The Shadow Map: A General Contact Definition for Capturing the Dynamics of Biomolecular Folding and Function

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dc.citation.firstpage8692en_US
dc.citation.issueNumber29en_US
dc.citation.journalTitleThe Journal of Physical Chemistry Ben_US
dc.citation.lastpage8702en_US
dc.citation.volumeNumber116en_US
dc.contributor.authorNoel, Jeffrey K.en_US
dc.contributor.authorWhitford, Paul C.en_US
dc.contributor.authorOnuchic, José N.en_US
dc.contributor.orgCenter for Theoretical Biological Physicsen_US
dc.date.accessioned2015-01-06T15:49:13Zen_US
dc.date.available2015-01-06T15:49:13Zen_US
dc.date.issued2012en_US
dc.description.abstractStructure-based models (SBMs) are simplified models of the biomolecular dynamics that arise from funneled energy landscapes. We recently introduced an all-atom SBM that explicitly represents the atomic geometry of a biomolecule. While this initial study showed the robustness of the all-atom SBM Hamiltonian to changes in many of the energetic parameters, an important aspect, which has not been explored previously, is the definition of native interactions. In this study, we propose a general definition for generating atomically grained contact maps called “Shadow”. The Shadow algorithm initially considers all atoms within a cutoff distance and then, controlled by a screening parameter, discards the occluded contacts. We show that this choice of contact map is not only well behaved for protein folding, since it produces consistently cooperative folding behavior in SBMs but also desirable for exploring the dynamics of macromolecular assemblies since, it distributes energy similarly between RNAs and proteins despite their disparate internal packing. All-atom structure-based models employing Shadow contact maps provide a general framework for exploring the geometrical features of biomolecules, especially the connections between folding and function.en_US
dc.identifier.citationNoel, Jeffrey K., Whitford, Paul C. and Onuchic, José N.. "The Shadow Map: A General Contact Definition for Capturing the Dynamics of Biomolecular Folding and Function." <i>The Journal of Physical Chemistry B,</i> 116, no. 29 (2012) American Chemical Society: 8692-8702. http://dx.doi.org/10.1021/jp300852d.en_US
dc.identifier.doihttp://dx.doi.org/10.1021/jp300852den_US
dc.identifier.urihttps://hdl.handle.net/1911/78888en_US
dc.language.isoengen_US
dc.publisherAmerican Chemical Societyen_US
dc.rightsThis is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the American Chemical Society.en_US
dc.titleThe Shadow Map: A General Contact Definition for Capturing the Dynamics of Biomolecular Folding and Functionen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpost-printen_US
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