MolBioPhys

Graduates Supported By NIH Traineeships

1990 - 2000

Jane M. Withka
Frank M. DiCapua 
Paul C. Harkins 
Michelle Fausel 
Shirley Louise-May 
Kieran I. Curley 
Ronald D. Lewis 
Matthew Young 
Kerry Cecere 
Karen Sheffield 
Vasilios (Bill) Marathias 
Kevin McConnell

 

Nota bene: This represents only a fraction of the total scientific activity of our program, since only US Citizens are eligible for NIH support and we only have three slots per year available for them. For a complete list of students mentored by participating faculty, see the entries under "Faculty" on this website. 

(in chronological order, 1990 - 2000):

Jane M. Withka 
(B.A. University of Rhode Island 1980); MBTG Yr. 01.

  • Dissertation Project: NMR and Theoretical Studies of Intact and Damaged DNA Oligonucleotides (Profs. P. H. Bolton and D. L. Beveridge, mentors)
  • Professional Activities: Attended Conference on Biomolecular Stereodynamics, Albany, 1987, 1989; NMR International Meeting, Warwich, 1990; CECAM Workshop on Biomolecular Electrostatics, Orsay, France, 1988 Biophysical Society, 1988.
  • Graduated with PhD in Chemistry (Major: Molecular Biophysics), Nov. 1992.
  • Postdoctoral Studies:  Prof. Gerhard Wagner at Harvard University Medical School, 
  • Current Placement:  Associate Research Fellow at Pfizer Pharmaceuticals
  • Publications Based on Dissertation Research:

1. "Coexistence of Conformations in a DNA Heteroduplex Revealed by Site Specific Labeling with 13C Labeled Nucleotides" M. Manoharan, J. A. Gerlt, J. A. Wilde, J. M. Withka, P. H. Bolton, J. Am. Chem. Soc. 109, 7217 (1987).

2. "NOEs in Duplex DNA Depend on Orientations of Internuclear Vectors to the Symmetry Axis" J. M. Withka, S. Swaminathan, P. H. Bolton, J. Magn. Reson. 89, 386 (1990).

3. "Molecular Dynamics of an in vacuo Model of Duplex d(CGCGAATTCGCG) in the B-Form Based on the AMBER 3.0 Force Field" J. Srinivasan, J. M. Withka, D. L. Beveridge, Biophys. J. 58, 533 (1990).

4. "A Critique of the Interpretation of Nuclear Overhauser Effects of Duplex DNA" J. M. Withka, S. Swaminathan, P. H. Bolton. In Proceedings of the NATO Advanced Research Workshop, Computational Aspects of the Study of Biological Macromolecules by NMR Spectroscopy (J. Hoch, ed.) Plenum, NY, 1991.

5.  "Characterization of Conformational Features of a DNA Heteroduplex Containing an Aldehydric Basic Site" J. M. Withka, J. A. Wilde, P. H. Bolton, A. Mazumder, J. A. Gerlt, Biochemistry 30, 9931 (1991). 

6. "Time Dependence of Nuclear Overhauser Effects in Duplex DNA from Molecular Dynamics Simulations" J. M. Withka, S. Swaminathan, D. L. Beveridge, P. H. Bolton, J. Am. Chem. Soc. 113, 5041 (1991).

7. "Methodological Considerations in Molecular Dynamics Simulations of DNA Oligonucleotides" D. L. Beveridge, S. Swaminathan, G. Ravishanker, J. Withka, J. Srinivasan, C. Prevost, S. Louise-May, F. M. DiCapua, P. H. Bolton. In Advances in Biomolecular Simulations (R. Lavery, J. Rivail, eds.) American Institute of Physics, New York, 1991.

8. "Stereochemical Studies of the B-Elimination Reactions at Aldehydic Abasic Sites in DNA: Endonuclease III from Escherichia coli, Sodium Hydroxide and Lys-Trp-Lys" A. Mazumder, J. A. Gerlt, M. J. Cunningham, J. M. Withka, P. H. Bolton, Biochemistry 30, 1119 (1991).

9. "Toward a Dynamical Structure of B-DNA in Solution: Comparison of Theoretical and Experimental NOE Intensities for d(CGCGAATTCGCG)2" J. M. Withka, S. Swaminathan, J. Srinivasan, D. L. Beveridge, P. H. Bolton, Science 255, 597-599 (1992).

10.  "Problems with, and Alternatives to, the NMR R Factor" J. M. Withka, J. Srinivasan, P. H. Bolton,J. Magn. Reson. 98, 611 (1992).

