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Zacharias M. Atomic Resolution Insight into Sac7d Protein Binding to DNA and Associated Global Changes by Molecular Dynamics Simulations. Angew Chem Int Ed Engl 2019; 58:5967-5972. [DOI: 10.1002/anie.201900935] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Martin Zacharias
- Physics Department T38Technical University of Munich 85748 Garching Germany
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2
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Zacharias M. Atomic Resolution Insight into Sac7d Protein Binding to DNA and Associated Global Changes by Molecular Dynamics Simulations. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Martin Zacharias
- Physics Department T38Technical University of Munich 85748 Garching Germany
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3
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Zhang X, Zheng QC. Exploring the influence of hyperthermophilic protein Ssh10b on the stability and conformation of RNA by molecular dynamics simulation. Biopolymers 2017; 109. [DOI: 10.1002/bip.23068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/27/2017] [Accepted: 09/15/2017] [Indexed: 01/22/2023]
Affiliation(s)
- Xue Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University; Changchun 130023 People's Republic of China
| | - Qing-Chuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University; Changchun 130023 People's Republic of China
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education; Jilin University; Changchun 130023 People's Republic of China
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Grishin DV, Pokrovskaya MV, Podobed OV, Gladilina JA, Pokrovsky VS, Aleksandrova SS, Sokolov NN. [Prediction of protein thermostability from their primary structure: the current state and development factors]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2017; 63:124-131. [PMID: 28414283 DOI: 10.18097/pbmc20176302124] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The construction of proteins and peptides with desired properties, including resistance to high temperatures, as well as optimization of their amino acid composition, is an important and complex task, which attracts much attention in various branches of the basic sciences, and also in biomedicine and biotechnology. This raises the question: what method is more relevant for the at the pilot stage of research in order to estimate the influence of the planned amino acid substitutions on the thermostability of the resultant protein construct? In this brief review we have classified existing basic practical and theoretical approaches used in studies and predicting the thermal stability of native and recombinant polypeptides. Particular attention has been paid to the predictive potential of statistical methods for studying the thermodynamic parameters of the primary protein structure and prospects of their use.
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Affiliation(s)
- D V Grishin
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - O V Podobed
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | | | - N N Sokolov
- Institute of Biomedical Chemistry, Moscow, Russia
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5
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BIKKINA SWETHA, BHATI AGASTYAP, PADHI SILADITYA, PRIYAKUMAR UDEVA. Temperature Dependence of the Stability of Ion Pair Interactions, and its Implications on the Thermostability of Proteins from Thermophiles. J CHEM SCI 2017. [DOI: 10.1007/s12039-017-1231-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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6
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Cruz-Teran CA, Carlin KB, Efimenko K, Genzer J, Rao BM. Targeted Mutagenesis and Combinatorial Library Screening Enables Control of Protein Orientation on Surfaces and Increased Activity of Adsorbed Proteins. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:8660-8667. [PMID: 27490089 DOI: 10.1021/acs.langmuir.6b01446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
While nonspecific adsorption is widely used for immobilizing proteins on solid surfaces, the random nature of protein adsorption may reduce the activity of immobilized proteins due to occlusion of the active site. We hypothesized that the orientation a protein assumes on a given surface can be controlled by systematically introducing mutations into a region distant from its active site, thereby retaining activity of the immobilized protein. To test this hypothesis, we generated a combinatorial protein library by randomizing six targeted residues in a binding protein derived from highly stable, nonimmunoglobulin Sso7d scaffold; mutations were targeted in a region that is distant from the binding site. This library was screened to isolate binders that retain binding to its cognate target (chicken immunoglobulin Y, cIgY) as well as exhibit adsorption on unmodified silica at pH 7.4 and high ionic strength conditions. A single mutant, Sso7d-2B5, was selected for further characterization. Sso7d-2B5 retained binding to cIgY with an apparent dissociation constant similar to that of the parent protein; both mutant and parent proteins saturated the surface of silica with similar densities. Strikingly, however, silica beads coated with Sso7d-2B5 could achieve up to 7-fold higher capture of cIgY than beads coated with the parent protein. These results strongly suggest that mutations introduced in Sso7d-2B5 alter its orientation relative to the parent protein, when adsorbed on silica surfaces. Our approach also provides a generalizable strategy for introducing mutations in proteins so as to improve their activity upon immobilization, and has direct relevance to development of protein-based biosensors and biocatalysts.
