ArticleBiophysical journal2008
Coevolution of function and the folding landscape: correlation with density of native contacts.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
8 citing papers in PubMed, 18 citations in OpenAlex.
- Evolution of a protein folding nucleus.Protein science : a publication of the Protein Society · 2016Article
- MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery.International journal of molecular sciences · 2015Review
- Sequence analysis on the information of folding initiation segments in ferredoxin-like fold proteins.BMC structural biology · 2014Article
- Energetic frustrations in protein folding at residue resolution: a homologous simulation study of Im9 proteins.PloS one · 2014Article
- Unfolding simulations reveal the mechanism of extreme unfolding cooperativity in the kinetically stable alpha-lytic protease.PLoS computational biology · 2010Article
- Characterization of the cofactor-induced folding mechanism of a zinc-binding peptide using computationally designed mutants.Journal of molecular biology · 2009Article
- Modeling signal propagation mechanisms and ligand-based conformational dynamics of the Hsp90 molecular chaperone full-length dimer.PLoS computational biology · 2009Article
- Insights from coarse-grained Gō models for protein folding and dynamics.International journal of molecular sciences · 2009Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The relationship between the folding landscape and function of evolved proteins is explored by comparison of the folding mechanisms for members of the flavodoxin fold. CheY, Spo0F, and NtrC have unrelated functions and low sequence homology but share an identical topology. Recent coarse-grained simulations show that their folding landscapes are uniquely tuned to properly suit their respective biological functions. Enhanced packing in Spo0F and its limited conformational dynamics compared to CheY or NtrC lead to frustration in its folding landscape. Simulation as well as experimental results correlate with the local density of native contacts for these and a sample of other proteins. In particular, protein regions of low contact density are observed to become structured late in folding; concomitantly, these dynamic regions are often involved in binding or conformational rearrangements of functional importance. These observations help to explain the widespread success of Gō-like coarse-grained models in reproducing protein dynamics.
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Registered trials
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