Ph.D., Department of Chemistry, Moscow State Univeristy, Russia. June 2002

Postdoctoral Research Associate, Department of Biochemistry and Cell Biology, State University of New York at Stony Brook, Stony Brook NY, USA. November 2002-October 2004.

Research Associate (part-time), Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook NY, USA. October 2004-December 2005.
Google Scholar profile

Research Interests

NMR spectroscopy.

1. Analysis of NMR spectra by lineshape fitting or other advanced methods. Conventional use of NMR spectra, with only the frequencies of the assigned peaks taken into account, wastes enormous amounts of spectral information. While it is beneficial to Varian and Bruker, it's really not fair that we have to spend millions on new spectrometers in order to solve problems for which we can get more than enough information on a ten times cheaper system.
2. Protein structure analysis by NMR. This is the field with the highest demand and toughest challenges for NMR spectroscopists, so I couldn't help getting into it. I assigned protein spectra with NMRDraw and NMRView, and calculated structures with CYANA (ex-DYANA), CNS, and ARIA. All these programs have their own strengths and weaknesses.

Computer science.

• I am interested in theory of algorithms, programming languages, and operating systems design. I also find the idea of artificial intellegence fascinating, but did not work in that area at all so far.

List of publications:

Articles

	Journal of Molecular Biology
	Zubkov, S., Gronenborn, A. M., Byeon, I-J. L., Mohanty S. Structural consequences of the pH-induced conformational switch in A. polyphemus pheromone-binding protein: mechanisms of ligand release J. Mol. Biol., December 2005; 354(5): 1081-1090. [PUBMED] [ABSTRACT] [PDF] [PDF (local copy)] Cited in: J. Biol. Chem., Nov 2009; 284(46): 32167-32177 J. Mol. Biol., Nov 2007; 373(4): 811-819 Structure, Oct 2006; 14(10): 1577-1586

	Proceedings of the National Academy of Sciences, U.S.A.
	Zubkov, S., Lennarz, W. J., Mohanty, S. Structural basis for the function of a minimembrane protein subunit of yeast oligosaccharyltransferase Proc. Natl. Acad. Sci. USA, March 2004; 101(11): 3821-3826. [PUBMED] [ABSTRACT] [PDF] [PDF (local copy)] Cited in: Proc. Natl. Acad. Sci. USA., Jun 2006; 103(24): 8947–8952 J. Biol. Chem., Jun 2005; 280(24): 22917-22924 Proc. Natl. Acad. Sci. USA., May 2005; 102(20): 7121-7126 J. Biol. Chem., Feb 2005; 280(5): 3121-3124

	Journal of Molecular Biology
	Mohanty, S., Zubkov, S., Gronenborn, A. M. The solution NMR structure of Antheraea polyphemus PBP provides new insight into pheronome recognition by pheronome binding proteins J. Mol. Biol., March 2004; 337(2): 443-451. [PUBMED] [ABSTRACT] [PDF] [PDF (local copy)] Cited in: J. Biol. Chem., Nov 2009; 284(46): 32167-32177 J. Mol. Biol., Nov 2007; 373(4): 811-819 Acta Entomologica Sinica, Jun 2006, 49(3): 355-362 Biochem. Biophys. Res. Commun., Jan 2006; 339(1): 157-164 J. Mol. Biol., Dec 2005; 354(5): 1081-1090 J. Chem. Ecol., Oct 2005; 31(10): 2493-2499 Proc. Natl. Acad. Sci. USA., Apr 2005; 102(15): 5386-5391 Chem Senses. Jun 2004; 29(5): 425-430

	Journal of Biomolecular NMR
	Mohanty, S., Zubkov, S., Campos-Olivas, R. 1H, 13C, and 15N backbone assignments of the pheromone binding protein from the silk moth Antheraea polyphemus (ApolPBP) J. Biomol. NMR, December 2003; 27(4): 393 - 394. [PUBMED] [Full Text] [PDF (local copy)] Cited in: J. Biol. Chem., Nov 2009; 284(46): 32167-32177 J. Mol. Biol., Mar 2004; 337(2): 443-451 J. Mol. Biol., Dec 2005; 354(5): 1081-1090 Naturwissenschaften, Jun 2006, 93(66): 267-277

	International Journal of Molecular Sciences
	Zubkov, S. V., Chertkov, V. A. Experimental determination of pseudorotation potentials for disubstituted cyclopentanes based on spin-spin coupling constants Int. J. Mol. Sci. March 2003; 4(3): 107 - 118. [PDF] [PDF (local copy)] Cited in: Annual Reports on NMR Spectroscopy, Volume 61, Academic Press, 2007, ISBN 0123739187, 9780123739186 J. Phys. Chem. A, 2007, 111(2): 295-298 Eur. J. Org. Chem., Apr 2007; 2007(18): 3028-3037 Dissertation of Olaf R. Ludek, 2005, Universität Hamburg

