TY - JOUR
T1 - Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites
AU - Bowman, Gregory R.
AU - Geissler, Phillip L.
PY - 2012/7/17
Y1 - 2012/7/17
N2 - Cryptic allosteric sites - transient pockets in a folded protein that are invisible to conventional experiments but can alter enzymatic activity via allosteric communication with the active site - are a promising opportunity for facilitating drug design by greatly expanding the repertoire of available drug targets. Unfortunately, identifying these sites is difficult, typically requiring resource-intensive screening of large libraries of small molecules. Here, we demonstrate that Markov state models built from extensive computer simulations (totaling hundreds of microseconds of dynamics) can identify prospective cryptic sites from the equilibrium fluctuations of three medically relevant proteins - β-lactamase, interleukin- 2, and RNase H - even in the absence of any ligand. As in previous studies, our methods reveal a surprising variety of conformations - including bound-like configurations - that implies a role for conformational selection in ligand binding. Moreover, our analyses lead to a number of unique insights. First, direct comparison of simulations with and without the ligand reveals that there is still an important role for an induced fit during ligand binding to cryptic sites and suggests new conformations for docking. Second, correlations between amino acid sidechains can convey allosteric signals even in the absence of substantial backbone motions. Most importantly, our extensive sampling reveals a multitude of potential cryptic sites - consisting of transient pockets coupled to the active site - even in a single protein. Based on these observations, we propose that cryptic allosteric sites may be even more ubiquitous than previously thought and that our methods should be a valuable means of guiding the search for such sites.
AB - Cryptic allosteric sites - transient pockets in a folded protein that are invisible to conventional experiments but can alter enzymatic activity via allosteric communication with the active site - are a promising opportunity for facilitating drug design by greatly expanding the repertoire of available drug targets. Unfortunately, identifying these sites is difficult, typically requiring resource-intensive screening of large libraries of small molecules. Here, we demonstrate that Markov state models built from extensive computer simulations (totaling hundreds of microseconds of dynamics) can identify prospective cryptic sites from the equilibrium fluctuations of three medically relevant proteins - β-lactamase, interleukin- 2, and RNase H - even in the absence of any ligand. As in previous studies, our methods reveal a surprising variety of conformations - including bound-like configurations - that implies a role for conformational selection in ligand binding. Moreover, our analyses lead to a number of unique insights. First, direct comparison of simulations with and without the ligand reveals that there is still an important role for an induced fit during ligand binding to cryptic sites and suggests new conformations for docking. Second, correlations between amino acid sidechains can convey allosteric signals even in the absence of substantial backbone motions. Most importantly, our extensive sampling reveals a multitude of potential cryptic sites - consisting of transient pockets coupled to the active site - even in a single protein. Based on these observations, we propose that cryptic allosteric sites may be even more ubiquitous than previously thought and that our methods should be a valuable means of guiding the search for such sites.
KW - Molecular dynamics
KW - Native state dynamics
UR - http://www.scopus.com/inward/record.url?scp=84863939894&partnerID=8YFLogxK
U2 - 10.1073/pnas.1209309109
DO - 10.1073/pnas.1209309109
M3 - Article
C2 - 22753506
AN - SCOPUS:84863939894
VL - 109
SP - 11681
EP - 11686
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
SN - 0027-8424
IS - 29
ER -