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Jocelyne Vreede - Publications

Affiliations: 
University of Amsterdam, Amsterdam, Netherlands 
Area:
Computational Chemistry
Website:
http://molsim.chem.uva.nl/users/vreede/index.html
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43 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 van Heesch T, Bolhuis PG, Vreede J. Decoding dissociation of sequence-specific protein-DNA complexes with non-equilibrium simulations. Nucleic Acids Research. 51: 12150-12160. PMID 37953329 DOI: 10.1093/nar/gkad1014  0.305
2022 Roet S, Hooft F, Bolhuis PG, Swenson DWH, Vreede J. Path Sampling Simulations Reveal How the Q61L Mutation Alters the Dynamics of KRas. The Journal of Physical Chemistry. B. PMID 36427204 DOI: 10.1021/acs.jpcb.2c06235  0.335
2020 Qin L, Bdira FB, Sterckx YGJ, Volkov AN, Vreede J, Giachin G, van Schaik P, Ubbink M, Dame RT. Structural basis for osmotic regulation of the DNA binding properties of H-NS proteins. Nucleic Acids Research. PMID 31925429 DOI: 10.1093/Nar/Gkz1226  0.462
2019 Vreede J, Pérez de Alba Ortíz A, Bolhuis PG, Swenson DWH. Atomistic insight into the kinetic pathways for Watson-Crick to Hoogsteen transitions in DNA. Nucleic Acids Research. PMID 31665440 DOI: 10.1093/Nar/Gkz837  0.347
2019 Riccardi E, van Mastbergen EC, Navarre WW, Vreede J. Predicting the mechanism and rate of H-NS binding to AT-rich DNA. Plos Computational Biology. 15: e1006845. PMID 30845209 DOI: 10.1371/Journal.Pcbi.1006845  0.364
2018 Muzdalo A, Saalfrank P, Vreede J, Santer M. cis to trans isomerization of azobenzene derivatives studied with transition path sampling and QM/MM molecular dynamics. Journal of Chemical Theory and Computation. PMID 29466663 DOI: 10.1021/Acs.Jctc.7B01120  0.353
2017 van der Valk RA, Vreede J, Qin L, Moolenaar GF, Hofmann A, Goosen N, Dame RT. Mechanism of environmentally driven conformational changes that modulate H-NS DNA bridging activity. Elife. 6. PMID 28949292 DOI: 10.7554/Elife.27369  0.331
2017 Valk RAvd, Vreede J, Qin L, Moolenaar GF, Hofmann A, Goosen N, Dame RT. Author response: Mechanism of environmentally driven conformational changes that modulate H-NS DNA-bridging activity Elife. DOI: 10.7554/Elife.27369.027  0.3
2017 Vreede J, Bolhuis PG, Swenson DW. Path Sampling Simulations of the Mechanisms and Rates of Transitions between Watson-Crick and Hoogsteen Base Pairing in DNA Biophysical Journal. 112: 214a. DOI: 10.1016/J.Bpj.2016.11.1181  0.341
2016 Meuzelaar H, Vreede J, Woutersen S. Influence of Glu/Arg, Asp/Arg, and Glu/Lys Salt Bridges on α-Helical Stability and Folding Kinetics. Biophysical Journal. 110: 2328-41. PMID 27276251 DOI: 10.1016/J.Bpj.2016.04.015  0.359
2016 Vreede J, Bolhuis PG, Swenson DW. Predicting the Mechanism and Kinetics of the Watson-Crick to Hoogsteen Base Pairing Transition Biophysical Journal. 110: 563a-564a. DOI: 10.1016/J.Bpj.2015.11.3014  0.369
2015 Singhal K, Vreede J, Mashaghi A, Tans SJ, Bolhuis PG. The Trigger Factor Chaperone Encapsulates and Stabilizes Partial Folds of Substrate Proteins. Plos Computational Biology. 11: e1004444. PMID 26512985 DOI: 10.1371/Journal.Pcbi.1004444  0.464
2015 Zhu J, Vreede J, Hospes M, Arents J, Kennis JT, van Stokkum IH, Hellingwerf KJ, Groot ML. Short hydrogen bonds and negative charge in photoactive yellow protein promote fast isomerization but not high quantum yield. The Journal of Physical Chemistry. B. 119: 2372-83. PMID 25144816 DOI: 10.1021/Jp506785Q  0.655
