Publications

Publications

2014

P.J. Buske, A. Mittal, R.V. Pappu, P.A. Levin (2014) An intrinsically disordered linker plays a critical role in bacterial cell division. Seminars in Cell and Developmental Biology. In Press

K. M. Ruff, S.J. Khan, R.V. Pappu (2014) A Coarse-Grained Model for Polyglutamine Aggregation Modulated by Amphipathic Flanking Sequences. Biophysical Journal 107: 1226-1235. Access Article - Highlighted on the Biophysical Journal home page

R.V. Pappu (2014) Frozen In Beta (Invited New & Notable Piece). Biophysical Journal 107: 795-797. Access Article

W. Xu, M.R. Edwards, D.M. Borek, A.R. Feagins, A. Mittal, J.B. Alinger, K.N. Berry, B.Yen, J. Hamilton, T.J. Brett, R.V. Pappu, D.W. Leung, C.F. Basler, G.K. Amarasinghe (2014) Ebola Virus VP24 Targets a Unique NLS Binding Site on Karyopherin Alpha 5 to Selectively Compete with Nuclear Import of Phosphorylated STAT1. Cell Host & Microbe, 16: 187-200. Free featured article. Access Article

A. Vitalis, R.V. Pappu (2014) A Simple Molecular Mechanics Integrator in Mixed Rigid Body and Dihedral Angle Space. Journal of Chemical Physics, 141: 034105. Access Article

A. Mittal, N. Lyle, T. S. Harmon, R. V. Pappu (2014) Hamiltonian Switch Metropolis Monte Carlo Simulations for Improved Conformational Sampling of Intrinsically Disordered Regions Tethered to Ordered Domains of Proteins. Journal of Chemical Theory and Computation, 10: 3550-3562. Access Article

A. T. Tubbs, Y. Dorsett, E. Chan, B. Helmink, B. Lee, P. Hung, R. George, A. L. Bredemeyer, A. Mittal, R. V. Pappu, D. Chowdhury, N. Mosammaparast, M. S. Krangel, B. P. Sleckman (2014) KAP-1 Promotes Resection of Broken DNA Ends Not Protected by γ-H2AX and 53BP1 in G1-Phase Lymphocytes. Molecular and Cellular Biology, 34: 2811-2821. Access Article

R. van der Lee, M. Buljan, B. Lang, R. J. Weatheritt, G.W. Daughdrill, A. K. Dunker, M.Fuxreiter, J. Gough, J. Gsponer, D. T. Jones, P. M. Kim, R. W. Kriwacki, C. J. Oldfield, R. V. Pappu, P. Tompa, V. N. Uversky, P. E. Wright, M. M. Babu (2014) Classification of Intrinsically Disordered Regions and Proteins. Chemical Reviews, 114: 6589-6631. Access Article

B. Luan, N. Lyle, R.V. Pappu, D.P. Raleigh (2014) Denatured State Ensembles with the Same Radius of Gyration Can Form Significantly Different Long-Range Contacts. Biochemistry, 53: 39-47. Access Article - Highlighted on the Biochemistry Journal home page


2013

S.L. Crick, K.M. Ruff, K. Garai, C. Frieden, R.V. Pappu (2013) Unmasking the Roles of N- and C-terminal Flanking Sequences From Exon 1 of Huntingtin as Modulators of Polyglutamine Aggregation. Proceedings of the National Academy of Sciences USA, 110: 20075-20080 Access Article

R.K. Das, R.V. Pappu (2013) Conformations of Intrinsically Disordered Proteins are Influenced by Linear Sequence Distributions of Oppositely Charged Residues. Proceedings of the National Academy of Sciences USA, 110: 13392-13397. Access Article - Highlighted as one of the 'hot new papers' at the 2014 IDR GRC

N. Lyle, R.K. Das, R.V. Pappu. (2013). A Quantitative Measure for Protein Conformational Heterogeneity. Journal of Chemical Physics. 139: 121907. Access Article.

