Single molecule force spectroscopy reveals engineered metal chelation is a general approach to enhance mechanical stability of proteins

Significant mechanical stability is an essential feature shared by many elastomeric proteins, which function as molecular springs in a wide variety of biological machinery and biomaterials of superb mechanical properties. Despite the progress in understanding molecular determinants of mechanical stability, it remains challenging to rationally enhance the mechanical stability of proteins. Using single molecule force spectroscopy and protein engineering techniques, we demonstrate that engineered bi-histidine metal chelation can enhance the mechanical stability of proteins significantly and reversibly. Based on simple thermodynamic cycle analysis, we engineered a bi-histidine metal chelation site into various locations of the small protein, GB1, to achieve preferential stabilization of the native state over the mechanical unfolding transition state of GB1 through the binding of metal ions. Our results demonstrate that the metal chelation can enhance the mechanical stability of GB1 by as much as 100 pN. Since bi-histidine metal chelation sites can be easily implemented, engineered metal chelation provides a general methodology to enhance the mechanical stability of a wide variety of proteins. This general approach in protein mechanics will enable the rational tuning of the mechanical stability of proteins. It will not only open new avenues toward engineering proteins of tailored nanomechanical properties, but also provide new approaches to systematically map the mechanical unfolding pathway of proteins.

[1]  Hongbin Li,et al.  Polyprotein of GB1 is an ideal artificial elastomeric protein. , 2007, Nature materials.

[2]  Stephen L. Mayo,et al.  Design, structure and stability of a hyperthermophilic protein variant , 1998, Nature Structural Biology.

[3]  Wolfgang A. Linke,et al.  Reverse engineering of the giant muscle protein titin , 2002, Nature.

[4]  Hongbin Li,et al.  Protein-protein interaction regulates proteins' mechanical stability. , 2008, Journal of molecular biology.

[5]  V. Eijsink,et al.  Selection of mutations for increased protein stability. , 2002, Current opinion in biotechnology.

[6]  H Li,et al.  Atomic force microscopy reveals the mechanical design of a modular protein. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[7]  F. Arnold,et al.  Engineered metal-binding proteins: purification to protein folding. , 1991, Science.

[8]  J. Clarke,et al.  Mechanical and chemical unfolding of a single protein: a comparison. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Andres F. Oberhauser,et al.  The molecular elasticity of the extracellular matrix protein tenascin , 1998, Nature.

[10]  Yi Lu,et al.  Engineering novel metalloproteins: design of metal-binding sites into native protein scaffolds. , 2001, Chemical reviews.

[11]  Julio M Fernandez,et al.  Ligand binding modulates the mechanical stability of dihydrofolate reductase. , 2005, Biophysical journal.

[12]  D. Makarov,et al.  Ubiquitin-like Protein Domains Show High Resistance to Mechanical Unfolding Similar to That of the I27 Domain in Titin: Evidence from Simulations , 2004 .

[13]  J. M. Sanchez-Ruiz Ligand effects on protein thermodynamic stability. , 2007, Biophysical chemistry.

[14]  Hongbin Li,et al.  Nonmechanical protein can have significant mechanical stability. , 2006, Angewandte Chemie.

[15]  Some Like It Hot: The Molecular Determinants of Protein Thermostability , 2002, Chembiochem : a European journal of chemical biology.

[16]  Hendrik Dietz,et al.  Anisotropic deformation response of single protein molecules , 2006, Proceedings of the National Academy of Sciences.

[17]  E. Evans,et al.  Dynamic strength of molecular adhesion bonds. , 1997, Biophysical journal.

[18]  L Regan,et al.  Protein design: novel metal-binding sites. , 1995, Trends in biochemical sciences.

[19]  Hongbin Li Engineering proteins with tailored nanomechanical properties: a single molecule approach. , 2007, Organic and biomolecular chemistry.

[20]  A. Gronenborn,et al.  A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G. , 1993, Science.

[21]  Siegfried Labeit,et al.  Titins: Giant Proteins in Charge of Muscle Ultrastructure and Elasticity , 1995, Science.

[22]  J. Scullion,et al.  To charge or not to charge? , 2009, Nursing standard (Royal College of Nursing (Great Britain) : 1987).

[23]  Yi Lu,et al.  Engineering Novel Metalloproteins: Design of Metal‐Binding Sites into Native Protein Scaffolds , 2001 .

[24]  D. Brockwell Force Denaturation of Proteins - an Unfolding Story , 2007 .

[25]  K. Schulten,et al.  Single-Molecule Experiments in Vitro and in Silico , 2007, Science.

[26]  D. Makarov,et al.  Mechanical unfolding of segment-swapped protein G dimer: results from replica exchange molecular dynamics simulations. , 2006, The journal of physical chemistry. B.

[27]  Hui Lu,et al.  Single-molecule force spectroscopy reveals a mechanically stable protein fold and the rational tuning of its mechanical stability , 2007, Proceedings of the National Academy of Sciences.

[28]  A. Oberhauser,et al.  Mechanical design of proteins studied by single-molecule force spectroscopy and protein engineering. , 2000, Progress in biophysics and molecular biology.

[29]  David Baker,et al.  Computer-based redesign of a protein folding pathway , 2001, Nature Structural Biology.

[30]  H. Clausen‐Schaumann,et al.  Mechanochemistry: the mechanical activation of covalent bonds. , 2005, Chemical reviews.

[31]  Joel P. Schneider,et al.  Templates That Induce .alpha.-Helical, .beta.-Sheet, and Loop Conformations , 1995 .

[32]  F. Arnold,et al.  Protein Stabilization by Engineered Metal Chelation , 1991, Bio/Technology.

[33]  M. Rief,et al.  Reversible unfolding of individual titin immunoglobulin domains by AFM. , 1997, Science.

[34]  T. Sosnick,et al.  Engineered metal binding sites map the heterogeneous folding landscape of a coiled coil , 2001, Nature Structural Biology.

[35]  E. Evans,et al.  Strength of a weak bond connecting flexible polymer chains. , 1999, Biophysical journal.

[36]  H. Hansma,et al.  Molecular nanosprings in spider capture-silk threads , 2003, Nature materials.

[37]  J. Clarke,et al.  Designing an extracellular matrix protein with enhanced mechanical stability , 2007, Proceedings of the National Academy of Sciences.

[38]  F. John,et al.  Stretching DNA , 2022 .

[39]  J. Arrondo,et al.  Advanced techniques in biophysics , 2006 .

[40]  Mario Viani,et al.  Molecular mechanistic origin of the toughness of natural adhesives, fibres and composites , 1999, Nature.

[41]  Robin S. Dothager,et al.  Characterizing the protein folding transition state using psi analysis. , 2006, Chemical reviews.

[42]  Udo Heinemann,et al.  Two exposed amino acid residues confer thermostability on a cold shock protein , 2000, Nature Structural Biology.

[43]  G. Makhatadze,et al.  To charge or not to charge? , 2001, Trends in biotechnology.

[44]  J. Gosline,et al.  Elastic proteins: biological roles and mechanical properties. , 2002, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[45]  Matthias Rief,et al.  Elastically Coupled Two-Level Systems as a Model for Biopolymer Extensibility , 1998 .

[46]  Hongbin Li,et al.  A functional single-molecule binding assay via force spectroscopy , 2007, Proceedings of the National Academy of Sciences.