Energy Landscape of the Prion Protein Helix 1 Probed by Metadynamics and NMR
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The characterization of the structural dynamics of proteins, including those that present a substantial degree of disorder, is currently a major scientific challenge. These dynamics are biologically relevant and govern the majority of functional and pathological processes. We exploited a combination of enhanced molecular simulations of metadynamics and NMR measurements to study heterogeneous states of proteins and peptides. In this way, we determined the structural ensemble and free-energy landscape of the highly dynamic helix 1 of the prion protein (PrP-H1), whose misfolding and aggregation are intimately connected to a group of neurodegenerative disorders known as transmissible spongiform encephalopathies. Our combined approach allowed us to dissect the factors that govern the conformational states of PrP-H1 in solution, and the implications of these factors for prion protein misfolding and aggregation. The results underline the importance of adopting novel integrated approaches that take advantage of experiments and theory to achieve a comprehensive characterization of the structure and dynamics of biological macromolecules.
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Metadynamics methods have been successfully applied to study free energy landscapes of flexible proteins, protein oligomers, peptide folding, ligand and selective ion permeation through membrane channels.
“These methods alone, or in combination with high-resolution experimental techniques such as x-ray crystallography and NMR, have been successfully applied to the study of the free energy landscape of flexible proteins and protein oligomers,36,388–389 peptide folding,390–392 ligand and selective ion permeation through cell membrane protein channels.393”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [388]
Cites
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. R. (2008) · Journal of Chemical Theory and Computation · doi:10.1021/ct700301q · Cited by 15,830 · see citing works
Jorgensen, W. L., Maxwell, D. S., & Tirado-Rives, J. (1996) · Journal of the American Chemical Society · doi:10.1021/ja9621760 · Cited by 14,078 · see citing works
NMR with Proteins and Nucleic Acids
Wüthrich, K. (1986) · Europhysics news · doi:10.1051/epn/19861701011 · Cited by 8,025 · see citing works
NMR of Proteins and Nucleic Acids
(2006) · Royal Society of Chemistry eBooks · doi:10.1039/9781847555236-00336 · Cited by 5,863 · see citing works
Laio, A., & Parrinello, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202427399 · Cited by 5,626 · see citing works
Prusiner, S. B. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.23.13363 · Cited by 5,373 · see citing works
Protein folding and misfolding
Dobson, C. M. (2003) · Nature · doi:10.1038/nature02261 · Cited by 4,791 · see citing works
Molecular dynamics simulations of biomolecules
Karplus, M., & McCammon, J. (2002) · Nature Structural Biology · doi:10.1038/nsb0902-646 · Cited by 3,401 · see citing works
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
Bonomi, M., Branduardi, D., Bussi, G., Camilloni, C., Provasi, D., Raiteri, P., Donadio, D., Marinelli, F., Pietrucci, F., Broglia, R. A., et al. (2009) · Computer Physics Communications · doi:10.1016/j.cpc.2009.05.011 · Cited by 1,890 · see citing works
Self-citationAccelerated molecular dynamics: A promising and efficient simulation method for biomolecules
Hamelberg, D., Mongan, J., & McCammon, J. A. (2004) · The Journal of Chemical Physics · doi:10.1063/1.1755656 · Cited by 1,536 · see citing works
A Perspective on Enzyme Catalysis