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Affiliation(s)
- Carlos A Cruz-Teran
- Department of Chemical and Biomolecular Engineering, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Kevin B Carlin
- Department of Chemical and Biomolecular Engineering, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Kirill Efimenko
- Department of Chemical and Biomolecular Engineering, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Jan Genzer
- Department of Chemical and Biomolecular Engineering, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Balaji M Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University , Raleigh, North Carolina 27695, United States
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Tych KM, Batchelor M, Hoffmann T, Wilson MC, Hughes ML, Paci E, Brockwell DJ, Dougan L. Differential Effects of Hydrophobic Core Packing Residues for Thermodynamic and Mechanical Stability of a Hyperthermophilic Protein. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:7392-7402. [PMID: 27338140 DOI: 10.1021/acs.langmuir.6b01550] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Proteins from organisms that have adapted to environmental extremes provide attractive systems to explore and determine the origins of protein stability. Improved hydrophobic core packing and decreased loop-length flexibility can increase the thermodynamic stability of proteins from hyperthermophilic organisms. However, their impact on protein mechanical stability is not known. Here, we use protein engineering, biophysical characterization, single-molecule force spectroscopy (SMFS), and molecular dynamics (MD) simulations to measure the effect of altering hydrophobic core packing on the stability of the cold shock protein TmCSP from the hyperthermophilic bacterium Thermotoga maritima. We make two variants of TmCSP in which a mutation is made to reduce the size of aliphatic groups from buried hydrophobic side chains. In the first, a mutation is introduced in a long loop (TmCSP L40A); in the other, the mutation is introduced on the C-terminal β-strand (TmCSP V62A). We use MD simulations to confirm that the mutant TmCSP L40A shows the most significant increase in loop flexibility, and mutant TmCSP V62A shows greater disruption to the core packing. We measure the thermodynamic stability (ΔGD-N) of the mutated proteins and show that there is a more significant reduction for TmCSP L40A (ΔΔG = 63%) than TmCSP V62A (ΔΔG = 47%), as might be expected on the basis of the relative reduction in the size of the side chain. By contrast, SMFS measures the mechanical stability (ΔG*) and shows a greater reduction for TmCSP V62A (ΔΔG* = 8.4%) than TmCSP L40A (ΔΔG* = 2.5%). While the impact on the mechanical stability is subtle, the results demonstrate the power of tuning noncovalent interactions to modulate both the thermodynamic and mechanical stability of a protein. Such understanding and control provide the opportunity to design proteins with optimized thermodynamic and mechanical properties.
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Affiliation(s)
- Katarzyna M Tych
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Matthew Batchelor
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Toni Hoffmann
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Michael C Wilson
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Megan L Hughes
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Emanuele Paci
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - David J Brockwell
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Lorna Dougan
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
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8
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Liu H, Gao YS, Chen XJ, Chen Z, Zhou HM, Yan YB, Gong H. A single residue substitution accounts for the significant difference in thermostability between two isoforms of human cytosolic creatine kinase. Sci Rep 2016; 6:21191. [PMID: 26879258 PMCID: PMC4754747 DOI: 10.1038/srep21191] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/19/2016] [Indexed: 11/14/2022] Open
Abstract
Creatine kinase (CK) helps maintain homeostasis of intracellular ATP level by catalyzing the reversible phosphotransfer between ATP and phosphocreatine. In humans, there are two cytosolic CK isoforms, the muscle-type (M) and the brain-type (B), which frequently function as homodimers (hMMCK and hBBCK). Interestingly, these isoenzymes exhibit significantly different thermostabilities, despite high similarity in amino acid sequences and tertiary structures. In order to investigate the mechanism of this phenomenon, in this work, we first used domain swapping and site-directed mutagenesis to search for the key residues responsible for the isoenzyme-specific thermostability. Strikingly, the difference in thermostability was found to principally arise from one single residue substitution at position 36 (Pro in hBBCK vs. Leu in hMMCK). We then engaged the molecular dynamics simulations to study the molecular mechanism. The calculations imply that the P36L substitution introduces additional local interactions around residue 36 and thus further stabilizes the dimer interface through a complex interaction network, which rationalizes the observation that hMMCK is more resistant to thermal inactivation than hBBCK. We finally confirmed this molecular explanation through thermal inactivation assays on Asp36 mutants that were proposed to devastate the local interactions and thus the dimer associations in both isoenzymes.
