February 2014 - compbio-allhands@cgl.ucsf.edu

[Compbio-allhands] Fwd: Postdoc Positions Available
by Jacobson, Matt 27 Feb '14

27 Feb '14

Begin forwarded message: From: Sharon Hammes-Schiffer <shs3(a)illinois.edu<mailto:shs3@illinois.edu>> Subject: Postdoc Positions Available Date: February 26, 2014 4:17:02 PM PST To: undisclosed-recipients:; Dear Colleague, I would appreciate your help in forwarding this e-mail to potential postdoc candidates. Best regards, Sharon POSTDOCTORAL POSITIONS AVAILABLE Several postdoctoral positions are currently available in my group at the University of Illinois at Urbana-Champaign. I am particularly seeking candidates interested in working on biologically oriented projects. These projects are focused on understanding the fundamental principles underlying enzyme and ribozyme catalysis, especially the roles of electrostatics, hydrogen bonding, and protein motion. One of the current projects centers on the use of nitrile probes placed at specific sites within an enzyme to examine the electrostatic and conformational changes along the catalytic cycle via the vibrational frequency shifts. Another current project uses mixed quantum mechanical/molecular mechanical (QM/MM) free energy methods to elucidate the mechanisms of several different ribozymes. Other projects focus on proton-coupled electron transfer (PCET) in enzymes. Two relevant papers are listed below, and additional information can be found on my group web site: http://www.scs.illinois.edu/schiffer/. Interested candidates should send a CV to me at shs3(a)illinois.edu<mailto:shs3@illinois.edu>. J. Layfield and S. Hammes-Schiffer, "Calculation of vibrational shifts of nitrile probes in the active site of ketosteroid isomerase upon ligand binding," J. Am. Chem. Soc. 135, 717-725 (2013). A. Ganguly, P. Thaplyal, E. Rosta, P. C. Bevilacqua, and S. Hammes-Schiffer, "Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme," J. Am. Chem. Soc. 136, 1483-1496 (2014). -- Sharon Hammes-Schiffer Swanlund Professor of Chemistry Department of Chemistry University of Illinois at Urbana-Champaign A410 Chemical & Life Sciences Laboratory 600 South Mathews Avenue Urbana, IL 61801-3364 Phone: (217) 300-0335 Fax: (217) 244-3186 e-mail: shs3(a)illinois.edu<mailto:shs3@illinois.edu> http://www.scs.illinois.edu/schiffer/ Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

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[Compbio-allhands] Stefan Boresch talk today
by Jacobson, Matt 25 Feb '14

25 Feb '14

Noon, BH212 Stefan Boresch, U. Vienna "Free energy simulations: from boring methodological work to a promising novel approach for QM/MM" http://www.mdy.univie.ac.at/en/people/boresch/boresch.html Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

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[Compbio-allhands] 2/27/14 Seminar with Bianxiao Cui
by Nicole Takesono Flowers 21 Feb '14

21 Feb '14

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Bianxiao Cui Stanford Light-controlled intracellular signaling pathways in cell fate determination February 27, 2014 B. Huang, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Cool Kinase Talk (hastily scheduled!) tomorrow (Friday) - 4PM - BH212
by Jacobson, Matt 21 Feb '14

