Influence of medium- and long-range interactions in different folding types of globular proteins.
Recognition of protein fold from amino acid sequence is a challenging task. The structure and stability of proteins from different fold are mainly dictated by inter-residue interactions. In our earlier work, we have successfully used the medium- and long-range contacts for predicting the protein folding rates, discriminating globular and membrane proteins and for distinguishing protein structural classes. In this work, we analyze the role of inter-residue interactions in commonly occurring folds of globular proteins in order to understand their folding mechanisms. In the medium-range contacts, the globin fold and four-helical bundle proteins have more contacts than that of DNA-RNA fold although they all belong to all-alpha class. In long-range contacts, only the ribonuclease fold prefers 4-10 range and the other folding types prefer the range 21-30 in alpha/beta class proteins. Further, the preferred residues and residue pairs influenced by these different folds are discussed. The information about the preference of medium- and long-range contacts exhibited by the 20 amino acid residues can be effectively used to predict the folding type of each protein.
Kumarevel
T S
TS
National Institute of Advanced Industrial Science and Technology (AIST), Institute of Molecular and Cell Biology, Functional Nucleic Acids Group, Tsukuba Central 6, 1-1 Higashi, Tsukuba Science City, Ibaraki, Japan. kumarevel-thirumananseri@aist.go.jp
Gromiha
M Michael
MM
Selvaraj
S
S
Gayatri
K
K
Kumar
P K R
PK
D000596:Amino Acids / Q000032:analysis* / Q000737:chemistry; D016208:Databases, Factual; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
D000596:Amino Acids; D011506:Proteins