This training grant supports graduate students at UC Berkeley working in Molecular Biophysics, substantially increasing opportunities for training in this discipline, enhancing the training and research experiences of the students, and encouraging new students to enter this field. This training grant stimulates interactions across the campus by increasing interactions between disciplines, and provides important support for the Structural and Quantitative Biology seminar series, that exposes students to the latest work in the field. Coursework, mostly during the first two years of study, covers a combination of contemporary problems in molecular biophysics and the methods used to analyze systems at the molecular level. Trainees are diverse both in background and interest, so there is flexibility in the coursework required yet we expect them all to gain a thorough grounding in quantitative skills for analyzing the function of biological systems at the molecular level, including knowledge of methods for structure analysis, determining localization and interactions in cells;computational methods for data collection and reduction;and methods for genomic analysis and database utilization. Advanced courses in chemistry and molecular biology provide the basis for combining these to examine the molecular basis for biological behavior. Additional, more specialized courses focus on particular systems or methods. All trainees also take a course in the ethical conduct of research and participate in career development activities. Regular attendance at seminars (particularly the Structural and Quantitative Biology Series) is expected throughout the graduate career. Graduate students enter Molecular Biophysics through the Graduate Programs in Biophysics, Molecular &Cell Biology, or Chemistry. MCB and Biophysics students carry out three 10-week rotation projects in different labs and then choose one of these labs/mentors and begin their thesis work. Chemistry students select a research director during the first 8-10 weeks of their first semester after talking with several faculty and attending lab meetings and begin research shortly thereafter. By the summer of the first year, all students are in labs and have initiated their research projects. Research projects focus on the function of biological systems at the molecular level, particularly using physical measurements, including: structural methods to understand the function biomolecules (including their complexes and how complexes change during function), their spatial distribution and transport;and their mechanisms of action. There is a very broad representation of measurement methods, with exceptional facilities for x-ray diffraction, NMR, EM, computation, and single molecule spectroscopy and manipulation housed in Stanley Hall, home of the interdisciplinary California Institute for Quantitative Biology. Students bridging between labs and applying a combination of methods are given priority for support. This training program is producing students well trained in modern methodologies for biophysical measurements and the principles of their operation, and knowledgeable of contemporary problems in biology.

Public Health Relevance

This program produces doctoral level trainees who are well prepared for research endeavors in basic and applied biomedical research. During their training they learn the latest breakthroughs in mechanistic understanding of biological systems and the best tools for the study of the behavior of biomolecules at the most detailed level possible. The students are ready for careers in research in either academics or the biotechnology industry to apply studies of biological systems at the molecular level to improve human health.

National Institute of Health (NIH)
Institutional National Research Service Award (T32)
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Flicker, Paula F
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University of California Berkeley
Schools of Arts and Sciences
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Ball, K Aurelia; Wemmer, David E; Head-Gordon, Teresa (2014) Comparison of structure determination methods for intrinsically disordered amyloid-? peptides. J Phys Chem B 118:6405-16
Carr, Cody A Marcus; Klinman, Judith P (2014) Hydrogen tunneling in a prokaryotic lipoxygenase. Biochemistry 53:2212-4
Hu, Shenshen; Sharma, Sudhir C; Scouras, Alexander D et al. (2014) Extremely elevated room-temperature kinetic isotope effects quantify the critical role of barrier width in enzymatic C-H activation. J Am Chem Soc 136:8157-60
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Hu, Wenbing; Walters, Benjamin T; Kan, Zhong-Yuan et al. (2013) Stepwise protein folding at near amino acid resolution by hydrogen exchange and mass spectrometry. Proc Natl Acad Sci U S A 110:7684-9
Ball, K Aurelia; Phillips, Aaron H; Wemmer, David E et al. (2013) Differences in *-strand populations of monomeric A*40 and A*42. Biophys J 104:2714-24
Nagel, Zachary D; Cun, Shujian; Klinman, Judith P (2013) Identification of a long-range protein network that modulates active site dynamics in extremophilic alcohol dehydrogenases. J Biol Chem 288:14087-97
Sterling, Harry J; Cassou, Catherine A; Susa, Anna C et al. (2012) Electrothermal supercharging of proteins in native electrospray ionization. Anal Chem 84:3795-801

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