Publications

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

Young, M. A., J. Srinivasan, I. Goljer, S. Kumar, D. L. Beveridge, and P. H. Bolton. 1995. Structure determination and analysis of local bending in an A-tract DNA duplex: comparison of results from crystallography, nuclear magnetic resonance, and molecular dynamics simulation on d(CGCAAAAATGCG). Methods Enzymol. 261:121-144.

Young, M. A., G. Ravishanker, D. L. Beveridge, and H. M. Berman. 1995. Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes. Biophys. J. 68:2454-2468.

Young, M. A., G. Ravishanker, and D. L. Beveridge. 1997. A 5-Nanosecond Molecular Dynamics Trajectory for B-DNA: Analysis of Structure, Motions and Solvation. Biophys. J. 73:2313-2336.

Flatters, D., M. A. Young, D. L. Beveridge, and R. Lavery. 1997. Conformational Properties of the TATA Box Binding Sequence of DNA. J. Biomol. Struct. Dyn. 14:1-8.

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

Sprous, D., M. A. Young, and D. L. Beveridge. 1997. Molecular Dynamics Studies of the Conformational Preferences of a DNA Double Helix in Water and in an Ethanol:Water Mixture:  Theoretical Considerations of the A/B Transition. J. Phys. Chem. 102:4658-4667.

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

Jayaram, B., D. Sprous, M. A. Young, and D. L. Beveridge. 1998. Molecular Origins of the Conformational Stability of A and B Forms of DNA in Solution. J. Am. Chem. Soc. 120:10629-10633.

Young, M. A., B. Jayaram, and D. L. Beveridge. 1998. The Local Dielectric Behavior Environment of B-DNA in Solution: Results from a 14 Nanosecond Molecular Dynamics Trajectory. J. Chem. Phys. 102(39):7666-7669..

Sprous, D., M. A. Young, and D. L. Beveridge. 1999. Molecular Dynamics Studies of Axis Bending in Oligonucleotide Duplexes d[G5-(GA4T4C)2-C5] and d[G5-(GA4T4C)2-C5] in Salt Solutions. J. Mol. Biol.285(4):1623-32.

Kombo, D. C., M. A. Young, and D. L. Beveridge. 2000. One Nanosecond Molecular Dynamics Simulation of the N-Terminal Domain of the l-Repressor Protein. Biopolymers. 53(7): 596-605.

Kombo, D. C., M. A. Young, and D. L. Beveridge. 2000. Molecular dynamics simulation accurately predicts the experimentally-observed distributions of the (C, N, O) protein atoms around water molecules and sodium ions. Proteins. 39(3):212-215.

Cheatham, T.E., 3rd, and Young, M.A. (2000). Molecular dynamics simulation of nucleic acids: successes, limitations, and promise. Biopolymers 56, 232-256.

Young, M.A., S. Gonfloni, G. Superti-Furga, B. Roux, J. Kuriyan. 2001. Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation. Cell. 105, 115–126.

Jeruzalmi D, Yurieva O, Zhao Y, Young M, Stewart J, Hingorani M, O'Donnell M, Kuriyan J. 2001. Mechanism of processivity clamp opening by the delta subunit wrench of the clamp loader complex of E. coli DNA polymerase III. Cell 106(4):417-28.

Kombo DC, McConnell KJ, Young MA, Beveridge DL. 2001. Molecular dynamics simulation reveals sequence-intrinsic and protein- induced geometrical features of the OL1 DNA operator. Biopolymers 59(4):205-25.

Wisniewski, D., Lambek, C. L., Liu, C., Strife, A., Veach, D. R., Nagar, B., Young, M. A., Schindler, T., Bornmann, W. G., Bertino, J. R., et al. 2002. Characterization of potent inhibitors of the Bcr-Abl and the c-kit receptor tyrosine kinases. Cancer Res 62, 4244-4255.

