个人简介

Professor in Molecular and Cell Biology, Chemistry, and Physics, University of California, Berkeley (1998 - present). Born 1951, Peru; B.S. Universidad Peruana Cayetano Heredia, M.S. Universidad Nacional Mayor de San Marcos, Ph.D. University of California, Berkeley; Kellogg Foundation Scholarship during the Master in Biochemistry (1973-1975); Fullbright Commission and Institute of International Education Fellow (1975-1976); Abraham Rosenberg Scholarship, University of California, Berkeley (1975-1976); Research Assistant, University of California, Berkeley (1976-1981); Postdoctoral Fellow, Lawrence Berkeley Laboratory, University of California, Berkely (1981-1982); Assistant Professor, Department of Chemistry, University of New Mexico (1982-1986); Searle Scholar (1984); Alfred P. Sloan Fellow (1985); Associate Professor, Department of Chemistry, University of New Mexico (1986-1989); Presidential Lecturer in Chemistry, University of New Mexico (1986); State of New Mexico Eminent Scholar (1989); Professor of Chemistry, Department of Chemistry, University of New Mexico (1989-1990); Professor of Chemistry and Member of the Institute of Molecular Biology, University of Oregon, Eugene, Oregon (1991-1998); (1994-1998) Howard Hughes Medical Institute Investigator; Elected Fellow of the American Physical Society (1995); Member of the Science Advisory Board of the Searle Scholars Program (1997-2000); Howard Hughes Medical Institute Investigator (2000).

研究领域

Biophysical Chemistry -- Scanning Force Microscope Our research is focused on the structural characterization of nucleo-protein assemblies. The structure of chromatin and the global structure of protein-nucleic acid complexes relevant to the molecular mechanisms of control of transcription in prokaryotes are investigated using high resolution scanning force microscopy (SFM). This microscope, also known as Atomic Force Microscope (AFM) works by scanning a tip over the sample to sense the topography of the surface, thus functioning in much the same way than old record players. In addition, we are studying the elastic response of long linear polymers, the forces responsible for maintaining the tertiary structure of proteins, and the mechanical properties of molecular motors, using methods of single molecule manipulation such as laser tweezers and the SFM. Our laboratory is involved in the study of the structural basis of protein-DNA interactions and their relevance in the processes of control of gene expression. In prokaryotes, and especially in eukaryotes, replication and transcription regulation involve the interaction of many specialized protein factors at regulator locations on the sequence to ensure correct sequence recognition, initiation, processivity, fidelity, and kinetic control. We wish to understand the multiple structural, spatial, and functional relationships among these regulatory factors. We are using the SFM as a high resolution tool to image initiation and elongation transcription complexes of E. coli RNA polymerase to characterize the spatial relationships between the enzyme and the DNA template. We are also beginning to investigate what structural changes are negotiated between RNA polymerase and chromatin during transcription. To this end, we are using the SFM to image complexes of nucleosome-containing DNA fragments carrying a promoter and a terminator upstream and downstream of the nucleosome positioning sequence, respectively. We plan to compare the behavior of various prokaryotic and eukaryotic polymerases as they transcribe through the nucleosome, to investigate whether transcription through a nucleosome is an inherent property of the core particle, or a property of each enzyme itself, and to characterize various intermediates of the translocation process. Our laboratory is also working actively in the development of methods of single-molecule manipulation, including the use of SFM cantilevers, optical or laser tweezers, and magnetic beads to investigate the mechanical properties of macromolecules. In one project, we first tether a single protein molecule of T-4 lysozyme between a surface and the end of an SFM cantilever. We can then separate the surfaces in a controlled fashion to induce the mechanical unfolding of the molecule to characterize the nature, range, and strength of the forces that maintain its three-dimensional structure. Our objective is to carry out the unfolding of the molecule at equilibrium so as to obtain the potential energy function of the molecule as a function of the mechanical extension. This function represents the most complete description of the folded state of the protein. We plan to investigate how external conditions in the medium, i.e. temperature, denaturant concentration, etc., or point-directed mutations affect the shape of the potential energy function. Finally, our laboratory is also engaged in the study of DNA-binding molecular motors (RNA polymerase, DNA polymerase, etc.) using optical tweezers to investigate the dynamics of these molecules during translocation, as well as the effect of external force load and nucleotide tri-phosphate concentration on their power and force generation. In parallel, we are developing both microscopic (chemical ratchet-type) and phenomenological models of molecular motors which will be tested experimentally. We believe that single molecule experiments can provide a unique look into the molecular mechanisms responsible for the mechano-chemical conversion process in these protein machines.