Benkovic, S. J., & Hammes‐Schiffer, S. (2003) · Science · doi:10.1126/science.1085515 · Cited by 1,281 · see citing works
Spera, S., & Bax, A. (1991) · Journal of the American Chemical Society · doi:10.1021/ja00014a071 · Cited by 1,101 · see citing works
The Nuclear Overhauser Effect in Structural and Conformational Analysis
Neuhaus, D., & Williamson, M. P. (1989) · Cited by 1,093 · see citing works
The nuclear overhauser effect in structural and conformational analysis
Lawless, G. A. (1989) · Journal of Organometallic Chemistry · doi:10.1016/0022-328x(89)85156-3 · Cited by 1,007 · see citing works
Sequence-Dependent Correction of Random Coil NMR Chemical Shifts
Schwarzinger, S., Kroon, G. J. A., Foss, T. R., Chung, J., Wright, P. E., & Dyson, H. J. (2001) · Journal of the American Chemical Society · doi:10.1021/ja003760i · Cited by 604 · see citing works
Self-citationEvidence for assembly of prions with left-handed β-helices into trimers
Govaerts, C., Wille, H., Prusiner, S. B., & Cohen, F. E. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0402254101 · Cited by 540 · see citing works
Defining Solution Conformations of Small Linear Peptides
Dyson, H. J., & Wright, P. E. (1991) · Annual Review of Biophysics and Biophysical Chemistry · doi:10.1146/annurev.bb.20.060191.002511 · Cited by 529 · see citing works
Free-Energy Landscape for β Hairpin Folding from Combined Parallel Tempering and Metadynamics
Bussi, G., Gervasio, F. L., Laio, A., & Parrinello, M. (2006) · Journal of the American Chemical Society · doi:10.1021/ja062463w · Cited by 507 · see citing works
Shen, Y., & Bax, A. (2007) · Journal of Biomolecular NMR · doi:10.1007/s10858-007-9166-6 · Cited by 362 · see citing works
Reconstructing the equilibrium Boltzmann distribution from well‐tempered metadynamics
Bonomi, M., Barducci, A., & Parrinello, M. (2009) · Journal of Computational Chemistry · doi:10.1002/jcc.21305 · Cited by 352 · see citing works
Ab Initio Folding of Proteins with All-Atom Discrete Molecular Dynamics
Ding, F., Tsao, D., Nie, H., & Dokholyan, N. V. (2008) · Structure · doi:10.1016/j.str.2008.03.013 · Cited by 326 · see citing works
Molecular architecture of human prion protein amyloid: A parallel, in-register β-structure
Cobb, N. J., Sönnichsen, F. D., Mchaourab, H. S., & Surewicz, W. K. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706522104 · Cited by 326 · see citing works
Observing biological dynamics at atomic resolution using NMR
Mittermaier, A., & Kay, L. E. (2009) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2009.07.004 · Cited by 322 · see citing works
Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins
Nettels, D., Müller-Späth, S., Küster, F., Hofmann, H., Haenni, D., Rüegger, S., Reymond, L., Hoffmann, A., Kubelka, J., Heinz, B., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0900622106 · Cited by 231 · see citing works
Dynamics connect substrate recognition to catalysis in protein kinase A
Masterson, L. R., Cheng, C. Y., Yu, T., Tonelli, M., Kornev, A. P., Taylor, S. S., & Veglia, G. (2010) · Nature Chemical Biology · doi:10.1038/nchembio.452 · Cited by 199 · see citing works
Local Structural Plasticity of the Prion Protein. Analysis of NMR Relaxation Dynamics
Viles, J. H., Donne, D. G., Kroon, G. J. A., Prusiner, S. B., Cohen, F. E., Dyson, H. J., & Wright, P. E. (2001) · Biochemistry · doi:10.1021/bi002898a · Cited by 174 · see citing works
The Effect of Disease-associated Mutations on the Folding Pathway of Human Prion Protein
Apetri, A. C., Surewicz, K. A., & Surewicz, W. K. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m313581200 · Cited by 155 · see citing works
Structural mobility of the human prion protein probed by backbone hydrogen exchange.
