Dr. Sudeep BhattacharyayProfessorEducation
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Office: Phillips 455
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Dr. Sudeep BhattacharyayProfessorEducation
|
Office: Phillips 455
|
General Chemistry
Physical Chemistry
Biophysical Chemistry
Computational Chemistry
One of my main interests is to foster active learning through discovery-guided projects. In the past few semesters, classroom research projects have been designed and introduced in biophysical and physical chemistry courses. These projects are computational and are being carried out using the in-house Blugold Super-Computing Cluster.
My research interest is focused on two broad topics:
We use theory, concepts of physical chemistry, and advanced computer simulation methods to explore these questions. In addition, we also collaborate with experimentalists to validate the theoretical findings.
Computing in Blugold Supercomputing Cluster
Peer-reviewed articles, reviews, and book chapters. UW-Eau Claire student collaborators are denoted with*
42. Polyethylene Glycol 20k. Does it Fluoresce?
Laatsch, B.*; Brandt, M.*, Finke, B.*,Fossum, C. J.*,Wackett, M. J.*, Lowater, H.R.*, Narkiewicz-Jodko, A.*, Le, C. J.*, Yang, T., Glowgowski, E. M., bailey-Hartsel, S.C., Hati, S. and Bhattacharyya, S. ACS Omega , 2023 , in press .
41. Evolution of Stronger SARS-CoV-2 Variants as Revealed Through the Lens of Molecular Dynamics Simulations
Wozney, A. J., Smith, M. A., Abdrabbo, M., Birch, C. M., Cicigoi, K. A., Dolan, C. C., Gerzema, A. E. L., Hansen, A., Henseler, E. J., LaBerge, B., Leavens, C. M., Le, C. N., Lindquist, A. C., Ludwig, R. K., O'Reilly, M. G., Reynolds, J. H., Sherman, B. A., Sillman, H. W., Smith, M. A., Snortheim, M. J., Svaren, L. M., Vanderpas, E. C., Wackett, M. J., Wwiss, M. M., Hati, S. and Bhattacharyya, S. Protein J. , 2022 , 41 , 444-456. (DOI: 10.1007/s10930-022-10065-6 ).
40. Pre-Existing Oxidative Stress Creates a Docking-Ready Conformation of the SARS-CoV-2 Receptor-Binding Domain
Fossum, C. J.*, Laatsch, B. F.*, Lowater, H. R.* Narkiewicz-Jodko*, A. R.*, Lonzarich, L.*, Hati S. and Bhattacharyya, S. ACS Bio & Med Chem Au , 2022 , 2, 84-93. (DOI: 10.1021/acsbiomedchemau.1c00040).
39. Vitamin D and COVID-19: A Review on the Role of Vitamin D in Preventing and Reducing the Severity of COVID-19 Infection
Abdrabbo, M., Birch, C. M., Brandt, M., K. A., Coffey, S. J., Dolan, C. C., Dvorak, H., Gehrke, A. C., Gerzema, A. E. L., Hansen, A., Henseler, E. J., Huelsbeck, A. C., LaBerge, B., Leavens, C. M., Le, C. N., Lindquist, A. C., Ludwig, R. K., Reynolds, J. H., Severson, N. J., Sherman, B. A., Sillman, H. W., Smith, M. A., Smith, M. A., Snortheim, M. J., Svaren, L. M., Vanderpas, E. C., Wackett, M. J., Wozney, A. J., Bhattacharyya, S., and Hati, S.* Protein Science , 2021 , 30 , 2206-2220. (DOI: 10.1002/pro.4190)).
38. Role of Oxidative Stress on SARS-CoV (SARS) and SARS-CoV-2 (COVID-19) Infection: A Review
Suhail, S.*; Zajac, Z.*; Fossum, C.*; Lowater, H.*; McCracken, C.*; Severson, N.*; Laatsch, B.*; Narkiewicz-Jodko, A.*; Johnson, B.*; Liebau, J.*; Bhattacharyya, S.; and Hati, S. Protein J. ,2020, 39,644-656 (DOI: 10.1007/s10930-020-09935-8).
37. Editing Domain Motions Preorganize the Synthetic Active Site of Prolyl-tRNA Synthetase
Hu, Q. H.*; Williams, M. T.*; Shulgina, I.*; Fossum, C.*; Weeks, K.*; Adams, L.A.*; Reinhardt, C. R.*; Musier-Forsyth K.; Hati, S.; and Bhattacharyya, S. ACS Catal., 2020, 10,10229-10242 (DOI:10.1021/acscatal.0c02381).
