Relative importance of secondary structure and solvent accessibility to the stability of protein mutants. A case study with amino acid properties and energetics on T4 and human lysozymes.
Understanding the factors influencing the stability of protein mutants is an important task in molecular and computational biology. In this work, we have approached this problem by examining the relative importance of secondary structure and solvent accessibility of the mutant residue for understanding/predicting the stability of protein mutants. We have used hydrophobic, electrostatic and hydrogen bond free energy terms and nine unique physicochemical, energetic and conformational properties of amino acids in the present study and these parameters have been related with changes in thermal stability (DeltaTm) of all the single mutants of lysozymes based on single and multiple correlation coefficients. As expected the properties reflecting hydrophobicity and hydrophobic free energy play a major role to distinguish stabilizing and destabilizing mutants. The hydrophobic free energy due to carbon and nitrogen atoms distinguish the stability of coil and strand mutations to the accuracy of 100 and 90%, respectively. In agreement with previous results, the subgroup classification based on secondary structure and the information about its location in the structure yielded good relationship with the experimental DeltaTm. We revealed that the secondary structure information is equally or more important than solvent accessibility for understanding the stability of protein mutants. The comparison of amino acid properties with free-energy terms indicate that the energetic contribution explains the mutant stability better in coil region whereas the amino acid properties do better in strand region. Further, the combination of free energies with amino acid properties increased the correlation significantly. The present study demonstrates the importance of classifying the mutants based on secondary structure to the stability of proteins upon mutations.
Saraboji
K
K
Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600025, India.
Gromiha
M Michael
MM
Ponnuswamy
M N
MN
D000596:Amino Acids / Q000737:chemistry / Q000235:genetics*; D017122:Bacteriophage T4 / Q000201:enzymology; D030562:Databases, Protein; D042822:Genomic Instability; D006801:Humans; D006863:Hydrogen-Ion Concentration; D057927:Hydrophobic and Hydrophilic Interactions; D009113:Muramidase / Q000737:chemistry / Q000235:genetics*; D009154:Mutation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012997:Solvents; D013816:Thermodynamics
D000596:Amino Acids; D012997:Solvents; D009113:Muramidase