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Simplified representation Fast Novel solvent model Extensible

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Poing. A dynamic model of protein folding. Simplified representation Fast Novel solvent model Extensible. Poing. Small hydrophilic sidechain. structure simplification. Backbone C-alpha. Protein backbone. Large hydrophobic sidechain. Poing. linear elastic springs. Poing.

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Presentation Transcript
slide1

Poing

A dynamic model of protein folding

  • Simplified representation
  • Fast
  • Novel solvent model
  • Extensible
slide2

Poing

Small hydrophilic sidechain

structure simplification

Backbone

C-alpha

Protein backbone

Large hydrophobic sidechain

slide3

Poing

linear elastic springs

slide4

Poing

Langevin dynamics is F = ma ... PLUS a model for solvent

a: acceleration

F: net force (sum of many forces)

γ: drag factor

v: current particle velocity

R: randomly distributed vector

m: particle mass

slide5

Poing

Secondary structure and hydrogen bonding

Solvent model leads tohydrophobic collapse

Sidechain size and shape

slide7

Phyre + Poing

HMM

ARNDLSLDLVCS…….

PSI-Blast

Hidden Markov Model DB of KNOWN STRUCTURES

HMM-HMM

matching

FINAL MODEL

POING: Synthesise from virtual ribosome.

Springs for constraints. Ab initio modelling

of missing regions.

Extract pairwise

distance constraints

slide8

Protein Folding Requires Crowd Control in a Simulated Cell.

Jefferys BR, Kelley LA and Sternberg MJE Journal of Molecular Biology (2010) Volume 397, Issue 5, 16 April 2010, Pages 1329-1338

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