Dave Bauer
Thesis title: "Influence of internal genome pressure for viral particle infectivity and stability"
Defense date: April 2015
Research interests:
Genome packaging during virus replication is an ATP-dependent process, resulting in a thermodynamically unstable state of packaged viral DNA. This energetically unfavorable confinement of the microns-long DNA molecule creates a large internal pressure inside the virus. The effects of tight genome confinement has previously been studied for multiple bacterial viruses. Recently, using a novel experimental assay, we have provided the first measurement of this DNA pressure within a eukaryotic herpesvirus, HSV-1. Dave's project focused on calorimetric investigations of internal pressure for specific viral systems, as well as comparative studies between evolutionarily diverse viruses. This experimental approach can uncover general physical properties of viruses that regulate viral infectivity.
Prior education:
B.S. Biology; B.S. Physics, Rowan University, Glassboro, NJ
Current location:
Research Scientist at Cybergenetics in Pittsburgh, PA
PhD Advisor: Dr Alex Evilevitch
Publications:
- D. W. Bauer, A. Evilevitch. Influence of internal DNA pressure on stability and infectivity of phage lambda. Journal of Molecular Biology. 427 (20), 3189–3200 (2015)
- D. W. Bauer, D. Li, J. Huffman, Fred Homa, K. Wilson, J. Leavitt, S. Casjens, J. Baines, A. Evilevitch. Exploring the balance between DNA pressure and capsid stability in Herpesviruses and phages. Journal of Virology. 89 (18), 9288–9298 (2015)
- D. W. Bauer, J. B. Huffman, F. L. Homa, A. Evilevitch. (2013) Herpes Virus Genome, The Pressure Is On. J. Am. Chem. Soc. 135, 11216-21
Naima Sharaf
Thesis Title: Solution NMR studies of HIV-1 reverse transcriptase
Graduation Date: Nov 21, 2016
Research Summary:
Naima used solution NMR as a method to study protein structure and dynamics. Standard NMR experiments use protein uniformly labeled with NMR active nuclei, such as 15N, 13C and 2H. Each nucleus reports on its surrounding environment and the ability to obtain structural information depends on being able to resolve, and unambiguously assign all resonance frequencies to unique nuclei. However, for large proteins (> 30 kDa) resonance overlap properties render this process difficult. Naima's goal was to help develop NMR methods to study large proteins in solution. Towards this goal, she applied selective labeling methods to study the structure and dynamics of the 118 kDa HIV-1 reverse transcriptase, a major drug target in the treatment of HIV-1 infection. The NMR spectra of RT produced by these labeling methods contain less resonance overlap since only a few residues are labeled.
Education:
Chemistry (biochemistry track) University of North Carolina at Chapel Hill
PhD Advisor: Dr Angela Gronenborn
Current Location: Postdoctoral associate in the Rees lab at CalTech / HHMI.
Publications:
- Sharaf, N. G.; Barnes, C. O.; Charlton, L. M.; Young, G. B.; Pielak, G. J., A bioreactor for in-cell protein NMR. J. Magn. Reson., 202 (2010) 140-146.
- Miklos AC, Li C, Sharaf NG, Pielak GJ. 2010. Volume exclusion and soft interaction effects on protein stability under crowded conditions. Biochemistry 49: 6984-6991.
- Sharaf NG, Poliner E, Slack RL, Christen MT, Byeon IJ, Parniak MA, Gronenborn AM, Ishima R. The p66 immature precursor of HIV-1 reverse transcriptase. Proteins. 2014; 82(10):2343-52
- Sharaf, N. G., and Gronenborn, A. M. 19F-Modified Proteins and 19F-Containing Ligands as Tools in Solution NMR Studies of Protein Interactions. Methods in Enzymology 2015; 565:67-95
- Sharaf NG, Ishima R, Gronenborn AM. Conformational Plasticity of the NNRTI-Binding Pocket in HIV-1 Reverse Transcriptase: A Fluorine Nuclear Magnetic Resonance Study. Biochemistry. 2016 Jul 19;55(28):3864-73>
- Sharaf NG, Brereton AE, Byeon IL, Andrew Karplus P, Gronenborn AM. NMR structure of the HIV-1 reverse transcriptase thumb subdomain. J Biomol NMR. 2016 66(4):273-280
- Sharaf NG, Xi Z, Ishima R, Gronenborn AM. The HIV-1 p66 homodimeric RT exhibits different conformations in the binding-competent and -incompetent NNRTI site. Proteins. 2017 doi: 10.1002/prot.25383 (in press)
Inventor in a provisional patent titled: Device for particulate NMR samples in a fluid.
