Skip to main content
NCBI home page
Biophysical Journal logoLink to Biophysical Journal
. 2001 May;80(5):2439–2454. doi: 10.1016/S0006-3495(01)76213-3

Protein folding and function: the N-terminal fragment in adenylate kinase.

S Kumar 1, Y Y Sham 1, C J Tsai 1, R Nussinov 1
PMCID: PMC1301432  PMID: 11325743

Abstract

Three-dimensional protein folds range from simple to highly complex architectures. In complex folds, some building block fragments are more important for correct protein folding than others. Such fragments are typically buried in the protein core and mediate interactions between other fragments. Here we present an automated, surface area-based algorithm that is able to indicate which, among all local elements of the structure, is critical for the formation of the native fold, and apply it to structurally well-characterized proteins. In particular, we focus on adenylate kinase. The fragment containing the phosphate binding, P-loop (the "giant anion hole") flanked by a beta-strand and an alpha-helix near the N-terminus, is identified as a critical building block. This building block shows a high degree of sequence and structural conservation in all adenylate kinases. The results of our molecular dynamics simulations are consistent with this identification. In its absence, the protein flips to a stable, non-native state. In this misfolded conformation, the other local elements of the structure are in their native-like conformations; however, their association is non-native. Furthermore, this element is critically important for the function of the enzyme, coupling folding, and function.

Full Text

The Full Text of this article is available as a PDF (2.2 MB).

