cached image

Jocelyne Vreede - Publications

Affiliations: 
University of Amsterdam, Amsterdam, Netherlands 
Area:
Computational Chemistry
Website:
http://molsim.chem.uva.nl/users/vreede/index.html

31 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
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  0.64
2019 Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, ... ... Vreede J, et al. Allostery in Its Many Disguises: From Theory to Applications. Structure (London, England : 1993). PMID 30744993 DOI: 10.1016/j.str.2019.01.003  0.64
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  1
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  1
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  1
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. DOI: 10.1371/journal.pcbi.1003797  1
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: 344-359. DOI: 10.1159/000368851  1
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 Journal of Physical Chemistry Letters. 5: 900-904. DOI: 10.1021/jz500029a  1
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  1
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  1
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  1
2012 Schor M, Vreede J, Bolhuis PG. Elucidating the locking mechanism of peptides onto growing amyloid fibrils through transition path sampling Biophysical Journal. 103: 1296-1304. PMID 22995502 DOI: 10.1016/j.bpj.2012.07.056  1
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  1
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  1
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  1
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  1
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  1
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  1
2009 Bussink AP, Verhoek M, Vreede J, Ghauharali-Van Der Vlugt K, Donker-Koopman WE, Sprenger RR, Hollak CE, Aerts JMFG, Boot RG. Common G102S polymorphism in chitotriosidase differentially affects activity towards 4-methylumbelliferyl substrates Febs Journal. 276: 5678-5688. PMID 19725875 DOI: 10.1111/j.1742-4658.2009.07259.x  1
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  1
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  1
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  1
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  1
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  1
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  0.64
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  1
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  1
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  1
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  1
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  1
2003 Rekvig L, Kranenburg M, Vreede J, Hafskjold B, Smit B. Investigation of surfactant efficiency using dissipative particle dynamics Langmuir. 19: 8195-8205. DOI: 10.1021/la0346346  1
Show low-probability matches.