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For: Vieira DS, Degrève L, Ward RJ. Characterization of temperature dependent and substrate-binding cleft movements in Bacillus circulans family 11 xylanase: a molecular dynamics investigation. Biochim Biophys Acta Gen Subj 2009;1790:1301-6. [PMID: 19409448 DOI: 10.1016/j.bbagen.2009.04.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2009] [Revised: 04/14/2009] [Accepted: 04/23/2009] [Indexed: 11/30/2022]
Number Cited by Other Article(s)
1
Wang L, Wang YY, Chen ZL, Li YH. Enzymatic characterization and thermostability improvement of an acidophilic endoxylanase PphXyn11 from Paenibacillus physcomitrellae XB. Protein Expr Purif 2024;219:106482. [PMID: 38583789 DOI: 10.1016/j.pep.2024.106482] [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: 07/11/2023] [Revised: 03/24/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
2
MacDonald ME, Wells NGM, Hassan BA, Dudley JA, Walters KJ, Korzhnev DM, Aramini JM, Smith CA. Effects of Xylanase A double mutation on substrate specificity and structural dynamics. J Struct Biol 2024;216:108082. [PMID: 38438058 DOI: 10.1016/j.jsb.2024.108082] [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: 12/16/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
3
Molina GA, Mendes LFS, Fuzo CA, Costa-Filho AJ, Ward RJ. Mapping secondary substrate-binding sites on the GH11 xylanase from Bacillus subtilis. FEBS Lett 2024;598:363-376. [PMID: 38253842 DOI: 10.1002/1873-3468.14799] [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: 09/18/2023] [Revised: 12/07/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024]
4
Vucinic J, Novikov G, Montanier CY, Dumon C, Schiex T, Barbe S. A Comparative Study to Decipher the Structural and Dynamics Determinants Underlying the Activity and Thermal Stability of GH-11 Xylanases. Int J Mol Sci 2021;22:ijms22115961. [PMID: 34073139 PMCID: PMC8199483 DOI: 10.3390/ijms22115961] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 11/23/2022]  Open
5
Marneth K, van den Elst H, Cramer‐Blok A, Codee J, Overkleeft HS, Aerts JMFG, Ubbink M, Ben Bdira F. Tuning the Transglycosylation Reaction of a GH11 Xylanase by a Delicate Enhancement of its Thumb Flexibility. Chembiochem 2021;22:1743-1749. [PMID: 33534182 PMCID: PMC8251542 DOI: 10.1002/cbic.202000856] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 02/01/2021] [Indexed: 12/31/2022]
6
Silva SRB, de Lima Neto JX, Fuzo CA, Fulco UL, Vieira DS. A quantum biochemistry investigation of the protein-protein interactions for the description of allosteric modulation on biomass-degrading chimera. Phys Chem Chem Phys 2020;22:25936-25948. [PMID: 33164009 DOI: 10.1039/d0cp04415f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
7
Greener approach for pulp and paper industry by Xylanase and Laccase. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101604] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
8
Interaction of drugs amlodipine and paroxetine with the metabolizing enzyme CYP2B4: a molecular dynamics simulation study. J Mol Model 2018;24:67. [DOI: 10.1007/s00894-018-3617-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/08/2018] [Indexed: 12/26/2022]
9
Ventorim RZ, de Oliveira Mendes TA, Trevizano LM, dos Santos Camargos AM, Guimarães VM. Impact of the removal of N-terminal non-structured amino acids on activity and stability of xylanases from Orpinomyces sp. PC-2. Int J Biol Macromol 2018;106:312-319. [DOI: 10.1016/j.ijbiomac.2017.08.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 07/19/2017] [Accepted: 08/01/2017] [Indexed: 11/17/2022]
10
Silva SB, Pinheiro MP, Fuzo CA, Silva SR, Ferreira TL, Lourenzoni MR, Nonato MC, Vieira DS, Ward RJ. The role of local residue environmental changes in thermostable mutants of the GH11 xylanase from Bacillus subtilis. Int J Biol Macromol 2017;97:574-584. [DOI: 10.1016/j.ijbiomac.2017.01.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/09/2017] [Accepted: 01/11/2017] [Indexed: 12/24/2022]
11
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: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
12
Gagné D, Narayanan C, Nguyen-Thi N, Roux LD, Bernard DN, Brunzelle JS, Couture JF, Agarwal PK, Doucet N. Ligand Binding Enhances Millisecond Conformational Exchange in Xylanase B2 from Streptomyces lividans. Biochemistry 2016;55:4184-96. [PMID: 27387012 DOI: 10.1021/acs.biochem.6b00130] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
