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Protein-protein interactions from linear-scaling first-principles quantum-mechanical calculations

Protein-protein interactions from linear-scaling first-principles quantum-mechanical calculations
Protein-protein interactions from linear-scaling first-principles quantum-mechanical calculations
A modification of the MM-PBSA technique for calculating binding affinities of biomolecular complexes is presented. Classical molecular dynamics is used to explore the motion of the extended interface between two peptides derived from the BRC4 repeat of BRCA2 and the eukaryotic recombinase RAD51. The resulting trajectory is sampled using the linear-scaling density functional theory code, onetep, to determine from first principles, and with high computational efficiency, the relative free energies of binding of the ~2800 atom receptor-ligand complexes. This new method provides the basis for computational interrogation of protein-protein and protein-ligand interactions within fields ranging from chemical biological studies to small-molecule binding behaviour, with both unprecedented chemical accuracy and affordable computational expense.
condensed matter, electrical, magnetic and optical, biological physics
0295-5075
37004-[6pp]
Cole, D.J.
9c443c7d-5291-40e8-b0a9-e0e3cf7948f1
Skylaris, C.-K.
8f593d13-3ace-4558-ba08-04e48211af61
Rajendra, E.
a7dbace9-48b3-412a-bbcb-27a0447a1ac7
Venkitaraman, A.R.
79e4a9f5-1f60-4b53-b035-6f378357507f
Payne, M.C.
090e6e2a-f537-4f23-8000-6f6814f8809a
Cole, D.J.
9c443c7d-5291-40e8-b0a9-e0e3cf7948f1
Skylaris, C.-K.
8f593d13-3ace-4558-ba08-04e48211af61
Rajendra, E.
a7dbace9-48b3-412a-bbcb-27a0447a1ac7
Venkitaraman, A.R.
79e4a9f5-1f60-4b53-b035-6f378357507f
Payne, M.C.
090e6e2a-f537-4f23-8000-6f6814f8809a

Cole, D.J., Skylaris, C.-K., Rajendra, E., Venkitaraman, A.R. and Payne, M.C. (2010) Protein-protein interactions from linear-scaling first-principles quantum-mechanical calculations. Europhysics Letters, 91 (3), 37004-[6pp]. (doi:10.1209/0295-5075/91/37004).

Record type: Article

Abstract

A modification of the MM-PBSA technique for calculating binding affinities of biomolecular complexes is presented. Classical molecular dynamics is used to explore the motion of the extended interface between two peptides derived from the BRC4 repeat of BRCA2 and the eukaryotic recombinase RAD51. The resulting trajectory is sampled using the linear-scaling density functional theory code, onetep, to determine from first principles, and with high computational efficiency, the relative free energies of binding of the ~2800 atom receptor-ligand complexes. This new method provides the basis for computational interrogation of protein-protein and protein-ligand interactions within fields ranging from chemical biological studies to small-molecule binding behaviour, with both unprecedented chemical accuracy and affordable computational expense.

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Published date: August 2010
Keywords: condensed matter, electrical, magnetic and optical, biological physics

Identifiers

Local EPrints ID: 179195
URI: http://eprints.soton.ac.uk/id/eprint/179195
ISSN: 0295-5075
PURE UUID: e642874a-1411-4c1b-80ac-1ecf2d079a1e
ORCID for C.-K. Skylaris: ORCID iD orcid.org/0000-0003-0258-3433

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Date deposited: 04 Apr 2011 10:19
Last modified: 29 Oct 2019 01:48

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