Skip to main content
NCBI home page
Biophysical Journal logoLink to Biophysical Journal
. 1998 Jan;74(1):72–81. doi: 10.1016/S0006-3495(98)77768-9

The loop opening/closing motion of the enzyme triosephosphate isomerase.

P Derreumaux 1, T Schlick 1
PMCID: PMC1299363  PMID: 9449311

Abstract

To explore the origin of the large-scale motion of triosephosphate isomerase's flexible loop (residues 166 to 176) at the active site, several simulation protocols are employed both for the free enzyme in vacuo and for the free enzyme with some solvent modeling: high-temperature Langevin dynamics simulations, sampling by a "dynamics driver" approach, and potential-energy surface calculations. Our focus is on obtaining the energy barrier to the enzyme's motion and establishing the nature of the loop movement. Previous calculations did not determine this energy barrier and the effect of solvent on the barrier. High-temperature molecular dynamics simulations and crystallographic studies have suggested a rigid-body motion with two hinges located at both ends of the loop; Brownian dynamics simulations at room temperature pointed to a very flexible behavior. The present simulations and analyses reveal that although solute/solvent hydrogen bonds play a crucial role in lowering the energy along the pathway, there still remains a high activation barrier. This finding clearly indicates that, if the loop opens and closes in the absence of a substrate at standard conditions (e.g., room temperature, appropriate concentration of isomerase), the time scale for transition is not in the nanosecond but rather the microsecond range. Our results also indicate that in the context of spontaneous opening in the free enzyme, the motion is of rigid-body type and that the specific interaction between residues Ala176 and Tyr208 plays a crucial role in the loop opening/closing mechanism.

