Publications

Folding-upon-binding pathways of an intrinsically disordered protein from a deep Markov state model. T Sisk & P Robustelli, (https://www.biorxiv.org/content/10.1101/2023.07.21.550103v)
In Press - Proceedings of the National Academy of Sciences (2024)
Rational optimization of a transcription factor activation domain inhibitor. S. Basu, P. Martinez-Cristoabl, M. Pesarrodona, M. Frigole-Viva, E. Szulc, M. Lewis, A. Banuelos, C. Sanchexz-Zarzalego, S. Bielskute, J. Zhu, C. Garcia-Cabau, C. Batlee, B. Mateos, M. Biesaga, A. Escobedo, L. Bardia, X. Verdaguer, A. Ruffoni, N.R. Mawji, J. Wang, T. Tam, I. Brun-Heath, S. Ventura, D. Meierhofer, J. Garcia, P. Robustelli, T.H. Stracker, M.D. Sadar, A. Riera, D. Hnisz, X. Salvatella,
https://www.nature.com/articles/s41594-023-01159-5 , Nature Structural and Molecular Biology (2023)
Dissecting the biophysics and biology of intrinsically disordered proteins. Banerjee, Priya R., Alex S. Holehouse, Richard Kriwacki, Paul Robustelli, Hao Jiang, Alexander I. Sobolevsky, Jennifer M. Hurley, and Joshua T. Mendell. https://doi.org/10.1016/j.tibs.2023.10.002, Trends in biochemical sciences (2023).
PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins. Ghafouri, H., Lazar, T., Del Conte, A., Ku, PED Consorium, P. Robustelli, L.G.T., Aspromonte, M., Bernadó, P., Chaves-Arquero, B., Chemes, L.B., Clementel, D., Cordeiro, T. and Elena-Real, C., 10.1093/nar/gkad947 Nucleic Acids Research (2023)
Structure-Based Experimental Datasets for Benchmarking of Protein Simulation Force Fields. C Cavender, D Case, J Chen, L Chong, D Keedy, K Lindorff-Larsen, D Mobley, O Ollila, C Oostenbrink, P Robustelli, V Voelz, M Wall, D Wych, M Gilson, https://arxiv.org/abs/2303.11056, arXiv (2023)
Clustering heterogenous ensembles of intrinsically disordered proteins with t-distributed stochastic neighbour embedding, R. Appadurai, JK Koneru, M Bonomi, P. Robustelli, A. Srivastava, Journal of Chemical Theory and Computation, 19, 14, 4711–4727 (2023)
Small Molecules Targeting the Disordered Transactivation Domain of the Androgen Receptor Induce the Formation of Collapsed Helical States. J Zhu, X Salvatella, P Robustelli, Nature Communications, 13 (1), 1-15 (2022)
Molecular basis of small-molecule binding to a-synuclein, P Robustelli, Ibanez-de-Opakua A, Campbell-Bezat C, Giordanetto F, Becker S, Zweckstette Mr, Pan AC, Shaw DE, Journal of the American Chemical Society,144, 6, 2501–2510 (2022)
Quantifying the Relationship between Conformational Dynamics and Enzymatic Activity in Ribonuclease HI Homologues, J Martin, P Robustelli, AG Palmer III, Biochemistry, 59 (35), 3201-3205 (2020)
The Mechanism of Coupled Folding-Upon-Binding of An Intrinsically Disordered Protein, P Robustelli, S Piana, DE Shaw, Journal of the American Chemical Society (2020)
Development of a Force Field for the Simulation of Single-Chain Proteins and Protein-Protein Complexes. S Piana*, P Robustelli*, D Tan, S Chen, DE Shaw (*=equal contributions), Journal of Chemical Theory and Computation, 16, 4, 2494-2507 (2020)
Developing a Molecular Dynamics Force Field for Both Folded and Disordered Protein States, P Robustelli, S Piana, DE Shaw, Proceedings of the National Academy of Sciences, p.201800690 (2018)
Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States, S Piana, A Donchev, P Robustelli, DE Shaw, Journal of Physical Chemistry B, 119 (16), 5113-5123 (2015)
Functional implications of large backbone amplitude motions of the glycoprotein 130-binding epitope of interleukin-6, R Bobby, P Robustelli, AV Kralicek, M Mobli, GF King, J Grötzinger, AJ Dingley, FEBS Journal, 281(10), 2471-83 (2014
Conformational Dynamics of the Partially Disordered Yeast Transcription Factor GCN4, P Robustelli, N Trbovic, RA Friesner, AG Palmer III, Journal of Chemical Theory and Computation, 9(11), 5190–5200 (2013)
Thermal Adaption of Conformational Dynamics in Ribonuclease H, KA Stafford, P Robustelli, AG Palmer III, PLoS Computational Biology, 9(10), e1003218 (2013)
Structure of an Intermediate State in Protein Folding and Aggregation, P Neudecker, P Robustelli, A Cavalli, P Walsh, P Lundstrom, A Zarrine-Afsar, S Sharpe, M Vendruscolo, LE Kay, Science, 336, 362-366 (2012)
Interpreting Protein Structural Dynamics from NMR Chemical Shifts, P Robustelli, KA Stafford, AG Palmer III, Journal of the American Chemical Society, 134, 6365-6374 (2012)
Characterization of the Conformational Equilibrium Between the Two Major Substates of RNase A using NMR chemical shifts, C Camilloni, P Robustelli, A De Simone, A Cavalli, M Vendruscolo, Journal of the American Chemical Society, 134, 3968-3971 (2012)
Effects of the Known Pathogenic Mutations on the Aggregation Pathway of the Amyloidogenic Peptide of Apolipoprotein A-I, S Raimondi, F Guglielmi, S Giorgetti, S Di Gaetano, A Arciello, DM Monti, A Relini, D Nichino, SM Doglia, A Natalello, P Pucci, P Mangione, L Obici, G Merlini, M Stoppini, P Robustelli, GG Tartaglia, M Vendruscolo, CM Dobson, R Piccoli, V Bellotti, Journal of Molecular Biology, 407(3), 465-76 (2011)
Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins, P Robustelli, KJ Kohlhoff, A Cavalli, M Vendrusculo, Structure, 18, 1-11 (2010)
Fast and Accurate Predictions of Protein NMR Chemical Shifts from Interatomic Distance, KJ Kohlhoff, P Robustelli, A Cavalli, X Salvatella, M Vendruscolo, Journal of the American Chemical Society, 131 (39), 13894-13895 (2009)
Folding of Small Proteins with Chemical Shift Restrained Monte Carlo Simulations without the use of Molecular Fragment Replacement or Structural Homology, P Robustelli, A Cavalli, CM Dobson, M Vendruscolo, X Salvatella, Journal of Physical Chemistry B, 113 (22), 7890-7896 (2009)
Determination of Protein Structures in the Solid State from NMR Chemical Shifts, P Robustelli, A Cavalli, M Vendruscolo, Structure, 16, 1764-1769 (2008)
Structure and Conformational Dynamics of Tricothecene Mycotoxins, WE Steinmetz, P Robustelli, E Edens, D Heineman, Journal of Natural Products, 71 (4), 589-594 (2008)
A Molecular switch based on a biologically important redox reaction, P Yan, MW Holman, P Robustelli, A Chowdhury, FI Ishak, DM Adams, Journal of Physical Chemistry B, 109, 130-137 (2005)

