Ezra Peisach, Ph.D. - Related publications

Brandeis University, Waltham, MA, United States 
relationship of protein three-dimensional structure to chemical function
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Maryam A, Khalid RR, Vedithi SC, Ece A, Çınaroğlu SS, Siddiqi AR, Blundell TL. Exploring the structural basis of conformational heterogeneity and autoinhibition of human cGMP-specific protein kinase Iα through computational modelling and molecular dynamics simulations. Computational and Structural Biotechnology Journal. 18: 1625-1638. PMID 32670503 DOI: 10.1016/j.csbj.2020.06.016   
2020 Bolgov A, Korban S, Luzik D, Zhemkov V, Kim M, Rogacheva O, Bezprozvanny I. Crystal structure of the SH3 domain of growth factor receptor-bound protein 2. Acta Crystallographica. Section F, Structural Biology Communications. 76: 263-270. PMID 32510467 DOI: 10.1107/S2053230X20007232   
2020 Potter ZE, Lau HT, Chakraborty S, Fang L, Guttman M, Ong SE, Fowler DM, Maly DJ. Parallel Chemoselective Profiling for Mapping Protein Structure. Cell Chemical Biology. PMID 32649906 DOI: 10.1016/j.chembiol.2020.06.014   
2020 Kaynak BT, Bahar I, Doruker P. Essential site scanning analysis: A new approach for detecting sites that modulate the dispersion of protein global motions. Computational and Structural Biotechnology Journal. 18: 1577-1586. PMID 32637054 DOI: 10.1016/j.csbj.2020.06.020   
2020 Piepoli S, Alt AO, Atilgan C, Mancini EJ, Erman B. Structural analysis of the PATZ1 BTB domain homodimer. Acta Crystallographica. Section D, Structural Biology. 76: 581-593. PMID 32496219 DOI: 10.1107/S2059798320005355   
2020 Visconti L, Toto A, Jarvis JA, Troilo F, Malagrinò F, De Simone A, Gianni S. Demonstration of Binding Induced Structural Plasticity in a SH2 Domain. Frontiers in Molecular Biosciences. 7: 89. PMID 32528972 DOI: 10.3389/fmolb.2020.00089   
2020 Na I, Choi S, Son SH, Uversky VN, Kim CG. Drug Discovery Targeting the Disorder-To-Order Transition Regions through the Conformational Diversity Mimicking and Statistical Analysis. International Journal of Molecular Sciences. 21. PMID 32722024 DOI: 10.3390/ijms21155248   
2020 Chan-Yao-Chong M, Marsin S, Quevillon-Cheruel S, Durand D, Ha-Duong T. Structural ensemble and biological activity of DciA intrinsically disordered region. Journal of Structural Biology. 107573. PMID 32679070 DOI: 10.1016/j.jsb.2020.107573   
2020 Zhu M, Ou D, Khan MH, Zhao S, Zhu Z, Niu L. Structural insights into the formation of oligomeric state by a type I Hsp40 chaperone. Biochimie. PMID 32621942 DOI: 10.1016/j.biochi.2020.06.009   
2020 Chang TH, Hsieh FL, Smallwood PM, Gabelli SB, Nathans J. Structure of the RECK CC domain, an evolutionary anomaly. Proceedings of the National Academy of Sciences of the United States of America. PMID 32541044 DOI: 10.1073/pnas.2006332117   
2020 Cao Y, Park SJ, Im W. A Systematic Analysis of Protein-Carbohydrate Interactions in the PDB. Glycobiology. PMID 32614943 DOI: 10.1093/glycob/cwaa062   
2020 Tomiczek B, Delewski W, Nierzwicki L, Stolarska M, Grochowina I, Schilke B, Dutkiewicz R, Uzarska MA, Ciesielski SJ, Czub J, Craig EA, Marszalek J. Two-step mechanism of J-domain action in driving Hsp70 function. Plos Computational Biology. 16: e1007913. PMID 32479549 DOI: 10.1371/journal.pcbi.1007913   