Clarke, A. R., Hosszu, L. L. P., Baxter, N. J., Jackson, G. S., Power, A., Waltho, J. P., Craven, C. J., & Collinge, J. (1999) · Nature Structural Biology · doi:10.1038/11507 · Cited by 148 · see citing works
Boehr, D. D., McElheny, D., Dyson, H. J., & Wright, P. E. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914163107 · Cited by 142 · see citing works
Targeting biomolecular flexibility with metadynamics
Leone, V., Marinelli, F., Carloni, P., & Parrinello, M. (2010) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2010.01.011 · Cited by 139 · see citing works
Eghiaian, F., Daubenfeld, T., Quenet, Y., van Audenhaege, M., Bouin, A., van der Rest, G., Grosclaude, J., & Rezaei, H. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0607745104 · Cited by 136 · see citing works
Evidence for the role of PrP C helix 1 in the hydrophilic seeding of prion aggregates
Morrissey, M., & Shakhnovich, E. I. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.20.11293 · Cited by 131 · see citing works
Crystal structure of human prion protein bound to a therapeutic antibody
Antonyuk, S. V., Trevitt, C. R., Strange, R. W., Jackson, G. S., Sangar, D., Batchelor, M., Cooper, S., Fraser, C., Jones, S., Georgiou, T., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0809170106 · Cited by 124 · see citing works
Probing the instabilities in the dynamics of helical fragments from mouse PrP C
Dima, R. I., & Thirumalai, D. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0404235101 · Cited by 122 · see citing works
Silva, J. L., Vieira, T. C. R. G., Gomes, M. P. B., Bom, A. P. A., Lima, L. M. T. R., de Freitas, M. S., Ishimaru, D., Cordeiro, Y., & Foguel, D. (2009) · Accounts of Chemical Research · doi:10.1021/ar900179t · Cited by 119 · see citing works
Toward a Unified Representation of Protein Structural Dynamics in Solution
Markwick, P. R. L., Bouvignies, G., Salmon, L., McCammon, J. A., Nilges, M., & Blackledge, M. J. (2009) · Journal of the American Chemical Society · doi:10.1021/ja907476w · Cited by 106 · see citing works
Exact Distances and Internal Dynamics of Perdeuterated Ubiquitin from NOE Buildups
Vögeli, B., Segawa, T. F., Leitz, D., Sobol, A., Choutko, A., Trzesniak, D., A, W. F. V. G., & Riek, R. (2009) · Journal of the American Chemical Society · doi:10.1021/ja905366h · Cited by 99 · see citing works
Accurate Random Coil Chemical Shifts from an Analysis of Loop Regions in Native States of Proteins
Simone, A. D., Cavalli, A., Hsu, S. D., Vranken, W., & Vendruscolo, M. (2009) · Journal of the American Chemical Society · doi:10.1021/ja904937a · Cited by 92 · see citing works
Kinetic Intermediate in the Folding of Human Prion Protein
Apetri, A. C., & Surewicz, W. K. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.c200507200 · Cited by 92 · see citing works
Structural and Hydration Properties of the Partially Unfolded States of the Prion Protein
Simone, A. D., Zagari, A., & Derreumaux, P. (2007) · Biophysical Journal · doi:10.1529/biophysj.107.108613 · Cited by 89 · see citing works
Experimental free energy surfaces reveal the mechanisms of maintenance of protein solubility
Simone, A. D., Dhulesia, A., Soldi, G., Vendruscolo, M., Hsu, S. D., Chiti, F., & Dobson, C. M. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1112197108 · Cited by 79 · see citing works
Protein dynamics from time resolved UV Raman spectroscopy
Balakrishnan, G., Weeks, C. L., Ibrahim, M., Soldatova, A. V., & Spiro, T. G. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2008.06.001 · Cited by 76 · see citing works
Exploring the protein G helix free‐energy surface by solute tempering metadynamics
Camilloni, C., Provasi, D., Tiana, G., & Broglia, R. A. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21852 · Cited by 76 · see citing works
