coagulation factor V (FV) is a large plasma glycoprotein with functions in both the pro- and anticoagulant pathways. In carriers of the so-called R2-FV haplotype, the FV D2194G mutation, in the C2 membrane-binding domain, is associated with low expression levels, suggesting a potential folding/stability problem. To analyze the molecular mechanisms potentially responsible for this in vitro phenotype, we used molecular dynamics (MD) and continuum electrostatic calculations. Implicit solvent simulations were performed on the x-ray structure of the wild-type C2 domain and on a model of the D2194G mutant. Because D2194 is located next to a disulfide bond (S-S bond), MD calculations were also performed on S-S bond depleted structures. D2194 is part of a salt-bridge network and investigations of the stabilizing/destabilizing role of these ionic interactions were carried out. Five mutant FV molecules were created and the expression levels measured with the aim of assessing the tolerance to amino acid changes in this region of molecule. Analysis of the MD trajectories indicated increased flexibility in some areas and energetic comparisons suggested overall destabilization of the structure due to the D2194G mutation. This substitution causes electrostatic destabilization of the domain by approximately 3 kcal/mol. Together these effects likely explain the lowered expression levels in R2-FV carriers.
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Affiliation(s)
- M A Miteva
- French National Institute of Health and Medical Research (INSERM) U428, University Paris V, 75006 Paris, France
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32
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Keskin O, Tsai CJ, Wolfson H, Nussinov R. A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. Protein Sci 2004; 13:1043-55. [PMID: 15044734 PMCID: PMC2280042 DOI: 10.1110/ps.03484604] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2003] [Revised: 12/23/2003] [Accepted: 01/09/2004] [Indexed: 10/26/2022]
Abstract
Here, we present a diverse, structurally nonredundant data set of two-chain protein-protein interfaces derived from the PDB. Using a sequence order-independent structural comparison algorithm and hierarchical clustering, 3799 interface clusters are obtained. These yield 103 clusters with at least five nonhomologous members. We divide the clusters into three types. In Type I clusters, the global structures of the chains from which the interfaces are derived are also similar. This cluster type is expected because, in general, related proteins associate in similar ways. In Type II, the interfaces are similar; however, remarkably, the overall structures and functions of the chains are different. The functional spectrum is broad, from enzymes/inhibitors to immunoglobulins and toxins. The fact that structurally different monomers associate in similar ways, suggests "good" binding architectures. This observation extends a paradigm in protein science: It has been well known that proteins with similar structures may have different functions. Here, we show that it extends to interfaces. In Type III clusters, only one side of the interface is similar across the cluster. This structurally nonredundant data set provides rich data for studies of protein-protein interactions and recognition, cellular networks and drug design. In particular, it may be useful in addressing the difficult question of what are the favorable ways for proteins to interact. (The data set is available at http://protein3d.ncifcrf.gov/~keskino/ and http://home.ku.edu.tr/~okeskin/INTERFACE/INTERFACES.html.)
