Molecular Simulations of Alternate Frame Folding in Engineered Protein-Based Switches

Living organisms take advantage of proteins in order to carry out most of the biological tasks that keep them alive. Although most proteins do not drastically change shape, some behave as conformational switches: in response to an outside signal from its environment, the protein will shape-change to either an “on” or “off” position. These properties of conformational switches have motivated recent efforts towards the conversion of regular ligand binding proteins into novel switches for use as optical sensors and therapeutics. Here we seek to examine one such design that exhibits an intermolecular tug-of-war between two alternate frames of folding that can be made sensitive to calcium. The challenges of elucidating structural and mechanistic details from a partially unfolded protein have led us to consider coarse-grained simulation techniques. We plan to demonstrate that results from these simulations are in agreement with experimental data and can provide novel insight into the mechanisms of switching in this class of engineered proteins.

[1]  S. Loh,et al.  Thermodynamic analysis of an antagonistic folding-unfolding equilibrium between two protein domains. , 2007, Journal of molecular biology.

[2]  S. Takada,et al.  Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model. , 2001, Journal of molecular biology.

[3]  A. Lewit-Bentley,et al.  EF-hand calcium-binding proteins. , 2000, Current opinion in structural biology.

[4]  William A. Catterall,et al.  Structure and function of voltage-gated ion channels , 1993, Trends in Neurosciences.

[5]  T. Hunter,et al.  Protein kinases and phosphatases: The Yin and Yang of protein phosphorylation and signaling , 1995, Cell.

[6]  V. Hilser,et al.  Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins , 2007, Proceedings of the National Academy of Sciences.

[7]  C. Fullmer,et al.  Role of facilitated diffusion of calcium by calbindin in intestinal calcium absorption. , 1992, The American journal of physiology.

[8]  Brian Kuhlman,et al.  Design of protein conformational switches. , 2006, Current opinion in structural biology.

[9]  A. Fersht,et al.  Exploring the folding funnel of a polypeptide chain by biophysical studies on protein fragments. , 1999, Journal of molecular biology.

[10]  Abhishek K. Jha,et al.  Statistical coil model of the unfolded state: resolving the reconciliation problem. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[11]  Hiromi Yamakawa,et al.  Transport Properties of Polymer Chains in Dilute Solution: Hydrodynamic Interaction , 1970 .

[12]  Adrian H Elcock,et al.  An Improved, Bias-Reduced Probabilistic Functional Gene Network of Baker's Yeast, Saccharomyces cerevisiae , 2007, PloS one.

[13]  Diana M. Mitrea,et al.  Engineering an artificial zymogen by alternate frame protein folding , 2010, Proceedings of the National Academy of Sciences.

[14]  Timothy A. Whitehead,et al.  Tying up the loose ends: circular permutation decreases the proteolytic susceptibility of recombinant proteins. , 2009, Protein engineering, design & selection : PEDS.

[15]  Cecilia Clementi,et al.  Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates. , 2004, Journal of the American Chemical Society.

[16]  G. Huber,et al.  Weighted-ensemble Brownian dynamics simulations for protein association reactions. , 1996, Biophysical journal.

[17]  M. Brunori,et al.  Folding and Misfolding in a Naturally Occurring Circularly Permuted PDZ Domain* , 2008, Journal of Biological Chemistry.

[18]  K. Moffat,et al.  The refined structure of vitamin D-dependent calcium-binding protein from bovine intestine. Molecular details, ion binding, and implications for the structure of other calcium-binding proteins. , 1986, The Journal of biological chemistry.

[19]  Zhen Qian,et al.  Improving the catalytic activity of Candida antarctica lipase B by circular permutation. , 2005, Journal of the American Chemical Society.

[20]  K. Luger,et al.  Correct folding of circularly permuted variants of a beta alpha barrel enzyme in vivo. , 1989, Science.

