Sequence or structure: using bioinformatics and homology modeling to understand functional relationships in cAMP/cGMP binding domains.
The relationship between sequence, structure, and function is examined by comparing nineteen cyclic nucleotide monophosphate binding domains of known structure from six different functional families. Comparisons are made by structure and sequence alignment and through the generation of 3610 homology models. This analysis suggests there are only weak relationships between functional families, sequence, and/or structure. However, we have identified that for cyclic nucleotide monophosphate binding domains privileged template structures occur for homology modeling. The existence of privileged template structures, capable of creating accurate modeling for a broad family of proteins, may lead to improved homology modeling protocols.
LaFranzo
Natalie A
NA
Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63110, USA.
Strulson
Matthew K
MK
Yanker
Dawn M
DM
Dang
Luke T
LT
Maurer
Joshua A
JA
D000595:Amino Acid Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D000242:Cyclic AMP / Q000378:metabolism*; D006152:Cyclic GMP / Q000378:metabolism*; D008969:Molecular Sequence Data; D015394:Molecular Structure; D054730:Protein Interaction Domains and Motifs / Q000235:genetics / Q000502:physiology; D017386:Sequence Homology, Amino Acid
D000242:Cyclic AMP; D006152:Cyclic GMP