ArticleProceedings of the National Academy of Sciences of the United States of America2008
Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 34 citations in OpenAlex.
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- Probing the effects of nonannular lipid binding on the stability of the calcium pump SERCA.Scientific reports · 2019Article
- Preexisting domain motions underlie protonation-dependent structural transitions of the P-type CaPhysical chemistry chemical physics : PCCP · 2017Article
- Differential Impact of the Monovalent Ions Li⁺, Na⁺, K⁺, and Rb⁺ on DNA Conformational Properties.The journal of physical chemistry letters · 2015Article
- Recapturing the Correlated Motions of Protein Using Coarse- Grained Models.Protein and peptide letters · 2015Article
- Capsid deformations reveal complex mechano-chemistry.Biophysical journal · 2013Article
- Conformational response to solvent interaction and temperature of a protein (Histone h3.1) by a multi-grained monte carlo simulation.PloS one · 2013Article
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- Induced fit, conformational selection and independent dynamic segments: an extended view of binding events.Trends in biochemical sciences · 2010Article
- Systematic study of anharmonic features in a principal component analysis of gramicidin A.Biophysical journal · 2010Article
- Proteins with weakly funneled energy landscapes challenge the classical structure-function paradigm.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Competing interactions create functionality through frustration.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
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3 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
The native state dynamics of the small globular serine protease inhibitor eglin c has been studied in a long 336 ns computer simulation in explicit solvent. We have elucidated the energy landscape explored during the course of the simulation by using Principal Component Analysis. We observe several basins in the energy landscape in which the system lingers for extended periods. Through an iterative process we have generated a tree-like hierarchy of states describing the observed dynamics. We observe a range of divergent contact types including salt bridges, hydrogen bonds, hydrophilic interactions, and hydrophobic interactions, pointing to the frustration between competing interactions. Additionally, we find evidence of competing water-mediated interactions. Divergence in water-mediated interactions may be found to supplement existing direct contacts, but they are also found to be independent of such changes. Water-mediated contacts facilitate interactions between residues of like charge as observed in the simulation. Our results provide insight into the complexity of the dynamic native state of a globular protein and directly probe the residual frustration in the native state.
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