Biophysical Chemistry -- Scanning Force Microscope Our research is focused on the structural characterization of nucleo-protein assemblies. The structure of chromatin and the global structure of protein-nucleic acid complexes relevant to the molecular mechanisms of control of transcription in prokaryotes are investigated using high resolution scanning force microscopy (SFM). This microscope, also known as Atomic Force Microscope (AFM) works by scanning a tip over the sample to sense the topography of the surface, thus functioning in much the same way than old record players. In addition, we are studying the elastic response of long linear polymers, the forces responsible for maintaining the tertiary structure of proteins, and the mechanical properties of molecular motors, using methods of single molecule manipulation such as laser tweezers and the SFM. Our laboratory is involved in the study of the structural basis of protein-DNA interactions and their relevance in the processes of control of gene expression. In prokaryotes, and especially in eukaryotes, replication and transcription regulation involve the interaction of many specialized protein factors at regulator locations on the sequence to ensure correct sequence recognition, initiation, processivity, fidelity, and kinetic control. We wish to understand the multiple structural, spatial, and functional relationships among these regulatory factors. We are using the SFM as a high resolution tool to image initiation and elongation transcription complexes of E. coli RNA polymerase to characterize the spatial relationships between the enzyme and the DNA template. We are also beginning to investigate what structural changes are negotiated between RNA polymerase and chromatin during transcription. To this end, we are using the SFM to image complexes of nucleosome-containing DNA fragments carrying a promoter and a terminator upstream and downstream of the nucleosome positioning sequence, respectively. We plan to compare the behavior of various prokaryotic and eukaryotic polymerases as they transcribe through the nucleosome, to investigate whether transcription through a nucleosome is an inherent property of the core particle, or a property of each enzyme itself, and to characterize various intermediates of the translocation process. Our laboratory is also working actively in the development of methods of single-molecule manipulation, including the use of SFM cantilevers, optical or laser tweezers, and magnetic beads to investigate the mechanical properties of macromolecules. In one project, we first tether a single protein molecule of T-4 lysozyme between a surface and the end of an SFM cantilever. We can then separate the surfaces in a controlled fashion to induce the mechanical unfolding of the molecule to characterize the nature, range, and strength of the forces that maintain its three-dimensional structure. Our objective is to carry out the unfolding of the molecule at equilibrium so as to obtain the potential energy function of the molecule as a function of the mechanical extension. This function represents the most complete description of the folded state of the protein. We plan to investigate how external conditions in the medium, i.e. temperature, denaturant concentration, etc., or point-directed mutations affect the shape of the potential energy function. Finally, our laboratory is also engaged in the study of DNA-binding molecular motors (RNA polymerase, DNA polymerase, etc.) using optical tweezers to investigate the dynamics of these molecules during translocation, as well as the effect of external force load and nucleotide tri-phosphate concentration on their power and force generation. In parallel, we are developing both microscopic (chemical ratchet-type) and phenomenological models of molecular motors which will be tested experimentally. We believe that single molecule experiments can provide a unique look into the molecular mechanisms responsible for the mechano-chemical conversion process in these protein machines.