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Affiliation(s)
- Huihui Liu
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yan-Song Gao
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing 314006, China
| | - Xiang-Jun Chen
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhe Chen
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing 314006, China
| | - Hai-Meng Zhou
- Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing 314006, China
| | - Yong-Bin Yan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haipeng Gong
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
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9
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Chen L, Li X, Wang R, Fang F, Yang W, Kan W. Thermal stability and unfolding pathways of hyperthermophilic and mesophilic periplasmic binding proteins studied by molecular dynamics simulation. J Biomol Struct Dyn 2016; 34:1576-89. [DOI: 10.1080/07391102.2015.1084480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Lin Chen
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, P.R. China
| | - Xue Li
- College of Chemistry and Biology, Beihua Uuniversity, Jilin 132000, P.R. China
| | - Ruige Wang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, P.R. China
| | - Fengqin Fang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, P.R. China
| | - Wanli Yang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, P.R. China
| | - Wei Kan
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, P.R. China
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SURESH GORLE, PRIYAKUMAR UDEVA. Atomistic details of the molecular recognition of DNA-RNA hybrid duplex by ribonuclease H enzyme. J CHEM SCI 2015. [DOI: 10.1007/s12039-015-0942-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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11
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Medvedev KE, Alemasov NA, Vorobjev YN, Boldyreva EV, Kolchanov NA, Afonnikov DA. Molecular dynamics simulations of the Nip7 proteins from the marine deep- and shallow-water Pyrococcus species. BMC STRUCTURAL BIOLOGY 2014; 14:23. [PMID: 25315147 PMCID: PMC4209456 DOI: 10.1186/s12900-014-0023-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 10/03/2014] [Indexed: 11/13/2022]
Abstract
Background The identification of the mechanisms of adaptation of protein structures to extreme environmental conditions is a challenging task of structural biology. We performed molecular dynamics (MD) simulations of the Nip7 protein involved in RNA processing from the shallow-water (P. furiosus) and the deep-water (P. abyssi) marine hyperthermophylic archaea at different temperatures (300 and 373 K) and pressures (0.1, 50 and 100 MPa). The aim was to disclose similarities and differences between the deep- and shallow-sea protein models at different temperatures and pressures. Results The current results demonstrate that the 3D models of the two proteins at all the examined values of pressures and temperatures are compact, stable and similar to the known crystal structure of the P. abyssi Nip7. The structural deviations and fluctuations in the polypeptide chain during the MD simulations were the most pronounced in the loop regions, their magnitude being larger for the C-terminal domain in both proteins. A number of highly mobile segments the protein globule presumably involved in protein-protein interactions were identified. Regions of the polypeptide chain with significant difference in conformational dynamics between the deep- and shallow-water proteins were identified. Conclusions The results of our analysis demonstrated that in the examined ranges of temperatures and pressures, increase in temperature has a stronger effect on change in the dynamic properties of the protein globule than the increase in pressure. The conformational changes of both the deep- and shallow-sea protein models under increasing temperature and pressure are non-uniform. Our current results indicate that amino acid substitutions between shallow- and deep-water proteins only slightly affect overall stability of two proteins. Rather, they may affect the interactions of the Nip7 protein with its protein or RNA partners.
