E.A. Newcombe*, K.M. Ruff*, A. Sethi, A. Ormsby, Y.M. Ramdzan, A. Fox, A.W. Purcell, P.R. Gooley, R.V. Pappu✝, D.M. Hatters✝ [*Co-first authors, ✝Co-corresponding authors] (2017) Tadpole-like conformations of huntingtin exon 1 with expanded polyglutamine engenders novel interactions in cells. Access pre-print
H. Mirbaha, O.A. Morozova, K.M. Ruff, A. Sharma, R.V. Pappu, D.W. Colby, H. Mirzaei, L.A. Joachimiak, M.I. Diamond (2017) Inert and seed-competent tau monomers elucidate the structural origins of aggregation. Access pre-print
L.P. Bergeron-Sandoval, H.K. Heris, A.G. Hendricks, A.J. Ehrlicher, P. Francois, R.V. Pappu, S.W. Michnick (2017) Endocytosis caused by liquid-liquid phase separation of proteins. Access pre-print
J. Fei*✝, M. Jadaliha*, T.S. Harmon$, I.T.S. Li$, B. Hua, Q. Hao, A.S. Holehouse, M. Reyer, Q. Sun, S.M. Freier, R.V. Pappu, K.V. Prasanth✝, and T. Ha (*Co-first authors, $ Equal contribution, ✝Co-corresponding authors) (2017) Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution.
Journal of Cell Science. Advanced Online Access
T.S. Harmon, A.S. Holehouse, M.K. Rosen, R.V. Pappu (2017) Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins.
eLife 6:30294. Access Article
A.S. Holehouse, R.V. Pappu (2017) FUS Zigzags Its Way to Cross Beta. (Invited Preview)
Cell, 171: 499-500. Access Article
J.B. Warner IV*, K.M. Ruff*, P.S. Tan, E.A. Lemke, R.V. Pappu✝, H.A. Lashuel✝ (*Co-first authors, ✝Co-corresponding authors) (2017) Monomeric huntingtin exon 1 has similar overall structural features for wild type and pathological polyglutamine lengths.
Journal of the American Chemical Society, 139:14456-14469. Access Article
** News coverage (C&E news)
** News coverage (Washington University)
K. Sherry, R.K. Das, R.V. Pappu✝, D. Barrick✝ [✝Co-corresponding authors] (2017) Control of transcriptional activity by design of charge patterning in the intrinsically disordered RAM region of the Notch receptor.
K.M. Ruff✝, A.S. Holehouse [✝Corresponding author] (2017) SAXS versus FRET: A matter of heterogeneity? (Invited New & Notable Piece),
G. Fuertes*, N. Banterle*, K.M. Ruff*, A. Chowdhury, D. Mercadante, C. Koehler, M. Kachala, G.E. Girona, S. Milles, A. Mishra, P.R. Onck, F. Gräter, S. Esteban-Martin, R.V. Pappu✝, D.I. Svergun✝, E.A. Lemke✝ [*Co-first authors, ✝Co-corresponding authors] (2017) Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS versus FRET measurements.
M.T. Wei*, S. Elbaum-Garfinkle*, A.S. Holehouse*, C.C.H. Chen, M. Feric, C.B. Arnold, R.D. Priestley, R.V. Pappu✝, C.P. Brangwynne✝ [*Co-first authors, ✝Co-corresponding authors] (2017) Phase behaviour of disordered proteins underlying low density and high permeability of liquid organelles.
** News coverage (EurekaAlert)
** News coverage (Princeton University)
** IDP State Letter Summary
S. Chatterjee, P. Luthra, E. Esaulova, E. Agapov, B. Yen, D. Borek, M. Edwards, A. Mittal, D. Jordan, P. Ramanan, M. Moore, R.V. Pappu, M. Holtzman, M.N. Artyomov, C. Basler, G. Amarasinghe, and D. Leung (2017) Structural basis for human respiratory syncytial virus NS1-mediated modulation of host responses.
