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Structural determinants of protein folding

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Abstract

The last several decades have seen an explosion of knowledge in the field of structural biology. With critical advances in spectroscopic techniques in examining structures of biomacromolecules, in maturation of molecular biology techniques, as well as vast improvements in computation prowess, protein structures are now being elucidated at an unprecedented rate. In spite of all the recent advances, the protein folding puzzle remains as one of the fundamental biochemical challenges. A facet to this empiric problem is the structural determinants of protein folding. What are the driving forces that pivot a polypeptide chain to a specific conformation amongst the vast conformation space? In this review, we shall discuss some of the structural determinants to protein folding that have been identified in the recent decades.

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References

  1. Honig B, Cohen FE (1996) Adding backbone to protein folding: why proteins are polypeptides. Fold Des 1:R17–R20

    PubMed  CAS  Google Scholar 

  2. Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181:223–230

    PubMed  CAS  Google Scholar 

  3. Anfinsen CB, Haber E, Sela M, White FH Jr (1961) The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. Proc Natl Acad Sci USA 47:1309–1314

    PubMed  CAS  Google Scholar 

  4. Levinthal C (1968) Are there protein folding pathways? J Chim Phys 65:44–45

    Google Scholar 

  5. Levinthal C (1969) How to fold graciously. In: DeBrunner JTP, Munck E (Eds) Mossbauer spectroscopy in biological systems. University of Illinois Bulletin, vol 67, pp 22–24

    Google Scholar 

  6. Karplus M (1997) The Levinthal paradox: yesterday and today. Fold Des 2:S69–S75

    PubMed  CAS  Google Scholar 

  7. Creighton TE (1986) Disulfide bonds as probes of protein folding pathways. Methods Enzymol 131:83–106

    PubMed  CAS  Google Scholar 

  8. Baldwin RL (2008) The search for folding intermediates and the mechanism of protein folding. Annu Rev Biophys 37:1–21

    PubMed  CAS  Google Scholar 

  9. Fine R, Dimmler G, Levinthal C (1991) FASTRUN: a special purpose, hardwired computer for molecular simulation. Proteins 11:242–253

    PubMed  CAS  Google Scholar 

  10. Chou PY, Fasman GD (1974) Prediction of protein conformation. Biochemistry 13:222–245

    PubMed  CAS  Google Scholar 

  11. Leopold PE, Montal M, Onuchic JN (1992) Protein folding funnels: a kinetic approach to the sequence-structure relationship. Proc Natl Acad Sci USA 89:8721–8725

    PubMed  CAS  Google Scholar 

  12. Dill KA, Ozkan SB, Shell MS, Weikl TR (2008) The protein folding problem. Annu Rev Biophys 37:289–316

    PubMed  CAS  Google Scholar 

  13. Wetlaufer DB (1973) Nucleation, rapid folding, and globular intrachain regions in proteins. Proc Natl Acad Sci USA 70:697–701

    PubMed  CAS  Google Scholar 

  14. Fersht AR (2008) From the first protein structures to our current knowledge of protein folding: delights and scepticisms. Nat Rev Mol Cell Biol 9:650–654

    PubMed  CAS  Google Scholar 

  15. Ptitsyn OB (1995) How the molten globule became. Trends Biochem Sci 20:376–379

    PubMed  CAS  Google Scholar 

  16. Kim PS, Baldwin RL (1982) Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. Annu Rev Biochem 51:459–489

    PubMed  CAS  Google Scholar 

  17. Karplus M, Weaver DL (1994) Protein folding dynamics: the diffusion-collision model and experimental data. Protein Sci 3:650–668

    Article  PubMed  CAS  Google Scholar 

  18. Ptitsyn O (1996) How molten is the molten globule? Nat Struct Biol 3:488–490

    PubMed  CAS  Google Scholar 

  19. Fersht AR (1995) Optimization of rates of protein folding: the nucleation–condensation mechanism and its implications. Proc Natl Acad Sci USA 92:10869–10873

    PubMed  CAS  Google Scholar 

  20. Fersht AR (1997) Nucleation mechanisms in protein folding. Curr Opin Struct Biol 7:3–9

    PubMed  CAS  Google Scholar 

  21. Gianni S, Guydosh NR, Khan F, Caldas TD, Mayor U, White GW, DeMarco ML, Daggett V, Fersht AR (2003) Unifying features in protein-folding mechanisms. Proc Natl Acad Sci USA 100:13286–13291

    PubMed  CAS  Google Scholar 

  22. Shortle D, Ackerman MS (2001) Persistence of native-like topology in a denatured protein in 8 M urea. Science 293:487–489

    PubMed  CAS  Google Scholar 

  23. Fersht AR, Matouschek A, Serrano L (1992) The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding. J Mol Biol 224:771–782

    PubMed  CAS  Google Scholar 

  24. Ivarsson Y, Travaglini-Allocatelli C, Brunori M, Gianni S (2008) Mechanisms of protein folding. Eur Biophys J 37:721–728

    PubMed  CAS  Google Scholar 

  25. Dyson HJ, Wright PE (2005) Elucidation of the protein folding landscape by NMR. Methods Enzymol 394:299–321

    PubMed  CAS  Google Scholar 

  26. Dyson HJ, Wright PE (2004) Unfolded proteins and protein folding studied by NMR. Chem Rev 104:3607–3622

    PubMed  CAS  Google Scholar 

  27. Borgia A, Williams PM, Clarke J (2008) Single-molecule studies of protein folding. Annu Rev Biochem 77:101–125

    PubMed  CAS  Google Scholar 

  28. Forman JR, Clarke J (2007) Mechanical unfolding of proteins: insights into biology, structure and folding. Curr Opin Struct Biol 17:58–66

    PubMed  CAS  Google Scholar 

  29. Balakrishnan G, Weeks CL, Ibrahim M, Soldatova AV, Spiro TG (2008) Protein dynamics from time resolved UV Raman spectroscopy. Curr Opin Struct Biol 18:623–629

    PubMed  CAS  Google Scholar 

  30. Schaeffer RD, Fersht A, Daggett V (2008) Combining experiment and simulation in protein folding: closing the gap for small model systems. Curr Opin Struct Biol 18:4–9

    PubMed  CAS  Google Scholar 

  31. Dokholyan NV (2006) Studies of folding and misfolding using simplified models. Curr Opin Struct Biol 16:79–85

    PubMed  CAS  Google Scholar 

  32. Caflisch A (2006) Network and graph analyses of folding free energy surfaces. Curr Opin Struct Biol 16:71–78

    PubMed  CAS  Google Scholar 

  33. Kubelka J, Hofrichter J, Eaton WA (2004) The protein folding ‘speed limit’. Curr Opin Struct Biol 14:76–88

    PubMed  CAS  Google Scholar 

  34. Brockwell DJ, Radford SE (2007) Intermediates: ubiquitous species on folding energy landscapes? Curr Opin Struct Biol 17:30–37