36. Effects of Distal Mutations on Prolyl-Adenylate Formation of Escherichia coli Prolyl-tRNA Synthetase
Zajac, J.*; Anderson, H.*; Adams, L. A.*; Wangmo, D.*; Suhail, S.*; Almen, A.*; Berns, L.*; Coerber, B.*; Dawson, L.*; Hunger, A.*; Jehn,
J.*; Johnson, J.*; Plack, N.*; Strasser, S.*; Williams, M. T.*; Bhattacharyya, S.; and Hati, S. Protein J. 2020, 39,542-553 (DOI:10.1007/s10930-020-09910-3).
35. Impact of Thiol-Disulfide Balance on the Binding of Covid-19 Spike Protein with Angiotensin-Converting Enzyme 2 Receptor
Hati, S. and Bhattacharyya, S. ACS Omega 2020, 5, 16292-16298.(DOI:10.1021/acsomega.0c02125).
34. Crowder-induced Conformational Ensemble Shift in Escherichia Coli Prolyl-tRNA Synthetase
Adams, L. A.*, Andrews, R. J.*, Hu, Q. H.*, Smit, H. L.*, Hati, S., and Bhattacharyya, S. Biophys. J. 2019 , 117, 1269-1284 (DOI:10.1016/j.bpj.2019.08.033).
33. Cyclic Changes in Active Site Polarization and Dynamics Drive the 'Ping-pong' Kinetics in NRH:Quinone Oxidoreductase 2: An Insight from QM/MM Simulations
Reinhardt, C. R.*, Hu, Q. H.*, Bresnahan, C. G.*, Hati, S., Bhattacharyya, S. ACS Catal. 2018, 8, 12015-12029 (DOI: 10.1021/acscatal.8b04193).
32. Integrating Research into the Curriculum: A Low-Cost Strategy for Promoting Undergraduate Research
Hati, S. and Bhattacharyya, S. in ACS Symposium Series "Best Practices for Supporting and Expanding Undergraduate Research in Chemistry" Eds. Gourley, B. L. and Jones, R. M. 2018, 119-141 (DOI:10.1021/bk-2018-1275.ch008).
31. Incorporating
Modeling and Simulations in Undergraduate Biophysical Chemistry Course to Promote Understanding of Structure-Dynamics-Function Relationships in
Proteins
Hati, S. and Bhattacharyya, S. Biochem. Mol. Biol. Ed. 2016, 44, 140-159 (DOI:10.1002/bmb.20942).
30. Insight into the
Kinetics and Thermodynamics of the Hydride Transfer Reactions between
Quinones and Lumiflavin: A Density Functional Theory Study
Reinhardt,
C. R.*, Jaglinski, T. C.*, Kastenschmidt, A. M.*, Song, E. H.*,
Krause, A. J.*, Gollmar, J. M.*, Meise, K. J.*, Stenerson, Z. S.*,
Weibel, T. J.*, Dison, A.*, Finnegan, M. R.*, Griesi, D. S.*, Gross, A.
K.*, Heltne, M. D.*, Hughes, T. G.*, Hunt, C. D.*, Jansen, K. A.*,
Xiong, A. H.*, Hati, S., and Bhattacharyya, S. J. Mol. Mod. 2016, 22, 199 (DOI: 10.1007/s00894-016-3074-1).
29. Effect
of Stacking Interactions on the Thermodynamics and Kinetics of
Lumiflavin: A Study with Improved Density Functionals and Density
Functional Tight-Binding Protocol
Bresnahan, C. G.*, Reinhardt, C. R.*, Bartholow, T. *, Rumpel, J. P.*, North, M. A.*, and Bhattacharyya, S. J. Phys. Chem. A 2015, 119, 172�182. (DOI:10.1021/jp510020v).
28. Probing the Global and Local Dynamics of Aminoacyl-tRNA Synthetases using All atom and Coarse-grained Simulations
Strom, A.,* Fehling, S.*, Bhattacharyya, S., Hati, S. J. Mol. Mod. 2014, 20, 2245 (doi:DOI:10.1007/s00894-014-2245-1).
27. Comparison of the Intrinsic Dynamics of Aminoacyl-tRNA Synthetases
*Warren, N.*, Strom, A.*, Nicolet, B.*, Albin, K.*,
Albrecht, J.,* Bausch, B.* Dobbe, M.*, Dudek, M.*, Firgens, S.*,
Fritsche, C.*, Gunderson, A.*, Heimann, J.*, Her, C.*, Hurt, J. *
Konorev, D.*, Lively, M.*, Meacham, S.*, Rodriguez, V*, Tadayon, S.*,
Trcka, D.*, Yang, Y.*, Bhattacharyya, S., and Hati, S. The Protein Journal 2014, 33,184-98. doi: DOI:10.1007/s10930-014-9548-z.
