Modelling functional motions of biological systems by customised natural moves

Journal article

Simulating the functional motions of biomolecular systems requires large computational resources. We introduce a computationally inexpensive protocol for the systematic testing of hypotheses regarding the dynamic behaviour of proteins and nucleic acids. The protocol is based on natural move Monte Carlo, a highly efficient conformational sampling method with in-built customisation capabilities that allows researchers to design and perform a large number of simulations to investigate functional motions in biological systems. We demonstrate the use of this protocol on both a protein and a DNA case study. Firstly, we investigate the plasticity of a class II major-histo-compatibility complex in the absence of a bound peptide. Secondly, we study the effects of the epigenetic mark 5-hydroxymethyl on cytosine on the structure of the Dickerson-Drew dodecamer. We show how our customised natural moves protocol can be used to investigate causal relationships of functional motions in biological systems.

Authors: Minary, P; Demharter, S; Knapp, B; Deane, C

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Biophysical Society
• Journal: Biophysical Journal
• Volume: 111
• Issue: 4
• Pages: 710–721
• Publication date: 2016-08-23
• Acceptance date: 2016-06-22
• DOI: 10.1016/j.bpj.2016.06.028
• EISSN: 1542-0086
• ISSN: 0006-3495