    PubMed  CAS  Google Scholar 

  35. Gianni S, Ivarsson Y, Jemth P, Brunori M, Travaglini-Allocatelli C (2007) Identification and characterization of protein folding intermediates. Biophys Chem 128:105–113

    PubMed  CAS  Google Scholar 

  36. Sanchez IE, Kiefhaber T (2003) Evidence for sequential barriers and obligatory intermediates in apparent two-state protein folding. J Mol Biol 325:367–376

    PubMed  CAS  Google Scholar 

  37. Gianni S, Geierhaas CD, Calosci N, Jemth P, Vuister GW, Travaglini-Allocatelli C, Vendruscolo M, Brunori M (2007) A PDZ domain recapitulates a unifying mechanism for protein folding. Proc Natl Acad Sci USA 104:128–133

    PubMed  CAS  Google Scholar 

  38. Zarrine-Afsar A, Larson SM, Davidson AR (2005) The family feud: do proteins with similar structures fold via the same pathway? Curr Opin Struct Biol 15:42–49

    PubMed  CAS  Google Scholar 

  39. Lindberg MO, Oliveberg M (2007) Malleability of protein folding pathways: a simple reason for complex behaviour. Curr Opin Struct Biol 17:21–29

    PubMed  CAS  Google Scholar 

  40. Daggett V, Fersht AR (2003) Is there a unifying mechanism for protein folding? Trends Biochem Sci 28:18–25

    PubMed  CAS  Google Scholar 

  41. Englander SW, Mayne L, Krishna MM (2007) Protein folding and misfolding: mechanism and principles. Q Rev Biophys 40:287–326

    PubMed  CAS  Google Scholar 

  42. Dill KA (1990) Dominant forces in protein folding. Biochemistry 29:7133–7155

    PubMed  CAS  Google Scholar 

  43. Yang JS, Chen WW, Skolnick J, Shakhnovich EI (2007) All-atom ab initio folding of a diverse set of proteins. Structure 15:53–63

    PubMed  Google Scholar 

  44. Cho JH, Raleigh DP (2006) Electrostatic interactions in the denatured state and in the transition state for protein folding: effects of denatured state interactions on the analysis of transition state structure. J Mol Biol 359:1437–1446

    PubMed  CAS  Google Scholar 

  45. Mirsky AE, Pauling L (1936) On the structure of native, denatured, and coagulated proteins. Proc Natl Acad Sci USA 22:439–447

    PubMed  CAS  Google Scholar 

  46. Chen J, Stites WE (2001) Packing is a key selection factor in the evolution of protein hydrophobic cores. Biochemistry 40:15280–15289

    PubMed  CAS  Google Scholar 

  47. Richards FM, Lim WA (1993) An analysis of packing in the protein folding problem. Q Rev Biophys 26:423–498

    PubMed  CAS  Google Scholar 

  48. Marin M (2008) Folding at the rhythm of the rare codon beat. Biotechnol J 3:1047–1057

    PubMed  CAS  Google Scholar 

  49. Sauer RT, Milla ME, Waldburger CD, Brown BM, Schildbach JF (1996) Sequence determinants of folding and stability for the P22 Arc repressor dimer. Faseb J 10:42–48

    PubMed  CAS  Google Scholar 

  50. Barrow CJ, Yasuda A, Kenny PT, Zagorski MG (1992) Solution conformations and aggregational properties of synthetic amyloid beta-peptides of Alzheimer’s disease. Analysis of circular dichroism spectra. J Mol Biol 225:1075–1093

    PubMed  CAS  Google Scholar 

  51. Haber E, Anfinsen CB (1961) Regeneration of enzyme activity by air oxidation of reduced subtilisin-modified ribonuclease. J Biol Chem 236:422–424

    PubMed  CAS  Google Scholar 

  52. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blocker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921

    PubMed  CAS  Google Scholar 

  53. Walsh CT (2006) Posttranslational modification of proteins. Roberts, Greenwood Village, CO

    Google Scholar 

  54. Sali A, Shakhnovich E, Karplus M (1994) How does a protein fold? Nature 369:248–251

    PubMed  CAS  Google Scholar 

  55. Wilson DR, Finlay BB (1997) The ‘Asx-Pro turn’ as a local structural motif stabilized by alternative patterns of hydrogen bonds and a consensus-derived model of the sequence Asn-Pro-Asn. Protein Eng 10:519–529

    PubMed  CAS  Google Scholar 

  56. Pauling L, Corey RB, Branson HR (1951) The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci USA 37:205–211

    PubMed  CAS  Google Scholar 

  57. Feyereisen C, Morcellet M, Loucheux C (1977) Preferential and absolute adsorption to poly[N5-(3-hydroxypropyl)-L-glutamine] in water/2-chloroethanol solvent mixtures. Macromolecules 10:485–488

    PubMed  CAS  Google Scholar 

  58. Schiffer M, Edmundson AB (1967) Use of helical wheels to represent the structures of proteins and to identify segments with helical potential. Biophys J 7:121–135

    PubMed  CAS  Google Scholar 

  59. Kotelchuck D, Scheraga HA (1969) The influence of short-range interactions on protein onformation. II. A model for predicting the alpha-helical regions of proteins. Proc Natl Acad Sci USA 62:14–21

    PubMed  CAS  Google Scholar 

  60. Creighton TE (1993) Proteins: structures and molecular properties. Freeman, New York

    Google Scholar 

  61. Marqusee S, Robbins VH, Baldwin RL (1989) Unusually stable helix formation in short alanine-based peptides. Proc Natl Acad Sci USA 86:5286–5290

    PubMed  CAS  Google Scholar 

  62. Chakrabartty A, Schellman JA, Baldwin RL (1991) Large differences in the helix propensities of alanine and glycine. Nature 351:586–588

    PubMed  CAS  Google Scholar 

  63. Altmann KH, Wojcik J, Vasquez M, Scheraga HA (1990) Helix-coil stability constants for the naturally occurring amino acids in water. XXIII. Proline parameters from random poly (hydroxybutylglutamine-co-L-proline). Biopolymers 30:107–120

    PubMed  CAS  Google Scholar 

  64. Shoemaker KR, Fairman R, Kim PS, York EJ, Stewart JM, Baldwin RL (1987) The C-peptide helix from ribonuclease A considered as an autonomous folding unit. Cold Spring Harb Symp Quant Biol 52:391–398

    PubMed  CAS  Google Scholar 

  65. Kim PS, Baldwin RL (1984) A helix stop signal in the isolated S-peptide of ribonuclease A. Nature 307:329–334

    PubMed  CAS  Google Scholar 

  66. Marqusee S, Baldwin RL (1987) Helix stabilization by Glu−···Lys + salt bridges in short peptides of de novo design. Proc Natl Acad Sci USA 84:8898–8902

