Multi-scale Ensemble Modeling of Modular Proteins with Intrinsically Disordered Linker Regions: Application to p53

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., & Kollman, P. A. (1995) · Journal of the American Chemical Society · doi:10.1021/ja00124a002 · Cited by 13,111 · see citing works

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., Shirts, M. R., Smith, J. C., Kasson, P. M., van der Spoel, D., et al. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt055 · Cited by 7,493 · see citing works

Intrinsically unstructured proteins and their functions

Dyson, H. J., & Wright, P. E. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1589 · Cited by 3,871 · see citing works

CRYSOL– a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates

Svergun, D. I., Barberato, C., & Koch, M. (1995) · Journal of Applied Crystallography · doi:10.1107/s0021889895007047 · Cited by 3,388 · see citing works

Why are ?natively unfolded? proteins unstructured under physiologic conditions?

Uversky, V. N., Gillespie, J. R., & Fink, A. L. (2000) · Proteins Structure Function and Bioinformatics · doi:10.1002/1097-0134(20001115)41:3 · Cited by 2,063 · see citing works

Peptide Folding: When Simulation Meets Experiment

Daura, X., Gademann, K., Jaun, B., Seebàch, D., van Gunsteren, W. F., & Mark, A. E. (1999) · Angewandte Chemie International Edition · doi:10.1002/(sici)1521-3773(19990115)38:1/2 · Cited by 2,059 · see citing works

Prediction and Functional Analysis of Native Disorder in Proteins from the Three Kingdoms of Life

Ward, J. J., Sodhi, J. S., McGuffin, L. J., Buxton, B. F., & Jones, D. T. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.02.002 · Cited by 2,010 · see citing works

Intrinsic Disorder and Protein Function

Dunker, A. K., Brown, C. J., Lawson, J. D., Iakoucheva, L. M., & Obradović, Z. (2002) · Biochemistry · doi:10.1021/bi012159+ · Cited by 1,731 · see citing works

Intrinsically Disordered Proteins in Human Diseases: Introducing the D 2 Concept

Uversky, V. N., Oldfield, C. J., & Dunker, A. K. (2008) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.37.032807.125924 · Cited by 1,406 · see citing works

Scaffold Proteins: Hubs for Controlling the Flow of Cellular Information

Good, M. C., Zalatan, J. G., & Lim, W. A. (2011) · Science · doi:10.1126/science.1198701 · Cited by 886 · see citing works

Mapping Long-Range Interactions in α-Synuclein using Spin-Label NMR and Ensemble Molecular Dynamics Simulations

Dedmon, M. M., Lindorff‐Larsen, K., Christodoulou, J. C., Vendruscolo, M., & Dobson, C. M. (2004) · Journal of the American Chemical Society · doi:10.1021/ja044834j · Cited by 718 · see citing works

Structural Biology of the Tumor Suppressor p53

Joerger, A. C., & Fersht, A. R. (2008) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.77.060806.091238 · Cited by 699 · see citing works

Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life

Xue, B., Dunker, A. K., & Uversky, V. N. (2012) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2012.675145 · Cited by 557 · see citing works

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

Piana, S., Klepeis, J. L., & Shaw, D. E. (2014) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2013.12.006 · Cited by 513 · see citing works

Fast procedure for reconstruction of full‐atom protein models from reduced representations

Rotkiewicz, P., & Skolnick, J. (2008) · Journal of Computational Chemistry · doi:10.1002/jcc.20906 · Cited by 395 · see citing works

Biophysical characterization of intrinsically disordered proteins

Eliezer, D. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2008.12.004 · Cited by 325 · see citing works

Nature of the protein universe

Levitt, M. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0905029106 · Cited by 316 · see citing works

Intrinsically disordered proteins are potential drug targets

Metallo, S. J. (2010) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2010.06.169 · Cited by 298 · see citing works

Unstructural biology coming of age

Tompa, P. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.03.012 · Cited by 292 · see citing works

Constructing ensembles for intrinsically disordered proteins

Fisher, C. K., & Stultz, C. M. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.04.001 · Cited by 276 · see citing works

The development/application of a ‘minimalist’ organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data

Kollman, P., Dixon, R., Cornell, W., Fox, T., Chipot, C., & Pohorille, A. (1997) · Computer Simulation of Biomolecular Systems · doi:10.1007/978-94-017-1120-3_2 · Cited by 242 · see citing works

Capturing the essence of folding and functions of biomolecules using coarse-grained models

Hyeon, C., & Thirumalai, D. (2011) · Nature Communications · doi:10.1038/ncomms1481 · Cited by 241 · see citing works

Multi-domain Proteins in the Three Kingdoms of Life: Orphan Domains and Other Unassigned Regions

