Multiple state transition interface sampling of alanine dipeptide in explicit solvent

Du, Wei-Na; Marino, Kristen A.; Bolhuis, Peter G.

doi:doi:10.1063/1.3644344

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Theory and simulation of diffusion-influenced, stochastically gated ligand binding to buried sites

We consider the diffusion-influenced rate coefficient of ligand binding to a site located in a deep pocket on a protein; the binding pocket is flexible and can reorganize in response to ligand entrance. We extend to this flexible protein-ligand system a formalism developed previously [A. M. Berezhkovskii, A, Szabo, and H.-X. Zhou, J. Chem. Phys. 135, 075103 (2011)10.1063/1.3609973] for breaking the ligand-binding problem into an exterior problem and an interior problem. Conformational fluctuatio...

Erratum: “Towards an accurate description of anharmonic infrared spectra in solution within the polarizable continuum model: Reaction field, cavity field and nonequilibrium effects” [J. Chem. Phys. 135, 104505 (2011)]

We have applied the recently developed multiple state transition interface sampling approach to alanine dipeptide in explicit water. We extract the rate constant matrix for configurational changes between each pair of metastable states. The results are comparable with values from previous literature and show that the method is applicable to biomolecular systems.

Article Outline

INTRODUCTION
METHODS
1. Multiple state transition path sampling
  1. Two-state transition path sampling
  2. Multiple state TPS/TIS
  3. Combining stable states
2. Simulation details
  1. System setup and equilibration
  2. Replica exchange molecular dynamics
  3. Path sampling simulation
RESULTS AND DISCUSSION
1. Stable states and interfaces from REMD simulation
2. Flux factor from MD
3. Rate constants from MD
4. Crossing probabilities P _i (λ _mi |λ _1i ) by TIS
5. The crossing probability P _i (λ _0j |λ _mi ) by MSTIS
6. Rate constants
7. Comparison with previous work
CONCLUSION

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KEYWORDS and PACS

Keywords

biochemistry, macromolecules, metastable states, molecular biophysics, molecular configurations, molecular dynamics method, solvation, solvent effects

PACS

87.15.ap

Molecular dynamics simulation
87.15.N-

Properties of solutions of macromolecules
36.20.Ey

Conformation (statistics and dynamics)
82.30.Nr

Association, addition, insertion, cluster formation

ARTICLE DATA

Digital Object Identifier

http://dx.doi.org/10.1063/1.3644344

PUBLICATION DATA

ISSN

0021-9606 (print)

1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef

American Institute of Physics

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