    PubMed  CAS  Google Scholar 

  67. Takahashi S, Kim EH, Hibino T, Ooi T (1989) Comparison of alpha-helix stability in peptides having a negatively or positively charged residue block attached either to the N- or C-terminus of an alpha-helix: the electrostatic contribution and anisotropic stability of the alpha-helix. Biopolymers 28:995–1009

    PubMed  CAS  Google Scholar 

  68. Zimm BH, Brag JK (1959) Theory of phase transition between helix and random coil in polypeptide chains. J Chem Phys 31:526

    CAS  Google Scholar 

  69. Finkelstein AV, Badretdinov AY, Ptitsyn OB (1991) Physical reasons for secondary structure stability: alpha-helices in short peptides. Proteins 10:287–299

    PubMed  CAS  Google Scholar 

  70. Munoz V, Serrano L (1994) Elucidating the folding problem of helical peptides using empirical parameters. Nat Struct Biol 1:399–409

    PubMed  CAS  Google Scholar 

  71. Munoz V, Serrano L (1995) Elucidating the folding problem of helical peptides using empirical parameters. II. Helix macrodipole effects and rational modification of the helical content of natural peptides. J Mol Biol 245:275–296

    PubMed  CAS  Google Scholar 

  72. Munoz V, Serrano L (1995) Elucidating the folding problem of helical peptides using empirical parameters. III. Temperature and pH dependence. J Mol Biol 245:297–308

    PubMed  CAS  Google Scholar 

  73. Smith C, Regan L (1997) Construction and design of β-sheets. Acc Chem Res 30:153–161

    CAS  Google Scholar 

  74. Lee J, Dubey VK, Longo LM, Blaber M (2008) A logical OR redundancy within the Asx-Pro-Asx-Gly type I beta-turn motif. J Mol Biol 377:1251–1264

    PubMed  CAS  Google Scholar 

  75. Chou PY, Fasman GD (1978) Empirical predictions of protein conformation. Annu Rev Biochem 47:251–276

    PubMed  CAS  Google Scholar 

  76. Williams RM, Obradovi Z, Mathura V, Braun W, Garner EC, Young J, Takayama S, Brown CJ, Dunker AK (2001) The protein non-folding problem: amino acid determinants of intrinsic order and disorder. Pac Symp Biocomput 89–100

  77. DeGrado W, Kezdy F, Kaiser E (1981) Design, synthesis and characterization of a cytotoxic peptide with melittin-like activity. J Am Chem Soc 103:679–681

    CAS  Google Scholar 

  78. Lupas AN, Gruber M (2005) The structure of alpha-helical coiled coils. Adv Protein Chem 70:37–78

    PubMed  CAS  Google Scholar 

  79. Han JH, Batey S, Nickson AA, Teichmann SA, Clarke J (2007) The folding and evolution of multidomain proteins. Nat Rev Mol Cell Biol 8:319–330

    PubMed  CAS  Google Scholar 

  80. MacArthur MW, Thornton JM (1991) Influence of proline residues on protein conformation. J Mol Biol 218:397–412

    PubMed  CAS  Google Scholar 

  81. Senes A, Engel DE, DeGrado WF (2004) Folding of helical membrane proteins: the role of polar, GxxxG-like and proline motifs. Curr Opin Struct Biol 14:465–479

    PubMed  CAS  Google Scholar 

  82. Chakrabarti P, Chakrabarti S (1998) C–H…O hydrogen bond involving proline residues in alpha-helices. J Mol Biol 284:867–873

    PubMed  CAS  Google Scholar 

  83. Barlow DJ, Thornton JM (1988) Helix geometry in proteins. J Mol Biol 201:601–619

    PubMed  CAS  Google Scholar 

  84. Kini RM (2002) Molecular moulds with multiple missions: functional sites in three-finger toxins. Clin Exp Pharmacol Physiol 29:815–822

    PubMed  CAS  Google Scholar 

  85. Carlier E, Fajloun Z, Mansuelle P, Fathallah M, Mosbah A, Oughideni R, Sandoz G, Di Luccio E, Geib S, Regaya I, Brocard J, Rochat H, Darbon H, Devaux C, Sabatier JM, de Waard M (2001) Disulfide bridge reorganization induced by proline mutations in maurotoxin. FEBS Lett 489:202–207

    PubMed  CAS  Google Scholar 

  86. Arias HR, Blanton MP (2000) Alpha-conotoxins. Int J Biochem Cell Biol 32:1017–1028

    PubMed  CAS  Google Scholar 

  87. Balaji RA, Ohtake A, Sato K, Gopalakrishnakone P, Kini RM, Seow KT, Bay BH (2000) λ-Conotoxins, a new family of conotoxins with unique disulfide pattern and protein folding. Isolation and characterization from the venom of Conus marmoreus. J Biol Chem 275:39516–39522

    PubMed  CAS  Google Scholar 

  88. Kang TS, Radic Z, Talley TT, Jois SD, Taylor P, Kini RM (2007) Protein folding determinants: structural features determining alternative disulfide pairing in alpha- and chi/lambda-conotoxins. Biochemistry 46:3338–3355

    PubMed  CAS  Google Scholar 

  89. Kemper B (2004) Structural basis for the role in protein folding of conserved proline-rich regions in cytochromes P450. Toxicol Appl Pharmacol 199:305–315

    PubMed  CAS  Google Scholar 

  90. Lorenzen S, Peters B, Goede A, Preissner R, Frommel C (2005) Conservation of cis prolyl bonds in proteins during evolution. Proteins 58:589–595

    PubMed  CAS  Google Scholar 

  91. Jenko Kokalj S, Guncar G, Stern I, Morgan G, Rabzelj S, Kenig M, Staniforth RA, Waltho JP, Zerovnik E, Turk D (2007) Essential role of proline isomerization in stefin B tetramer formation. J Mol Biol 366:1569–1579

    PubMed  CAS  Google Scholar 

  92. Martin A, Schmid FX (2003) A proline switch controls folding and domain interactions in the gene-3-protein of the filamentous phage fd. J Mol Biol 331:1131–1140

    PubMed  CAS  Google Scholar 

  93. Eckert B, Martin A, Balbach J, Schmid FX (2005) Prolyl isomerization as a molecular timer in phage infection. Nat Struct Mol Biol 12:619–623

    PubMed  CAS  Google Scholar 

  94. Kamen DE, Woody RW (2002) Identification of proline residues responsible for the slow folding kinetics in pectate lyase C by mutagenesis. Biochemistry 41:4724–4732

    PubMed  CAS  Google Scholar 

  95. Lu KP, Finn G, Lee TH, Nicholson LK (2007) Prolyl cis-trans isomerization as a molecular timer. Nat Chem Biol 3:619–629

    PubMed  CAS  Google Scholar 

  96. Takahashi N, Hayano T, Suzuki M (1989) Peptidyl-prolyl cis-trans isomerase is the cyclosporin A-binding protein cyclophilin. Nature 337:473–475

