Importance of surrounding residues for protein stability of partially buried mutations.
For understanding the factors influencing protein stability, we have analyzed the relationship between changes in protein stability caused by partially buried mutations and changes in 48 physico-chemical, energetic and conformational properties of amino acid residues. Multiple regression equations were derived to predict the stability of protein mutants and the efficiency of the method has been verified with both back-check and jack-knife tests. We observed a good agreement between experimental and computed stabilities. Further, we have analyzed the effect of sequence window length from 1 to 12 residues on each side of the mutated residue to include the sequence information for predicting protein stability and we found that the preferred window length for obtaining the highest correlation is different for each secondary structure; the preferred window length for helical, strand and coil mutations are, respectively, 0, 9 and 4 residues on both sides of the mutant residues. However, all the secondary structures have significant correlation for a window length of one residue on each side of the mutant position, implying the role of short-range interactions. Extraction of surrounding residue information for various distances (3 to 20A) around the mutant position showed the highest correlation at 8A, 6A and 7A, respectively, for mutations in helical, strand and coil segments. Overall, the information about the surrounding residues within the sphere of 7 to 8A, may explain better the stability in all subsets of partially buried mutations implying that this distance is sufficient to accommodate the residues influenced by major intramolecular interactions for the stability of protein structures.
Gromiha
M M
MM
RIKEN Tsukuba Institute, The Institute of Physical and Chemical Research, Ibaraki, Japan.
Oobatake
M
M
Kono
H
H
Uedaira
H
H
Sarai
A
A
D000596:Amino Acids / Q000737:chemistry; D016208:Databases, Factual; D015233:Models, Statistical; D009154:Mutation; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D012984:Software; D013816:Thermodynamics; D014867:Water / Q000378:metabolism
D000596:Amino Acids; D011506:Proteins; D014867:Water