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Affiliation(s)
- Ozlem Keskin
- NCI-Frederick, Building 469, Room 151, Frederick, MD 21702, USA
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33
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Mancusso R, Cruz E, Cataldi M, Mendoza C, Fuchs J, Wang H, Yang X, Tasayco ML. Reversal of Negative Charges on the Surface of Escherichia coli Thioredoxin: Pockets versus Protrusions. Biochemistry 2004; 43:3835-43. [PMID: 15049690 DOI: 10.1021/bi0354684] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent studies of proteins with reversed charged residues have demonstrated that electrostatic interactions on the surface can contribute significantly to protein stability. We have used the approach of reversing negatively charged residues using Arg to evaluate the effect of the electrostatics context on the transition temperature (T(m)), the unfolding Gibbs free energy change (DeltaG), and the unfolding enthalpy change (DeltaH). We have reversed negatively charged residues at a pocket (Asp9) and protrusions (Asp10, Asp20, Glu85), all located in interconnecting segments between elements of secondary structure on the surface of Arg73Ala Escherichia coli thioredoxin. DSC measurements indicate that reversal of Asp in a pocket (Asp9Arg/Arg73Ala, DeltaT(m) = -7.3 degrees C) produces a larger effect in thermal stability than reversal at protrusions: Asp10Arg/Arg73Ala, DeltaT(m) = -3.1 degrees C, Asp20Arg/Arg73Ala, DeltaT(m) = 2.0 degrees C, Glu85Arg/Arg73Ala, DeltaT(m) = 3.9 degrees ). The 3D structure of thioredoxin indicates that Asp20 and Glu85 have no nearby charges within 8 A, while Asp9 does not only have Asp10 as sequential neighbor, but it also forms a 5-A long-range ion pair with the solvent-exposed Lys69. Further DSC measurements indicate that neutralization of the individual charges of the ion pair Asp9-Lys69 with nonpolar residues produces a significant decrease in stability in both cases: Asp9Ala/Arg73Ala, DeltaT(m) = -3.7 degrees C, Asp9Met/Arg73Ala, DeltaT(m) = -5.5 degrees C, Lys69Leu/Arg73Ala, DeltaT(m) = -5.1 degrees C. However, thermodynamic analysis shows that reversal or neutralization of Asp9 produces a 9-15% decrease in DeltaH, while both reversal of Asp at protrusions and neutralization of Lys69 produce negligible changes. These results correlate well with the NMR analysis, which demonstrates that only the substitution of Asp9 produces extensive conformational changes and these changes occur in the surroundings of Lys69. Our results led us to suggest that reversal of a negative charge at a pocket has a larger effect on stability than a similar reversal at a protrusion and that this difference arises largely from short-range interactions with polar groups within the pocket, rather than long-range interactions with solvent-exposed charged groups.
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Affiliation(s)
- Romina Mancusso
- Biochemistry Division, Department of Chemistry, City College of New York, 138th Street and Convent Avenue, New York, New York 10031, USA
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34
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Georlette D, Damien B, Blaise V, Depiereux E, Uversky VN, Gerday C, Feller G. Structural and functional adaptations to extreme temperatures in psychrophilic, mesophilic, and thermophilic DNA ligases. J Biol Chem 2003; 278:37015-23. [PMID: 12857762 DOI: 10.1074/jbc.m305142200] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Psychrophiles, host of permanently cold habitats, display metabolic fluxes comparable to those exhibited by mesophilic organisms at moderate temperatures. These organisms have evolved by producing, among other peculiarities, cold-active enzymes that have the properties to cope with the reduction of chemical reaction rates induced by low temperatures. The emerging picture suggests that these enzymes display a high catalytic efficiency at low temperatures through an improved flexibility of the structural components involved in the catalytic cycle, whereas other protein regions, if not implicated in catalysis, may be even more rigid than their mesophilic counterparts. In return, the increased flexibility leads to a decreased stability of psychrophilic enzymes. In order to gain further advances in the analysis of the activity/flexibility/stability concept, psychrophilic, mesophilic, and thermophilic DNA ligases have been compared by three-dimensional-modeling studies, as well as regards their activity, surface hydrophobicity, structural permeability, conformational stabilities, and irreversible thermal unfolding. These data show that the cold-adapted DNA ligase is characterized by an increased activity at low and moderate temperatures, an overall destabilization of the molecular edifice, especially at the active site, and a high conformational flexibility. The opposite trend is observed in the mesophilic and thermophilic counterparts, the latter being characterized by a reduced low temperature activity, high stability and reduced flexibility. These results strongly suggest a complex relationship between activity, flexibility and stability. In addition, they also indicate that in cold-adapted enzymes, the driving force for denaturation is a large entropy change.
