Julio Fernandez - Publications

Columbia University, New York, NY 

64 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
2020 Alonso-Caballero A, Echelman DJ, Tapia-Rojo R, Haldar S, Eckels EC, Fernandez JM. Protein folding modulates the chemical reactivity of a Gram-positive adhesin. Nature Chemistry. PMID 33257887 DOI: 10.1038/s41557-020-00586-x  1
2020 Tapia-Rojo R, Alonso-Caballero A, Fernandez JM. Direct observation of a coil-to-helix contraction triggered by vinculin binding to talin. Science Advances. 6: eaaz4707. PMID 32494739 DOI: 10.1126/sciadv.aaz4707  1
2018 Berkovich R, Fernandez VI, Stirnemann G, Valle-Orero J, Fernandez JM. Segmentation and the Entropic Elasticity of Modular Proteins. The Journal of Physical Chemistry Letters. PMID 30058807 DOI: 10.1021/acs.jpclett.8b01925  1
2018 Giganti D, Yan K, Badilla CL, Fernandez JM, Alegre-Cebollada J. Disulfide isomerization reactions in titin immunoglobulin domains enable a mode of protein elasticity. Nature Communications. 9: 185. PMID 29330363 DOI: 10.1038/s41467-017-02528-7  1
2017 Haldar S, Tapia-Rojo R, Eckels EC, Valle-Orero J, Fernandez JM. Trigger factor chaperone acts as a mechanical foldase. Nature Communications. 8: 668. PMID 28939815 DOI: 10.1038/s41467-017-00771-6  1
2017 Valle-Orero J, Tapia-Rojo R, Eckels EC, Rivas-Pardo JA, Popa I, Fernandez JM. Proteins Breaking Bad: A Free Energy Perspective. The Journal of Physical Chemistry Letters. PMID 28723106 DOI: 10.1021/acs.jpclett.7b01509  1
2017 Valle Orero J, Rivas-Pardo JA, Tapia-Rojo R, Popa I, Echelman DJ, Haldar S, Fernandez JM. Mechanical deformation accelerates protein ageing. Angewandte Chemie (International Ed. in English). PMID 28470663 DOI: 10.1002/anie.201703630  1
2016 Popa I, Rivas-Pardo JA, Eckels EC, Echelman D, Valle-Orero J, Fernandez JM. A HaloTag Anchored Ruler for Week-Long Studies of Protein Dynamics. Journal of the American Chemical Society. PMID 27409974 DOI: 10.1021/jacs.6b05429  1
2015 Rivas-Pardo JA, Alegre-Cebollada J, Ramírez-Sarmiento CA, Fernandez JM, Guixé V. Identifying sequential substrate binding at the single-molecule level by enzyme mechanical stabilization. Acs Nano. 9: 3996-4005. PMID 25840594 DOI: 10.1021/nn507480v  1
2015 Valle-Orero J, Eckels EC, Stirnemann G, Popa I, Berkovich R, Fernandez JM. The elastic free energy of a tandem modular protein under force. Biochemical and Biophysical Research Communications. 460: 434-8. PMID 25796331 DOI: 10.1016/j.bbrc.2015.03.051  1
2015 Chen H, Yuan G, Winardhi RS, Yao M, Popa I, Fernandez JM, Yan J. Dynamics of equilibrium folding and unfolding transitions of titin immunoglobulin domain under constant forces. Journal of the American Chemical Society. 137: 3540-6. PMID 25726700 DOI: 10.1021/ja5119368  1
2014 Perez-Jimenez R, Alonso-Caballero A, Berkovich R, Franco D, Chen MW, Richard P, Badilla CL, Fernandez JM. Probing the effect of force on HIV-1 receptor CD4. Acs Nano. 8: 10313-20. PMID 25299596 DOI: 10.1021/nn503557w  1
2014 Solsona C, Kahn TB, Badilla CL, Álvarez-Zaldiernas C, Blasi J, Fernandez JM, Alegre-Cebollada J. Altered thiol chemistry in human amyotrophic lateral sclerosis-linked mutants of superoxide dismutase 1. The Journal of Biological Chemistry. 289: 26722-32. PMID 25096579 DOI: 10.1074/jbc.M114.565333  1
