Effects of side chains in helix nucleation differ from helix propagation

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 18, 2014, Pages 6636-6641

  Miller, Stephen E ^a   Watkins, Andrew M ^a   Kallenbach, Neville R ^a   Arora, Paramjit S ^a  

^a NEW YORK UNIVERSITY   (United States)

Author keywords

Helix propensity; Synthetic helices

Indexed keywords

ALANINE; ASPARTIC ACID; CARBON; LEUCINE; LYSINE; PEPTIDE; STABILIZING AGENT;

ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; HYDROGEN BOND; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN UNFOLDING; THERMODYNAMICS;

HELIX PROPENSITY; SYNTHETIC HELICES;

AMINO ACID SEQUENCE; AMINO ACIDS; CIRCULAR DICHROISM; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PEPTIDES; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 84899841805     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1322833111     Document Type: Article

References (51)

1. Dill KA, MacCallum JL (2012) The protein-folding problem, 50 years on. Science 338(6110):1042-1046
2. Zimm BH, Bragg JK (1959) Theory of the phase transition between helix and random coil in polypeptide chains. J Chem Phys 31(2):526-535.
3. Qian H Schellman J.A. 1992, Helix-coil theories: A comparative study for finite length preferences, J Phys Chem,96,10, 3987-3994..
4. Lifson S, Roig A (1961) On the th eory of helix-coil transitions in polypeptides. J Chem Phys 34(6):1963-1974
5. Munoz V, Serrano L (1997) Development of the multiple sequence approximation within the AGADIR model of alpha-helix fo rmation: Comparison with Zimm-Bragg and Lifson-Roig formalisms. Biopolymers 41(5):495-509
6. Rohl CA, Chakrabartty A, Baldwin RL (1996) Helix propagation and N-cap propensities of the amino aci ds measured in alanine-based peptides in 40 volume percent trifluoroethanol. Protein Sci 5(12):2623-2637
7. Blaber M, et al. (1994) Determination of alpha-helix propensity within the context of a f olded protein. Sites 44 and 131 in bacteriophage T4 lysozyme. J Mol Biol 235(2): 600-624
8. Wojcik J, Altmann KH, Scheraga HA (1990) Helix-coil stability constants for the naturally occurring amino acids in water. XXIV. Half-cystine parameters from random poly(hydroxybutylglutamine-CO-S-methylthio-L-cystei ne). Biopolymers 30(1- 2):121-134
9. Padmanabhan S, Marqusee S, Ridgeway T, Laue TM, Baldwin RL (1990) Relative helixforming tendencies of nonpolar amino acids. Nature 344(6263):268-270
10. O? Neil KT, DeGrado WF (1990) A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science 250(4981):646-651
11. Lyu PC, Liff MI, Marky LA, Kallenbach NR (1990) Side chain contributions to the stability of alpha-helical structure in peptides. Science 250(4981):669-673
12. Richardson JM, Lopez MM, Makhatadze GI (2005) Enthalpy of helix-coil transition: Missing link in rationalizing the thermodynamics of helix-forming propensities of the amino acid residues. Proc Natl Acad Sci USA 102(5):1413-1418.
13. Lyu PC, Sherman JC, Chen A, Kallenbach NR (1991) Alpha-helix stabilization by natural and unnatural amino acids with alkyl side chains. Proc Natl Acad Sci USA 88(12): 5317-5320
14. Neumaier S, Reiner A, Bü ttner M, Fierz B, Kiefhaber T (2013) Testing the diffusing boundary model for the helix-coil transition in peptides. Proc Natl Acad Sci USA 110(32):12905-12910
15. Aurora R, Rose GD (1998) Helix capping. Protein Sci 7(1):21-38
16. Lopez MM, Chin D-H, Baldwin RL, Makhatadze GI (2002) The enthalpy of the alanine peptide helix m easured by isothermal titration calorimetry using metal-binding to induce helix formation. Proc Natl Acad Sci USA 99(3):1298-1302
17. Sun JK, Penel S, Doig AJ (2000) Determination of -helix N1 energies after addition of N1, N2, and N3 preferences to helix/coil theory. Protein Sci 9(4):750-754
18. Creamer TP, Rose GD (1992) Side-chain entropy opposes alpha -helix formation but rationalizes experimentally determined helix-forming propensities. Proc Natl Acad Sci USA 89(13):5937-5941
19. Chakrabartty A, Kortemme T, Baldwin RL (1994) Helix propensit ies of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci 3(5):843-852
20. Patgiri A, Jochim AL, Arora PS (2008) A hydrogen bond s urrogate approach for stabilization of short peptide sequences in alpha-helical conformation. Acc Chem Res 41(10):1289-1300
21. Wang D, Chen K, Kulp JL, III, Arora PS (2006) Evaluation of b iologically relevant short alpha-helices stabilized by a main-chain hydrogen-bond surrogate. J Am Chem Soc 128(28):9248-9256
22. Liu J, Wang D, Zheng Q, Lu M, Arora PS (2008) Atomic str ucture of a short alpha-helix stabilized by a main chain hydrogen-bond surrogate. J Am Chem Soc 130(13): 4334-4337