Full Text

The Full Text of this article is available as a PDF (347.6 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Banner D. W., Bloomer A. C., Petsko G. A., Phillips D. C., Pogson C. I., Wilson I. A., Corran P. H., Furth A. J., Milman J. D., Offord R. E. Structure of chicken muscle triose phosphate isomerase determined crystallographically at 2.5 angstrom resolution using amino acid sequence data. Nature. 1975 Jun 19;255(5510):609–614. doi: 10.1038/255609a0. [DOI] [PubMed] [Google Scholar]
  2. Bash P. A., Field M. J., Davenport R. C., Petsko G. A., Ringe D., Karplus M. Computer simulation and analysis of the reaction pathway of triosephosphate isomerase. Biochemistry. 1991 Jun 18;30(24):5826–5832. doi: 10.1021/bi00238a003. [DOI] [PubMed] [Google Scholar]
  3. Borchert T. V., Abagyan R., Jaenicke R., Wierenga R. K. Design, creation, and characterization of a stable, monomeric triosephosphate isomerase. Proc Natl Acad Sci U S A. 1994 Feb 15;91(4):1515–1518. doi: 10.1073/pnas.91.4.1515. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Brown F. K., Kollman P. A. Molecular dynamics simulations of "loop closing" in the enzyme triose phosphate isomerase. J Mol Biol. 1987 Dec 5;198(3):533–546. doi: 10.1016/0022-2836(87)90298-1. [DOI] [PubMed] [Google Scholar]
  5. Brünger A. T., Karplus M. Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison. Proteins. 1988;4(2):148–156. doi: 10.1002/prot.340040208. [DOI] [PubMed] [Google Scholar]
  6. Derreumaux P., Schlick T. Long timestep dynamics of peptides by the dynamics driver approach. Proteins. 1995 Apr;21(4):282–302. doi: 10.1002/prot.340210403. [DOI] [PubMed] [Google Scholar]
  7. Joseph-McCarthy D., Lolis E., Komives E. A., Petsko G. A. Crystal structure of the K12M/G15A triosephosphate isomerase double mutant and electrostatic analysis of the active site. Biochemistry. 1994 Mar 15;33(10):2815–2823. doi: 10.1021/bi00176a010. [DOI] [PubMed] [Google Scholar]
  8. Joseph D., Petsko G. A., Karplus M. Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop. Science. 1990 Sep 21;249(4975):1425–1428. doi: 10.1126/science.2402636. [DOI] [PubMed] [Google Scholar]
  9. Lodi P. J., Chang L. C., Knowles J. R., Komives E. A. Triosephosphate isomerase requires a positively charged active site: the role of lysine-12. Biochemistry. 1994 Mar 15;33(10):2809–2814. doi: 10.1021/bi00176a009. [DOI] [PubMed] [Google Scholar]
  10. Lolis E., Alber T., Davenport R. C., Rose D., Hartman F. C., Petsko G. A. Structure of yeast triosephosphate isomerase at 1.9-A resolution. Biochemistry. 1990 Jul 17;29(28):6609–6618. doi: 10.1021/bi00480a009. [DOI] [PubMed] [Google Scholar]
  11. Lolis E., Petsko G. A. Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5-A resolution: implications for catalysis. Biochemistry. 1990 Jul 17;29(28):6619–6625. doi: 10.1021/bi00480a010. [DOI] [PubMed] [Google Scholar]
  12. Pompliano D. L., Peyman A., Knowles J. R. Stabilization of a reaction intermediate as a catalytic device: definition of the functional role of the flexible loop in triosephosphate isomerase. Biochemistry. 1990 Apr 3;29(13):3186–3194. doi: 10.1021/bi00465a005. [DOI] [PubMed] [Google Scholar]
  13. Sampson N. S., Knowles J. R. Segmental motion in catalysis: investigation of a hydrogen bond critical for loop closure in the reaction of triosephosphate isomerase. Biochemistry. 1992 Sep 15;31(36):8488–8494. doi: 10.1021/bi00151a015. [DOI] [PubMed] [Google Scholar]
  14. Sampson N. S., Knowles J. R. Segmental movement: definition of the structural requirements for loop closure in catalysis by triosephosphate isomerase. Biochemistry. 1992 Sep 15;31(36):8482–8487. doi: 10.1021/bi00151a014. [DOI] [PubMed] [Google Scholar]
  15. Wade R. C., Davis M. E., Luty B. A., Madura J. D., McCammon J. A. Gating of the active site of triose phosphate isomerase: Brownian dynamics simulations of flexible peptide loops in the enzyme. Biophys J. 1993 Jan;64(1):9–15. doi: 10.1016/S0006-3495(93)81335-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Wade R. C., Luty B. A., Demchuk E., Madura J. D., Davis M. E., Briggs J. M., McCammon J. A. Simulation of enzyme-substrate encounter with gated active sites. Nat Struct Biol. 1994 Jan;1(1):65–69. doi: 10.1038/nsb0194-65. [DOI] [PubMed] [Google Scholar]
  17. Wierenga R. K., Borchert T. V., Noble M. E. Crystallographic binding studies with triosephosphate isomerases: conformational changes induced by substrate and substrate-analogues. FEBS Lett. 1992 Jul 27;307(1):34–39. doi: 10.1016/0014-5793(92)80897-p. [DOI] [PubMed] [Google Scholar]
  18. Wierenga R. K., Noble M. E., Vriend G., Nauche S., Hol W. G. Refined 1.83 A structure of trypanosomal triosephosphate isomerase crystallized in the presence of 2.4 M-ammonium sulphate. A comparison with the structure of the trypanosomal triosephosphate isomerase-glycerol-3-phosphate complex. J Mol Biol. 1991 Aug 20;220(4):995–1015. doi: 10.1016/0022-2836(91)90368-g. [DOI] [PubMed] [Google Scholar]
  19. Williams J. C., McDermott A. E. Dynamics of the flexible loop of triosephosphate isomerase: the loop motion is not ligand gated. Biochemistry. 1995 Jul 4;34(26):8309–8319. doi: 10.1021/bi00026a012. [DOI] [PubMed] [Google Scholar]
  20. Yüksel K. U., Sun A. Q., Gracy R. W., Schnackerz K. D. The hinged lid of yeast triose-phosphate isomerase. Determination of the energy barrier between the two conformations. J Biol Chem. 1994 Feb 18;269(7):5005–5008. [PubMed] [Google Scholar]
  21. Zhang Z., Sugio S., Komives E. A., Liu K. D., Knowles J. R., Petsko G. A., Ringe D. Crystal structure of recombinant chicken triosephosphate isomerase-phosphoglycolohydroxamate complex at 1.8-A resolution. Biochemistry. 1994 Mar 15;33(10):2830–2837. doi: 10.1021/bi00176a012. [DOI] [PubMed] [Google Scholar]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society

RESOURCES