2013 Ingles-Prieto A, Ibarra-Molero B, Delgado-Delgado A, Perez-Jimenez R, Fernandez JM, Gaucher EA, Sanchez-Ruiz JM, Gavira JA. Conservation of protein structure over four billion years Structure. 21: 1690-1697. PMID 23932589 DOI: 10.1016/j.str.2013.06.020  1
2013 Popa I, Berkovich R, Alegre-Cebollada J, Badilla CL, Rivas-Pardo JA, Taniguchi Y, Kawakami M, Fernandez JM. Nanomechanics of HaloTag tethers. Journal of the American Chemical Society. 135: 12762-71. PMID 23909704 DOI: 10.1021/ja4056382  1
2013 Kan Z, Zheng H, Liu X, Li S, Barber TD, Gong Z, Gao H, Hao K, Willard MD, Xu J, Hauptschein R, Rejto PA, Fernandez J, Wang G, Zhang Q, et al. Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma. Genome Research. 23: 1422-33. PMID 23788652 DOI: 10.1101/gr.154492.113  0.44
2013 Popa I, Kosuri P, Alegre-Cebollada J, Garcia-Manyes S, Fernandez JM. Force dependency of biochemical reactions measured by single-molecule force-clamp spectroscopy. Nature Protocols. 8: 1261-76. PMID 23744288 DOI: 10.1038/nprot.2013.056  1
2013 Stirnemann G, Giganti D, Fernandez JM, Berne BJ. Elasticity, structure, and relaxation of extended proteins under force. Proceedings of the National Academy of Sciences of the United States of America. 110: 3847-52. PMID 23407163 DOI: 10.1073/pnas.1300596110  1
2013 Javadi Y, Fernandez JM, Perez-Jimenez R. Protein folding under mechanical forces: a physiological view. Physiology (Bethesda, Md.). 28: 9-17. PMID 23280353 DOI: 10.1152/physiol.00017.2012  1
2012 Berkovich R, Hermans RI, Popa I, Stirnemann G, Garcia-Manyes S, Berne BJ, Fernandez JM. Rate limit of protein elastic response is tether dependent. Proceedings of the National Academy of Sciences of the United States of America. 109: 14416-21. PMID 22895787 DOI: 10.1073/pnas.1212167109  1
2011 Dougan L, Genchev GZ, Lu H, Fernandez JM. Probing osmolyte participation in the unfolding transition state of a protein. Proceedings of the National Academy of Sciences of the United States of America. 108: 9759-64. PMID 21613570 DOI: 10.1073/pnas.1101934108  1
2011 Perez-Jimenez R, Inglés-Prieto A, Zhao ZM, Sanchez-Romero I, Alegre-Cebollada J, Kosuri P, Garcia-Manyes S, Kappock TJ, Tanokura M, Holmgren A, Sanchez-Ruiz JM, Gaucher EA, Fernandez JM. Single-molecule paleoenzymology probes the chemistry of resurrected enzymes. Nature Structural & Molecular Biology. 18: 592-6. PMID 21460845 DOI: 10.1038/nsmb.2020  1
2010 Li J, Fernandez JM, Berne BJ. Water's role in the force-induced unfolding of ubiquitin. Proceedings of the National Academy of Sciences of the United States of America. 107: 19284-9. PMID 20974922 DOI: 10.1073/pnas.1013159107  1
2010 Berkovich R, Garcia-Manyes S, Urbakh M, Klafter J, Fernandez JM. Collapse dynamics of single proteins extended by force. Biophysical Journal. 98: 2692-701. PMID 20513414 DOI: 10.1016/j.bpj.2010.02.053  1
2010 Rodriguez-Larrea D, Perez-Jimenez R, Sanchez-Romero I, Delgado-Delgado A, Fernandez JM, Sanchez-Ruiz JM. Role of conservative mutations in protein multi-property adaptation. The Biochemical Journal. 429: 243-9. PMID 20446918 DOI: 10.1042/BJ20100386  1
2010 Alegre-Cebollada J, Perez-Jimenez R, Kosuri P, Fernandez JM. Single-molecule force spectroscopy approach to enzyme catalysis. The Journal of Biological Chemistry. 285: 18961-6. PMID 20382731 DOI: 10.1074/jbc.R109.011932  1