** News coverage (EurekAlert)
J. Clarke & R.V. Pappu (2017) Protein Folding and Binding, Complexity Comes of Age.
P. Sormanni, D. Piovesan, G. Heller, M. Bonomi, P. Kukic, C. Camilloni, M. Fuxreiter, Z. Dosztanyi, R.V. Pappu, M.M. Babu, S. Longhi, P.S. Tompa, A.K. Dunker, V.N. Uversky, S. Tosatto, M. Vendruscolo (2017) Simultaneous quantification of protein order and disorder. (Commentary).
T.S. Harmon, A.S. Holehouse, R.V. Pappu (2017) To mix, or to demix, that is the question (Invited New & Notable Piece),
V. Kalas, J.S. Pinkner, T.J. Hannan, M.E. Hibbing, K.W. Dodson, A.S. Holehouse, H. Zhang, N.H. Tolia, M.L. Gross, R.V. Pappu, J. Janetka, S.J. Hultgren (2017) Evolutionary fine-tuning of conformational ensembles in FimH during host-pathogen interactions.
A.S. Holehouse✝, R.K. Das, J.N. Ahad, M.O.G. Richardson, R.V. Pappu✝ [✝Co-corresponding authors] (2017) CIDER: Resources to analyze sequence-ensemble relationships of intrinsically disordered proteins.
E.W. Martin*, A.S. Holehouse*, C.R. Grace, A. Hughs, R.V. Pappu✝, T. Mittag✝ [*Co-first authors, ✝Co-corresponding authors] (2016) Sequence Determinants of the Conformational Properties of an Intrinsically Disordered Protein Prior to and Upon Multisite Phosphorylation.
T.S. Harmon, M.D. Crabtree, S.L. Shammas, A.E. Posey, J. Clarke, R.V. Pappu (2016) GADIS: Algorithm for Designing Sequences to Achieve Target Secondary Structure Profiles of Intrinsically Disordered Proteins.
C.W. Pak, M. Kosno, A.S. Holehouse, S.B. Padrick, A. Mittal, R. Ali, A.A. Yunus, D.R. Liu, R.V. Pappu✝, M.K. Rosen✝ [✝Co-corresponding authors] (2016) Sequence Determinants of Intracellular Phase Separation by Complex Coacervation of a Disordered Protein.
M. Feric, N. Vaidya, T.S. Harmon, D.M. Mitrea, L. Zhu, T.M. Richardson, R.W. Kriwacki, R.V. Pappu, C.P. Brangwynne (2016) Coexisting Liquid Phases Underlie Nucleolar Subcompartments.
** News coverage (EurekAlert)
** News coverage (Princeton University)
R.K. Das, Y. Huang, A. H. Phillips, R.W. Kriwacki, R.V. Pappu (2016) Cryptic Sequence Features Within the Disordered Protein p27Kip1 Regulate Cell Cycle Signaling.
** News coverage (Phys.org)
** IDP State Letter Summary
S. Banjade, Q. Wu, A. Mittal, W.B. Peeples, R.V. Pappu, M.K. Rosen (2015) A Conserved Interdomain Linker Promotes Phase Separation of the Multivalent Adaptor Protein Nck.
K.M. Ruff, T.S. Harmon, R.V. Pappu (2015) CAMELOT: A Machine Learning Approach for Coarse-grained Simulations of Aggregation of Block-copolymeric Protein Sequences.
C.P. Brangwynne, P.S. Tompa, R.V. Pappu (2015) Polymer Physics of Intracellular Phase Transitions.
A.S. Holehouse, R.V. Pappu (2015) Encoding phase transitions. (Invited News & Views Piece),
R.K. Das, K.M. Ruff, R.V. Pappu (2015) Relating Sequence Encoded Information to Form and Function of Intrinsically Disordered Proteins.
M.I. Diamond, S. Cai, A. Boudreau, C.J. Carey Jr., N. Lyle, R.V. Pappu, S.J. Swamidass, M. Bissell, H. Piwnica-Worms, J. Shao (2015) Subcellular Localization and Ser-137 Phosphorylation Regulate Tumor-Suppressive Activity of Profilin-1.
