The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases

 David Volk, Ph.D.

David Volk, Ph.D.

Assistant Professor, Center for Proteomics and Systems Biology and
Department of Nanomedicine and Biomedical Engineering
David.Volk@uth.tmc.edu

713-500-3195

Fax 713.500.0319

Dr. Volk received his B.A. (Physics and Mathematics) from Minot State University and his Ph.D. (Chemistry) from North Dakota State University where his work focused on reaction mechanisms studied by low temperature NMR and quantum mechanics. His postdoctoral training at Duke University and UT Medical Branch focused on NMR-derived protein and DNA structure determinations. As a Research Scientist at UTMB, his work focused on structural biology, aptamers, NMR-based metabolomics/bioinformatics and quantum chemistry. He joined the IMM in 2009 and in 2010 became an Assistant Professor in the Center for Proteomics and Systems Biology.

Research Interests

Dr. Volk’s current research interests include using bioinformatics techniques applied to proteomic and metabolite studies of patient populations and in the development of novel classes of DNA thioaptamer libraries for use as therapeutic and diagnostic agents. Our recent work focuses on combining aptamers and nanoparticles.

Publications

Publications
(47)  Bone marrow endothelium-targeted therapeutics for metastatic breast cancer J Mai, Y Huang, C Mu, G Zhang, R Xu, X Guo, X Xia, D E Volk, G L Lokesh, V Thiviyanathan, D G Gorenstein, X Liu, M Ferrari, H Shen (2014) J. Control Release. (In Press)
(46) Aptaligner: Automated Software for Aligning Pseudo-Random DNA X-Aptamers from Next-Generation Sequencing Data. E. Lu, M.-A. Elizondo-Riojas, D. E. Volk (2014Biochemistry
(45) X-Aptamers: A bead-based selection method for random incorporation of drug-like moieties onto next-generation aptamers for enhanced binding
Weiguo He, Miguel-Angel Elizondo-Riojas, Xin Li, Ganesh Lakshmana Rao Lokesh, Anoma Somasunderam, Varatharasa Thiviyanathan, David E. Volk, Ross H. Durland, Johnnie Englehardt, Claudio N. Cavasotto, David G. Gorenstein,
Biochemistry
, 2012, 51(42):8321-8323.   Click here for PMC Free PDF
(44) Aggregation Behavior of Ibuprofen, cholic acid and dodecylphosphocholine
P. Prakash, A. Sayyed-Ahmad, Y. Zhou, D. E. Volk, D. G. Gorenstein, E. Dial, L. M. Lichtenberger, A. A. Gorfe, BBA- Mem, Epub - 2012 Aug 4, doi:dx.doi.org/10.1016/j.bbamem.2012.07.029
(43) Aptamers as attractive choices in diagnostic and therapeutic applications
V. Thiviyanathan, A. Somasunderam, D.E. Volk, J. Klostergaard, D.G. Gorenstein,
Proc. Inst. Chem. Sri Lanka
, 2012 (in press).
(42) 1H Nuclear Magnetic Resonance (NMR) Metabolomic Study of Chronic Organophosphate Exposure in Rats
Alam, T.*, Neerthilingam, M., Alam, K., Volk, D., Sarkar, S., Ansari, S. & Luxon, B., Metabolites, 2012, 2(3),:479-495. Free PDF
(41) NMR Structural studies of thymosin alpha-1 and b-thymosins
Volk, D. E., Tuthill, C.W., Elizondo-Riojas, M.-A. and Gorenstein, D.G., Ann. N.Y. Acad. Sci. 2012 1270:73-78.