2009 Fernandez VI, Kosuri P, Parot V, Fernandez JM. Extended Kalman filter estimates the contour length of a protein in single molecule atomic force microscopy experiments. The Review of Scientific Instruments. 80: 113104. PMID 19947714 DOI: 10.1063/1.3252982  1
2009 Grützner A, Garcia-Manyes S, Kötter S, Badilla CL, Fernandez JM, Linke WA. Modulation of titin-based stiffness by disulfide bonding in the cardiac titin N2-B unique sequence. Biophysical Journal. 97: 825-34. PMID 19651040 DOI: 10.1016/j.bpj.2009.05.037  1
2009 Perez-Jimenez R, Li J, Kosuri P, Sanchez-Romero I, Wiita AP, Rodriguez-Larrea D, Chueca A, Holmgren A, Miranda-Vizuete A, Becker K, Cho SH, Beckwith J, Gelhaye E, Jacquot JP, Gaucher EA, ... ... Fernandez JM, et al. Diversity of chemical mechanisms in thioredoxin catalysis revealed by single-molecule force spectroscopy. Nature Structural & Molecular Biology. 16: 890-6. PMID 19597482 DOI: 10.1038/nsmb.1627  1
2009 Dougan L, Li J, Badilla CL, Berne BJ, Fernandez JM. Single homopolypeptide chains collapse into mechanically rigid conformations. Proceedings of the National Academy of Sciences of the United States of America. 106: 12605-10. PMID 19549822 DOI: 10.1073/pnas.0900678106  1
2009 del Rio A, Perez-Jimenez R, Liu R, Roca-Cusachs P, Fernandez JM, Sheetz MP. Stretching single talin rod molecules activates vinculin binding. Science (New York, N.Y.). 323: 638-41. PMID 19179532 DOI: 10.1126/science.1162912  1
2008 Dougan L, Koti AS, Genchev G, Lu H, Fernandez JM. A single-molecule perspective on the role of solvent hydrogen bonds in protein folding and chemical reactions. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 9: 2836-47. PMID 19058277 DOI: 10.1002/cphc.200800572  1
2008 Perez-Jimenez R, Wiita AP, Rodriguez-Larrea D, Kosuri P, Gavira JA, Sanchez-Ruiz JM, Fernandez JM. Force-clamp spectroscopy detects residue co-evolution in enzyme catalysis. The Journal of Biological Chemistry. 283: 27121-9. PMID 18687682 DOI: 10.1074/jbc.M803746200  1
2008 Koti Ainavarapu SR, Wiita AP, Dougan L, Uggerud E, Fernandez JM. Single-molecule force spectroscopy measurements of bond elongation during a bimolecular reaction. Journal of the American Chemical Society. 130: 6479-87. PMID 18433129 DOI: 10.1021/ja800180u  1
2008 Dougan L, Feng G, Lu H, Fernandez JM. Solvent molecules bridge the mechanical unfolding transition state of a protein. Proceedings of the National Academy of Sciences of the United States of America. 105: 3185-90. PMID 18305176 DOI: 10.1073/pnas.0706075105  1
2008 Ainavarapu SR, Wiita AP, Huang HH, Fernandez JM. A single-molecule assay to directly identify solvent-accessible disulfide bonds and probe their effect on protein folding. Journal of the American Chemical Society. 130: 436-7. PMID 18088123 DOI: 10.1021/ja077851s  1
2008 Szoszkiewicz R, Ainavarapu SR, Wiita AP, Perez-Jimenez R, Sanchez-Ruiz JM, Fernandez JM. Dwell time analysis of a single-molecule mechanochemical reaction. Langmuir : the Acs Journal of Surfaces and Colloids. 24: 1356-64. PMID 17999545 DOI: 10.1021/la702368b  1
