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Peter EK, Manstein DJ, Shea JE, Schug A. CORE-MD II: A fast, adaptive, and accurate enhanced sampling method. J Chem Phys 2021; 155:104114. [PMID: 34525829 DOI: 10.1063/5.0063664] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this paper, we present a fast and adaptive correlation guided enhanced sampling method (CORE-MD II). The CORE-MD II technique relies, in part, on partitioning of the entire pathway into short trajectories that we refer to as instances. The sampling within each instance is accelerated by adaptive path-dependent metadynamics simulations. The second part of this approach involves kinetic Monte Carlo (kMC) sampling between the different states that have been accessed during each instance. Through the combination of the partition of the total simulation into short non-equilibrium simulations and the kMC sampling, the CORE-MD II method is capable of sampling protein folding without any a priori definitions of reaction pathways and additional parameters. In the validation simulations, we applied the CORE-MD II on the dialanine peptide and the folding of two peptides: TrpCage and TrpZip2. In a comparison with long time equilibrium Molecular Dynamics (MD), 1 µs replica exchange MD (REMD), and CORE-MD I simulations, we find that the level of convergence of the CORE-MD II method is improved by a factor of 8.8, while the CORE-MD II method reaches acceleration factors of ∼120. In the CORE-MD II simulation of TrpZip2, we observe the formation of the native state in contrast to the REMD and the CORE-MD I simulations. The method is broadly applicable for MD simulations and is not restricted to simulations of protein folding or even biomolecules but also applicable to simulations of protein aggregation, protein signaling, or even materials science simulations.
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Affiliation(s)
- Emanuel K Peter
- Institute for Biophysical Chemistry, Fritz-Hartmann-Centre for Medical Research, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover 30625, Germany
| | - Dietmar J Manstein
- Institute for Biophysical Chemistry, Fritz-Hartmann-Centre for Medical Research, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover 30625, Germany
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, Department of Physics, University of California, Santa Barbara, California 93106, USA
| | - Alexander Schug
- John von Neumann Institute for Computing and Jülich Supercomputing Centre, Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany
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Cai K, Zheng X, Du F. Electrostatic frequency maps for amide-I mode of β-peptide: Comparison of molecular mechanics force field and DFT calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 183:150-157. [PMID: 28448953 DOI: 10.1016/j.saa.2017.04.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/09/2017] [Accepted: 04/16/2017] [Indexed: 06/07/2023]
Abstract
The spectroscopy of amide-I vibrations has been widely utilized for the understanding of dynamical structure of polypeptides. For the modeling of amide-I spectra, two frequency maps were built for β-peptide analogue (N-ethylpropionamide, NEPA) in a number of solvents within different schemes (molecular mechanics force field based, GM map; DFT calculation based, GD map), respectively. The electrostatic potentials on the amide unit that originated from solvents and peptide backbone were correlated to the amide-I frequency shift from gas phase to solution phase during map parameterization. GM map is easier to construct with negligible computational cost since the frequency calculations for the samples are purely based on force field, while GD map utilizes sophisticated DFT calculations on the representative solute-solvent clusters and brings insight into the electronic structures of solvated NEPA and its chemical environments. The results show that the maps' predicted amide-I frequencies present solvation environmental sensitivities and exhibit their specific characters with respect to the map protocols, and the obtained vibrational parameters are in satisfactory agreement with experimental amide-I spectra of NEPA in solution phase. Although different theoretical schemes based maps have their advantages and disadvantages, the present maps show their potentials in interpreting the amide-I spectra for β-peptides, respectively.
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Affiliation(s)
- Kaicong Cai
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China.
| | - Xuan Zheng
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
| | - Fenfen Du
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
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3
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Simulation of the T-jump triggered unfolding and thermal unfolding vibrational spectroscopy related to polypeptides conformation fluctuation. Sci China Chem 2017. [DOI: 10.1007/s11426-016-9055-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Gupta M, Khatua P, Chakravarty C, Bandyopadhyay S. The sensitivity of folding free energy landscapes of trpzips to mutations in the hydrophobic core. Phys Chem Chem Phys 2017; 19:22813-22825. [DOI: 10.1039/c7cp03825a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The sensitivity of the stability of folded states and free energy landscapes to the differences in the hydrophobic content of the core residues has been studied for the set of 16-residue trpzips, namely, Trpzip4, Trpzip5 and Trpzip6.
