Protein folding: A problem with multiple solutions

Journal of Biomolecular Structure and Dynamics

Volumn 31, Issue 4, 2013, Pages 351-362

  Bywater, Robert Paul ^a  

^a MAGDALEN COLLEGE   (United Kingdom)

Author keywords

Aromatic interactions; Hydrogen bonding; Hydrophobic interactions; Protein activation; Protein folding

Indexed keywords

G PROTEIN COUPLED RECEPTOR; HYDROGEN; MEMBRANE PROTEIN;

ARTICLE; DYNDOM DATABASE; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE;

CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; HYDROGEN BONDING; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 84879217292     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2012.703062     Document Type: Article

References (38)

1. Andreeva, A., & Murzin, A.G. (2006). Evolution of protein fold in the presence of functional constraints. Current Opinion in Structural Biology, 16, 399-408.
2. Anfinsen, C.B. (1973). Principles that govern the folding of protein chains. Science, 181, 223-230.
3. Anfinsen, C.B., Haber, E., Sela, M., & White, F.H. (1961). The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. Proceedings of the National Academy of Sciences USA, 47, 1309-1314.
4. Beadle, G.W., & Tatum, E.L. (1941). Genetic control of biochemical reactions in Neurospora. Proceedings of the National Academy of Sciences USA, 27, 499-506.
5. Ben-Naim, A. (2006). On the driving forces for protein-protein association. Journal of Chemical Physics, 125, 24901-24911.
6. Berendsen, H.J.C. (2011). The relevance of distance statistics for protein folding. Journal of Biomolecular Structure & Dynamics, 28(4), 599-601.
7. Bywater, R.P. (2005). Location and nature of the residues important for ligand recognition in G-protein coupled receptor. Journal of Molecular Recognition, 18, 60-72.
8. Bywater, R.P., & Denny-Gouldson, P.R. (2006). Molecular mechanisms of G-protein activation. In D. Rognan (Ed.), Ligand design for G-protein coupled receptors (pp. 83-97). Weinheim: Wiley-VCH.
9. Bywater, R.P., Sørensen, A., Røgen, P., & Hjorth, P.G. (2002). Construction of the simplest model to explain complex receptor activation kinetics. Journal of Theoretical Biology, 218, 139-147.
10. Chou, K.C. (1995). A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins, 21, 310-344.
11. Chouard, T. (2011). Breaking the protein rules. Nature, 471, 151-153.
12. Cooper, A. (2000). Heat capacity of hydrogen bonded networks: An alternative view of protein folding thermodynamics. Biophysical Chemistry, 85, 25-39.
13. Dill, K.A. (1990). Dominant forces in protein folding. Biochemistry, 29, 7133-7155.
14. Dima, R.I. (2011). Stoichiometry and topology in protein folding. Journal of Biomolecular Structure & Dynamics, 28(4), 617-618.
15. Gether, U., & Kobilka, B.K. (1998). G protein-coupled receptors. II. Mechanism of activation. The Journal of Biological Chemistry, 273, 17979-17982.
16. Hayward, S., & Berendsen, H.J.C. (1998). Systematic analysis of domain motions in proteins from conformational change; new results on citrate synthase and T4 lysozyme. Proteins, 30, 144-154.
17. Head-Gordon, T., Sorenson, J.M., Pertsemlidis, A., & Glaeser, F.M. (1997). Differences in hydration structure near hydrophobic and hydrophilic amino acids. Biophysical Journal, 73, 2106-2115.
18. Henzler-Wildman, K., & Kern, D. (2007). Dynamic personalities of proteins. Nature, 450, 964-972.
19. Kamtekar, S., Schiffer, J.M., Xiong, H., Babik, J.M., & Hecht, H.M. (1993). Protein design by binary patterning of polar and nonpolar amino acids. Science, 262, 1680-1685.
20. Kidd, B.A., Baker, D., & Thomas, W.E. (2009). Computation of conformational coupling in allosteric proteins. PLoS Computational Biology, 5(8), e1000484.
21. Krieger, E., Koraimann, G., & Vriend, G. (2002). Increasing the precision of comparative models with YASARA NOVA - a self-parameterizing force field. Proteins, 47, 393-402.
22. Lee, R.A., Razaz, M., & Hayward, S. (2003). The DynDom database of protein domain motions. Bioinformatics, 19, 1290-1291.
23. Levinthal, C. (1968). Are there pathways for protein folding? Journal of Chimie Physiquw, 65, 44-45.
24. Marks, D.S., Colwell, L.J., Sheridan, R., Hopf, T.A., Pagnani, A., Zecchina, R., & Sander, C. (2011). Protein 3D structure computed from evolutionary sequence variation. PloS One, 6, e28766. doi: 10.1371/journal.pone. 0028766.g001.
25. Matthews, B.W. (2011). Stoichiometry versus hydrophobicity in protein folding. Journal of Biomolecular Structure & Dynamics, 28(4), 589-591.
26. Mittal, A., Jayaram, B., Shenoy, S., & Bawa, T.S. (2010). A stoichiometry driven universal spatial organization of backbones of folded proteins: Are there Chargaff's rules for protein folding? Journal of Biomolecular Structure & Dynamics, 28(4), 133-142.
27. Montgomerie, S., Sundararaj, S., Gallin, W.J., & Wishart, D.S. (2006). Improving the accuracy of protein secondary structure prediction using structural alignment. BMC Bioinformatics, 7, 301-314.
28. Perez, D., & Karnik, S.S. (2005). Multiple signaling states of G-protein-coupled receptors. Pharmacological Reviews, 57, 147-161.
29. Sarma, R.H. (2011). A conversation on protein folding. Journal of Biomolecular Structure & Dynamics, 28(4), 587-588.
30. Seeliger, D., & De Groot, B.L. (2010). Conformational transitions upon ligand binding: Holo-structure prediction from apo conformations. PLoS Computational Biology, 6(1), e1000634.
31. Sun, S., Thomas, P.D., & Dill, K.A. (1995). A simple protein folding algorithm using a binary code and secondary structure constraints. Protein Engineering, 8, 769-778.
32. Taylor, W.R., & Hatrick, K. (1994). Compensating changes in protein multiple sequence alignments. Protein Engineering, 7, 341-348.
33. Uversky, V.N., & Dunker, A.K. (2010). Understanding protein non-folding. Biochima et Biophysica Acta, 1804, 1231-1264.
34. Venselaar, H., Joosten, R.P., Vroling, B., Baakman, C.A., Hekkelman, M.L., Krieger, E., & Vriend, G. (2009). Homology modelling and spectroscopy, a never-ending love story. European Biophysics Journal, 39, 551-563.
35. Vriend, G. (1990). WHAT IF: A molecular modelling and drug design program. Journal of Molecular Graphics, 8, 52-56.
36. Vroling, B., Bywater, R.P., Oliveira, L., & Vriend, G. (2010). GPCRs: Past, present and future. In Structural bioinformatics of membrane proteins (pp. 251-278). Vienna: Springer-Verlag.
37. Wright, P.E., & Dyson, H.J. (1999). Intrinsically unstructured proteins: Re-assessing the protein structure-function paradigm. Journal of Molecular Biology, 293, 321-331.
38. Xue, B., Dunker, A.K., & Uversky, V.N. (2012). The roles of intrinsic disorder in orchestrating the Wnt-Pathway. Journal of Biomolecular Structure & Dynamics, 29(5), 843-861.