2020 Kumar R, Maksudov F, Kononova O, Marx KA, Barsegov V, Singh BR. Botulinum Endopeptidase: SAXS Experiments and MD Simulations Reveal Extended Solution Structures That Account for Its Biochemical Properties. The Journal of Physical Chemistry. B. PMID 32543194 DOI: 10.1021/acs.jpcb.0c02817   
2020 Lüthje S, Ramanathan K. In Silico Analysis of Class III Peroxidases: Hypothetical Structure, Ligand Binding Sites, Posttranslational Modifications, and Interaction with Substrates. Methods in Molecular Biology (Clifton, N.J.). 2139: 325-339. PMID 32462597 DOI: 10.1007/978-1-0716-0528-8_24   
2020 Hosford CJ, Adams MC, Niu Y, Chappie JS. The N-terminal domain of Staphylothermus marinus McrB shares structural homology with PUA-like RNA binding proteins Journal of Structural Biology. PMID 32652237 DOI: 10.1016/j.jsb.2020.107572   
2020 Geiger JH, Ghanbarpour A, Santos EM, Pinger CH, Assar Z, Nasr SH, Vasileiou C, Spence D, Borhan BH. Human Cellular Retinol Binding Protein II Forms a Domain-Swapped Trimer Representing a Novel Fold and a New Template for Protein Engineering. Chembiochem : a European Journal of Chemical Biology. PMID 32608180 DOI: 10.1002/cbic.202000405   
2020 Watanabe Y, Watanabe Y, Watanabe S. Structural Basis for Phosphatidylethanolamine Biosynthesis by Bacterial Phosphatidylserine Decarboxylase. Structure (London, England : 1993). PMID 32402247 DOI: 10.1016/j.str.2020.04.006   
2020 Bhat AS, Kinch LN, Grishin NV. β-Strand-mediated interactions of protein domains. Proteins. PMID 32543729 DOI: 10.1002/prot.25970   
2020 Min K, Yoon HJ, Park JY, Baidya M, Dwivedi-Agnihotri H, Maharana J, Chaturvedi M, Chung KY, Shukla AK, Lee HH. Crystal Structure of β-Arrestin 2 in Complex with CXCR7 Phosphopeptide. Structure (London, England : 1993). PMID 32579945 DOI: 10.1016/j.str.2020.06.002   
2020 Xu B, Liu D, Wang Z, Tian R, Zuo Y. Multi-substrate selectivity based on key loops and non-homologous domains: new insight into ALKBH family. Cellular and Molecular Life Sciences : Cmls. PMID 32642789 DOI: 10.1007/s00018-020-03594-9   
2020 Vignesh R, Aradhyam GK. Change in domain cooperativity drives function of calnuc. Biochemistry. PMID 32543177 DOI: 10.1021/acs.biochem.0c00207   
2020 Ha Y, Jang M, Lee S, Lee JY, Lee WC, Bae S, Kang J, Han M, Kim Y. Identification of inhibitor binding hotspots in Acinetobacter baumannii β-ketoacyl acyl carrier protein synthase III using molecular dynamics simulation. Journal of Molecular Graphics & Modelling. 100: 107669. PMID 32659632 DOI: 10.1016/j.jmgm.2020.107669   
2020 Panchamia B, Raimalani V, Prashar V, Kumar M, Ratna Prabha C. Structural and Functional Characterisation of the Domains of Ubiquitin-Activating Enzyme (E1) of Saccharomyces cerevisiae. Cell Biochemistry and Biophysics. PMID 32583128 DOI: 10.1007/s12013-020-00924-3   
2020 Campbell AC, Stiers KM, Martin Del Campo JS, Mehra-Chaudhary R, Sobrado P, Tanner JJ. Trapping conformational states of a flavin-dependent N-monooxygenase in crystallo reveals protein and flavin dynamics. The Journal of Biological Chemistry. PMID 32723870 DOI: 10.1074/jbc.RA120.014750   
