RIP 1.1 – Accelerated Molecular Dynamics

RIP 1.1


RIP (Rotamerically Induced Perturbation) generates local perturbations of residues in a protein. In picoseconds of a molecular-dynamics (MD) simulation, RIP generates motions that reveal certain mechanical properties of a protein. 1) Flexibility Analysis: using larger perturbations, RIP can induce several ?ngstroms of conformational change in loops, identifying potential allosteric effectors. E.g. on the right is the RIP perturbation on TRP-83 in the Ligand-Binding Domain of the Estrogen Receptor, which produces a dramatic 10 ? motion of the ligand-binding Helix 12 in a 10 ps simulation. 2) Coupling Analysis: using small RIP perturbations, residues that interact strongly can be identified. Analysis of the patterns of strongly interacting residues allows an analysis of tertiary structure dynamics.



Bosco K. Ho







Reference for Flexibility Analysis: “Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations” by Bosco K. Ho and David A. Agard. PLoS Comput Biol (2009) 5(4): e1000343.

Reference for Coupling Analysis: “Conserved tertiary couplings stabilize elements in the PDZ fold, leading to characteristic patterns of domain conformational flexibility“by Bosco K. Ho and David A. Agard. Protein Science (2010) 19:398-411.

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