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For: Suplatov D, Panin N, Kirilin E, Shcherbakova T, Kudryavtsev P, Svedas V. Computational design of a pH stable enzyme: understanding molecular mechanism of penicillin acylase's adaptation to alkaline conditions. PLoS One 2014;9:e100643. [PMID: 24959852 PMCID: PMC4069103 DOI: 10.1371/journal.pone.0100643] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 05/29/2014] [Indexed: 01/12/2023]  Open
Number Cited by Other Article(s)
1
Zhang Z, Wei Z, Qin Z, Wang L, Gong J, Shi J, Wu J, Deng Z. Advancing Enzyme Optimal pH Prediction via Retrieved Embedding Data Augmentation. J Chem Inf Model 2025. [PMID: 40418030 DOI: 10.1021/acs.jcim.5c00526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2025]
2
Yuan H, Ajeje SB, Wen Y, Chio C, Hu Y, Dou S, Qin W, Zhang E, Wu Q, Sun F. Enhancement of the catalytic activity of thermostable Endo-1,4-β-glucanase B (TnCelB) from Thermotoga neapolitana by error-prone PCR. Int J Biol Macromol 2025;308:142310. [PMID: 40122426 DOI: 10.1016/j.ijbiomac.2025.142310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Revised: 03/17/2025] [Accepted: 03/18/2025] [Indexed: 03/25/2025]
3
Zhang L, Luo K, Zhou Z, Yu Y, Jiang F, Wu B, Li M, Hong L. A Deep Retrieval-Enhanced Meta-Learning Framework for Enzyme Optimum pH Prediction. J Chem Inf Model 2025;65:3761-3770. [PMID: 40127128 PMCID: PMC12005191 DOI: 10.1021/acs.jcim.4c02291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2024] [Revised: 03/04/2025] [Accepted: 03/07/2025] [Indexed: 03/26/2025]
4
Song H, Chen WJ, Chen SF, Liu M, Si G, Zhu X, Bhatt K, Mishra S, Ghorab MA, Chen S. Unveiling the hydrolase Oph2876 mediated chlorpyrifos degradation mechanism in Pseudomonas nitroreducens and its potential for environmental bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2025;483:136570. [PMID: 39603136 DOI: 10.1016/j.jhazmat.2024.136570] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 10/15/2024] [Accepted: 11/17/2024] [Indexed: 11/29/2024]
5
Zhu M, Song Y, Yuan Q, Yang Y. Accurately predicting optimal conditions for microorganism proteins through geometric graph learning and language model. Commun Biol 2024;7:1709. [PMID: 39739114 DOI: 10.1038/s42003-024-07436-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 12/20/2024] [Indexed: 01/02/2025]  Open
6
Wu S, Xu G, Su Y, Huang H, Xu X, Zhang Y, Tian J, Zhang W, Zhang Z, Liu B. Mining and rational design of psychrophilic catalases using metagenomics and deep learning models. Appl Microbiol Biotechnol 2024;108:31. [PMID: 38175233 DOI: 10.1007/s00253-023-12926-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/21/2023] [Accepted: 09/30/2023] [Indexed: 01/05/2024]
7
Billerbeck S, Walker RSK, Pretorius IS. Killer yeasts: expanding frontiers in the age of synthetic biology. Trends Biotechnol 2024;42:1081-1096. [PMID: 38575438 DOI: 10.1016/j.tibtech.2024.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 04/06/2024]
8
Quiroga I, Hernández-González JA, Bautista-Rodríguez E, Benítez-Rojas AC. Exploring the Structurally Conserved Regions and Functional Significance in Bacterial N-Terminal Nucleophile (Ntn) Amide-Hydrolases. Int J Mol Sci 2024;25:6850. [PMID: 38999960 PMCID: PMC11241749 DOI: 10.3390/ijms25136850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 07/14/2024]  Open
9
Liu X, Lian M, Zhao M, Huang M. Advances in recombinant protease production: current state and perspectives. World J Microbiol Biotechnol 2024;40:144. [PMID: 38532149 DOI: 10.1007/s11274-024-03957-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024]
10
Zhang Y, Zhao Q, Ngolong Ngea GL, Godana EA, Yang Q, Zhang H. Biodegradation of patulin in fresh pear juice by an aldo-keto reductase from Meyerozyma guilliermondii. Food Chem 2024;436:137696. [PMID: 37862990 DOI: 10.1016/j.foodchem.2023.137696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/01/2023] [Accepted: 10/06/2023] [Indexed: 10/22/2023]
11
Amangeldina A, Tan ZW, Berezovsky IN. Living in trinity of extremes: Genomic and proteomic signatures of halophilic, thermophilic, and pH adaptation. Curr Res Struct Biol 2024;7:100129. [PMID: 38327713 PMCID: PMC10847869 DOI: 10.1016/j.crstbi.2024.100129] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 02/09/2024]  Open
