This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. We request resources to enable significantly more realistic QM-MM computations that aim to explore the extremely rugged electrostatic landscape of proteins through a detailed fundamental understanding of two phenomena that are widely exploited to study protein structure and dynamics: tryptophan (Trp) fluorescence quenching (by electron transfer from the excited state) and tryptophan fluorescence wavelength shifts due to hydration of the large excited state dipole. Particular focus during the next three years will be on (1) understanding ultrafast (0.5 -100 ps) fluorescence intensity decay (quenching) and wavelength shift experiments on proteins, (2) the spectacular fluctuation of quenching rates seen in single-molecule fluorescence of proteins, and (3) the underlying mechanisms of quenching variation used to monitor protein folding. These are areas of cutting edge experimental work. The project builds on 9 previous years of NSF support for mostly computational work that led to unprecedented progress in understanding Trp fluorescence wavelength variability in proteins using electrostatics, and to unprecedented progress in understanding of the previously unexplained--but widely exploited--Trp fluorescence intensity changes accompanying changes in protein structure. This work has recently been funded by NSF (NSF Proposal ID: 0847047) for the period Aug 2009-July 2012. Our recent ab initio computations of realistic electron transfer coupling elements during dynamics simulations led unexpectedly to an understanding of why wavelength and quenching are often strongly coupled and correlated. With the aid of the proposed multiple ns-scale simulations, the project is now immediately in a position to make insightful contributions to the contested notion that time resolved wavelength shifts speak solely to solvation dynamics, rather than a mixture of solvation dynamics and long term heterogeneity in protein conformation. This is particularly relevant to items (1) and (2) above. A constant theme of our work has shown the supreme importance of the enormous local electric field strength and direction in determining fluorescence behavior in proteins. Continued effort in these areas is encouraged by the emerging view that the catalytic power of enzymes is largely due to a specifically oriented, preorganized electrostatic environment, whose energy may come from reduction in folding energy. A constant theme from the Callis group has been that an ordered electrostatic environment coupled with large fluctuations is precisely what determines whether fluorescence will be strong or weak, and whether its average wavelength will be short or long. This meshes perfectly with the exciting recent observation by Marcus and others that the temporal behavior of fluctuations in electrostatic field is in common with that of other properties of proteins over the time scale of biological importance (milliseconds to seconds). Two students and a postdoctoral associate will work on subprojects entitled: (A) QM-MM simulations examining the relationship of solvent relaxation and heterogeneity in ultrafast TDSS measurements, and (B) Prediction of tryptophan fluorescence intensities during folding of the villin headpiece. The PI requests 500, 000 SU.

National Institute of Health (NIH)
National Center for Research Resources (NCRR)
Biotechnology Resource Grants (P41)
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Carnegie-Mellon University
Biostatistics & Other Math Sci
Schools of Arts and Sciences
United States
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