Recent Publications

All Publications 2002-Present

1.          Jayaram, B., K. McConnell, et al. (2002). “Free-energy component analysis of 40 protein-DNA complexes: A consensus view on the thermodynamics of binding at the molecular level.” Journal of Computational Chemistry 23(1): 1-14.

2.          Kombo, D.C., B., J., J., M.K. and Beveridge, D.L. (2002) Calculation of the Affinity of the lamda Repressor-Operator Complex Based on free Energy Component Analysis. Molecular Simulation, 28, 187-211.

3.          Liu, Y.X. and D.L. Beveridge (2002). “Exploratory studies of ab initio protein structure prediction: Multiple copy simulated annealing, AMBER energy functions, and a Generalized Born/Solvent Accessibility solvation model.” Proteins-Structure Function and Genetics 46(1): 128-146. 32. “Pitici, F., D. L. Beveridge, et al. (2002). “Molecular dynamics simulation studies of induced fit and conformational capture in U1A-RNA binding: Do molecular substrates code for specificity?” Biopolymers 65(6): 424-435.

4.           (2002). “Hidden Markov models from molecular dynamics simulations on DNA.” Proceedings of the National Academy of Sciences of the United States of America 99(13): 8642-8647.

5.           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.

6.           Beveridge, D.L., Barreiro, G., Byun, K.S., Case, D.A., Cheatham, T.E., 3rd, Dixit, S.B., Giudice, E., Lankas, F., Lavery, R., Maddocks, J.H. et al. (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, 3799-3813.

7.          “Beveridge, D. L., S. B. Dixit, et al. (2004). “Molecular dynamics of DNA and protein-DNA complexes: Progress on sequence effects, conformational stability, axis curvature, and structural bioinformatics.” Nucleic Acids: Curvature and Deformation 884: 13-64.

8.           “Beveridge, D. L., S. B. Dixit, et al. (2004). “Molecular dynamics simulations of DNA curvature and flexibility: Helix phasing and premelting.” Biopolymers 73(3): 380-403.

9.            “Byun, K. S. and D. L. Beveridge (2004). “Molecular dynamics simulation of papilloma virus E2 DNA sequences: Dynamical models for oligonucleotide structures in solution.” Biopolymers 73(3): 369-379.

10.          Dixit, S.B., Pitici, F. and Beveridge, D.L. (2004) Structure and axis curvature in two dA6 x dT6 DNA oligonucleotides: comparison of molecular dynamics simulations with results from crystallography and NMR spectroscopy. Biopolymers, 75, 468-479.

11.          “Beveridge, D.L., Barreiro, G. et al. (2004) “Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. I. Research Design and Results on d(cpG) Steps.” Biophysical Journal (87): 1-15. 10. Beveridge, D.L. (2004) “Nucleic acid science articles – Preface.” Biopolymers 73(3): 326-326.

12.           Knee, K.M., Aitken, C.E., Beveridge D.L. et al. (2005) “Theoretical and Experimental Evidence for a Sequential Mechanism for the DNA B ->A Transition.” Biophysical Journal 88(1): 58A-59A.

13.           Zhao, Y., et al. (2006) “Molecular dynamics simulation studies of a protein-RNA complex with a selectively modified binding interface,” Biopolymers 81 (4): 256-69. Morris, B. J., D. J. Adams, et al. (2004). “cAMP controls human renin mRNA stability via specific RNA-binding proteins.” Acta Physiol Scand 181(4): 369-73.

14.          “Ponomarev, S. Y., K. M. Thayer, et al. (2004). “Ion motions in molecular dynamics simulations on DNA.” Proceedings of the National Academy of Sciences of the United States of America 101(41): 14771-14775.

15.          Dixit, S.B. Andrews D.Q., Beveridge, D.L. et al. (2005) “Induced Fit an the Entropy of Structural Adaptation in the Complexation of CAP and Lambda-Repressor with Cognate DNA Sequences,” Biophysical Journal 88(5): 3147-3157.

16.          Dixit, S.B, Beveridge, D.L. (2005) “Axis Curvature and Ligand Induced Bending in the CAP-DNA Oligomers.” Biophysical Journal 88(1): L4-L6.

17.         Dixit, B. S., Beveridge, D.L., et al. (2005) “Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. II: Sequence Context Effects on the Dynamical Structures of the 10 Unique Dinucleotide Steps,” Biophysical Journal 89: 3721-3740

18.         Dixit, S.B, and Beveridge, D.L, (2006) “Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction,” Bioinformatics Applications Notes, Vol. 22 (8) 1007-1009.

