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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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Correct folding of an α-helix and a β-hairpin using a polarized 2D torsional potential. Sci Rep 2015; 5:10359. [PMID: 26039188 PMCID: PMC5380191 DOI: 10.1038/srep10359] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 04/09/2015] [Indexed: 01/12/2023] Open
Abstract
A new modification to the AMBER force field that incorporates the coupled two-dimensional main chain torsion energy has been evaluated for the balanced representation of secondary structures. In this modified AMBER force field (AMBER03(2D)), the main chain torsion energy is represented by 2-dimensional Fourier expansions with parameters fitted to the potential energy surface generated by high-level quantum mechanical calculations of small peptides in solution. Molecular dynamics simulations are performed to study the folding of two model peptides adopting either α-helix or β-hairpin structures. Both peptides are successfully folded into their native structures using an AMBER03(2D) force field with the implementation of a polarization scheme (AMBER03(2D)p). For comparison, simulations using a standard AMBER03 force field with and without polarization, as well as AMBER03(2D) without polarization, fail to fold both peptides successfully. The correction to secondary structure propensity in the AMBER03 force field and the polarization effect are critical to folding Trpzip2; without these factors, a helical structure is obtained. This study strongly suggests that this new force field is capable of providing a more balanced preference for helical and extended conformations. The electrostatic polarization effect is shown to be indispensable to the growth of secondary structures.
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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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Peter EK, Agarwal M, Kim B, Pivkin IV, Shea JE. How water layers on graphene affect folding and adsorption of TrpZip2. J Chem Phys 2014; 141:22D511. [DOI: 10.1063/1.4896984] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Emanuel K. Peter
- Insitute of Computational Science, Faculty of Informatics, University of Lugano, Switzerland
- Department of Chemistry and Biochemistry and Department of Physics, University of California Santa Barbara, California 93106, USA
| | - Mrigya Agarwal
- Insitute of Computational Science, Faculty of Informatics, University of Lugano, Switzerland
| | - BongKeun Kim
- Department of Chemistry and Biochemistry and Department of Physics, University of California Santa Barbara, California 93106, USA
| | - Igor V. Pivkin
- Insitute of Computational Science, Faculty of Informatics, University of 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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Gu S, Silva DA, Meng L, Yue A, Huang X. Quantitatively characterizing the ligand binding mechanisms of choline binding protein using Markov state model analysis. PLoS Comput Biol 2014; 10:e1003767. [PMID: 25101697 PMCID: PMC4125059 DOI: 10.1371/journal.pcbi.1003767] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 06/22/2014] [Indexed: 01/05/2023] Open
Abstract
Protein-ligand recognition plays key roles in many biological processes. One of the most fascinating questions about protein-ligand recognition is to understand its underlying mechanism, which often results from a combination of induced fit and conformational selection. In this study, we have developed a three-pronged approach of Markov State Models, Molecular Dynamics simulations, and flux analysis to determine the contribution of each model. Using this approach, we have quantified the recognition mechanism of the choline binding protein (ChoX) to be ∼90% conformational selection dominant under experimental conditions. This is achieved by recovering all the necessary parameters for the flux analysis in combination with available experimental data. Our results also suggest that ChoX has several metastable conformational states, of which an apo-closed state is dominant, consistent with previous experimental findings. Our methodology holds great potential to be widely applied to understand recognition mechanisms underlining many fundamental biological processes.