    PubMed  CAS  Google Scholar 

  97. Harding MW, Galat A, Uehling DE, Schreiber SL (1989) A receptor for the immunosuppressant FK506 is a cis-trans peptidyl-prolyl isomerase. Nature 341:758–760

    PubMed  CAS  Google Scholar 

  98. Kabsch W, Sander C (1984) On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations. Proc Natl Acad Sci USA 81:1075–1078

    PubMed  CAS  Google Scholar 

  99. Ambroggio XI, Kuhlman B (2006) Design of protein conformational switches. Curr Opin Struct Biol 16:525–530

    PubMed  CAS  Google Scholar 

  100. Siligardi G, Drake AF (1995) The importance of extended conformations and, in particular, the PII conformation for the molecular recognition of peptides. Biopolymers 37:281–292

    PubMed  CAS  Google Scholar 

  101. Rath A, Davidson AR, Deber CM (2005) The structure of “unstructured” regions in peptides and proteins: role of the polyproline II helix in protein folding and recognition. Biopolymers 80:179–185

    PubMed  CAS  Google Scholar 

  102. Waters ML (2004) Aromatic interactions in peptides: impact on structure and function. Biopolymers 76:435–445

    PubMed  CAS  Google Scholar 

  103. Hughes RM, Waters ML (2006) Effects of lysine acetylation in a beta-hairpin peptide: comparison of an amide-pi and a cation-pi interaction. J Am Chem Soc 128:13586–13591

    PubMed  CAS  Google Scholar 

  104. Rea AM, Simpson ER, Meldrum JK, Williams HE, Searle MS (2008) Aromatic residues engineered into the beta-turn nucleation site of ubiquitin lead to a complex folding landscape, non-native side-chain interactions, and kinetic traps. Biochemistry 47:12910–12922

    PubMed  CAS  Google Scholar 

  105. Li S, Yang W, Maniccia AW, Barrow D Jr, Tjong H, Zhou HX, Yang JJ (2008) Rational design of a conformation-switchable Ca(2+)- and Tb(3+)-binding protein without the use of multiple coupled metal-binding sites. FEBS J 275:5048–5061

    PubMed  CAS  Google Scholar 

  106. Uversky VN (2008) Amyloidogenesis of natively unfolded proteins. Curr Alzheimer Res 5:260–287

    PubMed  CAS  Google Scholar 

  107. Uversky VN, Fink AL (2004) Conformational constraints for amyloid fibrillation: the importance of being unfolded. Biochim Biophys Acta 1698:131–153

    PubMed  CAS  Google Scholar 

  108. Sevier CS, Kaiser CA (2002) Formation and transfer of disulphide bonds in living cells. Nat Rev Mol Cell Biol 3:836–847

    PubMed  CAS  Google Scholar 

  109. Mamathambika BS, Bardwell JC (2008) Disulfide-linked protein folding pathways. Annu Rev Cell Dev Biol 24:211–235

    PubMed  CAS  Google Scholar 

  110. Abkevich VI, Shakhnovich EI (2000) What can disulfide bonds tell us about protein energetics, function and folding: simulations and bioninformatics analysis. J Mol Biol 300:975–985

    PubMed  CAS  Google Scholar 

  111. Nakamura H (2005) Thioredoxin and its related molecules: update 2005. Antioxid Redox Signal 7:823–828

    PubMed  CAS  Google Scholar 

  112. Schmidt B, Ho L, Hogg PJ (2006) Allosteric disulfide bonds. Biochemistry 45:7429–7433

    PubMed  CAS  Google Scholar 

  113. Yokota A, Izutani K, Takai M, Kubo Y, Noda Y, Koumoto Y, Tachibana H, Segawa S (2000) The transition state in the folding-unfolding reaction of four species of three-disulfide variant of hen lysozyme: the role of each disulfide bridge. J Mol Biol 295:1275–1288

    PubMed  CAS  Google Scholar 

  114. Creighton TE (1995) Protein folding. An unfolding story. Curr Biol 5:353–356

    PubMed  CAS  Google Scholar 

  115. Narhi LO, Hua QX, Arakawa T, Fox GM, Tsai L, Rosenfeld R, Holst P, Miller JA, Weiss MA (1993) Role of native disulfide bonds in the structure and activity of insulin-like growth factor 1: genetic models of protein-folding intermediates. Biochemistry 32:5214–5221

    PubMed  CAS  Google Scholar 

  116. Thornton JM (1981) Disulphide bridges in globular proteins. J Mol Biol 151:261–287

    PubMed  CAS  Google Scholar 

  117. Guo ZY, Qiao ZS, Feng YM (2008) The in vitro oxidative folding of the insulin superfamily. Antioxid Redox Signal 10:127–139

    PubMed  CAS  Google Scholar 

  118. Weiss MA, Hua QX, Jia W, Chu YC, Wang RY, Katsoyannis PG (2000) Hierarchical protein “un-design”: insulin’s intrachain disulfide bridge tethers a recognition alpha-helix. Biochemistry 39:15429–15440

    PubMed  CAS  Google Scholar 

  119. Chang SG, Choi KD, Jang SH, Shin HC (2003) Role of disulfide bonds in the structure and activity of human insulin. Mol Cells 16:323–330

    PubMed  CAS  Google Scholar 

  120. Hua QX, Mayer JP, Jia W, Zhang J, Weiss MA (2006) The folding nucleus of the insulin superfamily: a flexible peptide model foreshadows the native state. J Biol Chem 281:28131–28142

    PubMed  CAS  Google Scholar 

  121. Zhu Q, Liang S, Martin L, Gasparini S, Menez A, Vita C (2002) Role of disulfide bonds in folding and activity of leiurotoxin I: just two disulfides suffice. Biochemistry 41:11488–11494

    PubMed  CAS  Google Scholar 

  122. Drakopoulou E, Vizzavona J, Neyton J, Aniort V, Bouet F, Virelizier H, Menez A, Vita C (1998) Consequence of the removal of evolutionary conserved disulfide bridges on the structure and function of charybdotoxin and evidence that particular cysteine spacings govern specific disulfide bond formation. Biochemistry 37:1292–1301

    PubMed  CAS  Google Scholar 

  123. Hober S, Forsberg G, Palm G, Hartmanis M, Nilsson B (1992) Disulfide exchange folding of insulin-like growth factor I. Biochemistry 31:1749–1756

    PubMed  CAS  Google Scholar 

  124. Huang QL, Zhao J, Tang YH, Shao SQ, Xu GJ, Feng YM (2007) The sequence determinant causing different folding behaviors of insulin and insulin-like growth factor-1. Biochemistry 46:218–224

    PubMed  CAS  Google Scholar 

  125. White CE, Hunter MJ, Meininger DP, Garrod S, Komives EA (1996) The fifth epidermal growth factor-like domain of thrombomodulin does not have an epidermal growth factor-like disulfide bonding pattern. Proc Natl Acad Sci USA 93:10177–10182

