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Robert M. Stroud - Related publications

University of California, San Francisco, San Francisco, CA 
membrane protein characterizations and crystal structures
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Seok J, Hong J, Park J, Kim KJ. Structural analysis of the peptidoglycan editing factor PdeF from Bacillus cereus ATCC 14579. Biochemical and Biophysical Research Communications. 583: 43-48. PMID 34735878 DOI: 10.1016/j.bbrc.2021.10.051   
2021 Catalano C, Al Mughram MH, Guo Y, Kellogg GE. 3D interaction homology: Hydropathic interaction environments of serine and cysteine are strikingly different and their roles adapt in membrane proteins. Current Research in Structural Biology. 3: 239-256. PMID 34693344 DOI: 10.1016/j.crstbi.2021.09.002   
2021 Jia Z, Liu C, Chen Y, Jiang H, Wang Z, Yao J, Yang J, Zhu J, Zhang B, Yuchi Z. Crystal structures of the SARS-CoV-2 nucleocapsid protein C-terminal domain and development of nucleocapsid-targeting nanobodies. The Febs Journal. PMID 34665939 DOI: 10.1111/febs.16239   
2021 Robertson AJ, Courtney JM, Shen Y, Ying J, Bax A. Concordance of X-ray and AlphaFold2 Models of SARS-CoV-2 Main Protease with Residual Dipolar Couplings Measured in Solution. Journal of the American Chemical Society. PMID 34757725 DOI: 10.1021/jacs.1c10588   
2021 Berta D, Badaoui M, Martino SA, Buigues PJ, Pisliakov AV, Elghobashi-Meinhardt N, Wells G, Harris SA, Frezza E, Rosta E. Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design. Chemical Science. 12: 13492-13505. PMID 34777769 DOI: 10.1039/d1sc02775a   
2021 Sheikh AY, Mattei A, Miglani Bhardwaj R, Hong RS, Abraham NS, Schneider-Rauber G, Engstrom KM, Diwan M, Henry RF, Gao Y, Juarez V, Jordan E, DeGoey DA, Hutchins CW. Implications of the Conformationally Flexible, Macrocyclic Structure of the First-Generation, Direct-Acting Anti-Viral Paritaprevir on Its Solid Form Complexity and Chameleonic Behavior. Journal of the American Chemical Society. PMID 34637297 DOI: 10.1021/jacs.1c06837   
2021 Collu G, Bierig T, Krebs AS, Engilberge S, Varma N, Guixà-González R, Sharpe T, Deupi X, Olieric V, Poghosyan E, Benoit RM. Chimeric single α-helical domains as rigid fusion protein connections for protein nanotechnology and structural biology. Structure (London, England : 1993). PMID 34587504 DOI: 10.1016/j.str.2021.09.002   
2021 Tanramluk D*, Pakotiprapha D, Phoochaijaroen S, Chantravisut P, Thampradid S, Vanichtanankul J, Narupiyakul L, Akavipat R, Yuvaniyama J. MANORAA: A machine learning platform to guide protein-ligand design by anchors and influential distances. Structure. PMID 34614393 DOI: 10.1016/j.str.2021.09.004   
2021 Schulze-Niemand E, Naumann M, Stein M. Substrate-Assisted Activation and Selectivity of the Bacterial RavD Effector Deubiquitinylase. Proteins. PMID 34825414 DOI: 10.1002/prot.26286   
2021 Numoto N, Kawano Y, Okumura H, Baba S, Fukumori Y, Miki K, Ito N. Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state. Iucrj. 8: 954-962. PMID 34804547 DOI: 10.1107/S2052252521009386   
2021 Cui H, Müller AU, Leibundgut M, Tian J, Ban N, Weber-Ban E. Structures of prokaryotic ubiquitin-like protein Pup in complex with depupylase Dop reveal the mechanism of catalytic phosphate formation. Nature Communications. 12: 6635. PMID 34789727 DOI: 10.1038/s41467-021-26848-x   
2021 Wong SWK, Liu Z. Conformational variability of loops in the SARS-CoV-2 spike protein. Proteins. PMID 34661307 DOI: 10.1002/prot.26266   
