Redesigning pH optimum of Geobacillus sp. TF16 endoxylanase through in silico designed DNA swapping strategy.

[1]  Ummuhan Cakmak,et al.  Gene cloning, expression, immobilization and characterization of endo-xylanase from Geobacillus sp. TF16 and investigation of its industrial applications , 2016 .

[2]  Renzhi Cao,et al.  3Drefine: an interactive web server for efficient protein structure refinement , 2016, Nucleic Acids Res..

[3]  Aihua Liu,et al.  Rational design of xylose dehydrogenase for improved thermostability and its application in development of efficient enzymatic biofuel cell. , 2016, Enzyme and microbial technology.

[4]  Shane A. Seabrook,et al.  Rational engineering of a mesohalophilic carbonic anhydrase to an extreme halotolerant biocatalyst , 2015, Nature Communications.

[5]  P. Agarwal,et al.  Perturbation of the Conformational Dynamics of an Active-Site Loop Alters Enzyme Activity. , 2015, Structure.

[6]  Xiaoqiong Pei,et al.  Improving the thermostability of feruloyl esterase by DNA shuffling and site-directed mutagenesis , 2015 .

[7]  M. Guenza,et al.  Predicting protein dynamics from structural ensembles. , 2015, The Journal of chemical physics.

[8]  Hongyu Ma,et al.  Functional diversity and properties of multiple xylanases from Penicillium oxalicum GZ-2 , 2015, Scientific Reports.

[9]  W. Bai,et al.  Structural Insight into and Mutational Analysis of Family 11 Xylanases: Implications for Mechanisms of Higher pH Catalytic Adaptation , 2015, PloS one.

[10]  Apolinaria García,et al.  Variations in periplasmic loop interactions determine the pH-dependent activity of the hexameric urea transporter UreI from Helicobacter pylori: a molecular dynamics study , 2015, BMC Structural Biology.

[11]  María Martín,et al.  UniProt: A hub for protein information , 2015 .

[12]  Minky Son,et al.  Structural importance of the C-terminal region in pig aldo-keto reductase family 1 member C1 and their effects on enzymatic activity , 2015, BMC Structural Biology.

[13]  Yang Zhang,et al.  The I-TASSER Suite: protein structure and function prediction , 2014, Nature Methods.

[14]  The Uniprot Consortium,et al.  UniProt: a hub for protein information , 2014, Nucleic Acids Res..

[15]  Faez Iqbal Khan,et al.  Creation of thermostable and alkaline stable xylanase variants by DNA shuffling. , 2014, Journal of biotechnology.

[16]  Dmitry Suplatov,et al.  Computational Design of a pH Stable Enzyme: Understanding Molecular Mechanism of Penicillin Acylase's Adaptation to Alkaline Conditions , 2014, PloS one.

[17]  Vahid Mirjalili,et al.  Physics‐based protein structure refinement through multiple molecular dynamics trajectories and structure averaging , 2014, Proteins.

[18]  A. Gusakov,et al.  Engineering the pH-optimum of activity of the GH12 family endoglucanase by site-directed mutagenesis. , 2013, Biochimie.

[19]  Xurong Xu,et al.  Rational design of thermostable vaccines by engineered peptide-induced virus self-biomineralization under physiological conditions , 2013, Proceedings of the National Academy of Sciences.

[20]  Jianfang Li,et al.  Engineering hyperthermostability into a mesophilic family 11 xylanase from Aspergillus oryzae by in silico design of N‐terminus substitution , 2013, Biotechnology and bioengineering.

[21]  Xiao-qiong Lin,et al.  Bleach boosting effect of xylanase A from Bacillus halodurans C-125 in ECF bleaching of wheat straw pulp. , 2013, Enzyme and microbial technology.

[22]  Modesto Orozco,et al.  Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field. , 2013, Journal of chemical theory and computation.

[23]  Manish Kumar Tiwari,et al.  From Protein Engineering to Immobilization: Promising Strategies for the Upgrade of Industrial Enzymes , 2013, International journal of molecular sciences.

[24]  Y. Yoo,et al.  Rational design of a Bacillus circulans xylanase by introducing charged residue to shift the pH optimum , 2012 .

[25]  Varad R Shende,et al.  Toward a molecular understanding of protein solubility: increased negative surface charge correlates with increased solubility. , 2012, Biophysical journal.

[26]  T. Satyanarayana,et al.  Cloning, expression and applicability of thermo-alkali-stable xylanase of Geobacillus thermoleovorans in generating xylooligosaccharides from agro-residues. , 2012, Bioresource technology.

[27]  S. Bozonnet,et al.  Engineering better biomass-degrading ability into a GH11 xylanase using a directed evolution strategy , 2012, Biotechnology for Biofuels.