Self-citationLinking Well-Tempered Metadynamics Simulations with Experiments
Barducci, A., Bonomi, M., & Parrinello, M. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2010.01.033 · Cited by 75 · see citing works
Toward an Accurate Determination of Free Energy Landscapes in Solution States of Proteins
Simone, A. D., Richter, B., Salvatella, X., & Vendruscolo, M. (2009) · Journal of the American Chemical Society · doi:10.1021/ja8087295 · Cited by 70 · see citing works
CD and NMR Studies of Prion Protein (PrP) Helix 1
Ziegler, J., Sticht, H., Marx, U., Müller, W., Rösch, P., & Schwarzinger, S. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m305234200 · Cited by 66 · see citing works
Self-citationSlow Conformational Dynamics in the Hamster Prion Protein
Kuwata, K., Kamatari, Y. O., Akasaka, K., & James, T. L. (2004) · Biochemistry · doi:10.1021/bi036123o · Cited by 64 · see citing works
Gianni, S., Ivarsson, Y., Simone, A. D., Travaglini‐Allocatelli, C., Brunori, M., & Vendruscolo, M. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1956 · Cited by 60 · see citing works
Factors Governing Helix Formation in Peptides Confined to Carbon Nanotubes
O’Brien, E. P., Stan, G., Thirumalai, D., & Brooks, B. R. (2008) · Nano Letters · doi:10.1021/nl8019328 · Cited by 47 · see citing works
Observation of intermediate states of the human prion protein by high pressure NMR spectroscopy
Kachel, N., Kremer, W., Zahn, R., & Kalbitzer, H. R. (2006) · BMC Structural Biology · doi:10.1186/1472-6807-6-16 · Cited by 47 · see citing works
Prion Protein Helix1 Promotes Aggregation but Is Not Converted into β-Sheet
Watzlawik, J. O., Skóra, L., Frense, D., Griesinger, C., Zweckstetter, M., Schulz‐Schaeffer, W., & Kramer, M. L. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m605141200 · Cited by 46 · see citing works
The Charge Structure of Helix 1 in the Prion Protein Regulates Conversion to Pathogenic PrPSc
Norstrom, E. M., & Mastrianni, J. A. (2006) · Journal of Virology · doi:10.1128/jvi.00366-06 · Cited by 41 · see citing works
Conformational Properties of β-PrP
Hosszu, L. L. P., Trevitt, C. R., Jones, S., Batchelor, M., Scott, D. J., Jackson, G. S., Collinge, J., Waltho, J. P., & Clarke, A. R. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m809173200 · Cited by 38 · see citing works
Unfolded‐State Structure and Dynamics Influence the Fibril Formation of Human Prion Protein
Gerum, C., Silvers, R., Wirmer, J., & Schwalbe, H. (2009) · Angewandte Chemie International Edition · doi:10.1002/anie.200903771 · Cited by 34 · see citing works
Putative aggregation initiation sites in prion protein
Ziegler, J., Viehrig, C., Geimer, S., ROSCH, P. J., & Schwarzinger, S. (2006) · FEBS Letters · doi:10.1016/j.febslet.2006.03.002 · Cited by 32 · see citing works
Self-citationReversible monomer-oligomer transition in human prion protein
Sasaki, K., Gaikwad, J. U., Hashiguchi, S., Kubota, T., Sugimura, K., Kremer, W., Kalbitzer, H. R., & Akasaka, K. (2008) · Prion · doi:10.4161/pri.2.3.7148 · Cited by 27 · see citing works
Mégy, S., Bertho, G., Kozin, S. A., Debey, P., Hoa, G. H. B., & Girault, J. (2004) · Protein Science · doi:10.1110/ps.04745004 · Cited by 27 · see citing works
Kremer, W., Kachel, N., Kuwata, K., Akasaka, K., & Kalbitzer, H. R. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m701884200 · Cited by 26 · see citing works
Sharman, G. J., Kenward, N., Williams, H. E. L., Landon, M., Mayer, R. J., & Searle, M. S. (1998) · Folding and Design · doi:10.1016/s1359-0278(98)00043-1 · Cited by 19 · see citing works
Mapping of protein structural ensembles by chemical shifts
Baskaran, K., Brunner, K., Munte, C. E., & Kalbitzer, H. R. (2010) · Journal of Biomolecular NMR · doi:10.1007/s10858-010-9438-4 · Cited by 17 · see citing works
