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Raul Perez-Jimenez - Publications

Affiliations: 
2007-2013 Department of Biological Sc Columbia University, New York, NY 
 2013- CIC nanoGUNE 
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44/47 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
2024 Reifs A, Fernandez-Calvo A, Alonso-Lerma B, Schönfelder J, Franco D, Ortega-Muñoz M, Casares S, Jimenez-Lopez C, Saa L, Cortajarena AL, De Sancho D, San Sebastian E, Perez-Jimenez R. High-throughput virtual search of small molecules for controlling the mechanical stability of human CD4. The Journal of Biological Chemistry. 300: 107133. PMID 38432632 DOI: 10.1016/j.jbc.2024.107133  0.36
2022 Herrero-Galán E, Martínez-Martín I, Sánchez-González C, Vicente N, Bonzón-Kulichenko E, Calvo E, Suay-Corredera C, Pricolo MR, Fernández-Trasancos Á, Velázquez-Carreras D, Careaga CB, Abdellatif M, Sedej S, Rainer PP, Giganti D, et al. Basal oxidation of conserved cysteines modulates cardiac titin stiffness and dynamics. Redox Biology. 52: 102306. PMID 35367810 DOI: 10.1016/j.redox.2022.102306  0.659
2022 Peters DT, Reifs A, Alonso-Caballero A, Madkour A, Waller H, Kenny B, Perez-Jimenez R, Lakey JH. Unraveling the molecular determinants of the anti-phagocytic protein cloak of plague bacteria. Plos Pathogens. 18: e1010447. PMID 35358289 DOI: 10.1371/journal.ppat.1010447  0.768
2022 Schönfelder J, Alonso-Caballero A, Perez-Jimenez R. Mechanochemical Evolution of Disulfide Bonds in Proteins. Methods in Molecular Biology (Clifton, N.J.). 2376: 283-300. PMID 34845615 DOI: 10.1007/978-1-0716-1716-8_15  0.811
2020 Corsetti F, Alonso-Caballero A, Poly S, Perez-Jimenez R, Artacho E. Entropic bonding of the type 1 pilus from experiment and simulation. Royal Society Open Science. 7: 200183. PMID 32431906 DOI: 10.1098/Rsos.200183  0.771
2018 De Sancho D, Schönfelder J, Best RB, Perez-Jimenez R, Muñoz V. Instrumental Effects in the Dynamics of an Ultrafast Folding Protein under Mechanical Force. The Journal of Physical Chemistry. B. PMID 30129367 DOI: 10.1021/Acs.Jpcb.8B05975  0.503
2018 Alonso-Caballero A, Schönfelder J, Poly S, Corsetti F, De Sancho D, Artacho E, Perez-Jimenez R. Mechanical architecture and folding of E. coli type 1 pilus domains. Nature Communications. 9: 2758. PMID 30013059 DOI: 10.1038/S41467-018-05107-6  0.78
2018 Schönfelder J, Alonso-Caballero A, De Sancho D, Perez-Jimenez R. The life of proteins under mechanical force. Chemical Society Reviews. PMID 29473060 DOI: 10.1039/C7Cs00820A  0.812
2017 Manteca A, Schönfelder J, Alonso-Caballero A, Fertin MJ, Barruetabeña N, Faria BF, Herrero-Galán E, Alegre-Cebollada J, De Sancho D, Perez-Jimenez R. Mechanochemical evolution of the giant muscle protein titin as inferred from resurrected proteins. Nature Structural & Molecular Biology. 24: 652-657. PMID 28671667 DOI: 10.1038/Nsmb.3426  0.771
2017 Manteca A, Alonso-Caballero Á, Fertin M, Poly S, De Sancho D, Perez-Jimenez R. The influence of disulfide bonds on the mechanical stability of proteins is context dependent. The Journal of Biological Chemistry. 292: 13374-13380. PMID 28642368 DOI: 10.1074/Jbc.M117.784934  0.81
2017 Alonso-Caballero A, Perez-Jimenez R. Mechanical Architecture and Genesis of Bacterial Pilus Domains Revealed by Single-Molecule Force Spectroscopy Biophysical Journal. 112: 490a. DOI: 10.1016/J.Bpj.2016.11.2654  0.8
2016 Schönfelder J, De Sancho D, Perez-Jimenez R. The Power of Force: Insights into the Protein Folding Process Using Single-Molecule Force Spectroscopy. Journal of Molecular Biology. 428: 4245-4257. PMID 27639437 DOI: 10.1016/J.Jmb.2016.09.006  0.501