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Affiliation(s)
- Daphné Georlette
- Laboratory of Biochemistry, Institute of Chemistry B6, University of Liège, B-4000 Liège, Belgium
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35
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Makhatadze GI, Loladze VV, Ermolenko DN, Chen X, Thomas ST. Contribution of surface salt bridges to protein stability: guidelines for protein engineering. J Mol Biol 2003; 327:1135-48. [PMID: 12662936 DOI: 10.1016/s0022-2836(03)00233-x] [Citation(s) in RCA: 185] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The small globular protein, ubiquitin, contains a pair of oppositely charged residues, K11 and E34, that according to the three-dimensional structure are located on the surface of this protein with a spatial orientation characteristic of a salt bridge. We investigated the strength of this salt bridge and its contribution to the global stability of the ubiquitin molecule. Using the "double mutant cycle" analysis, the strength of the pairwise interactions between K11 and E34 was estimated to be favorable by 3.6kJ/mol. Further, the salt bridge of the reverse orientation, i.e. E11/K34, can be formed and is found to have a strength (3.8kJ/mol) similar to that of the K11/E34 pair. However, the global stability of the K11/E34 variant of ubiquitin is 2.2kJ/mol higher than that of the E11/K34 variant. The difference in the contribution of the opposing salt bridge orientations to the overall stability of the ubiquitin molecule is attributed to the difference in the charge-charge interactions between residues forming the salt bridge and the rest of the ionizable groups in this protein. On the basis of these results, we concluded that surface salt bridges are stabilizing, but their contribution to the overall protein stability is strongly context-dependent, with charge-charge interactions being the largest determinant. Analysis of 16 salt bridges from six different proteins, for which detailed experimental data on energetics have been reported, support the conclusions made from the analysis of the salt bridge in ubiquitin. Implications of these findings for engineering proteins with enhanced thermostability are discussed.
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Affiliation(s)
- George I Makhatadze
- Department of Biochemistry and Molecular Biology, College of Medicine, Penn State University, 500 UniversityDrive, Hershey, PA 17033-2390, USA.
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36
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Alexov E. Role of the protein side-chain fluctuations on the strength of pair-wise electrostatic interactions: comparing experimental with computed pK(a)s. Proteins 2003; 50:94-103. [PMID: 12471602 DOI: 10.1002/prot.10265] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The effect of the protein side-chain fluctuations on the strength of electrostatic interactions was studied. The effect was modeled on 7 different crystal structures on the same enzyme as well as on 20 molecular dynamics snapshot structures. It was shown that the side-chain flexibility affects predominantly the magnitude of the strong pair-wise interactions, that is, the pair-wise interaction among ion pairs, and practically does not affect the interactions with the rest of the protein. This was used to suggest a correction function that should be applied to the original pair-wise electrostatic interaction to mimic the effects of the fluctuations. The procedure is applied on three ion pairs identified in lysozyme. It was shown that sampling different side-chain rotamers and modifying the strength of the pair-wise interaction energies makes calculated pK(a)s less sensitive to the fluctuations of the structure and improves the prediction accuracy.
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Affiliation(s)
- Emil Alexov
- Howard Hughes Medical Institute and Biochemistry Department, Columbia University, New York, New York 10032, USA.
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37
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Abstract
The electrostatic free energy contribution of an ion pair in a protein depends on two factors, geometrical orientation of the side-chain charged groups with respect to each other and the structural context of the ion pair in the protein. Conformers in NMR ensembles enable studies of the relationship between geometry and electrostatic strengths of ion pairs, because the protein structural contexts are highly similar across different conformers. We have studied this relationship using a dataset of 22 unique ion pairs in 14 NMR conformer ensembles for 11 nonhomologous proteins. In different NMR conformers, the ion pairs are classified as salt bridges, nitrogen-oxygen (N-O) bridges and longer-range ion pairs on the basis of geometrical criteria. In salt bridges, centroids of the side-chain charged groups and at least a pair of side-chain nitrogen and oxygen atoms of the ion-pairing residues are within a 4 A distance. In N-O bridges, at least a pair of the side-chain nitrogen and oxygen atoms of the ion-pairing residues are within 4 A distance, but the distance between the side-chain charged group centroids is greater than 4 A. In the longer-range ion pairs, the side-chain charged group centroids as well as the side-chain nitrogen and oxygen atoms are more than 4 A apart. Continuum electrostatic calculations indicate that most of the ion pairs have stabilizing electrostatic contributions when their side-chain charged group centroids are within 5 A distance. Hence, most (approximately 92%) of the salt bridges and a majority (68%) of the N-O bridges are stabilizing. Most (approximately 89%) of the destabilizing ion pairs are the longer-range ion pairs. In the NMR conformer ensembles, the electrostatic interaction between side-chain charged groups of the ion-pairing residues is the strongest for salt bridges, considerably weaker for N-O bridges, and the weakest for longer-range ion pairs. These results suggest empirical rules for stabilizing electrostatic interactions in proteins.