    PubMed  CAS  Google Scholar 

  126. Bulaj G, Olivera BM (2008) Folding of conotoxins: formation of the native disulfide bridges during chemical synthesis and biosynthesis of Conus peptides. Antioxid Redox Signal 10:141–155

    PubMed  CAS  Google Scholar 

  127. Kang TS, Vivekanandan S, Jois SD, Kini RM (2005) Effect of C-terminal amidation on folding and disulfide-pairing of alpha-conotoxin ImI. Angew Chem Int Ed Engl 44:6333–6337

    PubMed  CAS  Google Scholar 

  128. Zhang RM, Snyder GH (1991) Factors governing selective formation of specific disulfides in synthetic variants of alpha-conotoxin. Biochemistry 30:11343–11348

    PubMed  CAS  Google Scholar 

  129. Clarke J, Fersht AR (1993) Engineered disulfide bonds as probes of the folding pathway of barnase: increasing the stability of proteins against the rate of denaturation. Biochemistry 32:4322–4329

    PubMed  CAS  Google Scholar 

  130. Maleknia SD, Reixach N, Buxbaum JN (2006) Oxidation inhibits amyloid fibril formation of transthyretin. FEBS J 273:5400–5406

    PubMed  CAS  Google Scholar 

  131. Chugha P, Sage HJ, Oas TG (2006) Methionine oxidation of monomeric lambda repressor: the denatured state ensemble under nondenaturing conditions. Protein Sci 15:533–542

    PubMed  CAS  Google Scholar 

  132. Gao J, Yin DH, Yao Y, Sun H, Qin Z, Schoneich C, Williams TD, Squier TC (1998) Loss of conformational stability in calmodulin upon methionine oxidation. Biophys J 74:1115–1134

    PubMed  CAS  Google Scholar 

  133. Wood MJ, Becvar LA, Prieto JH, Melacini G, Komives EA (2003) NMR structures reveal how oxidation inactivates thrombomodulin. Biochemistry 42:11932–11942

    PubMed  CAS  Google Scholar 

  134. Dado GP, Gellman SH (1993) Redox control of secondary structure in a designed peptide. J Am Chem Soc 115:12609–12610

    CAS  Google Scholar 

  135. Wong CH (2005) Protein glycosylation: new challenges and opportunities. J Org Chem 70:4219–4225

    PubMed  CAS  Google Scholar 

  136. Helenius A, Aebi M (2004) Roles of N-linked glycans in the endoplasmic reticulum. Annu Rev Biochem 73:1019–1049

    PubMed  CAS  Google Scholar 

  137. Kornfeld S (1986) Trafficking of lysosomal enzymes in normal and disease states. J Clin Invest 77:1–6

    PubMed  CAS  Google Scholar 

  138. Sola RJ, Griebenow K (2009) Effects of glycosylation on the stability of protein pharmaceuticals. J Pharm Sci 98:1223–1245

    PubMed  CAS  Google Scholar 

  139. Sinclair AM, Elliott S (2005) Glycoengineering: the effect of glycosylation on the properties of therapeutic proteins. J Pharm Sci 94:1626–1635

    PubMed  CAS  Google Scholar 

  140. Berg-Fussman A, Grace ME, Ioannou Y, Grabowski GA (1993) Human acid beta-glucosidase. N-glycosylation site occupancy and the effect of glycosylation on enzymatic activity. J Biol Chem 268:14861–14866

    PubMed  CAS  Google Scholar 

  141. Kobayashi T, Honke K, Jin T, Gasa S, Miyazaki T, Makita A (1992) Components and proteolytic processing sites of arylsulfatase B from human placenta. Biochim Biophys Acta 1159:243–247

    PubMed  CAS  Google Scholar 

  142. Millat G, Froissart R, Maire I, Bozon D (1997) IDS transfer from overexpressing cells to IDS-deficient cells. Exp Cell Res 230:362–367

    PubMed  CAS  Google Scholar 

  143. Scriver CR (2001) The metabolic & molecular bases of inherited disease. McGraw-Hill, New York

    Google Scholar 

  144. Zhao KW, Faull KF, Kakkis ED, Neufeld EF (1997) Carbohydrate structures of recombinant human alpha-L-iduronidase secreted by Chinese hamster ovary cells. J Biol Chem 272:22758–22765

    PubMed  CAS  Google Scholar 

  145. Shental-Bechor D, Levy Y (2008) Effect of glycosylation on protein folding: a close look at thermodynamic stabilization. Proc Natl Acad Sci USA 105:8256–8261

    PubMed  CAS  Google Scholar 

  146. Wyss DF, Wagner G (1996) The structural role of sugars in glycoproteins. Curr Opin Biotechnol 7:409–416

    PubMed  CAS  Google Scholar 

  147. Wormald MR, Dwek RA (1999) Glycoproteins: glycan presentation and protein-fold stability. Structure 7:R155–R160

    PubMed  CAS  Google Scholar 

  148. Walsh MT, Watzlawick H, Putnam FW, Schmid K, Brossmer R (1990) Effect of the carbohydrate moiety on the secondary structure of beta 2-glycoprotein. I. Implications for the biosynthesis and folding of glycoproteins. Biochemistry 29:6250–6257

    PubMed  CAS  Google Scholar 

  149. Wyss DF, Choi JS, Li J, Knoppers MH, Willis KJ, Arulanandam AR, Smolyar A, Reinherz EL, Wagner G (1995) Conformation and function of the N-linked glycan in the adhesion domain of human CD2. Science 269:1273–1278

    PubMed  CAS  Google Scholar 

  150. O’Connor SE, Imperiali B (1996) Modulation of protein structure and function by asparagine-linked glycosylation. Chem Biol 3:803–812

    PubMed  Google Scholar 

  151. Rickert KW, Imperiali B (1995) Analysis of the conserved glycosylation site in the nicotinic acetylcholine receptor: potential roles in complex assembly. Chem Biol 2:751–759

    PubMed  CAS  Google Scholar 

  152. Shaanan B, Lis H, Sharon N (1991) Structure of a legume lectin with an ordered N-linked carbohydrate in complex with lactose. Science 254:862–866

    PubMed  CAS  Google Scholar 

  153. Helenius A (1994) How N-linked oligosaccharides affect glycoprotein folding in the endoplasmic reticulum. Mol Biol Cell 5:253–265

    PubMed  CAS  Google Scholar 

  154. Hickman S, Kornfeld S (1978) Effect of tunicamycin on IgM, IgA, and IgG secretion by mouse plasmacytoma cells. J Immunol 121:990–996

    PubMed  CAS  Google Scholar 

  155. Landolfi NF, Rich RR, Cook RG (1985) Differential glycosylation requirements for the cell surface expression of class I molecules. J Immunol 134:423–430

    PubMed  CAS  Google Scholar 

  156. Shackelford DA, Strominger JL (1983) Analysis of the oligosaccharides on the HLA-DR and DC1 B cell antigens. J Immunol 130:274–282

