Research Interest:

Research interest lies at the interface of biology and the physical sciences. The general thrust

of my research program is aimed at developing and applying computational methodologies to

understand structural characteristics, kinetics and thermodynamics of peptides, proteins and

carbohydrates.

Research Capabilities:

Molecular Dynamics Simulations

Enhanced sampling methods

Molecular Modeling & Forcefields

Coarse-grained approaches

Free energy and binding calculations

Research Programs:

Our basic science research program is aligned towards supporting emerging national security

missions. We apply our expertise in computational structural biology/immunology capabilities

towards both health and energy securities.

Research Projects:

* Energy landscapes and dynamics of signaling proteins

* Dynamics of surface proteins of HIV & Rational vaccine design

* Protein Folding & Secondary structural propensities of peptides

* Aggregation and misfolding of disease related peptides

* Protein conformational networks and folding pathways

* Interfacing All-atom simulations with spectral measurements

* Perturbation of local solvent and protein structures by metals

* Multi-scale Modeling of Plant Cell Wall Components

* Pretreatment and Enzymatic degradation of cellulose

* Rational enzyme design: Increasing turnover and Biasing chirality

Publications:

Rong Rong, Bing Li, Rebecca M. Lynch, Richard E. Haaland, Megan K. Murphy, Joseph Mulenga, Susan A. Allen, Jerry L. Blackwell, Abraham Pinter, George M. Shaw, Eric Hunter, James E. Robinson, S. Gnanakaran, and Cynthia A. Derdeyn. Escape from Autologous Neutralizing Antibodies in Acute/Early Subtype C HIV-1 Infection Requires Multiple Pathways. PLoS Pathogens. accepted (2009).

B. Korber and S. Gnanakaran. The implications of patterns in HIV Diversity for neutralizing antibody induction and susceptibility. Curr Opin in HIV and AIDS. in press (2009).

Tongye Shen and S. Gnanakaran. The stability of cellulose: A statistical perspective from a coarse grained model of hydrogen bond network. Biophys. J., 96, 3032-3040 (2009) –highlighted in cover]

Rebecca M., Tongye Shen, S. Gnanakaran and Cynthia A. Derdeyn. Appreciating HIV-1 Diversity: Subtypic Differences in Env. AIDS Res. and Hum. Retroviruses 25, 237-248 (2009).

Smita S. Kulkarni, Alan Lapedes, Haili Tang, S. Gnanakaran, Marcus G. Daniels, Ming Zhang, Tanmoy Bhattacharya, Ming Li, Victoria R. Polonis, Francine E. McCutchan, Lynn Morris, Dennis Ellenberger, Salvatore T. Butera, Robert C. Bollinger, Bette T. Korber, Ramesh S. Paranjape, and David C. Montefiori. Highly complex neutralization determinants on a monophyletic lineage of newly transmitted subtype C HIV-1 Env clones from India. Virology 385, 505-20 (2009)

D. Paschek, M. Puhse, A. Perez-Goicochea, S. Gnanakaran, A.E. Garcia, S. Decatur, A. Geiger and R. Winter. 2008. The solvent dependent shift of the amide-I band of a fully solvated peptide in Methanol/ Water mixture as a local probe for the solvent composition in the peptide/solvent interface. Chemphyschem. 9, 2742-50 (2008).

M.Vuyisich, S. Gnanakaran, JA. Lovchik, Rick Lyons, G. Gupta. A dual-purpose protein ligand for effective therapy and sensitive diagnosis of anthrax. Protein J. 27, 292-302 (2008)

S. Gnanakaran, B. Scott, T.M McCleskey and A. E. Garcia. Perturbation of Local Solvent Structure bSmall

Dication: Structural, Spectroscopic and Reactive Properties of Beryllium Ion in Water, J. Phys. Chem. B, 112, 2958-2963 (2008).

Erzsebet Ravasz, S. Gnanakaran, Zoltan Toroczkai, Network Structure of Protein Folding

Pathways. 2008. available at arXiv:0705.0912v1 [q-bio.BM].

Brian L. Scott, T. Mark McCleskey, Anu Chaudhary, Elizabeth Hong-Geller, and S. Gnanakaran. 2008.

The bioinorganic chemistry and associated immunology of Chronic Beryllium Disease, Chem. Comm.,

25, 2837-2847.

M. Kunkel, M. Vuyisich, S. Gnanakaran, G.E. Bruening, A.M. Dandekar, E. Civerolo, J.J. Marchalonis

and G. Gupta. 2007. Rapid clearance of bacteria and their toxins: Development of therapeutic proteins.

Crit. Rev. Immuno., 27, 233-245.

S. Gnanakaran, Dorothy Lang, Marcus Daniels, Tanmoy Bhattacharya, Cynthia A. Derdeyn, and Bette Korber. 2007. Clade Specific Differences in HIV-1: Diversity and Correlations in C3-V4 Regions of gp120. J. Virol. 81:4886-4891.

Rong, R., S. Gnanakaran, J.M. Decker, F. Bibollet-Ruche, J. Taylor, J.N. Sfakianos, J.L. Mokili, M. Muldoon, J. Mulenga, S. Allen, B.H. Hahn, G.M. Shaw, J.L. Blackwell, B.T. Korber, E. Hunter, and C.A. Derdeyn. 2007. Unique Mutational patterns in the envelope 2 amphipathic helix and acquisition of length in gp120 hypervariable domains are associated with resistance to autologous neutralization of subtype C HIV type 1. J. Virol. 81:5658-5668.

