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Simplified representation Fast Novel solvent model Extensible PowerPoint PPT Presentation


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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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Simplified representation Fast Novel solvent model Extensible

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Simplified representation fast novel solvent model extensible

Poing

A dynamic model of protein folding

  • Simplified representation

  • Fast

  • Novel solvent model

  • Extensible


Simplified representation fast novel solvent model extensible

Poing

Small hydrophilic sidechain

structure simplification

Backbone

C-alpha

Protein backbone

Large hydrophobic sidechain


Simplified representation fast novel solvent model extensible

Poing

linear elastic springs


Simplified representation fast novel solvent model extensible

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


Simplified representation fast novel solvent model extensible

Poing

Secondary structure and hydrogen bonding

Solvent model leads tohydrophobic collapse

Sidechain size and shape


Simplified representation fast novel solvent model extensible

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


Simplified representation fast novel solvent model extensible

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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