Julio Fernandez - Related publications

Affiliations: 
Columbia University, New York, NY 
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Yu M, Zhao Z, Chen Z, Le S, Yan J. Modulating mechanical stability of heterodimerization between engineered orthogonal helical domains. Nature Communications. 11: 4476. PMID 32900995 DOI: 10.1038/s41467-020-18323-w   
2020 Cook EC, Creamer TP. Influence of Electrostatic Forces on the Association Kinetics and Conformational Ensemble of an Intrinsically Disordered Protein. Proteins. PMID 32654182 DOI: 10.1002/prot.25979   
2020 Kirmizialtin S, Pitici F, Cardenas AE, Elber R, Thirumalai D. Dramatic Shape Changes Occur as Cytochrome Folds. The Journal of Physical Chemistry. B. PMID 32840372 DOI: 10.1021/acs.jpcb.0c05802   
2020 Smith Z, Ravindra P, Wang Y, Cooley R, Tiwary P. Discovering Protein Conformational Flexibility Through Artificial Intelligence Aided Molecular Dynamics. The Journal of Physical Chemistry. B. PMID 32841026 DOI: 10.1021/acs.jpcb.0c03985   
2020 Sala BM, Le Marchand T, Pintacuda G, Camilloni C, Natalello A, Ricagno S. Conformational Stability and Dynamics in Crystals Recapitulate Protein Behavior in Solution. Biophysical Journal. 119: 978-988. PMID 32758421 DOI: 10.1016/j.bpj.2020.07.015   
2020 Stenzoski NE, Zou J, Piserchio A, Ghose R, Holehouse AS, Raleigh DP. The Cold-Unfolded State is Expanded but Contains Long- and Medium-range Contacts and Is Poorly Described by Homopolymer Models. Biochemistry. PMID 32786415 DOI: 10.1021/acs.biochem.0c00469   
2020 Oliveira NFB, Pires IDS, Machuqueiro M. Improved GROMOS 54A7 charge sets for phosphorylated Tyr, Ser, and Thr to deal with pH-dependent binding phenomena. Journal of Chemical Theory and Computation. PMID 32809819 DOI: 10.1021/acs.jctc.0c00529   
2020 Dasari S, Mallik BS. Conformational Free Energy Landscapes of Alanine Dipeptide in Hydrated Ionic Liquids from Enhanced Sampling Methods. The Journal of Physical Chemistry. B. PMID 32666802 DOI: 10.1021/acs.jpcb.0c05629   
2020 Ma H, Zou T, Li H, Cheng H. The interaction of sodium dodecyl sulfate with trypsin: Multi-spectroscopic analysis, molecular docking, and molecular dynamics simulation. International Journal of Biological Macromolecules. PMID 32781131 DOI: 10.1016/j.ijbiomac.2020.08.020   
2020 Ma H, Zou T, Li H, Cheng H. The interaction of sodium dodecyl sulfate with trypsin: Multi-spectroscopic analysis, molecular docking, and molecular dynamics simulation. International Journal of Biological Macromolecules. PMID 32781131 DOI: 10.1016/j.ijbiomac.2020.08.020   
2020 Sluysmans D, Willet N, Thevenot J, Lecommandoux S, Duwez AS. Single-molecule mechanical unfolding experiments reveal a critical length for the formation of α-helices in peptides. Nanoscale Horizons. 5: 671-678. PMID 32226978 DOI: 10.1039/d0nh00036a   
2020 Parray ZA, Ahmad F, Hassan MI, Islam A. Conformational changes in cytochrome c directed by ethylene glycol accompanying complex formation: Protein-solvent preferential interaction or/and kosmotropic effect. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 242: 118788. PMID 32810818 DOI: 10.1016/j.saa.2020.118788   