11. "Effects of the Presence of an Aldehydic Abasic Site on the Thermal Stability Rate of Helix Opening of Duplex DNA" I. Goljer, J. M. Withka, P. H. Bolton, Biochemistry 31, 11614 (1992).

12. "Molecular Dynamics Simulations on the Hydration, Structure and Motions of DNA Oligomers," D. L. Beveridge, S. Swaminathan, G. Ravishanker, J. M. Withka, J. Srinivasan, C. Prevost, S. Louise-May, D. R. Langley, F. M. DiCapua, P. H. Bolton. In Topics in Molecular and Structure Biology: Waterand Biological Macromolecules, 19 (E. Westhof, ed.) McMillan Press Ltd., 1993.  

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Frank M. DiCapua 
(B.A. Boston College 1986); MBTG Yrs. 01,02.

  • Dissertation Project: Theoretical Studies of Protein Structure and Folding via Molecular Dynamics Simulation (Prof. D. L. Beveridge, mentor)
  • Professional Activities: Attended Conference on Biomolecular Stereodynamics, 1987, 1989; Meeting at NIH, 1989; Biophysical Society, 1990; Biopolymers Gordon Conference, 1990.
  • Graduated with PhD in Molecular Biology and Biochemistry (Major: Molecular Biophysics), Nov. 1992.
  • Current Placement: Senior Principal Scientist, Pfizer Pharmaceuticals
  • Publications Based on Dissertation Research:

1.   "Free Energy in Molecular Simulation: A Primer" D. L. Beveridge, F. M. DiCapua. In Computer Simulations in Protein Engineering and Drug Design, W. F. van Gunsteren and P. K. Weiner, eds., ASCOM Scientific Publishers, Leiden, 1989.

2.   "Free Energy via Molecular Simulation: Applications to Chemical and Biomolecular Systems" D. L. Beveridge, F. DiCapua, Ann. Rev. Biophys. Biophys. Chem18, 431 (1989).

3.      "Theoretical Evidence for the Destabilization of an a-Helix by Water Insertion: Molecular Dynamics Simulation of the Hydrated Deca Alanine" F. M. DiCapua, S. Swaminathan, D. L. Beveridge, J. Am. Chem. Soc. 112, 6768 (1990).

4.   "A Theoretical Study of Polyelectrolyte Effects in Protein-DNA Interactions: Monte Carlo Free Energy Simulations on the Ion Atmosphere Contribution to the Thermodynamics of l Repressor-Operator Complex Formation" B. Jayaram, F. M. DiCapua, D. L. Beveridge, J. Am. Chem. Soc. 113,5211 (1991).

5.     "Theoretical Evidence for Water Insertion in a-Helix Bending: Molecular Dynamics Simulations on [Gly]30 and [Ala]30 in Vacuo and in Solution" F. M. DiCapua, S. Swaminathan, D. L. Beveridge, J. Am. Chem. Soc. 113, 6145 (1991).

6.      "Methodological Considerations on Molecular Dynamics Simulations on DNA Oligonucleotides" D. L. Beveridge, S. Swaminathan, G. Ravishanker, J. M. Withka, J. Srinivasan, C. Prevost, S. Louise-May, F. M. DiCapua, P. H. Bolton. In Advances in Biomolecular Simulations(Lavery and Smith, eds.) American Institute of Physics, New York, 1991.

7.      "Molecular Dynamics Simulations on the Hydration, Structure and Motions of DNA Oligomers" D. L. Beveridge, S. Swaminathan, G. Ravishanker, J. M. Withka, J. Srinivasan, C. Prevost, S. Louise-May, D. R. Langley, F. M. DiCapua, P. H. Bolton. In Topics in Molecular and Structure Biology: Water and Biological Macromolecules, 19 (E. Westhof, ed.) Press Ltd., 1993.

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Paul C. Harkins 
(B.A. University of California, San Diego 1986); MBTG Yrs. 01,02.