A.S. Holehouse, K. Garai, N. Lyle, A. Vitalis, R.V. Pappu (2015) Quantitative Assessments of the Distinct Contributions of Polypeptide Backbone Amides versus Sidechain Groups to Chain Expansion via Chemical Denaturation.
A.G. Kozlov, E. Weiland, A. Mittal, V. Waldman, E. Antony, N. Fazio, R.V. Pappu, T.M. Lohman (2015) Intrinsically Disordered C-terminal Tails of E.coli Single Stranded DNA Binding Protein Regulate Cooperative Binding to Single Stranded DNA.
A. Mittal, R.K. Das, A. Vitalis, R.V. Pappu (2015) ABSINTH Implicit Solvation Model and Force Field Paradigm for Use in Simulations of Intrinsically Disordered Proteins. Book chapter in Computational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods, pp. 181-201. Ed. Monika Fuxreiter. CRC Press, Boca Raton, FL. Link to book (Amazon)
R.V. Pappu (2015) Cell Signaling, Division, and Organization Mediated by Intrinsically Disordered Proteins.
P.J. Buske, A. Mittal, R.V. Pappu, P.A. Levin (2015) An Intrinsically Disordered Linker Plays a Critical Role in Bacterial Cell Division.
L. Ripaud, V. Chumakova, M. Antonin, A. Hastie, S. Pinkert, R. Koerner, K.M. Ruff, R.V. Pappu, D. Hornburg, M. Mann, F. U. Hartl, M. S. Hipp (2014) Overexpression of Q-rich prion-like Proteins Suppresses PolyQ Cytotoxicity and Alters the PolyQ Interactome.
K. M. Ruff, S.J. Khan, R.V. Pappu (2014) A Coarse-Grained Model for Polyglutamine Aggregation Modulated by Amphipathic Flanking Sequences.
R.V. Pappu (2014) Frozen In Beta (Invited New & Notable Piece),
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.
A. Vitalis, R.V. Pappu (2014) A Simple Molecular Mechanics Integrator in Mixed Rigid Body and Dihedral Angle Space.
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.
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.
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.
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.
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.
R.K. Das, R.V. Pappu (2013) Conformations of Intrinsically Disordered Proteins are Influenced by Linear Sequence Distributions of Oppositely Charged Residues.
N. Lyle, R.K. Das, R.V. Pappu. (2013) A Quantitative Measure for Protein Conformational Heterogeneity.
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.
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.
A.H. Mao, N. Lyle, R.V. Pappu (2013) Describing Sequence-Ensemble Relationships for Intrinsically Disordered Proteins.
R.K. Das, A. Mittal, R.V. Pappu (2013) How is Functional Specificity Achieved Through Disordered Regions of Proteins?
M.M. Babu, R.W. Kriwacki, R.V. Pappu (2012) Versatility from Protein Disorder.
A.H. Mao, R.V. Pappu (2012) Crystal Lattice Properties Fully Determine Short-Range Interaction Parameters for Alkali and Halide Ions.
R.K. Das, A.H. Mao, R.V. Pappu (2012) Unmasking Functional Motifs within Disordered Regions of Proteins.
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.
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.
A. Vitalis, R.V. Pappu (2011) Assessing the Contribution of Heterogeneous Distributions of Oligomers to Aggregation Mechanisms of Polyglutamine Peptides.
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.
A.H. Mao, R.V. Pappu (2011) Exact Recording of Metropolis-Hastings-Class Monte Carlo Simulations Using One Bit Per Sample.
D.G. Thomas, R.V. Pappu, N.A. Baker (2011) NanoParticle Ontology for Cancer Nanotechnology Research.
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.
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.
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.
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.
A.A. Chen, M. Marucho, N.A. Baker, R.V. Pappu (2009) Simulations of RNA Interactions with Monovalent Ions.