[28]  S. Baker,et al.  A versatile toolkit for high throughput functional genomics with Trichoderma reesei , 2012, Biotechnology for Biofuels.

[29]  S. Brunak,et al.  SignalP 4.0: discriminating signal peptides from transmembrane regions , 2011, Nature Methods.

[30]  Mallur S. Madhusudhan,et al.  CLICK—topology-independent comparison of biomolecular 3D structures , 2011, Nucleic Acids Res..

[31]  Jan H. Jensen,et al.  PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions. , 2011, Journal of chemical theory and computation.

[32]  P. Bergquist,et al.  Alteration of the pH optimum of a family 11 xylanase, XynB6 of Dictyoglomus thermophilum. , 2010, New biotechnology.

[33]  Stefan Lutz,et al.  Beyond directed evolution--semi-rational protein engineering and design. , 2010, Current opinion in biotechnology.

[34]  Lantao Liu,et al.  Enzyme structure dynamics of xylanase I from Trichoderma longibrachiatum , 2010, BMC Bioinformatics.

[35]  R. Sharan,et al.  I-TASSER: a unified platform for automated protein structure and function prediction , 2010, Nature Protocols.

[36]  Vincent B. Chen,et al.  MolProbity: all-atom structure validation for macromolecular crystallography , 2009, Acta crystallographica. Section D, Biological crystallography.

[37]  Tim Beliën,et al.  Computational design-based molecular engineering of the glycosyl hydrolase family 11 B. subtilis XynA endoxylanase improves its acid stability. , 2009, Protein engineering, design & selection : PEDS.

[38]  G. Mamo,et al.  An alkaline active xylanase: insights into mechanisms of high pH catalytic adaptation. , 2009, Biochimie.

[39]  Y. Yoo,et al.  Shifting pH optimum of Bacillus circulans xylanase based on molecular modeling. , 2008, Journal of biotechnology.

[40]  A. Murdoch.  Cloning , 2007, Ethics & Medics.

[41]  Tao Xia,et al.  Enhancement of the thermostability and hydrolytic activity of GH10 xylanase by module shuffling between Cellulomonas fimi Cex and Thermomonospora alba XylA , 2007 .

[42]  M. Karplus,et al.  Molecular dynamics and protein function. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[43]  Sophia Hober,et al.  Engineering streptococcal protein G for increased alkaline stability. , 2002, Protein engineering.

[44]  S. Subramaniyan,et al.  Biotechnology of Microbial Xylanases: Enzymology, Molecular Biology, and Application , 2002, Critical reviews in biotechnology.

[45]  A. Sali,et al.  Protein Structure Prediction and Structural Genomics , 2001, Science.

[46]  T. Yamane,et al.  Crystal structure of alkaline cellulase K: insight into the alkaline adaptation of an industrial enzyme. , 2001, Journal of molecular biology.

[47]  S. Kaneko,et al.  Enhancement of the thermostability and hydrolytic activity of xylanase by random gene shuffling. , 2000, The Biochemical journal.

[48]  M. Uhlén,et al.  Stability towards alkaline conditions can be engineered into a protein ligand. , 2000, Journal of biotechnology.

[49]  B. Musafia,et al.  Complex salt bridges in proteins: statistical analysis of structure and function. , 1995, Journal of molecular biology.

[50]  R Tyler-Cross,et al.  Effects of amino acid sequence, buffers, and ionic strength on the rate and mechanism of deamidation of asparagine residues in small peptides. , 1991, The Journal of biological chemistry.

[51]  T. Kudo,et al.  Two types of xylanases of alkalophilic Bacillus sp. No. C-125 , 1985 .

[52]  M. M. Bradford.  A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. , 1976, Analytical biochemistry.

[53]  G. L. Miller.  Use of Dinitrosalicylic Acid Reagent for Determination of Reducing Sugar , 1959 .

[54]  Swati Joshi,et al.  In vitro engineering of microbial enzymes with multifarious applications: prospects and perspectives. , 2015, Bioresource technology.

[55]  Nucleic Acids Research Advance Access published June 21, 2007 PIC: Protein Interactions Calculator , 2007 .

[56]  G. Feller,et al.  Xylanases, xylanase families and extremophilic xylanases. , 2005, FEMS microbiology reviews.

[57]  N. Kruger,et al.  The bradford method for protein quantitation. , 1988, Methods in molecular biology.

[58]  Y Kuchino,et al.  [Gene cloning]. , 1982, Nihon rinsho. Japanese journal of clinical medicine.

[59]  C. Chuong,et al.  Article type Software , 2007 .