  • Dissertation Project: Interactions of Polar Peptides and Metal Ions with Phosphate Diesters (Prof. Paul Haake, mentor)
  • Professional Activities: Initially worked with Prof. N. Allewell and carried out a training period in the Wyckoff Lab at Yale University. Began dissertation research with Prof. Paul Haake, MB&B Dept., 6/90. Meetings at Biophysical Society 1990; ATCase Meeting, Brussels, AAAS Protein Folding Meeting, New Orleans, 1989.
  • Graduated with PhD in Molecular Biology and Biochemistry, June 1992.
  • Postdoctoral Studies: Yale University,  Prof. Fox in X-ray Crystallography 
  • Current Placement:  Southwestern Medical Center.
  • Publications Based on Dissertation Research:

1. "Crystalization and Preliminary X-Ray Investigation of the Recombinant Trypanosoma brucei rhodesiense Calmodulin" N. M. A. El-Sayed, P. C. Harkins, R. O. Fox, K. Anderson, C. L. Patton,Proteins: Structure, Function and Genetics 21, 354-357 (1995).

2. "Spectroscopic and Kinetic Properties of Unphosphorylated Rat Hepatic Phenylalanine Hydroxylase Expresssed in Escherichia coli. Comparison of Resting and Activated States" T. J. Kappock, P. C. Harkins, S. Friedenberg, J. P. Caradonna, J. Biol. Chem. 270, 30532-30550 (1995).

3. "Mutation of Position 52 in ERK2 Creates a Non-Productive Binding Mode of ATP" M. J. Robison, P. C. Harkins, J. Zhang, R. Baer, J. Haycock, M. Cobb, E. J. Goldsmith, Biochemistry 35, 5641-5646 (1996).

4. "Overpacking of a Cavity in Staphylococcal Nuclease" R. Wynn, P. C. Harkins, F. M. Richards, R. O. Fox, Protein Science 5, 1026-1031 (1996).

5. "Distortion of O-P-O Bond Angels in Phosphorous Monoanions: Ab Initio Studies" P. C. Harkins, G. Petersson, P. Haake. J. Inorg. Biochem. 61, 25-41 (1996).

6. "The Structure of Mitogen-activated Protein Kinase p38 at 2.1 A  Resolution" Z. Wang, P. C. Harkins, R. J. Ulevitch, J. Han, M. H. Cobb, E. J. Goldsmith, Proc. Nat. Acad. Sci. USA 94, 2327<2332 (1997).

7. "Simplification of a Protein Loop in Staphylococcal Nuclease" A. Hodel, P. C. Harkins, D. M. Adelman, R. O. Fox, Protein Science, in press.

8. "Comparison of Straight Chain and Cyclic Unnatural Amino Acids Embedded in the Core of Staphylococcal Nuclease" R. Wynn, P. C. Harkins, F. M. Richards, R. O. Fox. Protein Science, in press.

9.  "Analysis of Protein-Protein Associations and Coordinate Error from Isomorphous Structures and Ribonuclease A and S at 2.1 A Resolution" P. C. Harkins, H. W. Wyckoff, submitted.

10.  "Insights into Specificity and Substrate Binding of MAP Kinases Deduced from the Refined Structure of ERK2 at 1.sA Resolution" P. C. Harkins, J. Wilsbacher, J. Zhang, E. Goldsmith, manuscript in preparation.

11. "Short and Long Time Scale Molecular Dynamics Information Derived from Several Crystal Structures of Ribonuclease A and S" P. C. Harkins, H. W. Wyckoff, manuscript in preparation.

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Michelle Fausel 
(B.A. Rensselaer Polytechnical Institute 1989); MBTG Yrs. 02,03.

  • Dissertation Project: NMR Studies on EcoRI Endonuclease Interactions with DNA Oligonucleotides (Prof. I. M. Russu, mentor)
  • Professional Activities: Attended Biophysical Society, San Francisco, 1990; Biopolymers Gordon Conference, 1990
  • Graduated with MA in Molecular Biology and Biochemistry (Major: Molecular Biophysics), June 1994. Decided to terminate at the MA level due to family reasons.
  • Current Placement: Laboratory Research, Pfizer, Inc.

  • Publications Based on Dissertation Research:

1. "NMR Structural Comparison of the Recognition Sites for EcoRI and Bam HI Restriction Endonucleases" M. Fausel, I. M. Russu, J. Biomol. Str. Dyn., 1991.

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Shirley Louise-May 
(B.A. University of Maine 1987; M.A. Columbia University 1988);      MBTG Yrs. 03,04,05.