2016 Schönfelder J, Perez-Jimenez R, Muñoz V. A simple two-state protein unfolds mechanically via multiple heterogeneous pathways at single-molecule resolution. Nature Communications. 7: 11777. PMID 27248054 DOI: 10.1038/Ncomms11777  0.492
2016 Perez-Jimenez R, Manteca A, Sancho DD, Herrero-Galán E, Cebollada JA. Mechanochemical Evolution of the Giant Muscle Protein Titin as Inferred from Ancient Proteins Biophysical Journal. 110: 14. DOI: 10.1016/J.Bpj.2015.11.133  0.491
2015 Kahn TB, Fernández JM, Perez-Jimenez R. Monitoring Oxidative Folding of a Single Protein Catalyzed by the Disulfide Oxidoreductase DsbA. The Journal of Biological Chemistry. 290: 14518-27. PMID 25897077 DOI: 10.1074/Jbc.M115.646000  0.724
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  0.765
2014 Kahn TB, Fernandez JM, Perez-Jimenez R. Placeholder Mechanism of Catalyzed Oxidative Folding is Conserved Across Multiple Domains of Life Biophysical Journal. 106: 6-8. DOI: 10.1016/J.Bpj.2013.11.3753  0.396
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  0.689
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  0.757
2011 Naganathan AN, Perez-Jimenez R, Muñoz V, Sanchez-Ruiz JM. Estimation of protein folding free energy barriers from calorimetric data by multi-model Bayesian analysis. Physical Chemistry Chemical Physics : Pccp. 13: 17064-76. PMID 21769353 DOI: 10.1039/C1Cp20156E  0.353
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  0.789
2010 Naganathan AN, Li P, Perez-Jimenez R, Sanchez-Ruiz JM, Muñoz V. Navigating the downhill protein folding regime via structural homologues. Journal of the American Chemical Society. 132: 11183-90. PMID 20698685 DOI: 10.1021/Ja103612Q  0.412
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  0.731
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  0.815
2010 Perez-Jimenez R, Inglés-Prieto A, Sanchez-Romero I, Alegre-Cebollada J, Kosuri P, Garcia-Mañes S, Gaucher E, Sanchez-Ruiz JM, Fernandez JM. Paleoenzymology at the Single-Molecule Level: Probing the Chemistry of Resurrected Enzymes with Force-Clamp Spectroscopy Biophysical Journal. 98: 617a. DOI: 10.1016/J.Bpj.2009.12.3368  0.837
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, 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  0.833
2009 Sadqi M, de Alba E, Pérez-Jiménez R, Sanchez-Ruiz JM, Muñoz V. A designed protein as experimental model of primordial folding. Proceedings of the National Academy of Sciences of the United States of America. 106: 4127-32. PMID 19240216 DOI: 10.1073/Pnas.0812108106  0.411
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  0.746
2009 Sadqi M, Alba Ed, Perez-Jimenez R, Sanchez-Ruiz JM, Munoz V. Protein folding on a highly rugged landscape: Experimental observation of glassy dynamics and structural frustration Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb2K6R/Pdb  0.362
2009 Perez-Jimenez R, Li J, Kosuri P, Berne BJ, Fernandez JM. Chemical Diversity and Origin of Thioredoxin Catalysis Revealed by Force-clamp Spectroscopy Biophysical Journal. 96: 643a. DOI: 10.1016/J.Bpj.2008.12.3402  0.801
2009 Rodriguez-Larrea D, Perez-Jimenez R, Sanchez-Romero I, Arco-Gonzalez R, Delgado A, Fernandez JM, Sanchez-Ruiz JM. Super-proteins From Fitness-threshold Selection Statistics Biophysical Journal. 96. DOI: 10.1016/J.Bpj.2008.12.3098  0.722
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  0.801
2008 Halskau O, Perez-Jimenez R, Ibarra-Molero B, Underhaug J, Muñoz V, Martinez A, Sanchez-Ruiz JM. Large-scale modulation of thermodynamic protein folding barriers linked to electrostatics. Proceedings of the National Academy of Sciences of the United States of America. 105: 8625-30. PMID 18550823 DOI: 10.1073/Pnas.0709881105  0.412
