Analysis of the differences in the folding kinetics of structurally homologous proteins based on predictions of the gross features of residue contacts.
It is a general notion that proteins with very similar three-dimensional structures would show very similar folding kinetics. However, recent studies reveal that the folding kinetic properties of some proteins contradict this thought (i.e., the members in a same protein family fold through different pathways). For example, it has been reported that some beta-proteins in the intracellular lipid-binding protein family fold through quite different pathways (Burns et al., Proteins 1998;33:107-118). Similar differences in folding kinetics are also observed in the members of the globin family (Nishimura et al., Nat Struct Biol 2000;7:679-686). In our study, we examine the possibility of predicting qualitative differences in folding kinetics of the intracellular lipid-binding proteins and two globin proteins (i.e., myoglobin and leghemoglobin). The problem is tackled by means of a contact map based on the average distance statistics between residues, the Average Distance Map (ADM), as constructed from sequence. The ADMs for the three proteins show overall similarity, but some local differences among maps are also observed. Our results demonstrate that some properties of the protein folding kinetics are consistent with local differences in the ADMs. We also discuss the general possibility of predicting folding kinetics from sequence information.
Ichimaru
Takehiro
T
Department of Chemistry and Bioscience, College of Industrial Technology, Kurashiki University of Science and the Arts, Kurashiki, Okayama, Japan.
Kikuchi
Takeshi
T
D002352:Carrier Proteins / Q000737:chemistry; D050556:Fatty Acid-Binding Proteins; D005914:Globins / Q000737:chemistry; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D009363:Neoplasm Proteins; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D018168:Receptors, Retinoic Acid / Q000737:chemistry
D002352:Carrier Proteins; D050556:Fatty Acid-Binding Proteins; D009363:Neoplasm Proteins; D011506:Proteins; D018168:Receptors, Retinoic Acid; D005914:Globins