Daniel E. Koshland, Jr., Ph.D. - Related publications

Affiliations: 
1951-1965 Biochemistry Brookhaven National Laboratory, Upton, NY, United States 
 1965- Biochemistry University of California, Berkeley, Berkeley, CA 
Area:
enzyme reaction mechanisms
Website:
http://dx.doi.org/10.1073/pnas.0707644104
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50 most relevant papers in past 60 days:
Year Citation  Score
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 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 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 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 Harini K, Jayashree S, Tiwari V, Vishwanath S, Sowdhamini R. Ligand Docking Methods to Recognize Allosteric Inhibitors for G-Protein-Coupled Receptors. Bioinformatics and Biology Insights. 15: 11779322211037769. PMID 34733103 DOI: 10.1177/11779322211037769   
2021 Adegawa S, Yamaguchi N, Sato R. The base and root of domain II loops of Cry toxins contribute to binding to Bombyx mori ABC transporter C2. The Febs Journal. PMID 34618400 DOI: 10.1111/febs.16224   
2021 Cuy-Chaparro L, Bohórquez MD, Arévalo-Pinzón G, Castañeda-Ramírez JJ, Suárez CF, Pabón L, Ordóñez D, Gallego-López GM, Suárez CE, Moreno-Pérez DA, Patarroyo MA. Ligand-Receptor Interaction: AMA-1 Contains Small Regions Governing Bovine Erythrocyte Binding. International Journal of Molecular Sciences. 22. PMID 33450807 DOI: 10.3390/ijms22020714   
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 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 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 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 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 He T, Liu J, Wang JP. Development of a Dihydropteroate Synthase-Based Fluorescence Polarization Assay for Detection of Sulfonamides and Studying Its Recognition Mechanism. Journal of Agricultural and Food Chemistry. PMID 34783550 DOI: 10.1021/acs.jafc.1c05674   
2021 Huang Y, Ognjenovic J, Karandur D, Miller K, Merk A, Subramaniam S, Kuriyan J. A molecular mechanism for the generation of ligand-dependent differential outputs by the epidermal growth factor receptor. Elife. 10. PMID 34846302 DOI: 10.7554/eLife.73218   
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 Vongsouthi V, Whitfield JH, Unichenko P, Mitchell JA, Breithausen B, Khersonsky O, Kremers L, Janovjak H, Monai H, Hirase H, Fleishman SJ, Henneberger C, Jackson CJ. A Rationally and Computationally Designed Fluorescent Biosensor for d-Serine. Acs Sensors. 6: 4193-4205. PMID 34783546 DOI: 10.1021/acssensors.1c01803   
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 Huang Q, Ng EY, Li Q, Kang C.  H,  N and  C resonance assignments of the Q61H mutant of human KRAS bound to GDP. Biomolecular Nmr Assignments. PMID 34787842 DOI: 10.1007/s12104-021-10058-z   
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 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 Wu Y, Brooks CL. Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy. Journal of Chemical Information and Modeling. PMID 34704754 DOI: 10.1021/acs.jcim.1c01078   
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 Heyne M, Shirian J, Cohen I, Peleg Y, Radisky ES, Papo N, Shifman JM. Climbing Up and Down Binding Landscapes through Deep Mutational Scanning of Three Homologous Protein-Protein Complexes. Journal of the American Chemical Society. PMID 34609866 DOI: 10.1021/jacs.1c08707   
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 Patel MH, Dolinska MB, Sergeev YV. Tyrp1 Mutant Variants Associated with OCA3: Computational Characterization of Protein Stability and Ligand Binding. International Journal of Molecular Sciences. 22. PMID 34638544 DOI: 10.3390/ijms221910203   
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 Sherman MB, Williams AN, Smith HQ, Pettitt BM, Wobus CE, Smith TJ. Structural Studies on the Shapeshifting Murine Norovirus. Viruses. 13. PMID 34834968 DOI: 10.3390/v13112162   