  • Dissertation Project: Molecular Dynamics Studies of DNA Fine Structure and Bending (Prof. D. L Beveridge, mentor)
  • Professional Activities: CECAM Workshop on DNA Fine Structure and Bending, Paris, 1990; Biomolecular Stereodynamics, Albany, 1989, 1991, 1993; Biopolymers Gordon Conference, 1990.
  • Graduated with PhD in Chemistry, (Majors: Chemical Physics & Molecular Biophysics), June 1994.
  • Postdoctoral Studies: CNRS, Strasbourg, France with Prof. Eric Westhof; Dr. David Moreland at Parke-Davis Pharmaceutical Research.
  • Current Placement:  Computational Chemist, Neurogen Inc., Branford, CT.
  • Publications Based on Dissertation Research:

1. "Methodological Considerations on Molecular Dynamics Simulations on DNA Oligonucleotides" D. L. Beveridge, S. Swaminathan, G. Ravishanker, J. M. Withka, J. Srinivasan, C. Prevost, S. Louise-May, F. M. DiCapua and P. H. Bolton. In Advances in Biomolecular Simulations (Lavery and Smith, eds.) American Institute of Physics, New York, 1991.

2. "Molecular Dynamics Simulations on the Hydration, Structure and Motions of DNA Oligomers" D. L. Beveridge, S. Swaminathan, G. Ravishanker, J. M. Withka, J. Srinivasan, C. Prevost, S. Louise-May, D. R. Langley, F. M. DiCapua, P. H. Bolton. In Topics in Molecular and Structure Biology: Water and Biological Macromolecules, 19 (E. Westhof, ed.) Press Ltd., 1993.

3. "Persistence Analysis of the Static Dynamical Helix Deformations of DNA Oligonucleotides: Application to the Crystal Structure and Molecular Dynamics Trajectories of d(CGCGAATTCGCG)2" C. Prevost, S. Louise-May, G. Ravishanker, R. Lavery, D. L. Beveridge, Biopolymers 33, 335 (1993).

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Kieran I. Curley 
(B.S. University of Connecticut 1984; MS Fordham University 1989):      MBTG Yrs. 06,07.

  • Dissertation Project: Studies of Transition State Analog Inhibitors of B-Lactamase Enzymes: Enzyme Kinetics and Molecular Modeling. (Prof. R. Pratt, mentor)
  • Professional Activities: Excellence in Biochemistry, 1995; Scottsdale, AZ, 1995. The Peterson Fellowship Award for 14th Enzyme Mechanism Conference,
  • Graduated with PhD in Chemistry, June 1997.
  • Current Placement: Postdoctoral Fellow, Department of Biochemistry, Albert Einstein College of Medicine. Research chemist at Schein Pharmaceuticals, NY.
  • Publications Based on Dissertation Research:
  •  

1. "The Di-decameric Hemocyanin of the Atlantic Murex Snail Muricanthus Fulvescens" T. T. Herskovitz, K. I. Curley, M. D. Edwards, M. G. Hamilton. In Structure and Function of Invertebrate Oxygen Carriers, S. N. Vinogradov, O. H. Kapp eds., 1990.

2.  "Effectiveness of Tetrahedral Adducts as Transition State Analogs and Inhibitors of the Class C ß-Lactamase of Enterobacter Cloacea  P99" R. F. Pratt, K. I. Curley, J. Am. Chem. Soc. 118, 8207 (1996).

3. "Structure of an a-keto-ß-amido Acid, 3-(Phenylacetamido)pyruvic Acid, and its Methyl Ester in the Solid State and in Organic and Aqueous Solvents" R. F. Pratt, K. I. Curley, J. Org. Chem. 62, 4479 (1997).

4.    "Inhibition of Serine Amidohydrolases by Complexes of Vanadate with Hydroxamic Acids" J. H. Bell, K. Curley, R. F. Pratt, Biochem. Biophys. Res. Commun274, 732 (2000).

5.   "The Oxyanion Hole in Serine ß-Lactamase Catalysis: Interactions of Thiono Substrates with the Active Site" K. Curley, R. F. Pratt, Bioorg. Chem. 28, 338 (2000).  

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Ronald D. Lewis 
(B.A. Johns Hopkins University 1990): MBTG Yrs. 05,06,07.

  • Dissertation Project: Use of 2-Keto-3-deoxy-6-phosphogluconate Aldolase as a Biocatalyst in Organic Synthesis and Mechanistic Models (Prof. S. Sobolov, mentor).
  • Professional Activities: Gordon Research Conference, 1992; 204th ACS National Meeting, Washington, DC, 1992.
  • Graduated with PhD in Chemistry, May 1997.
  • Postdoctoral Studies: Postdoctoral Fellow at Scripps Research Institute.  
  • Current Placement: Postdoctoral Fellow at Scripps Research Institute.
  • Publications Based On Dissertation Research:

1. "Enzyme-Catalyzed Aldol Reactions with 2-Keto-3-Deoxy-6-Phospho-gluconate Aldolase" R. D. Lewis, II, S. B. Sobolov. Manuscript in preparation.

