Recognition of stable protein mutants with 3D stochastic average electrostatic potentials.
As more and more proteins are applied to biochemical research there is increasing interest in studying their stability. In this study, a Markov model has been used to calculate molecular descriptors of the protein structure and these are called the average electrostatic potentials (xi(k)). These descriptors were intended to encode indirect electrostatic pair-wise interactions between amino acids located at Euclidean distance k within a given 3D protein backbone. The different xi(k) values could be calculated for the protein as a whole or for specific protein regions (orbits), which include amino acids that lie within a given range of distances from the center of charge of the protein. In this work we calculated the xi(k) values for 657 mutants of different proteins. A Linear Discriminant Analysis model correctly classified a subset of 435 out of 493 proteins according to their thermal stability - a level of predictability of 88.2%. This experiment was repeated with three additional subsets of proteins selected at random from the initial series of 657. More specifically, the model predicted 314/356 (88.2%) of mutants with higher stability than the corresponding wild-type protein and 264/301 (86.7%) of proteins with near wild-type stability. These results illustrate the possibilities for the average stochastic potentials xi(k) in the study of 3D-structure/property relationships for biochemically relevant proteins.
González-Díaz
Humberto
H
Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela 15782, Spain. qohumbe@usc.es
Molina
Reinaldo
R
Uriarte
Eugenio
E
D008390:Markov Chains; D008958:Models, Molecular; D009154:Mutation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D055672:Static Electricity
D011506:Proteins