(40) Insight into NSAID-induced membrane alterations, pathogenesis and therapeutics: characterization of interaction of NSAIDs with phosphatidylcholine
L M Lichtenberger, V Jayaraman, J R Doyen, R G O’Neil, E J Dial, Y Yong Zhou, D E Volk, D G Gorenstein, U Marathi, M B Boggara, R Krishnamoorti, Biochim. et Biophys. Acta (BBA) - Molecular and Cell Biology of Lipids, 2012, 1821: 7. 994-1002.
(39) NMR Structure of Human Thymosin Alpha-1
Elizondo-Riojas, M.-A., Chamow, S.M., Tuthill, C.W., Gorenstein, D.G., Volk, D.E., Biochem. & Biophys. Res. Commun., 2011, 416:356-361. PMC3419375 (Free PDF)
(38) Thioaptamer Conjugated Liposomes for Tumor Vasculature Targeting.
A.P. Mann, R.C. Bhavane, A. Somasunderam, B.L. Montalvo-Ortiz, K.B. Ghaghada, D. Volk, R. Nieves-Alicea, K.S. Suh, M. Ferrari, A. Annapragada, D.G. Gorenstein, T. Tanaka, Oncotarget 2011, 2(4), 298-304. Free PDF
(37) Role of BC loop residues in structure, function and antigenicity of the West Nile virus envelope protein receptor binding domain III.
S. Zhang, E. E. Bovshik, R. Maillard, G. D. Gromowski, D. E. Volk, C. H. Schein, C.Y.-H. Huang, D. G. Gorenstein, J. C. Lee, A. D. T. Barrett, D. W. C. Beasley, Virology 2010, 403: 85-91. PMC2897250 (Free PDF)
(36) 1H and 31P NMR-Based Lipidomics of Ethanol-Induced Fatty Liver.
H. Fernando, S. Kondraganti, K. K. Bhopale, D. E. volk, M. Neerathilingam, B. S. Kaphalia, B. A. Luxon, P. J. Poor, G. A. S. Ansari,
Alcoholism: Clinical and Experimental Research 2010, 34,: 1937-1947. PMC3095964 (Free PDF)
(35) 1H NMR-Based Metabonomic Investigation of Tributyl Phosphate Exposure in Rats.
M. Neerathilingam, D. E. Volk, S. Sarkar, T. M. Alam, K. M. Alam, S. G. Ansari, B. A. Luxon,  
Toxicology Letters 2010, 199: 10-16.
(34) 1H NMR Metabonomic Study of Rat Responce to Tri-Phenyl Phosphate and Tri-Butyl Phosphate Exposure.
T.M. Alam, K. M. Alam, M. Neerathilingam, D. E. Volk, S. Sarkar, G. A. Shakeel Ansari, B. A. Luxon
Metabonomics 2010, 6: 386-394.
(33)Structure of Yellow Fever Virus Envelope Protein Domain III.
D. E. Volk, F. J. May, S. H. Gandham, A. Anderson, J. von Lindern,
D. Beasley, A. D.T. Barrett and D. G. Gorenstein.
Virology 2009, 394:12-18. PMC2787094 (Free PDF)
(32)Investigation of Chemometric Instrumental Transfer Methods for High-Resolution NMR.
T. M. Alam, M. K. Alam, S. K. McIntyre, D. E. Volk, M. Neerathilingam & B. A. Luxon
Analytical Chemistry81:4433-4443, 2009 .
(31)NMR Assignments of the Sylvatic Dengue 1 Virus Envelope Protein Domain III.
D. E. Volk, K. M. Anderson, S. H. A. Gandham, F. J. May, L. Li, David W. C. Beasley, A. D. T. Barrett and D. G. Gorenstein
Biomol. NMR Assigments 2008, 2:155-157. PMC2593834 (Free PDF)
(30) Base-pairing Properties of the Oxidized Cytosine Derivative, 5-Hydroxy Uracil.
V. Thiviyanathan, A. Somasunderam, D. E. Volk, T.K. Hazra, S. Mitra and D. G. Gorenstein
Biochem. Biophys. Res. Commun. 366:752-757, 2008. PMC2262052 (Free PDF)
(29) Ab initio base-pairing energies of an oxidized thymine product, 5-formyluracil,
with standard DNA bases at the BSSE-free DFT and MP2 theory levels.

