ArticleBiophysical journal2009
Helix/coil nucleation: a local response to global demands.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Rigidity Emerges during Antibody Evolution in Three Distinct Antibody Systems: Evidence from QSFR Analysis of Fab Fragments.PLoS computational biology · 2015Article
- AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular Systems.Entropy (Basel, Switzerland) · 2015Article
- A virtual pebble game to ensemble average graph rigidity.Algorithms for molecular biology : AMB · 2015Article
- Flexibility Correlation between Active Site Regions Is Conserved across Four AmpC β-Lactamase Enzymes.PloS one · 2015Article
- Thermodynamic stability and flexibility characteristics of antibody fragment complexes.Protein and peptide letters · 2014Article
- A case study comparing quantitative stability-flexibility relationships across five metallo-β-lactamases highlighting differences within NDM-1.Methods in molecular biology (Clifton, N.J.) · 2014Article
- Redistribution of flexibility in stabilizing antibody fragment mutants follows Le Châtelier's principle.PloS one · 2014Article
- Variations within class-A β-lactamase physiochemical properties reflect evolutionary and environmental patterns, but not antibiotic specificity.PLoS computational biology · 2013Article
- Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged.PLoS computational biology · 2012Article
- Ensemble properties of network rigidity reveal allosteric mechanisms.Methods in molecular biology (Clifton, N.J.) · 2012Article
- Article
- Direct assessment of the α-helix nucleation time.The journal of physical chemistry. B · 2011Article
- Nonadditivity in the alpha-helix to coil transition.Biopolymers · 2011Article
- Nonadditivity in conformational entropy upon molecular rigidification reveals a universal mechanism affecting folding cooperativity.Biophysical journal · 2011Article
- Ensemble-based methods for describing protein dynamics.Current opinion in pharmacology · 2010Review
- Predicting the melting point of human C-type lysozyme mutants.Current protein & peptide science · 2010Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
A complete description of protein structure and function must include a proper treatment of mechanisms that lead to cooperativity. The helix/coil transition serves as a simple example of a cooperative folding process, commonly described by a nucleation-propagation mechanism. The prevalent view is that coil structure must first form a short segment of helix in a localized region despite paying a free energy cost (nucleation). Afterward, helical structure propagates outward from the nucleation site. Both processes entail enthalpy-entropy compensation that derives from the loss in conformational entropy on helix formation with concomitant gain in favorable interactions. Nucleation-propagation models inherently assume that cooperativity arises from a sequential series of local events. An alternative distance constraint model asserts there is a direct link between available degrees of freedom and cooperativity through the nonadditivity in conformational entropy. That is, helix nucleation is a concerted manifestation of rigidity propagating through atomic structure. The link between network rigidity and nonadditivity of conformational entropy is shown in this study by solving the distance constraint model using a simple global constraint counting approximation. Cooperativity arises from competition between excess and deficiency in available degrees of freedom in the coil and helix states respectively.
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Registered trials
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