2020 Herrera-Nieto P, Pérez A, De Fabritiis G. Small molecule modulation of intrinsically disordered proteins using molecular dynamics simulations. Journal of Chemical Information and Modeling. PMID 32786705 DOI: 10.1021/acs.jcim.0c00381   
2020 Kuhar N, Umapathy S. Probing the stepwise unfolding of bovine serum albumin using 2D correlation Raman spectroscopic analysis. Analytical Chemistry. PMID 32865392 DOI: 10.1021/acs.analchem.0c02968   
2020 Cheng Y, Zhang Y, Gong Z, Zhang XH, Li Y, Shi X, Pei Y, You H. High Mechanical Stability and Slow Unfolding Rates Are Prevalent in Parallel-Stranded DNA G-Quadruplexes. The Journal of Physical Chemistry Letters. PMID 32885976 DOI: 10.1021/acs.jpclett.0c02229   
2020 Tan YS, Verma CS. Straightforward incorporation of multiple ligand types into molecular dynamics simulations for efficient binding site detection and characterization. Journal of Chemical Theory and Computation. PMID 32810406 DOI: 10.1021/acs.jctc.0c00405   
2020 Younas T, Vidallon MLP, Tabor RF, He L. Open-Closed Structure of Light Responsive Protein LOV2 Regulates its Molecular Interaction with Binding Partner. The Journal of Physical Chemistry Letters. PMID 32945680 DOI: 10.1021/acs.jpclett.0c02252   
2020 Bhunia A, Ilyas H, Bhattacharjya S. Salt Dependence Conformational Stability of the Dimeric SAM Domain of MAPKKK Ste11 from Budding Yeast: A Native State H/D Exchange NMR Study". Biochemistry. PMID 32667811 DOI: 10.1021/acs.biochem.0c00522   
2020 Stojanovski BM, Pelc LA, Zuo X, Di Cera E. Zymogen and activated protein C have similar structural architecture. The Journal of Biological Chemistry. PMID 32855236 DOI: 10.1074/jbc.RA120.014789   
2020 Macchiagodena M, Pagliai M, Andreini C, Rosato A, Procacci P. Upgraded AMBER Force Field for Zinc-Binding Residues and Ligands for Predicting Structural Properties and Binding Affinities in Zinc-Proteins. Acs Omega. 5: 15301-15310. PMID 32637803 DOI: 10.1021/acsomega.0c01337   
2020 Bhattacharjee K, Gopi S, Naganathan AN. A Disordered Loop Mediates Heterogeneous Unfolding of an Ordered Protein by Altering the Native Ensemble. The Journal of Physical Chemistry Letters. 6749-6756. PMID 32787218 DOI: 10.1021/acs.jpclett.0c01848   
2020 Neelamraju S, Wales DJ, Gosavi S. Protein energy landscape exploration with structure-based models. Current Opinion in Structural Biology. 64: 145-151. PMID 32795948 DOI: 10.1016/j.sbi.2020.07.003   
2020 Sidhu A, Grosbart M, Sánchez H, Verhagen B, van der Zon NLL, Ristić D, van Rossum-Fikkert SE, Wyman C. Conformational flexibility and oligomerization of BRCA2 regions induced by RAD51 interaction. Nucleic Acids Research. PMID 32785644 DOI: 10.1093/nar/gkaa648   
2020 Chrabąszczewska M, Sieradzan AK, Rodziewicz-Motowidło S, Grubb A, Dobson CM, Kumita JR, Kozak M. Structural Characterization of Covalently Stabilized Human Cystatin C Oligomers. International Journal of Molecular Sciences. 21. PMID 32824145 DOI: 10.3390/ijms21165860   
2020 Frank M, Beccati D, Leeflang BR, Vliegenthart JFG. C-Mannosylation Enhances the Structural Stability of Human RNase 2. Iscience. 23: 101371. PMID 32739833 DOI: 10.1016/j.isci.2020.101371   
2020 Dajnowicz S, Cheng Y, Daemen LL, Weiss KL, Gerlits O, Mueser TC, Kovalevsky A. Substrate Binding Stiffens Aspartate Aminotransferase by Altering the Enzyme Picosecond Vibrational Dynamics. Acs Omega. 5: 18787-18797. PMID 32775880 DOI: 10.1021/acsomega.0c01900   