W. Meng, B. Luan, N. Lyle, R.V. Pappu, D.P. Raleigh (2013) The Denatured State Ensemble Contains Significant Local and Long-range Structure Under Native Condition: Analysis of the N-terminal Domain of the Ribosomal Protein L9. Biochemistry, 52: 2662-2671. Access Article

W. Meng*, N. Lyle*, B. Luan, D.P. Raleigh, R.V. Pappu [*Co-first-authors] (2013) Experiments and Simulations Show How Long-Range Contacts Can Form in Expanded Unfolded Proteins with Negligible Secondary Structure. Proceedings of the National Academy of Sciences USA, 110: 2123-2128. Access Article

A.H. Mao, N. Lyle, R.V. Pappu (2013) Describing Sequence-Ensemble Relationships for Intrinsically Disordered Proteins. Biochemical Journal, 449: 307-318. Access Article - Cover article

R.K. Das, A. Mittal, R.V. Pappu (2013) How is Functional Specificity Achieved Through Disordered Regions of Proteins? BioEssays, 35:17-22 . Access Article


2012

M.M. Babu, R.W. Kriwacki, R.V. Pappu (2012) Versatility from Protein Disorder. Science, 337:1460-1461. Access Article

A.H. Mao, R.V. Pappu (2012) Crystal Lattice Properties Fully Determine Short-Range Interaction Parameters for Alkali and Halide Oons. Journal of Chemical Physics, 137: 064104(1-9). Access Article

R.K. Das, A.H. Mao, R.V. Pappu (2012) Unmasking Functional Motifs within Disordered Regions of Proteins. Science Signaling, 5: pe17. Access Article

A. Radhakrishnan, A. Vitalis, A.H. Mao, A.T. Steffen, R.V. Pappu (2012) Improved Atomistic Monte Carlo Simulations Demonstrate that Poly-L-Proline Adopts Heterogeneous Ensembles of Conformations of Semi-Rigid Segments Interrupted by Kinks. Journal of Physical Chemistry B, 116: 6862-6871. Access Article

S.L. Crick, R.V. Pappu (March 27, 2012) Thermodynamic and Kinetic Models for Aggregation of Intrinsically Disordered Proteins. Book chapter in Peptide Folding, Misfolding, and Nonfolding, pp. 413-440. Ed. Reinhard Schweitzer-Stenner, Vladimir Uversky. John Wiley & Sons, Hoboken, NJ. Access Article or Download Copy

R.K. Das, S.L. Crick, R.V. Pappu (2012) N-terminal Segments Modulate the α-Helical Propensities of the Intrinsically Disordered Basic Regions of bZIP Proteins. Journal of Molecular Biology, 416: 287-299. Access Article - Selected and evaluated by Faculty of 1000


2011

A. Vitalis, R.V. Pappu (2011) Assessing the Contribution of Heterogeneous Distributions of Oligomers to Aggregation Mechanisms of Polyglutamine Peptides. Biophysical Chemistry, 159: 14-23. Access Article

R. Halfmann, S. Alberti, R. Krishnan, N. Lyle, C.W. O'Donnell, O.D. King, B. Berger, R.V. Pappu, S. Lindquist (2011) Opposing Effects of Glutamine and Asparagine Govern Prion Formation by Intrinsically Disordered Proteins. Molecular Cell, 43: 72-84. Access Article

A.H. Mao, R.V. Pappu (2011) Exact Recording of Metropolis-Hastings-Class Monte Carlo Simulations Using One Bit Per Sample. Computer Physics Communications, 182: 1452-1454. Access Article

D.G. Thomas, R.V. Pappu, N.A. Baker (2011) NanoParticle Ontology for Cancer Nanotechnology Research. Journal of Biomedical Informatics, 44: 59-74. Access Article.