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Affiliation(s)
- Shuo Gu
- Department of Chemistry, Institute for Advance Study and School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Daniel-Adriano Silva
- Department of Chemistry, Institute for Advance Study and School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Luming Meng
- Department of Chemistry, Institute for Advance Study and School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Alexander Yue
- Department of Chemistry, Institute for Advance Study and School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xuhui Huang
- Department of Chemistry, Institute for Advance Study and School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Division of Biomedical Engineering, Institute for Advance Study and School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Center of Systems Biology and Human Health, Institute for Advance Study and School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- * E-mail:
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Chodera JD, Noé F. Markov state models of biomolecular conformational dynamics. Curr Opin Struct Biol 2014; 25:135-44. [PMID: 24836551 DOI: 10.1016/j.sbi.2014.04.002] [Citation(s) in RCA: 493] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 04/08/2014] [Accepted: 04/12/2014] [Indexed: 10/25/2022]
Abstract
It has recently become practical to construct Markov state models (MSMs) that reproduce the long-time statistical conformational dynamics of biomolecules using data from molecular dynamics simulations. MSMs can predict both stationary and kinetic quantities on long timescales (e.g. milliseconds) using a set of atomistic molecular dynamics simulations that are individually much shorter, thus addressing the well-known sampling problem in molecular dynamics simulation. In addition to providing predictive quantitative models, MSMs greatly facilitate both the extraction of insight into biomolecular mechanism (such as folding and functional dynamics) and quantitative comparison with single-molecule and ensemble kinetics experiments. A variety of methodological advances and software packages now bring the construction of these models closer to routine practice. Here, we review recent progress in this field, considering theoretical and methodological advances, new software tools, and recent applications of these approaches in several domains of biochemistry and biophysics, commenting on remaining challenges.
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Affiliation(s)
- John D Chodera
- Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany.
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Wu T, Zhang R, Li H, Yang L, Zhuang W. Discriminating trpzip2 and trpzip4 peptides' folding landscape using the two-dimensional infrared spectroscopy: a simulation study. J Chem Phys 2014; 140:055101. [PMID: 24511982 DOI: 10.1063/1.4863562] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We analyzed, based on the theoretical spectroscopic modeling, how the differences in the folding landscapes of two β-hairpin peptides trpzip2 and trpzip4 are reflected in their thermal unfolding infrared measurements. The isotope-edited equilibrium FTIR and two dimensional infrared spectra of the two peptides were calculated, using the nonlinear exciton propagation method, at a series of temperatures. The spectra calculations were based on the configuration distributions generated using the GB(OBC) implicit solvent MD simulation and the integrated tempering sampling technique. Conformational analysis revealed the different local thermal stabilities for these two peptides, which suggested the different folding landscapes. Our study further suggested that the ellipticities of the isotope peaks in the coherent IR signals are more sensitive to these local stability differences compared with other spectral features such as the peak intensities. Our technique can thus be combined with the relevant experimental measurements to achieve a better understanding of the peptide folding behaviors.
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Affiliation(s)
- Tianmin Wu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, People's Republic of China
| | - Ruiting Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, People's Republic of China
| | - Huanhuan Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, People's Republic of China
| | - Lijiang Yang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Wei Zhuang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, People's Republic of China
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Wu T, Yang L, Zhang R, Shao Q, Zhuang W. Modeling the thermal unfolding 2DIR spectra of a β-hairpin peptide based on the implicit solvent MD simulation. J Phys Chem A 2013; 117:6256-63. [PMID: 23496267 DOI: 10.1021/jp400625a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We simulated the equilibrium isotope-edited FTIR and 2DIR spectra of a β-hairpin peptide trpzip2 at a series of temperatures. The simulation was based on the configuration distributions generated using the GB(OBC) implicit solvent model and the integrated tempering sampling (ITS) technique. A soaking procedure was adapted to generate the peptide in explicit solvent configurations for the spectroscopy calculations. The nonlinear exciton propagation (NEP) method was then used to calculate the spectra. Agreeing with the experiments, the intensities and ellipticities of the isotope-shifted peaks in our simulated signals have the site-specific temperature dependences, which suggest the inhomogeneous local thermal stabilities along the peptide chain. Our simulation thus proposes a cost-effective means to understand a peptide's conformational change and related IR spectra across its thermal unfolding transition.
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Affiliation(s)
- Tianmin Wu
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
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