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Parametrization of reversible digitally filtered molecular dynamics simulations

Parametrization of reversible digitally filtered molecular dynamics simulations
Parametrization of reversible digitally filtered molecular dynamics simulations
Reversible Digitally Filtered Molecular Dynamics (RDFMD) is a method of amplifying or suppressing motions in a molecular dynamics simulation, through the application of a digital filter to the simulation velocities. RDFMD and its derivatives have been previously used to promote conformational motions in liquid-phase butane, the Syrian hamster prion protein, alanine dipeptide, and the pentapeptide, YPGDV. The RDFMD method has associated with it a number of parameters that require specification to optimize the desired response. In this paper methods for the systematic analysis of these parameters are presented and applied to YPGDV with the specific emphasis of ensuring a gentle and progressive method that produces maximum conformation change from the energy put into the system. The portability of the new parameter set is then shown with an application to the M20 loop of E-coli dihydrofolate reductase. A conformational change is induced from a closed to an open structure similar to that seen in the DHFR-NADP+ complex.
coli dihydrofolate-reductase, escherichia-coli, free-energy, loop, constraints, integration, algorithms, proteins, water
1549-9618
24-35
Wiley, Adrian P.
f35459c6-40b2-4572-acb6-669fca3b13f7
Swain, Martin T.
9fc7fee8-524a-4bcd-9a0e-bc42ea4aa14a
Phillips, Stephen C.
47610c30-a543-4bac-a96a-bc1fce564a59
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Edge, Colin M.
7cb32b1b-4e31-4d58-becc-c65d76dc9370
Wiley, Adrian P.
f35459c6-40b2-4572-acb6-669fca3b13f7
Swain, Martin T.
9fc7fee8-524a-4bcd-9a0e-bc42ea4aa14a
Phillips, Stephen C.
47610c30-a543-4bac-a96a-bc1fce564a59
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Edge, Colin M.
7cb32b1b-4e31-4d58-becc-c65d76dc9370

Wiley, Adrian P., Swain, Martin T., Phillips, Stephen C., Essex, Jonathan W. and Edge, Colin M. (2005) Parametrization of reversible digitally filtered molecular dynamics simulations. Journal of Chemical Theory and Computation, 1 (1), 24-35. (doi:10.1021/ct049970t S1549-9618(04)09970-9).

Record type: Article

Abstract

Reversible Digitally Filtered Molecular Dynamics (RDFMD) is a method of amplifying or suppressing motions in a molecular dynamics simulation, through the application of a digital filter to the simulation velocities. RDFMD and its derivatives have been previously used to promote conformational motions in liquid-phase butane, the Syrian hamster prion protein, alanine dipeptide, and the pentapeptide, YPGDV. The RDFMD method has associated with it a number of parameters that require specification to optimize the desired response. In this paper methods for the systematic analysis of these parameters are presented and applied to YPGDV with the specific emphasis of ensuring a gentle and progressive method that produces maximum conformation change from the energy put into the system. The portability of the new parameter set is then shown with an application to the M20 loop of E-coli dihydrofolate reductase. A conformational change is induced from a closed to an open structure similar to that seen in the DHFR-NADP+ complex.

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More information

e-pub ahead of print date: 17 December 2004
Published date: 2005
Keywords: coli dihydrofolate-reductase, escherichia-coli, free-energy, loop, constraints, integration, algorithms, proteins, water

Identifiers

Local EPrints ID: 20936
URI: http://eprints.soton.ac.uk/id/eprint/20936
ISSN: 1549-9618
PURE UUID: 439ba4fe-3118-4ce6-9b0e-930033f46363
ORCID for Stephen C. Phillips: ORCID iD orcid.org/0000-0002-7901-0839
ORCID for Jonathan W. Essex: ORCID iD orcid.org/0000-0003-2639-2746

Catalogue record

Date deposited: 28 Feb 2006
Last modified: 05 Nov 2019 02:04

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Contributors

Author: Adrian P. Wiley
Author: Martin T. Swain
Author: Stephen C. Phillips ORCID iD
Author: Colin M. Edge

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