    PubMed  CAS  Google Scholar 

  157. Hebert DN, Zhang JX, Chen W, Foellmer B, Helenius A (1997) The number and location of glycans on influenza hemagglutinin determine folding and association with calnexin and calreticulin. J Cell Biol 139:613–623

    PubMed  CAS  Google Scholar 

  158. Hermans MM, Wisselaar HA, Kroos MA, Oostra BA, Reuser AJ (1993) Human lysosomal alpha-glucosidase: functional characterization of the glycosylation sites. Biochem J 289:681–686

    PubMed  CAS  Google Scholar 

  159. Ioannou YA, Zeidner KM, Grace ME, Desnick RJ (1998) Human alpha-galactosidase A: glycosylation site 3 is essential for enzyme solubility. Biochem J 332:789–797

    PubMed  CAS  Google Scholar 

  160. Kotch FW, Guzei IA, Raines RT (2008) Stabilization of the collagen triple helix by O-methylation of hydroxyproline residues. J Am Chem Soc 130:2952–2953

    PubMed  CAS  Google Scholar 

  161. Raines RT (2006) 2005 Emil Thomas Kaiser Award. Protein Sci 15:1219–1225

    PubMed  CAS  Google Scholar 

  162. Brodsky B, Ramshaw JA (1997) The collagen triple-helix structure. Matrix Biol 15:545–554

    PubMed  CAS  Google Scholar 

  163. Buczek O, Bulaj G, Olivera BM (2005) Conotoxins and the posttranslational modification of secreted gene products. Cell Mol Life Sci 62:3067–3079

    PubMed  CAS  Google Scholar 

  164. Lopez-Vera E, Walewska A, Skalicky JJ, Olivera BM, Bulaj G (2008) Role of hydroxyprolines in the in vitro oxidative folding and biological activity of conotoxins. Biochemistry 47:1741–1751

    PubMed  CAS  Google Scholar 

  165. Kubo S, Chino N, Kimura T, Sakakibara S (1996) Oxidative folding of omega-conotoxin MVIIC: effects of temperature and salt. Biopolymers 38:733–744

    PubMed  CAS  Google Scholar 

  166. Koivunen P, Salo KE, Myllyharju J, Ruddock LW (2005) Three binding sites in protein-disulfide isomerase cooperate in collagen prolyl 4-hydroxylase tetramer assembly. J Biol Chem 280:5227–5235

    PubMed  CAS  Google Scholar 

  167. Martinez A, Treston AM (1996) Where does amidation take place? Mol Cell Endocrinol 123:113–117

    PubMed  CAS  Google Scholar 

  168. Merkler DJ (1994) C-terminal amidated peptides: production by the in vitro enzymatic amidation of glycine-extended peptides and the importance of the amide to bioactivity. Enzyme Microb Technol 16:450–456

    PubMed  CAS  Google Scholar 

  169. Sforca ML, Oyama S Jr, Canduri F, Lorenzi CC, Pertinhez TA, Konno K, Souza BM, Palma MS, Ruggiero Neto J, Azevedo WF Jr, Spisni A (2004) How C-terminal carboxyamidation alters the biological activity of peptides from the venom of the eumenine solitary wasp. Biochemistry 43:5608–5617

    PubMed  CAS  Google Scholar 

  170. Yasin B, Lehrer RI, Harwig SS, Wagar EA (1996) Protegrins: structural requirements for inactivating elementary bodies of Chlamydia trachomatis. Infect Immun 64:4863–4866

    PubMed  CAS  Google Scholar 

  171. Katayama H, Ohira T, Aida K, Nagasawa H (2002) Significance of a carboxyl-terminal amide moiety in the folding and biological activity of crustacean hyperglycemic hormone. Peptides 23:1537–1546

    PubMed  CAS  Google Scholar 

  172. Mor A, Nicolas P (1994) The NH2-terminal alpha-helical domain 1–18 of dermaseptin is responsible for antimicrobial activity. J Biol Chem 269:1934–1939

    PubMed  CAS  Google Scholar 

  173. Sandvik AK, Dockray GJ (1999) Biological activity of carboxy-terminal gastrin analogs. Eur J Pharmacol 364:199–203

    PubMed  CAS  Google Scholar 

  174. Ali MF, Soto A, Knoop FC, Conlon JM (2001) Antimicrobial peptides isolated from skin secretions of the diploid frog, Xenopus tropicalis (Pipidae). Biochim Biophys Acta 1550:81–89

    PubMed  CAS  Google Scholar 

  175. Meredith J, Ring M, Macins A, Marschall J, Cheng NN, Theilmann D, Brock HW, Phillips JE (1996) Locust ion transport peptide (ITP): primary structure, cDNA and expression in a baculovirus system. J Exp Biol 199:1053–1061

    PubMed  CAS  Google Scholar 

  176. Fuller E, Green BR, Catlin P, Buczek O, Nielsen JS, Olivera BM, Bulaj G (2005) Oxidative folding of conotoxins sharing an identical disulfide bridging framework. FEBS J 272:1727–1738

    PubMed  CAS  Google Scholar 

  177. Shearer MJ (1992) Vitamin K metabolism and nutriture. Blood Rev 6:92–104

    PubMed  CAS  Google Scholar 

  178. Hauschka PV, Lian JB, Gallop PM (1975) Direct identification of the calcium-binding amino acid, gamma-carboxyglutamate, in mineralized tissue. Proc Natl Acad Sci USA 72:3925–3929

    PubMed  CAS  Google Scholar 

  179. Howard JB, Nelsestuen GL (1975) Isolation and characterization of vitamin K-dependent region of bovine blood clotting factor X. Proc Natl Acad Sci USA 72:1281–1285

    PubMed  CAS  Google Scholar 

  180. Suttie JW (1985) Vitamin K-dependent carboxylase. Annu Rev Biochem 54:459–477

    PubMed  CAS  Google Scholar 

  181. McIntosh JM, Olivera BM, Cruz LJ, Gray WR (1984) Gamma-carboxyglutamate in a neuroactive toxin. J Biol Chem 259:14343–14346

    PubMed  CAS  Google Scholar 

  182. Rigby AC, Lucas-Meunier E, Kalume DE, Czerwiec E, Hambe B, Dahlqvist I, Fossier P, Baux G, Roepstorff P, Baleja JD, Furie BC, Furie B, Stenflo J (1999) A conotoxin from Conus textile with unusual posttranslational modifications reduces presynaptic Ca2+ influx. Proc Natl Acad Sci USA 96:5758–5763

    PubMed  CAS  Google Scholar 

  183. Bulaj G, Buczek O, Goodsell I, Jimenez EC, Kranski J, Nielsen JS, Garrett JE, Olivera BM (2003) Efficient oxidative folding of conotoxins and the radiation of venomous cone snails. Proc Natl Acad Sci USA 100(Suppl 2):14562–14568

