Universal positions in globular proteins.
The description of globular protein structures as an ensemble of contiguous 'closed loops' or 'tightened end fragments' reveals fold elements crucial for the formation of stable structures and for navigating the very process of protein folding. These are the ends of the loops, which are spatially close to each other but are situated apart in the polypeptide chain by 25-30 residues. They also correlate with the locations of highly conserved hydrophobic residues (referred to as topohydrophobic), in a structural alignment of the members of a protein family. This study analysed these positions in 111 representatives of different protein folds, and then carried out dynamic Monte Carlo simulations of the first steps of the folding process, aimed at predicting the origins of the assembling folds. The simulations demonstrated that there is an obvious trend for certain sets of residues, named 'mostly interacting residues', to be buried at the early stages of the folding process. Location of these residues at the loop ends and correlation with topohydrophobic positions are demonstrated, thereby giving a route to simulations of the protein folding process.
Papandreou
Nikolaos
N
Laboratory of Genetics, Agricultural University of Athens, Greece. papandre@aua.gr
Berezovsky
Igor N
IN
Lopes
Anne
A
Eliopoulos
Elias
E
Chomilier
Jacques
J
D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid
D011506:Proteins