scholarly journals Using motion planning to map protein folding landscapes and analyze folding kinetics of known native structures

2002 ◽  
Author(s):  
Nancy M. Amato ◽  
Ken A. Dill ◽  
Guang Song
Keyword(s):  
Protein Folding ◽  
Motion Planning ◽  
Folding Kinetics ◽  
Kinetics Of

Probing Protein Folding with Substitution-Inert Metal Ions. Folding Kinetics of Cobalt(III)-Cytochromec

1999 ◽  
Vol 121 (50) ◽  
pp. 11918-11919 ◽  
Author(s):  
F. Akif Tezcan ◽  
Jay R. Winkler ◽  
Harry B. Gray
Keyword(s):  
Protein Folding ◽  
Metal Ions ◽  
Folding Kinetics ◽  
Kinetics Of

scholarly journals Size and topology modulate the effects of frustration in protein folding

2018 ◽  
Vol 115 (37) ◽  
pp. 9234-9239 ◽  
Author(s):  
Alex Kluber ◽  
Timothy A. Burt ◽  
Cecilia Clementi
Keyword(s):  
Protein Folding ◽  
Folding Kinetics ◽  
Native Structure ◽  
And Topology ◽  
Folding Dynamics ◽  
Helical Proteins ◽  
Experimental Findings ◽  
State Size ◽  
Kinetics Of ◽  
Β Sheet

The presence of conflicting interactions, or frustration, determines how fast biomolecules can explore their configurational landscapes. Recent experiments have provided cases of systems with slow reconfiguration dynamics, perhaps arising from frustration. While it is well known that protein folding speed and mechanism are strongly affected by the protein native structure, it is still unknown how the response to frustration is modulated by the protein topology. We explore the effects of nonnative interactions in the reconfigurational and folding dynamics of proteins with different sizes and topologies. We find that structural correlations related to the folded state size and topology play an important role in determining the folding kinetics of proteins that otherwise have the same amount of nonnative interactions. In particular, we find that the reconfiguration dynamics of α-helical proteins are more susceptible to frustration than β-sheet proteins of the same size. Our results may explain recent experimental findings and suggest that attempts to measure the degree of frustration due to nonnative interactions might be more successful with α-helical proteins.

scholarly journals Simulation of Folding Kinetics for Aligned RNAs

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 347
Author(s):  
Jiabin Huang ◽  
Björn Voß
Keyword(s):  
Evolutionary Conservation ◽  
Folding Kinetics ◽  
New Approach ◽  
Computational Approaches ◽  
Reasonable Time ◽  
Valuable Method ◽  
Kinetics Of ◽  
Insight Into ◽  
Folding Space ◽  
Standing Problem

Studying the folding kinetics of an RNA can provide insight into its function and is thus a valuable method for RNA analyses. Computational approaches to the simulation of folding kinetics suffer from the exponentially large folding space that needs to be evaluated. Here, we present a new approach that combines structure abstraction with evolutionary conservation to restrict the analysis to common parts of folding spaces of related RNAs. The resulting algorithm can recapitulate the folding kinetics known for single RNAs and is able to analyse even long RNAs in reasonable time. Our program RNAliHiKinetics is the first algorithm for the simulation of consensus folding kinetics and addresses a long-standing problem in a new and unique way.

scholarly journals Cooperativity in protein-folding kinetics.

1993 ◽  
Vol 90 (5) ◽  
pp. 1942-1946 ◽  
Author(s):  
K. A. Dill ◽  
K. M. Fiebig ◽  
H. S. Chan
Keyword(s):  
Protein Folding ◽  
Folding Kinetics

scholarly journals Modulation of Folding Kinetics of Repeat Proteins: Interplay between Intra- and Interdomain Interactions

2012 ◽  
Vol 103 (7) ◽  
pp. 1555-1565 ◽  
Author(s):  
Tzachi Hagai ◽  
Ariel Azia ◽  
Emmanuel Trizac ◽  
Yaakov Levy
Keyword(s):  
Folding Kinetics ◽  
Repeat Proteins ◽  
Interdomain Interactions ◽  
Kinetics Of

Stability and Folding Kinetics of Structurally Characterized Cytochromec-b562†,‡

Biochemistry ◽  
2006 ◽  
Vol 45 (35) ◽  
pp. 10504-10511 ◽  
Author(s):  
Jasmin Faraone-Mennella ◽  
F. Akif Tezcan ◽  
Harry B. Gray ◽  
Jay R. Winkler
Keyword(s):  
Folding Kinetics ◽  
Kinetics Of
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