2020 Bryant P, Elofsson A. Decomposing Structural Response Due to Sequence Changes in Protein Domains with Machine Learning. Journal of Molecular Biology. PMID 32485208 DOI: 10.1016/j.jmb.2020.05.021   
2020 Stelzl LL, Mavridou DAI, Saridakis E, Gonzalez D, Baldwin AJ, Ferguson SJ, Sansom MS, Redfield C. Local frustration determines loop opening during the catalytic cycle of an oxidoreductase. Elife. 9. PMID 32568066 DOI: 10.7554/eLife.54661   
2020 Baptista FR, Devereux SJ, Gurung SP, Hall JP, Sazanovich IV, Towrie M, Cardin CJ, Brazier JA, Kelly JM, Quinn SJ. The influence of loops on the binding of the [Ru(phen)dppz] light-switch compound to i-motif DNA structures revealed by time-resolved spectroscopy. Chemical Communications (Cambridge, England). PMID 32699864 DOI: 10.1039/d0cc03702h   
2020 Prajapat M, Sarma P, Shekhar N, Prakash A, Avti P, Bhattacharyya A, Kaur H, Kumar S, Bansal S, Sharma AR, Medhi B. Update on the target structures of SARS-CoV-2: A systematic review. Indian Journal of Pharmacology. 52: 142-149. PMID 32565603 DOI: 10.4103/ijp.IJP_338_20   
2020 Tahara S, Mizuno M, Mizutani Y. Nonbonded Atomic Contacts Drive Ultrafast Helix Motions in Myoglobin. The Journal of Physical Chemistry. B. PMID 32510952 DOI: 10.1021/acs.jpcb.0c04772   
2020 Dutoit R, Brandt N, Van Gompel T, Van Elder D, Van Dyck J, Sobott F, Droogmans L. M42 aminopeptidase catalytic site: the structural and functional role of a strictly conserved aspartate residue. Proteins. PMID 32673419 DOI: 10.1002/prot.25982   
2020 Sevcnikar B, Schaffner I, Chuang CY, Gamon L, Paumann-Page M, Hofbauer S, Davies MJ, Furtmüller PG, Obinger C. The leucine-rich repeat domain of human peroxidasin 1 promotes binding to laminin in basement membranes. Archives of Biochemistry and Biophysics. 108443. PMID 32485152 DOI: 10.1016/j.abb.2020.108443   
2020 Lee BG, Merkel F, Allegretti M, Hassler M, Cawood C, Lecomte L, O'Reilly FJ, Sinn LR, Gutierrez-Escribano P, Kschonsak M, Bravo S, Nakane T, Rappsilber J, Aragon L, Beck M, et al. Cryo-EM structures of holo condensin reveal a subunit flip-flop mechanism. Nature Structural & Molecular Biology. PMID 32661420 DOI: 10.1038/s41594-020-0457-x   
2020 Lara J, Diacovich L, Trajtenberg F, Larrieux N, Malchiodi EL, Fernández MM, Gago G, Gramajo H, Buschiazzo A. Mycobacterium tuberculosis FasR senses long fatty acyl-CoA through a tunnel and a hydrophobic transmission spine. Nature Communications. 11: 3703. PMID 32710080 DOI: 10.1038/s41467-020-17504-x   
2020 Deb A, Kaur Grewal R, Roy S, Mitra D. Residue Interaction Dynamics in Vaucheria Aureochrome1 LOV: Bridging Theory and Experiments. Proteins. PMID 32683714 DOI: 10.1002/prot.25984   
2020 Ye Q, West AMV, Silletti S, Corbett KD. Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein. Protein Science : a Publication of the Protein Society. PMID 32654247 DOI: 10.1002/pro.3909   
2020 Yang F, Mao C, Guo L, Lin J, Ming Q, Xiao P, Wu X, Shen Q, Guo S, Shen DD, Lu R, Zhang L, Huang S, Ping Y, Zhang C, et al. Structural basis of GPBAR activation and bile acid recognition. Nature. PMID 32698187 DOI: 10.1038/s41586-020-2569-1   
