Topological principles of protein folding

2021 ◽  
Author(s):  
Barbara Scalvini ◽  
Vahid Sheikhhassani ◽  
Alireza Mashaghi
Keyword(s):  
Protein Folding ◽  
Folding Kinetics ◽  
Folding Rate ◽  
Topological Relationships ◽  
Protein Loops

Native topology correlates with folding rate: entangled topological relationships between protein loops facilitate folding. High numbers of topologically independent units (circuits) – normalized by size – are associated with fast folding kinetics.

Predicting Protein Folding Rate From Amino Acid Sequence

2011 ◽  
Vol 37 (12) ◽  
pp. 1331-1338 ◽  
Author(s):  
Jian-Xiu GUO ◽  
Ni-Ni RAO ◽  
Guang-Xiong LIU ◽  
Jie LI ◽  
Yun-He WANG
Keyword(s):  
Protein Folding ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Folding Rate ◽  
Protein Folding Rate

An Effective Cumulative Torsion Angles Model for Prediction of Protein Folding Rates

2020 ◽  
Vol 27 (4) ◽  
pp. 321-328 ◽  
Author(s):  
Yanru Li ◽  
Ying Zhang ◽  
Jun Lv
Keyword(s):  
Protein Folding ◽  
Size Structure ◽  
Conformational Space ◽  
Coefficient Of Determination ◽  
Folding Rate ◽  
Torsion Angles ◽  
Folding Rates ◽  
Protein Folding Rate ◽  
Optimal Set ◽  
Conformation Space

Background: Protein folding rate is mainly determined by the size of the conformational space to search, which in turn is dictated by factors such as size, structure and amino-acid sequence in a protein. It is important to integrate these factors effectively to form a more precisely description of conformation space. But there is no general paradigm to answer this question except some intuitions and empirical rules. Therefore, at the present stage, predictions of the folding rate can be improved through finding new factors, and some insights are given to the above question. Objective: Its purpose is to propose a new parameter that can describe the size of the conformational space to improve the prediction accuracy of protein folding rate. Method: Based on the optimal set of amino acids in a protein, an effective cumulative backbone torsion angles (CBTAeff) was proposed to describe the size of the conformational space. Linear regression model was used to predict protein folding rate with CBTAeff as a parameter. The degree of correlation was described by the coefficient of determination and the mean absolute error MAE between the predicted folding rates and experimental observations. Results: It achieved a high correlation (with the coefficient of determination of 0.70 and MAE of 1.88) between the logarithm of folding rates and the (CBTAeff)0.5 with experimental over 112 twoand multi-state folding proteins. Conclusion: The remarkable performance of our simplistic model demonstrates that CBTA based on optimal set was the major determinants of the conformation space of natural proteins.

The Influences of Palindromes in mRNA on Protein Folding Rates

2020 ◽  
Vol 27 (4) ◽  
pp. 303-312 ◽  
Author(s):  
Ruifang Li ◽  
Hong Li ◽  
Sarula Yang ◽  
Xue Feng
Keyword(s):  
Protein Folding ◽  
Regression Analysis ◽  
Linear Regression ◽  
Linear Regression Analysis ◽  
Folding Rate ◽  
Folding Rates ◽  
Negative Linear Correlation ◽  
Protein Folding Rate ◽  
The Relationship ◽  
Structure Environment

Background: It is currently believed that protein folding rates are influenced by protein structure, environment and temperature, amino acid sequence and so on. We have been working for long to determine whether and in what ways mRNA affects the protein folding rate. A large number of palindromes aroused our attention in our previous research. Whether these palindromes do have important influences on protein folding rates and what’s the mechanism? Very few related studies are focused on these problems. Objective: In this article, our motivation is to find out if palindromes have important influences on protein folding rates and what’s the mechanism. Method: In this article, the parameters of the palindromes were defined and calculated, the linear regression analysis between the values of each parameter and the experimental protein folding rates were done. Furthermore, to compare the results of different kinds of proteins, proteins were classified into the two-state proteins and the multi-state proteins. For the two kinds of proteins, the above linear regression analysis were performed respectively. Results : Protein folding rates were negatively correlated to the palindrome frequencies for all proteins. An extremely significant negative linear correlation appeared in the relationship between palindrome densities and protein folding rates. And the repeatedly used bases by different palindromes simultaneously have an important effect on the relationship between palindrome density and protein folding rate. Conclusion: The palindromes have important influences on protein folding rates, and the repeatedly used bases in different palindromes simultaneously play a key role in influencing the protein folding rates.

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 Protein folding kinetics and thermodynamics from atomistic simulation

2012 ◽  
Vol 109 (44) ◽  
pp. 17845-17850 ◽  
Author(s):  
S. Piana ◽  
K. Lindorff-Larsen ◽  
D. E. Shaw
Keyword(s):  
Protein Folding ◽  
Atomistic Simulation ◽  
Folding Kinetics ◽  
Kinetics And Thermodynamics

scholarly journals Predicting Experimental Quantities in Protein Folding Kinetics Using Stochastic Roadmap Simulation

2006 ◽  
pp. 410-424 ◽  
Author(s):  
Tsung-Han Chiang ◽  
Mehmet Serkan Apaydin ◽  
Douglas L. Brutlag ◽  
David Hsu ◽  
Jean-Claude Latombe
Keyword(s):  
Protein Folding ◽  
Folding Kinetics

Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory†

2004 ◽  
Vol 108 (21) ◽  
pp. 6571-6581 ◽  
Author(s):  
William C. Swope ◽  
Jed W. Pitera ◽  
Frank Suits
Keyword(s):  
Molecular Dynamics ◽  
Protein Folding ◽  
Molecular Dynamics Simulations ◽  
Folding Kinetics ◽  
Dynamics Simulations
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