M. Vuyisich, S. Gnanakaran, J.A. Lovchik, CR. Lyons, K.L. DeBord, and G. Gupta. 2007. Novel therapy for anthrax. J. Biomol. Struct. Dyn. 24:727-728.

S. Gnanakaran, R. Nussinov, and A.E. Garcia. 2006. Atomic level description of amyloid beta dimer formation. J. Am. Chem. Soc. 128:2158-2159.

W. Blay, S. Gnanakaran, B. Foley, N. Doria-Rose, B.T. Korber, and N.L. Haigwood. 2006. Consistent Patterns of Change During Divergence of Human Immunodeficiency Virus Type 1 Envelope in SHIV-Infected Macaques. J. Virol. 80:999-1014.

S. Gnanakaran and A.E. Garcia. 2005. Helix-coil transition of alanine peptides in water: Force field dependence on the folded and unfolded structures. Proteins-Structure Function and Genetics. 59:773-782.

D. Paschek, S. Gnanakaran, and A.E. Garcia. 2005. Simulations of the pressure and temperature unfolding of an alpha-helical peptide. Proc. Natl. Acad. Sci. USA. 102:6765-6770.

S. Gnanakaran, R.M. Hochstrasser, and A.E. Garcia. 2004. Nature of structural inhomogeneities on folding a helix and their influence on spectral measurements. Proc. Natl. Acad. Sci. USA. 101:9229-9234.

H. Nymeyer, S. Gnanakaran, and A.E. Garcia. 2004. Atomic simulations of protein folding, using the replica exchange algorithm. Methods Enzymol. 383:119-149.

S. Gnanakaran and A.E. Garcia. 2003. Validation of an all-atom protein force field: From dipeptides to larger peptides. J. Phys. Chem. B. 107:12555-12557.

S. Gnanakaran, H. Nymeyer, J. Portman, K. Sanbonmatsu, and A.E. Garcia. 2003. Peptide folding simulations. Curr. Opin. Struct. Biol. 13:168-174.

S. Gnanakaran and A.E. Garcia. 2003. Folding of a highly conserved diverging turn motif from the SH3 domain. Biophys. J. 84:1548-1562.

R.M. Hochstrasser, N. Ge, S. Gnanakaran, and M. Zanni. 2002. Two dimensional infrared spectroscopy: Studies of the dynamics of structures with femtosecond pulse Fourier transform correlation spectroscopy. Bull. Chem. Soc. Japan. 75:1103.

S. Gnanakaran and R.M. Hochstrasser. 2001. Conformational preferences of short peptides in relation to multidimensional IR spectroscopy. J. Am. Chem. Soc. 123:12886-12898.

M.T. Zanni, S. Gnanakaran, J. Stenger, and R.M. Hochstrasser. 2001. Two-dimensional infrared spectroscopy of solvent dependent conformations of acetylproline-NH2. J. Phys. Chem. 105:6520-6535.

S. Gnanakaran, G. Haran, R. Kumble, and R.M. Hochstrasser. 1999. Energy transfer and localization: Applications to photosynthetic systems. Chapter in book titled “Resonance Energy Transfer”. J. Wiley Publishing Co.

S. Gnanakaran and R.M. Hochstrasser. 1999. Effect of vibrational coherence on rotational dynamics in solution. Int. J. Quantum Chem. 72:451-462.

S. Gnanakaran, M. Lim, M. Volk, E. Gooding, Y. Kholodenko, and R.M. Hochstrasser. 1998. Chemical reaction dynamics of some simple molecules in solution. Phil. Trans. R. Soc. Lond. A. 356:377-388.

M. Volk, S. Gnanakaran, M. Lim, E. Gooding, Y. Kholodenko, and R.M. Hochstrasser. 1997. Anisotropy measurements of the solvated HgI2; Transition state and fragment rotational dynamics. J. Phys. Chem. A.101:638-643.

M. Lim, S. Gnanakaran, and R.M. Hochstrasser. 1997. Charge shifting in the ultrafast photo-reactions of ClO^- in water. J. Chem. Phys. 106:3485-3493.

S. Gnanakaran and R.M. Hochstrasser. 1996. Vibrational relaxation of HgI in ethanol: Equilibrium molecular dynamics simulations. J. Chem. Phys. 105:3486-3496.

N. Pugliano, S. Gnanakaran, and R.M. Hochstrasser. 1996. The dynamics of photo-dissociation reaction. J. Photochem. & Photobiol. A. 102:21-28.

N. Pugliano, A. Szarka, S. Gnanakaran, and R.M. Hochstrasser. 1995. Vibrational populational dynamics of the HgI photofragment in ethanol solution. J. Chem. Phys. 103:6498-6511.

K. Wynne, S. Gnanakaran, C. Galli, F. Zhu, and R.M. Hochstrasser. 1994. Luminescence studies of ultrafast energy transfer oscillations in dimmers. J. Lumin. 60-1:735-738.

P.G. Smith, S. Gnanakaran, A.G. Kasziska, A.L. Motyka, S.M. Hong, R.M. Hochstrasser, and M. Topp. 1994. Electronic coupling and conformational barrier crossing of 9’,9-Bifluorenyl studied in a supersonic jet. J. Chem. Phys. 100:3384-3493.