D. E. Volk, V. Thiviyanathan, A. Somasunderam and D. G. Gorenstein,
Org. Biomol. Chem. 2007, 5(10), 1554-1558.
(28) NMR Assignments of the Yellow Fever Virus Envelope Protein Domain III
D. E. Volk, S. A. Gandham, F. J. May, A. Anderson, A. D. T. Barrett and D. G. Gorenstein.
Biomolecular NMR Assignments 2007, 1(1):49-50, 2007.
(27) Solution Structure of the Envelope Protein Domain III of Dengue-4 Virus
D. E. Volk, Y.-C. Lee, X. Li, V. Thiviyanathan, G. D. Gromowski, L. Li, A. Lamb, D. W. Beasley, A. D. T. Barrett and D. G. Gorenstein,
Virology 2007, 364(1), 147-154. (PMCID: PMC1950219)
(26) NMR Assignment of the Dengue 4 Virus Envelope Protein Domain III
D. E. Volk, Y.-C. Lee, X. Li, A. D. T. Barrett and D. G. Gorenstein,
Journal of Biomolecular NMR 2006, 36(suppl. 5):62.
(25) Ab Initio Base-pairing Energies of Uracil and 5-Hydroxy-Uracil with Standard DNA Bases at the BSSE-free DFT and MP2 Theory Levels
D. E. Volk, V. Thiviyanathan, A. Somasunderam and D. G. Gorenstein
Organic and Biomolecular Chemistry 2006, 4(9), 1741-1745.
(24) Structure of the Envelope Protein Domain III of Omsk Hemorrhagic Fever Virus.
D. E. Volk, L. Chavez, D. W. C. Beasley, A. D. T. Barrett, M. R. Holbrook and D. G. Gorenstein
Virology 2006, 351(1), 188-195.
(23) NMR structure of the viral peptide linked to the genome (VPg) of poliovirus.
C. Schein, N. Oezguen, D. E. Volk, R. Garimella, A. Paul and W. Braun
Peptides 2006, 27(7), 1676-1684. PMC1629084 (Free PDF))
(22) Novel, structure-based mechanism for uridylylation of the genome-linked peptide (VPg) of picornaviruses.
C. Schein, D. E. Volk, N. Oezguen, A. Paul and W. Braun
PROTEINS:Structure, Function, and Bioinformatics 2006, 63:719-726.
(21) Selection of Thioaptamers for Diagnostics and Therapeutics
X. Yang, H. Wang, D.W.C. Beasley, D. E. Volk, X. Zhao, B. A. Luxon,
L. O. Lomas, N. Herzog, J. F. Aronson, A.D.T. Barrett, J. F. Leary and D. G. Gorenstein
Annal. N. Y. Acad. Sci. 2006, 1082:116-119.
(20) 5-Hydroxy Uracil Can Form Stable Base Pairs With all Four Bases in a DNA Duplex.
V. Thiviyanathan, A. Somasunderam, D.E. Volk, and D.G. Gorenstein
Chemical Communications. 2005(3) 400-402.
(19) TATA-Box Binding Protein Induces Structure in the Recombinant Glucocorticoid Receptor AF1 Domain.
R. Kumar, D.E. Volk, J. Li, J.C. Lee, D.G. Gorenstein and E.B. Thompson
Proc. Nat. Acad. Sci. U.S.A. 2004, 101, 16425-16430. (PMCID: PMC534534 (Free PDF))
(18) Solution structure and antibody binding studies of the envelope protein domain III from the New York strain of West Nile virus.
D.E. Volk, D. W. C. Beasley, D. A. Kallick, M.R. Holbrook, A.D.T. Barrett and D. G. Gorenstein
J. Biolog. Chem. 2004, 279,38755-38761.
(17) 1H, 13C, and 15N resonance assignments for domain III of the West Nile Virus envelope protein.
D.E. Volk, D. A. Kallick, M.R. Holbrook, D.W.C. Beasley, A.D.T. Barrett and D.G. Gorenstein
J. Biomol. NMR 2004, 29, 445-446.
(16) NMR Structure of the Apo-S100P protein.
Y.-C. Lee, D.E. Volk, V. Thiviyanathan, Q. Kleerekoper, A.X. Gribenko, S. Zhang D.G. Gorenstein, G. I. Makhatadze and B. A. Luxon.
J. Biomol. NMR 2004, 29, 399-402.
(15) Solution Structure of a Cis-Opened (10R)-N6- Deoxyadenosine Adduct of
(9S,10R)-9,10-Epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a DNA Duplex