2021 Kumar A, Kumar P, Saumya KU, Giri R. Investigating the conformational dynamics of SARS-CoV-2 NSP6 protein with emphasis on non-transmembrane 91-112 & 231-290 regions. Microbial Pathogenesis. 161: 105236. PMID 34648928 DOI: 10.1016/j.micpath.2021.105236   
2021 Zhang C, Li Y, Samad A, Zheng P, Ji Z, Chen F, Zhang H, Jin T. Structure and mutation analysis of the hexameric P4 from Pseudomonas aeruginosa phage phiYY. International Journal of Biological Macromolecules. PMID 34856215 DOI: 10.1016/j.ijbiomac.2021.11.129   
2021 Conseil G, Cole SPC. The First Cytoplasmic Loop in the Core Structure of the ABCC1 (Multidrug Resistance Protein 1; MRP1) Transporter Contains Multiple Amino Acids Essential for Its Expression. International Journal of Molecular Sciences. 22. PMID 34575890 DOI: 10.3390/ijms22189710   
2021 Adams M, Sharma R, Colby T, Weis F, Matic I, Bhogaraju S. Structural basis for protein glutamylation by the Legionella pseudokinase SidJ. Nature Communications. 12: 6174. PMID 34702826 DOI: 10.1038/s41467-021-26429-y   
2021 Modi V, Dunbrack RL. Kincore: a web resource for structural classification of protein kinases and their inhibitors. Nucleic Acids Research. PMID 34643709 DOI: 10.1093/nar/gkab920   
2021 Zhao Q, Yuan JJ, Hu F, Qian C, Tian CF, Wang JT, Gao D, Yi W, Wang HB. Isolation, physicochemical, and structure-function relationship of the hydrophobic variant of Fc-fusion proteins that bind to TNF-α receptor, HS002 and HS002A. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. 1186: 123026. PMID 34781108 DOI: 10.1016/j.jchromb.2021.123026   
2021 Chen Y, Fleetwood O, Pérez-Conesa S, Delemotte L. Allosteric Effect of Nanobody Binding on Ligand-Specific Active States of the β2 Adrenergic Receptor. Journal of Chemical Information and Modeling. PMID 34780174 DOI: 10.1021/acs.jcim.1c00826   
2021 Grahame DAS, Dupuis JH, Bryksa BC, Tanaka T, Yada RY. Improving the alkaline stability of pepsin through rational protein design using renin, an alkaline-stable aspartic protease, as a structural and functional reference. Enzyme and Microbial Technology. 150: 109871. PMID 34489030 DOI: 10.1016/j.enzmictec.2021.109871   
2021 Lamichhane TR, Ghimire MP. Evaluation of SARS-CoV-2 main protease and inhibitor interactions using dihedral angle distributions and radial distribution function. Heliyon. 7: e08220. PMID 34693066 DOI: 10.1016/j.heliyon.2021.e08220   
2021 Ramírez CS, Tolmie C, Opperman DJ, González PJ, Rivas MG, Brondino CD, Ferroni FM. Copper nitrite reductase from Sinorhizobium meliloti 2011: Crystal structure and interaction with the physiological versus a nonmetabolically related cupredoxin-like mediator. Protein Science : a Publication of the Protein Society. 30: 2310-2323. PMID 34562300 DOI: 10.1002/pro.4195   
2021 Sun Z, Zheng S, Zhao H, Niu Z, Lu Y, Pan Y, Yang Y. To improve the predictions of binding residues with DNA, RNA, carbohydrate, and peptide via multi-task deep neural networks. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 34637380 DOI: 10.1109/TCBB.2021.3118916   
2021 Liu X, Yang S, Hart JR, Xu Y, Zou X, Zhang H, Zhou Q, Xia T, Zhang Y, Yang D, Wang MW, Vogt PK. Cryo-EM structures of PI3Kα reveal conformational changes during inhibition and activation. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34725156 DOI: 10.1073/pnas.2109327118   
