Analysis of conserved hydrophobic cores in proteins and supramolecular complexes.
The conserved hydrophobic core is an important feature of a family of protein domains. We suggest a procedure for finding and the analysis of conserved hydrophobic cores. The procedure is based on using an original program called CluD (http://monkey.belozersky.msu.ru/CluD/cgi-bin/hftri.pl). Conserved hydrophobic cores of several families including homeodomains and interlock-containing domains are described. Hydrophobic clusters on some protein-DNA and protein-protein interfaces were also analyzed.
Karyagina
Anna
A
Gamaleya Institute of Epidemiology and Microbiology, Gamaleya Str. 18, Moscow 123098, Russia. akaryagina@rambler.ru
Ershova
Anna
A
Titov
Mikhail
M
Olovnikov
Ivan
I
Aksianov
Evgeniy
E
Ryazanova
Alexandra
A
Kubareva
Elena
E
Spirin
Sergei
S
Alexeevski
Andrei
A
D001665:Binding Sites; D016000:Cluster Analysis; D017124:Conserved Sequence; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D018398:Homeodomain Proteins / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D046911:Macromolecular Substances / Q000737:chemistry; D008956:Models, Chemical; D008958:Models, Molecular; D010363:Pattern Recognition, Automated / Q000379:methods; D011485:Protein Binding; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid
D004268:DNA-Binding Proteins; D018398:Homeodomain Proteins; D046911:Macromolecular Substances; D004247:DNA