Müller‐Schiffmann, A., Petsch, B., Leliveld, S. R., Kutzsche, J., Salwierz, A., Mangels, C., Schwarzinger, S., Riesner, D., Stitz, L., & Korth, C. (2008) · Molecular Immunology · doi:10.1016/j.molimm.2008.07.023 · Cited by 16 · see citing works
Self-citationRare Large Scale Subdomain Motions in Prion Protein can Initiate Aggregation
Schwarzinger, S., Horn, A. H. C., Ziegler, J., & Sticht, H. (2006) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2006.10507083 · Cited by 12 · see citing works
Self-citationMangels, C., Kellner, R., Einsiedel, J., Weiglmeier, P. R., ROSCH, P. J., Gmeiner, P., & Schwarzinger, S. (2010) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2010.10507340 · Cited by 11 · see citing works
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Flagged first, then by citations
1 of the 64 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Wei, G., Xi, W., Nussinov, R., & Ma, B. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00562 · Cited by 436 · see citing works
Jensen, M. R., Zweckstetter, M., Huang, J., & Blackledge, M. J. (2014) · Chemical Reviews · doi:10.1021/cr400688u · Cited by 298 · see citing works
Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates
Ilie, I. M., & Caflisch, A. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00731 · Cited by 177 · see citing works
Computational Studies of Protein Aggregation: Methods and Applications
Morriss-Andrews, A., & Shea, J. (2015) · Annual Review of Physical Chemistry · doi:10.1146/annurev-physchem-040513-103738 · Cited by 168 · see citing works
Sutto, L., Marsili, S., & Gervasio, F. L. (2012) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1103 · Cited by 160 · see citing works
Protein aggregation: Mechanisms and functional consequences
Invernizzi, G., Papaleo, E., Sabaté, R., & Ventura, S. (2012) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2012.05.023 · Cited by 158 · see citing works
Intrinsic disorder modulates protein self-assembly and aggregation
Simone, A. D., Kitchen, C., Kwan, A. H., Sunde, M., Dobson, C. M., & Frenkel, D. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1118048109 · Cited by 112 · see citing works
Michel, J., & Cuchillo, R. (2012) · PLoS ONE · doi:10.1371/journal.pone.0041070 · Cited by 74 · see citing works
Camilloni, C., Cavalli, A., & Vendruscolo, M. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct4006272 · Cited by 71 · see citing works
Self-citationConformational Recognition of an Intrinsically Disordered Protein
Krieger, J. M., Fusco, G., Lewitzky, M., Simister, P. C., Marchant, J., Camilloni, C., Feller, S. M., & De Simone, A. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2014.03.004 · Cited by 56 · see citing works
Self-citationMechanism of misfolding of the human prion protein revealed by a pathological mutation
Sanz-Hernández, M., Barritt, J. D., Sobek, J., Hornemann, S., Aguzzi, A., & Simone, A. D. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2019631118 · Cited by 47 · see citing works
Peng, Y., Chuanyang, W., Yu, J. C., Wu, J., Wang, F., Liu, Y., & Li, X. (2023) · Food Hydrocolloids · doi:10.1016/j.foodhyd.2023.108867 · Cited by 44 · see citing works
Molecular determinants of the interaction of EGCG with ordered and disordered proteins
Fusco, G., Sanz-Hernández, M., Ruggeri, F. S., Vendruscolo, M., Dobson, C. M., & Simone, A. D. (2018) · Biopolymers · doi:10.1002/bip.23117 · Cited by 44 · see citing works
Mechanism of Unfolding of Human Prion Protein
Singh, R. K., Chamachi, N. G., Chakrabarty, S., & Mukherjee, A. (2016) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.6b11416 · Cited by 39 · see citing works
Luo, Y., Pu, C., Zhang, J., Fu, Z., Tang, W., & Sun, Q. (2024) · Food Hydrocolloids · doi:10.1016/j.foodhyd.2024.110530 · Cited by 36 · see citing works
