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Why Do Protein Folding Rates Correlate with Metrics of Native Topology?
- Source :
- E-Prints Complutense. Archivo Institucional de la UCM, instname, E-Prints Complutense: Archivo Institucional de la UCM, Universidad Complutense de Madrid, PLoS ONE, PLoS ONE, Vol 7, Iss 4, p e35599 (2012)
- Publication Year :
- 2012
- Publisher :
- Public Library of Science, 2012.
-
Abstract
- For almost 15 years, the experimental correlation between protein folding rates and the contact order parameter has been under scrutiny. Here, we use a simple simulation model combined with a native-centric interaction potential to investigate the physical roots of this empirical observation. We simulate a large set of circular permutants, thus eliminating dependencies of the folding rate on other protein properties (e.g. stability). We show that the rate-contact order correlation is a consequence of the fact that, in high contact order structures, the contact order of the transition state ensemble closely mirrors the contact order of the native state. This happens because, in these structures, the native topology is represented in the transition state through the formation of a network of tertiary interactions that are distinctively long-ranged.
- Subjects :
- Models, Molecular
Bioquímica
Protein Folding
Biophysics
lcsh:Medicine
Topology
01 natural sciences
Biochemistry
Protein Chemistry
Biophysics Simulations
03 medical and health sciences
Interaction potential
Protein structure
0103 physical sciences
Native state
Química física
Denaturation (biochemistry)
Computer Simulation
lcsh:Science
Biology
Computerized Simulations
030304 developmental biology
Physics
0303 health sciences
Quantitative Biology::Biomolecules
Multidisciplinary
010304 chemical physics
lcsh:R
Proteins
Computational Biology
Contact order
Protein Structure, Tertiary
Kinetics
Protein Interaction Networks
Computer Science
Experimental correlation
Thermodynamics
lcsh:Q
Protein folding
Biophysic Al Simulations
Research Article
Subjects
Details
- Database :
- OpenAIRE
- Journal :
- E-Prints Complutense. Archivo Institucional de la UCM, instname, E-Prints Complutense: Archivo Institucional de la UCM, Universidad Complutense de Madrid, PLoS ONE, PLoS ONE, Vol 7, Iss 4, p e35599 (2012)
- Accession number :
- edsair.doi.dedup.....2408e09ddb654dad61747fd4ce542460