    PubMed  CAS  Google Scholar 

  184. Gowd KH, Twede V, Watkins M, Krishnan KS, Teichert RW, Bulaj G, Olivera BM (2008) Conantokin-P, an unusual conantokin with a long disulfide loop. Toxicon 52:203–213

    PubMed  CAS  Google Scholar 

  185. Chen Z, Blandl T, Prorok M, Warder SE, Li L, Zhu Y, Pedersen LG, Ni F, Castellino FJ (1998) Conformational changes in conantokin-G induced upon binding of calcium and magnesium as revealed by NMR structural analysis. J Biol Chem 273:16248–16258

    PubMed  CAS  Google Scholar 

  186. Latzer J, Shen T, Wolynes PG (2008) Conformational switching upon phosphorylation: a predictive framework based on energy landscape principles. Biochemistry 47:2110–2122

    PubMed  Google Scholar 

  187. Johnson LN, Lewis RJ (2001) Structural basis for control by phosphorylation. Chem Rev 101:2209–2242

    PubMed  CAS  Google Scholar 

  188. Jacobs SA, Khorasanizadeh S (2002) Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. Science 295:2080–2083

    PubMed  CAS  Google Scholar 

  189. Tatko CD, Waters ML (2004) Comparison of C-H…pi and hydrophobic interactions in a beta-hairpin peptide: impact on stability and specificity. J Am Chem Soc 126:2028–2034

    PubMed  CAS  Google Scholar 

  190. Hughes RM, Waters ML (2005) Influence of N-methylation on a cation-pi interaction produces a remarkably stable beta-hairpin peptide. J Am Chem Soc 127:6518–6519

    PubMed  CAS  Google Scholar 

  191. Hughes RM, Waters ML (2006) Arginine methylation in a beta-hairpin peptide: implications for Arg-pi interactions, DeltaCp(o), and the cold denatured state. J Am Chem Soc 128:12735–12742

    PubMed  CAS  Google Scholar 

  192. Hilfiker A, Hilfiker-Kleiner D, Pannuti A, Lucchesi JC (1997) mof, a putative acetyl transferase gene related to the Tip60 and MOZ human genes and to the SAS genes of yeast, is required for dosage compensation in Drosophila. EMBO J 16:2054–2060

    PubMed  CAS  Google Scholar 

  193. Reynolds MR, Berry RW, Binder LI (2007) Nitration in neurodegeneration: deciphering the “Hows” “nYs”. Biochemistry 46:7325–7336

    PubMed  CAS  Google Scholar 

  194. Pylypenko O, Schonichen A, Ludwig D, Ungermann C, Goody RS, Rak A, Geyer M (2008) Farnesylation of the SNARE protein Ykt6 increases its stability and helical folding. J Mol Biol 377:1334–1345

    PubMed  CAS  Google Scholar 

  195. Bowie JU, Reidhaar-Olson JF, Lim WA, Sauer RT (1990) Deciphering the message in protein sequences: tolerance to amino acid substitutions. Science 247:1306–1310

    PubMed  CAS  Google Scholar 

  196. Plaxco KW, Riddle DS, Grantcharova V, Baker D (1998) Simplified proteins: minimalist solutions to the ‘protein folding problem’. Curr Opin Struct Biol 8:80–85

    PubMed  CAS  Google Scholar 

  197. Miller JH (1979) Genetic studies of the lac repressor. XI. On aspects of lac repressor structure suggested by genetic experiments. J Mol Biol 131:249–258

    PubMed  CAS  Google Scholar 

  198. Miller JH, Coulondre C, Hofer M, Schmeissner U, Sommer H, Schmitz A, Lu P (1979) Genetic studies of the lac repressor. IX. Generation of altered proteins by the suppression of nonsence mutations. J Mol Biol 131:191–222

    PubMed  CAS  Google Scholar 

  199. Miller JH, Schmeissner U (1979) Genetic studies of the lac repressor. X. Analysis of missense mutations in the lacI gene. J Mol Biol 131:223–248

    PubMed  CAS  Google Scholar 

  200. Brown BM, Sauer RT (1999) Tolerance of Arc repressor to multiple-alanine substitutions. Proc Natl Acad Sci USA 96:1983–1988

    PubMed  CAS  Google Scholar 

  201. Islam MM, Sohya S, Noguchi K, Yohda M, Kuroda Y (2008) Crystal structure of an extensively simplified variant of bovine pancreatic trypsin inhibitor in which over one-third of the residues are alanines. Proc Natl Acad Sci USA 105:15334–15339

    PubMed  CAS  Google Scholar 

  202. Kuroda Y, Kim PS (2000) Folding of bovine pancreatic trypsin inhibitor (BPTI) variants in which almost half the residues are alanine. J Mol Biol 298:493–501

    PubMed  CAS  Google Scholar 

  203. Munson M, O’Brien R, Sturtevant JM, Regan L (1994) Redesigning the hydrophobic core of a four-helix-bundle protein. Protein Sci 3:2015–2022

    PubMed  CAS  Google Scholar 

  204. Baldwin RL (1986) Temperature dependence of the hydrophobic interaction in protein folding. Proc Natl Acad Sci USA 83:8069–8072

    PubMed  CAS  Google Scholar 

  205. Bashford D, Chothia C, Lesk AM (1987) Determinants of a protein fold. Unique features of the globin amino acid sequences. J Mol Biol 196:199–216

    PubMed  CAS  Google Scholar 

  206. Chothia C, Levitt M, Richardson D (1981) Helix to helix packing in proteins. J Mol Biol 145:215–250

    PubMed  CAS  Google Scholar 

  207. Kellis JT Jr, Nyberg K, Sali D, Fersht AR (1988) Contribution of hydrophobic interactions to protein stability. Nature 333:784–786

    PubMed  CAS  Google Scholar 

  208. Eriksson AE, Baase WA, Zhang XJ, Heinz DW, Blaber M, Baldwin EP, Matthews BW (1992) Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science 255:178–183

    PubMed  CAS  Google Scholar 

  209. Gassner NC, Baase WA, Matthews BW (1996) A test of the “jigsaw puzzle” model for protein folding by multiple methionine substitutions within the core of T4 lysozyme. Proc Natl Acad Sci USA 93:12155–12158

    PubMed  CAS  Google Scholar 

  210. Lim WA, Sauer RT (1991) The role of internal packing interactions in determining the structure and stability of a protein. J Mol Biol 219:359–376

    PubMed  CAS  Google Scholar 

  211. Baldwin EP, Hajiseyedjavadi O, Baase WA, Matthews BW (1993) The role of backbone flexibility in the accommodation of variants that repack the core of T4 lysozyme. Science 262:1715–1718

    PubMed  CAS  Google Scholar 

  212. Pielak GJ, Auld DS, Beasley JR, Betz SF, Cohen DS, Doyle DF, Finger SA, Fredericks ZL, Hilgen-Willis S, Saunders AJ (1995) Protein thermal denaturation, side-chain models, and evolution: amino acid substitutions at a conserved helix–helix interface. Biochemistry 34:3268–3276