26. Strictly Conserved Lysine of Prolyl-tRNA Synthetase Editing Domain Facilitates Binding and Positioning of Misacylated tRNAPro
Bartholow, T. G.,* Sanford, B. L., Cao, B.V.,* Schmidt, H.
L., Johnson, J. M., Meitzner, J. Bhattacharyya, S., Musier-Forsyth, K.
M., Hati, S. Biochemistry 2014, 53, 1059-68: DOI:10.1021/bi401279r.
25. Multiple Pathways Promote Dynamical Coupling Between Catalytic Domains in Escherichia Coli Prolyl-tRNA Synthetase
Johnson, J. M., Sanford, B. L., Strom, A. S,* Tadayon, S.,*
Brent, L., Zirbes, A., Bhattacharyya, S., Musier-Forsyth, K. M., Hati,
S. Biochemistry 2013, 52, 4399-4412. [PDF]
24. Role of coupled-dynamics in the catalytic activity of prokaryotic-like prolyl-tRNA synthetases
Sanford, B.L., Cao, B.V.,* Johnson, J., Zimmerman, C., Strom,
A. S.,* Mueller, R. M.,* Bhattacharyya, S., Musier-Forsyth, K. M., Hati,
S. Biochemistry 2012, 51, 2146-2156. [PDF]
23. Interplay of flavin's redox states and protein dynamics: an insight from QM/MM simulations of dihydronicotinamide riboside quinone oxidoreductase 2
Mueller, R. M.,* North, M. A.,* Yang, C.,* Hati, S., Bhattacharyya, S. J. Phys. Chem. B 2011, 115, 3632-3641. [PDF]
22. Improved density functional description of the electrochemistry and structure-property descriptors of substituted flavins
North, M. A.,* Bhattacharyya, S., and Truhlar, D. G. J. Phys. Chem. B 2010, 114, 14907�14915. [PDF]
21. Theoretical determination of the
redox potentials of NRH:quinone oxidoreductase 2 using quantum mechanical/molecular
mechanical simulations
Rauschnot, J. C. Jr.,* Yang, C.,* Yang,
V.,* and Bhattacharyya, S. J. Phys. Chem. B 2009, 113, 8149-8157. [PDF]
20. Evolutionary basis for the coupled-domain
motions in Thermus thermophilus leucyl-tRNA synthetase
Weimer, K. M. E.,* Shane, B. L., Brunetto,
M., Bhattacharyya, S. and Hati, S. J. Biol. Chem. 2009, 284,
10088-99. [PDF]
19. Critical role of substrate conformational
change in the proton transfer process catalyzed by 4-oxalocrotonate tautomerase
Ruiz-Pernia, J. J.; Garcia-Viloca, M.;
Bhattacharyya, S.; Gao, J.; Truhlar, D. G. and Tunon, I. J. Am. Chem.
Soc. 2009, 131, 2687-2698. [PDF]
From post-doctoral and graduate studies
18. Combined quantum mechanical and
molecular mechanical simulations of one- and two-electron reduction potentials
of flavin cofactor in water, medium-chain acyl-CoA dehydrogenase, and cholesterol
oxidase
Bhattacharyya, S.; Stankovich, M. T.;
Truhlar, D. G. and Gao, J. J. Phys. Chem. A 2007,
111,
5729-5742.[PDF]
17. Potential of mean force calculation
for the proton and hydride transfer reactions catalyzed by medium-chain
acyl-CoA dehydrogenase: effect of mutations on enzyme catalysis
Bhattacharyya, S.; Ma, S.; Stankovich,
M. T.; Truhlar, D. G. and Gao, J.
Biochemistry 2005,
44,
16549-16562.[PDF]
16. Comparative modeling of the phosphatase
and kinase domains of protein tyrosine phosphatase and insulin receptor
kinase from Drosophila melanogaster (DPTP61fm), and a computational
study of their mutual interactions
Hati, S.; Bhattacharyya, S.; Price, J.
V. and Tracey, A. S. Biochemistry and Cell Biology 2002,
80,
225-239.[PDF]
15. V(V) Complexes in Enzyme Systems:
Aqueous chemistry, inhibition and molecular modelling in inhibitor design
Bhattacharyya, S.; Tracey, A. S. J.
Inorg. Biochem. 2001,
85, 9-13.[PDF]
14. Fluorescent derivatives of nucleotide
sugars as probes for studying the glucohydrolase activities of C. difficile
toxin A
Bhattacharyya, S.; Kerzman, A. and Feig,
A. L. Eur. J. Biochem.
2002,
269, 3425-3432.[PDF]
13. Synthesis, characterization and
reactivity of mononuclear O, N-chelated Vanadium-(IV) and (III) complexes
of methyl 2-aminocyclopent-1-ene-1-dithiocarboxylate based ligands: reporting
a rare type of conformational isomerism
Bhattacharyya, S.; Mukhopadhyay, S.; Samanta,
S.; Weakley, T. J. R. and Chaudhury, M.