2015 Zhu J, Vreede J, Hospes M, Arents J, Kennis JTM, Van Stokkum IHM, Hellingwerf KJ, Groot ML. Short hydrogen bonds and negative charge in photoactive yellow protein promote fast isomerization but not high quantum yield Journal of Physical Chemistry B. 119: 2372-2383. DOI: 10.1021/jp506785q  0.586
2015 van Mastbergen EC, Vreede J. Modeling the Binding of H-NS to DNA Biophysical Journal. 108: 537a-538a. DOI: 10.1016/J.Bpj.2014.11.2948  0.333
2014 van der Valk RA, Vreede J, Crémazy F, Dame RT. Genomic looping: a key principle of chromatin organization. Journal of Molecular Microbiology and Biotechnology. 24: 344-59. PMID 25732337 DOI: 10.1159/000368851  0.328
2014 A Rohrdanz M, Zheng W, Lambeth B, Vreede J, Clementi C. Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble. Plos Computational Biology. 10: e1003797. PMID 25356903 DOI: 10.1371/Journal.Pcbi.1003797  0.381
2014 Meuzelaar H, Tros M, Huerta-Viga A, van Dijk CN, Vreede J, Woutersen S. Solvent-Exposed Salt Bridges Influence the Kinetics of α-Helix Folding and Unfolding. The Journal of Physical Chemistry Letters. 5: 900-904. PMID 24634715 DOI: 10.1021/Jz500029A  0.397
2013 Singhal K, Vreede J, Mashaghi A, Tans SJ, Bolhuis PG. Hydrophobic Collapse of Trigger Factor Monomer in Solution Plos One. 8. PMID 23565160 DOI: 10.1371/Journal.Pone.0059683  0.396
2013 Joyeux M, Vreede J. A model of H-NS mediated compaction of bacterial DNA Biophysical Journal. 104: 1615-1622. PMID 23561538 DOI: 10.1016/J.Bpj.2013.02.043  0.365
2013 Zhu L, Bolhuis PG, Vreede J. The HAMP Signal Relay Domain Adopts Multiple Conformational States through Collective Piston and Tilt Motions Plos Computational Biology. 9. PMID 23468603 DOI: 10.1371/Journal.Pcbi.1002913  0.443
2013 Singhal K, Vreede J, Mashaghi A, Tans SJ, Bolhuis PG. A Molecular Dynamics Study of the Flexibility and Protein-Binding of the Trigger Factor Chaperone in Solution Biophysical Journal. 104: 571a. DOI: 10.1016/J.Bpj.2012.11.3172  0.518
2012 Vreede J, Dame RT. Predicting the effect of ions on the conformation of the H-NS dimerization domain Biophysical Journal. 103: 89-98. PMID 22828335 DOI: 10.1016/J.Bpj.2012.05.040  0.445
2012 Juraszek J, Vreede J, Bolhuis PG. Transition path sampling of protein conformational changes Chemical Physics. 396: 30-34. DOI: 10.1016/J.Chemphys.2011.04.032  0.414
2011 Kwakman PH, Krijgsveld J, de Boer L, Nguyen LT, Boszhard L, Vreede J, Dekker HL, Speijer D, Drijfhout JW, te Velde AA, Crielaard W, Vogel HJ, Vandenbroucke-Grauls CM, Zaat SA. Native thrombocidin-1 and unfolded thrombocidin-1 exert antimicrobial activity via distinct structural elements. The Journal of Biological Chemistry. 286: 43506-14. PMID 22025617 DOI: 10.1074/Jbc.M111.248641  0.649
2011 Rupenyan AB, Vreede J, van Stokkum IH, Hospes M, Kennis JT, Hellingwerf KJ, Groot ML. Proline 68 enhances photoisomerization yield in photoactive yellow protein. The Journal of Physical Chemistry. B. 115: 6668-77. PMID 21542640 DOI: 10.1021/Jp112113S  0.692
2011 Rupenyan AB, Vreede J, Van Stokkum IHM, Hospes M, Kennis JTM, Hellingwerf KJ, Louise GM. Proline 68 enhances photoisomerization yield in photoactive yellow protein Journal of Physical Chemistry B. 115: 6668-6677. DOI: 10.1021/jp112113s  0.625
2011 Zhu L, Bolhuis PG, Vreede J. Exploring Signal Transduction Mechanism of HAMP Domains via Molecular Dynamics and Metadynamics Biophysical Journal. 100: 195a. DOI: 10.1016/J.Bpj.2010.12.1281  0.455
