Mechanism and evolution of protein dimerization

Protein Science

Volumn 7, Issue 3, 1998, Pages 533-544

  Xu, Dong ^a,c   Tsai, Chung Jung ^a   Nussinov, Ruth ^a,b  

^a NATIONAL CANCER INSTITUTE   (United States)

^b TEL AVIV UNIVERSITY   (Israel)

^c OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

Compactness; Dimerization; Domain swapping; Intermediate; Kinetics; Oligomer evolution

Indexed keywords

OLIGOMER; PROTEIN;

ARTICLE; DIMERIZATION; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STABILITY; PROTEIN STRUCTURE;

EID: 0031913197     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560070301     Document Type: Article

References (48)

1. Aceto A, Caccuri AM, Sacchetta P, Bucciarelli T, Dragani B, Rosato N, Federici G, Di Ilio C. 1992. Dissociation and unfolding of Pi-class glutathione transferase. Evidence for a monomeric inactive intermediate. Biochem J 285:241-245.
2. Akasaka K, Fujii S, Hayashi F, Rokushika S, Hatano H. 1982. A novel technique for the detection of dissociation-association equilibrium in highly associable macromolecular systems. Biochem Int 5:637-642.
3. Baker EN, Hubbard RE. 1984. Hydrogen bonding in globular proteins. Prog Biophys Molec Biol 44:97-179.
4. Banik U, Saha R, Mandal NC, Bhattacharyya B, Roy S. 1992. Multiphasic denaturation of the lambda repressor by urea and its implications for the repressor structure. Eur J Biochem 206:15-21.
5. Bennett MJ, Choe S, Eisenberg D. 1994. Domain swapping: Entangling alliances between proteins. Proc Natl Acad Sci USA 91:3127-3131.
6. Bennett MJ, Schlunegger MP, Eisenberg D. 1995. 3D domain swapping: A mechanism for oligomer assembly. Protein Sci 4:2455-2468.
7. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. 1977. The protein data bank: A computer based archival file for macromolecular structures. J Mol Biol 112:535-542.
8. Borchert TV, Zeelen JP, Schliebs W, Callens M, Minke W, Jaenicke R, Wierenga RK. 1995. An interface point-mutation variant of triosephosphate isomerase is compactly folded and monomeric at low protein concentrations. FEBS Lett 367:315-318.
9. Bourne Y, Arvai AS, Bernstein SL, Watson MH, Reedand SI, Endicott JE, Noble ME, Johnson LN, Tainer JA. 1995. Crystal structure of the cell cycle-regulatory protein suc1 reveals a β-hinge conformational switch. Proc Natl Acad Sci USA 92:10232-10236.
10. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. 1983. CHARMm: A program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 4:187-217.
11. Cheng YS, Yin FH, Foundling S, Blomstrom D, Kettner CA. 1990. Stability and activity of human immunodeficiency virus protease: Comparison of the natural dimer with a homologous, single-chain tethered dimer. Proc Natl Acad Sci USA 87:9660-9664.
12. Connolly ML. 1983. Analytical molecular surface calculation. J Appl Cryst 16:548-558.
13. Connolly ML. 1993. The molecular surface package. J Mol Graphics 11:139-141.
14. Cunningham BC, Wells JA. 1993. Comparison of a structural and a functional epitope. J Mol Biol 234:554-563.
15. D'Alessio G. 1995. Oligomer evolution in action. Nature Struct Biol 2:11-13.
16. De Francesco R, Pastore A, Vecchio G, Cortese R. 1991. Circular dichroism study on the conformational stability of the dimerization domain of transcription factor LFB1. Biochemistry 30:143-147.
17. Dill KA, Chan HS. 1997. From Levinthal to pathways to funnels. Nature Struct Biol 4:10-19.
18. Grant SK, Deckman IC, Culp JS, Minnich MD, Brooks IS, Hensley P, Debouck C, Meek DT. 1992. Use of protein unfolding studies to determine the conformational and dimeric stabilities of HIV-1 and SIV proteases. Biochemistry 31:9491-9501.
19. Green SM, Gittis AG, Meeker AK, Lattman EE. 1995. One-step evolution of a dimer from a monomeric protein. Nat Struct Biol 2:746-751.
20. Herold M, Kirschner K. 1990. Reversible dissociation and unfolding of aspartate aminotransferase from escherichia coli: Characterization of a monomeric intermediate. Biochemistry 29:1907-1913.
21. Kippen AD, Sancho J, Fersht AR. 1994. Folding of barnase in parts. Biochemistry 33:3778-3786.
