Engineering proteins for thermostability through rigidifying flexible sites.

Engineering proteins for thermostability is an exciting and challenging field since it is critical for broadening the industrial use of recombinant proteins. Thermostability of proteins arises from the simultaneous effect of several forces such as hydrophobic interactions, disulfide bonds, salt bridges and hydrogen bonds. All of these interactions lead to decreased flexibility of polypeptide chain. Structural studies of mesophilic and thermophilic proteins showed that the latter need more rigid structures to compensate for increased thermal fluctuations. Hence flexibility can be an indicator to pinpoint weak spots for enhancing thermostability of enzymes. A strategy has been proven effective in enhancing proteins' thermostability with two steps: predict flexible sites of proteins firstly and then rigidify these sites. We refer to this approach as rigidify flexible sites (RFS) and give an overview of such a method through summarizing the methods to predict flexibility of a protein, the methods to rigidify residues with high flexibility and successful cases regarding enhancing thermostability of proteins using RFS.

[1]  Uwe T Bornscheuer,et al.  Thermostabilization of an esterase by alignment-guided focussed directed evolution. , 2010, Protein engineering, design & selection : PEDS.

[2]  Nicholas J Turner,et al.  Directed evolution drives the next generation of biocatalysts. , 2009, Nature chemical biology.

[3]  Robert Kourist,et al.  Protein engineering and discovery of lipases , 2010 .

[4]  D. Bevan,et al.  Study and design of stability in GH5 cellulases , 2012, Biotechnology and bioengineering.

[5]  S. Pack,et al.  Thermostabilization of Bacillus circulans xylanase: computational optimization of unstable residues based on thermal fluctuation analysis. , 2011, Journal of biotechnology.

[6]  Roberto A Chica,et al.  Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design. , 2005, Current opinion in biotechnology.

[7]  Manfred T Reetz,et al.  Addressing the Numbers Problem in Directed Evolution , 2008, Chembiochem : a European journal of chemical biology.

[8]  Yosephine Gumulya,et al.  Iterative saturation mutagenesis accelerates laboratory evolution of enzyme stereoselectivity: rigorous comparison with traditional methods. , 2010, Journal of the American Chemical Society.

[9]  Michael McDuffie,et al.  FlexPred: a web-server for predicting residue positions involved in conformational switches in proteins , 2008, Bioinformation.

[10]  Michail Yu. Lobanov,et al.  FoldUnfold: web server for the prediction of disordered regions in protein chain , 2006, Bioinform..

[11]  Hue Sun Chan,et al.  Kinetic consequences of native state optimization of surface‐exposed electrostatic interactions in the Fyn SH3 domain , 2012, Proteins.

[12]  M. Perutz Electrostatic effects in proteins. , 1978, Science.

[13]  Holger Gohlke,et al.  Protein rigidity and thermophilic adaptation , 2011, Proteins.

[14]  Holger Gohlke,et al.  Change in protein flexibility upon complex formation: Analysis of Ras‐Raf using molecular dynamics and a molecular framework approach , 2004, Proteins.

[15]  H. Gohlke,et al.  Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory , 2006, Proteins.

[16]  M. Oobatake,et al.  Conformational Stabilities of Escherichia coli RNase HI Variants with a Series of Amino Acid Substitutions at a Cavity within the Hydrophobic Core* , 1997, The Journal of Biological Chemistry.

[17]  S. Pack,et al.  Thermostabilization of Bacillus circulans xylanase via computational design of a flexible surface cavity. , 2010, Journal of biotechnology.

[18]  Ruth Nussinov,et al.  HingeProt: Automated prediction of hinges in protein structures , 2008, Proteins.

[19]  Robert L Jernigan,et al.  vGNM: a better model for understanding the dynamics of proteins in crystals. , 2007, Journal of molecular biology.

[20]  Dick B Janssen,et al.  Molecular dynamics simulations as a tool for improving protein stability. , 2002, Protein engineering.

[21]  Andreas Vogel,et al.  Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability. , 2006, Angewandte Chemie.

[22]  Xian-Ming Pan,et al.  Salt Bridges in the Hyperthermophilic Protein Ssh10b Are Resilient to Temperature Increases* , 2008, Journal of Biological Chemistry.

[23]  George I Makhatadze,et al.  Protein stabilization by the rational design of surface charge-charge interactions. , 2009, Methods in molecular biology.

[24]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[25]  Yi Liu,et al.  RosettaDesign server for protein design , 2006, Nucleic Acids Res..

[26]  Yosephine Gumulya,et al.  Increasing the stability of an enzyme toward hostile organic solvents by directed evolution based on iterative saturation mutagenesis using the B-FIT method. , 2010, Chemical communications.

[27]  Jory Z. Ruscio,et al.  The influence of protein dynamics on the success of computational enzyme design. , 2009, Journal of the American Chemical Society.

