AMBER-based hybrid force field for conformational sampling of polypeptides

Kamiya, Narutoshi; Watanabe, Yukihisa S.; Ono, Satoshi; Higo, Junichi

doi:10.1016/j.cplett.2004.11.070

Cited by 73 publications

(78 citation statements)

References 23 publications

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“…24 The parameters included the harmonic force field and nuclear derivatives of electric dipole-electric dipole (a), electric dipole-magnetic dipole (G 0 ), and electric dipole-electric quadrupole (A) polarizability derivatives. 25 For the MD simulations the periodic boundary conditions were used by default, with the Amber99 force field, 26 1 fs integration time step and an NpT ensemble (pressure p 5 1 atm, temperature T 5 298 K). The solute MD structures were compared atom-by-atom with these precalculated geometries so that the best local overlap could be found and the spectra generated from the transferred parameters.…”

Section: Methodsmentioning

confidence: 99%

Molecular dynamics with restrictions derived from optical spectra

2008

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The information about molecular structure coded in the optical spectra must often be deciphered by complicated computational procedures. A combination of spectral modeling with the molecular dynamic simulations makes the process simpler, by implicit accounting for the inhomogeneous band broadening and Boltzmann averaging of many conformations. Ideally, geometries of studied systems can be deduced by a direct confrontation of such modeling with the experiment. In this work, the comparison is enhanced by restrictions to molecular dynamics propagations based on the Raman and Raman optical activity spectra. The methodology is introduced and tested on model systems comprising idealized H 2 O 2 , H 2 O 3 molecules, and the alanine zwitterion. An additional gradient term based on the spectral overlap smoothed by Fourier transformation is constructed and added to the molecular energy during the molecular dynamics run. For systems with one prevalent conformation the method did allow to enrich the Boltzmann ensemble by a spectroscopically favored structure. For systems with multiconformational equilibria families preferential conformations can be selected. An alternative algorithm based on the comparison of the averaged spectra with the reference enabling iterative updates of the conformer probabilities provided even more distinct distributions in shorter times. It also accounts for multiconformer equilibria and provided realistic spectra and conformer distribution for the alanine.

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Section: Methodsmentioning

confidence: 99%

Molecular dynamics with restrictions derived from optical spectra

2008

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“…Results show that a w value of 0.75 is optimal. 51 Furthermore, McMD simulations with E(0.75) revealed that a peptide with a helical propensity folds into an α-helix, whereas a peptide with a β-hairpin propensity forms a β-hairpin. 51 Therefore, we used E(0.75) for the current study.…”

Section: A Setting the Systemmentioning

confidence: 99%

“…51 Furthermore, McMD simulations with E(0.75) revealed that a peptide with a helical propensity folds into an α-helix, whereas a peptide with a β-hairpin propensity forms a β-hairpin. 51 Therefore, we used E(0.75) for the current study. We have successfully applied this force field to protein folding 22,23,25 and coupled folding and binding.…”

Section: A Setting the Systemmentioning

confidence: 99%

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A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein–protein interaction with an all-atom model in explicit solvent

Higo

Umezawa²,

Nakamura³

2013

The Journal of Chemical Physics

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We propose a novel generalized ensemble method, a virtual-system coupled multicanonical molecular dynamics (V-McMD), to enhance conformational sampling of biomolecules expressed by an all-atom model in an explicit solvent. In this method, a virtual system, of which physical quantities can be set arbitrarily, is coupled with the biomolecular system, which is the target to be studied. This method was applied to a system of an Endothelin-1 derivative, KR-CSH-ET1, known to form an antisymmetric homodimer at room temperature. V-McMD was performed starting from a configuration in which two KR-CSH-ET1 molecules were mutually distant in an explicit solvent. The lowest freeenergy state (the most thermally stable state) at room temperature coincides with the experimentally determined native complex structure. This state was separated to other non-native minor clusters by a free-energy barrier, although the barrier disappeared with elevated temperature.

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“…The former results from the difficulty in determining physical parameters to calculate the potential energy. For example, the torsion energy for the protein backbone affects the secondary structure contents of the snapshots (Ikebe et al 2007;Kamiya et al 2005). Tuning of the torsionenergy parameters is still an extremely active research topic in this field (Maier et al 2015;Sakae and Okamoto 2014).…”

Section: Introductionmentioning

confidence: 99%

Enhanced sampling simulations to construct free-energy landscape of protein–partner substrate interaction

2016

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Molecular dynamics (MD) simulations using allatom and explicit solvent models provide valuable information on the detailed behavior of protein-partner substrate binding at the atomic level. As the power of computational resources increase, MD simulations are being used more widely and easily. However, it is still difficult to investigate the thermodynamic properties of protein-partner substrate binding and protein folding with conventional MD simulations. Enhanced sampling methods have been developed to sample conformations that reflect equilibrium conditions in a more efficient manner than conventional MD simulations, thereby allowing the construction of accurate free-energy landscapes. In this review, we discuss these enhanced sampling methods using a series of case-by-case examples. In particular, we review enhanced sampling methods conforming to trivial trajectory parallelization, virtual-system coupled multicanonical MD, and adaptive lambda square dynamics. These methods have been recently developed based on the existing method of multicanonical MD simulation. Their applications are reviewed with an emphasis on describing their practical implementation. In our concluding remarks we explore extensions of the enhanced sampling methods that may allow for even more efficient sampling.

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AMBER-based hybrid force field for conformational sampling of polypeptides

Cited by 73 publications

References 23 publications

Molecular dynamics with restrictions derived from optical spectra

Molecular dynamics with restrictions derived from optical spectra

A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein–protein interaction with an all-atom model in explicit solvent

Enhanced sampling simulations to construct free-energy landscape of protein–partner substrate interaction

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