Patricia C. Babbitt - Related publications

Affiliations: 
Biophysics University of California, San Francisco, San Francisco, CA 
Area:
Bioinformatics Biology, Biochemistry, General Biophysics
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Sugiura S, Nakano S, Niwa M, Hasebe F, Matsui D, Ito S. Catalytic Mechanism of Ancestral L-Lysine Oxidase Assigned by Sequence Data Mining. The Journal of Biological Chemistry. 101043. PMID 34358565 DOI: 10.1016/j.jbc.2021.101043   
2021 Sirota FL, Maurer-Stroh S, Li Z, Eisenhaber F, Eisenhaber B. Functional Classification of Super-Large Families of Enzymes Based on Substrate Binding Pocket Residues for Biocatalysis and Enzyme Engineering Applications. Frontiers in Bioengineering and Biotechnology. 9: 701120. PMID 34409021 DOI: 10.3389/fbioe.2021.701120   
2021 Sung JY, Lee YJ, Cho YJ, Shin MN, Lee SJ, Lee HS, Koh H, Bae JW, Shin JH, Kim HJ, Lee DW. A Large-Scale Metagenomic Study for Enzyme Profiles Using the Focused Identification of the NGS-Based Definitive Enzyme Research (FINDER) Strategy. Biotechnology and Bioengineering. PMID 34309016 DOI: 10.1002/bit.27904   
2021 Sung JY, Lee YJ, Cho YJ, Shin MN, Lee SJ, Lee HS, Koh H, Bae JW, Shin JH, Kim HJ, Lee DW. A Large-Scale Metagenomic Study for Enzyme Profiles Using the Focused Identification of the NGS-Based Definitive Enzyme Research (FINDER) Strategy. Biotechnology and Bioengineering. PMID 34309016 DOI: 10.1002/bit.27904   
2021 Gerrard Wheeler MC, Arias CL, E Mello JDFR, Cirauqui Diaz N, Rodrigues CR, Drincovich MF, de Souza AMT, Alvarez CE. Structural insights into the allosteric site of Arabidopsis NADP-malic enzyme 2: role of the second sphere residues in the regulatory signal transmission. Plant Molecular Biology. PMID 34333694 DOI: 10.1007/s11103-021-01176-2   
2021 Kummer MJ, Lee YS, Yuan M, Alkotaini B, Zhao J, Blumenthal E, Minteer SD. Substrate Channeling by a Rationally Designed Fusion Protein in a Biocatalytic Cascade. Jacs Au. 1: 1187-1197. PMID 34467357 DOI: 10.1021/jacsau.1c00180   
2021 Lou D, Liu X, Tan J. An Overview of 7α- and 7β-Hydroxysteroid Dehydrogenases: Structure, Specificity and Practical Application. Protein and Peptide Letters. PMID 34397319 DOI: 10.2174/0929866528666210816114032   
2021 Marshall AC, Bruning JB. Engineering potassium activation into biosynthetic thiolase. The Biochemical Journal. PMID 34338286 DOI: 10.1042/BCJ20210455   
2021 Thompson NK, LeClaire L, Rodriguez Perez S, Wakarchuk W. Investigation of sequon engineering for improved O-glycosylation by the human polypeptide N-acetylgalactosaminyl transferase T2 isozyme and two orthologues. The Biochemical Journal. PMID 34523671 DOI: 10.1042/BCJ20210382   
2021 Jia Q, Zeng H, Li H, Xiao N, Tang J, Gao S, Zhang J, Xie W. The C-terminal loop of guanosine deaminase is essential to catalysis. Chemical Communications (Cambridge, England). PMID 34477187 DOI: 10.1039/d1cc03042f   
2021 Wu H, Chen Q, Zhang W, Mu W. Overview of strategies for developing high thermostability industrial enzymes: Discovery, mechanism, modification and challenges. Critical Reviews in Food Science and Nutrition. 1-18. PMID 34445912 DOI: 10.1080/10408398.2021.1970508   
2021 Hamdan SH, Maiangwa J, Ali MSM, Normi YM, Sabri S, Leow TC. Thermostable lipases and their dynamics of improved enzymatic properties. Applied Microbiology and Biotechnology. PMID 34487207 DOI: 10.1007/s00253-021-11520-7   
