I am interested in deciphering the structural basis of protein-protein interactions between HIV protein and host cell proteins. I will be using various structural methods to deepen our understanding of how HIV protein Nef activates Tec family kinases.
B.A. in Biochemistry and Molecular Biology, The College of Wooster (Wooster, OH), May 2014
PhD Advisor: Dr. Thomas Smithgall
University of Pittsburgh
Department of Microbiology and Molecular Genetics
533 Bridgeside Point II
450 Technology Dr.
Pittsburgh, PA 15219
email: manish.aryal - AT - pitt.edu
- Fraga D, Aryal M, Hall JE, Rae E, Snider M. Characterization of the arginine kinase isoforms in Caenorhabditis elegans. Comp Biochem Physiol B Biochem Mol Biol 2015; 187:85-101
Li, W. F., Aryal, M., Shu, S. T., and Smithgall, T. E. (2020) HIV-1 Nef dimers short-circuit immune receptor signaling by activating Tec-family kinases at the host cell membrane. J Biol Chem 295, 5163-5174
Fraga, D., Stock, K., Aryal, M., Demoll, C., Fannin, L., and Snider, M. J. (2019) Bacterial arginine kinases have a highly skewed distribution within the proteobacteria. Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology 233, 60-71
Fraga, D., Aryal, M., Hall, J. E., Rae, E., and Snider, M. (2015) Characterization of the arginine kinase isoforms in Caenorhabditis elegans. Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology 187, 85-101
The Dahl group primarily interested in studying and understanding the mechanical properties of the nucleus and actin cytoskeleton. I primarily use confocal microscopy, to study biophysical characteristics of force mechanotransduction through particle tracking, immunofluorescence, and FRET tension-sensor measurements. Cellular forces have been identified to play critical roles in the cell life cycle, but how the cell interprets and propagates mechanical perturbation is largely unknown. We endeavor to develop a better understanding of how force plays pivotal roles in determining cell fate.
BS Biophysics, Loyola University Chicago, December 2014
PhD Advisor: Kris Noel Dahl
5000 Forbes Ave
Pittsburgh PA 15213
Piperazine Derivatives Enhance Epithelial Cell Monolayer Permeability by Increased Cell Force Generation and Loss of Cadherin Structures, Shiyuan Zheng, Kirill Lavrenyuk, Nicholas G. Lamson, Katherine C. Fein, Kathryn A. Whitehead, and Kris Noel Dahl, ACS Biomaterials Science & Engineering 2020 6 (1), 367-374 , DOI: 10.1021/acsbiomaterials.9b01660
Thesis Title: Solution NMR studies of HIV-1 reverse transcriptase
Graduation Date: Nov 21, 2016
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.
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.
- 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.
Thesis title: "Influence of internal genome pressure for viral particle infectivity and stability"
Defense date: April 2015
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.
B.S. Biology; B.S. Physics, Rowan University, Glassboro, NJ
Research Scientist at Cybergenetics in Pittsburgh, PA
PhD Advisor: Dr Alex Evilevitch
- 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
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).
Biomedical Engineering BE, State University of New York at Stony Brook, 2013
PhD Advisor: Dr. Jacob Durrant
A318 Langley Hall
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
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