Inferring protein interactions from phylogenetic distance matrices.
Finding the interacting pairs of proteins between two different protein families whose members are known to interact is an important problem in molecular biology. We developed and tested an algorithm that finds optimal matches between two families of proteins by comparing their distance matrices. A distance matrix provides a measure of the sequence similarity of proteins within a family. Since the protein sets of interest may have dozens of proteins each, the use of an efficient approximate solution is necessary. Therefore the approach we have developed consists of a Metropolis Monte Carlo optimization algorithm which explores the search space of possible matches between two distance matrices. We demonstrate that by using this algorithm we are able to accurately match chemokines and chemokine-receptors as well as the tgfbeta family of ligands and their receptors.
Gertz
Jason
J
Department of Mathematics, 310 Malott Hall, Cornell University, Ithaca, NY 14853-4201, USA.
Elfond
Georgiy
G
Shustrova
Anna
A
Weisinger
Matt
M
Pellegrini
Matteo
M
Cokus
Shawn
S
Rothschild
Bruce
B
D000465:Algorithms; D000595:Amino Acid Sequence; D001665:Binding Sites; D018925:Chemokines / Q000737:chemistry / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods*; D016000:Cluster Analysis; D017124:Conserved Sequence; D020869:Gene Expression Profiling / Q000379:methods*; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D010802:Phylogeny; D011485:Protein Binding / Q000235:genetics; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D019707:Receptors, Chemokine / Q000737:chemistry / Q000235:genetics; D018125:Receptors, Transforming Growth Factor beta / Q000737:chemistry / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D016212:Transforming Growth Factor beta / Q000737:chemistry / Q000235:genetics
D018925:Chemokines; D011506:Proteins; D019707:Receptors, Chemokine; D018125:Receptors, Transforming Growth Factor beta; D016212:Transforming Growth Factor beta