[28]  Uwe T Bornscheuer,et al.  Natural Diversity to Guide Focused Directed Evolution , 2010, Chembiochem : a European journal of chemical biology.

[29]  J. Joo,et al.  Development of thermostable Candida antarctica lipase B through novel in silico design of disulfide bridge , 2012, Biotechnology and bioengineering.

[30]  S. Parthasarathy,et al.  Protein thermal stability: insights from atomic displacement parameters (B values). , 2000, Protein engineering.

[31]  A. Rader,et al.  Thermostability in rubredoxin and its relationship to mechanical rigidity , 2009, Physical biology.

[32]  Jianpeng Ma,et al.  CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..

[33]  K. S. Yip,et al.  Protein thermostability above 100°C: A key role for ionic interactions , 1998 .

[34]  M. Reetz,et al.  A thermostable variant of P. aeruginosa cold-adapted LipC obtained by rational design and saturation mutagenesis , 2012 .

[35]  M. Lehmann,et al.  Engineering proteins for thermostability: the use of sequence alignments versus rational design and directed evolution. , 2001, Current opinion in biotechnology.

[36]  Keiko Watanabe,et al.  Designing thermostable proteins: ancestral mutants of 3-isopropylmalate dehydrogenase designed by using a phylogenetic tree. , 2006, Journal of molecular biology.

[37]  Manfred T Reetz,et al.  Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes , 2007, Nature Protocols.

[38]  Sebastian Doniach,et al.  Protein flexibility in solution and in crystals , 1999 .

[39]  Janna K Blum,et al.  Improved thermostability of AEH by combining B-FIT analysis and structure-guided consensus method. , 2012, Journal of biotechnology.

[40]  Lennart Nilsson,et al.  Dynamic arrangement of ion pairs and individual contributions to the thermal stability of the cofactor-binding domain of glutamate dehydrogenase from Thermotoga maritima. , 2007, Biochemistry.

[41]  Raghavan Varadarajan,et al.  MODIP revisited: re-evaluation and refinement of an automated procedure for modeling of disulfide bonds in proteins. , 2003, Protein engineering.

[42]  Pierrick Craveur,et al.  PredyFlexy: flexibility and local structure prediction from sequence , 2012, Nucleic Acids Res..

[43]  Alan A. Dombkowski,et al.  Disulfide by DesignTM: a computational method for the rational design of disulfide bonds in proteins , 2003, Bioinform..

[44]  George I Makhatadze,et al.  Effects of charge-to-alanine substitutions on the stability of ribosomal protein L30e from Thermococcus celer. , 2005, Biochemistry.

[45]  Jeremy C. Smith,et al.  Fluctuations and correlations in crystalline protein dynamics: a simulation analysis of staphylococcal nuclease. , 2005, Biophysical journal.

[46]  Avner Schlessinger,et al.  PROFbval: predict flexible and rigid residues in proteins , 2006, Bioinform..

[47]  Yong Hwan Kim,et al.  Development of thermostable lipase B from Candida antarctica (CalB) through in silico design employing B-factor and RosettaDesign , 2010 .

[48]  H. Nakano,et al.  Improving thermostability of phosphatidylinositol-synthesizing Streptomyces phospholipase D. , 2012, Protein engineering, design & selection : PEDS.

[49]  Igor B Kuznetsov,et al.  Simplified computational methods for the analysis of protein flexibility. , 2009, Current protein & peptide science.

[50]  Shuangyan Han,et al.  High-throughput screening of B factor saturation mutated Rhizomucor miehei lipase thermostability based on synthetic reaction. , 2012, Enzyme and microbial technology.

[51]  M. Koksharov,et al.  Thermostabilization of firefly luciferase by in vivo directed evolution. , 2011, Protein engineering, design & selection : PEDS.

[52]  H Frauenfelder,et al.  Variations on a theme by Debye and Waller: From simple crystals to proteins , 1997, Proteins.

[53]  O. Galzitskaya,et al.  Stability and rigidity/flexibility-two sides of the same coin? , 2013, Biochimica et biophysica acta.

[54]  Modesto Orozco,et al.  FlexServ: an integrated tool for the analysis of protein flexibility , 2009, Bioinform..

[55]  Manfred T. Reetz,et al.  Enhancing the Thermal Robustness of an Enzyme by Directed Evolution: Least Favorable Starting Points and Inferior Mutants Can Map Superior Evolutionary Pathways , 2011, Chembiochem : a European journal of chemical biology.

[56]  E. Bayer,et al.  Improved Thermostability of Clostridium thermocellum Endoglucanase Cel8A by Using Consensus-Guided Mutagenesis , 2012, Applied and Environmental Microbiology.

[57]  Berk Hess,et al.  GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .

[58]  Modesto Orozco,et al.  A consensus view of protein dynamics , 2007, Proceedings of the National Academy of Sciences.