近期论文

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Shannon Yan, Jin-Der Wen, Carlos Bustamante, & Ignacio Tinoco Jr.; Ribosome Excursions during mRNA Translocation Mediate Broad Branching of Frameshift Pathways; Cell 2015 in Press PDF Not yet available Clement Riedel, Ronen Gabizon, Christian A.M. Wilson, Kambiz Hamadani, Konstatinos Tsekourasl, Susan Marqusee, Steve Presse & Carlos Bustamante; The heat released during catalytic turnover enhances the diffusion of an enzyme; Nature 517, pp.227-230, January 8, 2015 Geoffrey C. Rollins, Jae Yen Shin, Carlos Bustamante & Steve Presse; Stochastic approach to the molecular counting problem in super resolution microscopy; PNAS, Vol. 112, 2, pp. E110-E118, January 13, 2015 Yara Mejia, Evgeny Nudler & Carlos Bustamante; Trigger loop folding determines rate of Escheriachia coli?s RNA polymerase; PNAS, Vol. 111, 52, December 31, 2014 Rosenbloom A.B, Lee Sang-Hyuk, Milton T, Lee A, Shin Jae Yen, Bustamante C,; Optimized two-color super resolution imaging of Drp1 during kitochondrial fission with a slow-switching Dronpa variant; PNAS, Vol. 111, 36, pp 13093-13098, September 9, 2014 Tingting Liu, Ariel Kaplan, Lisa Alexander, Shannon Yan, Jin-Der Wen, Laura Lancaster, Charlie E. Wickersham, Kurt Fredrick, Harry Noller, Ignacio Tinoco Jr., Carlos Bustamante; Direct measurement of the mechanical work during translocation by the ribosome; eLife 2014;3:e03406, August 11, 2014 Onoa B, Schneider AR, Brooks MD, Grob P, Nogales E, Geissler P, Niyogi K, Bustamante C.; Atomic Force Microscopy of Photosystem II and Its Unit Cell Clustering Quantitatively Delineate the Mesoscale Variability in Arabidopsis Thylakoids; Plos One, Vol. 9, Issue 7, e101470, July 2014 Isabel Llorente-Garcia, Tchern Lenn, Heiko Erhardt, Oliver L. Harriman, Lu-Ning Liu, Alex Robson, Sheng-Wen Chiu, Sarah Matthews, Nicky J. Willis, Christopher D. Bray, Sang-Hyuk Lee, Jae Yen Shin, Carlos Bustamante, Jan Liphardt, Thorsten Friedrich, Conrad W. Mullineaux, Mark C. Leake; Single-molecule in vivo imaging of bacterial respiratory complexes indicates delocalized oxidative phosphorylation; Elsevier, Vol. 1837, pp 811-824, June 2014 Kaiser C.M, Maillard R.A, Goldman D.H, Wilson C.A.M, Bustamante, C.; Mechanisms of Cellular Proteostasis: Insights from Single-Molecule Approaches; Annual Review of Biophysics, Vol. 43 pp 119-140, May 2014 Liu S, Chistol G, Bustamante C.; Mechanical Operation and Intersubunit Coordination of Ring-Shaped Molecular Motors: Insights from Single-Molecule Studies; Biophys. J., Vol. 106 pp. 1844-1858, May 2014 Steve Presse, Jack Peterson, Julian Lee, Phillip Elms, Justin L. MacCallum, Susan Marqusee, Carlos Bustamante and Ken Dill; Single Molecule Conformational Memory Extraction: P5ab RNA Hairpin ; J. Phys. Chem. B, 2014, 118 (24), pp 6597-6603 Liu S, Chistol G, Hetherington CL, Tafoya S, Aathavan K, Schnitzbauer J, Grimes S, Jardine PJ, & Bustamante C.; A viral packaging motor varies its DNA rotation and step size to preserve subunit coordination as the capsid fills; Cell, Vol. 157 pp.702-713, April 24, 2014 Kim HK, Liu F, Fei J, Bustamante C, Gonzalez RL Jr, & Tinoco I Jr.; A frameshifting stimulatory stem loop destabilizes the hybrid state and impedes ribosomal translocation; PNAS Vol. 111 No. 15, April 15, 2014 Walter NG & Bustamante C.; Introduction to single molecule imaging and mechanics:seeing and touching molecules one at a time; Chem. Rev., 2014, 114, pp 3069-3071 Dangkulwanich M, Ishibashi T, Bintu L, & Bustamante C.; Molecular Mechanisms of Transcription through Single-Molecule Experiments; Chem. Rev., 2014, 114, pp 3203-3223 Toyotaka Ishibashi, Manchuta Dangkulwanich, Yves Coello, Troy A. Lionberger,Lucyna Lubkowska, Alfred S. Ponticelli, Mikhail Kashlev, & Carlos Bustamante; Transcription factors IIS and IIF enhance transcription efficiency by differentially modifying RNA polymerase pausing dynamics; PNAS,Vol. 111. no. 7, February 18, 2014 Strycharska MS, Arias-Palomo E, Lyubimov AY, Erzberger JP, O'Shea VL, Bustamante CJ, & Berger JM; Nucleotide and Partner-Protein Control of Bacterial Replicative Helicase Structure and Function; Mol. Cell., Vol. 52, no. 6, pp.844-854, December 26, 2013 Jeffrey R. Moffitt and Carlos Bustamante; Extracting Signal from Noise: Kinetic Mechanisms from a Michaelis-Menten-Like Expression for Enzymatic Fluctuations; the Febs Journal, pp.1-36, September 25, 2013 Manchuta Dangkulwanich, Toyotaka Ishibashi, Shixin Liu, Maria L. Kireeva, Lucyna Lubkowska, Mikhail Kashlev, and Carlos J. Bustamante; Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism; eLIFE pp. 1-22, September 24, 2013 Sen, M., Maillard, R.A., Nyquist, K., Rodriguez-Aliaga, P., Presse, S., Martin, A. and Bustamante C. ; The ClpXP protease unfolds substrates using a constant rate of pulling but different gears; CELL, Vol. 155, pp.636-646, October 24, 2013