2010 Vreede J, Juraszek J, Bolhuis PG. Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein Proceedings of the National Academy of Sciences of the United States of America. 107: 2397-2402. PMID 20133754 DOI: 10.1073/Pnas.0908754107  0.488
2010 Zhu L, Bolhuis P, Vreede J. Molecular Dynamics Simulation Study of Isolated Hamp Domain Biophysical Journal. 98: 26a. DOI: 10.1016/J.Bpj.2009.12.155  0.46
2009 Avila-Pérez M, Vreede J, Tang Y, Bende O, Losi A, Gärtner W, Hellingwerf K. In vivo mutational analysis of YtvA from bacillus subtilis. Mechanism of light activation of the general stress response Journal of Biological Chemistry. 284: 24958-24964. PMID 19581299 DOI: 10.1074/Jbc.M109.033316  0.624
2009 Vreede J, Wolf MG, de Leeuw SW, Bolhuis PG. Reordering hydrogen bonds using hamiltonian replica exchange enhances sampling of conformational changes in biomolecular systems. The Journal of Physical Chemistry. B. 113: 6484-94. PMID 19358572 DOI: 10.1021/Jp809641J  0.397
2009 Vreede J, Wolf MG, de Leeuw SW, Bolhuis PG. Reordering Hydrogen Bonds In The Protein Backbone In Hamiltonian Exchange MD Enhances Sampling Of Conformational Changes Biophysical Journal. 96: 589a. DOI: 10.1016/J.Bpj.2008.12.3086  0.425
2009 Vreede J, Juraszek J, Hellingwerf KJ, Bolhuis PG. Sampling the unfolding pathways towards the signaling state of Photoactive Yellow Protein Biophysical Journal. 96: 524a. DOI: 10.1016/J.Bpj.2008.12.2703  0.702
2008 Bussink AP, Vreede J, Aerts JMFG, Boot RG. A single histidine residue modulates enzymatic activity in acidic mammalian chitinase Febs Letters. 582: 931-935. PMID 18294964 DOI: 10.1016/J.Febslet.2008.02.032  0.327
2008 Vreede J, Hellingwerf KJ, Crielaard W. TraR auto-inducer enhances protein backbone fluctuations in DNA binding domain Febs Letters. 582: 805-809. PMID 18275856 DOI: 10.1016/J.Febslet.2008.01.062  0.744
2008 Vreede J, Hellingwerf KJ, Bolhuis PG. Helix formation is a dynamical bottleneck in the recovery reaction of Photoactive Yellow Protein Proteins: Structure, Function and Genetics. 72: 136-149. PMID 18214984 DOI: 10.1002/Prot.21902  0.686
2007 Leenders EJ, Guidoni L, Röthlisberger U, Vreede J, Bolhuis PG, Meijer EJ. Protonation of the chromophore in the photoactive yellow protein. The Journal of Physical Chemistry. B. 111: 3765-73. PMID 17388542 DOI: 10.1021/Jp067158B  0.452
2007 Leenders EJM, Guidoni L, Röthlisberger U, Vreede J, Bolhuis PG, Meijer EJ. Protonation of the chromophore in the photoactive yellow protein Journal of Physical Chemistry B. 111: 3765-3773. DOI: 10.1021/jp067158b  0.314
2005 Vreede J, Crielaard W, Hellingwerf KJ, Bolhuis PG. Predicting the signaling state of photoactive yellow protein Biophysical Journal. 88: 3525-3535. PMID 15722437 DOI: 10.1529/Biophysj.104.055103  0.752
2005 van Der Horst MA, Hendriks J, Vreede J, Yeremenko S, Crielaard W, Hellingwerf KJ. Photoactive Yellow Protein, the Xanthopsin Handbook of Photosensory Receptors. 391-415. DOI: 10.1002/352760510X.ch19  0.724
2004 Vreede J, Van Der Horst MA, Kort R, Crielaard W, Hellingwerf KJ. Measuring and modelling dynamical changes in the structure of photoactive yellow protein Phase Transitions. 77: 3-20. DOI: 10.1080/01411590310001621384  0.726
2003 Vreede J, Van der Horst MA, Hellingwerf KJ, Crielaard W, Van Aalten DMF. PAS domains. Common structure and common flexibility Journal of Biological Chemistry. 278: 18434-18439. PMID 12639952 DOI: 10.1074/Jbc.M301701200  0.744
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