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 Rübbelke M, Hamilton J, Binder F, Bauer M, King J, Nar H, Zeeb M. Discovery and Structure-Based Optimization of Fragments Binding the Mixed Lineage Kinase Domain-like Protein Executioner Domain. Journal of Medicinal Chemistry. PMID 34672548 DOI: 10.1021/acs.jmedchem.1c00686   
2021 Chen YJ, Li PY, Yang CN. Molecular dynamics study of enhanced autophosphorylation by S904F mutation of the RET kinase domain. Journal of Structural Biology. 213: 107799. PMID 34563653 DOI: 10.1016/j.jsb.2021.107799   
2021 Hu X, Pang J, Zhang J, Shen C, Chai X, Wang E, Chen H, Wang X, Duan M, Fu W, Xu L, Kang Y, Li D, Xia H, Hou T. Discovery of Novel GR Ligands toward Druggable GR Antagonist Conformations Identified by MD Simulations and Markov State Model Analysis. Advanced Science (Weinheim, Baden-Wurttemberg, Germany). e2102435. PMID 34825505 DOI: 10.1002/advs.202102435   
2021 Nagata T, Shinya S, Ohnuma T, Fukamizo T. Multi-functionality of a tryptophan residue conserved in substrate-binding groove of GH19 chitinases. Scientific Reports. 11: 2494. PMID 33510258 DOI: 10.1038/s41598-021-81903-3   
2021 Khan A, Mohammad A, Haq I, Nasar M, Ahmad W, Yousafi Q, Suleman M, Ahmad S, Albutti A, Khan T, Marafie SK, Alshawaf E, Ali SS, Abubaker J, Wei DQ. Structural-Dynamics and Binding Analysis of RBD from SARS-CoV-2 Variants of Concern (VOCs) and GRP78 Receptor Revealed Basis for Higher Infectivity. Microorganisms. 9. PMID 34835456 DOI: 10.3390/microorganisms9112331   
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 Rottinghaus AG, Xi C, Amrofell MB, Yi H, Moon TS. Engineering ligand-specific biosensors for aromatic amino acids and neurochemicals. Cell Systems. PMID 34767760 DOI: 10.1016/j.cels.2021.10.006   
2021 Sapienza PJ, Currie MM, Lancaster NM, Li K, Aubé J, Goldfarb D, Cloer EW, Major MB, Lee AL. Visualizing an Allosteric Intermediate Using CuAAC Stabilization of an NMR Mixed Labeled Dimer. Acs Chemical Biology. PMID 34784173 DOI: 10.1021/acschembio.1c00617   
2021 Kuo CW, Yang TJ, Chien YC, Yu PY, Hsu SD, Khoo KH. Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. Glycobiology. PMID 34735575 DOI: 10.1093/glycob/cwab102   
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 Saporiti S, Parravicini C, Pergola C, Guerrini U, Rossi M, Centola F, Eberini I. IgG1 conformational behavior: elucidation of the N-glycosylation role via molecular dynamics. Biophysical Journal. PMID 34710380 DOI: 10.1016/j.bpj.2021.10.026   
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 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 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 Das JK, Thakuri B, MohanKumar K, Roy S, Sljoka A, Sun GQ, Chakraborty A. Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. Acs Omega. 6: 31312-31327. PMID 34805715 DOI: 10.1021/acsomega.1c05155   
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 Hussain M, Cummins MC, Endo-Streeter S, Sondek J, Kuhlman B. Designer proteins that competitively inhibit Gα by targeting its effector site. The Journal of Biological Chemistry. 101348. PMID 34715131 DOI: 10.1016/j.jbc.2021.101348   
2021 Liu S, Huynh T, Stauft CB, Wang TT, Luan B. Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Journal of Chemical Information and Modeling. PMID 34648284 DOI: 10.1021/acs.jcim.1c01058   
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   
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 Nakayoshi T, Kato K, Kurimoto E, Oda A. Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. International Journal of Molecular Sciences. 22. PMID 34576002 DOI: 10.3390/ijms22189837   
2021 La Sala G, Gunnarsson A, Edman K, Tyrchan C, Hogner A, Frolov AI. Unraveling the Allosteric Cross-Talk between the Coactivator Peptide and the Ligand-Binding Site in the Glucocorticoid Receptor. Journal of Chemical Information and Modeling. 61: 3667-3680. PMID 34156843 DOI: 10.1021/acs.jcim.1c00323