2.  "Use of 2-Keto-3-Deoxy-6-Phosphogluconate Aldolase in Aldol Reactions: Synthesis of Proline and Pipecolinic Acid Analogues" R. D. Lewis, II,S.B. Sobolov. Manuscript in preparation.

3. "Identification of Aldolase Binding Sites for Substrates and Inhibitors" R. D. Lewis, M. A. Young, S. Sobolov, et al., manuscript in preparation.  

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Matthew Young 
(B.A. Wesleyan University 1992) MBTG Yrs. 07,08,09.

  • Dissertation Project: "Sequence Dependent Fine Structure and Bending in DNA Oligonucleotides" (Prof. D. L. Beveridge, mentor)
  • Professional Activities: Conference -- Mathematical Applications to Biology, Berkeley, CA, 1992; Conference in Biomolecular Structure and Dynamics, Albany, NY, 1993; Poster: Biophysical Society Meeting, New Orleans, LA, 1994; Poster: Biophysical Society Meeting, San Francisco, CA, 1995; Two posters: Conference in Biomolecular Structure and Dynamics, 1995; Presentation: "Investigations involving the NDB," Nucleic Acids Database Conference, Rutgers, NJ, 1995; Presentation: "Refining the dynamic atomic resolution picture of DNA" Biochemistry evening seminar, Wesleyan University, 1995; Presentation: "Nanosecond molecular dynamics on DNA oligonucleotides with water and counterions," IBPC, Paris, France, 1995.; Two posters: Biophysical Society Meeting, Baltimore, MD, 1996; Invited Talk: "Structure, Solvation and Counterion Condensation for Oligonucleotides Based on Molecular Dynamics Simulation" American Chemical Society Meeting, Orlando, FL, 1996. Poster, Biophysical Society Meeting, New Orleans 1997; Poster, American Chemical Society Meeting, San Francisco, CA, April 1997. Lecture and Poster (Titles: TBA) - Conference in Biomolecular Structure and Dynamics (June 1997); Conference: CECAM Workshop, "Theoretical and experimental approaches to nucleic acid structure and activity, Lyon, France (September 1997).
  • Graduated with PhD in Molecular Biology and Biochemistry, Nov. 1998.
  • Current placement: Assistant Professor, University of Michigan
  • Postdoctoral Studies: Damon Runyan Society Postdoctoral Fellow at Rockefeller University and University of California, Berkeley with Prof. J. Kuriyan.
  • Publications Based on Dissertation Research:

1. "Analysis of Helix Bending in Crystal Structures and Molecular Dynamics Simulations of DNA Oligonucleotides," M. A. Young, R. Nirmala, J. Srinivasan, K. J. McConnell, G. Ravishanker, D. L. Beveridge, H. M. Berman. In Structural Biology: The State of the Art. R. H. Sarma, M. H. Sarma, eds. Adenine Press, Albany, NY, 197-214, 1993.

2. "Molecular Dynamics Simulations of DNA and Protein-DNA Complexes Including Solvent" D. L. Beveridge, K. J. McConnell, R. Nirmala, M. A. Young, S. Vijayakumar, G. Ravishanker. In Structure and Reactivity in Aqueous Solution: Characterization of Chemical and Biological Systems, C. J. Cramer, D. G. Truhar, eds., ACS Symposium Series, Washington, DC, 381-394, 1994.

3. "A Nanosecond Molecular Dynamics Trajectory for a B-DNA Double Helix: Evidence for Substrates" K. J. McConnell, R. Nirmala, M. A. Young, G. Ravishanker, D. L. Beveridge, J. Am. Chem. Soc. 116, 4461-4462 (1994).

4. "Analysis of Local Helix Bending in Crystal Structures of DNA Oligonucleotides and DNA-Protein Complexes" M. A. Young, G. Ravishanker, D. L. Beveridge, H. M. Berman, Biophys. J. 68, 2454-2468 (1995).

5. "Molecular Dynamics Simulations of DNA and a Protein-DNA Complex Including Solvent" D. L. Beveridge, K. J. McConnell, M. A. Young, S. Vijayakumar, G. Ravishanker. In Modeling of Biomolecular Structures and Mechanisms, A. Pullman et al., eds., Kluew Academic Publishers, Netherlands, 409-423, 1995.