Chamachi, N. G., & Chakrabarty, S. (2017) · Biochemistry · doi:10.1021/acs.biochem.6b01042 · Cited by 35 · see citing works
Characterizing Intermolecular Interactions That Initiate Native-Like Protein Aggregation
Bemporad, F., Simone, A. D., Chiti, F., & Dobson, C. M. (2012) · Biophysical Journal · doi:10.1016/j.bpj.2012.03.057 · Cited by 34 · see citing works
Protein Aggregation and Molecular Crowding
Musiani, F., & Giorgetti, A. (2016) · International review of cytology · doi:10.1016/bs.ircmb.2016.08.009 · Cited by 30 · see citing works
Role of Conformational Motions in Enzyme Function: Selected Methodologies and Case Studies
Narayanan, C., Bernard, D., & Doucet, N. (2016) · Catalysts · doi:10.3390/catal6060081 · Cited by 29 · see citing works
Mercadante, D., Melton, L. D., Jameson, G. B., Williams, M. A. K., & Simone, A. D. (2013) · Biophysical Journal · doi:10.1016/j.bpj.2013.02.049 · Cited by 29 · see citing works
Protein disorder-to-order transition enhances the nucleosome-binding affinity of H1
Sridhar, A., Orozco, M., & Collepardo‐Guevara, R. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa285 · Cited by 28 · see citing works
Salmon, L., & Blackledge, M. J. (2015) · Reports on Progress in Physics · doi:10.1088/0034-4885/78/12/126601 · Cited by 27 · see citing works
Myers, R. R., Cembran, A., & Fernández-Fúnez, P. (2020) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2020.00254 · Cited by 26 · see citing works
Simone, A. D., Mote, K. R., & Veglia, G. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2014.03.026 · Cited by 21 · see citing works
Qu, F., ElOmari, K., Wagner, A., Simone, A. D., & Beis, K. (2019) · Biochemical Journal · doi:10.1042/bcj20190779 · Cited by 20 · see citing works
Free-Energy Landscape of the Amino-Terminal Fragment of Huntingtin in Aqueous Solution
Binette, V., Côté, S., & Mousseau, N. (2016) · Biophysical Journal · doi:10.1016/j.bpj.2016.01.015 · Cited by 16 · see citing works
Menon, S., & Sengupta, N. (2015) · Molecular BioSystems · doi:10.1039/c4mb00689e · Cited by 13 · see citing works
The PROSECCO server for chemical shift predictions in ordered and disordered proteins
Sanz-Hernández, M., & Simone, A. D. (2017) · Journal of Biomolecular NMR · doi:10.1007/s10858-017-0145-2 · Cited by 13 · see citing works
Enhancing Biomolecular Simulations with Hybrid Potentials Incorporating NMR Data
Qi, G., Vrettas, M. D., Biancaniello, C., Sanz-Hernández, M., Cafolla, C. T., Morgan, J. W. R., Wang, Y., Simone, A. D., & Wales, D. J. (2022) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.2c00657 · Cited by 12 · see citing works
Chatterjee, S., Salimi, A., & Lee, J. Y. (2021) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.1c00376 · Cited by 12 · see citing works
Haerteis, S., Schaal, D., Brauer, F., Brüschke, S., Schweimer, K., Rauh, R. D., Sticht, H., ROSCH, P. J., Schwarzinger, S., & Korbmacher, C. (2012) · Cellular Physiology and Biochemistry · doi:10.1159/000312590 · Cited by 9 · see citing works
Self-citationTaurine ABC transporter substrate binding protein TauA from E. coli in complex with taurine
Beis, K., Qu, F., Wagner, A., & ElOmari, K. (2019) · Worldwide Protein Data Bank · doi:10.2210/pdb6stl/pdb · Cited by 9 · see citing works
Palaniappan, C., Rahul, C. N., & Sekar, K. (2021) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.1c00142 · Cited by 8 · see citing works
Meloni, R., Camilloni, C., & Tiana, G. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400879v · Cited by 8 · see citing works
Self-citationQuantifying the Sources of Kinetic Frustration in Folding Simulations of Small Proteins
Savol, A. J., & Chennubhotla, C. S. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct500361w · Cited by 6 · see citing works
