Journal
JOURNAL OF PHYSICAL CHEMISTRY B
Volume 116, Issue 29, Pages 8692-8702Publisher
AMER CHEMICAL SOC
DOI: 10.1021/jp300852d
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Funding
- Center for Theoretical Biological Physics
- NSF [PHY-0822283]
- Cancer Prevention and Research Institute of Texas
- NSF through TeraGrid
- TACC [TGMCB110021]
- NIH [T32 GM08326]
- [NSF-MCB-1214457]
- Direct For Biological Sciences
- Div Of Molecular and Cellular Bioscience [1214457] Funding Source: National Science Foundation
- Direct For Mathematical & Physical Scien
- Division Of Physics [1308264] Funding Source: National Science Foundation
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Structure-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.
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