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Predicting folding free energy changes upon single point mutations

Zhe Zhang, Lin Wang, Yang Gao, Jie Zhang, Maxim Zhenirovskyy, Emil Alexov
2012 Computer applications in the biosciences : CABIOS  
In both cases, it is desirable to predict the change of the folding free energy upon single point mutations in order to either provide insights of the molecular mechanism of the change or to design new  ...  Results: We report an approach that predicts the free energy change upon single point mutation by utilizing the 3D structure of the wild-type protein.  ...  Folding free energy calculation The folding free energy changes upon single point mutations were calculated as described in our previous works (Witham et al., 2011; Zhang et al., 2011; Zhang et al., 2010  ... 
doi:10.1093/bioinformatics/bts005 pmid:22238268 pmcid:PMC3289912 fatcat:g2f5gt5yo5gwhlvffblngvusyu

Predicting the Viability of Beta-Lactamase: How Folding and Binding Free Energies Correlate with Beta-Lactamase Fitness [article]

Jordan Yang, Nandita Naik, Jagdish Suresh Patel, Christopher S. Wylie, Wenze Gu, Jessie Huang, Marty Ytreberg, Mandar T. Naik, Daniel M. Weinreich, Brenda M. Rubenstein
2020 bioRxiv   pre-print
folding free energies can meaningfully, although not perfectly, predict the experimental folding free energies of single mutants.  ...  free energies will be to the large data sets of multiply-mutated proteins forthcoming.  ...  resources were provided by the Brown Center for Computation and Visualization (CCV) and the high-performance computing center at Idaho National Laboratory, which is supported by the Office of Nuclear Energy  ... 
doi:10.1101/2020.04.15.043661 fatcat:cxren3sq3feuxkzt3yyciycaq4

Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness

Jordan Yang, Nandita Naik, Jagdish Suresh Patel, Christopher S. Wylie, Wenze Gu, Jessie Huang, F. Marty Ytreberg, Mandar T. Naik, Daniel M. Weinreich, Brenda M. Rubenstein, Jose M. Sanchez-Ruiz
2020 PLoS ONE  
as FoldX and PyRosetta can meaningfully, although not perfectly, predict the experimental folding free energies of single mutants.  ...  Based upon a set of 21 β-lactamase single and double mutants expressly designed to influence protein folding, we first demonstrate that modeling software designed to compute folding free energies such  ...  resources were provided by the Brown Center for Computation and Visualization (CCV) and the high-performance computing center at Idaho National Laboratory, which is supported by the Office of Nuclear Energy  ... 
doi:10.1371/journal.pone.0233509 pmid:32470971 fatcat:mojihcc47vbc7e3xgjmptojwtu

PROTS-RF: A Robust Model for Predicting Mutation-Induced Protein Stability Changes

Yunqi Li, Jianwen Fang, Narayanaswamy Srinivasan
2012 PLoS ONE  
Contrary to previous suggestions, our results clearly demonstrate that a robust predictive model trained for predicting single point mutation induced thermostability changes can be capable of predicting  ...  In this report we present PROTS-RF, a robust model based on the Random Forest algorithm capable of predicting thermostability changes induced by not only single-, but also double- or multiple-point mutations  ...  of experimental data for free energy changes upon mutations of this enzyme [46] .  ... 
doi:10.1371/journal.pone.0047247 pmid:23077576 pmcid:PMC3471942 fatcat:poqnn3jzwjbhdo4u3573y4hm4e

Proteins Evolution Upon Point Mutations [article]

J.A. Vila
2021 arXiv   pre-print
The preliminary results -- without considering epistasis effects explicitly -- indicate that the protein marginal-stability change upon point mutations provides the necessary and sufficient information  ...  This finding is of paramount importance because it illustrates the impact of point mutations on both the protein marginal-stability and the ensemble of folded conformations coexisting with the native state  ...  Before we proceed, let us remember: firstly, that G ~ GU will provide us with the Gibbs free energy change in the protein's marginal stability upon point mutation; secondly, the amide HX protection  ... 
arXiv:2111.04199v2 fatcat:fyhc2uswjfc5lhpdh63ngipaxm

SIMPLE estimate of the free energy change due to aliphatic mutations: Superior predictions based on first principles

Marta Bueno, Carlos J. Camacho, Javier Sancho
2007 Proteins: Structure, Function, and Bioinformatics  
point mutations predicts 20-30% less false positives and yields more accurate predictions than any published empirical energy function.  ...  Our first principle analysis strongly suggests that both the solute-solute van der Waals interactions in the folded state and the electrostatics free energy change of exposed aliphatic mutations are almost  ...  A simplified version of this problem is predicting changes in structure and stability induced by single point-mutations.  ... 
doi:10.1002/prot.21453 pmid:17523191 fatcat:hjr25ppg4nd43hli7aoqlm2die

SAAFEC-SEQ: A Sequence-Based Method for Predicting the Effect of Single Point Mutations on Protein Thermodynamic Stability

Gen Li, Shailesh Kumar Panday, Emil Alexov
2021 International Journal of Molecular Sciences  
Here, we report a new development of the SAAFEC method, the SAAFEC-SEQ, which is a gradient boosting decision tree machine learning method to predict the change of the folding free energy caused by amino  ...  Modeling the effect of mutations on protein thermodynamics stability is useful for protein engineering and understanding molecular mechanisms of disease-causing variants.  ...  the change of folding free energy resulting from a single amino acid mutation.  ... 
doi:10.3390/ijms22020606 pmid:33435356 fatcat:oksdyq2uuvffdapxhjqpnhk3ea

