All Title Author
Keywords Abstract

Mechanism of Action of Cyclophilin A Explored by Metadynamics Simulations

DOI: 10.1371/journal.pcbi.1000309

Full-Text   Cite this paper   Add to My Lib


Trans/cis prolyl isomerisation is involved in several biological processes, including the development of numerous diseases. In the HIV-1 capsid protein (CA), such a process takes place in the uncoating and recruitment of the virion and is catalyzed by cyclophilin A (CypA). Here, we use metadynamics simulations to investigate the isomerization of CA's model substrate HAGPIA in water and in its target protein CypA. Our results allow us to propose a novel mechanistic hypothesis, which is finally consistent with all of the available molecular biology data.


[1]  Fischer S, Dunbrack RL, Karplus M Jr (1994) Cis-trans imide isomerization of the proline dipeptide. J Am Chem Soc 116: 11931–11937.
[2]  Hodel A, Rice LM, Simonson T, Fox RO, Brunger AT (1995) Proline cis-trans isomerization in Staphylococcal nuclease: multi-substrate free energy perturbation calculations. Protein Sci 4: 636–654.
[3]  Harrar Y, Bellini C, Faure JD (2001) FKBPs: at the crossroads of folding and transduction. Trends Plant Sci 6: 426–431.
[4]  Wang P, Heitman J (2005) The cyclophilins. Genome Biol 6: 226.
[5]  Lummis SCR, Beene DL, Lee LW, Lester HA, Broadhurst RW, et al. (2005) Cis-trans isomerization at a proline opens the pore of a neurotransmitter-gated ion channel. Nature 438: 243–252.
[6]  Wulf G, Finn G, Suizu F, Lu KP (2005) Phosphorylation-specific prolyl isomerization: is there an underlying theme? Nat Cell Biol 7: 435–441.
[7]  Scarlata S, Carter C (2003) Role of HIV-1 Gag domains in virial assembly. Biochim Biophys Acta 1614: 62–72.
[8]  G?thel SF, Marahiel MA (1999) Peptidyl-prolyl cis-trans isomerases, a superfamily of ubiquitous folding catalysts. Cell Mol Life Sci 55: 423–436.
[9]  Pastorino L, Sun A, Lu PJ, Zhou XZ, Balastik M, et al. (2006) The prolyl isomerase Pin1 regulates amyloid precursor protein processing and amyloid-β production. Nature 440: 528–534.
[10]  Finkelstein AV, Ptitsyn OB (2002) Lecture 2. Protein Physics: A Course of Lectures. Amsterdam: Academic Press. pp. 15–22.
[11]  van Holde KE, Jonson WC, Ho PS (1998) Biological macromolecules. Principles of Physical Biochemistry. Upper Saddle River, NJ: Prentice Hall. pp. 2–67.
[12]  Bosco DA, Eisenmesser EZ, Pochapsky S, Sundquist WI, Kern D (2002) Catalysis of cis/trans isomerization in native HIV-1 capsid by human cyclophilin A. Proc Natl Acad Sci U S A 99: 5247–5252.
[13]  Howard BR, Vajdos FF, Li S, Sundquist WI, Hill CP (2003) Structural insights into the catalytic mechanism of cyclophilin A. Nat Struct Biol 10: 475–481.
[14]  Li G, Cui Q (2003) What is so special about Arg 55 in the catalysis of cyclophilin A? insights from hybrid QM/MM simulations. J Am Chem Soc 125: 15028–15038.
[15]  Agarwal PK, Geist A, Gorin A (2004) Protein dynamics and enzymatic catalysis: investigating the peptidyl-prolyl cis-trans isomerization activity of cyclophilin A. Biochemistry 43: 10605–10618.
[16]  Kofron JL, Kuzmic P, Kishore V, Colón-Bonilla E, Rich DH (1991) Determination of kinetic constants for peptidyl prolyl cis-trans isomerases by an improved spectrophotometric assay. Biochemistry 30: 6127–6134.
[17]  Kern D, Kern G, Scherer G, Fischer G, Drakenberg T (1995) Kinetic analysis of cyclophilin-catalyzed prolyl cis/trans isomerization by dynamic NMR spectroscopy. Biochemistry 34: 13594–13602.
[18]  Hur S, Bruice TC (2002) The mechanism of cis-trans isomerization of prolyl peptides by cyclophilin. J Am Chem Soc 124: 7303–7313.
[19]  Fangh?nel J, Fischer G (2004) Insights into the catalytic mechanism of peptidyl prolyl cis/trans isomerases. Front Biosci 9: 3453–3478.
[20]  Zydowsky LD, Etzkorn FA, Chang HY, Ferguson SB, Stolz LA, et al. (1992) Active site mutants of human cyclophilin A separate peptidyl-prolyl isomerase activity from cyclosporin A binding and calcineurin inhibition. Protein Sci 1: 1092–1099.
[21]  Eisenmesser EZ, Bosco DA, Akke M, Kern D (2002) Enzyme dynamics during catalysis. Science 295: 1520–1523.
[22]  Agarwal PK (2004) Cis/trans isomerization in HIV-1 capsid protein catalyzed by cyclophilin A: insights from computational and theoretical studies. Proteins 56: 449–463.
[23]  Agarwal PK (2005) Role of protein dynamics in reaction rate enhancement by enzymes. J Am Chem Soc 127: 15248–15256.
[24]  Zhao Y, Ke H (1996) Crystal structure implies that cyclophilin predominantly catalyzes the trans to cis isomerization. Biochemistry 35: 7356–7361.
[25]  Fischer S, Dunbrack RL, Karplus M Jr (1994) Cis-trans imide isomerization of the proline dipeptide. J Am Chem Soc 116: 11931–11937.
[26]  Laio A, Parrinello M (2002) Escaping free-energy minima. Proc Natl Acad Sci U S A 99: 12562–12566.