2021 Ho TNT, Lee HS, Swaminathan S, Goodwin L, Rai N, Ushay B, Lewis RJ, Rosengren KJ, Conibear AC. Posttranslational modifications of α-conotoxins: sulfotyrosine and C-terminal amidation stabilise structures and increase acetylcholine receptor binding. Rsc Medicinal Chemistry. 12: 1574-1584. PMID 34671739 DOI: 10.1039/d1md00182e   
2021 Yan XF, Yang C, Wang M, Yong Y, Deng Y, Gao YG. Structural analyses of the AAA+ ATPase domain of the transcriptional regulator GtrR in the BDSF quorum sensing system in Burkholderia cenocepacia. Febs Letters. PMID 34837384 DOI: 10.1002/1873-3468.14244   
2021 Chan HTH, Moesser MA, Walters RK, Malla TR, Twidale RM, John T, Deeks HM, Johnston-Wood T, Mikhailov V, Sessions RB, Dawson W, Salah E, Lukacik P, Strain-Damerell C, Owen CD, et al. Discovery of SARS-CoV-2 M peptide inhibitors from modelling substrate and ligand binding. Chemical Science. 12: 13686-13703. PMID 34760153 DOI: 10.1039/d1sc03628a   
2021 Poelman H, Ippel H, Gürkan B, Boelens R, Vriend G, Veer CV', Lutgens E, Nicolaes GAF. Structural anomalies in a published NMR-derived structure of IRAK-M. Journal of Molecular Graphics & Modelling. 111: 108061. PMID 34837785 DOI: 10.1016/j.jmgm.2021.108061   
2021 Hallinan JP, Doyle LA, Shen BW, Gewe MM, Takushi B, Kennedy MA, Friend D, Roberts JM, Bradley P, Stoddard BL. Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces. Communications Biology. 4: 1240. PMID 34716407 DOI: 10.1038/s42003-021-02766-y   
2021 Patel VR, Salinas AM, Qi D, Gupta S, Sidote DJ, Goldschen-Ohm MP. Single-molecule imaging with cell-derived nanovesicles reveals early binding dynamics at a cyclic nucleotide-gated ion channel. Nature Communications. 12: 6459. PMID 34753946 DOI: 10.1038/s41467-021-26816-5   
2021 Liu W, Chen J, Jin L, Liu ZY, Lu M, Jiang G, Yang Q, Quan C, Nam KH, Xu Y. Functional and structural analysis of catabolite control protein C that responds to citrate. Scientific Reports. 11: 20285. PMID 34645869 DOI: 10.1038/s41598-021-99552-x   
2021 Schwarz M, Eno RFM, Freitag-Pohl S, Coxon CR, Straker HE, Wortley DJ, Hughes DJ, Mitchell G, Moore J, Cummins I, Onkokesung N, Brazier-Hicks M, Edwards R, Pohl E, Steel PG. Flavonoid-based inhibitors of the Phi-class glutathione transferase from black-grass to combat multiple herbicide resistance. Organic & Biomolecular Chemistry. PMID 34643629 DOI: 10.1039/d1ob01802g   
2021 Yang F, Guo L, Li Y, Wang G, Wang J, Zhang C, Fang GX, Chen X, Liu L, Yan X, Liu Q, Qu C, Xu Y, Xiao P, Zhu Z, et al. Structure, function and pharmacology of human itch receptor complexes. Nature. PMID 34789875 DOI: 10.1038/s41586-021-04077-y   
2021 Correia VG, Trovão F, Pinheiro BA, Brás JLA, Silva LM, Nunes C, Coimbra MA, Liu Y, Feizi T, Fontes CMGA, Mulloy B, Chai W, Carvalho AL, Palma AS. Mapping Molecular Recognition of β1,3-1,4-Glucans by a Surface Glycan-Binding Protein from the Human Gut Symbiont Bacteroides ovatus. Microbiology Spectrum. e0182621. PMID 34817219 DOI: 10.1128/Spectrum.01826-21   
2021 Pacheco-Garcia JL, Anoz-Carbonell E, Vankova P, Kannan A, Palomino-Morales R, Mesa-Torres N, Salido E, Man P, Medina M, Naganathan AN, Pey AL. Structural basis of the pleiotropic and specific phenotypic consequences of missense mutations in the multifunctional NAD(P)H:quinone oxidoreductase 1 and their pharmacological rescue. Redox Biology. 46: 102112. PMID 34537677 DOI: 10.1016/j.redox.2021.102112   
2021 Kolos JM, Pomplun S, Jung S, Rieß B, Purder PL, Voll AM, Merz S, Gnatzy M, Geiger TM, Quist-Løkken I, Jatzlau J, Knaus P, Holien T, Bracher A, Meyners C, et al. Picomolar FKBP inhibitors enabled by a single water-displacing methyl group in bicyclic [4.3.1] aza-amides. Chemical Science. 12: 14758-14765. PMID 34820091 DOI: 10.1039/d1sc04638a   