Using DelPhi capabilities to mimic protein's conformational reorganization with amino acid specific dielectric constants

Lin Wang, Zhe Zhang, Walter Rocchia, Emil Alexov
2013 Communications in Computational Physics  
The predicted energy changes are benchmarked against experimentally measured changes of the folding energy on a set of 257 single mutations.  ...  Here we report a large scale investigation of modeling the changes of the folding energy due to single mutations involving charged group.  ...  upon single point mutations involving charged amino acid.  ... 
pmid:24683422 pmcid:PMC3966310 fatcat:xds7mfycrrhuraebgvvjgmx6vm

Predictive shifts in free energy couple mutations to their phenotypic consequences

Griffin Chure, Manuel Razo-Mejia, Nathan M. Belliveau, Tal Einav, Zofii A. Kaczmarek, Stephanie L. Barnes, Mitchell Lewis, Rob Phillips
2019 Proceedings of the National Academy of Sciences of the United States of America  
Finally, we show that the induction profiles and resulting free energies associated with pairwise double mutants can be predicted with quantitative accuracy given knowledge of the single mutants, providing  ...  Changing these subsets of parameters tunes the free energy of the system in a way that is concordant with theoretical expectations.  ...  To determine the free energy for a given set of fold-change measurements (for 1 unique strain at a single inducer concentration), we modeled the observed fold-change measurements as being drawn from a  ... 
doi:10.1073/pnas.1907869116 pmid:31451655 pmcid:PMC6744869 fatcat:mkinwoovoneoxeq4x3362m7kni

On the physics of thermal-stability changes upon mutations of a protein

Shota Murakami, Hiraku Oshima, Tomohiko Hayashi, Masahiro Kinoshita
2015 Journal of Chemical Physics  
It is of great interest from both scientific and practical viewpoints to theoretically predict the thermal-stability changes upon mutations of a protein.  ...  Our approach is compared with one of the most popular approaches, FOLD-X, in terms of the prediction performance not only for single mutations but also for double, triple, and higher-fold (up to sevenfold  ...  The free-energy function of FOLD-X is parameterized using only the experimental data for single mutations.  ... 
doi:10.1063/1.4931814 pmid:26429043 fatcat:b27w6v3qj5fhjlorarguj4yize

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability

Carlos HM Rodrigues, Douglas EV Pires, David B Ascher
2018 Nucleic Acids Research  
upon static structures.  ...  DynaMut integrates our graph-based signatures along with normal mode dynamics to generate a consensus prediction of the impact of a mutation on protein stability.  ...  The change in folding free energy is a thermodynamic state function, and it has been proposed that the change in folding free energy of a mutation from a wild-type protein to its mutant ( G WT→MT ) should  ... 
doi:10.1093/nar/gky300 pmid:29718330 pmcid:PMC6031064 fatcat:q6mxi3iz5fhn5mf4r3yd4cnnke

Prediction of protein thermostability with a direction- and distance-dependent knowledge-based potential

Christian Hoppe, Dietmar Schomburg
2005 Protein Science  
A total of 76% of the mutations could be predicted correctly as being either stabilizing or destabilizing. The results for the test set are r = 0.74 (747 data points) and 72%, respectively.  ...  The increasing use of enzymes in industrial processes and the importance of understanding protein folding and stability have led to several attempts to predict and quantify the effect of every possible  ...  Predicting protein stability changes upon mutation  ... 
doi:10.1110/ps.04940705 pmid:16155198 pmcid:PMC2253293 fatcat:albymq675fh4hne5ymemhzrhh4

I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure

E. Capriotti, P. Fariselli, R. Casadio
2005 Nucleic Acids Research  
I-Mutant2.0 is a support vector machine (SVM)-based tool for the automatic prediction of protein stability changes upon single point mutations.  ...  I-Mutant2.0 can be used both as a classifier for predicting the sign of the protein stability change upon mutation and as a regression estimator for predicting the related DDG values.  ...  I-Mutant2.0 was also trained/tested to predict the value of the free energy stability change upon single point mutation, starting from the protein structure or sequence.  ... 
doi:10.1093/nar/gki375 pmid:15980478 pmcid:PMC1160136 fatcat:rhp4qihyizasnijx5yaqusm33u

Using DelPhi Capabilities to Mimic Protein's Conformational Reorganization with Amino Acid Specific Dielectric Constants

Lin Wang, Zhe Zhang, Walter Rocchia, Emil Alexov
2013 Communications in Computational Physics  
The predicted energy changes are benchmarked against experimentally measured changes of the folding energy on a set of 257 single mutations.  ...  Here we report a large scale investigation of modeling the changes of the folding energy due to single mutations involving charged group.  ...  The compiled folding energy changes, the corresponding structures and in silico made mutant structures, along with calculated energies are available from http://compbio. clemson.edu/delphi.php and clicking  ... 
doi:10.4208/cicp.300611.120911s fatcat:pzikfyizgberjky5irovopednq

Biophysical ambiguities prevent accurate genetic prediction

Xianghua Li, Ben Lehner
2020 Nature Communications  
This apparent paradox arises because mutations can have different biophysical effects to cause the same change in a phenotype and the outcome in a double mutant depends upon what these hidden biophysical  ...  changes actually are.  ...  of changes in the free energy of folding (ΔΔG F ) and DNA binding (ΔΔG B ).  ... 
doi:10.1038/s41467-020-18694-0 pmid:33004824 fatcat:lttls7z3xfcbjnsx42rv5gk6rm
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