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The Role of Water in Molecular Recognition and Hydrophobic Assembly

Aneesur Rahman Lecture in Computational Molecular Science
Professor Bruce J. Berne, Columbia University
October 31, 2013 11:00AM to 12:00PM
Building 402, Auditorium
Professor Bruce J. Berne will present “The Role of Water in Molecular Recognition and Hydrophobic Assembly” at the Rahman Lecture Thursday, October 31, at 11 a.m. in the Building 402 Auditorium.

Shuttle Service Provided

Continuous shuttle service will be provided starting at 10:15 a.m. with first stop at 201, then 212, 202, 240, 223, 203, 208, 200, 205 and 362. Return trips following lecture.


A model of protein–ligand binding kinetics, in which slow solvent dynamics results from hydrophobic drying transitions, is investigated. Molecular dynamics simulations show that solvent in the hydrophobic receptor pocket can fluctuate between wet and dry states with lifetimes in each state that are long enough for the extraction of a separate potentials of mean force for the wet and dry states and the rate constants for wet-to-dry transitions. We present a diffusive surface-hopping model that is represented by a 2D Markovian master equation.

One dimension is the standard re- action coordinate, the ligand–pocket separation, and the other is the solvent state in the region between ligand and binding pocket which specifies whether it is wet or dry. When the rate constants for the wet to dry transitions this theory collapses into the usual Smoluchowsky description of diffusion controlled reactions. In our model, the ligand diffuses on a dynamic free-energy surface which undergoes kinetic transitions between the wet and dry states. The model yields good agreement with results from explicit solvent molecular dynamics simulation and an improved description of the kinetics of hydrophobic assembly.

Furthermore, it is consistent with a “non-Markovian Brownian theory” for the ligand–pocket separation coordinate alone. Molecular dynamics, stochastic dynamics and various sampling methods are used in these simulations. Aneesur Rahman pioneered many of these techniques over forty years ago.

About the Lectureship

The Aneesur Rahman Lecture in Computational Molecular Science is an annual event featuring the most innovative and thought-provoking speakers. True to its namesake, the lectureship will present before the community new ideas and innovative methods of research.

About Bruce J. Berne, Ph.D.

Bruce J. Berne received his Bachelors of Science in Chemistry from The City University of New York (CUNY) in 1961 and his Ph.D. in Chemical Physics from the University of Chicago in 1964. He was a NATO postdoctoral fellow at the Universite Libre de Bruxelles in 1965 with Ilya Prigogine working on problems in the theory of irreversible processes.

Berne joined the faculty of Columbia University in 1966 receiving tenure in 1969. He was a Guggenheim Fellow at the University of Tel Aviv, Israel in 1973, Miller Institute Professor at the University of California, Berkeley in 1994 and Humboldt researcher at the University of Augsburg, Germany in 1992.

His major early contribution was to show how to use memory functions to model the non-Markovian dynamics of liquids. Shortly after arriving at Columbia he and his student George Harp developed the methodology for and performed the first molecular dynamics simulation ever done on a molecular liquid.