Ekman, D. S., Björklund, Å. K., Frey‐Skött, J., & Elofsson, A. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.02.007 · Cited by 235 · see citing works

CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work

Kenzaki, H., Koga, N., Hori, N., Kanada, R., Li, W., Okazaki, K.-I., Yao, X., & Takada, S. (2011) · Journal of Chemical Theory and Computation · doi:10.1021/ct2001045 · Cited by 232 · see citing works

A single-molecule characterization of p53 search on DNA

Tafvizi, A., Huang, F. L., Fersht, A. R., Mirny, L. A., & van Oijen, A. M. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1016020107 · Cited by 231 · see citing works

Coarse-grained molecular simulations of large biomolecules

Takada, S. (2012) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2012.01.010 · Cited by 221 · see citing works

Describing intrinsically disordered proteins at atomic resolution by NMR

Jensen, M. R., Ruigrok, R. W. H., & Blackledge, M. J. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2013.02.007 · Cited by 219 · see citing works

Quantitative Description of Backbone Conformational Sampling of Unfolded Proteins at Amino Acid Resolution from NMR Residual Dipolar Couplings

Nodet, G., Salmon, L., Ozenne, V., Meier, S., Jensen, M. R., & Blackledge, M. J. (2009) · Journal of the American Chemical Society · doi:10.1021/ja9069024 · Cited by 210 · see citing works

Intrinsically disordered regions as affinity tuners in protein–DNA interactions

Vuzman, D., & Levy, Y. (2011) · Molecular BioSystems · doi:10.1039/c1mb05273j · Cited by 199 · see citing works

Coarse-Grained (Multiscale) Simulations in Studies of Biophysical and Chemical Systems

Kamerlin, S. C. L., Vicatos, S., Dryga, A., & Warshel, A. (2011) · Annual Review of Physical Chemistry · doi:10.1146/annurev-physchem-032210-103335 · Cited by 193 · see citing works

Quaternary structures of tumor suppressor p53 and a specific p53–DNA complex

Tidow, H., Melero, R., Mylonas, E., Freund, S. M. V., Großmann, J., Carazo, J. M., Svergun, D. I., Valle, M., & Fersht, A. R. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0705069104 · Cited by 182 · see citing works

Modeling Intrinsically Disordered Proteins with Bayesian Statistics

Fisher, C. K., Huang, A., & Stultz, C. M. (2010) · Journal of the American Chemical Society · doi:10.1021/ja105832g · Cited by 166 · see citing works

The modular logic of signaling proteins: building allosteric switches from simple binding domains

Lim, W. A. (2002) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(02)00290-7 · Cited by 151 · see citing works

Crystal Structure of the p53 Core Domain Bound to a Full Consensus Site as a Self-Assembled Tetramer

Chen, Y., Dey, R., & Chen, L. (2010) · Structure · doi:10.1016/j.str.2009.11.011 · Cited by 151 · see citing works

Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot

Li, W., Terakawa, T., Wang, W., & Takada, S. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1201807109 · Cited by 149 · see citing works

Effect of interdomain dynamics on the structure determination of modular proteins by small-angle scattering

Bernadó, P. (2009) · European Biophysics Journal · doi:10.1007/s00249-009-0549-3 · Cited by 117 · see citing works

Improved Structural Characterizations of the drkN SH3 Domain Unfolded State Suggest a Compact Ensemble with Native-like and Non-native Structure

Marsh, J. A., Neale, C., Jack, F. E., Choy, W., Lee, A. Y., Crowhurst, K. A., & Forman-Kay, J. D. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.01.038 · Cited by 116 · see citing works

Genome-scale prediction of proteins with long intrinsically disordered regions

Peng, Z., Mizianty, M. J., & Kurgan, L. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24348 · Cited by 112 · see citing works

A Free-Energy Landscape for Coupled Folding and Binding of an Intrinsically Disordered Protein in Explicit Solvent from Detailed All-Atom Computations

Higo, J., Nishimura, Y., & Nakamura, H. (2011) · Journal of the American Chemical Society · doi:10.1021/ja110338e · Cited by 106 · see citing works

Multiscale Ensemble Modeling of Intrinsically Disordered Proteins: p53 N-Terminal Domain

Terakawa, T., & Takada, S. (2011) · Biophysical Journal · doi:10.1016/j.bpj.2011.08.003 · Cited by 105 · see citing works

Interaction of the p53 DNA-Binding Domain with Its N-Terminal Extension Modulates the Stability of the p53 Tetramer

Natan, E., Baloğlu, Ç., Pagel, K., Freund, S. M. V., Morgner, N., Robinson, C. V., Fersht, A. R., & Joerger, A. C. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.03.047 · Cited by 98 · see citing works

p53 Searches on DNA by Rotation-Uncoupled Sliding at C-Terminal Tails and Restricted Hopping of Core Domains