6.  "Structure Determination and Analysis of Local Bending in an A-Tract Duplex: Comparison of Results from Crystallography, Nuclear Magnetic Resonance, and Molecular Dynamics Simulation on d(CGCAAAAATGCG)" D. L. Beveridge, P. H. Bolton, I. Goljer, S. Kumar, J. Srinivasan, M. A. Young, Methods in Enzymology 261, 121-144 (1995). 

7. "Treatment of Counterions in Computer Simulations of DNA" G. Ravishanker, P. Auffinger, D. R. Langley, B. Jayaram, M. A. Young, D. L. Beveridge. In Reviews in Comp. Chem. K. B. Lipkovitz, D. B. Boyd, eds., Wiley-UCH, NY, 11, 317-372 (1997).

8. "Intrusion of Counterions into the Spine of Hydration in the Minor Groove of B DNA: Fractional Occupancy of Electronegative Pockets" M. A. Young, B. Jayaram, D. L. Beveridge, J. Am. Chem. Soc. 119, 59-69 (1997).

9. "A Five Nanosecond Molecular Dynamics Trajectory for B-DNA: Analysis of Structure, Motions and Solvation" M. A. Young, G. Ravishanker, D. L. Beveridge, Biophys. J. 73, 2313-2336 (1997).

10. "Conformational Properties of the TATA Box Binding Sequence of DNA" D. Flatters, M. A. Young, D. L. Beveridge, R. Lavery, J. Biomol. Struct. & Dyn. 14 (1997).

11. "Molecular Dynamics Information Extraction" D. Sprous, W. Wang, G. Ravishanker, M. A. Young, D. L. Beveridge. In IMA Volumes in Mathematics and its Applications, "Mathematical and Computational Issues in Drug Design" J. Blaney, et al., Eds. Springer-Verlag, NY, 1997.

12. "Modeling of DNA via Molecular Dynamics Simulation: Structure, Bending, in Conformational Transitions" D. L. Beveridge, M. A. Young, D. Sprous. In Molecular Modeling of Nucleic Acids, N. Leontis, J. Santa Lucia, Eds, ACS Symp. Series682, 260-284, 1998.

13. "Molecular Dynamics Studies of the Conformational Preferences of a DNA Double Helix in Water and an Ethanol/Water Mixture: Theoretical Considerations of the A®B Transition" D. Sprous, M. A. Young, D. L. Beveridge, J. Phys. Chem. 102, 4658-4667 (1998).

14. "Molecular Dynamics Simulations of an Oligonucleotide Duplex with Adenine Tracts Phased by a Full Helix Turn, M. A. Young, D. L. Beveridge, J. Mol. Biol. 281, 675-687 (1998).

15. "Monte Carlo Simulation of the Ion Atmosphere Distribution Around the Operator Binding Domain of the l-Repressor Protein" D. C. Kombo, M. A. Young, D. L. Belveridge, Biophys. J. (1998).

16. "Molecular Dynamics Simulation of the OL1 DNA Operator: The Unusual Geometrical Features at the Center of the DNA Operator Site Occur in the Absence of Bound Protein" D. C. Kombo, M. A. Young, D. L. Beveridge, Biophys. J. (1998).

17. "Free Energy Analysis of the Conformational Stability of A and B Forms of DNA in Solution, B. Jayaram, D. Sprous, M. A. Young, D. L. Beveridge, J. Am. Chem. Soc. 120, 10629-10633 (1998).

18. "The Local Dielectric Environment of B-DNA in Solution: Results from a 14 Nanosecond Molecular Dynamics Trajectory" M. A. Young, B. Jayaram, D. L. Beveridge, J. Phys. Chem. 102, 7666-7669 (1998).

19. "Molecular Dynamics Studies of Axis Bending in Oligonucleotide Duplexes d[G5(GA4T4C)2-C5] and d[G5-(GA4T4C2)-C5]: Effects of Sequence Polarity on DNA Curvature" D. Sprous, M. A. Young, D. L. Beveridge, J. Mol. Biol. 285, 1623-1632 (1999). 

20.  "Molecular Dynamics Simulation Accurately Predicts the Experimentally-Observed Distributions of the (C,N,O) Protein Atoms Around Water Molecules and Sodium Ions" D. C. Kombo, M. A. Young, D. L. Beveridge, Proteins 39, 212-215 (2000).

21. "One Nanosecond Molecular Dynamics Simulation of the N-Terminal Domain of the l-Repressor Protein" D. C. Kombo, M. A. Young, D. L. Beveridge, Biopolymers 53, 596-605 (2000).

