Multiscale characterization of macromolecular dynamics

Application to photoacitve yellow protein

Mary A. Rohrdanz, Wenwei Zheng, Bradley Lambeth, Cecilia Clementi

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

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.

Original languageEnglish (US)
Title of host publicationProceedings of the XSEDE 2013 Conference
Subtitle of host publicationGateway to Discovery
DOIs
StatePublished - Aug 26 2013
Externally publishedYes
EventConference on Extreme Science and Engineering Discovery Environment, XSEDE 2013 - San Diego, CA, United States
Duration: Jul 22 2013Jul 25 2013

Other

OtherConference on Extreme Science and Engineering Discovery Environment, XSEDE 2013
CountryUnited States
CitySan Diego, CA
Period7/22/137/25/13

Fingerprint

Proteins
Molecular dynamics
Chromophores
Isomerization
Bacteria
Hydrogen bonds
DNA
Photons
Atoms
Computer simulation

Keywords

  • Molecular dynamics
  • Proteins

ASJC Scopus subject areas

  • Human-Computer Interaction
  • Computer Networks and Communications
  • Computer Vision and Pattern Recognition
  • Software

Cite this

Rohrdanz, M. A., Zheng, W., Lambeth, B., & Clementi, C. (2013). Multiscale characterization of macromolecular dynamics: Application to photoacitve yellow protein. In Proceedings of the XSEDE 2013 Conference: Gateway to Discovery [4] https://doi.org/10.1145/2484762.2484836

Multiscale characterization of macromolecular dynamics : Application to photoacitve yellow protein. / Rohrdanz, Mary A.; Zheng, Wenwei; Lambeth, Bradley; Clementi, Cecilia.

Proceedings of the XSEDE 2013 Conference: Gateway to Discovery. 2013. 4.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Rohrdanz, MA, Zheng, W, Lambeth, B & Clementi, C 2013, Multiscale characterization of macromolecular dynamics: Application to photoacitve yellow protein. in Proceedings of the XSEDE 2013 Conference: Gateway to Discovery., 4, Conference on Extreme Science and Engineering Discovery Environment, XSEDE 2013, San Diego, CA, United States, 7/22/13. https://doi.org/10.1145/2484762.2484836
Rohrdanz MA, Zheng W, Lambeth B, Clementi C. Multiscale characterization of macromolecular dynamics: Application to photoacitve yellow protein. In Proceedings of the XSEDE 2013 Conference: Gateway to Discovery. 2013. 4 https://doi.org/10.1145/2484762.2484836
Rohrdanz, Mary A. ; Zheng, Wenwei ; Lambeth, Bradley ; Clementi, Cecilia. / Multiscale characterization of macromolecular dynamics : Application to photoacitve yellow protein. Proceedings of the XSEDE 2013 Conference: Gateway to Discovery. 2013.
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