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. 2001 Jun;80(6):2527–2535. doi: 10.1016/S0006-3495(01)76224-8

Brownian dynamics simulations of aldolase binding glyceraldehyde 3-phosphate dehydrogenase and the possibility of substrate channeling.

I V Ouporov 1, H R Knull 1, A Huber 1, K A Thomasson 1
PMCID: PMC1301442  PMID: 11371431

Abstract

Brownian dynamics (BD) simulations test for channeling of the substrate, glyceraldehyde 3-phosphate (GAP), as it passes between the enzymes fructose-1,6-bisphosphate aldolase (aldolase) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH). First, BD simulations determined the favorable complexes between aldolase and GAPDH; two adjacent subunits of GAPDH form salt bridges with two subunits of aldolase. These intermolecular contacts provide a strong electrostatic interaction between the enzymes. Second, BD simulates GAP moving out of the active site of the A or D aldolase subunit and entering any of the four active sites of GAPDH. The efficiency of transfer is determined as the relative number of BD trajectories that reached any active site of GAPDH. The distribution functions of the transfer time were calculated based on the duration of successful trajectories. BD simulations of the GAP binding from solution to aldolase/GAPDH complex were compared to the channeling simulations. The efficiency of transfer of GAP within an aldolase/GAPDH complex was 2 to 3% compared to 1.3% when GAP was binding to GAPDH from solution. There is a preference for GAP channeling between aldolase and GAPDH when compared to binding from solution. However, this preference is not large enough to be considered as a theoretical proof of channeling between these proteins.