Structure and Dynamics of the Misfolding Intermediate in the Pathogenic T183A Prion Protein Mutant
Biancaniello, C., Emendato, A., & Simone, A. D. (2025) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5c00742 · Cited by 5 · see citing works
Computational Insights into Dynamics of Protein Aggregation and Enzyme–Substrate Interactions
Özbil, M., Barman, A., Bora, R. P., & Prabhakar, R. S. (2012) · The Journal of Physical Chemistry Letters · doi:10.1021/jz301597k · Cited by 5 · see citing works
Sanz-Hernández, M., & Simone, A. D. (2021) · Biomolecular NMR Assignments · doi:10.1007/s12104-021-10005-y · Cited by 3 · see citing works
Exploring the Binding Mechanism of ADGRG2 Through Metadynamics and Biochemical Analysis
Zhang, C., Zhang, R., Qi, Y., Wen, X., Sun, J., & Xiao, P. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms26010167 · Cited by 3 · see citing works
Antibody binding increases the flexibility of the prion protein
Ilie, I. M., & Caflisch, A. (2022) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2022.140827 · Cited by 3 · see citing works
The intrinsic stability of the human prion β-sheet region investigated by molecular dynamics
Simone, A. D., Stanzione, F., Marasco, D., Vitagliano, L., & Esposito, L. (2013) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2012.703070 · Cited by 2 · see citing works
Structural and cellular properties of human prion protein oligomers
Emendato, A., Divisato, G., Giannino, E., Mansueto, S., Zizolfi, M. C., Peltrini, R., Parisi, S., & Simone, A. D. (2025) · Communications Biology · doi:10.1038/s42003-025-09105-5 · Cited by 1 · see citing works
Lorenzo, D. D., Bisi, N., Bucci, R., Ennen, I., Presti, L. L., Dodero, V. I., Brandt, R., Ongeri, S., Gelmi, M. L., & Tonali, N. (2025) · iScience · doi:10.1016/j.isci.2025.112272 · Cited by 1 · see citing works
Path to Diversity and to Resistant Uniformity: Intracellular Adaptation to Nutrient EnvironmentPreprint
Korogodina, V. L. (2021) · doi:10.21203/rs.3.rs-153775/v1
Lorenzo, D. D., Bisi, N., Bucci, R., Ennen, I., Presti, L. L., Dodero, V. I., Brandt, R., Ongeri, S., Gelmi, M. L., & Tonali, N. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.04.616679
Dynamical Protein Interaction Pathways: A Molecularroot to DiseasesPreprint
ASIR, M. P. (2025) · SSRN Electronic Journal · doi:10.2139/ssrn.5111478
- Authors
- Camilloni, C., Schaal, D., Schweimer, K., Schwarzinger, S., & De Simone, A.
- Affiliations
- University of Cambridge (GB)
- University of Bayreuth (DE)
- Corresponding author
- Schwarzinger, Stephan
- Venue
- Biophysical Journal
- Publisher
- Elsevier BV
- Published
- 2012-01
- Volume
- 102
- Issue
- 1
- Pages
- 158-167
- ISSN
- 0006-3495 (ISSN-L)
- PMC
- PMC3250675
- OpenAlex
- W2153865022
- Cited by
- 45
- References
- 64
- Citations by year
- 2025: 4 · 2024: 3 · 2023: 1 · 2022: 2 · 2021: 5 · 2020: 2 · 2019: 2 · 2018: 1 · 2017: 2 · 2016: 5 · 2015: 3 · 2014: 4 · 2013: 3 · 2012: 8
- FWCI
- 2.32
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Biophysical Journal (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- ERef Bayreuth (University of Bayreuth) (submittedVersion)
- Funders
- Engineering and Physical Sciences Research Council (EP/G049998/2)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Prion Diseases and Protein Misfolding
- Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
- Keywords
- prion protein, helix 1, free energy landscape, structural ensembles, protein dynamics, intrinsically disordered regions, protein misfolding, prion aggregation, prion disease, conformational heterogeneity
- MeSH terms
- Amino Acid Sequence, Computer Simulation, Energy Transfer, Models, Chemical, Models, Molecular, Molecular Sequence Data, Prions, Protein Conformation
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