Home Faculty and Research Faculty by Name Eva Nogales

Eva Nogales

Howard Hughes Investigator and Professor of Biochemistry and Molecular Biology*
*And Affiliate, Division of Cell and Developmental Biology

Lab Homepage: http://cryoem.berkeley.edu/

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Research Interests

My lab is involved in the structural characterization of complex biological assemblies, their architecture, conformational flexibility, and their interactions with ligands and cellular partners. Of special interest to us are the structural basis of microtubule dynamics and its cellular function, and the assembly and complex interactions of a number of molecular machines involved in nucleic acid transactions. We use electron microscopy, image analysis, and functional biochemical assays, with the final aim of a mechanistic understanding of their function and regulation.

Current Projects

Microtubule Cytoskeleton

The dynamic behavior of microtubules, an intrinsic property of tubulin GTPase activity, is essential to their functions. Our studies of tubulin in polymerized, straight protofilaments established the structural basis of nucleotide exchange and polymerization-coupled hydrolysis. More recently we have obtained the structure of two structural intermediates corresponding to the start and end points in the polymerization cycle that illustrate the conformational consequences of the nucleotide state, and how they relate to longitudinal and lateral assembly. The flexibility of tubulin and the consequent versatility of its self-assembly can hardly be an accident. We propose that the polymorphism of assembly unique to tubulin reflects an exquisite tuning mechanism for the complex interaction of different microtubule intermediates with cellular factors that need to detect or make direct use of the growing or shortening state of microtubules in order to play functional roles at the right time and place in the cell. Our lab is now dedicated to the characterization of these molecular interplays. These studies promise to create new paradigms of microtubule cellular function, where tubulin polymers are not seen as passive platforms but as molecular machines capable of work by switching conformational and polymerization states.

As a prominent example, we are studying the dynamic interaction of microtubules with components of the yeast kinetochore. We have shown that the Dam1 complex self-assembles around microtubules into rings and spiral-like structures. The Dam1 ring diffuses along microtubules and this diffusion becomes unidirectional when the microtubule depolymerizes and effectively pushes along the ring. Thus, the Dam1 complex uses the conformational strain of GDP tubulin within the lattice as tubulin relaxes into its curved state, to move processively, and without energy consumption of its own. We are carrying out structural analysis in order to characterize the self-assembly of Dam1 complexes, their interaction with microtubules and other kinetochore components, and their regulation by spindle check-point kinases.

Eukaryotic Gene Regulation

Regulated gene transcription in eukaryotes requires the assembly of a complex molecular machinery that includes general factors, activators, cofactor complexes and chromatin remodeling factors. Our most recent work has highlighted the highly flexible nature of these large protein assemblies and its potential relevance in their affinity for DNA, their catalytic cycles, or the integration of regulatory signals. Present projects include the study of TFIID interaction with promoter DNA, with other basal factor and with mediator; the regulatory effect of non-coding RNAs on RNAP II; and the mechanochemistry of chromatin remodeling complexes.

 Transcription-Coupled DNA Repair

My lab is part of a large NCI funded project in Structural Biology of DNA Repair that aims at producing biologically relevant DNA repair structures and identifying fundamental structural principles for repair proteins. The role of electron microscopy is to provide structures of large macromolecular complexes involved in these processes that complement the X-ray crystallographic structures of individual components. Of special interest to us is the mechanism of transcription-coupled DNA repair (TCR) and the role of human TFIIH and RNA Pol II in this process. Our future plans include to produce structures of TCR supracomplexes in the context of the damaged DNA.

Additional studies include the structural characterization of the Origin Recognition Complex (ORC), the architecture and self-assembly properties of yeast septins, and studies of a number of eukaryotic molecular machines involved in RNA transactions.

Selected Publications

Selected Recent Publications

H.-W. Wang, V.H. Ramey, S. Westermann, A.E. Leschziner, J.P.I. Welburn, Y. Nakajima, D.G. Drubin, G. Barnes, and E. Nogales. Architecture of the Dam1 kinetochore ring complex: implications for microtubule-driven assembly and force-coupling mechanisms. (2007) Nat Struct Mol Biol., Epub ahead of print.

A.E. Leschziner, A. Saha, J. Wittmeyer, Y. Zhang, C. Bustamante, B.R. Cairns, and E. Nogales. Conformational flexibility in the chromatin remodeler RSC observed by electron microscopy and the orthogonal tilt reconstruction method. (2007) PNAS, 104, 4913-4918.

S.A. Kostek, P. Grob, S. De Carlo, J.S. Lipscomb, F. Garczarek, and E. Nogales. Molecular architecture and conformational flexibility of human RNA polymerase II. (2006) Structure, 14, 1691-1700.

M.G. Clarey, J.P. Erzberger, P. Grob, A.E. Leschziner, J.M. Berger, E. Nogales, and M. Botchan. Nucleotide-dependent conformational changes in the DnaA-like core of the origin recognition complex. (2006) Nat Struct Mol Biol., 13, 684-690.

S. De Carlo, B. Chen, T.R. Hoover, E. Kondrashkina, E. Nogales, and B.T. Nixon. The structural basis of regulated assembly and function of the transcriptional activator NtrC. (2006) Genes & Devel., 20, 1485-1495.

H.-W. Wang and E. Nogales. Structural intermediates in microtubule assembly and disassembly: how and why? (2006) Curr Opin Cell Biol., 18(2), 179-284.

P. Grob, M.J. Cruse, C. Inoue, M. Peris, P.A. Penczek, R. Tjian, and E. Nogales. Cryo-electron microscopy studies of human TFIID: Conformational breathing in the integration of gene regulatory cues. (2006) Structure, 14, 511-520.

S. Westermann, H.-W. Wang, A. Avila-Sakar, D.G. Drubin, E. Nogales, and G. Barnes. The Dam1 kinetochore ring complex moves processively on depolymerizing microtubule ends. (2006) Nature, 440, 565-569.

B. Siridechadilok, C.S. Fraser, R.J. Hall, J.A. Doudna, and E. Nogales. Structural roles for human translation factor eIF3 in the initiation of protein synthesis. (2005) Science, 310, 1513-1515.

A.H. Sarker, S.E. Tsutakawa, S. Kostek, C. Ng, D.S. Shin, M. Peris, E. Campeau, J.A. Tainer, E. Nogales, and P.K. Cooper. Recognition of RNA PolII and transcription bubbles by XPG, CSB and TFIIH: Insights for transcription-coupled repair and Cockayne Syndrome. (2005) Mol Cell., 20, 1-12. 

H.-W. Wang and E. Nogales. The nucleotide-dependent bending flexibility of tubulin regulates microtubule assembly. (2005) Nature, 435, 911-915

S. Westermann, A. Avila-Sakar, H.-W. Wang, H. Niederstrasser, H. Wong, D.G. Drubin, E. Nogales, and G. Barnes. Formation of a dynamic kinetochore-microtubule interface through assembly of the Dam1 ring complex. (2005) Mol Cell, 17, 1-20.

For a full publication listing please visit http://cryoem.berkeley.edu/pubs.shtml

Last Updated 2007-08-13