Theoretical Biophysics

The study of the mechanism of association and dissociation of macromolecules is important for many biological structures and processes, and some examples are the binding and dissociation of ligand to/from receptors, the recognition of ligands by their receptors or the recognition of DNA sequences by the DNA binding domains of regulatory proteins. These processes can be studied through molecular dynamics simulations with the addition of an external forces. This approach closely mimics the micromanipulation through atomic force microscopy or optical tweezers.

Selected Publications

Dissecting the molecular origins of protein-nucleic acid recognition: Hydrostatic pressure and molecular dynamics. Thomas W. Lynch, Dorina Kosztin, Mark A. McLean, Klaus Schulten, and Stephen G. Sligar. Biophysical Journal, 82:93-98, 2002.

Structural determinants of MscL gating studied by molecular dynamics simulations. Justin Gullingsrud, Dorina Kosztin, and Klaus Schulten. Biophysical Journal, 80:2074-2081, 2001.

Steered Molecular Dynamics Investigations of Protein Function. Barry Isralewitz, Jerome Baudry, Justin Gullingsrud, Dorina Kosztin, and Klaus Schulten. In Protein Flexibility and Folding Proceedings, 2000.

Probing the role of structural water in a duplex olygodeoxyribonucleotide containing a water-mimicking base analogue. D. Kosztin, R. Gumport and K. Schulten. Nucleic Acids Research, 27:3550--3556, 1999

Unbinding of retinoic acid from its receptor studied by Steered Molecular Dynamics. D. Kosztin, S. Izrailev and K. Schulten. Biophysical J., 76:188--197, 1999

Binding of the Estrogen Receptor to DNA: The Role of Waters. D. Kosztin, T. C. Bishop and K. Schulten. Biophysical J., 73:557--570, 1997

How hormone receptor--DNA binding affects nucleosomal DNA: The role of symmetry. T. C. Bishop, D. Kosztin, and K. Schulten. Biophysical J, 72:2056--2067, 1997

Steered molecular Dynamics. Sergei Izrailev, Sergey Stepaniants, Barry Isralewitz, Dorina Kosztin, Hui Lu, Ferenc Molnar, Willy Wriggers, and Klaus Schulten. In P. Deuflhard, J. Hermans, B. Leimkuhler, A. E. Mark, S. Reich, and R. D. Skeel, editors, Computational Molecular Dynamics: Challenges, Methods,Ideas, volume 4 of Lecture Notes in Computational Science and Engineering, pages 39--65, Springer-Verlag, Berlin, 1998.