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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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Sang P, Yang Q, Du X, Yang N, Yang LQ, Ji XL, Fu YX, Meng ZH, Liu SQ. Effect of the Solvent Temperatures on Dynamics of Serine Protease Proteinase K. Int J Mol Sci 2016; 17:254. [PMID: 26907253 DOI: 10.3390/ijms17020254] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 01/21/2016] [Accepted: 02/06/2016] [Indexed: 11/16/2022] Open
Abstract
To obtain detailed information about the effect of the solvent temperatures on protein dynamics, multiple long molecular dynamics (MD) simulations of serine protease proteinase K with the solute and solvent coupled to different temperatures (either 300 or 180 K) have been performed. Comparative analyses demonstrate that the internal flexibility and mobility of proteinase K are strongly dependent on the solvent temperatures but weakly on the protein temperatures. The constructed free energy landscapes (FELs) at the high solvent temperatures exhibit a more rugged surface, broader spanning range, and higher minimum free energy level than do those at the low solvent temperatures. Comparison between the dynamic hydrogen bond (HB) numbers reveals that the high solvent temperatures intensify the competitive HB interactions between water molecules and protein surface atoms, and this in turn exacerbates the competitive HB interactions between protein internal atoms, thus enhancing the conformational flexibility and facilitating the collective motions of the protein. A refined FEL model was proposed to explain the role of the solvent mobility in facilitating the cascade amplification of microscopic motions of atoms and atomic groups into the global collective motions of the protein.
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Affiliation(s)
- Peng Sang
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
- Laboratory of Molecular Cardiology, Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, China.
| | - Qiong Yang
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
| | - Xing Du
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
| | - Nan Yang
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
| | - Li-Quan Yang
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
- College of Agriculture and Biological Science, Dali University, Dali 671003, China.
| | - Xing-Lai Ji
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
| | - Yun-Xin Fu
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
- Human Genetics Center, School of Public Health, the University of Texas Health Science Center, Houston, TX 77030, USA.
| | - Zhao-Hui Meng
- Laboratory of Molecular Cardiology, Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, China.
| | - Shu-Qun Liu
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China.
- Laboratory of Molecular Cardiology, Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, China.
- Key Laboratory for Tumor molecular biology of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming 650091, China.
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Selection of effective and highly thermostable Bacillus subtilis lipase A template as an industrial biocatalyst-A modern computational approach. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s11515-015-1379-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Rydzewski J, Jakubowski R, Nowak W. Communication: Entropic measure to prevent energy over-minimization in molecular dynamics simulations. J Chem Phys 2015; 143:171103. [PMID: 26547151 DOI: 10.1063/1.4935370] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This work examines the impact of energy over-minimization on an ensemble of biological molecules subjected to the potential energy minimization procedure in vacuum. In the studied structures, long potential energy minimization stage leads to an increase of the main- and side-chain entropies in proteins. We show that such over-minimization may diverge the protein structures from the near-native attraction basin which possesses a minimum of free energy. We propose a measure based on the Pareto front of total entropy for quality assessment of minimized protein conformation. This measure may help in selection of adequate number of energy minimization steps in protein modelling and, thus, in preservation of the near-native protein conformation.
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Affiliation(s)
- J Rydzewski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun, Poland
| | - R Jakubowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun, Poland
| | - W Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun, Poland
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Li H, Xie Y, Liu C, Liu S. Physicochemical bases for protein folding, dynamics, and protein-ligand binding. SCIENCE CHINA-LIFE SCIENCES 2014; 57:287-302. [PMID: 24554472 DOI: 10.1007/s11427-014-4617-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 09/27/2013] [Indexed: 01/02/2023]
Abstract
Proteins are essential parts of living organisms and participate in virtually every process within cells. As the genomic sequences for increasing number of organisms are completed, research into how proteins can perform such a variety of functions has become much more intensive because the value of the genomic sequences relies on the accuracy of understanding the encoded gene products. Although the static three-dimensional structures of many proteins are known, the functions of proteins are ultimately governed by their dynamic characteristics, including the folding process, conformational fluctuations, molecular motions, and protein-ligand interactions. In this review, the physicochemical principles underlying these dynamic processes are discussed in depth based on the free energy landscape (FEL) theory. Questions of why and how proteins fold into their native conformational states, why proteins are inherently dynamic, and how their dynamic personalities govern protein functions are answered. This paper will contribute to the understanding of structure-function relationship of proteins in the post-genome era of life science research.