D.E. Volk, V. Thiviyanathan, J.S. Rice, B.A. Luxon, J.H. Shah, H. Yagi, J.M. Sayer, D.M. Jerina, and D.G. Gorenstein
Biochemistry 2003, 42, 1410-1420.
(14) Initiation of Repair of A:G Mismatches is Modulated by Sequence Context
A.M. Sanchez, D.E. Volk, D.G. Gorenstein, and R.S. Lloyd
DNA Repair 2003, 2(8), 863-878.
(13) Solution Structure, Dynamics and Thermodynamics of the Native
State Ensemble of the Sem-5 C-terminal SH3 Domain

J.C. Ferreon, D.E. Volk, B.A. Luxon, D.G. Gorenstein and V.J. Hilser,
Biochemistry 2003, 42, 5582-5591.
(12) Solution structure and design of dithiophosphate backbone
aptamers targeting transcription factor NF-kappa B

D.E. Volk, X. Yang, S.M. Fennewald, D.J. King, S. Bassett,
S. Venkitachalam, N. Herzog, B.A. Luxon, and D.G. Gorenstein,
Bioorganic Chemistry 2002, 30, 396-419.
(11) An ab initio study of phosphorothioate and phosphorodithioate interactions with sodium cation.
D.E. Volk, T.D. Power, D.G. Gorenstein and B.A. Luxon,
Tetrahedron Letters 2002, 43, 4443-4447.
(10) Potential Double-Flipping Mechanism by E. coli MutY.
P.G. House, D.E. Volk, V. Thiviyanathan, R.C. Manual, B.A. Luxon, D.G. Gorenstein, and R.S. Lloyd,
Progress in Nucleic Acid Research and Molecular Biology, 2001, 68, 349-364.
(9) NMR Evidence for Syn-Anti Interconversion of a Trans Opened (10R)-dA Adduct of Benzo[a]pyrene (7S,8R)-Diol (9R,10S)-Epoxide in a DNA Duplex.
D.E. Volk, J.S. Rice, B.A. Luxon, H.J.C. Yeh, C. Liang, G. Xie, J.M. Sayer, D.M. Jerina, and D.G. Gorenstein,
Biochemistry 2000, 39, 14040-14053.
(8) Structural Similarities between MutT and the C-Terminal Domain of MutY.
D.E. Volk, P.G. House,V. Thiviyanathan, B.A. Luxon, S. Zhang, R.S. Lloyd and D.G. Gorenstein,
Biochemistry (Accelerated Publication) 2000, 39, 7331-7336.
(7) 1H, 13C, and 15N resonance assignments of the C-terminal domain of MutY: An Adenine glycosylase active on G:A mismatches.
D.E. Volk, V. Thiviyanathan, P.G. House, R.S. Lloyd and D.G. Gorenstein,
J. Biomol. NMR: 1999, 14, 385-386.
(6) SnCl4
S. Castellino and D.E. Volk,
"Encyclopedia of Reagents for Organic Synthesis".
Leo Paquette, Editor-in-Chief, Wiley: 1995.
(5) Allyltributylstannane
S. Castellino and D.E. Volk,
"Encyclopedia of Reagents for Organic Synthesis".
Leo Paquette, Editor-in-Chief, Wiley: 1995.
(4) Crotylstannane
S. Castellino and D.E. Volk,
"Encyclopedia of Reagents for Organic Synthesis".
Leo Paquette, Editor-in-Chief, Wiley: 1995.
(3) SnCl4/ZnCl2
S. Castellino and D.E. Volk,
"Encyclopedia of Reagents for Organic Synthesis".
Leo Paquette, Editor-in-Chief, Wiley: 1995.
(2) Chelation Controlled Reactions of Et2AlCl and Carbomethoxy Substituted Dioxolanes.
S. Castellino and D.E. Volk,
Tetrahedron Letters: 1993, 34, 967.
(1) Substituent Effects on the Gas Phase Acidity of Silane.
M.S. Gordon, D.E. Volk, and D.R. Gano,
J. Am. Chem. Soc.: 1989, 111, 9273.