2010

M.A. Wyczalkowski, A. Vitalis, R.V. Pappu (2010) New Estimators for Calculating Solvation Entropy and Enthalpy and Comparative Assessments of their Accuracy and Precision. Journal of Physical Chemistry B, 114: 8166-8180. Access Article

A.H. Mao, S.L. Crick, A. Vitalis, C. Chicoine, R.V. Pappu (2010) Net Charge Per Residue Modulates Conformational Ensembles of Intrinsically Disordered Proteins. Proceedings of the National Academy of Sciences USA, 107: 8183-8188. Access Article

T.E. Williamson, A. Vitalis, S.L. Crick, R.V. Pappu (2010) Modulation of Polyglutamine Conformations and Dimer Formation by the N-terminus of Huntingtin. Journal of Molecular Biology, 396: 1295-1309. Access Article


2009

X. Hu, S.L. Crick, G. Bu, C. Frieden, R.V. Pappu, J-M. Lee (2009) Amyloid Seeds Formed by Cellular Uptake, Concentration, and Aggregation of the Amyloid-Beta Peptide. Proceedings of the National Academy of Sciences USA, 106: 20324-20329. Access Article

A.A. Chen, M. Marucho, N.A. Baker, R.V. Pappu (2009) Simulations of RNA Interactions with Monovalent Ions. Methods in Enzymology, 469: 406-426.Access Article

D.G. Thomas, R.V. Pappu, N.A. Baker (2009) NPO: Ontology for Cancer Nanotechnology Research. Nature Precedings, EMBC 2009, Annual International Conference of the IEEE 3-6 Sept. 2009. Access Article

H.A. Lashuel, R.V. Pappu (2009) Amyloids Go Genomic: Insights Regarding the Sequence Determinants of Prion Formation from Genome-Wide Studies. ChemBioChem , 10: 1951-1954. Access Article

A. Vitalis, N. Lyle, R.V. Pappu (2009) Thermodynamics of beta sheet formation in polyglutamine. Biophysical Journal, 97: 303-311. Feature Article Access Article

A.A. Chen, D.E. Draper, R.V. Pappu (2009) Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop. Journal of Molecular Biology, 390: 805-819. Access Article

A. Vitalis, R.V. Pappu (2009) Methods for Monte Carlo Simulations of Biomacromolecules. Annual Reports in Computational Chemistry, 5: 49-76. Access Article (**Please note that there is a typo in equation (1) where max should be min).

R.V. Pappu, R. Nussinov (2009) Protein folding: Lessons Learned and New Frontiers. Physical Biology, 6: 010301. Access Article

A. Vitalis, R.V. Pappu(2009) ABSINTH: A New Continuum Solvation Model for Simulations of Polypeptides in Aqueous Solutions. Journal of Computational Chemistry, 30: 673-700. Access Article - Cover picture


2008

A. Vitalis, X. Wang, R.V. Pappu (2008) Atomistic Simulations of the Effects of Polyglutamine Chain Length and Solvent Quality on Conformational Equilibria and Spontaneous Homodimerization. Journal of Molecular Biology, 384: 279-297. Access Article

H.T. Tran, A. Mao, R.V. Pappu (2008) Role of Backbone-Solvent Interactions in Determining Conformational Equilibria of Intrinsically Disordered Polypeptides. Journal of the American Chemical Society, 130: 7380-7392. Access Article

M. A. Wyczalkowski, R.V. Pappu (2008) Satisfying the Fluctuation Theorem in Free Energy Calculations with Hamiltonian Replica Exchange. Physical Review E, 77: 026104. Access Article

R.V. Pappu, X. Wang, A. Vitalis, S.L. Crick (2008) A Polymer Physics Pperspective on Driving Forces and Mechanisms for Protein Aggregation. Archives of Biochemstry and Biophysics, 469: 132-141. Access Article


2007

A.A. Chen, R.V. Pappu (2007) Parameters of Monovalent Ions in the AMBER-99 Forcefield: Assessment of Inaccuracies and Proposed Improvements. Journal of Physical Chemstry B, 111: 11884-11887. Access Article