2007 Dougan L, Fernandez JM. Tandem repeating modular proteins avoid aggregation in single molecule force spectroscopy experiments. The Journal of Physical Chemistry. A. 111: 12402-8. PMID 18020430 DOI: 10.1021/jp076095+  1
2007 Wiita AP, Perez-Jimenez R, Walther KA, Gräter F, Berne BJ, Holmgren A, Sanchez-Ruiz JM, Fernandez JM. Probing the chemistry of thioredoxin catalysis with force. Nature. 450: 124-7. PMID 17972886 DOI: 10.1038/nature06231  1
2007 Walther KA, Gräter F, Dougan L, Badilla CL, Berne BJ, Fernandez JM. Signatures of hydrophobic collapse in extended proteins captured with force spectroscopy. Proceedings of the National Academy of Sciences of the United States of America. 104: 7916-21. PMID 17470816 DOI: 10.1073/pnas.0702179104  1
2007 Brujic J, Hermans RI, Garcia-Manyes S, Walther KA, Fernandez JM. Dwell-time distribution analysis of polyprotein unfolding using force-clamp spectroscopy. Biophysical Journal. 92: 2896-903. PMID 17259284 DOI: 10.1529/biophysj.106.099481  1
2007 Sarkar A, Caamano S, Fernandez JM. The mechanical fingerprint of a parallel polyprotein dimer. Biophysical Journal. 92: L36-8. PMID 17158577 DOI: 10.1529/biophysj.106.097741  1
2007 Ainavarapu SR, Brujic J, Huang HH, Wiita AP, Lu H, Li L, Walther KA, Carrion-Vazquez M, Li H, Fernandez JM. Contour length and refolding rate of a small protein controlled by engineered disulfide bonds. Biophysical Journal. 92: 225-33. PMID 17028145 DOI: 10.1529/biophysj.106.091561  1
2006 Perez-Jimenez R, Garcia-Manyes S, Ainavarapu SR, Fernandez JM. Mechanical unfolding pathways of the enhanced yellow fluorescent protein revealed by single molecule force spectroscopy. The Journal of Biological Chemistry. 281: 40010-4. PMID 17082195 DOI: 10.1074/jbc.M609890200  1
2006 Ainavarapu SR, Li L, Fernandez JM. Fingerprinting DHFR in single-molecule AFM studies. Biophysical Journal. 91: 2009-10, discussion . PMID 16782796 DOI: 10.1529/biophysj.106.085126  1
2006 Wiita AP, Ainavarapu SR, Huang HH, Fernandez JM. Force-dependent chemical kinetics of disulfide bond reduction observed with single-molecule techniques. Proceedings of the National Academy of Sciences of the United States of America. 103: 7222-7. PMID 16645035 DOI: 10.1073/pnas.0511035103  1
2006 Li L, Wetzel S, Plückthun A, Fernandez JM. Stepwise unfolding of ankyrin repeats in a single protein revealed by atomic force microscopy. Biophysical Journal. 90: L30-2. PMID 16387766 DOI: 10.1529/biophysj.105.078436  1
2005 Sato T, Esaki M, Fernandez JM, Endo T. Comparison of the protein-unfolding pathways between mitochondrial protein import and atomic-force microscopy measurements. Proceedings of the National Academy of Sciences of the United States of America. 102: 17999-8004. PMID 16326810 DOI: 10.1073/pnas.0504495102  1
2005 Fernandez JM. Fingerprinting single molecules in vivo. Biophysical Journal. 89: 3676-7. PMID 16319078 DOI: 10.1529/biophysj.105.072223  1
2005 Ainavarapu SR, Li L, Badilla CL, Fernandez JM. Ligand binding modulates the mechanical stability of dihydrofolate reductase. Biophysical Journal. 89: 3337-44. PMID 16100277 DOI: 10.1529/biophysj.105.062034  1
2005 Sarkar A, Caamano S, Fernandez JM. The elasticity of individual titin PEVK exons measured by single molecule atomic force microscopy. The Journal of Biological Chemistry. 280: 6261-4. PMID 15632200 DOI: 10.1074/jbc.C400573200  1
