Free energy barrier estimation of unfolding the α-helical surfactant-associated polypeptide c

Proteins: Structure, Function and Genetics

Volumn 43, Issue 4, 2001, Pages 395-402

  Zangi, Ronen ^a   Kovacs, Helena ^b,c   Van Gunsteren, Wilfred F ^b   Johansson, Jan ^d   Mark, Alan E ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b ETH ZURICH   (Switzerland)

^c Bruker AG   (Switzerland)

^d KAROLINSKA INSTITUTE   (Sweden)

Author keywords

SP C; Free energy barrier; MD simulations; Protein unfolding

Indexed keywords

POLYPEPTIDE; SURFACTANT PROTEIN C;

ALPHA HELIX; ARTICLE; ENERGY; MOLECULAR DYNAMICS; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; SIMULATION; THERMODYNAMICS;

AMINO ACID SEQUENCE; ANIMALS; COMPUTER SIMULATION; HUMANS; MODELS, MOLECULAR; PEPTIDES; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEOLIPIDS; PULMONARY SURFACTANTS; SOLVENTS; THERMODYNAMICS;

EID: 0035370881     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.1052     Document Type: Article

References (26)

1. Goerke J. Pulmonary surfactant: functions and molecular composition. Biochim Biophys Acta 1998;1408:79-89.
2. Johansson J, Szyperski T, Curstedt T, Wüthrich K. The NMR structure of the pulmonary surfactant-associated polypeptide SP-C in an apolar solvent contains a valyl-rich α-helix. Biochemistry 1994;33:6015-6023.
3. Pastrana B, Mautone AJ, Mendelsohn R. Fourier transform infrared studies of secondary structure and orientation of pulmonary surfactant SP-C and its effect on the dynamic surface properties of phospholipids. Biochemistry 1991;30: 10058-10064.
4. Vandenbussche G, Clercx A, Curstedt T, Johansson J, Ruysschaert JM. Structure and orientation of the surface-associated protein C in a lipid bilayer. Eur J Biochem 1992;203:201-209.
5. Johansson J, Szyperski T, Wüthrich K. Pulmonary surfactant-associated polypeptide SP-C in lipid micelles: CD studies of intact SP-C and NMR secondary structure determination of depalmitoyl-SP-C (1-17). FEBS Lett 1995;362:261-265.
6. Johansson J, Nilsson G, Strömberg R, Robertson B, Jörnvall H, Curstedt T. Secondary structure and biophysical activity of synthetic analogs of the pulmonary surfactant polypeptide SP-C. Biochem J 1995;307:535-541.
7. Baatz JE, Smyth KL, Whitsett JA, Baxter C, Absalom DR. Structure and functions of a dimeric form of surfactant protein SP-C: a Fourier transform infrared and surfactometry study. Chem Phys Lipids 1992;63:91-104.
8. Beers MF, Kim CY, Dodia C, Fisher A. Localization, synthesis and processing of surfactant protein SP-C in rat lung analyzed by epitope-specific antipeptide antibodies. J Biol Chem 1994;269: 20318-20328.
9. Szyperski T, Vandenbussche G, Curstedt T, Ruysschaert J-M, Wüthrich K, Johansson J. Pulmonary surfactant-associated polypeptide C in a mixed organic solvent transforms from a monomeric α-helical state into β-sheet aggregates. Protein Sci 1998;7:2533-2540.
10. Gustafsson M, Thyberg J, Näslund J, Eliasson E, Johansson J. Amyloid fibril formation by pulmonary surfactant protein C. FEBS Lett 1999;464:138-142.
11. Rost B, Sander C. Combining evolutionary information and the neural networks to predict protein secondary structure. Proteins 1994;19:55-72.
12. Li S-C, Deber CM. A measure of helical propensity for amino acids in membrane environments. Nature Struct Biol 1994;1:368-373.
13. Kovacs H, Mark AE, Johansson J, van Gunsteren WF. The effect of environment on the stability of an integral membrane helix: molecular dynamics simulations of surfactant protein C in chloroform, methanol and water. J Mol Biol 1995;247:808-822.
14. Brooks CL. Helix-coil kinetics: folding time scales for helical peptides from a sequential kinetic model. J Phys Chem 1996;100: 2546-2549.
15. Berendsen HJC, van der Spoel D, van Drunen R. GROMACS: a message-passing parallel molecular dynamics implementation. Comp Phys Commun 1995;91:43-56.
16. van der Spoel D, Hess B, Feenstra KA, Lindahl E, Berendsen HJC. GROMACS user manual version 2.0. Groningen, The Netherlands: Nijenborgh AG; 1999. http://md.chem.rug.nl/~gmx.
17. van Gunsteren WF, Billeter SR, Eising AA, Hünenberger PH, Krüger P, Mark AE, Scott WRP, Tironi IG. Biomolecular simulation: GROMOS96 manual and user guide. Groningen, The Netherlands: BIOMOS BV; 1996.
18. Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J. Interaction models for water in relation to protein hydration. In: Pullman B, editor. Intermolecular forces. Dordrecht, The Netherlands: D. Reidel; 1981. p 331-342.
19. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
20. Miyamoto S, Kollman PA. SETTLE: an analytical version of the SHAKE and RATTLE algorithms for rigid water models. J Comp Chem 1992; 13:952-962.
21. Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the Cartesian equations of motion of a system with constraints; molecular dynamics of n-alkanes. J Comp Phys 1977;23:327-341.
22. Tirado-Rives J, Jorgensen WL. Molecular dynamics simulations of the unfolding of an α-helical analogue of ribonuclease A S-peptide in water. Biochemistry 1991;30:3864-3871.
23. Englander SW, Sosnick TR, Englander JJ, Mayne L. Mechanisms and uses of hydrogen exchange. Curr Opin Struct Biol 1996;6:18-23.
24. Mark AE, van Gunsteren WF. Decomposition of the free energy of a system in terms of specific interactions: implications for theoretical and experimental studies. J Mol Biol 1994;240:167-176.
25. Brooks CL, Nilsson L. Promotion of helix formation in peptides dissolved in alcohol and water-alcohol mixtures. J Am Chem Soc 1993;115:11034-11035.
26. Eaton WA, Thompson PA, Chan C-K, Hagen SJ, Hofrichter J. Fast events in protein folding. Structure 1996;4:1133-1139.