2020 Young TA, Gheorghe R, Duarte F. cgbind: A Python Module and Web App for Automated Metallocage Construction and Host-Guest Characterization. Journal of Chemical Information and Modeling. PMID 32579847 DOI: 10.1021/acs.jcim.0c00519   
2020 Le CA, Harvey DS, Aller SG. Structural definition of polyspecific compensatory ligand recognition by P-glycoprotein. Iucrj. 7: 663-672. PMID 32695413 DOI: 10.1107/S2052252520005709   
2020 Nutho B, Pengthaisong S, Tankrathok A, Lee VS, Ketudat Cairns JR, Rungrotmongkol T, Hannongbua S. Structural Basis of Specific Glucoimidazole and Mannoimidazole Binding by Os3BGlu7. Biomolecules. 10. PMID 32549280 DOI: 10.3390/biom10060907   
2020 Maharjan R, Fukuda Y, Nakayama T, Nakayama T, Hamada H, Ozaki SI, Inoue T. Crown-ether-mediated crystal structures of the glycosyltransferase PaGT3 from Phytolacca americana. Acta Crystallographica. Section D, Structural Biology. 76: 521-530. PMID 32496214 DOI: 10.1107/S2059798320005306   
2020 Horvath A, Miskei M, Ambrus V, Vendruscolo M, Fuxreiter M. Sequence-based prediction of protein binding mode landscapes. Plos Computational Biology. 16: e1007864. PMID 32453748 DOI: 10.1371/journal.pcbi.1007864   
2020 Kilgore H, Latham AP, Ressler VT, Zhang B, Raines RT. Structure and Dynamics of -Glycosylated Human Ribonuclease 1. Biochemistry. PMID 32544330 DOI: 10.1021/acs.biochem.0c00191   
2020 Stepanenko OV, Stepanenko OV, Turoverov KK, Kuznetsova IM. Probing the allostery in dimeric near-infrared biomarkers derived from the bacterial phytochromes: The impact of the T204A substitution on the inter-monomer interaction. International Journal of Biological Macromolecules. 162: 894-902. PMID 32569685 DOI: 10.1016/j.ijbiomac.2020.06.162   
2020 Bonjack M, Avnir D. The near-symmetry of protein oligomers: NMR-derived structures. Scientific Reports. 10: 8367. PMID 32433550 DOI: 10.1038/s41598-020-65097-8   
2020 Lou JW, Mazhab-Jafari MT. Steric occlusion regulates proximal interactions of acyl carrier protein domain in fungal fatty acid synthase. Communications Biology. 3: 274. PMID 32471977 DOI: 10.1038/s42003-020-0997-y   
2020 Jaworek MW, Ruggiero A, Graziano G, Winter R, Vitagliano L. On the extraordinary pressure stability of the Thermotoga maritima arginine binding protein and its folded fragments - a high-pressure FTIR spectroscopy study. Physical Chemistry Chemical Physics : Pccp. 22: 11244-11248. PMID 32400824 DOI: 10.1039/d0cp01618g   
2020 Cross TJ, Takahashi GR, Diessner EM, Crosby MG, Farahmand V, Zhuang S, Butts CT, Martin RW. Sequence characterization and molecular modeling of clinically relevant variants of the SARS-CoV-2 main protease. Biorxiv : the Preprint Server For Biology. PMID 32511408 DOI: 10.1101/2020.05.15.097493   
2020 Tamirat MZ, Kurppa KJ, Elenius K, Johnson MS. Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation. Journal of Visualized Experiments : Jove. PMID 32510498 DOI: 10.3791/61125   
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 Sheetz JB, Mathea S, Karvonen H, Malhotra K, Chatterjee D, Niininen W, Perttilä R, Preuss F, Suresh K, Stayrook SE, Tsutsui Y, Radhakrishnan R, Ungureanu D, Knapp S, Lemmon MA. Structural Insights into Pseudokinase Domains of Receptor Tyrosine Kinases. Molecular Cell. PMID 32619402 DOI: 10.1016/j.molcel.2020.06.018