Selected References

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

  1. Abele U., Schulz G. E. High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer. Protein Sci. 1995 Jul;4(7):1262–1271. doi: 10.1002/pro.5560040702. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Baldwin R. L., Rose G. D. Is protein folding hierarchic? I. Local structure and peptide folding. Trends Biochem Sci. 1999 Jan;24(1):26–33. doi: 10.1016/s0968-0004(98)01346-2. [DOI] [PubMed] [Google Scholar]
  3. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  4. Berry M. B., Meador B., Bilderback T., Liang P., Glaser M., Phillips G. N., Jr The closed conformation of a highly flexible protein: the structure of E. coli adenylate kinase with bound AMP and AMPPNP. Proteins. 1994 Jul;19(3):183–198. doi: 10.1002/prot.340190304. [DOI] [PubMed] [Google Scholar]
  5. Berry M. B., Phillips G. N., Jr Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+. Proteins. 1998 Aug 15;32(3):276–288. doi: 10.1002/(sici)1097-0134(19980815)32:3<276::aid-prot3>3.0.co;2-g. [DOI] [PubMed] [Google Scholar]
  6. 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]
  7. Byeon L., Shi Z., Tsai M. D. Mechanism of adenylate kinase. The "essential lysine" helps to orient the phosphates and the active site residues to proper conformations. Biochemistry. 1995 Mar 14;34(10):3172–3182. doi: 10.1021/bi00010a006. [DOI] [PubMed] [Google Scholar]
  8. Chan H. S., Dill K. A. Origins of structure in globular proteins. Proc Natl Acad Sci U S A. 1990 Aug;87(16):6388–6392. doi: 10.1073/pnas.87.16.6388. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Dreusicke D., Karplus P. A., Schulz G. E. Refined structure of porcine cytosolic adenylate kinase at 2.1 A resolution. J Mol Biol. 1988 Jan 20;199(2):359–371. doi: 10.1016/0022-2836(88)90319-1. [DOI] [PubMed] [Google Scholar]
  10. Dreusicke D., Schulz G. E. The glycine-rich loop of adenylate kinase forms a giant anion hole. FEBS Lett. 1986 Nov 24;208(2):301–304. doi: 10.1016/0014-5793(86)81037-7. [DOI] [PubMed] [Google Scholar]
  11. Elamrani S., Berry M. B., Phillips G. N., Jr, McCammon J. A. Study of global motions in proteins by weighted masses molecular dynamics: adenylate kinase as a test case. Proteins. 1996 May;25(1):79–88. doi: 10.1002/(SICI)1097-0134(199605)25:1<79::AID-PROT6>3.0.CO;2-F. [DOI] [PubMed] [Google Scholar]
  12. Gegg C. V., Bowers K. E., Matthews C. R. Probing minimal independent folding units in dihydrofolate reductase by molecular dissection. Protein Sci. 1997 Sep;6(9):1885–1892. doi: 10.1002/pro.5560060909. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Gerstein M., Schulz G., Chothia C. Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers. J Mol Biol. 1993 Jan 20;229(2):494–501. doi: 10.1006/jmbi.1993.1048. [DOI] [PubMed] [Google Scholar]
  14. Haney P., Konisky J., Koretke K. K., Luthey-Schulten Z., Wolynes P. G. Structural basis for thermostability and identification of potential active site residues for adenylate kinases from the archaeal genus Methanococcus. Proteins. 1997 May;28(1):117–130. doi: 10.1002/(sici)1097-0134(199705)28:1<117::aid-prot12>3.0.co;2-m. [DOI] [PubMed] [Google Scholar]
  15. Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983 Dec;22(12):2577–2637. doi: 10.1002/bip.360221211. [DOI] [PubMed] [Google Scholar]
  16. Kern P., Brunne R. M., Folkers G. Nucleotide-binding properties of adenylate kinase from Escherichia coli: a molecular dynamics study in aqueous and vacuum environments. J Comput Aided Mol Des. 1994 Aug;8(4):367–388. doi: 10.1007/BF00125373. [DOI] [PubMed] [Google Scholar]
  17. Lazaridis T., Karplus M. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J Mol Biol. 1999 May 7;288(3):477–487. doi: 10.1006/jmbi.1999.2685. [DOI] [PubMed] [Google Scholar]
  18. Lazaridis T., Karplus M. Effective energy function for proteins in solution. Proteins. 1999 May 1;35(2):133–152. doi: 10.1002/(sici)1097-0134(19990501)35:2<133::aid-prot1>3.0.co;2-n. [DOI] [PubMed] [Google Scholar]
  19. Lim W. A., Farruggio D. C., Sauer R. T. Structural and energetic consequences of disruptive mutations in a protein core. Biochemistry. 1992 May 5;31(17):4324–4333. doi: 10.1021/bi00132a025. [DOI] [PubMed] [Google Scholar]
  20. Lim W. A., Sauer R. T. The role of internal packing interactions in determining the structure and stability of a protein. J Mol Biol. 1991 May 20;219(2):359–376. doi: 10.1016/0022-2836(91)90570-v. [DOI] [PubMed] [Google Scholar]
  21. Ma B., Tsai C. J., Nussinov R. Binding and folding: in search of intramolecular chaperone-like building block fragments. Protein Eng. 2000 Sep;13(9):617–627. doi: 10.1093/protein/13.9.617. [DOI] [PubMed] [Google Scholar]
  22. Matte A., Tari L. W., Delbaere L. T. How do kinases transfer phosphoryl groups? Structure. 1998 Apr 15;6(4):413–419. doi: 10.1016/s0969-2126(98)00043-4. [DOI] [PubMed] [Google Scholar]
  23. Matthews B. W. Structural and genetic analysis of protein stability. Annu Rev Biochem. 1993;62:139–160. doi: 10.1146/annurev.bi.62.070193.001035. [DOI] [PubMed] [Google Scholar]
  24. Müller C. W., Schlauderer G. J., Reinstein J., Schulz G. E. Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding. Structure. 1996 Feb 15;4(2):147–156. doi: 10.1016/s0969-2126(96)00018-4. [DOI] [PubMed] [Google Scholar]