Ryan Slack
Research Interests:
I study the structural basis of dimerization and maturation of HIV-1 reverse transcriptase (RT). This viral enzyme is a primary target in the current treatments for HIV-1 infection. The biologically active form of the enzyme requires dimerization of the RT subunits and proteolytic processing of one of these subunits. Little structural data currently exists regarding the mechanisms of these dimerization and maturation processes which could provide attractive therapeutic targets for future antiretroviral therapies. Our lab uses solution nuclear magnetic resonance (NMR) spectroscopy to determine structures of viral enzymes, and integrate our structural understanding into further mechanistic and functional studies.
Education:
B. Sc. in Biophysics, Centenary College of Louisiana, 2006
PhD Advisor: Dr. Rieko Ishima
Lab Address:
Room 1037
Biomedical Science Tower 3
3501 Fifth Ave.
Pittsburgh, PA 15260
email: rls128{AT}pitt.edu
Publications:
- Cornelius J, Tran T, Turner N, Piazza A, Mills L, Slack R, Hauser S, Alexander JS, Grisham MB, Feelisch M, Rodriguez J. “Isotope tracing enhancement of chemiluminescence assays for nitric oxide research” Biol Chem. Feb;390(2):181-9 (2009)
- Sharaf NG, Poliner E, Slack RL, Christen MT, Byeon IJ, Parniak MA, Gronenborn AM, Ishima R. The p66 immature precursor of HIV-1 reverse transcriptase. Proteins. 2014; 82(10):2343-52
- Slack RL, Spiriti J, Ahn J, Parniak MA, Zuckerman DM, Ishima R. (2015) Structural integrity of the ribonuclease H domain in HIV-1 reverse transcriptase. Proteins. 83(8):1526-38
- Karki I, Christen MT, Spiriti J, Slack RL, Oda M, Kanaori K, Zuckerman DM, Ishima R. Entire-Dataset Analysis of NMR Fast-Exchange Titration Spectra: A Mg2+ Titration Analysis for HIV-1 Ribonuclease H Domain. J Phys Chem B. 2016; 120(49):12420-12431.
- Ilina TV, Slack RL, Elder JH, Sarafianos SG, Parniak MA, Ishima R. Effect of tRNA on the Maturation of HIV-1 Reverse Transcriptase. J Mol Biol. 2018;430(13):1891-1900
Jacob Spiegel
Research Interests:
While at the University of Pittsburgh I've had the opportunity to work on a number of projects across several fields.
From 2013 to 2017 I worked with Dr. Roger Hendrix researching fundamental phage biology. I worked on two projects while in his lab. I studied non-canonical ribosome translation in bacteriophage ΦHau3, in which the ribosome bypassed a 10 nucleotide region and continued translation downstream. My other project was crystallizing and studying the chaperone tail assembly proteins in bacteriophage λ.
Following the passing of Dr. Roger Hendrix, I join the lab or Dr. Jacob Durrant, working on computation biology with focuses in computer-aided drug design (CADD), Molecular Dynamics, and program development. My dissertation focuses on the development of the genetic algorithm for de novo computer-aided drug design, AutoGrow4, and its application to poly(ADP-ribose) polymerase 1 (PARP-1).
Education:
Biomedical Engineering BE, State University of New York at Stony Brook, 2013
PhD Advisor: Dr. Jacob Durrant
Lab Address:
A318 Langley Hall
email: jspiegel[at]pitt.edu
Publications:
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Spiegel, J.O., Durrant, J.D. AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization. J Cheminform 12, 25 (2020). https://doi.org/10.1186/s13321-020-00429-4
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Ropp, P.J., Spiegel, J.O., Walker, J.L. et al. Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening. J Cheminform 11, 34 (2019). https://doi.org/10.1186/s13321-019-0358-3
David Punihaole
Thesis title: Molecular Structural Insights of Polyglutamine-rich Amyloid-like Fibrils using UV Resonance Raman Spectroscopy
Graduation date: June 2016
MBSB PhD Advisor: Dr Sanford Asher (Dept. Chemistry; University of Pittsburgh)
Research Interests:
David worked on the development of UV Resonance Raman (UVRR) spectroscopic methods to study amyloid fibril structure and aggregation kinetics. UVRR is exquisitely sensitive to protein/peptide conformations and can be used to selectively probe the electronic structure of UV-absorbing chromophores.
