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Samuel Krimm |
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Vibrational Spectroscopic and Energy Function Studies of Protein Structure |
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Research Scientist |
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Ph.D., Princeton University |
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| Dept: Physics | ||||||||
| Office Address: 3303 Chemistry | ||||||||
| Phone: (734) 763-8081 | ||||||||
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Email: skrimm@umich.edu |
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| Our
research program has two main goals: developing infrared and Raman
spectroscopy as a rigorous technique for studying the three-dimensional
structures of peptides and proteins, and developing physically reliable
potential energy functions for studying the conformation and molecular
dynamics of biomacromolecules. The vibrational spectroscopic studies involve experimental determination of infrared and Raman spectra combined with normal mode calculations of expected vibrational frequencies. Our goal is to provide rigorous predictions of the spectra to be associated with any given structure. Since the reliability of a normal mode calculation is determined by the validity of the force field, we have devoted significant effort to developing such force fields. Our early work concentrated on empirically refined peptide force fields, and these have proven quite successful in analyzing the vibrational spectra of peptides, polypeptides and proteins. In an effort to develop conformation-dependent force fields, we have turned to the refinement of better molecular mechanics energy functions. We have found a method for converting spectroscopic force fields analytically into molecular mechanics energy functions. In this approach, we use ab initio structures, energies, and scaled force fields, and since this treatment preserves spectroscopic accuracy, we call these spectroscopically determined force fields (SDFF). This research involves ab initio computations, spectroscopic assignments, and development of optimum molecular mechanics functional forms. For the latter, we give special attention to detailed characterization of the electrostatics, including polarizability and conformational dependence of charges, to a proper physical description of hydrogen bonding, and to subtle structural properties of the peptide group. We work on peptides, polypeptides, and proteins. Problems are chosen for their inherent biological relevance as well as for how they can elucidate and advance the use of the techniques. |
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Representative Publications |
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Mannfors, B., Sundius, T., Palmo, K., Pietila, L.-O., and Krimm, S. "Spectroscopically Determined Force Fields for Macromolecules. 3. Alkene Chains" J. Mol. Struct. 521 (2000) 49-75. |
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