[59]  Y. Yoo,et al.  The development of a thermostable CiP (Coprinus cinereus peroxidase) through in silico design , 2010, Biotechnology progress.

[60]  K. Teilum,et al.  Functional aspects of protein flexibility , 2009, Cellular and Molecular Life Sciences.

[61]  M. Thorpe,et al.  Protein flexibility using constraints from molecular dynamics simulations , 2005, Physical biology.

[62]  Bosco K. Ho,et al.  The Ramachandran plots of glycine and pre-proline , 2005, BMC Structural Biology.

[63]  Kaare Teilum,et al.  Protein stability, flexibility and function. , 2011, Biochimica et biophysica acta.

[64]  M. Reetz Controlling the selectivity and stability of proteins by new strategies in directed evolution: the case of organocatalytic enzymes. , 2007, Ernst Schering Foundation symposium proceedings.

[65]  Zheng Yuan,et al.  Prediction of protein B‐factor profiles , 2005, Proteins.

[66]  M. Thorpe,et al.  Constrained geometric simulation of diffusive motion in proteins , 2005, Physical biology.

[67]  Jie Chen,et al.  Improving stability of nitrile hydratase by bridging the salt-bridges in specific thermal-sensitive regions. , 2013, Journal of biotechnology.

[68]  V. Eijsink,et al.  Rational engineering of enzyme stability. , 2004, Journal of biotechnology.

[69]  D. Jacobs,et al.  Protein flexibility predictions using graph theory , 2001, Proteins.

[70]  John L. Klepeis,et al.  Millisecond-scale molecular dynamics simulations on Anton , 2009, Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis.

[71]  Tim J Kamerzell,et al.  The complex inter-relationships between protein flexibility and stability. , 2008, Journal of pharmaceutical sciences.

[72]  Kyle E. Watters,et al.  Comparative void-volume analysis of psychrophilic and mesophilic enzymes: Structural bioinformatics of psychrophilic enzymes reveals sources of core flexibility , 2011, BMC Structural Biology.

[73]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[74]  Kerstin Steiner,et al.  Recent advances in rational approaches for enzyme engineering , 2012, Computational and structural biotechnology journal.

[75]  T. Tan,et al.  Improving the thermostability of lipase Lip2 from Yarrowia lipolytica. , 2013, Journal of biotechnology.

[76]  Shina Caroline Lynn Kamerlin,et al.  Computational Protein Engineering: Bridging the Gap between Rational Design and Laboratory Evolution , 2012, International journal of molecular sciences.

[77]  H. Gohlke,et al.  Exploiting the Link between Protein Rigidity and Thermostability for Data‐Driven Protein Engineering , 2008 .

[78]  Yu Cao,et al.  A multi-factors rational design strategy for enhancing the thermostability of Escherichia coli AppA phytase , 2013, Journal of Industrial Microbiology & Biotechnology.

[79]  R. Dror,et al.  Long-timescale molecular dynamics simulations of protein structure and function. , 2009, Current opinion in structural biology.

[80]  Rajni Verma,et al.  Computer-Aided Protein Directed Evolution: a Review of Web Servers, Databases and other Computational Tools for Protein Engineering , 2012, Computational and structural biotechnology journal.

[81]  Ping Wang,et al.  Enhanced thermostability of methyl parathion hydrolase from Ochrobactrum sp. M231 by rational engineering of a glycine to proline mutation , 2010, The FEBS journal.

[82]  S. Hosseinkhani,et al.  Design and introduction of a disulfide bridge in firefly luciferase: increase of thermostability and decrease of pH sensitivity , 2010, Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology.

[83]  Bert L. de Groot,et al.  tCONCOORD‐GUI: Visually supported conformational sampling of bioactive molecules , 2009, J. Comput. Chem..

[84]  J A McCammon,et al.  Molecular dynamics simulations of the hyperthermophilic protein sac7d from Sulfolobus acidocaldarius: contribution of salt bridges to thermostability. , 1999, Journal of molecular biology.

[85]  Wim Soetaert,et al.  Increasing the thermostability of sucrose phosphorylase by a combination of sequence- and structure-based mutagenesis. , 2011, Protein engineering, design & selection : PEDS.

[86]  Huimin Yu,et al.  Insights into thermal stability of thermophilic nitrile hydratases by molecular dynamics simulation. , 2008, Journal of molecular graphics & modelling.

[87]  B. Pletschke,et al.  Stabilization of Escherichia coli uridine phosphorylase by evolution and immobilization , 2011 .

[88]  Holger Gohlke,et al.  Thermostabilizing mutations preferentially occur at structural weak spots with a high mutation ratio. , 2012, Journal of biotechnology.

[89]  Ron O. Dror,et al.  Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations , 2010, The Journal of general physiology.

[90]  Donald J. Jacobs,et al.  Structural rigidity in the capsid assembly of cowpea chlorotic mottle virus , 2004 .