Practical Applications of Time-averaged Restrained Molecular Dynamics to Ligand-receptor Systems: FK506 Bound to the Q50R,A95H,K98I Triple Mutant of FKBP-13

Overview

Journal J Biomol NMR

Publisher Springer

Specialties Molecular Biology
Nuclear Medicine

Date 2010 Dec 8

PMID 21136324

Authors

C A Lepre

D A Pearlman

O Futer

D J Livingston

J M Moore

Affiliations

Soon will be listed here.

Abstract

The ability of time-averaged restrained molecular dynamics (TARMD) to escape local low-energy conformations and explore conformational space is compared with conventional simulated-annealing methods. Practical suggestions are offered for performing TARMD calculations with ligand-receptor systems, and are illustrated for the complex of the immunosuppressant FK506 bound to Q50R,A95H,K98I triple mutant FKBP-13. The structure of (13)C-labeled FK506 bound to triple-mutant FKBP-13 was determined using a set of 87 NOE distance restraints derived from HSQC-NOESY experiments. TARMD was found to be superior to conventional simulated-annealing methods, and produced structures that were conformationally similar to FK506 bound to wild-type FKBP-12. The individual and combined effects of varying the NOE restraint force constant, using an explicit model for the protein binding pocket, and starting the calculations from different ligand conformations were explored in detail.

References

Futer O, DeCenzo M, Aldape R, Livingston D . FK506 binding protein mutational analysis. Defining the surface residue contributions to stability of the calcineurin co-complex. J Biol Chem. 1995; 270(32):18935-40. DOI: 10.1074/jbc.270.32.18935. View

Griffith J, Kim J, Kim E, Sintchak M, Thomson J, Fitzgibbon M . X-ray structure of calcineurin inhibited by the immunophilin-immunosuppressant FKBP12-FK506 complex. Cell. 1995; 82(3):507-22. DOI: 10.1016/0092-8674(95)90439-5. View

Pearlman D . How is an NMR structure best defined? An analysis of molecular dynamics distance-based approaches. J Biomol NMR. 2012; 4(1):1-16. DOI: 10.1007/BF00178332. View

Michnick S, Rosen M, Wandless T, Karplus M, Schreiber S . Solution structure of FKBP, a rotamase enzyme and receptor for FK506 and rapamycin. Science. 1991; 252(5007):836-9. DOI: 10.1126/science.1709301. View

Sigal N, Dumont F . Cyclosporin A, FK-506, and rapamycin: pharmacologic probes of lymphocyte signal transduction. Annu Rev Immunol. 1992; 10:519-60. DOI: 10.1146/annurev.iy.10.040192.002511. View

Torda A, Scheek R, van Gunsteren W . Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat. J Mol Biol. 1990; 214(1):223-35. DOI: 10.1016/0022-2836(90)90157-H. View

Scheek R, van Nuland N, de Groot B, Amadei A . Structure from NMR and molecular dynamics: Distance restraining inhibits motion in the essential subspace. J Biomol NMR. 2012; 6(1):106-11. DOI: 10.1007/BF00417496. View

Lepre C, Pearlman D, Cheng J, DeCenzo M, Livingston D, Moore J . Solution structure of FK506 bound to the R42K, H87V double mutant of FKBP-12. Biochemistry. 1994; 33(46):13571-80. DOI: 10.1021/bi00250a009. View

Cheng J, Lepre C, Moore J . 15N NMR relaxation studies of the FK506 binding protein: dynamic effects of ligand binding and implications for calcineurin recognition. Biochemistry. 1994; 33(14):4093-100. DOI: 10.1021/bi00180a001. View

10.

Clipstone N, Crabtree G . Identification of calcineurin as a key signalling enzyme in T-lymphocyte activation. Nature. 1992; 357(6380):695-7. DOI: 10.1038/357695a0. View

11.

Lepre C, Thomson J, Moore J . Solution structure of FK506 bound to FKBP-12. FEBS Lett. 1992; 302(1):89-96. DOI: 10.1016/0014-5793(92)80292-o. View

12.

Jin Y, Albers M, Lane W, Bierer B, Schreiber S, Burakoff S . Molecular cloning of a membrane-associated human FK506- and rapamycin-binding protein, FKBP-13. Proc Natl Acad Sci U S A. 1991; 88(15):6677-81. PMC: 52151. DOI: 10.1073/pnas.88.15.6677. View

13.

OKeefe S, Tamura J, Kincaid R, Tocci M, ONeill E . FK-506- and CsA-sensitive activation of the interleukin-2 promoter by calcineurin. Nature. 1992; 357(6380):692-4. DOI: 10.1038/357692a0. View

14.

Cheng J, Lepre C, Chambers S, Fulghum J, Thomson J, Moore J . 15N NMR relaxation studies of the FK506 binding protein: backbone dynamics of the uncomplexed receptor. Biochemistry. 1993; 32(35):9000-10. DOI: 10.1021/bi00086a004. View

15.

Moore J, Peattie D, Fitzgibbon M, Thomson J . Solution structure of the major binding protein for the immunosuppressant FK506. Nature. 1991; 351(6323):248-50. DOI: 10.1038/351248a0. View

16.

Van Duyne G, Standaert R, Karplus P, Schreiber S, Clardy J . Atomic structure of FKBP-FK506, an immunophilin-immunosuppressant complex. Science. 1991; 252(5007):839-42. DOI: 10.1126/science.1709302. View

17.

Liu J, Farmer Jr J, Lane W, Friedman J, Weissman I, Schreiber S . Calcineurin is a common target of cyclophilin-cyclosporin A and FKBP-FK506 complexes. Cell. 1991; 66(4):807-15. DOI: 10.1016/0092-8674(91)90124-h. View