22. "Molecular Dynamics Simulations on Crystallographic Unit Cells of d(CGCGAATTCGCG)2 and d(CGCAAAATGCG)2 Comparison with Predicted Solution Structures and Studies of Packing Effects" K. J. McConnell, M. A. Young, D. L. Beveridge, in preparation.

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Kerry Cecere 
(B.A. Fairfield University, 1996) MBTG Yr. 10.

  • Dissertation Project: "Contribution of Stacking Interactions to the UIA Protein - UIsn RNA Complex" (Prof. A. Baranger, mentor)
  • Graduated with MA in Chemistry, June 1999. Decided to terminate at the MA level for a career change.
  • Current Placement: Research chemist with Purdue Pharma L.P.
  • Publications Based on Dissertation Research:

1.     "Recognition of an Essential Adenine at a Protein:RNA Interface: Comparison of the Contributions of Hydrogen Bonding and Stacking Interactions" S. J. Nolan, J. C. Shiels, J. B. Tuite, K. L. Cecere, A. M. Baranger, J. Am. Chem. Soc. 121, 8951-8952 (1999).

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Karen Sheffield 
(B.A Connecticut College 1995) MBTG Yrs. 07,09.

  • Dissertation Project: The Effects of Anti-Sickling Drugs on Sickle Cell Hemoglobin Fiber Formation. (Prof. I. Mukerji, mentor)
  • Professional Activities: Poster, Tenth Conversation in Biomolecular Stereodynamics, "Polymerization of Fluoromet Sickle Cell Hb" L. Sokolov, K. Sheffield, I. Mukerji. (1997)
  • Graduated with MA in Molecular Biology and Biochemistry, June 1999.
  • Current Placement: Research chemist for Pfizer Pharmaceuticals.
  • Publications Based on Dissertation Research:

1.     "Polymerization of Fluoromet Sickle Cell Hb" L. Sokolov, K. Sheffield, I. Mukerji, manuscript in preparation.

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Vasilios (Bill) Marathias 
(B.A. Clark University 1992) MBTG Yrs. 08,09.

  • Dissertation Project: Solution Structure and Function of DNA Quadruplexes (Prof. P. H. Bolton, mentor)
  • Professional Activities: Connecticut Magnetic Resonance Discussion Group, 1994, 1995, 1996.
  • Graduated with PhD in Chemistry, June 2000.
  • Current Placement: CN, Princeton
  • Publications Based on Dissertation Research:

1.      "Determination of the Number and Location of the Manganese Binding Sites of DNA Quadruplexes in Solution by EPR and NMR in the Presence and Absence of Thrombin" V. M. Marathias, K. Y. Wang, S. Kumar, T. Pham, P. H. Bolton, J. Mol. Biol. 260, 378<394 (1996).

2.     "Determination of Internuclear Angles of DNA Using Paramagnetic Assisted Magnetic Alignment" R. D. Beger, V. M. Marathias, B. F. Volkman, P. H. Bolton, J. Magn. Reson. 135, 256-259 (1998).

3.      "Determinants of DNA Quadruplex Structural Type: Sequence and Potassium Binding" V. M. Marathias, P. H. Bolton, Biochemistry 38, 4355-4364 (1999).

4.   "Damage Increases the Flexibility of Duplex DNA" V. M. Marathias, B. Jerkovic, P. H. Bolton,Nuc. Acids Res. 227, 1854-1858 (1999).

5.   "6-Thioguanine Alters the Structure and Stability of Duplex DNA and Inhibits Quadruplex DNA Formation" V. M. Marathias, M. J. Sawicki, P. H. Bolton, Nucleic Acids Res. 27, 2860-2867 (1999).

6.     "Flexibility and Curvature of Duplex DNA Containing Mismatched Sites as a Function of Temperature" V. M. Marathias, B. Jerkovic, H. Arthanari, P. H. Bolton, Biochemistry 39, 153 (2000).

7.     "Structures of the Potassium Saturated, 2:1, and Intermediate, 1:1, Forms of a Quadruplex DNA" V. M. Marathias, P. H. Bolton, Nucl. Acids. Res. 28, 1969 (2000).  

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Kevin McConnell 
(B.S. Marquette University 1990) MBTG Yrs. 03,04,05,06,11,12.

