Quality Matters: Extension of Clusters of Residues with Good Hydrophobic Contacts Stabilize (Hyper)Thermophilic Proteins

Identifying determinant(s) of protein thermostability is key for rational and data-driven protein engineering. By analyzing more than 130 pairs of mesophilic/(hyper)thermophilic proteins, we identified the quality (residue-wise energy) of hydrophobic interactions as a key factor for protein thermostability. This distinguishes our study from previous ones that investigated predominantly structural determinants. Considering this key factor, we successfully discriminated between pairs of mesophilic/(hyper)thermophilic proteins (discrimination accuracy: ∼80%) and searched for structural weak spots in E. coli dihydrofolate reductase (classification accuracy: 70%).

[1]  Y. Yoo,et al.  Hydrophobic interaction network analysis for thermostabilization of a mesophilic xylanase. , 2012, Journal of biotechnology.

[2]  G. Antranikian,et al.  Extremophiles as a source of novel enzymes for industrial application , 1999, Applied Microbiology and Biotechnology.

[3]  C. Vieille,et al.  Hyperthermophilic Enzymes: Sources, Uses, and Molecular Mechanisms for Thermostability , 2001, Microbiology and Molecular Biology Reviews.

[4]  L. Randall,et al.  Folding of maltose-binding protein. Evidence for the identity of the rate-determining step in vivo and in vitro. , 1993, The Journal of biological chemistry.

[5]  Akinori Sarai,et al.  ProTherm and ProNIT: thermodynamic databases for proteins and protein–nucleic acid interactions , 2005, Nucleic Acids Res..

[6]  D. L. Diamond,et al.  Interaction of SecB with intermediates along the folding pathway of maltose‐binding protein , 1995, Protein science : a publication of the Protein Society.

[7]  B. Honig,et al.  A hierarchical approach to all‐atom protein loop prediction , 2004, Proteins.

[8]  V. Eijsink,et al.  Directed evolution of enzyme stability. , 2005, Biomolecular engineering.

[9]  Iosif I Vaisman,et al.  Discrimination of thermophilic and mesophilic proteins , 2009, 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshop.

[10]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[11]  Hervé Minoux,et al.  An electrostatic basis for the stability of thermophilic proteins , 2004, Proteins.

[12]  G. Taylor,et al.  The crystal structure of citrate synthase from the thermophilic archaeon, Thermoplasma acidophilum. , 1994, Structure.

[13]  C. Matthews,et al.  The coordination of the isomerization of a conserved non-prolyl cis peptide bond with the rate-limiting steps in the folding of dihydrofolate reductase. , 2003, Journal of molecular biology.

[14]  Carl Frieden,et al.  Effects of point mutations in a hinge region on the stability, folding, and enzymatic activity of Escherichia coli dihydrofolate reductase. , 1991, Biochemistry.

[15]  Z. Xiang,et al.  On the role of the crystal environment in determining protein side-chain conformations. , 2002, Journal of molecular biology.

[16]  A. Bowman,et al.  Applied smoothing techniques for data analysis : the kernel approach with S-plus illustrations , 1999 .

[17]  S. L. Mayo,et al.  Automated design of the surface positions of protein helices , 1997, Protein science : a publication of the Protein Society.

[18]  Effect of single amino acid replacements on the folding and stability of dihydrofolate reductase from Escherichia coli. , 1987, Biochemistry.

[19]  Karen M Polizzi,et al.  Better library design: data‐driven protein engineering , 2007, Biotechnology journal.

[20]  B. van den Burg,et al.  Extremophiles as a source for novel enzymes. , 2003, Current opinion in microbiology.

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

[22]  M. Gittelman,et al.  Long-range electrostatic interactions can influence the folding, stability, and cooperativity of dihydrofolate reductase. , 1989, Biochemistry.

[23]  R. Nussinov,et al.  Factors enhancing protein thermostability. , 2000, Protein engineering.

[24]  J. M. Scholtz,et al.  Lessons in stability from thermophilic proteins , 2006, Protein science : a publication of the Protein Society.

[25]  T. Taylor.  Discrimination of thermophilic and mesophilic proteins , 2009, BIBM 2009.

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

[27]  E. Nadaraya.  On Non-Parametric Estimates of Density Functions and Regression Curves , 1965 .

[28]  E. Querol,et al.  Analysis of protein conformational characteristics related to thermostability. , 1996, Protein engineering.

[29]  R. Bannen,et al.  Bioinformatic method for protein thermal stabilization by structural entropy optimization , 2008, Proceedings of the National Academy of Sciences.

[30]  Munehito Arai,et al.  Testing the relationship between foldability and the early folding events of dihydrofolate reductase from Escherichia coli. , 2003, Journal of molecular biology.

[31]  A. Elcock.  The stability of salt bridges at high temperatures: implications for hyperthermophilic proteins. , 1998, Journal of molecular biology.

[32]  Garabed Antranikian,et al.  Industrial relevance of thermophilic Archaea. , 2005, Current opinion in microbiology.

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

[34]  A. Surolia,et al.  Thermodynamic effects of replacements of pro residues in helix interiors of maltose‐binding protein , 2003, Proteins.

[35]  P. Privalov,et al.  Stability of protein structure and hydrophobic interaction. , 1988, Advances in protein chemistry.

[36]  P Argos,et al.  Protein thermal stability, hydrogen bonds, and ion pairs. , 1997, Journal of molecular biology.

[37]  Chiwook Park,et al.  Mapping transient partial unfolding by protein engineering and native-state proteolysis. , 2009, Journal of molecular biology.

[38]  N. Xuong,et al.  An engineered disulfide bond in dihydrofolate reductase. , 1987, Biochemistry.

[39]  Richard S. Rosenstein,et al.  Intramolecular catalysis of a proline isomerization reaction in the folding of dihydrofolate reductase. , 1992, Biochemistry.

[40]  Michail Yu. Lobanov,et al.  Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms , 2007, Bioinform..

[41]  M Vihinen,et al.  Relationship of protein flexibility to thermostability. , 1987, Protein engineering.

[42]  Matti Leisola,et al.  Protein engineering: opportunities and challenges , 2007, Applied Microbiology and Biotechnology.

[43]  J. Schellman,et al.  Temperature, stability, and the hydrophobic interaction. , 1997, Biophysical journal.

[44]  A hydrophobic cluster forms early in the folding of dihydrofolate reductase , 1989, Proteins.

[45]  William L. Jorgensen,et al.  Journal of Chemical Information and Modeling , 2005, J. Chem. Inf. Model..

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

[47]  B. Silverman.  Density estimation for statistics and data analysis , 1986 .

[48]  N. Kannan,et al.  Aromatic clusters: a determinant of thermal stability of thermophilic proteins. , 2000, Protein engineering.

[49]  M Michael Gromiha,et al.  Hydrophobic environment is a key factor for the stability of thermophilic proteins , 2013, Proteins.

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

[51]  D. Demirjian,et al.  Enzymes from extremophiles. , 2001, Current opinion in chemical biology.

[52]  Woody Sherman,et al.  Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments , 2013, Journal of Computer-Aided Molecular Design.

[53]  Saraswathi Vishveshwara,et al.  Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks , 2010, BMC Bioinformatics.

[54]  Munehito Arai,et al.  Probing the interactions between the folding elements early in the folding of Escherichia coli dihydrofolate reductase by systematic sequence perturbation analysis. , 2005, Journal of molecular biology.

[55]  C. Schleper,et al.  Metagenome—a challenging source of enzyme discovery , 2002 .

[56]  Bertus van den Burg,et al.  Extremophiles as a source for novel enzymes. , 2003 .