Inorg. Chem. 2002,
41,
2433-40.
[PDF]
12. Interactions of N,N-dimethylhydroxamidovanadium(V)
with sulfhydryl-containing ligands:V(V) equilibria and the structure of
a V(IV) dithiothreitol complex
Bhattacharyya, S.; Martinsson, A., Bachelor,
R., Einstein, F. W. B.; Tracey, A. S.
Can. J. Chem. 2001,
79,
938 - 948.[PDF]
11. Syntheses, structure and properties
of cobalt(II) and (III) complexes of pentadentate (N4S) ligands
with appended pyrazolyl groups: evidence for cobalt(II)-dioxygen reversible
binding
Bhattacharyya, S.; Ghosh, D.; Mukhopadhyay,
S.; Jensen, Willium, P.; Tiekink, E. R. T.; Chaudhury, M.
J. Chem.
Soc., Dalton Trans.2000, 4677-4682.[PDF]
10. Nickel(II) in N4S donor
environment: an unprecedented alcoholysis reaction due to metal ion induced
activation of carbon-nitrogen single bond
Bhattacharyya, S.; Weakley, T. J. R.;
Chaudhury, M. Inorg. Chem.
1999,
38, 633-638.[PDF]
9. Nickel(II)-induced activation of
carbon-nitrogen single bond of coordinated ligand by hydroxylated substrates:
generation of mono- and binuclear complexes with modified ligand frameworks
Bhattacharyya, S.; Ghosh, D.; Endo, A.;
Shimizu, K.; Weakley, T. J. R.; Chaudhury, M.
J. Chem. Soc., Dalton
Trans. 1999, 3859-3865.[PDF]
8. Crystal structure and solution studies
of the product of the reaction of b-mercaptoethanol with vanadate
Bhattacharyya, S.; Batchelor, R. J.; Einstein,
F. W. B.; Tracey, A. S. Can. J. Chem. 1999, 77,
2088-2094.
7. Palladium(II)-induced activation
of carbon-nitrogen single bond of coordinated N4S ligand. Characterization
of product with modified ligand structure
Bhattacharyya, S.; Weakley, T. J. R.;
Chaudhury, M. Inorg. Chem.
1999,
38, 5453-5456.[PDF]
6. Crystal and molecular structure of
cis-bis(monothiodibenzoylmethanato)dioxomolybdenum (VI)
Bhattacharyya, S.; Dutta, S. K.; Chaudhury,
M.; Tiekink, E. R. T.
Z. Kristallogr. 1998, 213,
436.
5. Intra molecular electron transfer
in [(BzIm)(LVO)2O] (H2L = S-methyl-(2-hydroxy phenyl)methylenedithiocarbazate):
A novel (5-oxo) dinuclear oxovanadium(IV/V) compound with a trapped-valence
(V2O3
)3+
core
Dutta, S. K.; Kumar, S. B.; Bhattacharyya,
S.; Tiekink, E. R. T.; Chaudhury, M.
Inorg. Chem.1997,
36,
4954-4960.
4. Zinc(II) and copper(II) complexes
of pentacoordinating (N4S) ligands with flexible pyrazolyl arms:
syntheses, structure, redox and spectroscopic properties.
Bhattacharyya, S.; Kumar, S. B.; Dutta,
S. K.; Tiekink, E. R. T.; Chaudhury, M.
Inorg. Chem.1996,
35,
1967-1973.[PDF]
3. Mononuclear manganese(III) complexes
of a heterodonor (N2OS) ligand containing thiolate type sulfur:
synthesis, structure, redox and spectroscopic properties
Kumar, S. B.; Bhattacharyya, S.; Dutta,
S. K.; Tiekink, E. R. T.; Chaudhury, M.
J. Chem. Soc., Dalton Trans.1995,
2619.
2. Chemistry of molybdenum, part 9.
Non-oxomolybdenum(IV) and mononuclear oxomolybdenum(V) complexes with dithioacid
ligands
Dutta, S. K.; Kumar, S. B.; Bhattacharyya,
S.; Chaudhury, M. J. Chem. Soc., Dalton Trans. 1994,
97.
1. Oxalic acid
mediated coupled electron-proton transfer to sulfur rich cis-dioxomolybdenum
(VI), (IV) and bridged oxalato dinuclear molybdenum(V) complexes: synthesis,
spectra and electrochemical studies
Dutta, S. K.; Kumar, S. B.; Bhattacharyya,
S.; Chaudhury, M. J. Inorg. Biochem. 1993, 51,
168.