Terakawa, T., Kenzaki, H., & Takada, S. (2012) · Journal of the American Chemical Society · doi:10.1021/ja305369u · Cited by 92 · see citing works

Recognition of DNA by p53 Core Domain and Location of Intermolecular Contacts of Cooperative Binding

Rippin, T. M., Freund, S. M. V., Veprintsev, D. B., & Fersht, A. R. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00326-1 · Cited by 80 · see citing works

AMBER-based hybrid force field for conformational sampling of polypeptides

Kamiya, N., Watanabe, Y. S., Ono, S., & Higo, J. (2004) · Chemical Physics Letters · doi:10.1016/j.cplett.2004.11.070 · Cited by 71 · see citing works

Coupling of tandem Smad ubiquitination regulatory factor (Smurf) WW domains modulates target specificity

Chong, P. A., Lin, H., Wrana, J. L., & Forman-Kay, J. D. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1003023107 · Cited by 71 · see citing works

Optimal Combination of Theory and Experiment for the Characterization of the Protein Folding Landscape of S6: How Far Can a Minimalist Model Go?

Matysiak, S., & Clementi, C. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.08.006 · Cited by 70 · see citing works

Crystallization and structure solution of p53 (residues 326–356) by molecular replacement using an NMR model as template

Mittl, P. R. E., Chêne, P., & Grütter, M. G. (1998) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444997006550 · Cited by 69 · see citing works

Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water

Ikebe, J., Umezawa, K., Kamiya, N., et al. (2010) · Journal of Computational Chemistry · doi:10.1002/jcc.21710 · Cited by 65 · see citing works

Insight into the Structural Basis of Pro- and Antiapoptotic p53 Modulation by ASPP Proteins

Ahn, J., Byeon, I. L., Byeon, C., & Gronenborn, A. M. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m808821200 · Cited by 51 · see citing works

Domain–domain interactions in full-length p53 and a specific DNA complex probed by methyl NMR spectroscopy

Biśta, M., Freund, S. M. V., & Fersht, A. R. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1214176109 · Cited by 39 · see citing works

A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein–protein interaction with an all-atom model in explicit solvent

Higo, J., Umezawa, K., & Nakamura, H. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4803468 · Cited by 34 · see citing works

Modulation of Integrin Activation by an Entropic Spring in the β-Knee

Smagghe, B. J., Huang, P., Ban, Y. A., Baker, D. A., & Springer, T. A. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.145177 · Cited by 34 · see citing works

Analysis of Molecular Recognition Features (MoRFs) in membrane proteins

Kotta‐Loizou, I., Tsaousis, G., & Hamodrakas, S. J. (2013) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2013.01.006 · Cited by 32 · see citing works

Finding Order within Disorder: Elucidating the Structure of Proteins Associated with Neurodegenerative Disease

Huang, A., & Stultz, C. M. (2009) · Future Medicinal Chemistry · doi:10.4155/fmc.09.40 · Cited by 25 · see citing works

Ab initio simulation of a 57‐residue protein in explicit solvent reproduces the native conformation in the lowest free‐energy cluster

Ikebe, J., Standley, D. M., Nakamura, H., & Higo, J. (2010) · Protein Science · doi:10.1002/pro.553 · Cited by 19 · see citing works

Conformational sampling of a 40-residue protein consisting of α and β secondary-structure elements in explicit solvent

Ikebe, J., Kamiya, N., Shindo, H., et al. (2007) · Chemical Physics Letters · doi:10.1016/j.cplett.2007.06.102 · Cited by 12 · see citing works

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

Wei, G., Xi, W., Nussinov, R., & Ma, B. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00562 · Cited by 436 · see citing works

Intrinsically Disordered Proteins (IDPs)

Ando, T. (2022) · Nanoscience and technology · doi:10.1007/978-3-662-64785-1_13 · Cited by 1 · see citing works

Structural Characterization of Nucleic Acid Nanoparticles Using SAXS and SAXS-Driven MD

Byrnes, J., Chopra, K., Rolband, L. A., et al. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-3417-2_4 · Cited by 7 · see citing works

Integrative SAXS ‐Driven Computational Modeling of Biomolecular Complexes

Song, L., Lu, L., Huang, W., Ravikumar, K. M., Meng, J., & Yang, S. (2018) · Wiley eBooks · doi:10.1002/9783527697106.ch17 · Cited by 1 · see citing works

SAXS investigations of polyethylene modified with methacrylic acid

Włochowicz, A., Ślusarczyk, C., Wycisk, R. J., et al. (1993) · Journal de Physique IV (Proceedings) · doi:10.1051/jp4:1993816