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Xie L, Cheng H, Fang D, Chen ZN, Yang M. Enhanced QM/MM sampling for free energy calculation of chemical reactions: A case study of double proton transfer. J Chem Phys 2019; 150:044111. [PMID: 30709281 DOI: 10.1063/1.5072779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Free energy calculations for chemical reactions with a steep energy barrier require well defined reaction coordinates (RCs). However, when multiple parallel channels exist along selected RC, the application of conventional enhanced samplings is difficult to generate correct sampling within limited simulation time and thus cannot give correct prediction about the favorable pathways, the relative stability of multiple products or intermediates. Here, we implement the selective integrated tempering sampling (SITS) method with quantum mechanical and molecular mechanical (QM/MM) potential to investigate the chemical reactions in solution. The combined SITS-QM/MM scheme is used to identify possible reaction paths, intermediate and product states, and the free energy profiles for the different reaction paths. Two double proton transfer reactions were studied to validate the implemented method and simulation protocol, from which the independent and correlated proton transfer processes are identified in two representative systems, respectively. This protocol can be generalized to various kinds of chemical reactions for both academic studies and industry applications, such as in exploration and optimization of potential reactions in DNA encoded compound library and halogen or deuterium substitution of the hit discovery and lead optimization stages of drug design via providing a better understanding of the reaction mechanism along the designed chemical reaction pathways.
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Affiliation(s)
- Liangxu Xie
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 21300, China
| | - Huimin Cheng
- XtalPi Inc. (Shenzhen Jingtai Technology Co., Ltd.), Times Science & Tech Mansion E. 20F, 7028 Shennan Ave, Futian District, Shenzhen, China
| | - Dong Fang
- XtalPi Inc. (Shenzhen Jingtai Technology Co., Ltd.), Times Science & Tech Mansion E. 20F, 7028 Shennan Ave, Futian District, Shenzhen, China
| | - Zhe-Ning Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yangqiao Road West, Fuzhou 350002, China
| | - Mingjun Yang
- XtalPi Inc. (Shenzhen Jingtai Technology Co., Ltd.), Times Science & Tech Mansion E. 20F, 7028 Shennan Ave, Futian District, Shenzhen, China
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Abstract
The folding simulations of three ββα-motifs and β-barrel structured proteins (NTL9, NuG2b, and CspA) were performed to determine the important roles of native and nonnative contacts in protein folding.
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Affiliation(s)
- Qiang Shao
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
| | - Weiliang Zhu
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
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3
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Shao Q, Zhu W. Assessing AMBER force fields for protein folding in an implicit solvent. Phys Chem Chem Phys 2018; 20:7206-7216. [PMID: 29480910 DOI: 10.1039/c7cp08010g] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Molecular dynamics (MD) simulation implemented with a state-of-the-art protein force field and implicit solvent model is an attractive approach to investigate protein folding, one of the most perplexing problems in molecular biology. But how well can force fields developed independently of implicit solvent models work together in reproducing diverse protein native structures and measuring the corresponding folding thermodynamics is not always clear. In this work, we performed enhanced sampling MD simulations to assess the ability of six AMBER force fields (FF99SBildn, FF99SBnmr, FF12SB, FF14ipq, FF14SB, and FF14SBonlysc) as coupled with a recently improved pair-wise GB-Neck2 model in modeling the folding of two helical and two β-sheet peptides. Whilst most of the tested force fields can yield roughly similar features for equilibrium conformational ensembles and detailed folding free-energy profiles for short α-helical TC10b in an implicit solvent, the measured counterparts are significantly discrepant in the cases of larger or β-structured peptides (HP35, 1E0Q, and GTT). Additionally, the calculated folding/unfolding thermodynamic quantities can only partially match the experimental data. Although a combination of the force fields and GB-Neck2 implicit model able to describe all aspects of the folding transitions towards the native structures of all the considered peptides was not identified, we found that FF14SBonlysc coupled with the GB-Neck2 model seems to be a reasonably balanced combination to predict peptide folding preferences.
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Affiliation(s)
- Qiang Shao
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
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Shao Q, Zhu W. The effects of implicit modeling of nonpolar solvation on protein folding simulations. Phys Chem Chem Phys 2018; 20:18410-18419. [PMID: 29946610 DOI: 10.1039/c8cp03156h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Implicit solvent models, in which the polar and nonpolar solvation free-energies of solute molecules are treated separately, have been widely adopted for molecular dynamics simulation of protein folding. While the development of the implicit models is mainly focused on the methodological improvement and key parameter optimization for polar solvation, nonpolar solvation has been either ignored or described by a simplistic surface area (SA) model. In this work, we performed the folding simulations of multiple β-hairpin and α-helical proteins with varied surface tension coefficients embedded in the SA model to clearly demonstrate the effects of nonpolar solvation treated by a popular SA model on protein folding. The results indicate that the change in the surface tension coefficient does not alter the ability of implicit solvent simulations to reproduce a protein native structure but indeed controls the components of the equilibrium conformational ensemble and modifies the energetic characterization of the folding transition pathway. The suitably set surface tension coefficient can yield explicit solvent simulations and/or experimentally suggested folding mechanism of protein. In addition, the implicit treatment of both polar and nonpolar components of solvation free-energy contributes to the overestimation of the secondary structure in implicit solvent simulations.