[21]  Diana M. Mitrea,et al.  A Ca2+-sensing molecular switch based on alternate frame protein folding. , 2008, ACS chemical biology.

[22]  Bin W. Zhang,et al.  Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin , 2007, Proceedings of the National Academy of Sciences.

[23]  J. Ha,et al.  Allosteric switching by mutually exclusive folding of protein domains. , 2003, Journal of molecular biology.

[24]  Diana M. Mitrea,et al.  Modular enzyme design: regulation by mutually exclusive protein folding. , 2006, Journal of molecular biology.

[25]  A. Sali,et al.  Comparative protein structure modeling of genes and genomes. , 2000, Annual review of biophysics and biomolecular structure.

[26]  Sara Linse,et al.  Coupling of ligand binding and dimerization of helix‐loop‐helix peptides: Spectroscopic and sedimentation analyses of calbindin D9k EF‐hands , 2002, Proteins.

[27]  J. G. Torre,et al.  Hydration from hydrodynamics. General considerations and applications of bead modelling to globular proteins. , 2001 .

[28]  Kevin W Plaxco,et al.  Structure-switching biosensors: inspired by Nature. , 2010, Current opinion in structural biology.

[29]  S. Loh,et al.  On the mechanism of protein fold‐switching by a molecular sensor , 2010, Proteins.

[30]  G. Bifulco,et al.  Hydrophobic core substitutions in calbindin D9k: effects on Ca2+ binding and dissociation. , 1998, Biochemistry.

[31]  S. Prager,et al.  Variational Treatment of Hydrodynamic Interaction in Polymers , 1969 .

[32]  D. Ermak,et al.  Brownian dynamics with hydrodynamic interactions , 1978 .

[33]  Structural characterization of two alternate conformations in a calbindin D₉k-based molecular switch. , 2011, Biochemistry.

[34]  Valerie Daggett,et al.  The present view of the mechanism of protein folding , 2003, Nature Reviews Molecular Cell Biology.

[35]  L. Chong,et al.  Efficient Explicit-Solvent Molecular Dynamics Simulations of Molecular Association Kinetics: Methane/Methane, Na(+)/Cl(-), Methane/Benzene, and K(+)/18-Crown-6 Ether. , 2011, Journal of chemical theory and computation.

[36]  J. García de la Torre,et al.  Calculation of hydrodynamic properties of globular proteins from their atomic-level structure. , 2000, Biophysical journal.

[37]  S. Loh,et al.  Converting a protein into a switch for biosensing and functional regulation , 2011, Protein science : a publication of the Protein Society.

[38]  Luis Serrano,et al.  Different folding transition states may result in the same native structure , 1996, Nature Structural Biology.

[39]  C. Vogel,et al.  Duplication, divergence and formation of novel protein topologies. , 2006, BioEssays : news and reviews in molecular, cellular and developmental biology.

[40]  R. Tsien,et al.  Circular permutation and receptor insertion within green fluorescent proteins. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[41]  K. Plaxco,et al.  Engineering a signal transduction mechanism for protein-based biosensors. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[42]  Cecilia Clementi,et al.  Coarse-grained models of protein folding: toy models or predictive tools? , 2008, Current opinion in structural biology.

[43]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using MODELLER , 2007, Current protocols in protein science.

[44]  Marc Ostermeier,et al.  Engineering allosteric protein switches by domain insertion. , 2005, Protein engineering, design & selection : PEDS.

[45]  Lillian T Chong,et al.  Effect of interdomain linker length on an antagonistic folding-unfolding equilibrium between two protein domains. , 2009, Journal of molecular biology.

[46]  A. Elcock,et al.  Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins. , 2009, Journal of chemical theory and computation.

[47]  L. Pearl,et al.  Structure and mechanism of the Hsp90 molecular chaperone machinery. , 2006, Annual review of biochemistry.

[48]  L. Chong,et al.  Molecular simulations of mutually exclusive folding in a two-domain protein switch. , 2011, Biophysical journal.