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Affiliation(s)
- Kirill E Medvedev
- Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia.
| | - Nikolay A Alemasov
- Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia.
| | - Yuri N Vorobjev
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Prospekt Lavrentyeva 8, Novosibirsk, 630090, Russia.
| | - Elena V Boldyreva
- Novosibirsk State University, Pirogova str. 2, Novosibirsk, 630090, Russia. .,Institute of Solid Chemistry and Mechanochemistry, SB RAS, Novosibirsk, 630090, Russia.
| | - Nikolay A Kolchanov
- Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Pirogova str. 2, Novosibirsk, 630090, Russia. .,NRC Kurchatov Institute, 1, Akademika Kurchatova pl., Moscow, 123182, Russia.
| | - Dmitry A Afonnikov
- Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Pirogova str. 2, Novosibirsk, 630090, Russia.
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12
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Suresh G, Priyakumar UD. DNA–RNA hybrid duplexes with decreasing pyrimidine content in the DNA strand provide structural snapshots for the A- to B-form conformational transition of nucleic acids. Phys Chem Chem Phys 2014; 16:18148-55. [DOI: 10.1039/c4cp02478h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A gradual increase in the deoxypyrimidine content in DNA–RNA hybrids leads to B- to A-form nucleic acid transition. Possible factors that govern nuclease activity on hybrid duplexes are presented.
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Affiliation(s)
- Gorle Suresh
- Centre for Computational Natural Sciences and Bioinformatics
- International Institute of Information Technology
- Hyderabad 500 032, India
| | - U. Deva Priyakumar
- Centre for Computational Natural Sciences and Bioinformatics
- International Institute of Information Technology
- Hyderabad 500 032, India
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13
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Terpe K. Overview of thermostable DNA polymerases for classical PCR applications: from molecular and biochemical fundamentals to commercial systems. Appl Microbiol Biotechnol 2013; 97:10243-54. [DOI: 10.1007/s00253-013-5290-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/20/2013] [Accepted: 09/22/2013] [Indexed: 11/29/2022]
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14
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Chu WT, Zheng QC. Conformational changes of enzymes and DNA in molecular dynamics: influenced by pH, temperature, and ligand. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 92:179-217. [PMID: 23954102 DOI: 10.1016/b978-0-12-411636-8.00005-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Protein conformation, which has been a research hotspot for human diseases, is an important factor of protein properties. Recently, a series of approaches have been utilized to investigate the conformational changes under different conditions. Some of them have gained promising achievements, but it is still deficient in the detail researches at the atomic level. In this chapter, a series of computational examples of protein conformational changes under different pH environment, temperature, and ligand binding are described. We further show some useful methods, such as constant pH molecular dynamics simulations, molecular docking, and molecular mechanics Poisson-Boltzmann surface area/generalized Born surface area calculations. In comparison with the experimental results, the methods mentioned above are reasonable to detect and predict the interaction between residue and residue, residue and DNA, and residue and ligand. Additionally, some crucial interactions that cause protein conformational changes are discovered and discussed in this chapter. In summary, our work can give penetrating information to understand the pH-, temperature-, and ligand-induced conformational change mechanisms.