His my main research focus was the aggregation mechanism(s) of polyglutamine (polyQ) peptides and how they lead to amyloid fibril formation. There are at least nine neurodegenerative diseases associated with expansions in polyQ repeat segments of proteins. These simple polyQ peptides are useful model systems for studying the fundamental biophysics of larger, more complicated polyQ rich protein systems. Another focus was on the development of instrumentation for use in studying new biological systems with UVRR. For this, he worked on creating a high-resolution, high-throughput UV double monochromoter to study biologicals with ~200 nm-excited UVRR and on refurbishing a picosecond Nd:YAG laser so that it can directly probe picosecond dynamics of model peptides and organic molecules.
Current location: postdoctoral researcher in the Frontiera lab at the University of Minnesota.
Education:
B.S., Molecular Biology/Biochemistry, University of Pittsburgh, 2009
Ph.D., Molecular Biophysics & Structural Biology, University of Pittsburgh, 2016
Publications:
- Levine AB, Punihaole D, Levine TB (2012) Characterization of the Role of Nitric Oxide and Its Clinical Applications. Cardiology 2012;122:55-68
- Xiong, K., D. Punihaole, & Asher, S.A. (2012). "UV Resonance Raman Spectroscopy Monitors Polyglutamine Backbone and Side Chain Hydrogen Bonding and Fibrillization." Biochemistry 51(29): 5822-5830.
- Cai Z, Zhang JT, Xue F, Hong Z, Punihaole D, Asher SA. 2D photonic crystal protein hydrogel coulometer for sensing serum albumin ligand binding. Anal Chem. 2014; 86(10):4840-7
- Punihaole, D.; Jakubek, R. S.; Dahlburg, E. M. ; Hong, Z.; Myshakina, N. S.; Geib, S.; Asher, S. A. UV Resonance Raman Investigation of the Aqueous Solvation Dependence of Primary Amide Vibrations. J. Phys. Chem. B. 119(10):3931-9
- Punihaole D, Hong Z, Jakubek RS, Dahlburg EM, Geib S, Asher SA. (2015) Glutamine and Asparagine Side Chain Hyperconjugation-Induced Structurally Sensitive Vibrations. J Phys Chem B. 119(41):13039-51
- Cai Z, Kwak DH, Punihaole D, Hong Z, Velankar SS, Liu X, Asher SA. (2015) A Photonic Crystal Protein Hydrogel Sensor for Candida albicans. Angew Chem Int Ed Engl. 54(44):13036-40
- Punihaole D, Workman RJ, Hong Z, Madura JD, Asher SA. (2016) Polyglutamine Fibrils: New Insights into Antiparallel β-Sheet Conformational Preference and Side Chain Structure. J Phys Chem B. 120(12):3012-26
- Sharma B, Cardinal MF, Ross MB, Zrimsek AB, Bykov SV, Punihaole D, Asher SA, Schatz GC, Van Duyne RP. (2016) Aluminum Film-Over-Nanosphere Substrates for Deep-UV Surface-Enhanced Resonance Raman Spectroscopy. Nano Lett. 2016 Dec 14;16(12):7968-7973.
- Punhaole D, Jakubek RS, Workman RJ, Marbella LE, Campbell P, Madura JD, Asher SA. (2017) Moomeric Polyglutamine Structures That Evolve into Fibrils. J Phys Chem B. 2017; 121(24): 5953-5967
- Punihaole D, Jakubek RS, Workman RJ, Asher SA. Interaction Enthalpy of Side Chain and Backbone Amides in Polyglutamine Solution Monomers and Fibrils. J Phys Chem Lett. 2018;9(8):1944-1950