Computational Modelling Group

Seminar  13th December 2011 2 p.m.  85/2207

Analyzing biomacromolecular flexibility by constraint counting

Prof. Dr. Holger Gohlke
Heinrich-Heine-Universität Düsseldorf

Agent-Based Negotiation, AMBER, Bioinformatics, Biomedical, Biomolecular Organisation, Biomolecular simulations, C, C#, Complex Systems, Computer Science, Digital Economy, Economics, Emacs, FFT, Fortran, Gaussian, Gromacs, HECToR, HPCx, Iridis, Jaguar, Lattice Field Theory, Mathematica, Molecular Dynamics, Molecular Mechanics, Monte Carlo, MPI, Multi-physics, Multi-scale, Multigrid solvers, Multipole methods, Nanoscale Assemblies, NWCHEM, Onetep, Optimisation, Quantum Chemistry, Scientific Computing, Systems biology, Vim, Windows, Xmgrace
Chris-Kriton Skylaris

Professor. Dr. Holger Gohlke

Protein flexibility is important for a wide range of biological phenomena, such as enzymatic reaction and control, complex formation, and macromolecular stability.[1] In the case of protein-protein or protein-ligand complex formation, flexibility of the binding partners provides the origin for their plasticity, enabling them to conformationally adapt to each other. Equally important as flexibility per se are changes in the flexibility upon complex formation. Thus, analyzing flexibility and modeling plasticity of macromolecules without having to do expensive calculations is of great importance. Here, flexibility concepts grounded in rigidity theory are applied and further developed to investigate flexibility changes upon macromolecular association,[2] to link protein thermostability and rigidity,[3][4] and to efficiently estimate changes in receptor vibrational entropy upon complex formation.

[1] Ahmed, A.; Kazemi, S.; Gohlke, H., Frontiers Drug Des. Discov. 2007, 3, 455-476.

[2] Gohlke, H.; Kuhn, L. A.; Case, D. A., Proteins 2004, 56, 322-337.

[3] Radestock, S.; Gohlke, H., Eng. Life Sci. 2008, 8, 507-522.

[4] Radestock, S.; Gohlke, H., Proteins 2011, 79, 1089-1108.