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.
:: MORE INFORMATION
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.