21 Feb '14

-- Matt Sent from my iPad Begin forwarded message: From: James Fraser <jaimefraser(a)gmail.com<mailto:jaimefraser@gmail.com>> Date: February 20, 2014 at 6:02:33 PM PST To: "Taunton, Jack (Jack.Taunton(a)ucsf.edu<mailto:Jack.Taunton@ucsf.edu>)" <Jack.Taunton(a)ucsf.edu<mailto:Jack.Taunton@ucsf.edu>>, "Kevan Shokat" <shokat(a)cmp.ucsf.edu<mailto:shokat@cmp.ucsf.edu>>, Natalia Jura <natalia.jura(a)ucsf.edu<mailto:natalia.jura@ucsf.edu>>, "Michael Grabe" <mdgrabe(a)pitt.edu<mailto:mdgrabe@pitt.edu>>, David Sivak <david.sivak(a)gmail.com<mailto:david.sivak@gmail.com>>, "Matthew Jacobson" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>>, Andrej Sali <sali(a)salilab.org<mailto:sali@salilab.org>>, Jim Wells <Jim.Wells(a)ucsf.edu<mailto:Jim.Wells@ucsf.edu>>, "Lim, Wendell" <Wendell.Lim(a)ucsf.edu<mailto:Wendell.Lim@ucsf.edu>>, Tanja Kortemme <kortemme(a)cgl.ucsf.edu<mailto:kortemme@cgl.ucsf.edu>>, "Fujimori, Danica" <Danica.Fujimori(a)ucsf.edu<mailto:Danica.Fujimori@ucsf.edu>>, Fletterick Robert <flett(a)msg.ucsf.edu<mailto:flett@msg.ucsf.edu>>, Agard Dave <agard(a)msg.ucsf.edu<mailto:agard@msg.ucsf.edu>>, Robert Stroud <stroud(a)msg.ucsf.edu<mailto:stroud@msg.ucsf.edu>>, Trever Bivona <TBivona(a)medicine.ucsf.edu<mailto:TBivona@medicine.ucsf.edu>>, Mark von Zastrow <vonzastrow(a)gmail.com<mailto:vonzastrow@gmail.com>>, "Jeff Cox" <jeffery.cox(a)ucsf.edu<mailto:jeffery.cox@ucsf.edu>> Subject: Cool Kinase Talk (hastily scheduled!) tomorrow (Friday) - 4PM - BH212 Matthew Young (Prof at UMichigan, was a postdoc once upon a time with John Kuriyan) was in town for BPS. He has some cool new mechanistic stories on Kinase regulation (and also some new directions on deubiquitinase inhibitors) that you all might be interested in! The seminar will be at 4PM Friday (tomorrow) in BH212. Please forward to your labs! https://dl.dropboxusercontent.com/u/7403581/matt_young.pdf If you want to meet with Matt, let me know, he'll get to campus around 2:30-3 and be free until 4. I'm happy to direct him your way - first come first served! The plan was to grab a beer after the talk at Terzetto, to which everyone is invited. Hope to see you there! And apologies for the last minute nature of the invite, Jaime ABSTRACT: Matthew Young - University of Michigan Allosteric Regulation Of Protein Kinase Enzymes Via An Electrostatic Switch That Modulates Active Site Dynamics Protein kinase (PK) enzymes are a large family of signaling proteins that play a central role in signal transduction pathways. Robust regulation of their catalytic activity is critical, and many oncogenes harbor mutations that result in misregulated PK activity. The chemical basis for how some PK regulatory factors ultimately affect the rate of chemistry is still not completely understood. We have identified a long-range electrostatic switch that we believe is used by allosteric PK regulatory factors to modulate the rate of chemistry by tuning active-site dynamics. We applied a combination of crystallography, kinetics, and molecular dynamics to determine the chemical kinetic basis for how this electrostatic switch, toggled by regulatory subunit binding, affects each step of the catalytic cycle of CDK2 kinase. We engineered point mutants to deconstruct the kinetic, dynamic, and thermodynamic consequences of the switch. We also evaluated other PKs and find that, although it has evolved to be triggered in different ways by diverse PK regulatory factors, the mechanics of this switch can be conserved. We demonstrate that a key component of the switch is that it affects a significant change in the electrostatic potential within the ATP*Mg binding site of the enzyme. This electrostatic effect is propagated through the low-dielectric protein interior and directly affects the two dominant rate-determining steps of catalysis: attenuating both the recruitment of catalytically essential Mg cofactors (affecting both kcat and KM) as well as the release of the ADP product. Conclusion: We present a chemical hypothesis that provides a mechanistic explanation for one way that a large-scale conformation transition, observed in diverse PK family members, is able to significantly affect the rate of chemistry by acting at a distance from the active site. -- -- James Fraser, PhD Assistant Professor Department of Bioengineering and Therapeutic Sciences Office: N212C Genentech Hall, Lab: N216 Genentech Hall james.fraser(a)ucsf.edu<mailto:james.fraser@ucsf.edu> // jaimefraser(a)gmail.com<mailto:jaimefraser@gmail.com> (415) 493-8421 http://www.fraserlab.com

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[Compbio-allhands] Biomolecular Discovery Dome - TODAY ONLY 11:30-1:30 Byers Hall 2nd floor atrium
by Tom Ferrin 20 Feb '14

20 Feb '14

If you didn't get a chance to experience the 3D Biomolecular Discovery Dome this week at the Biophysical Society annual meeting, you've still got a chance to see it. The dome will be running in the 1st floor atrium area of Genentech Hall TODAY Feb 20th between noon and 3pm. Short videos that examine macromolecular complexes and explore datasets from electron microscopy will be shown. Co-sponsored by the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI) and the National Center for Macromolecular Imaging (NCMI).

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[Compbio-allhands] 2/20/14 Seminar with Claudio Joazeiro
by Nicole Takesono Flowers 14 Feb '14

14 Feb '14

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Claudio Joazeiro Scripps Listerin/Ltn1 links Co-translational Protein Quality Control and Neurodegeneration. February 20, 2014 J. Weissman, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Postdoc opportunity: design of HIV entry inhibitors
by Andrej Sali 01 Feb '14

01 Feb '14

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org Begin forwarded message: > From: Cameron Abrams <cfa22(a)drexel.edu> > Subject: Postdoc opportunity: design of HIV entry inhibitors > Date: January 31, 2014 at 7:49:20 AM PST > To: sali(a)salilab.org > > Dear Andrej, > > My name is Cameron Abrams and I am the director of the computational core of an NIH-P01 program project entitled "Structure-based antagonism of HIV-1 envelope function in cell entry". I have immediate need to hire a postdoc with experience in docking calculations and molecular dynamics. I have attached a description of the position to this email. I would very much appreciate it if you could let me know if any members of your group would be interested in learning more about this position. > > Thanks in advance, > Cameron > ---- > Cameron F Abrams, Professor > Department of Chemical and Biological Engineering > Drexel University, Philadelphia, Pennsylvania > t 215-895-2231

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