12
Hu J, Du S, Qiu H, Wu Y, Hong Q, Wang G, Mohamed SR, Lee YW, Xu J. A Hydrolase Produced by Rhodococcus erythropolis HQ Is Responsible for the Detoxification of Zearalenone. Toxins (Basel) 2023;15:688. [PMID: 38133192 PMCID: PMC10747462 DOI: 10.3390/toxins15120688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023]  Open
13
Zhang Z, Zhao Z, Huang K, Liang Z. Acid-resistant enzymes: the acquisition strategies and applications. Appl Microbiol Biotechnol 2023;107:6163-6178. [PMID: 37615723 DOI: 10.1007/s00253-023-12702-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 08/25/2023]
14
Ru WJ, Xia BB, Zhang YX, Yang JW, Zhang HB, Hu XQ. Development of thermostable dextranase from Streptococcus mutans (SmdexTM) through in silico design employing B-factor and Cartesian-ΔΔG. J Biotechnol 2022;360:142-151. [PMID: 36343755 DOI: 10.1016/j.jbiotec.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022]
15
Hao M, Cui R, Zhu X, Han L, Zhou Z, Liu Z. Improving the activity and synergistic catalysis of l-aspartate β-decarboxylase by arginine introduction on the surface. Catal Sci Technol 2022. [DOI: 10.1039/d2cy00700b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
16
Ardila-Leal LD, Poutou-Piñales RA, Pedroza-Rodríguez AM, Quevedo-Hidalgo BE. A Brief History of Colour, the Environmental Impact of Synthetic Dyes and Removal by Using Laccases. Molecules 2021;26:3813. [PMID: 34206669 PMCID: PMC8270347 DOI: 10.3390/molecules26133813] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/12/2021] [Accepted: 06/16/2021] [Indexed: 12/07/2022]  Open
17
Ardila-Leal LD, Monterey-Gutiérrez PA, Poutou-Piñales RA, Quevedo-Hidalgo BE, Galindo JF, Pedroza-Rodríguez AM. Recombinant laccase rPOXA 1B real-time, accelerated and molecular dynamics stability study. BMC Biotechnol 2021;21:37. [PMID: 34088291 PMCID: PMC8178886 DOI: 10.1186/s12896-021-00698-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/24/2021] [Indexed: 12/28/2022]  Open
18
Li J, Chu Y, Yang R, Lin J, Shao L, Wang L. An alkali-tolerant phospholipase D from Sphingobacterium thalpophilum 2015: Gene cloning, overproduction and characterization. J GEN APPL MICROBIOL 2021;67:1-8. [PMID: 32981922 DOI: 10.2323/jgam.2020.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
19
Suplatov D, Sharapova Y, Švedas V. Mustguseal and Sister Web-Methods: A Practical Guide to Bioinformatic Analysis of Protein Superfamilies. Methods Mol Biol 2021;2231:179-200. [PMID: 33289894 DOI: 10.1007/978-1-0716-1036-7_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
20
Chen J, Wei H, Guo Y, Li Q, Wang H, Liu J. Chaperone-mediated protein folding enhanced D-psicose 3-epimerase expression in engineered Bacillus subtilis. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.02.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
21
Aricov L, Leonties AR, Gîfu IC, Preda D, Raducan A, Anghel DF. Enhancement of laccase immobilization onto wet chitosan microspheres using an iterative protocol and its potential to remove micropollutants. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020;276:111326. [PMID: 32891981 DOI: 10.1016/j.jenvman.2020.111326] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/21/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
22
Surface charge-based rational design of aspartase modifies the optimal pH for efficient β-aminobutyric acid production. Int J Biol Macromol 2020;164:4165-4172. [DOI: 10.1016/j.ijbiomac.2020.08.229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/29/2020] [Accepted: 08/29/2020] [Indexed: 12/19/2022]
23
Mogany T, Kumari S, Swalaha FM, Bux F. An in silico structural and physiochemical analysis of C-Phycocyanin of halophile Euhalothece sp. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.102025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
24
Suplatov D, Sharapova Y, Geraseva E, Švedas V. Zebra2: advanced and easy-to-use web-server for bioinformatic analysis of subfamily-specific and conserved positions in diverse protein superfamilies. Nucleic Acids Res 2020;48:W65-W71. [PMID: 32313959 PMCID: PMC7319439 DOI: 10.1093/nar/gkaa276] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/29/2020] [Accepted: 04/08/2020] [Indexed: 12/17/2022]  Open
