August 27, 2009
No Speaker
September 3, 2009
Steven Cannon
Agronomy and USDA ARS
Publications to review:
Kwak M, Velasco D, Gepts P (2008) Mapping homologous sequences for determinacy and photoperiod sensitivity in common bean (Phaseolus vulgaris). Journal of Heredity 99: 283-291 http://jhered.oxfordjournals.org/cgi/content/abstract/99/3/283
Jeffrey A. Fawcett, Steven Maere, and Yves Van de Peer (2009) Plants with double genomes might have had a better chance to survive the CretaceousTertiary extinction event http://www.pnas.org/content/106/14/5455
And perspective on the Fawcett et al. article: Douglas E. Soltis and J. Gordon Burleigh (2009) Surviving the K-T mass extinction: New perspectives of polyploidization in angiosperms http://www.pnas.org/content/106/14/5737
September 10, 2009
Drena Dobbs
Department of Genetics, Development and Cell Biology
Title: "Interrogating RNA-Protein Interactions in Viruses"
Ihm, Y., Sparks, W.O., Lee, J.H., Cao, H., Culver, G., Carpenter, S., Wang, C.Z., Ho, K.M., Dobbs, D. (2009) Structural model of the Rev regulatory protein from equine infectious anemia virus. PLoS ONE 3:e4178.
Lee, J.-H., Culver, G., Carpenter, S., Dobbs, D. (2008). Analysis of the EIAV Rev-responsive element (RRE) reveals a conserved RNA motif required for high affinity Rev binding in both HIV-1 and EIAV. PLoS ONE 3:e2272.
Lee, J.H., Murphy, S.C., Belshan, M., Sparks, W.O., Wannemuehler, Y., Liu, S., Hope, T.J., Dobbs, D., Carpenter, S. (2006) Characterization of functional domains of equine infectious anemia virus Rev suggests a bipartite RNA-binding domain. J Virol 80:3844-3852.
September 17, 2009
Steve Whitham
Department of Plant Pathology
Title: Characterization of soybean gene networks specifying pathogen recognition and defense
Three publications to read prior to lecture for BCB 691 participants:
zhang_et_al_MPMI-22-2-0123.pdf
Meyer_et_al_PlantPhys_2009.pdf
vandemortel_et_al_MPMI-20-8-0887.pdf
September 24, 2009
Ed Yu
Department of Physics and Astronomy
Title: Structural basis of bacterial protein machinery that mediates antibiotic resistance
This seminar addresses fundamental questions regarding the nature multi-ligand recognition and gene regulation in multi-drug efflux systems that mediate the phenomenon of antibiotic resistance in bacteria. The primary system is the Escherichia coli AcrB multi-drug efflux transporter, which recognizes structurally dissimilar toxic chemicals, including most of the currently used antibiotics, disinfectants, dyes, bile salts, fatty acids, and detergents.
The expression of the AcrB transporter in E. coli is tightly regulated and controlled by the repressor protein AcrR, which acts as a molecular switch in the system. In the presence of toxic chemicals, the AcrR regulator allows the expression of the AcrB efflux transporter, which, in turn, promotes efflux of chemicals from the bacterium, thus protecting it from toxic substances.
How can AcrR and AcrB recognize a variety of toxic chemicals? How do they respond to changing environmental conditions? An understanding of the structures of these proteins at the atomic level may allow us to uncover the mechanisms that these proteins use to bind multiple ligands, regulate gene expression, and mediate antibiotic resistance in bacteria.
Publications:
Gu, R., C.-C. Su, F. Shi, M. Li, G. McDermott, Q. Zhang, and E. W. Yu. 2007. Crystal structure of the transcriptional regulator CmeR from Campylobacter jejuni. J. Mol. Biol. 372:583-593.
Li, M., R. Gu, C.-C. Su, M. D. Routh, K. C. Harris, E. S. Jewell, G. McDermott, and E. W. Yu. 2007. Crystal structure of the transcriptional regulator AcrR from Escherichia coli. J. Mol. Biol. 374:591-603.
Su, C.-C., F. Yang, F. Long, D. Reyon, M. D. Routh, D. W. Kuo, A. K. Mokhtari, J. D. Van Ornam, K. L. Rabe, J. A. Hoy, Y. J. Lee, K. R. Rajashankar, and E. W. Yu. 2009. Crystal structure of the membrane fusion protein CusB from Escherichia coli. J. Mol. Biol. doi:10.1016/j.jmb.2009.08.029.
October 1, 2009
Alex Travesset
Department of Physics and Ames Laboratory
"Understanding how signaling phospholipids act at the molecular level"
References:
"Hydrogen Bonding and the Binding of Polybasic Residues with
Negatively Charged Mixed Lipid Monolayers" C.D. Lorenz , J. Faraudo
and A. Travesset, Langmuir 24, 1654 (2008).