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Affiliation(s)
- Qiang Shao
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
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Shao Q, Zhu W. How Well Can Implicit Solvent Simulations Explore Folding Pathways? A Quantitative Analysis of α-Helix Bundle Proteins. J Chem Theory Comput 2017; 13:6177-6190. [DOI: 10.1021/acs.jctc.7b00726] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Qiang Shao
- Drug
Discovery and Design Center, CAS Key Laboratory of Receptor Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of
Chinese Academy of Sciences, Beijing 100049, China
| | - Weiliang Zhu
- Drug
Discovery and Design Center, CAS Key Laboratory of Receptor Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of
Chinese Academy of Sciences, Beijing 100049, China
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6
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Shao Q, Shi J, Zhu W. Determining Protein Folding Pathway and Associated Energetics through Partitioned Integrated-Tempering-Sampling Simulation. J Chem Theory Comput 2017; 13:1229-1243. [DOI: 10.1021/acs.jctc.6b00967] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Qiang Shao
- Drug
Discovery and Design Center, CAS Key Laboratory of Receptor Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jiye Shi
- UCB Biopharma
SPRL, Chemin du Foriest, 1420 Braine-l’Alleud, Belgium
| | - Weiliang Zhu
- Drug
Discovery and Design Center, CAS Key Laboratory of Receptor Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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7
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Xie L, Shen L, Chen ZN, Yang M. Efficient free energy calculations by combining two complementary tempering sampling methods. J Chem Phys 2017; 146:024103. [PMID: 28088161 DOI: 10.1063/1.4973607] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Liangxu Xie
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Lin Shen
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zhe-Ning Chen
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Yangqiao West Road 155, Fuzhou, Fujian 350002, China
| | - Mingjun Yang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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Yang M, Yang L, Gao Y, Hu H. Combine umbrella sampling with integrated tempering method for efficient and accurate calculation of free energy changes of complex energy surface. J Chem Phys 2015; 141:044108. [PMID: 25084882 DOI: 10.1063/1.4887340] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Umbrella sampling is an efficient method for the calculation of free energy changes of a system along well-defined reaction coordinates. However, when there exist multiple parallel channels along the reaction coordinate or hidden barriers in directions perpendicular to the reaction coordinate, it is difficult for conventional umbrella sampling to reach convergent sampling within limited simulation time. Here, we propose an approach to combine umbrella sampling with the integrated tempering sampling method. The umbrella sampling method is applied to chemically more relevant degrees of freedom that possess significant barriers. The integrated tempering sampling method is used to facilitate the sampling of other degrees of freedom which may possess statistically non-negligible barriers. The combined method is applied to two model systems, butane and ACE-NME molecules, and shows significantly improved sampling efficiencies as compared to standalone conventional umbrella sampling or integrated tempering sampling approaches. Further analyses suggest that the enhanced performance of the new method come from the complemented advantages of umbrella sampling with a well-defined reaction coordinate and integrated tempering sampling in orthogonal space. Therefore, the combined approach could be useful in the simulation of biomolecular processes, which often involves sampling of complex rugged energy landscapes.
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Affiliation(s)
- Mingjun Yang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Lijiang Yang
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yiqin Gao
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Hao Hu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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Shao Q. Important roles of hydrophobic interactions in folding and charge interactions in misfolding of α-helix bundle protein. RSC Adv 2015. [DOI: 10.1039/c4ra14265a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
An enhanced-sampling molecular dynamics simulation is presented to quantitatively demonstrate the important roles of hydrophobic and charge interactions in the folding and misfolding of α-helix bundle protein, respectively.
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Affiliation(s)
- Qiang Shao
- Drug Discovery and Design Center
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
- China
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Shao Q. Probing Sequence Dependence of Folding Pathway of α-Helix Bundle Proteins through Free Energy Landscape Analysis. J Phys Chem B 2014; 118:5891-900. [DOI: 10.1021/jp5043393] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Qiang Shao
- Drug Discovery and Design
Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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Hansen N, Allison JR, Hodel FH, van Gunsteren WF. Relative free enthalpies for point mutations in two proteins with highly similar sequences but different folds. Biochemistry 2013; 52:4962-70. [PMID: 23802564 DOI: 10.1021/bi400272q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enveloping distribution sampling was used to calculate free-enthalpy changes associated with single amino acid mutations for a pair of proteins, GA95 and GB95, that show 95% sequence identity yet fold into topologically different structures. Of the L → A, I → F, and L → Y mutations at positions 20, 30, and 45, respectively, of the 56-residue sequence, the first and the last contribute the most to the free-enthalpy difference between the native and non-native sequence-structure combinations, in agreement with the experimental findings for this protein pair. The individual free-enthalpy changes are almost sequence-independent in the four-strand/one-helix structure, the stable form of GB95, while in the three-helix bundle structure, the stable form of GA95, an interplay between residues 20 and 45 is observed.
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Affiliation(s)
- Niels Hansen
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology , ETH, CH-8093 Zürich, Switzerland
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