25
Thakur N, Sharma N, Kumar V, Bhalla TC. Computational Analysis of the Primary and Secondary Structure of Amidases in Relation to their pH Adaptation. CURR PROTEOMICS 2020. [DOI: 10.2174/1570164616666190718150627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
26
Kumar AP, Verma CS, Lukman S. Structural dynamics and allostery of Rab proteins: strategies for drug discovery and design. Brief Bioinform 2020;22:270-287. [PMID: 31950981 DOI: 10.1093/bib/bbz161] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/29/2019] [Accepted: 11/15/2019] [Indexed: 01/09/2023]  Open
27
Anuar NFSK, Wahab RA, Huyop F, Halim KBA, Hamid AAA. In silico mutation on a mutant lipase from Acinetobacter haemolyticus towards enhancing alkaline stability. J Biomol Struct Dyn 2019;38:4493-4507. [DOI: 10.1080/07391102.2019.1683074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
28
Laccase isoform diversity in basidiomycete Lentinus strigosus 1566: Potential for phenylpropanoid polymerization. Int J Biol Macromol 2019;137:1199-1210. [DOI: 10.1016/j.ijbiomac.2019.07.056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/23/2019] [Accepted: 07/07/2019] [Indexed: 11/17/2022]
29
Suplatov DA, Kopylov KE, Popova NN, Voevodin VV, Švedas VK. Mustguseal: a server for multiple structure-guided sequence alignment of protein families. Bioinformatics 2019;34:1583-1585. [PMID: 29309510 DOI: 10.1093/bioinformatics/btx831] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/21/2017] [Indexed: 01/23/2023]  Open
30
Tuning the pH profile of β-glucuronidase by rational site-directed mutagenesis for efficient transformation of glycyrrhizin. Appl Microbiol Biotechnol 2019;103:4813-4823. [PMID: 31055652 DOI: 10.1007/s00253-019-09790-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/16/2019] [Accepted: 03/20/2019] [Indexed: 02/05/2023]
31
Liu Z, Zhao H, Han L, Cui W, Zhou L, Zhou Z. Improvement of the acid resistance, catalytic efficiency, and thermostability of nattokinase by multisite‐directed mutagenesis. Biotechnol Bioeng 2019;116:1833-1843. [DOI: 10.1002/bit.26983] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 03/22/2019] [Accepted: 03/28/2019] [Indexed: 11/07/2022]
32
Rouhani M, Khodabakhsh F, Norouzian D, Cohan RA, Valizadeh V. Molecular dynamics simulation for rational protein engineering: Present and future prospectus. J Mol Graph Model 2018;84:43-53. [DOI: 10.1016/j.jmgm.2018.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/05/2018] [Accepted: 06/08/2018] [Indexed: 12/19/2022]
33
Biophysical characterization of a recombinant lipase KV1 from Acinetobacter haemolyticus in relation to pH and temperature. Biochimie 2018;152:198-210. [PMID: 30036604 DOI: 10.1016/j.biochi.2018.07.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/18/2018] [Indexed: 01/05/2023]
34
Lee SY, Shin WR, Sekhon SS, Lee JP, Kim YC, Ahn JY, Kim YH. Molecular Docking Analysis and Biochemical Evaluation of Levansucrase from Sphingobium chungbukense DJ77. ACS COMBINATORIAL SCIENCE 2018;20:414-422. [PMID: 29812898 DOI: 10.1021/acscombsci.8b00002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
35
Synthesis, Characterization, and Applications of Nanographene-Armored Enzymes. Methods Enzymol 2018;609:83-142. [DOI: 10.1016/bs.mie.2018.05.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
36
Farrokh P, Yakhchali B, Karkhane AA. Role of Q177A and K173A/Q177A substitutions in thermostability and activity of the ELBn12 lipase. Biotechnol Appl Biochem 2017;65:203-211. [DOI: 10.1002/bab.1576] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 06/09/2017] [Accepted: 07/15/2017] [Indexed: 11/06/2022]
37
Obeng EM, Budiman C, Ongkudon CM. Identifying additives for cellulase enhancement—A systematic approach. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2017.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
38
Uzuner U, Canakci S, Bektas KI, Sapmaz MT, Belduz AO. Redesigning pH optimum of Geobacillus sp. TF16 endoxylanase through in silico designed DNA swapping strategy. Biochimie 2017;137:174-189. [PMID: 28351672 DOI: 10.1016/j.biochi.2017.03.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 03/23/2017] [Indexed: 12/27/2022]