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Affiliation(s)
- Wen-Ting Chu
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, PR China
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15
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Chen L, Zhang JL, Yu LY, Zheng QC, Chu WT, Xue Q, Zhang HX, Sun CC. Influence of hyperthermophilic protein Cren7 on the stability and conformation of DNA: insights from molecular dynamics simulation and free energy analysis. J Phys Chem B 2012; 116:12415-25. [PMID: 23013198 DOI: 10.1021/jp305860h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cren7, a novel chromatin protein highly conserved among crenarchaea, plays an important role in genome packaging and gene regulation. However, the detail dynamical structural characteristic of the Cren7-DNA complex and the detail study of the DNA in the complex have not been done. Focused on two specific Cren7-DNA complexes (PDB codes 3LWH and 3LWI ), we applied molecular dynamics (MD) simulations at four different temperatures (300, 350, 400, and 450 K) and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation at 300 and 350 K to examine the role of Cren7 protein in enhancing the stability of DNA duplexes via protein-DNA interactions, and to study the structural transition in DNA. The simulation results indicate that Cren7 stabilizes DNA duplex in a certain temperature range in the binary complex compared with the unbound DNA molecules. At the same time, DNA molecules were found to undergo B-like to A-like form transitions with increased temperature. The results of statistical analyses of the H-bond and hydrophobic contacts show that some residues have significant influence on the structure of DNA molecules. Our work can give important information to understand the interactions of proteins with nucleic acids and other ligands.
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Affiliation(s)
- Lin Chen
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People's Republic of China
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16
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Chen L, Zheng QC, Yu LY, Chu WT, Zhang JL, Xue Q, Zhang HX, Sun CC. Insights into the thermal stabilization and conformational transitions of DNA by hyperthermophile protein Sso7d: molecular dynamics simulations and MM-PBSA analysis. J Biomol Struct Dyn 2012; 30:716-27. [PMID: 22731116 DOI: 10.1080/07391102.2012.689702] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the assembly of DNA-protein complex, the DNA kinking plays an important role in nucleoprotein structures and gene regulation. Molecular dynamics (MD) simulations were performed on specific protein-DNA complexes in this study to investigate the stability and structural transitions of DNA depending on temperature. Furthermore, we introduced the molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) approach to analyze the interactions between DNA and protein in hyperthermophile. Focused on two specific Sso7d-DNA complexes (PDB codes: 1BNZ and 1BF4), we performed MD simulations at four temperatures (300, 360, 420, and 480 K) and MM-PBSA at 300 and 360 K to illustrate detailed information on the changes of DNA. Our results show that Sso7d stabilizes DNA duplex over a certain temperature range and DNA molecules undergo B-like to A-like form transitions in the binary complex with the temperature increasing, which are consistent with the experimental data. Our work will contribute to a better understanding of protein-DNA interaction.
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Affiliation(s)
- Lin Chen
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, P.R. China
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17
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Priyakumar UD. Role of Hydrophobic Core on the Thermal Stability of Proteins—Molecular Dynamics Simulations on a Single Point Mutant of Sso7d. J Biomol Struct Dyn 2012; 29:961-71. [DOI: 10.1080/07391102.2012.10507415] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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18
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Xu X, Su J, Chen W, Wang C. Thermal stability and unfolding pathways of Sso7d and its mutant F31A: insight from molecular dynamics simulation. J Biomol Struct Dyn 2011; 28:717-27. [PMID: 21294584 DOI: 10.1080/07391102.2011.10508601] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The thermo-stability and unfolding behaviors of a small hyperthermophilic protein Sso7d as well as its single-point mutation F31A are studied by molecular dynamics simulation at temperatures of 300 K, 371 K and 500 K. Simulations at 300 K show that the F31A mutant displays a much larger flexibility than the wild type, which implies that the mutation obviously decreases the protein's stability. In the simulations at 371 K, although larger fluctuations were observed, both of these two maintain their stable conformations. High temperature simulations at 500 K suggest that the unfolding of these two proteins evolves along different pathways. For the wild-type protein, the C-terminal alpha-helix is melted at the early unfolding stage, whereas it is destroyed much later in the unfolding process of the F31A mutant. The results also show that the mutant unfolds much faster than its parent protein. The deeply buried aromatic cluster in the F31A mutant dissociates quickly relative to the wild-type protein at high temperature. Besides, it is found that the triple-stranded antiparallel β-sheet in the wild-type protein plays an important role in maintaining the stability of the entire structure.