  • Dissertation Project: Studies of Protein DNA Complexes (Profs. D. L. Beveridge and I. Russu, mentors)
  • Professional Activities: Symposium on Biomolecular Stereodynamics, 1991, 1993 and 1995; Protein: Structure Function and Dynamics (Richards Symposium), 1991; Mathematical Physiology Workshop, 1992; Member, Sigma Xi: The Scientific Research Society, since 1992; Member, Biophysical Society, since 1994; Biophysical Society Annual Meeting, 1994, 1995, 1996; Advances in Protein Science (Nemethy Memorial Symposium) 1994, 1995; Poster, Biophysical Society Meeting, New Orleans 1997.
  • Graduated with PhD in Chemistry (Major: Molecular Biophysics), Aug. 2000.
  • Current Placement: Research Bioinformatics with Agilix Corporation, New Haven, CT.
  • Publications Based on Dissertation Research:

1. "Analysis of Helix Bending in Crystal Structures and Molecular Dynamics Simulations of DNA Oligonucleotides" M. A. Young, R. Nirmala, J. Srinivasan, K. J. McConnell, G. Ravishanker, D. L. Beveridge, H. M. Berman. In Structural Biology: State of the Art, 1993, Proc. 8th Conv. R. H. Sarma, M. H. Sarma, eds., Adenine Press Albany, NY, 1993.

2. "A Nanosecond Molecular Dynamics Trajectory for a B<DNA Double Helix: Evidence for Substrates" K. J. McConnell, R. Nirmala, M. A. Young, G. Ravishanker, D. L. Beveridge, J. Am. Chem. Soc. 116, 4461 (1994).

3. "Molecular Dynamics Simulations of DNA and Protein<DNA Complexes Including Solvent" D.L. Beveridge, K.J. McConnell, R. Nirmala, M.A. Young, S. Vijayakumar, G. Ravishanker. In Structure and Reactivity in Aqueous Solution: Characterization of Chemical and Biological Systems, C. J. Cramer, D. G. Truhar, eds., ACS Symposium Series, Washington, DC, 1994.

4. "Molecular Dynamics Simulations of DNA and a Protein<DNA Complex Including Solvent" D.L. Beveridge, K.J. McConnell, M.A. Young, S. Vijayakumar, G. Ravishanker. In Modeling of Biomolecular Structure and Mechanisms (eds. A. Pullman et al.) Kluwer Academic Publishers: Netherlands, 1995.

5. "Free Energy Analysis of Protein-DNA Binding: The Eco RI Endonuclease-DNA Complex" B. Jayaram, K. McConnell, S. B. Dixit, D. L. Beveridge, J. Comp. Phys. 151, 333-357 (1999).

6. "Nucleic Acids: Theory and Computer Simulation, Y2K" D. L. Beveridge, K. J. McConnell, Curr. Opin. Struct. Biol10, 182-196 (2000).

7. "Analysis of the Binding Free Energy of Protein-DNA Complexes Based on 40 X-Ray Crystal Structures" B. Jayaram, K. J. McConnell, S. B. Dixit, D. L. Beveridge, submitted (2000).

8. DNA Structure: What's in 'Charge'? K. J. McConnell, D. L. Beveridge, J. Mol. Biol., 304, 803-820 (2000).

9. "Molecular Dynamics and Thermodynamics of a Protein-RNA complex: Mutation of a Conserved Aromatic Residue Modifies Stacking Interactions and Structural Adaptation in the U1A-stem Loop 2 RNA Complex" D. M. Blakaj, K. J. McConnell, D. L. Beveridge, A. M. Baranger,  J. Am. Chem. Soc.123, 2548 (2001).

10. "Molecular Dynamics Simulations of B'-DNA: Sequence Effects on A-tract Bending and Bendability" K. J. McConnell, D. L. Beveridge, J. Mol. Biol. (2001), submitted.

11. "Molecular Dynamics Simulations on Crystallographic Unit Cells of d(CGCGAATTCGCG)2 and d(CGCAAAATGCG)2 Comparison with Predicted Solution Structures and Studies of Packing Effects" K. J. McConnell, M. A. Young, D. L. Beveridge, submitted.

12.  "Solution Structure of DNA: Comparing Molecular Dynamics and NMR Results on the Duplexes d(CGCGAATTCGCG) and d(CGCAAAAATGCG), K. J. McConnell and D. L. Beveridge, submitted.

Note : Mr McConnell took a one-year leave of absence from the graduate program and served at Wesleyan as Coordinator of the Life Sciences Divisional Data Laboratory. He returned to full-time graduate research as of June 1997.

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