  25. Müller C. W., Schulz G. E. Crystal structures of two mutants of adenylate kinase from Escherichia coli that modify the Gly-loop. Proteins. 1993 Jan;15(1):42–49. doi: 10.1002/prot.340150106. [DOI] [PubMed] [Google Scholar]
  26. Müller C. W., Schulz G. E. Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state. J Mol Biol. 1992 Mar 5;224(1):159–177. doi: 10.1016/0022-2836(92)90582-5. [DOI] [PubMed] [Google Scholar]
  27. Polverino de Laureto P., Scaramella E., Frigo M., Wondrich F. G., De Filippis V., Zambonin M., Fontana A. Limited proteolysis of bovine alpha-lactalbumin: isolation and characterization of protein domains. Protein Sci. 1999 Nov;8(11):2290–2303. doi: 10.1110/ps.8.11.2290. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Reinstein J., Brune M., Wittinghofer A. Mutations in the nucleotide binding loop of adenylate kinase of Escherichia coli. Biochemistry. 1988 Jun 28;27(13):4712–4720. doi: 10.1021/bi00413a020. [DOI] [PubMed] [Google Scholar]
  29. Reinstein J., Schlichting I., Wittinghofer A. Structurally and catalytically important residues in the phosphate binding loop of adenylate kinase of Escherichia coli. Biochemistry. 1990 Aug 14;29(32):7451–7459. doi: 10.1021/bi00484a014. [DOI] [PubMed] [Google Scholar]
  30. Rose T., Brune M., Wittinghofer A., Le Blay K., Surewicz W. K., Mantsch H. H., Bârzu O., Gilles A. M. Structural and catalytic properties of a deletion derivative (delta 133-157) of Escherichia coli adenylate kinase. J Biol Chem. 1991 Jun 15;266(17):10781–10786. [PubMed] [Google Scholar]
  31. Saint Girons I., Gilles A. M., Margarita D., Michelson S., Monnot M., Fermandjian S., Danchin A., Bârzu O. Structural and catalytic characteristics of Escherichia coli adenylate kinase. J Biol Chem. 1987 Jan 15;262(2):622–629. [PubMed] [Google Scholar]
  32. Saraste M., Sibbald P. R., Wittinghofer A. The P-loop--a common motif in ATP- and GTP-binding proteins. Trends Biochem Sci. 1990 Nov;15(11):430–434. doi: 10.1016/0968-0004(90)90281-f. [DOI] [PubMed] [Google Scholar]
  33. Schlauderer G. J., Proba K., Schulz G. E. Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP. J Mol Biol. 1996 Feb 23;256(2):223–227. doi: 10.1006/jmbi.1996.0080. [DOI] [PubMed] [Google Scholar]
  34. Schulz G. E., Müller C. W., Diederichs K. Induced-fit movements in adenylate kinases. J Mol Biol. 1990 Jun 20;213(4):627–630. doi: 10.1016/S0022-2836(05)80250-5. [DOI] [PubMed] [Google Scholar]
  35. Sham Y. Y., Ma B., Tsai C. J., Nussinov R. Molecular dynamics simulation of Escherichia coli dihydrofolate reductase and its protein fragments: relative stabilities in experiment and simulations. Protein Sci. 2001 Jan;10(1):135–148. doi: 10.1110/ps.33301. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Tsai C. J., Kumar S., Ma B., Nussinov R. Folding funnels, binding funnels, and protein function. Protein Sci. 1999 Jun;8(6):1181–1190. doi: 10.1110/ps.8.6.1181. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Tsai C. J., Maizel J. V., Jr, Nussinov R. Anatomy of protein structures: visualizing how a one-dimensional protein chain folds into a three-dimensional shape. Proc Natl Acad Sci U S A. 2000 Oct 24;97(22):12038–12043. doi: 10.1073/pnas.97.22.12038. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Tsai C. J., Maizel J. V., Jr, Nussinov R. Distinguishing between sequential and nonsequentially folded proteins: implications for folding and misfolding. Protein Sci. 1999 Aug;8(8):1591–1604. doi: 10.1110/ps.8.8.1591. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Tsai C. J., Nussinov R. Hydrophobic folding units at protein-protein interfaces: implications to protein folding and to protein-protein association. Protein Sci. 1997 Jul;6(7):1426–1437. doi: 10.1002/pro.5560060707. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Tsai C. J., Nussinov R. Hydrophobic folding units derived from dissimilar monomer structures and their interactions. Protein Sci. 1997 Jan;6(1):24–42. doi: 10.1002/pro.5560060104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Tsai C. J., Xu D., Nussinov R. Protein folding via binding and vice versa. Fold Des. 1998;3(4):R71–R80. doi: 10.1016/S1359-0278(98)00032-7. [DOI] [PubMed] [Google Scholar]
  42. Vonrhein C., Bönisch H., Schäfer G., Schulz G. E. The structure of a trimeric archaeal adenylate kinase. J Mol Biol. 1998 Sep 11;282(1):167–179. doi: 10.1006/jmbi.1998.2003. [DOI] [PubMed] [Google Scholar]
  43. Wu L. C., Grandori R., Carey J. Autonomous subdomains in protein folding. Protein Sci. 1994 Mar;3(3):369–371. doi: 10.1002/pro.5560030301. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Yan H., Tsai M. D. Nucleoside monophosphate kinases: structure, mechanism, and substrate specificity. Adv Enzymol Relat Areas Mol Biol. 1999;73:103-34, x. doi: 10.1002/9780470123195.ch4. [DOI] [PubMed] [Google Scholar]
  45. Yoneya T., Tagaya M., Kishi F., Nakazawa A., Fukui T. Site-directed mutagenesis of Gly-15 and Gly-20 in the glycine-rich region of adenylate kinase. J Biochem. 1989 Feb;105(2):158–160. doi: 10.1093/oxfordjournals.jbchem.a122631. [DOI] [PubMed] [Google Scholar]

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

RESOURCES