A model study of protein nascent chain and cotranslational folding using hydrophobic-polar residues

Proteins: Structure, Function and Genetics

Volumn 70, Issue 2, 2008, Pages 442-449

  Lu, Hsiao Mei ^a   Liang, Jie ^a,b  

^a University of Illinois at Chicago   (United States)

^b Chinese National Human Genome Center at Shanghai   (China)

Author keywords

Cotranslational folding; Lattice model; Nascent polypeptide; Off lattice model; Protein folding

Indexed keywords

AMINO ACID; CHAPERONE; POLYMER; PROTEIN;

ARTICLE; HYDROPHOBICITY; MODEL; POINT MUTATION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE;

MODELS, MOLECULAR; POINT MUTATION; PROTEIN BIOSYNTHESIS; PROTEIN CONFORMATION; PROTEIN FOLDING;

EID: 37849006746     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21575     Document Type: Article

References (44)

1. Frydman J. Folding of newly translated proteins in vivo: the role of molecular chaperones. Annu Rev Biochem 2001;70:603-647.
2. Thulasiraman V, Yang CF, Frydman J. In vivo newly translated polypeptides are sequestered in a protected folding environment. EMBO J 1999;18:85-95.
3. Bukau B, Deuerling E, Pfund C, Craig EA. Getting newly synthesized proteins into shape. Cell 2000;101:119-122.
4. Ellis RJ, Hemmingsen SM. Molecular chaperones: proteins essential for the biogenesis of some macromolecular structures. Trends Biochem Sci 1989;14:339-342.
5. Hartl FU. Molecular chaperones in cellular protein folding. Nature 1996;381:571-579.
6. Hartl F, Hayer-Hartl M. Molecular chaperones in the cytosol: from nascent chain to folded protein. Science 2002;295:1852-1858.
7. Clark P. Protein folding in the cell: reshaping the folding funnel. Trends Biochem Sci 2004;29:527-534.
8. Ferbitz L, Maier T, Patzelt H, Bukau B, Deuerling E, Ban N. Trigger factor in complex with the ribosome forms a molecular cradle for nascent proteins. Nature 2004;431:590-596.
9. Nissen P, Hansen J, Ban N, Moore P, Steitz TA. The structural basis of ribosome activity in peptide bond synthesis. Science 2000;289:920-930.
10. Dobson C. Protein folding and misfolding, Nature 2003;426:884-890.
11. Eaton W, Munoz V, Thompson P, Henry E, Hofrichter J. Kinetics and dynamics of loops, α-helices, β-hairpins, and fast-folding proteins. Ace Chem Res 1998;31:745-753.
12. Snow C, Nguyen H, Pande V, Gruebele M. Absolute comparison of simulated and experimental protein-folding dynamics. Nature 2002; 420:102-106.
13. Yang WY, Gruebele M. Folding at the speed limit. Nature 2003; 423:193-197.
14. Mayor U, Guydosh NR, Johnson CM, Grossmann JG, Sato S, Jas GS, Freund SM, Alonso DO, Daggett V, Fersht AR. The complete folding pathway of a protein from nanoseconds to microseconds. Nature 2003;421:863-867.
15. Fedorov A, Baldwin T. Contribution of cotranslational folding to the rate of formation of native protein structure. Proc Natl Acad Sci USA 1995;92:1227-1231.
16. Komar A, Kommer A, Krasheninnikov I, Spirin A. Cotranslational folding of globin. J Biol Chem 1997;272:10646-10651.
17. Fedorov A, Baldwin T, Cotranslational protein folding. J Biol Chem 1997;272:32715-32718.
18. Kolb V. Cotranslational protein folding. Mol Biol Mosk 2001; 35:682-90.
19. Laio A, Micheletti C. Are structural biases at protein termini a signature of vectorial folding? Proteins 2006;62:17-23.
20. Lau KF, Dill KA. A lattice statistical mechanics model of the conformation and sequence spaces of proteins. Macromolecules 1989;22: 3986.
21. Chan HS, Dill KA. Compact polymers. Macromolecules 1989;22: 1559-1573.
22. Dill KA. Dominant forces in protein folding. Biochemistry 1990;29: 7133-7155.
23. Shakhnovich EI, Gutin A. Enumeration of all conformations of copolymers with random sequence of links. J Chem Phys 1990;93: 5967-5971.
24. Camacho CJ, Thirumalai D. Kinetice and therodynamics of foding in model proteins. Proc Natl Acad Sci USA 1993;90:6369-6372.
25. Pande VS, Grosberg AY, Joerg C, Tanaka T. Enumeration of the Hamiltonian walks on a cubic sublattice. J Phys A Math Gen 1996; 29:4753-4756.
26. Socci ND, Onuchic JN. Folding kinetics of protein like heteropolymers. J Chem Phys 1994;101:1519.
27. Dill KA, Bromberg S, Yue K, Fiebig KM, Yee DP, Thomas PD, Chan HS. Principles of protein folding - a perspective from simple exact models. Protein Sci 1995;4:561-602.
28. Sali A, Shakhnovich EI, Karplus M. How does a protein fold? Nature 1994;369:248-251.
29. Shrivastava I, Vishveshwara S, Cieplak M, Maritan A, Banavar JR. Lattice model for rapidly folding protein-like heteropolymers. Proc Natl Acad Sci USA 1995;92:9206-9209.
30. Klimov DK, Thirumalai D. Criterion that determines the foldability of proteins. Phys Rev Lett 1996;76:4070-4073.
31. Melin R, Li H, Wingreen N, Tang C. Designability, thermodynamic stability, and dynamics in protein folding: a lattice model study. J Chem Phys 1999;110:1252.
32. Chan HS, Dill KA. The effects of internal constraints on the configurations of chain molecules. J Chem Phys 1990;92:3118-3135.
33. Liang J, Zhang J, Chen R. Statistical geometry of packing defects of lattice chain polymer from enumeration and sequential Monte Carlo method. J Chem Phys 2002;117:3511-3521.
34. Zhang J, Chen Y, Chen R, Liang J. Importance of chirality and reduced flexibility of protein side chains: a study with square and tetrahedral lattice models. J Chem Phys 2004;121:592-603.
35. Chan H, Shimizu S, Kaya H. Cooperativity principles in protein folding. Methods Enzymol 2004;380:350-79.
36. Wallin S, Chan H. A critical assessment of the topomer search model of protein folding using a continuum explicit-chain model with extensive conformational sampling. Protein Sci 2005;14:1643-60.
37. Zhang J, Chen Y, Chen R, Liang J. Emprirical protein function for simplified protein models: combining contact and local sequence-structure descriptors. Proteins 2006;63:949-960.
38. Park B, Levitt M. The complexity and accuracy of discrete state models of protein structure. J Mol Biol 1995;249:493-507.
39. Eilers M, Schatz G. Binding of a specific ligand inhibits import of a purified precursor protein into mitochondria. Nature 1986;322:228-232.
40. Neupert W, Hartl FU, Craig EA, Pfanner N. How do polypeptides cross the mitochondrial membranes? Cell 1990;63:447-450.
41. Landry SJ, Gierasch LM. Recognition of nascent polypeptides for targeting and folding. Trends Biochem Sci 1991;16:159-163.
42. von Heijne G. Signal sequences. The limits of variation. J Mol Biol 1985;184:99-105.
43. Chan H. Modeling protein density of states: additive hydrophobic effects are insufficient for calorimetric two-state cooperativity. Proteins 2000;40:543-571.
44. Gillespie B, Plaxco KW. Using protein folding rates to test protein folding theories. Annu Rev Biochem 2004;73:837-859.