Aromatic Side Chain Water-to-Lipid Transfer Free Energies Show a Depth Dependence across the Membrane Normal

Journal of the American Chemical Society

Volumn 138, Issue 25, 2016, Pages 7946-7950

  McDonald, Sarah K ^a   Fleming, Karen G ^a  

^a JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC COMPOUNDS; AROMATIZATION; BIOLOGICAL MEMBRANES; CHAINS; CYTOLOGY; FREE ENERGY; GIBBS FREE ENERGY; MEMBRANES; MOLECULAR BIOLOGY;

AROMATIC SIDE CHAINS; AROMATIC-AROMATIC INTERACTIONS; CONCENTRATION GRADIENTS; GIBBS FREE ENERGY CHANGES; HYDROPHOBIC SEQUENCES; NEAREST-NEIGHBOR COUPLING; PROTEIN-LIPID INTERACTIONS; TRANSFER ENERGETICS;

PROTEINS;

LIPID; MEMBRANE PROTEIN; WATER; COPPER; TRYPTOPHAN; TYROSINE;

ARTICLE; BILAYER MEMBRANE; ENERGY; ENERGY TRANSFER; MEASUREMENT; MEMBRANE; BINDING SITE; CELL MEMBRANE; CHEMICAL PHENOMENA; CHEMISTRY; CRYSTALLIZATION; ESCHERICHIA COLI; LIPID BILAYER; METABOLISM; MOLECULAR DYNAMICS; MUTAGENESIS; MUTATION; ORGANIC CHEMISTRY; PROCEDURES; PROTEIN FOLDING; PROTEIN STABILITY; THERMODYNAMICS;

BINDING SITES; CELL MEMBRANE; CHEMISTRY, ORGANIC; COPPER; CRYSTALLIZATION; ESCHERICHIA COLI; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; LIPID BILAYERS; LIPIDS; MEMBRANE PROTEINS; MOLECULAR DYNAMICS SIMULATION; MUTAGENESIS; MUTATION; PROTEIN FOLDING; PROTEIN STABILITY; THERMODYNAMICS; TRYPTOPHAN; TYROSINE; WATER;

EID: 84976599704     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/jacs.6b03460     Document Type: Article

References (29)

1. Yildirim, M. A.; Goh, K. I.; Cusick, M. E.; Barabasi, A. L.; Vidal, M. Nat. Biotechnol. 2007, 25, 1119 10.1038/nbt1338
2. Dill, K. A. Biochemistry 1990, 29, 7133 10.1021/bi00483a001
3. Rose, G. D.; Geselowitz, A. R.; Lesser, G. J.; Lee, R. H.; Zehfus, M. H. Science 1985, 229, 834 10.1126/science.4023714
4. Rees, D. C.; DeAntonio, L.; Eisenberg, D. Science 1989, 245, 510 10.1126/science.2667138
5. Schiffer, M.; Chang, C.-H.; Stevens, F. Protein Eng., Des. Sel. 1992, 5, 213 10.1093/protein/5.3.213
6. Wallin, E.; Tsukihara, T.; Yoshikawa, S.; von Heijne, G.; Elofsson, A. Protein Sci. 1997, 6, 808 10.1002/pro.5560060407
7. Ulmschneider, M. B.; Sansom, M. S.; Di Nola, A. Proteins: Struct., Funct., Genet. 2005, 59, 252 10.1002/prot.20334
8. Senes, A.; Chadi, D. C.; Law, P. B.; Walters, R. F.; Nanda, V.; Degrado, W. F. J. Mol. Biol. 2007, 366, 436 10.1016/j.jmb.2006.09.020
9. Hsieh, D.; Davis, A.; Nanda, V. Protein Sci. 2012, 21, 50 10.1002/pro.758
10. Slusky, J. S.; Dunbrack, R. L., Jr. Bioinformatics 2013, 29, 2122 10.1093/bioinformatics/btt355
11. Killian, J. A.; von Heijne, G. Trends Biochem. Sci. 2000, 25, 429 10.1016/S0968-0004(00)01626-1
12. Jacobs, R. E.; White, S. H. Biochemistry 1989, 28, 3421 10.1021/bi00434a042
13. Wimley, W. C.; White, S. H. Nat. Struct. Biol. 1996, 3, 842 10.1038/nsb1096-842
14. Yau, W.-M.; Wimley, W. C.; Gawrisch, K.; White, S. H. Biochemistry 1998, 37, 14713 10.1021/bi980809c
15. Wolfenden, R. J. Gen. Physiol. 2007, 129, 357 10.1085/jgp.200709743
16. Wiener, M. C.; White, S. H. Biophys. J. 1992, 61, 434 10.1016/S0006-3495(92)81849-0
17. White, S. H.; Wimley, W. C. Biochim. Biophys. Acta, Rev. Biomembr. 1998, 1376, 339 10.1016/S0304-4157(98)00021-5
18. MacCallum, J. L.; Bennett, W. F.; Tieleman, D. P. Biophys. J. 2008, 94, 3393 10.1529/biophysj.107.112805
19. Snijder, H. J.; Ubarretxena-Belandia, I.; Blaauw, M.; Kalk, K. H.; Verheij, H. M.; Egmond, M. R.; Dekker, N.; Dijkstra, B. W. Nature 1999, 401, 717 10.1038/401717a0
20. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996, 14, 33 10.1016/0263-7855(96)00018-5
21. Serrano, L.; Bycroft, M.; Fersht, A. R. J. Mol. Biol. 1991, 218, 465 10.1016/0022-2836(91)90725-L
22. Hong, H.; Rinehart, D.; Tamm, L. K. Biochemistry 2013, 52, 4413 10.1021/bi400344b
23. Hong, H.; Park, S.; Jimenez, R. H. F.; Rinehart, D.; Tamm, L. K. J. Am. Chem. Soc. 2007, 129, 8320 10.1021/ja068849o
24. Kannan, N.; Vishveshwara, S. Protein Eng., Des. Sel. 2000, 13, 753 10.1093/protein/13.11.753
25. Chourasia, M.; Sastry, G. M.; Sastry, G. N. Int. J. Biol. Macromol. 2011, 48, 540 10.1016/j.ijbiomac.2011.01.008
26. Hessa, T.; Meindl-Beinker, N. M.; Bernsel, A.; Kim, H.; Sato, Y.; Lerch-Bader, M.; Nilsson, I.; White, S. H.; von Heijne, G. Nature 2007, 450, 1026 10.1038/nature06387
27. Lin, M.; Gessmann, D.; Naveed, H.; Liang, J. J. Am. Chem. Soc. 2016, 138, 2592 10.1021/jacs.5b10307
28. Capponi, S.; Heyden, M.; Bondar, A.-N.; Tobias, D. J.; White, S. H. Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 9016 10.1073/pnas.1424483112
29. Tsuzuki, S.; Uchimaru, T. Curr. Org. Chem. 2006, 10, 745 10.2174/138527206776818937