title: Modeling Functional Motions of Biological Systems by Customized Natural Moves.
abstract: 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 behavior of proteins and nucleic acids. The protocol is based on natural move Monte Carlo, a highly efficient conformational sampling method with built-in customization 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 histocompatibility 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 customized natural moves protocol can be used to investigate causal relationships of functional motions in biological systems.
authors: Department of Computer Science, University of Oxford, Oxford, UK.
authors: Samuel
authors: S
authors: Demharter
authors: Department of Statistics, University of Oxford, Oxford, UK.
authors: Bernhard
authors: B
authors: Knapp
authors: Department of Statistics, University of Oxford, Oxford, UK.
authors: Charlotte M
authors: CM
authors: Deane
authors: Department of Computer Science, University of Oxford, Oxford, UK. Electronic address: peter.minary@cs.ox.ac.uk.
authors: Peter
authors: P
authors: Minary
mesh_terms: D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D044127:Epigenesis, Genetic; D006684:HLA-DR Antigens / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D009010:Monte Carlo Method; D009068:Movement; D009690:Nucleic Acid Conformation; D000072757:Protein Conformation, beta-Strand
chemical_list: D006684:HLA-DR Antigens; D004247:DNA