Modelling functional motions of biological systems by customised natural moves
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 Ca...
| Main Authors: | , , , |
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| Format: | Journal article |
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Biophysical Society
2016
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| _version_ | 1797064873490776064 |
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| author | Minary, P Demharter, S Knapp, B Deane, C |
| author_facet | Minary, P Demharter, S Knapp, B Deane, C |
| author_sort | Minary, P |
| collection | OXFORD |
| description | 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. |
| first_indexed | 2024-03-06T21:20:36Z |
| format | Journal article |
| id | oxford-uuid:415026a9-0923-4d74-a38e-45e3306a32dd |
| institution | University of Oxford |
| last_indexed | 2024-03-06T21:20:36Z |
| publishDate | 2016 |
| publisher | Biophysical Society |
| record_format | dspace |
| spelling | oxford-uuid:415026a9-0923-4d74-a38e-45e3306a32dd2022-03-26T14:42:57ZModelling functional motions of biological systems by customised natural movesJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:415026a9-0923-4d74-a38e-45e3306a32ddSymplectic Elements at OxfordBiophysical Society2016Minary, PDemharter, SKnapp, BDeane, CSimulating 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. |
| spellingShingle | Minary, P Demharter, S Knapp, B Deane, C Modelling functional motions of biological systems by customised natural moves |
| title | Modelling functional motions of biological systems by customised natural moves |
| title_full | Modelling functional motions of biological systems by customised natural moves |
| title_fullStr | Modelling functional motions of biological systems by customised natural moves |
| title_full_unstemmed | Modelling functional motions of biological systems by customised natural moves |
| title_short | Modelling functional motions of biological systems by customised natural moves |
| title_sort | modelling functional motions of biological systems by customised natural moves |
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