Folding Kinetics of Villin 14T, a Protein Domain with a Central β-Sheet and Two Hydrophobic Cores†

Biochemistry ◽  
1998 ◽  
Vol 37 (41) ◽  
pp. 14508-14518 ◽  
Author(s):  
Sung E. Choe ◽  
Paul T. Matsudaira ◽  
John Osterhout ◽  
Gerhard Wagner ◽  
Eugene I. Shakhnovich
Keyword(s):  
Protein Domain ◽  
Folding Kinetics ◽  
Hydrophobic Cores ◽  
Villin 14T ◽  
Kinetics Of ◽  
Β Sheet

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 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

Analysis of the pH-dependent stability and millisecond folding kinetics of horse cytochrome c

2015 ◽  
Vol 585 ◽  
pp. 52-63 ◽  
Author(s):  
Rishu Jain ◽  
Rajesh Kumar ◽  
Sandeep Kumar ◽  
Ritika Chhabra ◽  
Mukesh Chand Agarwal ◽  
...  
Keyword(s):  
Cytochrome C ◽  
Folding Kinetics ◽  
Ph Dependent ◽  
Kinetics Of ◽  
Horse Cytochrome

scholarly journals Ultrafast folding kinetics of WW domains reveal how the amino acid sequence determines the speed limit to protein folding

2019 ◽  
Vol 116 (17) ◽  
pp. 8137-8142 ◽  
Author(s):  
Malwina Szczepaniak ◽  
Manuel Iglesias-Bexiga ◽  
Michele Cerminara ◽  
Mourad Sadqi ◽  
Celia Sanchez de Medina ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Essential Element ◽  
Nanosecond Laser ◽  
Speed Limit ◽  
Free Energy Barrier ◽  
Folding Kinetics ◽  
Folding Rate ◽  
Ww Domains ◽  
Kinetics Of

Protein (un)folding rates depend on the free-energy barrier separating the native and unfolded states and a prefactor term, which sets the timescale for crossing such barrier or folding speed limit. Because extricating these two factors is usually unfeasible, it has been common to assume a constant prefactor and assign all rate variability to the barrier. However, theory and simulations postulate a protein-specific prefactor that contains key mechanistic information. Here, we exploit the special properties of fast-folding proteins to experimentally resolve the folding rate prefactor and investigate how much it varies among structural homologs. We measure the ultrafast (un)folding kinetics of five natural WW domains using nanosecond laser-induced temperature jumps. All five WW domains fold in microseconds, but with a 10-fold difference between fastest and slowest. Interestingly, they all produce biphasic kinetics in which the slower phase corresponds to reequilibration over the small barrier (<3RT) and the faster phase to the downhill relaxation of the minor population residing at the barrier top [transition state ensemble (TSE)]. The fast rate recapitulates the 10-fold range, demonstrating that the folding speed limit of even the simplest all-β fold strongly depends on the amino acid sequence. Given this fold’s simplicity, the most plausible source for such prefactor differences is the presence of nonnative interactions that stabilize the TSE but need to break up before folding resumes. Our results confirm long-standing theoretical predictions and bring into focus the rate prefactor as an essential element for understanding the mechanisms of folding.

scholarly journals Folding Kinetics of Multiple G-Quadruplex Telomeric DNA Structures

2020 ◽  
Vol 118 (3) ◽  
pp. 335a
Author(s):  
Emil L. Kristoffersen ◽  
Andrea Coletta ◽  
Line Lund ◽  
Birgit Schiøtt ◽  
Victoria Birkedal
Keyword(s):  
Folding Kinetics ◽  
Telomeric Dna ◽  
Dna Structures ◽  
G Quadruplex ◽  
Kinetics Of

scholarly journals Folding Kinetics of G-Quadruplexes: Duplex Stem Loops Drive and Accelerate G-Quadruplex Folding

2020 ◽  
Vol 124 (25) ◽  
pp. 5122-5130 ◽  
Author(s):  
Thi Quynh Ngoc Nguyen ◽  
Kah Wai Lim ◽  
Anh Tuân Phan
Keyword(s):  
Folding Kinetics ◽  
G Quadruplex ◽  
Kinetics Of
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