TY - GEN
T1 - Multiscale characterization of macromolecular dynamics
T2 - Conference on Extreme Science and Engineering Discovery Environment, XSEDE 2013
AU - Rohrdanz, Mary A.
AU - Zheng, Wenwei
AU - Lambeth, Bradley
AU - Clementi, Cecilia
N1 - Copyright:
Copyright 2013 Elsevier B.V., All rights reserved.
PY - 2013
Y1 - 2013
N2 - Photoactive yellow protein was first discovered in Halorho- dospira halophilia, causing the bacterium to flee potentially DNA-damaging light, and serves as a model system for signaling proteins. Upon absorption of a blue photon, PYP's chromophore undergoes a trans-to-cis isomerization that disrupts the hydrogen bond network in the core of the protein, resulting in a large conformational change and transformation into the signaling state. Because of the timescales involved, conventional molecular dynamics simulation of this system is practically impossible. In addition, due to the short signaling state lifetime, experimental determination of the signaling-state structure is also challenging. Here we use a combination of tools we have developed: A coarse-grain model [4], an all-atom reconstruction technique [5], locally scaled diffusion maps [9], and our most recent technique diffusion map-directed molecular dynamics [14], to explore the elusive structure of the signaling state of PYP.
AB - Photoactive yellow protein was first discovered in Halorho- dospira halophilia, causing the bacterium to flee potentially DNA-damaging light, and serves as a model system for signaling proteins. Upon absorption of a blue photon, PYP's chromophore undergoes a trans-to-cis isomerization that disrupts the hydrogen bond network in the core of the protein, resulting in a large conformational change and transformation into the signaling state. Because of the timescales involved, conventional molecular dynamics simulation of this system is practically impossible. In addition, due to the short signaling state lifetime, experimental determination of the signaling-state structure is also challenging. Here we use a combination of tools we have developed: A coarse-grain model [4], an all-atom reconstruction technique [5], locally scaled diffusion maps [9], and our most recent technique diffusion map-directed molecular dynamics [14], to explore the elusive structure of the signaling state of PYP.
KW - Molecular dynamics
KW - Proteins
UR - http://www.scopus.com/inward/record.url?scp=84882418413&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84882418413&partnerID=8YFLogxK
U2 - 10.1145/2484762.2484836
DO - 10.1145/2484762.2484836
M3 - Conference contribution
AN - SCOPUS:84882418413
SN - 9781450321709
T3 - ACM International Conference Proceeding Series
BT - Proceedings of the XSEDE 2013 Conference
Y2 - 22 July 2013 through 25 July 2013
ER -