2005 Li L, Huang HH, Badilla CL, Fernandez JM. Mechanical unfolding intermediates observed by single-molecule force spectroscopy in a fibronectin type III module. Journal of Molecular Biology. 345: 817-26. PMID 15588828 DOI: 10.1016/j.jmb.2004.11.021  1
2004 Sarkar A, Robertson RB, Fernandez JM. Simultaneous atomic force microscope and fluorescence measurements of protein unfolding using a calibrated evanescent wave. Proceedings of the National Academy of Sciences of the United States of America. 101: 12882-6. PMID 15326308 DOI: 10.1073/pnas.0403534101  1
2004 Schlierf M, Li H, Fernandez JM. The unfolding kinetics of ubiquitin captured with single-molecule force-clamp techniques. Proceedings of the National Academy of Sciences of the United States of America. 101: 7299-304. PMID 15123816 DOI: 10.1073/pnas.0400033101  1
2004 Fernandez JM, Li H. Force-clamp spectroscopy monitors the folding trajectory of a single protein. Science (New York, N.Y.). 303: 1674-8. PMID 15017000 DOI: 10.1126/science.1092497  1
2003 Li H, Fernandez JM. Mechanical design of the first proximal Ig domain of human cardiac titin revealed by single molecule force spectroscopy. Journal of Molecular Biology. 334: 75-86. PMID 14596801 DOI: 10.1016/j.jmb.2003.09.036  1
2003 Marszalek PE, Oberhauser AF, Li H, Fernandez JM. The force-driven conformations of heparin studied with single molecule force microscopy. Biophysical Journal. 85: 2696-704. PMID 14507732 DOI: 10.1016/S0006-3495(03)74692-X  1
2003 Kenniston JA, Baker TA, Fernandez JM, Sauer RT. Linkage between ATP consumption and mechanical unfolding during the protein processing reactions of an AAA+ degradation machine. Cell. 114: 511-20. PMID 12941278 DOI: 10.1016/S0092-8674(03)00612-3  1
2003 Carrion-Vazquez M, Li H, Lu H, Marszalek PE, Oberhauser AF, Fernandez JM. The mechanical stability of ubiquitin is linkage dependent. Nature Structural Biology. 10: 738-43. PMID 12923571 DOI: 10.1038/nsb965  1
2002 Linke WA, Fernandez JM. Cardiac titin: molecular basis of elasticity and cellular contribution to elastic and viscous stiffness components in myocardium. Journal of Muscle Research and Cell Motility. 23: 483-97. PMID 12785099 DOI: 10.1023/A:1023462507254  1
2002 Li H, Linke WA, Oberhauser AF, Carrion-Vazquez M, Kerkvliet JG, Lu H, Marszalek PE, Fernandez JM. Reverse engineering of the giant muscle protein titin. Nature. 418: 998-1002. PMID 12198551 DOI: 10.1038/nature00938  1
2002 Linke WA, Kulke M, Li H, Fujita-Becker S, Neagoe C, Manstein DJ, Gautel M, Fernandez JM. PEVK domain of titin: an entropic spring with actin-binding properties. Journal of Structural Biology. 137: 194-205. PMID 12064946 DOI: 10.1006/jsbi.2002.4468  1
2002 Oberhauser AF, Badilla-Fernandez C, Carrion-Vazquez M, Fernandez JM. The mechanical hierarchies of fibronectin observed with single-molecule AFM Journal of Molecular Biology. 319: 433-447. PMID 12051919 DOI: 10.1016/S0022-2836(02)00306-6  1
2002 Marszalek PE, Li H, Oberhauser AF, Fernandez JM. Chair-boat transitions in single polysaccharide molecules observed with force-ramp AFM Proceedings of the National Academy of Sciences of the United States of America. 99: 4278-4283. PMID 11917130 DOI: 10.1073/pnas.072435699  1
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