The role of Buergi-Dunitz interactions in the structural stability of proteins

Proteins: Structure, Function and Bioinformatics

Volumn 78, Issue 13, 2010, Pages 2831-2838

  Fufezan, Christian ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

Author keywords

Buergi Dunitz; N *; Protein stability

Indexed keywords

CARBON; OXYGEN;

ARTICLE; BUERGI DUNITZ TRAJECTORY; HYDROGEN BOND; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; SIMULATION;

CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; HYDROGEN BONDING; MODELS, MOLECULAR; PROTEIN STABILITY; PROTEIN STRUCTURE, SECONDARY; PROTEINS; STATIC ELECTRICITY;

EID: 77957975318     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22800     Document Type: Article

References (36)

1. Burgi HB, Dunitz JD, Shefter E. Geometrical reaction coordinates. II. Nucleophilic addition to a carbonyl group. J Am Chem Soc 1973;95:5065-5067.
2. Paulini R, Muller K, Diederich F. Orthogonal multipolar interactions in structural chemistry and biology. Angew Chem Int Ed Engl 2005;44:1788-1805.
3. Burgi HB, Dunitz JD, Shefter E. Pharmacological implications of the conformation of the methadone base. Nat New Biol 1973;244:186-187.
4. Hall SR, Ahmed FR. The crystal structure of cryptopine, C21H23OsN. Acta Cryst 1968;B24:346-355.
5. DeRider ML, Wilkens SJ, Waddell MJ, Bretscher LE, Weinhold F, Raines RT, Markley JL. Collagen stability: insights from NMR spectroscopic and hybrid density functional computational investigations of the effect of electronegative substituents on prolyl ring conformations. J Am Chem Soc 2002;124:2497-2505.
6. Choudhary A, Gandla D, Krow GR, Raines RT. Nature of amide carbonyl-carbonyl interactions in proteins. J Am Chem Soc 2009;131:7244.
7. Panasik N, Eberhardt ES, Edison AS, Powell DR, Raines RT. Inductive effects on the structure of proline residues. Int J Peptide Protein Res 1994;44:262-269.
8. Eberhardt ES, Panasik N, Jr, Raines RT. Inductive effects on the energetics of prolyl peptide bond isomerization: implications for collagen folding and stability. J Am Chem Soc 1996;118:12261-12266.
9. Holmgren SK, Taylor KM, Bretscher LE, Raines RT. Code for collagen's stability deciphered. Nature 1998;392:666-667.
10. Hinderaker MP, Raines RT. An electronic effect on protein structure. Protein Sci 2003;12:1188-1194.
11. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
12. Wang G, Dunbrack RL, Jr. PISCES: recent improvements to a PDB sequence culling server. Nucleic Acids Res 2005;33:W94-W98.
13. Fufezan C, Specht M. p3d, python module for structural bioinformatics. BMC Bioinformatics 2009;10:258.
14. Esposito L, Vitagliano L, Zagari A, Mazzarella L. Pyramidalization of backbone carbonyl carbon atoms in proteins. Protein Sci 2000;9:2038-2042.
15. Engh RA, Huber R. Structure quality and target parameters. In: Rossmann MG, Arnold E, editors. International tables for crystallography. Dordrecht: Kluwer Academic Publishers; 2001. Vol. F, Ch. 18.3, pp 382-392.
16. Fufezan C, Specht M. Available at: http://p3d.fufezan.net. 2009 (Accessed June 1, 2010).
17. Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph 1996;14:33-38,27-28.
18. Bondi A. van der Waals volumes and radii. J Phys Chem 1964;68:441-451.
19. Karplus PA. Experimentally observed conformation-dependent geometry and hidden strain in proteins. Protein Sci 1996;5:1406-1420.
20. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
21. Ramachandran GN, Sasisekharan V. Conformation of polypeptides and proteins. Adv Protein Chem 1968;23:283-438.
22. Scholtz JM, Marqusee S, Baldwin RL, York EJ, Stewart JM, Santoro M, Bolen DW. Calorimetric determination of the enthalpy change for the alpha-helix to coil transition of an alanine peptide in water. Proc Natl Acad Sci USA 1991;88:2854-2858.
23. Ooi T, Oobatake M. Prediction of the thermodynamics of protein unfolding: the helix-coil transition of poly(L-alanine). Proc Natl Acad Sci USA 1991;88:2859-2863.
24. Dwyer DS. Electronic properties of amino acid side chains: quantum mechanics calculation of substituent effects. BMC Chem Biol 2005;5:2.
25. Marqusee S, Robbins VH, Baldwin RL. Unusually stable helix formation in short alanine-based peptides. Proc Natl Acad Sci USA 1989;86:5286-5290.
26. Zimm BH, Bragg JK. Theory of the phase transition between helix and random coil in polypeptide chains. J Chem Phys 1959;31:526.
27. Mu-oz V, Serrano L. Elucidating the folding problem of helical peptides using empirical parameters. Nat Struct Mol Biol 1994;1:399-409.
28. Barlow DJ, Thornton JM. Helix geometry in proteins. J Mol Biol 1988;201:601-619.
29. Yang AS, Honig B. Free energy determinants of secondary structure formation: I.a-helices. J Mol Biol 1995;252:351-365.
30. Fu H, Grimsley GR, Razvi A, Scholtz JM, Pace CN. Increasing protein stability by improving beta-turns. Proteins 2009;77:491-498.
31. Suzuki Y. A general principle of increasing protein thermostability. Proc Jpn Acad Ser B 1989;65:146-148.
32. Watanabe K, Masuda T, Ohashi H, Mihara H, Suzuki Y. Multiple proline substitutions cumulatively thermostabilize Bacillus cereus ATCC7064 oligo-1,6-glucosidase. Irrefragable proof supporting the proline rule. Eur J Biochem 1994;226:277-283.
33. Matthews BW, Nicholson H, Becktel WJ. Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding. Proc Natl Acad Sci USA 1987;84:6663-6667.
34. Steiner T, Hess P, Bae JH, Wiltschi B, Moroder L, Budisa N. Synthetic biology of proteins: tuning GFPs folding and stability with fluoroproline. PLoS One 2008;3:e1680.
35. Ho BK, Thomas A, Brasseur R. Revisiting the Ramachandran plot: hard-sphere repulsion, electrostatics, and H-bonding in the alphahelix. Protein Sci 2003;12:2508-2522.
36. MacArthur MW, Thornton JM. Deviations from planarity of the peptide bond in peptides and proteins. J Mol Biol 1996;264:1180-1195.