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Selected References

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  1. Berman H. M., Westbrook J., Feng Z., Gilliland G., Bhat T. N., Weissig H., Shindyalov I. N., Bourne P. E. The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235–242. doi: 10.1093/nar/28.1.235. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Cheung C. W., Cohen N. S., Raijman L. Channeling of urea cycle intermediates in situ in permeabilized hepatocytes. J Biol Chem. 1989 Mar 5;264(7):4038–4044. [PubMed] [Google Scholar]
  3. Clegg J. S., Jackson S. A. Glucose metabolism and the channeling of glycolytic intermediates in permeabilized L-929 cells. Arch Biochem Biophys. 1990 May 1;278(2):452–460. doi: 10.1016/0003-9861(90)90284-6. [DOI] [PubMed] [Google Scholar]
  4. Elcock A. H., Huber G. A., McCammon J. A. Electrostatic channeling of substrates between enzyme active sites: comparison of simulation and experiment. Biochemistry. 1997 Dec 23;36(51):16049–16058. doi: 10.1021/bi971709u. [DOI] [PubMed] [Google Scholar]
  5. Elcock A. H., McCammon J. A. Evidence for electrostatic channeling in a fusion protein of malate dehydrogenase and citrate synthase. Biochemistry. 1996 Oct 1;35(39):12652–12658. doi: 10.1021/bi9614747. [DOI] [PubMed] [Google Scholar]
  6. Elcock A. H., Potter M. J., Matthews D. A., Knighton D. R., McCammon J. A. Electrostatic channeling in the bifunctional enzyme dihydrofolate reductase-thymidylate synthase. J Mol Biol. 1996 Sep 27;262(3):370–374. doi: 10.1006/jmbi.1996.0520. [DOI] [PubMed] [Google Scholar]
  7. Larsen T. A., Olson A. J., Goodsell D. S. Morphology of protein-protein interfaces. Structure. 1998 Apr 15;6(4):421–427. doi: 10.1016/s0969-2126(98)00044-6. [DOI] [PubMed] [Google Scholar]
  8. Lo Conte L., Chothia C., Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol. 1999 Feb 5;285(5):2177–2198. doi: 10.1006/jmbi.1998.2439. [DOI] [PubMed] [Google Scholar]
  9. Matthew J. B. Electrostatic effects in proteins. Annu Rev Biophys Biophys Chem. 1985;14:387–417. doi: 10.1146/annurev.bb.14.060185.002131. [DOI] [PubMed] [Google Scholar]
  10. Northrup S. H., Luton J. A., Boles J. O., Reynolds J. C. Brownian dynamics simulation of protein association. J Comput Aided Mol Des. 1988 Jan;1(4):291–311. doi: 10.1007/BF01677278. [DOI] [PubMed] [Google Scholar]
  11. Northrup S. H., Thomasson K. A., Miller C. M., Barker P. D., Eltis L. D., Guillemette J. G., Inglis S. C., Mauk A. G. Effects of charged amino acid mutations on the bimolecular kinetics of reduction of yeast iso-1-ferricytochrome c by bovine ferrocytochrome b5. Biochemistry. 1993 Jul 6;32(26):6613–6623. doi: 10.1021/bi00077a014. [DOI] [PubMed] [Google Scholar]
  12. Orosz F., Ovádi J. A simple approach to identify the mechanism of intermediate transfer: enzyme system related to triose phosphate metabolism. Biochim Biophys Acta. 1987 Sep 2;915(1):53–59. doi: 10.1016/0167-4838(87)90124-5. [DOI] [PubMed] [Google Scholar]
  13. Ouporov I. V., Knull H. R., Lowe S. L., Thomasson K. A. Interactions of glyceraldehyde-3-phosphate dehydrogenase with G- and F-actin predicted by Brownian dynamics. J Mol Recognit. 2001 Jan-Feb;14(1):29–41. doi: 10.1002/1099-1352(200101/02)14:1<29::AID-JMR517>3.0.CO;2-T. [DOI] [PubMed] [Google Scholar]
  14. Ouporov I. V., Knull H. R., Thomasson K. A. Brownian dynamics simulations of interactions between aldolase and G- or F-actin. Biophys J. 1999 Jan;76(1 Pt 1):17–27. doi: 10.1016/S0006-3495(99)77174-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Pettersson H., Pettersson G. Mechanism of metabolite transfer in coupled two-enzyme reactions involving aldolase. Eur J Biochem. 1999 Jun;262(2):371–376. doi: 10.1046/j.1432-1327.1999.00386.x. [DOI] [PubMed] [Google Scholar]
  16. Shatalin K., Lebreton S., Rault-Leonardon M., Vélot C., Srere P. A. Electrostatic channeling of oxaloacetate in a fusion protein of porcine citrate synthase and porcine mitochondrial malate dehydrogenase. Biochemistry. 1999 Jan 19;38(3):881–889. doi: 10.1021/bi982195h. [DOI] [PubMed] [Google Scholar]
  17. Sheinerman F. B., Norel R., Honig B. Electrostatic aspects of protein-protein interactions. Curr Opin Struct Biol. 2000 Apr;10(2):153–159. doi: 10.1016/s0959-440x(00)00065-8. [DOI] [PubMed] [Google Scholar]
  18. Shire S. J., Hanania G. I., Gurd F. R. Electrostatic effects in myoglobin. Hydrogen ion equilibria in sperm whale ferrimyoglobin. Biochemistry. 1974 Jul 2;13(14):2967–2974. doi: 10.1021/bi00711a028. [DOI] [PubMed] [Google Scholar]
  19. Sumegi B., Sherry A. D., Malloy C. R., Srere P. A. Evidence for orientation-conserved transfer in the TCA cycle in Saccharomyces cerevisiae: 13C NMR studies. Biochemistry. 1993 Nov 30;32(47):12725–12729. doi: 10.1021/bi00210a022. [DOI] [PubMed] [Google Scholar]
  20. Tanford C., Roxby R. Interpretation of protein titration curves. Application to lysozyme. Biochemistry. 1972 May 23;11(11):2192–2198. doi: 10.1021/bi00761a029. [DOI] [PubMed] [Google Scholar]
  21. Tsai C. J., Lin S. L., Wolfson H. J., Nussinov R. Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect. Protein Sci. 1997 Jan;6(1):53–64. doi: 10.1002/pro.5560060106. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Vértessy B., Ovádi J. A simple approach to detect active-site-directed enzyme-enzyme interactions. The aldolase/glycerol-phosphate-dehydrogenase enzyme system. Eur J Biochem. 1987 May 4;164(3):655–659. doi: 10.1111/j.1432-1033.1987.tb11176.x. [DOI] [PubMed] [Google Scholar]

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