"Phosphatidic Acid Domains in Membranes: effect of Divalent
Counterions", J. Faraudo and A. Travesset, Biophys. J., 92, 2806 (2007).
"Phosphoinositides in cell regulation and membrane dynamics"
D. Di Paolo and P. De Camilli, Nature 443, 651 (2006)
October 8, 2009
Volker Brendel
Department of Genetics, Development and Cell Biology
Title: "Genome-wide studies of intron evolution in the context of orthologous genes"
References:
Zhu, W. & Brendel, V. (2003) Identification, characterization, and molecular phylogeny of U12-dependent introns in the Arabidopsis thaliana genome. Nucl. Acids Res. 31, 4561-4572. [PubMed ID: 12888517]
Sparks, M.E. & Brendel, V. (2005) Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plants. Bioinformatics 21, iii20-iii30. [PubMed ID: 16306388]
Rogozin IB, Sverdlov AV, Babenko VN, Koonin EV. (2005) Analysis of evolution of exon-intron structure of eukaryotic genes.Brief. Bioinf. 6, 118-132. [PubMed ID: 15975222]
October 15, 2009
Robert Jernigan
Department of Biochemistry, Biophysics and Molecular Biology and L.H. Baker Center for Bioinformatics and Biological Statistics
Title: Functional Protein Motions
Abstract: Computing the functional motions from protein structures is an important challenge in computational biology. Elastic network models provide strong evidence that proteins control their functional motions through their slow, domain motions. These models represent the structures as highly cohesive rubbery materials. Such models exhibit strong control over their motions, including control of the motions of functional surface loops by domain motions and even the motion of reactive atoms at enzyme active sites in coordination with domain motions. These can even be used to suggest enzyme mechanisms. There is accumulating evidence that the behavior of protein machines can be understood with these models, and the important large domain motions can be obtained readily. For the ribosome, the results clearly indicate that its motions relate strongly to the multiple aspects of its function. Already we have seen that the large ribosomal ratchet motion simultaneously causes the t-RNAs and mRNA to move in the processing direction. The control of the mRNA at the codon/anti-codon binding site is extremely strong, to ensure fidelity of copying, with the mRNA being moved translationally as a fully rigid body, with no internal motions. The peptide channel undergoes peristaltic motions that relate to extrusion of the growing peptide.
The elastic network models are entropic models, and their success in describing protein functional motions suggests the importance of entropy. An important lesson from these computations is that protein entropies depend on the entire structure but not on the details of the structure.
References:
1. Kurkcuoglu O, Turgut OT, Cansu S, Jernigan RL, Doruker P. Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model. Biophys J. 2009;97:1178-87.
2. Yang L, Song G, Jernigan RL. Protein elastic network models and the ranges of cooperativity. Proc Natl Acad Sci U S A. 2009;106:12347-52.
3. Kurkcuoglu O, Doruker P, Sen TZ, Kloczkowski A, Jernigan RL. The ribosome structure controls and directs mRNA entry, translocation and exit dynamics. Phys Biol. 2008;5:46005.
October 22, 2009
Shi-Jie Chen and Xiaoqin Zou - Baker Seminar Speakers
University of Missouri
Shi-Jie -- "RNA Folding, anti-HIV Aptamer Design, and Human Telomerase RNA activity"
Xiaoqin -- "A scoring framework for selecting structural models"
Abstract
October 29, 2009
Tobin Sosick - Baker Seminar Speaker
University of Chicago
"Protein folding mechanisms and their application to structure prediction"
Abstract
November 5, 2009
Roger Wise
Department of Plant Pathology
"Regulation of innate immunity in cereal-fungal interactions"
References:
http://www.plantphysiol.org/cgi/content/full/149/1/271
http://www.plantcell.org/cgi/content/abstract/tpc.109.066167v1
November 12, 2009
Basil Nikolau
Department of Biochemistry, Biophysics and Molecular Biology
November 19, 2009
Dan Gusfield -Baker Seminar Speaker
University of CA, Davis
"The Multi-State Perfect Phylogeny Problem: The Chordal Graph Approach"
Abstract
November 26, 2009
No Class - Thanksgiving Break
December 3, 2009
Max Alekseyev - Baker Seminar Speaker
Department of Computer Science and Engineering
University of South Carolina
"Genome Rearrangements: from Models to Predictions"
Abstract
December 10, 2009
Xun Gu
Department of Genetics, Development and Cell Biology
December 17, 2009
Finals Week (Dec. 14-18)
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