Warning: file_get_contents(https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=27327045
&cmd=llinks): Failed to open stream: HTTP request failed! HTTP/1.1 429 Too Many Requests
in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 215
Warning: imagejpeg(C:\Inetpub\vhosts\kidney.de\httpdocs\phplern\27327045
.jpg): Failed to open stream: No such file or directory in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 117 Protein+Sci
2016 ; 25
(9
): 1659-71
Nephropedia Template TP
gab.com Text
Twit Text FOAVip
Twit Text #
English Wikipedia
Landscape of protein-small ligand binding modes
#MMPMID27327045
Kasahara K
; Kinoshita K
Protein Sci
2016[Sep]; 25
(9
): 1659-71
PMID27327045
show ga
Elucidating the mechanisms of specific small-molecule (ligand) recognition by
proteins is a long-standing conundrum. While the structures of these molecules,
proteins and ligands, have been extensively studied, protein-ligand interactions,
or binding modes, have not been comprehensively analyzed. Although methods for
assessing similarities of binding site structures have been extensively
developed, the methods for the computational treatment of binding modes have not
been well established. Here, we developed a computational method for encoding the
information about binding modes as graphs, and assessing their similarities. An
all-against-all comparison of 20,040 protein-ligand complexes provided the
landscape of the protein-ligand binding modes and its relationships with protein-
and chemical spaces. While similar proteins in the same SCOP Family tend to bind
relatively similar ligands with similar binding modes, the correlation between
ligand and binding similarities was not very high (R(2) ?=?0.443). We found many
pairs with novel relationships, in which two evolutionally distant proteins
recognize dissimilar ligands by similar binding modes (757,474 pairs out of
200,790,780 pairs were categorized into this relationship, in our dataset). In
addition, there were an abundance of pairs of homologous proteins binding to
similar ligands with different binding modes (68,217 pairs). Our results showed
that many interesting relationships between protein-ligand complexes are still
hidden in the structure database, and our new method for assessing binding mode
similarities is effective to find them.
free
free
free