2020 Kozak JJ, Gray HB, Garza-López RA. Unfolding cytochromes c-b and Rd apo b. Journal of Inorganic Biochemistry. 211: 111209. PMID 32818710 DOI: 10.1016/j.jinorgbio.2020.111209   
2020 Zang Z, Chou S, Tian J, Lang Y, Shen Y, Ran X, Gao N, Li B. Effect of whey protein isolate on the stability and antioxidant capacity of blueberry anthocyanins: A mechanistic and in vitro simulation study. Food Chemistry. 336: 127700. PMID 32768906 DOI: 10.1016/j.foodchem.2020.127700   
2020 Miller MC, Nesmelova IV, Daragan VA, Ippel H, Michalak M, Dregni A, Kaltner H, Kopitz J, Gabius HJ, Mayo KH. Pro4 prolyl peptide bond isomerization in human galectin-7 modulates the monomer-dimer equilibrum to affect function. The Biochemical Journal. PMID 32766716 DOI: 10.1042/BCJ20200499   
2020 Xiong X, Qu K, Ciazynska KA, Hosmillo M, Carter AP, Ebrahimi S, Ke Z, Scheres SHW, Bergamaschi L, Grice GL, Zhang Y, , Nathan JA, Baker S, James LC, et al. A thermostable, closed SARS-CoV-2 spike protein trimer. Nature Structural & Molecular Biology. PMID 32737467 DOI: 10.1038/s41594-020-0478-5   
2020 Xiong X, Qu K, Ciazynska KA, Hosmillo M, Carter AP, Ebrahimi S, Ke Z, Scheres SHW, Bergamaschi L, Grice GL, Zhang Y, , Nathan JA, Baker S, James LC, et al. A thermostable, closed SARS-CoV-2 spike protein trimer. Nature Structural & Molecular Biology. PMID 32737467 DOI: 10.1038/s41594-020-0478-5   
2020 Michael E, Polydorides S, Simonson T, Archontis G. Hybrid MC/MD for protein design. The Journal of Chemical Physics. 153: 054113. PMID 32770896 DOI: 10.1063/5.0013320   
2020 Vattepu R, Klausmeyer RA, Ayella A, Yadav R, Dille JT, Saiz SV, Beck MR. Conserved tryptophan mutation disrupts structure and function of immunoglobulin domain revealing unusual tyrosine fluorescence. Protein Science : a Publication of the Protein Society. PMID 32797644 DOI: 10.1002/pro.3929   
2020 Guo X, Yu J, Abell AD, Chen X, Yeoh YQ, He Y, Zhou C, Horsley JR. Unravelling structural dynamics within a photoswitchable single-peptide: A step towards multi-modal bio-inspired nanodevices. Angewandte Chemie (International Ed. in English). PMID 32851761 DOI: 10.1002/anie.202004701   
2020 Ramanathan A, Parvatikar A, Chennubhotla SC, Mei Y, Sinha SC. Transient Unfolding and Long-Range Interactions in Viral BCL2 M11 Enable Binding to the BECN1 BH3 Domain. Biomolecules. 10. PMID 32932757 DOI: 10.3390/biom10091308   
2020 Narang D, Lento C, J Wilson D. HDX-MS: An Analytical Tool to Capture Protein Motion in Action. Biomedicines. 8. PMID 32709043 DOI: 10.3390/biomedicines8070224   
2020 Schneider J, Korshunova K, Si Chaib Z, Giorgetti A, Alfonso-Prieto M, Carloni P. Ligand Pose Predictions for Human G Protein-Coupled Receptors: Insights from the Amber-Based Hybrid Molecular Mechanics/Coarse-Grained Approach. Journal of Chemical Information and Modeling. PMID 32786708 DOI: 10.1021/acs.jcim.0c00661   
2020 Henderson JN, Simmons CR, Fahmi NE, Jeffs JW, Borges CR, Mills JH. Structural insights into how protein environments tune the spectroscopic properties of a non-canonical amino acid fluorophore. Biochemistry. PMID 32845612 DOI: 10.1021/acs.biochem.0c00474   
