1469-896X/asset/olbannerleft.gif?v=1&s=d218899ae53b2862ab119790ed504b8d72122fb3)
1469-896X/asset/olbannerright.gif?v=1&s=59470eb9a1d9b7b13b1be75e9445e6c46ee2214f)
Article
You have full text access to this OnlineOpen article
Characterizing and controlling the inherent dynamics of cyclophilin-A
Article first published online: 12 FEB 2009
DOI: 10.1002/pro.89
Copyright © 2009 The Protein Society
Additional Information
How to Cite
Schlegel, J., Armstrong, G. S., Redzic, J. S., Zhang, F. and Eisenmesser, E. Z. (2009), Characterizing and controlling the inherent dynamics of cyclophilin-A. Protein Science, 18: 811–824. doi: 10.1002/pro.89
Publication History
- Issue published online: 25 MAR 2009
- Article first published online: 12 FEB 2009
- Accepted manuscript online: 12 FEB 2009 12:00AM EST
- Manuscript Accepted: 17 JAN 2009
- Manuscript Revised: 15 JAN 2009
- Manuscript Received: 23 SEP 2008
Funded by
- NSF. Grant Number: MCB-0820567
References
- 1, , ( 2003) Disulfide bond isomerization in basic pancreatic trypsin inhibitor: multisite chemical exchange quantified by CPMG relaxation dispersion and chemical shift modeling. J Am Chem Soc 125: 14324–14335.
- 2, , , ( 2000) Molecular motions and protein folding: characterization of the backbone dynamics and folding equilibrium of alpha D-2 using C-13 NMR spin relaxation. J Am Chem Soc 122: 11610–11619.
- 3, , , , ( 2001) Slow dynamics in folded and unfolded states of an SH3 domain. J Am Chem Soc 123: 11341– 11352.
- 4, , , ( 2003) NMR detection of multiple transitions to low-populated states in azurin. Protein Sci 12: 56–65.Direct Link:
- 5, , , , ( 2006b) Abp1p and fyn SH3 domains fold through similar low-populated intermediate states. Biochemistry 45: 10175–10183.
- 6, ( 2005) Off-resonance rotating-frame amide proton spin relaxation experiments measuring microsecond chemical exchange in proteins. J Biomol NMR 32: 163–173.
- 7, , , , , , , , , ( 1994) Synthesis, structure and mechanism in immunophilin research. Synlett 381-392.
- 8, , , , , , , , ( 2005) Intrinsic dynamics of an enzyme underlies catalysis. Nature 438: 117–121.
- 9, , , ( 2006b) The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313: 1638–1642.
- 10, , ( 2006a) An NMR perspective on enzyme dynamics. Chem Rev 106: 3055– 3079.
- 11, ( 2002) Evidence for flexibility in the function of ribonuclease A. Biochemistry 41: 6072–6081.
- 12, , , ( 2005) Conservation of mu s-ms enzyme motions in the apo- and substrate-mimicked state. J Am Chem Soc 127: 9167–9176.
- 13, ( 2006) Enzyme dynamics along the reaction coordinate: critical role of a conserved residue. Biochemistry 45: 2636–2647.
- 14, , , ( 2002) Enzyme dynamics during catalysis. Science 295: 1520– 1523.
- 15( 2003) Native state proline isomerization: an intrinsic molecular switch. Biochemistry 42: 9515–9524.
- 16, , , , , ( 2005) Roles of cyclophilins in cancers and other organ systems. World J Surg 29: 276–280.
- 17, , ( 2006) Dealing with the family: CD147 interactions with cyclophilins. Immunology 117: 301–309.Direct Link:
- 18, , , , , ( 2006) Structure-based design, synthesis, and biological evaluation of novel inhibitors of human cyclophilin A. J Med Chem 49: 900–910.
- 19, , , , , , , , , , ( 2007) Structure-based identification of small molecule compounds targeting cell cyclophilin A with anti-HIV-1 activity. Eur J Pharmacol 565: 54–59.