22. Lee B, Richards FM. 1971. The interpretation of protein structures: Estimation of static accessibility. J Mol Biol 55:379-400.
23. Liang H, Terwilliger TC. 1991. Reversible denaturation of the gene V protein of bacteriophage f1. Biochemistry 30:2772-2782.
24. Mann CJ, Royer CA, Matthews CR. 1993. Tryptophan replacements in the trp aporepressor from escherichia coli: Probing the equilibrium and kinetic folding models. Protein Sci 2:1853-1861.
25. McDonald I, Naylor D, Jones D, Thornton J. 1993. HBPLUS : Hydrogen Bond Calculator version 2.25. University College London.
26. McDonald IK, Thornton JM. 1994. Satisfying hydrogen bonding potential in proteins. J Mol Biol 238:777-793.
27. Mei G, Rosato N, Silva N, Rusch R, Gratton E, Savini I, Finazzi-Agro A. 1992. Denaturation of human Cu/Zn superoxide dismutase by guanidine hydrochloride: A dynamic fluorescence study. Biochemistry 31:7224-7230.
28. Milla ME, Sauer RT. 1994. P22 Arc repressor: Folding kinetics of a single-domain, dimeric protein. Biochemistry 33:1125-1133.
29. Molecular Simulations Inc. 1994. QUANTA 4.0. Burlington, Massachusetts: Molecular Simulations Inc.
30. 2+ affinity, formation, and stability of a two-site domain in troponin C. Protein Sci 1:945-955.
31. Neet KE, Timm DE. 1994. Conformational stability of dimeric proteins: Quantitative studies by equilibrium denaturation. Protein Sci 3:2167-2174.
32. Novotny J, Bruccoleri RE, Saul FA. 1989. On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5. Biochemistry 28:4735-4749.
33. Piccoli R, Tamburrini M, Piccialli G, Di Donato A, Parente A, D'Alessio G. 1992. The dual-mode quaternary structure of seminal mase. Proc Natl Acad Sci USA 89:1870-1874.
34. Richards FM. 1977. Areas, volumes, packing, and protein structure. Ann Rev Biochem Bioeng 6:151-176.
35. Russell RB. 1994. Domain insertion. Protein Eng 7:1407-1410.
36. Shaw A, Fortes PA, Stout CD, Vacquier VD. 1995. Crystal structure and subunit dynamics of the abalone sperm lysin dimer: Egg envelopes dissociate dimers, the monomer is the active species. J Cell Biol 31:1117-1125.
37. Steif C, Weber P, Hinz HJ, Flossdorf J, Cesareni G, Kokkinidis M. 1993. Subunit interactions provide a significant contribution to the stability of the dimeric four-alpha-helical-bundle protein rop. Biochemistry 32:3867-3876.
38. Tasayco ML, Carey J. 1992. Ordered self-assembly of polypeptide fragments to form nativelike dimeric trp repressor. Science 255:594-597.
39. Tegoni M, Ramoni R, Bignetti E, Spinelli S, Cambillau C. 1996. Domain swapping creates a third putative combining site in bovine odorant binding protein dimer. Nat Struct Biol 3:863-867.
40. Timm DE, de Haseth PL, Neet KE. 1994. Comparative equilibrium denaturation studies of the neurotrophins: Nerve growth factor, brain-derived neurotrophic factor, neurotrophin 3, and neurotrophin 4/5. Biochemistry 33:4667-4676.
41. Tsai C-J, Nussinov R. 1997a. Hydrophobic folding units derived from dissimilar monomer structures and their interactions. Protein Sci 6:24-42.
42. Tsai C-J, Nussinov R. 1997b. Hydrophobic folding units at protein-protein interfaces: Implications to protein folding and to protein-protein association. Protein Sci 6:1426-1437.
43. Tsai C-J, Xu D, Nussinov R. 1997. Structural motifs at protein-protein interfaces: Protein cores versus two-state and three-state model complexes. Protein Sci 6:1793-1805.
44. Wu LC, Grandori R, Carey J. 1994. Autonomous subdomains in protein foldin. Protein Sci 3:359-371.
45. Xu D, Lin SL, Nussinov R. 1997. Protein binding versus protein folding: The role of hydrophilic bridges in protein associations. J Mol Biol 265:68-84.
46. Zehfus MH, Rose GD. 1986. Compact units in proteins. Biochemistry 25:5759-5765.
47. Zetina CR, Goldberg ME. 1980. Reversible unfolding of the β2 subunit of escherichia coli tryptophan synthetase and its proteolytic fragments. J Mol Biol 137:401-414.
48. Zwanzig R. 1997. Two-state models of protein folding kinetics. Proc Natl Acad Sci USA 94:148-150.