39
Chakravorty D, Khan MF, Patra S. Multifactorial level of extremostability of proteins: can they be exploited for protein engineering? Extremophiles 2017;21:419-444. [PMID: 28283770 DOI: 10.1007/s00792-016-0908-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 12/19/2016] [Indexed: 12/20/2022]
40
Osiro KO, de Camargo BR, Satomi R, Hamann PRV, Silva JP, de Sousa MV, Quirino BF, Aquino EN, Felix CR, Murad AM, Noronha EF. Characterization of Clostridium thermocellum (B8) secretome and purified cellulosomes for lignocellulosic biomass degradation. Enzyme Microb Technol 2017;97:43-54. [DOI: 10.1016/j.enzmictec.2016.11.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 11/04/2016] [Accepted: 11/05/2016] [Indexed: 11/16/2022]
41
Childers MC, Daggett V. Insights from molecular dynamics simulations for computational protein design. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2017;2:9-33. [PMID: 28239489 PMCID: PMC5321087 DOI: 10.1039/c6me00083e] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
42
Tong X, Barberi TT, Botting CH, Sharma SV, Simmons MJH, Overton TW, Goss RJM. Rapid enzyme regeneration results in the striking catalytic longevity of an engineered, single species, biocatalytic biofilm. Microb Cell Fact 2016;15:180. [PMID: 27769259 PMCID: PMC5073922 DOI: 10.1186/s12934-016-0579-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 10/14/2016] [Indexed: 11/10/2022]  Open
43
Buchholz PCF, Vogel C, Reusch W, Pohl M, Rother D, Spieß AC, Pleiss J. BioCatNet: A Database System for the Integration of Enzyme Sequences and Biocatalytic Experiments. Chembiochem 2016;17:2093-2098. [DOI: 10.1002/cbic.201600462] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Indexed: 12/12/2022]
44
Bezsudnova EY, Stekhanova TN, Suplatov DA, Mardanov AV, Ravin NV, Popov VO. Experimental and computational studies on the unusual substrate specificity of branched-chain amino acid aminotransferase from Thermoproteus uzoniensis. Arch Biochem Biophys 2016;607:27-36. [PMID: 27523731 DOI: 10.1016/j.abb.2016.08.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/09/2016] [Accepted: 08/10/2016] [Indexed: 01/26/2023]
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Goyal B, Srivastava KR, Patel K, Durani S. Modulation of β-Hairpin Peptide Self-Assembly: A Twenty-Residue Poly-lβ-Hairpin Modified Rationally as a Mixed-l,dHydrolase. ChemistrySelect 2016. [DOI: 10.1002/slct.201600078] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Suplatov D, Popova N, Zhumatiy S, Voevodin V, Švedas V. Parallel workflow manager for non-parallel bioinformatic applications to solve large-scale biological problems on a supercomputer. J Bioinform Comput Biol 2016;14:1641008. [DOI: 10.1142/s0219720016410080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Panigrahi P, Chand D, Mukherji R, Ramasamy S, Suresh CG. Sequence and structure-based comparative analysis to assess, identify and improve the thermostability of penicillin G acylases. ACTA ACUST UNITED AC 2015;42:1493-506. [DOI: 10.1007/s10295-015-1690-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 09/14/2015] [Indexed: 11/28/2022]
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Suplatov D, Švedas V. Study of Functional and Allosteric Sites in Protein Superfamilies. Acta Naturae 2015;7:34-45. [PMID: 26798490 PMCID: PMC4717248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
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Miller DM, Gulbis JM. Engineering protocells: prospects for self-assembly and nanoscale production-lines. Life (Basel) 2015;5:1019-53. [PMID: 25815781 PMCID: PMC4500129 DOI: 10.3390/life5021019] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 03/09/2015] [Accepted: 03/16/2015] [Indexed: 11/16/2022]  Open
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Shcherbakova TA, Panin NV, Suplatov DA, Shapovalova IV, Švedas VK. The βD484N mutant of penicillin acylase from Escherichia coli is more resistant to inactivation by substrates and can effectively perform peptide synthesis in aqueous medium. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2014.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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