A. Vitalis, X. Wang, R.V. Pappu (2007) Quantitative Characterization of Intrinsic Disorder in Polyglutamine: Insights from Analysis Based on Polymer Theories. Biophyscal Journal, 93: 1923-1937. Access Article

A.A. Chen, R.V. Pappu (2007) Quantitative Characterization of Ion Pairing and Cluster Formation in Strong 1:1 Electrolytes. Journal of Physical Chemistry B, 111: 6469-6478. Access Article


2006

S.L. Crick, M. Jayaraman, C. Frieden, R. Wetzel, R.V. Pappu (2006) Fluorescence Correlation Spectroscopy Shows That Monomeric Polyglutamine Molecules Form Collapsed Structures in Aqueous Solutions. Proceedings of the National Academy of Sciences USA, 103: 1674-1679. Access Article

H.T. Tran, R.V. Pappu (2006) Toward an Accurate Theoretical Framework for Describing Ensembles for Proteins Under Strongly Denaturing Donditions. Biophyscal Journal, 91: 1868-1886. Access Article

X. Wang, A. Vitalis, M.A. Wyczalkowski, R.V. Pappu (2006) Characterizing the Conformational Ensemble of Monomeric Polyglutamine. Proteins: Structure, Function and Bioinformatics, 63: 297-311. Access Article


2005 and earlier

H.T. Tran, X. Wang, R.V. Pappu (2005) Reconciling Observations of Sequence-Specific Conformational Preferences with the Generic Behavior of Denatured Proteins. Biochemistry, 44: 11369-11380. Access Article

A. Patriciu, G.S. Chirikjian, R.V. Pappu (2004) Analysis of the Conformational Dependence of Mass-metric Tensor Determinants in Serial polymers with Constraints. Journal of Chemical Physics, 121: 12708-12720. Access Article

A.N. Drozdov, A. Grossfield, R.V. Pappu (2004) The Role of Solvent in Determining Conformational Preferences of Alanine Dipeptide in Water. Journal of the American Chemical Society, 126: 2574-2581. Access Article

R.V. Pappu, G.D.Rose (2002) A Simple Model for Polyproline II Structure in Unfolded States of Alanine-Based Peptides. Protein Science, 11: 2437-2455. Access Article

R.V. Pappu, R. Srinivasan, G.D. Rose (2000) The Flory Isolated Pair Hypothesis is not Valid for Polypeptide Chains: Implications for Protein Folding. Proceedings of the National Academy of Sciences USA, 97: 12565-12570. Access Article

R.K. Hart, R.V. Pappu, J.W. Ponder (2000) Exploring the Similarities Between Potential Smoothing and Simulated Annealing. Journal of Computational Chemistry, 97: 12565-12570. Access Article

R.V. Pappu (1999) Review of the Fourth Johns Hopkins Protein Folding Meeting. Proteins: Structure Function, Genetics, 36: 263-269. Access Article

R.V. Pappu, G.R. Marshall, J.W. Ponder (1999) A Potential Smoothing Algorithm Accurately Predicts Transmembrane Helix Packing. Nature Structural Biology, 6: 50-55. Access Article

R.V. Pappu, R.K. Hart, J.W. Ponder (1998) Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization. Journal of Physical Chemistry B, 102: 9725-9742. Access Article

E.S. Huang, P. Koehl, M. Levitt, R.V. Pappu, J.W. Ponder (1998) Accuracy of Side-Chain Prediction Upon Near-Native Protein Backbones Generated by Ab Initio Folding Methods. Proteins: Structure, Function, Genetics, 33: 204-217. Access Article

R.V. Pappu, D.L. Weaver (1998) The Early Folding Kinetics of Apomyoglobin. Protein Science, 7: 480-9742. Access Article

R.V. Pappu, W.J. Schneller, D.L. Weaver (1996) Electrostatic Multipole Representation of a Polypeptide Chain: An Algorithm for Simulation of Polypeptide Properties. Journal of Computational Chemistry, 17: 1033-1045. Access Article