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
(52) Thioaptamers targeting Dengue virus type-2 envelope protein domain III
S H A Gandham, D E Volk, L G L Rao, N. Neerathilingam and D G Gorenstein
Biochem Biophys Res Commun. 2014 (in press)
(51) 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
J. Control Release 187, 22-29, 2014.
(50) Aptaligner: Automated Software for Aligning Pseudo-Random DNA X-Aptamers from Next-Generation Sequencing Data.
E. Lu, M.-A. Elizondo-Riojas, J. T. Chang and D. E. Volk
Biochemistry 53(22), 3523-3525, 2014.
(49) 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 51(42):8321-8323, 2012. Free PDF
(48) 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-Biomembranes 1818(12), 3040-3047, 2012.
(47) Aptamers as attractive choices in diagnostic and therapeutic applications
V. Thiviyanathan, A. Somasunderam, D.E. Volk, J. Klostergaard, D.G. Gorenstein
Proc. Inst. Chem. Ceylon (Sri Lanka), 204-209, June 2012.
(46) 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., and Luxon, B.
Metabolites2(3):479-495, 2012. Free PDF
(45) 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. 1270:73-78, 2012.
(44) 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 , 1821(7): 994-1002, 2012.
(43) 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. , 416:356-361, 2011.
PMC3419375 (Free PDF)
(42) 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 2(4), 298-304, 2011. Free PDF
(41) 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 403: 85-91, 2010. PMC2897250 (Free PDF)
(40) 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, 34,: 1937-1947, 2010. PMC3095964 (Free PDF)
(39) 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 199, 10-16, 2010 .
(38) 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 6, 386-394, 2010.
(37) Allyltributylstannane
S. Castellino, D. E. Volk, N. T. Patil, Y. Yamamoto (2009) in
Encyclopedia of Reagents for Organic Synthesis, Second Edition,
Edited by: Leo A. Paquette, David Crinch, Philip Fuchs and Gary A. Molander. Wiley. ISBN 978-0-470-01754-8.
(36) Crotyltributylstannane
S. Castellino and D. E. Volk (2009) in
Encyclopedia of Reagents for Organic Synthesis, Second Edition,
Edited by: Leo A. Paquette, David Crinch, Philip Fuchs and Gary A. Molander. Wiley. ISBN 978-0-470-01754-8.
(35) Tin (IV) Chloride-Zinc Chloride
S. Castellino and D. E. Volk (2009) in
Encyclopedia of Reagents for Organic Synthesis, Second Edition,
Edited by: Leo A. Paquette, David Crinch, Philip Fuchs and Gary A. Molander. Wiley. ISBN 978-0-470-01754-8.
(34) Tin (IV) Chloride
S. Castellino, D. E. Volk and C. J. Chany (2009) in
Encyclopedia of Reagents for Organic Synthesis, Second Edition,
Edited by: Leo A. Paquette, David Crinch, Philip Fuchs and Gary A. Molander. Wiley. ISBN 978-0-470-01754-8.
(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 394, 12-18, 2009. 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 and B. A. Luxon
Analytical Chemistry 81, 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 2, 155-157, 2008. 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. 5(10), 1554-1558, 2007.
(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 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 364(1), 147-154, 2007. (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 36(suppl. 5):62, 2006.
(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 4(9), 1741-1745, 2006.
(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 351(1), 188-195, 2006.
(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
27(7), 1676-1684, 2006. 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 63:719-726, 2006.
(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. 1082, 116-119, 2006.
(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, 2005.
(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. 101, 16425-16430, 2004. 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. 279,38755-38761, 2004.
(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 29, 445-446. 2004.
(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 29, 399-402, 2004.
(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 42, 1410-1420, 2003.
(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 2(8), 863-878, 2003.
(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 42, 5582-5591, 2003.
(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 30, 396-419, 2002.
(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 43, 4443-4447, 2002.
(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 68, 349-364, 2001.
(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 39, 14040-14053, 2000.
(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 (Rapid Report) 39, 7331-7336, 2000.
(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 14, 385-386, 1999.
(6) Tin (IV) Chloride
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 in
"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 34, 967, 1993.
(1) Substituent Effects on the Gas Phase Acidity of Silane.
M.S. Gordon, D.E. Volk, and D.R. Gano,
J. Am. Chem. Soc.: 111, 9273, 1989.