Tamara Frembgen-Kesner

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Successful modeling of the processes of protein folding and aggregation may ultimately require accurate descriptions of proteins' diffusive characteristics, which are expected to be influenced by hydrodynamic effects; a comprehensive study of the diffusion and folding of 11 model proteins with an established simulation model extended to include hydrodynamic(More)
Theory and computation have long been used to rationalize the experimental association rate constants of protein-protein complexes, and Brownian dynamics (BD) simulations, in particular, have been successful in reproducing the relative rate constants of wild-type and mutant protein pairs. Missing from previous BD studies of association kinetics, however,(More)
An increasing number of structural studies reveal alternative binding sites in protein receptors that become apparent only when an inhibitor binds, and correct prediction of these situations presents a significant challenge to computer-aided drug design efforts. A striking example is provided by recent crystal structures of the p38 MAP kinase, where a 10A(More)
Disordered Proteins (IDPs) Francois-Xavier Theillet,†,∇ Andres Binolfi,†,∇ Tamara Frembgen-Kesner,‡ Karan Hingorani, Mohona Sarkar, Ciara Kyne, Conggang Li, Peter B. Crowley, Lila Gierasch, Gary J. Pielak, Adrian H. Elcock,‡ Anne Gershenson, and Philipp Selenko*,† †Department of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of(More)
Ever since the pioneering work of Minton, it has been recognized that the highly crowded interior of biological cells has the potential to cause dramatic changes to both the kinetics and thermodynamics of protein folding and association events relative to behavior that might be observed in dilute solution conditions. One very productive way to explore the(More)
Recently, we reported the parametrization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for(More)
Understanding the intrinsic conformational preferences of amino acids and the extent to which they are modulated by neighboring residues is a key issue for developing predictive models of protein folding and stability. Here we present the results of 441 independent explicit-solvent MD simulations of all possible two-residue peptides that contain the 20(More)
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