scholarly journals Contact order dependent protein folding rates: Kinetic consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences

2003 ◽  
Vol 52 (4) ◽  
pp. 524-533 ◽  
Author(s):  
Hüseyin Kaya ◽  
Hue Sun Chan
Keyword(s):  
Protein Folding ◽  
Nonlocal Interactions ◽  
Folding Rates ◽  
Contact Order ◽  
Conformational Preferences ◽  
Dependent Protein

Capturing protein folding-relevant topology via absolute contact order variants

2014 ◽  
Vol 13 (01) ◽  
pp. 1450005 ◽  
Author(s):  
Amy S. Wagaman ◽  
Sheila S. Jaswal
Keyword(s):  
Protein Folding ◽  
Heavy Atom ◽  
Folding Rate ◽  
Data Set ◽  
Structural Class ◽  
Protein Structural Class ◽  
Folding Rates ◽  
Contact Order ◽  
Energetic Interactions ◽  
Structural Classes

Absolute contact order is one of the simplest parameters used to predict protein folding rates. Many variants of contact order (CO) have been applied to highlight different aspects of contact neighborhoods and their relationship to folding. However, a systematic study of the influence of CO variants on correlation with folding rate has not been performed for a large combined set of multi- and two-state proteins. We explore different contact neighborhoods and resulting CO by varying the distance thresholds and weighting of sequence separation for heavy atom and residue-based counting methods for a set of 136 proteins diverse across folding and structural classes. We examine the changes in contact neighborhoods and compare correlations with our CO variants and the protein folding rates across our data set as well as by folding type and structural class. Different CO variants lead to the strongest correlations within each protein structural class. Our results demonstrate that backbone topology at a distance beyond where energetic interactions dominate is able to capture folding determinants, and suggest that more sensitive methods of characterizing contact relationships may improve ln kf prediction for diverse protein sets.

scholarly journals Topological complexity, contact order, and protein folding rates

2002 ◽  
Vol 117 (18) ◽  
pp. 8587-8591 ◽  
Author(s):  
P. F. N. Faisca ◽  
R. C. Ball
Keyword(s):  
Protein Folding ◽  
Topological Complexity ◽  
Folding Rates ◽  
Contact Order

Topology-dependent protein folding rates analyzed by a stereochemical model

2005 ◽  
Vol 123 (15) ◽  
pp. 154906 ◽  
Author(s):  
Inês R. Silva ◽  
Lucila M. Dos Reis ◽  
A. Caliri
Keyword(s):  
Protein Folding ◽  
Folding Rates ◽  
Dependent Protein

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.

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