2021 Jang H, Lee C, Hwang Y, Lee SJ. Concanavalin A: coordination diversity to xenobiotic metal ions and biological consequences. Dalton Transactions (Cambridge, England : 2003). PMID 34806716 DOI: 10.1039/d1dt03501k   
2021 Zhou S, Wang W, Zhou X, Zhang Y, Lai Y, Tang Y, Xu J, Li D, Lin J, Yang X, Ran T, Chen H, Guddat LW, Wang Q, Gao Y, et al. Structure of cytochrome in complex with Q203 and TB47, two anti-TB drug candidates. Elife. 10. PMID 34819223 DOI: 10.7554/eLife.69418   
2021 Mikkelsen MD, Cao HTT, Roret T, Rhein-Knudsen N, Holck J, Tran VTT, Nguyen TT, Tran VHN, Lezyk MJ, Muschiol J, Pham TD, Czjzek M, Meyer AS. A novel thermostable prokaryotic fucoidan active sulfatase PsFucS1 with an unusual quaternary hexameric structure. Scientific Reports. 11: 19523. PMID 34593864 DOI: 10.1038/s41598-021-98588-3   
2021 Morgan BR, Massi F. The Role of Substrate Mediated Allostery in the Catalytic Competency of the Bacterial Oligosaccharyltransferase PglB. Frontiers in Molecular Biosciences. 8: 740904. PMID 34604309 DOI: 10.3389/fmolb.2021.740904   
2021 James JK, Nanda V. A Folding Insulator Defines Cryptic Domains in Tropomyosin. Journal of Molecular Biology. 433: 167281. PMID 34606830 DOI: 10.1016/j.jmb.2021.167281   
2021 Saitoh Y, Mitani-Ueno N, Saito K, Matsuki K, Huang S, Yang L, Yamaji N, Ishikita H, Shen JR, Ma JF, Suga M. Structural basis for high selectivity of a rice silicon channel Lsi1. Nature Communications. 12: 6236. PMID 34716344 DOI: 10.1038/s41467-021-26535-x   
2021 Vankayala SL, Warrensford LC, Pittman AR, Pollard BC, Kearns FL, Larkin JD, Woodcock HL. CIFDock: A novel CHARMM-based flexible receptor-flexible ligand docking protocol. Journal of Computational Chemistry. PMID 34741467 DOI: 10.1002/jcc.26759   
2021 Suleman M, Yousafi Q, Ali J, Ali SS, Hussain Z, Ali S, Waseem M, Iqbal A, Ahmad S, Khan A, Wang Y, Wei DQ. Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. Computers in Biology and Medicine. 138: 104936. PMID 34655895 DOI: 10.1016/j.compbiomed.2021.104936   
2021 Wang J, Yu X, Ding ZJ, Zhang X, Luo Y, Xu X, Xie Y, Li X, Yuan T, Zheng SJ, Yang W, Guo J. Structural basis of ALMT1-mediated aluminum resistance in Arabidopsis. Cell Research. PMID 34799726 DOI: 10.1038/s41422-021-00587-6   
2021 Nijhawan AK, Chan AM, Hsu DJ, Chen LX, Kohlstedt KL. Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures. The Journal of Physical Chemistry. B. PMID 34748336 DOI: 10.1021/acs.jpcb.1c05820   
2021 Do HN, Haldane A, Levy RM, Miao Y. Unique features of different classes of G-protein-coupled receptors revealed from sequence coevolutionary and structural analysis. Proteins. PMID 34599827 DOI: 10.1002/prot.26256   
2021 Jiang Z, Xiao SR, Liu R. Dissecting and predicting different types of binding sites in nucleic acids based on structural information. Briefings in Bioinformatics. PMID 34624074 DOI: 10.1093/bib/bbab411   
2021 Zagotta WN, Sim BS, Nhim AK, Raza MM, Evans EG, Venkatesh Y, Jones CM, Mehl RA, Petersson EJ, Gordon SE. An improved fluorescent noncanonical amino acid for measuring conformational distributions using time-resolved transition metal ion FRET. Elife. 10. PMID 34623258 DOI: 10.7554/eLife.70236   
2021 Heltberg ML, Miné-Hattab J, Taddei A, Walczak AM, Mora T. Physical observables to determine the nature of membrane-less cellular sub-compartments. Elife. 10. PMID 34677123 DOI: 10.7554/eLife.69181