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Affiliation(s)
- HuiMin Li
- School of Mathematics and Computer Science, Yunnan University of Nationalities, Kunming, 650500, China
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of Ministry of Education, Yunnan University, Kunming, 650091, China
| | - YueHui Xie
- Teaching and Research Section of Computer, Department of Basic Medical, Kunming Medical University, Kunming, 650031, China
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of Ministry of Education, Yunnan University, Kunming, 650091, China
| | - CiQuan Liu
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of Ministry of Education, Yunnan University, Kunming, 650091, China
- Southwest Biological Diversity Laboratory, Kunming Branch of Chinese Academy of Sciences, Kunming, 650223, China
| | - ShuQun Liu
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of Ministry of Education, Yunnan University, Kunming, 650091, China.
- Southwest Biological Diversity Laboratory, Kunming Branch of Chinese Academy of Sciences, Kunming, 650223, China.
- Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, Kunming, 650091, China.
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Yang LQ, Sang P, Tao Y, Fu YX, Zhang KQ, Xie YH, Liu SQ. Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms. J Biomol Struct Dyn 2013; 32:372-93. [PMID: 23527883 PMCID: PMC3919177 DOI: 10.1080/07391102.2013.770372] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Proteins are dynamic entities in cellular solution with functions governed essentially by their dynamic personalities. We review several dynamics studies on serine protease proteinase K and HIV-1 gp120 envelope glycoprotein to demonstrate the importance of investigating the dynamic behaviors and molecular motions for a complete understanding of their structure–function relationships. Using computer simulations and essential dynamic (ED) analysis approaches, the dynamics data obtained revealed that: (i) proteinase K has highly flexible substrate-binding site, thus supporting the induced-fit or conformational selection mechanism of substrate binding; (ii) Ca2+ removal from proteinase K increases the global conformational flexibility, decreases the local flexibility of substrate-binding region, and does not influence the thermal motion of catalytic triad, thus explaining the experimentally determined decreased thermal stability, reduced substrate affinity, and almost unchanged catalytic activity upon Ca2+ removal; (iii) substrate binding affects the large concerted motions of proteinase K, and the resulting dynamic pocket can be connected to substrate binding, orientation, and product release; (iv) amino acid mutations 375 S/W and 423 I/P of HIV-1 gp120 have distinct effects on molecular motions of gp120, facilitating 375 S/W mutant to assume the CD4-bound conformation, while 423 I/P mutant to prefer for CD4-unliganded state. The mechanisms underlying protein dynamics and protein–ligand binding, including the concept of the free energy landscape (FEL) of the protein–solvent system, how the ruggedness and variability of FEL determine protein's dynamics, and how the three ligand-binding models, the lock-and-key, induced-fit, and conformational selection are rationalized based on the FEL theory are discussed in depth.
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Affiliation(s)
- Li-Quan Yang
- a Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education , Yunnan University , Kunming , 650091 , P.R. China
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Yang LQ, Ji XL, Liu SQ. The free energy landscape of protein folding and dynamics: a global view. J Biomol Struct Dyn 2013; 31:982-92. [PMID: 23297835 DOI: 10.1080/07391102.2012.748536] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Li-Quan Yang
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, PR China
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Mittal A, Jayaram B. The Newest View on Protein Folding: Stoichiometric and Spatial Unity in Structural and Functional Diversity. J Biomol Struct Dyn 2011. [DOI: 10.1080/073911011010524984] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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