	Russian Chemical Bulletin
	Zubkov, S. V., Chertkov, V. A., Golotvin, S. S. A new program for total lineshape analysis of NMR spectra. Conformational analysis of trans-1,2-dibromocyclopentane. Russ. Chem. Bull. 2002; 51(7): 1222 - 1230. [Abstract] Cited in: Nuclear magnetic resonance, Volume 24, Royal Society of Chemistry, 1993, ISBN 0854043470, 9780854043477

	Russian NMR Newsletter
	Zubkov, S. V., Golotvin, S. S., Chertkov, V. A. New program VALISA. Conformational analysis of some substituted cyclopentanes and cyclohexanes. Russian NMR Newsletter. (Russian) 2000; 2000(1-2): 917 - 922.

	Chemistry of Heterocyclic Compounds
	Chertkov, V. A., Zubkov, S. V., Ovcharenko, A. A., Karchava, A. V., Yurovskaya, M. A. Determination of ultra long-range spin-spin coupling constants using analysis of full form of line in 1H NMR spectra of fullerene C60 cycloadducts with 1-(4-nitrophenyl)-3-phenylnitrililide. Chem. Heterocycl. Compd. (Engl. Transl.), 1999; 389(11): 1500 - 1505.

	Russian NMR Newsletter
	Zubkov, S. V. Total lineshape NMR spectra analysis. Russian NMR Newsletter. (Russian) 1998; 1998(1): 593 - 602.

	Chemistry of Heterocyclic Compounds
	Makarkina, A. V., Zubkov, S. V., Chertkov, V. A. Orientation of benzothiophene by a magnetic field in the isotropic liquid phase. Chem. Heterocycl. Compd. (Engl. Transl.), 1997; 357(3): 266-270.

Books

		DMK Press
		Zubkov, S. V. Assembler for DOS, Windows and UNIX - 2nd ed, corr.&add. Russian 2003, DMK Press, Moscow, Russia, 608 pages. ISBN: 5-94074-259-9 (2nd edition, 2003, bestseller series) ISBN: 5-94074-003-0 (2nd edition, 2003, paperback) ISBN: 5-89818-082-6 (2nd edition, 2000, hard cover) 640 pages. ISBN: 5-89818-019-2 (1st edition, 1999) [Review]

	DMK Press
	Zubkov, S. V. Linux. Russian versions. Russian 2000, DMK Press, Moscow, Russia, 352 pages ISBN: 5-94074-013-8 [Review]

Conference Presentations

	18th Symposium of the Protein Society August 9-20, 2004, La Jolla, CA
	Mohanty, S., Zubkov, S., Gronenborn, A.M. Structural characterization of theAntheraea polyphemus pheromone binding protein in acidic pH Mohanty, S., Nestor, Z., Zubkov, S., Maslyanskaya, S. Biophysical characterization of the human glutaminase interacting protein containing a PDZ domain and its interaction with C-terminus peptide of glutaminase

	17th Symposium of the Protein Society July 26-30, 2003, Boston, MA
	Mohanty, S., Zubkov, S. NMR Assignment and secondary structure of the silk moth Antheraea polyphemus pheromone binding protein ApolPBP Protein Science, vol 12 suppl 2, 121.

	15th European Experimental NMR Conference (EENC2000) June 12-17, 2000, Leipzig, Germany
	Zubkov, S. V., Golotvin, S. S., Chertkov, V. A. Solving multi-site conformational problems with total lineshape analysis of NMR spectral multiplets Proceedings of the 15th European Experimental NMR Conference (EENC 2000), page 42. [PDF] [PDF (local copy)]

	3rd Russian Conference "New achievements of NMR in structural research" April 4-7, 2000, Kazan, Russia
	Chertkov V. A., Zubkov, S. V., Golotvin, S. S. Proceedings of the III Russian Conference "New achievements of NMR in structural research", page 59 (Russian)

I solved the structures of these proteins:

	Protein Data Bank
	Mohanty, S., Zubkov, S. NMR structure of the pheromone binding protein from Antheraea polyphemus at acidic pH July 1, 2004 PDB Identifier: 1TWO

	Protein Data Bank
	Zubkov, S., Lennarz, W. J., Mohanty, S. NMR structure of yeast oligosaccharyltransferase subunit Ost4p November 21, 2003 PDB Identifier: 1RKL BMRB Identifier: 6056

PDB	Protein Data Bank
	Mohanty, S., Zubkov, S. NMR structure of D. punctata allatostatin 5 in micelles October 15, 2003 PDB Identifier: 1R6I (to be reinserted when finished) BMRB Identifier: 5990 (to be reinserted when finished)

	Protein Data Bank
	Mohanty, S., Zubkov, S., Gronenborn, A. M. Solution structure of Antheraea polyphemus pheromone binding protein (ApolPBP) September 3, 2003 PDB Identifier: 1QWV BMRB Identifier: 5689