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Affiliation(s)
- Xianjin Xu
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
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19
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Bleicher L, Prates ET, Gomes TCF, Silveira RL, Nascimento AS, Rojas AL, Golubev A, Martínez L, Skaf MS, Polikarpov I. Molecular Basis of the Thermostability and Thermophilicity of Laminarinases: X-ray Structure of the Hyperthermostable Laminarinase from Rhodothermus marinus and Molecular Dynamics Simulations. J Phys Chem B 2011; 115:7940-9. [DOI: 10.1021/jp200330z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lucas Bleicher
- Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador São-Carlense, 400, CEP 13560-970 São Carlos, SP, Brazil
| | - Erica T. Prates
- Institute of Chemistry, State University of Campinas − UNICAMP, Cx.P. 6154, Campinas, SP 13084-862, Brazil
| | - Thiago C. F. Gomes
- Institute of Chemistry, State University of Campinas − UNICAMP, Cx.P. 6154, Campinas, SP 13084-862, Brazil
| | - Rodrigo L. Silveira
- Institute of Chemistry, State University of Campinas − UNICAMP, Cx.P. 6154, Campinas, SP 13084-862, Brazil
| | - Alessandro S. Nascimento
- Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador São-Carlense, 400, CEP 13560-970 São Carlos, SP, Brazil
| | - Adriana L. Rojas
- Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador São-Carlense, 400, CEP 13560-970 São Carlos, SP, Brazil
- Structural Biology Unit, Center for Cooperative Research in Biosciences bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Alexander Golubev
- Petersburg Nuclear Physics Institute, Gatchina, St. Petersburg, 188300, Russia
| | - Leandro Martínez
- Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador São-Carlense, 400, CEP 13560-970 São Carlos, SP, Brazil
| | - Munir S. Skaf
- Institute of Chemistry, State University of Campinas − UNICAMP, Cx.P. 6154, Campinas, SP 13084-862, Brazil
| | - Igor Polikarpov
- Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador São-Carlense, 400, CEP 13560-970 São Carlos, SP, Brazil
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Martinez R, Schwaneberg U, Roccatano D. Temperature effects on structure and dynamics of the psychrophilic protease subtilisin S41 and its thermostable mutants in solution. Protein Eng Des Sel 2011; 24:533-44. [DOI: 10.1093/protein/gzr014] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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21
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Priyakumar UD, Harika G, Suresh G. Molecular simulations on the thermal stabilization of DNA by hyperthermophilic chromatin protein Sac7d, and associated conformational transitions. J Phys Chem B 2010; 114:16548-57. [PMID: 21086967 DOI: 10.1021/jp101583d] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Sac7d belongs to a family of chromosomal proteins, which are crucial for thermal stabilization of DNA at higher growth temperatures. It is capable of binding DNA nonspecifically, and is responsible for the increase in the melting temperature of DNA in the bound form up to 85 °C. Molecular dynamics (MD) simulations were performed at different temperatures on two protein-DNA complexes of Sac7d. Various structural and energetic parameters were calculated to examine the DNA stability and to investigate the conformational changes in DNA and the protein-DNA interactions. Room temperature simulations indicated very good agreement with the experimental structures. The protein structure is nearly unchanged at both 300 and 360 K, and only up to five base pairs of the DNA are stabilized by Sac7d at 360 K. However, the MD simulations on DNA alone systems show that they lose their helical structures at 360 K further supporting the role of Sac7d in stabilizing the oligomers. At higher temperatures (420 and 480 K), DNA undergoes denaturation in the presence and the absence of the protein. The DNA molecules were found to undergo B- to A-form transitions consistent with experimental studies, and the extent of these transitions are examined in detail. The extent of sampling B- and A-form regions was found to show temperature and sequence dependence. Multiple MD simulations yielded similar results validating the proposed model. Interaction energy calculations corresponding to protein-DNA binding indicates major contribution due to DNA backbone, explaining the nonspecific interactions of Sac7d.
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Affiliation(s)
- U Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India.
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