How sequence determines elasticity of disordered proteins.

How nature tunes sequences of disordered protein to yield the desired coiling properties is not yet well understood. To shed light on the relationship between protein sequence and elasticity, we here investigate four different natural disordered proteins with elastomeric function, namely: FG repeats in the nucleoporins; resilin in the wing tendon of dragonfly; PPAK in the muscle protein titin; and spider silk. We obtain force-extension curves for these proteins from extensive explicit solvent molecular dynamics simulations, which we compare to purely entropic coiling by modeling the four proteins as entropic chains. Although proline and glycine content are in general indicators for the entropic elasticity as expected, divergence from simple additivity is observed. Namely, coiling propensities correlate with polyproline II content more strongly than with proline content, and given a preponderance of glycines for sufficient backbone flexibility, nonlocal interactions such as electrostatic forces can result in strongly enhanced coiling, which results for the case of resilin in a distinct hump in the force-extension curve. Our results, which are directly testable by force spectroscopy experiments, shed light on how evolution has designed unfolded elastomeric proteins for different functions.

[1]  O. Medalia,et al.  Structural analysis of the nuclear pore complex by integrated approaches. , 2009, Current opinion in structural biology.

[2]  Brigida Bochicchio,et al.  Polyproline II structure in proteins: identification by chiroptical spectroscopies, stability, and functions. , 2002, Chirality.

[3]  Sarah Rauscher,et al.  Proline and glycine control protein self-organization into elastomeric or amyloid fibrils. , 2006, Structure.

[4]  Fritz Vollrath,et al.  Structural disorder in silk proteins reveals the emergence of elastomericity. , 2008, Biomacromolecules.

[5]  T. Vuocolo,et al.  Synthesis and properties of crosslinked recombinant pro-resilin , 2005, Nature.

[6]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[7]  W. L. Jorgensen,et al.  The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.

[8]  S. O. Andersen,et al.  Tentative identification of a resilin gene in Drosophila melanogaster. , 2001, Insect biochemistry and molecular biology.

[9]  Misook Kim,et al.  A synthetic resilin is largely unstructured. , 2008, Biophysical journal.

[10]  B. Berne,et al.  Dissecting entropic coiling and poor solvent effects in protein collapse. , 2008, Journal of the American Chemical Society.

[11]  A. Sarkar,et al.  The Elasticity of Individual Titin PEVK Exons Measured by Single Molecule Atomic Force Microscopy* , 2005, Journal of Biological Chemistry.

[12]  B. Berne,et al.  Signatures of hydrophobic collapse in extended proteins captured with force spectroscopy , 2007, Proceedings of the National Academy of Sciences.

[13]  Chris Oostenbrink,et al.  A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6 , 2004, J. Comput. Chem..

[14]  H. C. Andersen,et al.  Role of Repulsive Forces in Determining the Equilibrium Structure of Simple Liquids , 1971 .

[15]  Ralf P. Richter,et al.  FG-Rich Repeats of Nuclear Pore Proteins Form a Three-Dimensional Meshwork with Hydrogel-Like Properties , 2006, Science.

[16]  J. Marsh,et al.  Sequence determinants of compaction in intrinsically disordered proteins. , 2010, Biophysical journal.

[17]  U. Aebi,et al.  Flexible phenylalanine-glycine nucleoporins as entropic barriers to nucleocytoplasmic transport. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Brigida Bochicchio,et al.  Investigating by CD the molecular mechanism of elasticity of elastomeric proteins. , 2008, Chirality.

[19]  T. Creamer,et al.  Polyproline II helical structure in protein unfolded states: Lysine peptides revisited , 2002, Protein science : a publication of the Protein Society.

[20]  R. Swendsen,et al.  THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method , 1992 .

[21]  J. Gosline,et al.  The effect of proline on the network structure of major ampullate silks as inferred from their mechanical and optical properties , 2008, Journal of Experimental Biology.

[22]  Wilfred F van Gunsteren,et al.  Force field evaluation for biomolecular simulation: free enthalpies of solvation of polar and apolar compounds in various solvents. , 2006, Chemphyschem : a European journal of chemical physics and physical chemistry.

[23]  Andreas Möglich,et al.  Effect of proline and glycine residues on dynamics and barriers of loop formation in polypeptide chains. , 2005, Journal of the American Chemical Society.

[24]  Christopher J. Oldfield,et al.  The unfoldomics decade: an update on intrinsically disordered proteins , 2008, BMC Genomics.

[25]  K. Schulten,et al.  Transport-related structures and processes of the nuclear pore complex studied through molecular dynamics. , 2009, Structure.

[26]  E. Siggia,et al.  Entropic elasticity of lambda-phage DNA. , 1994, Science.

[27]  H. Hansma,et al.  Segmented nanofibers of spider dragline silk: Atomic force microscopy and single-molecule force spectroscopy , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[28]  Justin L. MacCallum,et al.  Calculation of the water–cyclohexane transfer free energies of neutral amino acid side‐chain analogs using the OPLS all‐atom force field , 2003, J. Comput. Chem..

[29]  A. Oberhauser,et al.  Multiple conformations of PEVK proteins detected by single-molecule techniques , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[30]  W. V. Gunsteren,et al.  Validation of the 53A6 GROMOS force field , 2005, European Biophysics Journal.

[31]  M. Greaser,et al.  Identification of new repeating motifs in titin , 2001, Proteins.

[32]  J. Gosline,et al.  The role of proline in the elastic mechanism of hydrated spider silks , 2008, Journal of Experimental Biology.

[33]  V. Pande,et al.  Unusual compactness of a polyproline type II structure. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[34]  D. Porter,et al.  Proline and processing of spider silks. , 2008, Biomacromolecules.

[35]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[36]  J. Gosline,et al.  The mechanical design of spider silks: from fibroin sequence to mechanical function. , 1999, The Journal of experimental biology.