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  0.79
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  0.802
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  0.788
2006 Godoy-Ruiz R, Ariza F, Rodriguez-Larrea D, Perez-Jimenez R, Ibarra-Molero B, Sanchez-Ruiz JM. Natural selection for kinetic stability is a likely origin of correlations between mutational effects on protein energetics and frequencies of amino acid occurrences in sequence alignments. Journal of Molecular Biology. 362: 966-78. PMID 16935299 DOI: 10.1016/J.Jmb.2006.07.065  0.364
2006 Perez-Jimenez R, Godoy-Ruiz R, Parody-Morreale A, Ibarra-Molero B, Sanchez-Ruiz JM. A simple tool to explore the distance distribution of correlated mutations in proteins. Biophysical Chemistry. 119: 240-6. PMID 16239060 DOI: 10.1016/J.Bpc.2005.09.010  0.328
2005 Lidón-Moya MC, Barrera FN, Bueno M, Pérez-Jiménez R, Sancho J, Mateu MG, Neira JL. An extensive thermodynamic characterization of the dimerization domain of the HIV-1 capsid protein. Protein Science : a Publication of the Protein Society. 14: 2387-404. PMID 16131662 DOI: 10.1110/Ps.041324305  0.309
2005 Godoy-Ruiz R, Perez-Jimenez R, Ibarra-Molero B, Sanchez-Ruiz JM. A stability pattern of protein hydrophobic mutations that reflects evolutionary structural optimization. Biophysical Journal. 89: 3320-31. PMID 16100262 DOI: 10.1529/Biophysj.105.067025  0.317
2005 Naganathan AN, Perez-Jimenez R, Sanchez-Ruiz JM, Muñoz V. Robustness of downhill folding: guidelines for the analysis of equilibrium folding experiments on small proteins. Biochemistry. 44: 7435-49. PMID 15895987 DOI: 10.1021/Bi050118Y  0.369
2005 Godoy-Ruiz R, Perez-Jimenez R, Garcia-Mira MM, Plaza del Pino IM, Sanchez-Ruiz JM. Empirical parametrization of pK values for carboxylic acids in proteins using a genetic algorithm. Biophysical Chemistry. 115: 263-6. PMID 15752616 DOI: 10.1016/J.Bpc.2004.12.028  0.344
2005 Perez-Jimenez R, Godoy-Ruiz R, Ibarra-Molero B, Sanchez-Ruiz JM. The effect of charge-introduction mutations on E. coli thioredoxin stability. Biophysical Chemistry. 115: 105-7. PMID 15752590 DOI: 10.1016/J.Bpc.2004.12.012  0.319
2004 Godoy-Ruiz R, Perez-Jimenez R, Ibarra-Molero B, Sanchez-Ruiz JM. Relation between protein stability, evolution and structure, as probed by carboxylic acid mutations. Journal of Molecular Biology. 336: 313-8. PMID 14757046 DOI: 10.1016/J.Jmb.2003.12.048  0.332
Low-probability matches (unlikely to be authored by this person)
2004 Perez-Jimenez R, Godoy-Ruiz R, Ibarra-Molero B, Sanchez-Ruiz JM. The efficiency of different salts to screen charge interactions in proteins: a Hofmeister effect? Biophysical Journal. 86: 2414-29. PMID 15041679 DOI: 10.1016/S0006-3495(04)74298-8  0.281
2023 Alonso-Lerma B, Jabalera Y, Samperio S, Morin M, Fernandez A, Hille LT, Silverstein RA, Quesada-Ganuza A, Reifs A, Fernández-Peñalver S, Benitez Y, Soletto L, Gavira JA, Diaz A, Vranken W, ... ... Perez-Jimenez R, et al. Evolution of CRISPR-associated endonucleases as inferred from resurrected proteins. Nature Microbiology. 8: 77-90. PMID 36593295 DOI: 10.1038/s41564-022-01265-y  0.244
2021 Alonso-Lerma B, Larraza I, Barandiaran L, Ugarte L, Saralegi A, Corcuera MA, Perez-Jimenez R, Eceiza A. Enzymatically produced cellulose nanocrystals as reinforcement for waterborne polyurethane and its applications. Carbohydrate Polymers. 254: 117478. PMID 33357930 DOI: 10.1016/j.carbpol.2020.117478  0.133
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