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Affiliation(s)
- Sandeep Kumar
- Laboratory of Experimental and Computational Biology, National Cancer Institute, Frederick Cancer Research and Development Center, Frederick, Maryland 21702 USA
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38
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Kursula I, Partanen S, Lambeir AM, Wierenga RK. The importance of the conserved Arg191-Asp227 salt bridge of triosephosphate isomerase for folding, stability, and catalysis. FEBS Lett 2002; 518:39-42. [PMID: 11997014 DOI: 10.1016/s0014-5793(02)02639-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Triosephosphate isomerase (TIM) has a conserved salt bridge 20 A away from both the active site and the dimer interface. In this study, four salt bridge mutants of Trypanosoma brucei brucei TIM were characterized. The folding and stability of the mutants are impaired compared to the wild-type enzyme. This salt bridge is part of a hydrogen bonding network which tethers the C-terminal beta7alpha7beta8alpha8 unit to the bulk of the protein. In the variants D227N, D227A, and R191S, this network is preserved, as can be deduced from the structure of the R191S variant. In the R191A variant, the side chain at position 191 cannot contribute to this network. Also the catalytic power of this variant is most affected.
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Affiliation(s)
- Inari Kursula
- Department of Biochemistry and Biocenter Oulu, University of Oulu, P.O. Box 3000, FIN-90014 Oulu, Finland
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39
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Ma B, Shatsky M, Wolfson HJ, Nussinov R. Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci 2002; 11:184-97. [PMID: 11790828 PMCID: PMC2373439 DOI: 10.1110/ps.21302] [Citation(s) in RCA: 316] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2001] [Revised: 10/12/2001] [Accepted: 11/01/2001] [Indexed: 10/16/2022]
Abstract
Here, we comment on the steadily increasing body of data showing that proteins with specificity actually bind ligands of diverse shapes, sizes, and composition. Such a phenomenon is not surprising when one considers that binding is a dynamic process with populations in equilibrium and that the shape of the binding site is strongly influenced by the molecular partner. It derives implicitly from the concept of populations. All proteins, specific and nonspecific, exist in ensembles of substates. If the library of ligands in solution is large enough, favorably matching ligands with altered shapes and sizes can be expected to bind, with a redistribution of the protein populations. Point mutations at spatially distant sites may exert large conformational rearrangements and hinge effects, consistent with mutations away from the binding site leading to population shifts and (cross-)drug resistance. A similar effect is observed in protein superfamilies, in which different sequences with similar topologies display similar large-scale dynamic motions. The hinges are frequently at analogous sites, yet with different substrate specificity. Similar topologies yield similar conformational isomers, although with different distributions of population times, owing to the change in the conditions, that is, the change in the sequences. In turn, different distributions relate to binding of different sizes and shapes. Hence, the binding site shape and size are defined by the ligand. They are not independent entities of fixed proportions and cannot be analyzed independently of the binding partner. Such a proposition derives from viewing proteins as dynamic distributions, presenting to the incoming ligands a range of binding site shapes. It illustrates how presumably specific binding molecules can bind multiple ligands. In terms of drug design, the ability of a single receptor to recognize many dissimilar ligands shows the need to consider more diverse molecules. It provides a rationale for higher affinity inhibitors that are not derived from substrates at their transition states and indicates flexible docking schemes.
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Affiliation(s)
- Buyong Ma
- Laboratory of Experimental and Computational Biology, National Cancer Institute-Frederick, Frederick, Maryland 21702, USA
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