- 20, ( 1972) A General two-site solution for the chemical exchange produced dependence of T2 upon the Carr–Purcell pulse seperation. J Magn Reson 6: 89–105.
- 21( 1978) Chemical exchange and NMR T2 Relaxation—multisite case. J Magn Reson 30: 111–128.
- 22, , ( 1994) Direct measurements of the dissociation-rate constant for inhibitor-enzyme complexes via the T-1-Rho and T-2 (Cpmg) methods. J Magn Reson Ser B 104: 266–275.
- 23, , , , ( 2000) The static magnetic field dependence of chemical exchange linebroadening defines the NMR chemical shift time scale. J Am Chem Soc 122: 2867–2877.
- 24, ( 1996a) Crystal structure implies that cyclophilin predominantly catalyzes the trans to cis isomerization. Biochemistry 35: 7356–7361.
- 25, ( 1996b) Mechanistic implication of crystal structures of the cyclophilin-dipeptide complexes. Biochemistry 35: 7362–7368.
- 26, , , ( 2006) Faithful estimation of dynamics parameters from CPMG relaxation dispersion measurements. J Magn Reson 180: 93–104.
- 27, , ( 2002) Reconstructing NMR spectra of “invisible” excited protein states using HSQC and HMQC experiments. J Am Chem Soc 124: 12352–12360.
- 28, , , , , ( 1999) Antigen recognition by conformational selection. FEBS Lett 450: 149–153.
- 29, , , , ( 1995) Kinetic analysis of cyclophilin-catalyzed prolyl cis/trans isomerization by dynamic NMR spectroscopy. Biochemistry 34: 13594–13602.
- 30, , ( 1965). On the nature of allosteric transitions: a plausible model. J Mol Biol 12: 88–118.
- 31, , , , , , , , ( 2006a) Probing the transition state ensemble of a protein folding reaction by pressure-dependent NMR relaxation dispersion. J Am Chem Soc 128: 5262–5269.
- 32, , , , , , ( 1996) Crystal structure of human cyclophilin A bound to the amino-terminal domain of HIV-1 capsid. Cell 87: 1285–1294.
- 33, ( 2004) Crystal structures of cyclophilin and its partners. Front Biosci 9: 2285–2296.
- 34, , , , ( 2003) Structural insights into the catalytic mechanism of cyclophilin A. Nat Struct Biol 10: 475–481.
- 35, , , , , , ( 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.Direct Link:
- 36, , , , , ( 2005) Cyclophilin a binds to linear peptide motifs containing a consensus that is present in many human proteins. J Biol Chem 280: 23668–23674.
- 37, , ( 1999b) A TROSY CPMG sequence for characterizing chemical exchange in large proteins. J Biomol NMR 15: 151–155.
- 38, , ( 1999a) A relaxation-compensated Carr-Purcell-Meiboom-Gill sequence for characterizing chemical exchange by NMR spectroscopy. J Am Chem Soc 121: 2331–2332.
- 39, ( 2003) Solution NMR methods for quantitative identification of chemical exchange in N-15-labeled proteins. Magn Reson Chem 41: 866– 876.Direct Link:
- 40, , , , ( 2001) Measurement of slow (mu s-ms) time scale dynamics in protein side chains by N-15 relaxation dispersion NMR spectroscopy: Application to Asn and Gln residues in a cavity mutant of T4 lysozyme. J Am Chem Soc 123: 967–975.
- 41, , , , , ( 1995) NMRPipe - a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6: 277–293.
- 42, ( 1963) Nuclear magnetic resonance study of the protolysis of trimethylammonium ion in acqueous solution-order of the reaction with respect to solvent. J Chem Phys 39: 366–370.
- 43, , , , , , , , , ( 2005) The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins-Structure Function and Bioinformatics 59: 687–696.Direct Link: