Analyzing dynamical simulations of intrinsically disordered proteins using spectral clustering

Joshua L. Phillips, Edmond Y Lau, Michael E. Colvin, Shawn Newsam

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

4 Citations (Scopus)

Abstract

Continuing improvements in algorithms and computer speeds promise that an increasing number of biomolecular phenomena can be simulated by molecular dynamics to produce accurate "trajectories" of their molecular motions on the nanosecond to microsecond time scale. An important target for such simulations will be non-equilibrium biochemical processes, such as protein folding, but existing tools for analyzing molecular dynamics trajectories are not well suited to non-equilibrium processes and progress will require improvements in tools for classifying the range and types of dynamics exhibited by these systems. An extreme example of a non-equilibrium biochemical process is the function of "intrinsically disordered" proteins - proteins that function without ever folding into a unique structure. In this paper, we demonstrate the use of spectral clustering methods to analyze the data produced from simulations of several forms from one class of intrinsically disordered proteins, the phenylalanine-glycine nucleoporins (FG-Nups). We explain why such methods are well-suited for the data produced by our simulations and show that clustering methods provide a direct, quantitative measure of how effectively single simulations independently sample regions of structural phase space. Moreover, our clustering results show distinct dynamical behavior in different forms of the FGNups, which may provide insights into their biological function.

Original languageEnglish (US)
Title of host publicationProceedings - 2008 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW
Pages17-24
Number of pages8
DOIs
StatePublished - 2008
Externally publishedYes
Event2008 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW - Philadelphia, PA, United States
Duration: Nov 3 2008Nov 5 2008

Other

Other2008 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW
CountryUnited States
CityPhiladelphia, PA
Period11/3/0811/5/08

Fingerprint

Intrinsically Disordered Proteins
Biochemical Phenomena
Cluster Analysis
Molecular Dynamics Simulation
Proteins
Molecular dynamics
Trajectories
Nuclear Pore Complex Proteins
Protein folding
Protein Folding
Phenylalanine
Glycine
Amino acids

ASJC Scopus subject areas

  • Molecular Biology
  • Information Systems
  • Biomedical Engineering

Cite this

Phillips, J. L., Lau, E. Y., Colvin, M. E., & Newsam, S. (2008). Analyzing dynamical simulations of intrinsically disordered proteins using spectral clustering. In Proceedings - 2008 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW (pp. 17-24). [4686204] https://doi.org/10.1109/BIBMW.2008.4686204

Analyzing dynamical simulations of intrinsically disordered proteins using spectral clustering. / Phillips, Joshua L.; Lau, Edmond Y; Colvin, Michael E.; Newsam, Shawn.

Proceedings - 2008 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW. 2008. p. 17-24 4686204.

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

Phillips, JL, Lau, EY, Colvin, ME & Newsam, S 2008, Analyzing dynamical simulations of intrinsically disordered proteins using spectral clustering. in Proceedings - 2008 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW., 4686204, pp. 17-24, 2008 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW, Philadelphia, PA, United States, 11/3/08. https://doi.org/10.1109/BIBMW.2008.4686204
Phillips JL, Lau EY, Colvin ME, Newsam S. Analyzing dynamical simulations of intrinsically disordered proteins using spectral clustering. In Proceedings - 2008 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW. 2008. p. 17-24. 4686204 https://doi.org/10.1109/BIBMW.2008.4686204
Phillips, Joshua L. ; Lau, Edmond Y ; Colvin, Michael E. ; Newsam, Shawn. / Analyzing dynamical simulations of intrinsically disordered proteins using spectral clustering. Proceedings - 2008 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW. 2008. pp. 17-24
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