13
Thermostabilization of Bacillus subtilis GH11 xylanase by surface charge engineering. Int J Biol Macromol 2016;87:522-8. [DOI: 10.1016/j.ijbiomac.2016.03.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 11/24/2022]
14
Ribeiro LF, Tullman J, Nicholes N, Silva SRB, Vieira DS, Ostermeier M, Ward RJ. A xylose-stimulated xylanase-xylose binding protein chimera created by random nonhomologous recombination. BIOTECHNOLOGY FOR BIOFUELS 2016;9:119. [PMID: 27274356 PMCID: PMC4896006 DOI: 10.1186/s13068-016-0529-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/19/2016] [Indexed: 05/05/2023]
15
Rapid asymmetric reduction of ethyl 4-chloro-3-oxobutanoate using a thermostabilized mutant of ketoreductase ChKRED20. Appl Microbiol Biotechnol 2015;100:3567-75. [DOI: 10.1007/s00253-015-7200-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/19/2015] [Accepted: 11/24/2015] [Indexed: 11/25/2022]
16
Mixed Enzyme Systems for Delignification of Lignocellulosic Biomass. Catalysts 2014. [DOI: 10.3390/catal4010001] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
17
Activity enhancement of a Bacillus circulans xylanase by introducing ion-pair interactions into an α-helix. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
18
Jaeger VW, Pfaendtner J. Structure, dynamics, and activity of xylanase solvated in binary mixtures of ionic liquid and water. ACS Chem Biol 2013;8:1179-86. [PMID: 23517495 DOI: 10.1021/cb3006837] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
19
Singh RK, Tiwari MK, Kim D, Kang YC, Ramachandran P, Lee JK. Molecular cloning and characterization of a GH11 endoxylanase from Chaetomium globosum, and its use in enzymatic pretreatment of biomass. Appl Microbiol Biotechnol 2012. [PMID: 23184220 DOI: 10.1007/s00253-012-4577-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
20
Pan D, Xue W, Zhang W, Liu H, Yao X. Understanding the drug resistance mechanism of hepatitis C virus NS3/4A to ITMN-191 due to R155K, A156V, D168A/E mutations: A computational study. Biochim Biophys Acta Gen Subj 2012;1820:1526-34. [DOI: 10.1016/j.bbagen.2012.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Revised: 06/03/2012] [Accepted: 06/04/2012] [Indexed: 12/19/2022]
21
Foley BL, Tessier MB, Woods RJ. Carbohydrate force fields. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2012;2:652-697. [PMID: 25530813 PMCID: PMC4270206 DOI: 10.1002/wcms.89] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
22
Paës G, Cortés J, Siméon T, O'Donohue MJ, Tran V. Thumb-loops up for catalysis: a structure/function investigation of a functional loop movement in a GH11 xylanase. Comput Struct Biotechnol J 2012;1:e201207001. [PMID: 24688637 PMCID: PMC3962102 DOI: 10.5936/csbj.201207001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 05/23/2012] [Accepted: 05/27/2012] [Indexed: 12/17/2022]  Open
23
Song L, Siguier B, Dumon C, Bozonnet S, O'Donohue MJ. Engineering better biomass-degrading ability into a GH11 xylanase using a directed evolution strategy. BIOTECHNOLOGY FOR BIOFUELS 2012;5:3. [PMID: 22244361 PMCID: PMC3299623 DOI: 10.1186/1754-6834-5-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 01/13/2012] [Indexed: 05/23/2023]
24
Paës G, Berrin JG, Beaugrand J. GH11 xylanases: Structure/function/properties relationships and applications. Biotechnol Adv 2011;30:564-92. [PMID: 22067746 DOI: 10.1016/j.biotechadv.2011.10.003] [Citation(s) in RCA: 284] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 10/06/2011] [Accepted: 10/13/2011] [Indexed: 01/02/2023]
25
Vieira DS, Ward RJ. Conformation analysis of a surface loop that controls active site access in the GH11 xylanase A from Bacillus subtilis. J Mol Model 2011;18:1473-9. [PMID: 21785938 DOI: 10.1007/s00894-011-1172-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 06/29/2011] [Indexed: 11/29/2022]
26
Morin A, Kaufmann KW, Fortenberry C, Harp JM, Mizoue LS, Meiler J. Computational design of an endo-1,4-beta-xylanase ligand binding site. Protein Eng Des Sel 2011;24:503-16. [PMID: 21349882 DOI: 10.1093/protein/gzr006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
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