    PubMed  CAS  Google Scholar 

  213. Axe DD, Foster NW, Fersht AR (1996) Active barnase variants with completely random hydrophobic cores. Proc Natl Acad Sci USA 93:5590–5594

    PubMed  CAS  Google Scholar 

  214. Kamtekar S, Schiffer JM, Xiong H, Babik JM, Hecht MH (1993) Protein design by binary patterning of polar and nonpolar amino acids. Science 262:1680–1685

    PubMed  CAS  Google Scholar 

  215. Moffet DA, Hecht MH (2001) De novo proteins from combinatorial libraries. Chem Rev 101:3191–3203

    PubMed  CAS  Google Scholar 

  216. Harbury PB, Zhang T, Kim PS, Alber T (1993) A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants. Science 262:1401–1407

    PubMed  CAS  Google Scholar 

  217. Schafmeister CE, LaPorte SL, Miercke LJ, Stroud RM (1997) A designed four helix bundle protein with native-like structure. Nat Struct Biol 4:1039–1046

    PubMed  CAS  Google Scholar 

  218. Riddle DS, Santiago JV, Bray-Hall ST, Doshi N, Grantcharova VP, Yi Q, Baker D (1997) Functional rapidly folding proteins from simplified amino acid sequences. Nat Struct Biol 4:805–809

    PubMed  CAS  Google Scholar 

  219. Taylor SV, Walter KU, Kast P, Hilvert D (2001) Searching sequence space for protein catalysts. Proc Natl Acad Sci USA 98:10596–10601

    PubMed  CAS  Google Scholar 

  220. Walter KU, Vamvaca K, Hilvert D (2005) An active enzyme constructed from a 9-amino acid alphabet. J Biol Chem 280:37742–37746

    PubMed  CAS  Google Scholar 

  221. Silverman JA, Balakrishnan R, Harbury PB (2001) Reverse engineering the (beta/alpha)8 barrel fold. Proc Natl Acad Sci USA 98:3092–3097

    PubMed  CAS  Google Scholar 

  222. Hemmingsen JM, Gernert KM, Richardson JS, Richardson DC (1994) The tyrosine corner: a feature of most Greek key beta-barrel proteins. Protein Sci 3:1927–1937

    PubMed  CAS  Google Scholar 

  223. Yao J, Dyson HJ, Wright PE (1994) Three-dimensional structure of a type VI turn in a linear peptide in water solution. Evidence for stacking of aromatic rings as a major stabilizing factor. J Mol Biol 243:754–766

    PubMed  CAS  Google Scholar 

  224. Moore DT, Berger BW, DeGrado WF (2008) Protein–protein interactions in the membrane: sequence, structural, and biological motifs. Structure 16:991–1001

    PubMed  CAS  Google Scholar 

  225. Gsponer J, Vendruscolo M (2006) Theoretical approaches to protein aggregation. Protein Pept Lett 13:287–293

    PubMed  CAS  Google Scholar 

  226. Carrell RW, Lomas DA (1997) Conformational disease. Lancet 350:134–138

    PubMed  CAS  Google Scholar 

  227. Conn PM, Ulloa-Aguirre A, Ito J, Janovick JA (2007) G protein-coupled receptor trafficking in health and disease: lessons learned to prepare for therapeutic mutant rescue in vivo. Pharmacol Rev 59:225–250

    PubMed  CAS  Google Scholar 

  228. Brady RO (2006) Enzyme replacement for lysosomal diseases. Annu Rev Med 57:283–296

    PubMed  CAS  Google Scholar 

  229. Santucci R, Sinibaldi F, Fiorucci L (2008) Protein folding, unfolding and misfolding: role played by intermediate States. Mini Rev Med Chem 8:57–62

    PubMed  CAS  Google Scholar 

  230. Dahiyat BI, Mayo SL (1997) De novo protein design: fully automated sequence selection. Science 278:82–87

    PubMed  CAS  Google Scholar 

  231. Kortemme T, Ramirez-Alvarado M, Serrano L (1998) Design of a 20-amino acid, three-stranded beta-sheet protein. Science 281:253–256

    PubMed  CAS  Google Scholar 

  232. Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302:1364–1368

    PubMed  CAS  Google Scholar 

  233. Hecht MH, Richardson JS, Richardson DC, Ogden RC (1990) De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence. Science 249:884–891

    PubMed  CAS  Google Scholar 

  234. Magliery TJ, Regan L (2004) Combinatorial approaches to protein stability and structure. Eur J Biochem 271:1595–1608

    PubMed  CAS  Google Scholar 

  235. Baltzer L, Nilsson H, Nilsson J (2001) De novo design of proteins—what are the rules? Chem Rev 101:3153–3163

    PubMed  CAS  Google Scholar 

  236. Moult J, Fidelis K, Kryshtafovych A, Rost B, Hubbard T, Tramontano A (2007) Critical assessment of methods of protein structure prediction-Round VII. Proteins 69(Suppl 8):3–9

    PubMed  CAS  Google Scholar 

  237. Honig B (1999) Protein folding: from the levinthal paradox to structure prediction. J Mol Biol 293:283–293

    PubMed  CAS  Google Scholar 

  238. Walsh G, Jefferis R (2006) Post-translational modifications in the context of therapeutic proteins. Nat Biotechnol 24:1241–1252

    PubMed  CAS  Google Scholar 

  239. Bradbury AF, Smyth DG (1991) Peptide amidation. Trends Biochem Sci 16:112–115

    PubMed  CAS  Google Scholar 

  240. Dong J, Ye P, Schade AJ, Gao S, Romo GM, Turner NT, McIntire LV, Lopez JA (2001) Tyrosine sulfation of glycoprotein I(b)alpha. Role of electrostatic interactions in von Willebrand factor binding. J Biol Chem 276:16690–16694

    PubMed  CAS  Google Scholar 

  241. Tarcsa E, Marekov LN, Mei G, Melino G, Lee SC, Steinert PM (1996) Protein unfolding by peptidylarginine deiminase. Substrate specificity and structural relationships of the natural substrates trichohyalin and filaggrin. J Biol Chem 271:30709–30716

    PubMed  CAS  Google Scholar 

  242. Janke C, Rogowski K, van Dijk J (2008) Polyglutamylation: a fine-regulator of protein function? ‘Protein modifications: beyond the usual suspects’ review series. EMBO Rep 9:636–641

    PubMed  CAS  Google Scholar 

  243. MacRae TH (1997) Tubulin post-translational modifications—enzymes and their mechanisms of action. Eur J Biochem 244:265–278

    PubMed  CAS  Google Scholar 

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Acknowledgement

Tse Siang Kang is supported by the National University of Singapore under the Overseas Postdoctoral Fellowship.

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Kang, T.S., Kini, R.M. Structural determinants of protein folding. Cell. Mol. Life Sci. 66, 2341–2361 (2009). https://doi.org/10.1007/s00018-009-0023-5

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