2021 Kuriya Y, Inoue M, Yamamoto M, Murata M, Araki M. Knowledge extraction from literatures and enzyme sequences complements FBA analysis in metabolic engineering. Biotechnology Journal. e2000443. PMID 34516717 DOI: 10.1002/biot.202000443   
2021 Bai Y, Parker EJ. Reciprocal allostery arising from a bi-enzyme assembly controls aromatic amino acid biosynthesis in Prevotella nigrescens. The Journal of Biological Chemistry. 101038. PMID 34343567 DOI: 10.1016/j.jbc.2021.101038   
2021 Zhang X, Huang Z, Wang D, Zhang Y, Eser BE, Gu Z, Dai R, Gao R, Guo Z. A new thermophilic extradiol dioxygenase promises biodegradation of catecholic pollutants. Journal of Hazardous Materials. 422: 126860. PMID 34399224 DOI: 10.1016/j.jhazmat.2021.126860   
2021 Jia B, Han X, Kim KH, Jeon CO. Discovery and mining of enzymes from the human gut microbiome. Trends in Biotechnology. PMID 34304905 DOI: 10.1016/j.tibtech.2021.06.008   
2021 Bakunova AK, Nikolaeva AY, Rakitina TV, Isaikina TY, Khrenova MG, Boyko KM, Popov VO, Bezsudnova EY. The Uncommon Active Site of D-Amino Acid Transaminase from : Biochemical and Structural Insights into the New Enzyme. Molecules (Basel, Switzerland). 26. PMID 34443642 DOI: 10.3390/molecules26165053   
2021 Ma L, Li F, Zhang X, Chen H, Huang Q, Su J, Liu X, Sun T, Fang B, Liu K, Tang D, Wu D, Zhang W, Du L, Li S. Development of MEMS directed evolution strategy for multiplied throughput and convergent evolution of cytochrome P450 enzymes. Science China. Life Sciences. PMID 34480693 DOI: 10.1007/s11427-021-1994-1   
2021 Cheng F, Zhai QY, Gao XF, Liu HT, Qiu S, Wang YJ, Zheng YG. Tuning enzymatic properties by protein engineering toward catalytic tetrad of carbonyl reductase. Biotechnology and Bioengineering. PMID 34436762 DOI: 10.1002/bit.27925   
2021 James MO. Enzyme Kinetics of PAPS-Sulfotransferase. Methods in Molecular Biology (Clifton, N.J.). 2342: 285-300. PMID 34272699 DOI: 10.1007/978-1-0716-1554-6_11   
2021 James MO. Enzyme Kinetics of PAPS-Sulfotransferase. Methods in Molecular Biology (Clifton, N.J.). 2342: 285-300. PMID 34272699 DOI: 10.1007/978-1-0716-1554-6_11   
2021 Jeter VL, Escalante-Semerena JC. Sirtuin-dependent reversible lysine acetylation controls the activity of acetyl-Coenzyme A synthetase in . Journal of Bacteriology. JB0033321. PMID 34309396 DOI: 10.1128/JB.00333-21   
2021 Xiang G, Leemhuis H, van der Maarel MJEC. Structural elements determining the transglycosylating activity of glycoside hydrolase family 57 glycogen branching enzymes. Proteins. PMID 34346105 DOI: 10.1002/prot.26200   
2021 Mondal S, Thakur A, Fontes CMGA, Goyal A. A trimodular family 16 glycoside hydrolase from the cellulosome of displays highly specific licheninase (EC 3.2.1.73) activity. Microbiology (Reading, England). 167. PMID 34297654 DOI: 10.1099/mic.0.001055   
2021 Nguyen TM, Goto M, Noda S, Matsutani M, Hodoya Y, Kataoka N, Adachi O, Matsushita K, Yakushi T. The 5-ketofructose reductase of sp. strain CHM43 is a novel class in the shikimate dehydrogenase family. Journal of Bacteriology. JB0055820. PMID 34309403 DOI: 10.1128/JB.00558-20   
2021 Somma V, Calvio C, Rabuffetti M, Rama E, Speranza G, Morelli CF. An overall framework for the E. coli γ-glutamyltransferase-catalyzed transpeptidation reactions. Bioorganic Chemistry. 115: 105217. PMID 34364051 DOI: 10.1016/j.bioorg.2021.105217   