Publications

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Folding-upon-binding pathways of an intrinsically disordered protein from a deep Markov state model. T Sisk & P Robustelli, (https://www.biorxiv.org/content/10.1101/2023.07.21.550103v) In Press - Proceedings of the National Academy of Sciences (2024)

Structure-Based Experimental Datasets for Benchmarking of Protein Simulation Force Fields. C Cavender, D Case, J Chen, L Chong, D Keedy, K Lindorff-Larsen, D Mobley, O Ollila, C Oostenbrink, P Robustelli, V Voelz, M Wall, D Wych, M Gilson, https://arxiv.org/abs/2303.11056, arXiv (2023)

Clustering heterogenous ensembles of intrinsically disordered proteins with t-distributed stochastic neighbour embedding, R. Appadurai, JK Koneru, M Bonomi, P. Robustelli, A. Srivastava, Journal of Chemical Theory and Computation, 19, 14, 4711–4727 (2023)

Small Molecules Targeting the Disordered Transactivation Domain of the Androgen Receptor Induce the Formation of Collapsed Helical States. J Zhu, X Salvatella, P Robustelli, Nature Communications, 13 (1), 1-15 (2022)

Molecular basis of small-molecule binding to a-synuclein, P Robustelli, Ibanez-de-Opakua A, Campbell-Bezat C, Giordanetto F, Becker S, Zweckstette Mr, Pan AC, Shaw DE, Journal of the American Chemical Society,144, 6, 2501–2510 (2022)