D.G. Thomas, R.V. Pappu, N.A. Baker (2009) NPO: Ontology for Cancer Nanotechnology Research.
H.A. Lashuel, R.V. Pappu (2009) Amyloids Go Genomic: Insights Regarding the Sequence Determinants of Prion Formation from Genome-Wide Studies.
A. Vitalis, N. Lyle, R.V. Pappu (2009) Thermodynamics of beta sheet formation in polyglutamine.
A.A. Chen, D.E. Draper, R.V. Pappu (2009) Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop.
A. Vitalis, R.V. Pappu (2009) Methods for Monte Carlo Simulations of Biomacromolecules.
R.V. Pappu, R. Nussinov (2009) Protein folding: Lessons Learned and New Frontiers.
A. Vitalis, R.V. Pappu(2009) ABSINTH: A New Continuum Solvation Model for Simulations of Polypeptides in Aqueous Solutions.
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.
H.T. Tran, A. Mao, R.V. Pappu (2008) Role of Backbone-Solvent Interactions in Determining Conformational Equilibria of Intrinsically Disordered Polypeptides.
M. A. Wyczalkowski, R.V. Pappu (2008) Satisfying the Fluctuation Theorem in Free Energy Calculations with Hamiltonian Replica Exchange.
R.V. Pappu, X. Wang, A. Vitalis, S.L. Crick (2008) A Polymer Physics Perspective on Driving Forces and Mechanisms for Protein Aggregation.
A.A. Chen, R.V. Pappu (2007) Parameters of Monovalent Ions in the AMBER-99 Forcefield: Assessment of Inaccuracies and Proposed Improvements.
A. Vitalis, X. Wang, R.V. Pappu (2007) Quantitative Characterization of Intrinsic Disorder in Polyglutamine: Insights from Analysis Based on Polymer Theories.
A.A. Chen, R.V. Pappu (2007) Quantitative Characterization of Ion Pairing and Cluster Formation in Strong 1:1 Electrolytes.
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.
H.T. Tran, R.V. Pappu (2006) Toward an Accurate Theoretical Framework for Describing Ensembles for Proteins Under Strongly Denaturing Donditions.
X. Wang, A. Vitalis, M.A. Wyczalkowski, R.V. Pappu (2006) Characterizing the Conformational Ensemble of Monomeric Polyglutamine.
H.T. Tran, X. Wang, R.V. Pappu (2005) Reconciling Observations of Sequence-Specific Conformational Preferences with the Generic Behavior of Denatured Proteins.
A. Patriciu, G.S. Chirikjian, R.V. Pappu (2004) Analysis of the Conformational Dependence of Mass-metric Tensor Determinants in Serial polymers with Constraints.
A.N. Drozdov, A. Grossfield, R.V. Pappu (2004) The Role of Solvent in Determining Conformational Preferences of Alanine Dipeptide in Water.
R.V. Pappu, G.D.Rose (2002) A Simple Model for Polyproline II Structure in Unfolded States of Alanine-Based Peptides.
R.V. Pappu, R. Srinivasan, G.D. Rose (2000) The Flory Isolated Pair Hypothesis is not Valid for Polypeptide Chains: Implications for Protein Folding.
R.K. Hart, R.V. Pappu, J.W. Ponder (2000) Exploring the Similarities Between Potential Smoothing and Simulated Annealing.
R.V. Pappu (1999) Review of the Fourth Johns Hopkins Protein Folding Meeting.
R.V. Pappu, G.R. Marshall, J.W. Ponder (1999) A Potential Smoothing Algorithm Accurately Predicts Transmembrane Helix Packing.
R.V. Pappu, R.K. Hart, J.W. Ponder (1998) Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization.
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.
R.V. Pappu, D.L. Weaver (1998) The Early Folding Kinetics of Apomyoglobin.
R.V. Pappu, W.J. Schneller, D.L. Weaver (1996) Electrostatic Multipole Representation of a Polypeptide Chain: An Algorithm for Simulation of Polypeptide Properties.