2021 Moses ME, Lund PM, Bohr SS, Iversen JF, Kæstel-Hansen J, Kallenbach AS, Iversen L, Christensen SM, Hatzakis NS. Single-Molecule Study of Lipase in a Detergency Application System Reveals Diffusion Pattern Remodeling by Surfactants and Calcium. Acs Applied Materials & Interfaces. 13: 33704-33712. PMID 34235926 DOI: 10.1021/acsami.1c08809   
2021 Darrouzet E, Rinaldi C, Zambelli B, Ciurli S, Cavazza C. Revisiting the CooJ family, a potential chaperone for nickel delivery to [NiFe]‑carbon monoxide dehydrogenase. Journal of Inorganic Biochemistry. 225: 111588. PMID 34530332 DOI: 10.1016/j.jinorgbio.2021.111588   
2021 Wang Y, Mittermaier AK. Characterizing Bi-substrate Enzyme Kinetics at High Resolution by 2D-ITC. Analytical Chemistry. PMID 34514786 DOI: 10.1021/acs.analchem.1c02705   
2021 Espina G, Atalah J, Blamey JM. Extremophilic Oxidoreductases for the Industry: Five Successful Examples With Promising Projections. Frontiers in Bioengineering and Biotechnology. 9: 710035. PMID 34458243 DOI: 10.3389/fbioe.2021.710035   
2021 Becker D, Bharatam PV, Gohlke H. F/G Region Rigidity is Inversely Correlated to Substrate Promiscuity of Human CYP Isoforms Involved in Metabolism. Journal of Chemical Information and Modeling. 61: 4023-4030. PMID 34370479 DOI: 10.1021/acs.jcim.1c00558   
2021 Currie MJ, Manjunath L, Horne CR, Rendle PM, Subramanian R, Friemann R, Fairbanks AJ, Muscroft-Taylor AC, North RA, Dobson RCJ. N-Acetylmannosamine-6-phosphate 2-epimerase uses a novel substrate-assisted mechanism to catalyze amino sugar epimerization. The Journal of Biological Chemistry. 101113. PMID 34437902 DOI: 10.1016/j.jbc.2021.101113   
2021 Li Q, Pan Y, Li H, Lenertz M, Reed K, Jordahl D, Bjerke T, Ugrinov A, Chen B, Yang Z. Cascade/Parallel Biocatalysis via Multi-enzyme Encapsulation on Metal-Organic Materials for Rapid and Sustainable Biomass Degradation. Acs Applied Materials & Interfaces. PMID 34478257 DOI: 10.1021/acsami.1c12209   
2021 Tohar R, Ansbacher T, Sher I, Afriat-Jurnou L, Weinberg E, Gal M. Screening Collagenase Activity in Bacterial Lysate for Directed Enzyme Applications. International Journal of Molecular Sciences. 22. PMID 34445258 DOI: 10.3390/ijms22168552   
2021 Jiang D, Li Y, Wu W, Zhang H, Xu R, Xu H, Zhan R, Sun L. Identification and engineering on the non-conserved residues of metallo-β-lactamase-type thioesterase to improve the enzymatic activity. Biotechnology and Bioengineering. PMID 34427915 DOI: 10.1002/bit.27921   
2021 Guo J, Wang Y, Gao W, Wang X, Gao X, Man Z, Cai Z, Qing Q. Gene Cloning, Functional Expression, and Characterization of a Novel GH46 Chitosanase from Streptomyces avermitilis (SaCsn46A). Applied Biochemistry and Biotechnology. PMID 34542822 DOI: 10.1007/s12010-021-03687-6   
2021 Piper IM, Struyvenberg SA, Valgardson JD, Alex Johnson D, Gao M, Johnston K, Svendsen JE, Kodama HM, Hvorecny KL, Antos JM, Amacher JF. Sequence variation in the β7-β8 loop of bacterial Class A sortase enzymes alters substrate selectivity. The Journal of Biological Chemistry. 100981. PMID 34302812 DOI: 10.1016/j.jbc.2021.100981   
2021 Gabrielli V, Muñoz-García JC, Pergolizzi G, de Andrade P, Khimyak Y, Field RA, Angulo J. Molecular recognition of natural and non-natural substrates by cellodextrin phosphorylase from Ruminiclostridium thermocellum investigated by NMR spectroscopy. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 34436794 DOI: 10.1002/chem.202102039   