[27]  Piana S, Laio A (2007) A bias-exchange approach to protein folding. J Phys Chem B 111: 4553–4559.
[28]  Fiorin G, Pastore A, Carloni P, Parrinello M (2006) Using metadynamics to understand the mechanism of calmodulin/target recognition at atomic detail. Biophys J 9: 2768–2777.
[29]  Wang JM, Cieplak P, Kollman PA (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 21: 1049–1074.
[30]  Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, et al. (2006) Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 65: 712–725.
[31]  Bashford D, Karplus M (1990) pKa's of ionizable groups in proteins - Atomic detail from a continuum electrostatic model. Biochemistry 29: 10219–10225.
[32]  Gordon JC, Myers JB, Folta T, Shoja V, Heath LS, et al. (2005) H++: a server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Res 33: W368–W371.
[33]  Kelly BN, Kyere S, Kinde I, Tang C, Howard BR, et al. (2007) Structure of the antiviral assembly inhibitor CAP-1 complex with the HIV-1 CA protein. J Mol Biol 373: 355–366.
[34]  Mahoney MW, Jorgensen WL (2000) A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J Chem Phys 112: 8910–8922.
[35]  Feller SE, Zhang YH, Pastor RW, Brooks BR (1995) Constant-pressure molecular-dynamics simulation: the Langevin piston method. J Chem Phys 103: 4613–4621.
[36]  Paterlini MG, Ferguson DM (1998) Constant temperature simulations using the Langevin equation with velocity Verlet integration. Chem Phys 236: 243–252.
[37]  Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, et al. (1995) A smooth particle mesh Ewald method. J Chem Phys 103: 8577–8593.
[38]  Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, et al. (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26: 1781–1802.
[39]  Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) Equation of state calculations by fast computing machines. J Chem Phys 21: 1087–1092.
[40]  Daura X, Gademann K, Jaun B, Seebach D, van Gunsteren WF, et al. (1999) Peptide folding: when simulation meets experiment. Angew Chem Int Ed Engl 38: 236–240.
[41]  Marinelli F, Pietrucci F, Piana S, Laio A (2008) A kinetic model of Trp-cage folding from multiple biased molecular dynamics simulations. Submitted.
[42]  Evans DJ, Holian BL (1985) The Nose-Hoover thermostat. J Chem Phys 83: 4069–4074.
[43]  Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: a linear constraint solver for molecular simulations. J Comput Chem 18: 1463–1472.
[44]  Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7: 306–317.
[45]  Berendsen HJC, Vanderspoel D, Vandrunen R (1995) GROMACS: a message-passing parallel molecular dynamics implementation. Comput Phys Commun 91: 43–56.
[46]  Piana S, Laio A, Marinelli F, Van Troys M, Bourry D, et al. (2008) Predicting the effect of a point mutation on a protein fold: the villin and advillin headpieces and their Pro62Ala mutants. J Mol Biol 375: 460–470.
[47]  Ho BK, Coutsias EA, Seok C, Dill KA (2005) The flexibility in the proline ring couples to the protein backbone. Protein Sci 14: 1011–1018.
[48]  Garcia AE (1992) Large-amplitude nonlinear motions in proteins. Phys Rev Lett 68: 2696–2699.
[49]  Amadei A, Linssen AB, Berendsen HJ (1993) Essential dynamics of proteins. Proteins 17: 412–425.
[50]  Lee CT, Yang WT, Parr RG (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 37: 785–789.
[51]  Becke AD (1993) Density-functional thermochemistry III. The role of exact exchange. J Chem Phys 98: 5648–5652.
[52]  Vosko SH, Wilk L, Nusair M (1980) Accurate spin-dependent electron liquid correlation energies for local spin density calculations: a critical analysis. Can J Phys 58: 1200–1211.
[53]  Stephens PJ, Devlin FJ, Chabalowski CF, Frisch MJ (1994) Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields. J Phys Chem 98: 11623–11627.
[54]  Frisch MJ, et al. (1998) GImage 98. Pittsburgh, PA: Gaussian Inc.
[55]  Stein RL (1993) Mechanism of enzymatic and nonenzymatic prolyl cis-trans isomerization. Adv Protein Chem 44: 1–24.
[56]  Eberhardt ES, Loh SN, Hinck AP, Raines RT (1992) Solvent effects on the energetics of prolyl peptide bond isomerization. J Am Chem Soc 114: 5437–5439.
[57]  Trzesniak D, van Gunsteren WF (2006) Catalytic mechanism of cyclophilin as observed in molecular dynamics simulations: pathway prediction and reconciliation of X-ray crystallographic and NMR solution data. Protein Sci 15: 2544–2551.
[58]  Mark P, Nilsson L (2007) A molecular dynamics study of cyclophilin A free and in complex with the Ala-Pro dipeptide. Eur Biophys J 36: 213–224.
[59]  McDowell SE, ?pa?ková N, ?poner J, Walter NG (2007) Molecular dynamics simulations of RNA: an in silico single molecule approach. Biopolymers 85: 169–184.
[60]  Jhon JS, Kang YK (1999) Imide Cis-Trans isomerization of N-Acetyl-N′-methyl proline amide and solvent effects. J Phys Chem A 103: 5436–5439.


comments powered by Disqus