Quantifying the Relationship between Conformational Dynamics and Enzymatic Activity in Ribonuclease HI Homologues, J Martin, P Robustelli, AG Palmer III, Biochemistry, 59 (35), 3201-3205 (2020)

The Mechanism of Coupled Folding-Upon-Binding of An Intrinsically Disordered Protein, P Robustelli, S Piana, DE Shaw, Journal of the American Chemical Society (2020)

Development of a Force Field for the Simulation of Single-Chain Proteins and Protein-Protein Complexes. S Piana*, P Robustelli*, D Tan, S Chen, DE Shaw (*=equal contributions), Journal of Chemical Theory and Computation, 16, 4, 2494-2507 (2020)

Developing a Molecular Dynamics Force Field for Both Folded and Disordered Protein States, P Robustelli, S Piana, DE Shaw, Proceedings of the National Academy of Sciences, p.201800690 (2018)

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States, S Piana, A Donchev, P Robustelli, DE Shaw, Journal of Physical Chemistry B, 119 (16), 5113-5123 (2015)

Functional implications of large backbone amplitude motions of the glycoprotein 130-binding epitope of interleukin-6, R Bobby, P Robustelli, AV Kralicek, M Mobli, GF King, J Grötzinger, AJ Dingley, FEBS Journal, 281(10), 2471-83 (2014

Conformational Dynamics of the Partially Disordered Yeast Transcription Factor GCN4, P Robustelli, N Trbovic, RA Friesner, AG Palmer III, Journal of Chemical Theory and Computation, 9(11), 5190–5200 (2013)

Thermal Adaption of Conformational Dynamics in Ribonuclease H, KA Stafford, P Robustelli, AG Palmer III, PLoS Computational Biology, 9(10), e1003218 (2013)

Structure of an Intermediate State in Protein Folding and Aggregation, P Neudecker, P Robustelli, A Cavalli, P Walsh, P Lundstrom, A Zarrine-Afsar, S Sharpe, M Vendruscolo, LE Kay, Science, 336, 362-366 (2012)

Interpreting Protein Structural Dynamics from NMR Chemical Shifts, P Robustelli, KA Stafford, AG Palmer III, Journal of the American Chemical Society, 134, 6365-6374 (2012)

Characterization of the Conformational Equilibrium Between the Two Major Substates of RNase A using NMR chemical shifts, C Camilloni, P Robustelli, A De Simone, A Cavalli, M Vendruscolo, Journal of the American Chemical Society, 134, 3968-3971 (2012)

Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins, P Robustelli, KJ Kohlhoff, A Cavalli, M Vendrusculo, Structure, 18, 1-11 (2010)

Fast and Accurate Predictions of Protein NMR Chemical Shifts from Interatomic Distance, KJ Kohlhoff, P Robustelli, A Cavalli, X Salvatella, M Vendruscolo, Journal of the American Chemical Society, 131 (39), 13894-13895 (2009)

Folding of Small Proteins with Chemical Shift Restrained Monte Carlo Simulations without the use of Molecular Fragment Replacement or Structural Homology, P Robustelli, A Cavalli, CM Dobson, M Vendruscolo, X Salvatella, Journal of Physical Chemistry B, 113 (22), 7890-7896 (2009)

Determination of Protein Structures in the Solid State from NMR Chemical Shifts, P Robustelli, A Cavalli, M Vendruscolo, Structure, 16, 1764-1769 (2008)

Structure and Conformational Dynamics of Tricothecene Mycotoxins, WE Steinmetz, P Robustelli, E Edens, D Heineman, Journal of Natural Products, 71 (4), 589-594 (2008)

A Molecular switch based on a biologically important redox reaction, P Yan, MW Holman, P Robustelli, A Chowdhury, FI Ishak, DM Adams, Journal of Physical Chemistry B, 109, 130-137 (2005)

Folding-upon-binding pathways of an intrinsically disordered protein from a deep Markov state model. T Sisk & P Robustelli, (https://www.biorxiv.org/content/10.1101/2023.07.21.550103v)
In Press - Proceedings of the National Academy of Sciences (2024)

Development of a Force Field for the Simulation of Single-Chain Proteins and Protein-Protein Complexes. S Piana, P Robustelli, D Tan, S Chen, DE Shaw (*=equal contributions), Journal of Chemical Theory and Computation, 16, 4, 2494-2507 (2020)