2021 Qian Y, Gao Z, Wang J, Wang C, Li G, Fu F, Guo J, Shan Y. Safety Evaluation and Whole Genome Sequencing of PJ01 Reveal Its Potential to Degrade Citrus Segments in Juice Processing. Foods (Basel, Switzerland). 10. PMID 34441514 DOI: 10.3390/foods10081736   
2021 Ali A, Ellinger B, Brandt SC, Betzel C, Rühl M, Wrenger C, Schlüter H, Schäfer W, Brognaro H, Gand M. Genome and Secretome Analysis of DSM105789 Cultured on Agro-Residual and Chitinous Biomass. Microorganisms. 9. PMID 34442660 DOI: 10.3390/microorganisms9081581   
2021 Morzywolek A, Plotka M, Kaczorowska AK, Szadkowska M, Kozlowski LP, Wyrzykowski D, Makowska J, Waters JJ, Swift SM, Donovan DM, Kaczorowski T. Novel Lytic Enzyme of Prophage Origin from E3 Strain Alaska E43 with Bactericidal Activity against Clostridial Cells. International Journal of Molecular Sciences. 22. PMID 34502443 DOI: 10.3390/ijms22179536   
2021 Hagedoorn PL, Hollmann F, Hanefeld U. Novel oleate hydratases and potential biotechnological applications. Applied Microbiology and Biotechnology. PMID 34350478 DOI: 10.1007/s00253-021-11465-x   
2021 Zaru R, Onwubiko J, Ribeiro AJM, Cochrane K, Tyzack JD, Muthukrishnan V, Pravda L, Thornton JM, O'Donovan C, Velanker S, Orchard S, Leach A, Martin MJ. The Enzyme Portal: an integrative tool for enzyme information and analysis. The Febs Journal. PMID 34437766 DOI: 10.1111/febs.16168   
2021 Chao RR, Lau IC, Coleman T, Churchman LR, Child SA, Lee JHZ, Bruning JB, De Voss JJ, Bell SG. The stereoselective oxidation of para-substituted benzenes by a cytochrome P450 biocatalyst. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 34350662 DOI: 10.1002/chem.202102757   
2021 Aregbesola OA, Kumar A, Mokoena MP, Olaniran AO. Classic Pentachlorophenol Hydroxylating Phenylalanine 4-Monooxygenase from Indigenous Bacillus tropicus Strain AOA-CPS1: Cloning, Overexpression, Purification, Characterization and Structural Homology Modelling. Applied Biochemistry and Biotechnology. PMID 34417677 DOI: 10.1007/s12010-021-03645-2   
2021 Pandey S, Mahanta P, Berger BW, Acharya R. Structural insights into the mechanism of pH-selective substrate specificity of the polysaccharide lyase Smlt1473. The Journal of Biological Chemistry. 101014. PMID 34358563 DOI: 10.1016/j.jbc.2021.101014   
2021 Feehan R, Montezano D, Slusky JSG. Machine learning for enzyme engineering, selection and design. Protein Engineering, Design & Selection : Peds. 34. PMID 34296736 DOI: 10.1093/protein/gzab019   
2021 Kröß C, Engele P, Sprenger B, Fischer A, Lingg N, Baier M, Öhlknecht C, Lier B, Oostenbrink C, Cserjan-Puschmann M, Striedner G, Jungbauer A, Schneider R. PROFICS: A bacterial selection system for directed evolution of proteases. The Journal of Biological Chemistry. 101095. PMID 34418435 DOI: 10.1016/j.jbc.2021.101095   
2021 Vicker SL, Maina EN, Showalter AK, Tran N, Davidson EE, Bailey MR, McGarry SW, Freije WM, West JD. Broader than expected tolerance for substitutions in the WCGPCK catalytic motif of yeast thioredoxin 2. Free Radical Biology & Medicine. PMID 34530076 DOI: 10.1016/j.freeradbiomed.2021.09.009   
2021 Chua SMH, Wizrah MSI, Luo Z, Lim BYJ, Kappler U, Kobe B, Fraser JA. Structural features of Cryptococcus neoformans bifunctional GAR/AIR synthetase may present novel antifungal drug targets. The Journal of Biological Chemistry. 101091. PMID 34416230 DOI: 10.1016/j.jbc.2021.101091