This subproject is one of many research subprojects utilizing theresources provided by a Center grant funded by NIH/NCRR. The subproject andinvestigator (PI) may have received primary funding from another NIH source,and thus could be represented in other CRISP entries. The institution listed isfor the Center, which is not necessarily the institution for the investigator.The recent resurgence of interest in the unfolded state is partly motivated by the development of NMR methods that are capable of providing site-resolved structural information. The measurements indicate that unfolded proteins have far richer structural diversity than earlier believed. These recent works seem at odds with classic studies by Tanford and coworkers which demonstrate using hydrodynamic methods that the global dimensions of denatured proteins exhibit the size dependence expected for self-avoiding random coil polymers. We have developed a statistical coil model for the unfolded state which successfully reproduces the global dimensions and the local structure of proteins in the denatured state thereby resolving the reconciliation problem. We generate an unfolded state ensemble using a statistical coil model that is based on backbone conformational frequencies in a coil library, a restricted subset of the protein data bank, and is subjected to excluded volume constraints. The model successfully reproduces both the global dimensions (radius of gyration) and local conformational preferences (NMR residual dipolar couplings (RDCs)) of the chemically denatured state for a variety of proteins. The most stretched members of the ensemble of unfolded state structures contribute most to the RDC signal, while the sign of the couplings follows from the preponderance of polyproline II and beta conformers in the coil library. The agreement with the NMR data improves when the backbone conformational preferences include correlations with the chemical and conformational identity of neighboring residues. Using the computational resources available on teragrid we can run multiple short trajectories of solvated conformations. These simulations will yield a thermalized equilibriated ensemble of unfolded states which will then be made availbale to the biophysics community for various thermodynamic and kinetic studies.In addition, we can also generate realistic unfolded starting configurations for simulations. Thus, a physically realistic model for the unfolded state should save computational resources while increasing accuracy.
Showing the most recent 10 out of 292 publications