2020 Bergasa-Caceres F, Rabitz HA. Interdiction of Protein Folding for Therapeutic Drug Development in SARS CoV-2. The Journal of Physical Chemistry. B. PMID 32790379 DOI: 10.1021/acs.jpcb.0c03716   
2020 Palomino-Hernandez O, Buratti FA, Sacco PS, Rossetti G, Carloni P, Fernandez CO. Role of Tyr-39 for the Structural Features of α-Synuclein and for the Interaction with a Strong Modulator of Its Amyloid Assembly. International Journal of Molecular Sciences. 21. PMID 32709107 DOI: 10.3390/ijms21145061   
2020 Jonker HRA, Saxena K, Shcherbakova A, Tiemann B, Bakker H, Schwalbe H. NMR characterization of the C-mannose conformation in a thrombospondin repeat using a selective labeling approach. Angewandte Chemie (International Ed. in English). PMID 32745319 DOI: 10.1002/anie.202009489   
2020 Liu R, Wu L, Feng H, Tang F, Si H, Yao X, He W. The study on the interactions of two 1,2,3-triazoles with several biological macromolecules by multiple spectroscopic methodologies and molecular docking. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 243: 118795. PMID 32814256 DOI: 10.1016/j.saa.2020.118795   
2020 Pal S, Banerjee S, Prabhakaran EN. Helix-Coil Transition at a Glycine Following a Nascent α-Helix: A Synergetic Guidance Mechanism for Helix Growth. The Journal of Physical Chemistry. A. PMID 32877193 DOI: 10.1021/acs.jpca.0c05489   
2020 Staffler R, Pasternack R, Hils M, Kaiser W, Möller FM. Nucleotide binding kinetics and conformational change analysis of tissue transglutaminase with switchSENSE. Analytical Biochemistry. 605: 113719. PMID 32697952 DOI: 10.1016/j.ab.2020.113719   
2020 Polyakov IV, Kniga AE, Grigorenko BL, Nemukhin AV. Structure of the Brain -Acetylaspartate Biosynthetic Enzyme NAT8L Revealed by Computer Modeling. Acs Chemical Neuroscience. 11: 2296-2302. PMID 32639720 DOI: 10.1021/acschemneuro.0c00250   
2020 Ryzhov P, Tian Y, Yao Y, Bobkov AA, Im W, Marassi FM. Conformational States of the Cytoprotective Protein Bcl-xL. Biophysical Journal. PMID 32888404 DOI: 10.1016/j.bpj.2020.08.014   
2020 Batista JAD, Oliveira L, Moura TA, Dos Anjos VC, Bell MJV, Rocha MS. On the use of Europium (Eu) for designing new metal-based anticancer drugs. Biochemical and Biophysical Research Communications. PMID 32800544 DOI: 10.1016/j.bbrc.2020.07.080   
2020 Strotz D, Orts J, Kadavath H, Friedmann M, Ghosh D, Olsson S, Chi C, Pokharna A, Güntert P, Vögeli B, Riek R. Protein allostery at atomic resolution. Angewandte Chemie (International Ed. in English). PMID 32797659 DOI: 10.1002/anie.202008734   
2020 Iuliano JN, Tolentino Collado J, Gil AA, Ravindran PT, Lukacs A, Shin S, Woroniecka HA, Adamczyk K, Aramini JM, Edupuganti UR, Hall CR, Greetham GM, Sazanovich IV, Clark IP, Daryaee T, et al. Unraveling the Mechanism of a LOV Domain Optogenetic Sensor: A Glutamine Lever Induces Unfolding of the Jα Helix. Acs Chemical Biology. PMID 32880430 DOI: 10.1021/acschembio.0c00543   
2020 Stylianakis I, Shalev A, Scheiner S, Sigalas MP, Arkin IT, Glykos N, Kolocouris A. The balance between side-chain and backbone-driven association in folding of the α-helical influenza A transmembrane peptide. Journal of Computational Chemistry. PMID 32735736 DOI: 10.1002/jcc.26381