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Affiliation(s)
- Madhulika Gupta
- Department of Chemistry
- Indian Institute of Technology-Delhi
- New Delhi 110016
- India
| | - Prabir Khatua
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur 721302
- India
| | | | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur 721302
- India
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Cai K, Du F, Zheng X, Liu J, Zheng R, Zhao J, Wang J. General Applicable Frequency Map for the Amide-I Mode in β-Peptides. J Phys Chem B 2016; 120:1069-79. [PMID: 26824578 DOI: 10.1021/acs.jpcb.5b11643] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In this work, a general applicable amide-I vibrational frequency map (GA map) for β-peptides in a number of common solvents was constructed, based on a peptide derivative, N-ethylpropionamide (NEPA). The map utilizes force fields at the ab initio computational level to accurately describe molecular structure and solute-solvent interactions, and also force fields at the molecular mechanics level to take into account long-range solute-solvent interactions. The results indicate that the GA map works reasonably for mapping the vibrational frequencies of the amide-I local-modes for β-peptides, holding promises for understanding the complicated infrared spectra of the amide-I mode in β-polypeptides.
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Affiliation(s)
- Kaicong Cai
- College of Chemistry and Chemical Engineering, Fujian Normal University , Fuzhou, Fujian 350007, P. R. China.,Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry , Xiamen, Fujian 361005, P. R. China
| | - Fenfen Du
- College of Chemistry and Chemical Engineering, Fujian Normal University , Fuzhou, Fujian 350007, P. R. China.,Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry , Xiamen, Fujian 361005, P. R. China
| | - Xuan Zheng
- College of Chemistry and Chemical Engineering, Fujian Normal University , Fuzhou, Fujian 350007, P. R. China.,Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry , Xiamen, Fujian 361005, P. R. China
| | - Jia Liu
- College of Chemistry and Chemical Engineering, Fujian Normal University , Fuzhou, Fujian 350007, P. R. China.,Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry , Xiamen, Fujian 361005, P. R. China
| | - Renhui Zheng
- Beijing National Laboratory for Molecular Sciences, Structural Chemistry of Unstable and Stable Species Laboratory, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P. R. China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P. R. China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P. R. China
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Pan Z, Wu T, Jin T, Liu Y, Nagata Y, Zhang R, Zhuang W. Low frequency 2D Raman-THz spectroscopy of ionic solution: A simulation study. J Chem Phys 2015; 142:212419. [DOI: 10.1063/1.4917260] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Zhijun Pan
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Tianmin Wu
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Tan Jin
- State Key Lab of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yong Liu
- State Key Lab of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yuki Nagata
- Department for Molecular Spectroscopy, Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Ruiting Zhang
- State Key Lab of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Wei Zhuang
- State Key Lab of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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Peter EK, Pivkin IV, Shea JE. A kMC-MD method with generalized move-sets for the simulation of folding of α-helical and β-stranded peptides. J Chem Phys 2015; 142:144903. [DOI: 10.1063/1.4915919] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Emanuel K. Peter
- Faculty of Informatics, Institute of Computational Science, University of Lugano, Lugano, Switzerland
| | - Igor V. Pivkin
- Faculty of Informatics, Institute of Computational Science, University of Lugano, Lugano, Switzerland
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, USA
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Cai K, Du F, Liu J, Su T. Solvent induced conformational fluctuation of alanine dipeptide studied by using vibrational probes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 137:701-710. [PMID: 25260065 DOI: 10.1016/j.saa.2014.08.126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/05/2014] [Accepted: 08/24/2014] [Indexed: 06/03/2023]
Abstract
The solvation effect on the three dimensional structure and the vibrational feature of alanine dipeptide (ALAD) was evaluated by applying the implicit solvents from polarizable continuum solvent model (PCM) through ab initio calculations, by using molecular dynamic (MD) simulations with explicit solvents, and by combining these two approaches. The implicit solvent induced potential energy fluctuations of ALAD in CHCl3, DMSO and H2O are revealed by means of ab initio calculations, and a global view of conformational and solvation environmental dependence of amide I frequencies is achieved. The results from MD simulations with explicit solvents show that ALAD trends to form PPII, αL, αR, and C5 in water, PPII and C5 in DMSO, and C5 in CHCl3, ordered by population, and the demonstration of the solvated structure, the solute-solvent interaction and hydrogen bonding is therefore enhanced. Representative ALAD-solvent clusters were sampled from MD trajectories and undergone ab initio calculations. The explicit solvents reveal the hydrogen bonding between ALAD and solvents, and the correlation between amide I frequencies and the CO bond length is built. The implicit solvents applied to the ALAD-solvent clusters further compensate the solvation effect from the bulk, and thus enlarge the degree of structural distortion and the amide I frequency red shift. The combination of explicit solvent in the first hydration shell and implicit solvent in the bulk is helpful for our understanding about the conformational fluctuation of solvated polypeptides through vibrational probes.
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Affiliation(s)
- Kaicong Cai
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China.
| | - Fenfen Du
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China
| | - Jia Liu
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China
| | - Tingting Su
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China
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