23. Kushal S, et al. (2013) Protein domain mimetics as in vivo modulators of hypoxia-inducible factor signaling. Proc Natl Acad Sci USA 110(39):15602-15607.
24. Patgiri A, Yadav KK, Arora PS, Bar-Sagi D (2011, An orthosteric inhibitor of the Ras- Sos interaction, Nat Chem Biol,7,9, 585-587..
25. Miller SE, Kallenbach NR, Arora PS (2012) Reversible -helix formation controlled by a hydrogen bond surrogate. Tetrahedron 68(23):4434-4437
26. Serrano AL, Tucker MJ, Gai F (2011) Direct assessment of the -helix nucleation time. J Phys Chem B 115(22):7472-7478
27. Lin MM, Mohammed OF, Jas GS, Zewail AH (2011) Speed limit of protein folding evidenced in secondary structure dynamics. Proc Natl Acad Sci USA 108(40): 16622-16627
28. De Sancho D, Best RB (2011) What is the time scale for -helix nucleation J Am Chem Soc 133(17):6809-6816
29. Huang C-Y, Klemke JW, Getahun Z, DeGrado WF, Gai F (2001) Temperaturedependent helix-coil transition of an alanine based peptide. J Am Chem Soc 123(38): 9235-9238
30. Tam JP, Wu CR, Liu W, Zhang JW (1991) Disulfide bond formation in peptides by dimethyl sulfoxide. Scope and applications. J Am Chem Soc 113(17):6657-6662
31. Haney CM, Loch MT, Horne WS (2011) Promoting peptide -helix formation with dynamic covalent oxime side-chain cross-links. Chem Commun 47(39):10915-10917
32. Bredenbeck J, Helbing J, Kumita JR, Woolley GA, Hamm P (2005) -Helix formation in a photoswitchable peptide tracked from picoseconds to microseconds by time-resolved IR spectroscopy. Proc Natl Acad Sci USA 102(7):2379-2384
33. Ihalainen JA, et al. (2008) -Helix folding in the presence of structural constraints. Proc Natl Acad Sci USA 105(28):9588-9593
34. Li M, Yamato K, Ferguson JS, Gong B (2006) Sequence-specific association in aqueous media by integrating hydrogen bonding and dynamic covalent interactions. J Am Chem Soc 128(39):12628-12629
35. Kussie PH, et al. (1996) Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science 274(5289):948-953
36. Patgiri A, Joy ST, Arora PS (2012) Nucleation effects in peptide foldamers. J Am Chem Soc 134(28):11495-11502
37. Mahon AB, Arora PS (2012) Design, synthesis and protein-targeting properties of thioether-linked hydrogen bond surrogate helices. Chem Commun (Camb) 48(10): 1416-1418
38. Henchey LK, Porter JR, Ghosh I, Arora PS (2010) High specificity in protein recognition by hydrogen-bond-surrogate -helices: Selective inhibition of th e p53/MDM2 complex. ChemBioChem 11(15):2104-2107
39. Young WS, Brooks CL, 3rd (1996) A microscopic view of helix propagation: N and Cterminal helix growth in alanine helices. J Mol Biol 259(3):560-572
40. Cochran DAE, Doig AJ (2001) Effect of the N2 residue on the stability of the -helix for all 20 amino acids. Protein Sci 10(7):1305-1311
41. Wa ng Y, Nip AM, Wishart DS (1997) A simple method to quantitatively measure polypeptide JHNH coupling constants from TOCSY or NOESY spectra. J Biomol NMR 10(4):373-382
42. Pardi A, Billeter M, Wü thrich K (1984) Calibration of the angular dependence of the amide proton-C alpha proton coupling constants, 3JHN alpha, in a globular protein. Use of 3JHN alpha for identification of helical secondary structure. J Mol Biol 180 (3): 741-751
43. Brantley RK, Haeffner-Gormley L, Wetlaufer DB (1984) Preparation of a positively charged maleimide and its application to the high-performance liquid chromatographic separation of the tr yptic peptides of lysozyme. J Chromatogr A 295(1): 220-225
44. Huyghues-Despointes BM, Scholtz JM, Baldwin RL (1993) Effect of a single aspartate on helix stability at different positions in a neutral alanine-based peptide. Protein Sci 2(10):1604-1611
45. Yang JX, Zhao K, Gong YX, Vologodskii A, Kallenbach NR (1998) Alpha-helix nucleation constant in copolypeptides of alanine and ornithine or lysine. J Am Chem Soc 120(41):10646-10652
46. Shoemaker KR, Kim PS, York EJ, Stewart JM, Baldwin RL (1987) Tests of the helix dipole model for stabilization of alpha-helices. Nature 326(6113):563-567
47. Laio A, Gervasio FL (2008) Metadynamics: A method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science. Rep Prog Phys 71(12):126601
48. Ensing B, De Vivo M, Liu Z, Moore P, Klein ML (2005) Metadynamics as a tool for exploring free energy landscapes of chemical reactions. Acc Chem Res 39(2):73-81
49. Daggett V, Levitt M (1992) Molecular dynamics simulations of helix denaturation. J Mol Biol 223(4):1121-1138
50. Bowers KJ, et al. (2006) Scalable algorithms for mo lecular dynamics simulations on commodity clusters. Proceedings of the 2006 ACM/IEEE Conference on Supercomputing (ACM, Tampa, FL), p 84. 51. Case DA (2012) AMBER 12 (Univ of California, San Francisco)
51. Joung IS, Cheatham TE, 3rd (2008) Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. J Phys Chem B 112(30):9020-9041