19.         Dixit, S.B., Ponomarev, S.Y., and Beveridge, D.L., (2006) “Root Mean Square Deviation Probability Analysis of Molecular Dynamics Trajectories on DNA,” J Chem Inf Model, 46, 1084-1093. Hatchell, E.C., S.M. Colley, et al. (2006). “SLIRP, a small SRA binding protein, is a nuclear receptor compressor.” Mol Cell 22(5): 657-68

20.         Kormos, B.L., Baranger, A.M. and Beveridge, D.L. (2006) Do collective atomic fluctuations account for cooperative effects? Molecular dynamic studies of U1A-RNA complex. J AM Chem Soc, 128, 8992-8993.

21.          Zhao, Y., Kormos, B.L., Beveridge, D.L. and Baranger, A.M. (2006) Molecular dynamics simulation studies of a protein-RNA complex with a selectively modified binding interface.Biopolymers, 81, 256-269.

22.          Kormos, B.L., Baranger, A.M. and Beveridge, D.L. (2007) A Study of collective atomic fluctuations and cooperativity in the U1A-RNA complex based on molecular dynamics simulations. J. Struc. Biol., 157, 500-513.

23.           Kormos, B.L., Benitex, Y., Baranger, A.M. and Beveridge, D.L. (2007) Affinity and Specificity of Protein U1A-RNA Complex Formation Based on an Additive Component Free Energy Model. J Mol Biol, 371, 1405-1419.

24.           Yan, Z., Sikri, S., Beveridge, D.L. and Baranger, A.M. (2007) Identification of an aminoacridine derivative that binds to RNA tetraloops. J Med Chem, 50, 4096-4104.

25.          Zhong, W., Dixit, S. B., Mallis, R. J., Arthanari, H., Lugovskoy, A. A., Beveridge, D. L., Wagner, G. & Reinherz, E. L. (2007). CTL recognition of a protective immunodominant influenza A virus nucleoprotein epitope utilizes a highly restricted Vbeta but diverse Valpha repertoire: functional and structural implications. J Mol Biol 372, 535-48.

26.         Anunciado, D., Agumeh, M., Kormos, B. L., Beveridge, D. L., Knee, J. L. & Baranger, A. M. (2008). Characterization of the dynamics of an essential helix in the U1A protein by time-resolved fluorescence measurements. J Phys Chem B 112, 6122-30.

27.         Knee, K. M., Dixit, S. B., Aitken, C. E., Ponomarev, S., Beveridge, D. L. & Mukerji, I. (2008). Spectroscopic and molecular dynamics evidence for a sequential mechanism for the A-to-B transition in DNA. Biophys J 95, 257-72.

28.          Saunus, J. M., J.D. French, et al. (2008). “Posttranscriptional regulation of the breast cancer susceptibility gene BRCA1 by the RNA binding protein HuR.” Cancer Res 68(22):9469-78

29.          Singhal, P., Jayaram, B., Dixit, S. B. & Beveridge, D. L. (2008). Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations. Biophys J 94, 4173-83.

30.          Sen, S., Andreatta, D., Ponomarev, S. Y., Beveridge, D. L. & Berg, M. A. (2009). Dynamics of water and ions near DNA: comparison of simulation to time-resolved stokes-shift experiments. J Am Chem Soc 131, 1724-35.

31.          Lavery, R., Zakrzewska, K., Beveridge, D., Bishop, T. C., Case, D. A., Cheatham, T., 3rd, Dixit, S., Jayaram, B., Lankas, F., Laughton, C., Maddocks, J. H., Michon, A., Osman, R., Orozco, M., Perez, A., Singh, T., Spackova, N. & Sponer, J. (2010). A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformat. Nucleic Acids Res. 38, 299-313.

32.           Kormos, B. L. Pieniazek, S., Beveridge, D.L. (2010) U1A Protein -Stem Loop 2 RNA Recognition: Structural Differences in F56 Mutants from MD Simulations, Biopolymers, .

33.           Pieniazek, S. Hingorani, M., Beveridge, (2011) D.L. Dynamical Allosterism in a Mismatch Repair Protein, MutS, Biophysical Journal, 101, 1730-9.

34.           Wheatley, E.G., Pieniazek, S.N., Mukerji, I., Beveridge, D.L, (2012) Molecular dynamics of a DNA Holliday junction: the inverted repeat sequence d(CCGGTACCGG)(4), Biophys J. 102, 552-60.

35.           Beveridge, D.L., Cheatham, T.E., 3rd, Mezei, M., (2012) The ABCs of molecular dynamics simulations on B-DNA, circa 2012, J. Biosci. 37, 379-97.

36.           Dixit, S.B., Mezei, M., Beveridge, D.L. (2012) Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations, J Biosci., 37, 399-421.

37.           Khandelwal, G., Lee, R.A., Jayaram, B., Beveridge, D.L. (2014) A statistical thermodynamic model for investigating the stability of DNA sequences from oligonucleotides to genomes, Biophys. J., 106, 2465-73.