 

Nagar, B., O. Hantschel, M.A. Young, K. Scheffzek, D. Veach, W. Bornmann, B. Clarkson, G. Superti-Furga, and J. Kuriyan. 2003. Structural basis for the auto-inhibition of c-Abl tyrosine kinase, Cell, 112, 859-871.

 

Arthanari, H., McConnell, K. J., Beger, R., Young, M. A., Beveridge, D. L., and Bolton, P. H. 2003. Assessment of the molecular dynamics structure of DNA in solution based on calculated and observed NMR NOESY volumes and dihedral angles from scalar coupling constants. Biopolymers 68, 3-15.

 

Beveridge, D. L., G. Barreiro, K. S. Byun, D. A. Case, T. E. Cheatham, 3rd, S. B. Dixit, E. Giudice, F. Lankas, R. Lavery, J. H. Maddocks, R. Osman, E. Seibert, H. Sklenar, G. Stoll, K. M. Thayer, P. Varnai and M. A. Young 2004. Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps. Biophys J 87(6): 3799-813.

 

Seeliger, M. A., M. Young, M. N. Henderson, P. Pellicena, D. S. King, A. M. Falick and J. Kuriyan 2005. High yield bacterial expression of active c-Abl and c-Src tyrosine kinases. Protein Sci.

 

Young, M.A., N.P. Shah, L.H. Chao, M. Seeliger, Z.V. Milanov, W.H.B. III, D.K. Treiber, H.K. Patel, P.P. Zarrinkar, D.J. Lockhart, C.L. Sawyers and J. Kuriyan 2006. Structure of the kinase domain of an imatinib-resistant Abl mutant in complex with the Aurora kinase inhibitor VX-680. Cancer Research. 66(2): 1007-1014.

 

Nicholas M. Levinson, Olga Kuchment, Kui Shen, Matthew A.Young, Michael Koldobskiy, Martin Karplus, Philip A. Cole, John Kuriyan. 2006. A Src-Like Inactive Conformation in the Abl Tyrosine Kinase Domain. PLoS Biology.

 

Eric S. Simon, Matthew Young, Antonia Chan, Zhao-Qin Bao, and Philip C. Andrews. 2008. Improved Enrichment Strategies for Phosphorylated Peptides on Titanium Dioxide Using Methyl Esterification and pH Gradient Elution. Analytical Biochemistry (in press).

 

Articles Accepted for Publication

Anil K. Nair, Matthew A. Young and K. M. J. Menon. 2008. Regulation of Luteinizing Hormone Receptor mRNA Expression by Mevalonate Kinase:  Role of the Catalytic Center in mRNA Recognition. FEBS Journal.

 

Chapters in Books

Young, M. A., R. Nirmala, J. Srinivasan, K. J. McConnell, G. Ravishanker, D. L. Beveridge, and H. M. Berman. 1994. Analysis of Helix Bending in Crystal Structures and Molecular Dynamics Simulations of DNA Oligonucleotides. In Structural Biology: The State of the Art. Proceedings of the 8th Conversation. Adenine Press, Albany, New York. 197-214.

Beveridge, D. L., K. J. McConnell, R. Nirmala, and M. A. Young. 1994. Molecular Dynamics Simulations of DNA and Protein-DNA Complexes Including Solvent: Recent Progress.  ACS symposium series. 568:381-394.

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

Sprous, D., W. Wang, G. Ravishanker, M. A. Young, and D. L. Beveridge. 1998. Molecular Dynamics Information Extraction. In Rational Drug Design. Springer-Verlag, New York. 127-148.

Beveridge, D. L., M. A. Young, and D. Sprous. 1998. Modeling of DNA via Molecular Dynamics Simulation: Structure, Bending, and Conformational Transitions. In Molecular Modeling of Nucleic Acids. American Chemical Society, Washington, D.C. 260-284.

Young, M.A., and Kuriyan, J.  Structures of Ser/Thr and Tyr Kinases.  In Handbook of Cell Signalling. Academic Press. 2003.