Structure-based statistical analysis of transmembrane helices

European Biophysics Journal

Volumn 42, Issue 2-3, 2013, Pages 199-207

  Baeza Delgado, Carlos ^a   Marti Renom, Marc A ^b,c   Mingarro, Ismael ^a  

^a UNIVERSITY OF VALENCIA   (Spain)

^b Structural Genomics Team   (Spain)

^c CENTRE FOR GENOMIC REGULATION CRG   (Spain)

Author keywords

Amino acid distribution; Membrane protein; Statistical analysis; Transmembrane helices

Indexed keywords

MEMBRANE PROTEIN; WATER;

BIOLOGY; CELL MEMBRANE; CHEMICAL STRUCTURE; CHEMISTRY; CONFERENCE PAPER; METABOLISM; PROTEIN DATABASE; PROTEIN SECONDARY STRUCTURE; SOLUBILITY; THERMODYNAMICS;

CELL MEMBRANE; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MEMBRANE PROTEINS; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY; SOLUBILITY; THERMODYNAMICS; WATER;

EID: 84876250689     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-012-0813-9     Document Type: Conference Paper

References (37)

1. Arkin IT, Brunger AT (1998) Statistical analysis of predicted transmembrane alpha-helices. Biochim Biophys Acta 1429:113-128
2. Berman HM, Berman HM, Westbrook J, Westbrook J, Feng Z, Feng Z, Gilliland G, Gilliland G, Bhat TN, Bhat TN, Weissig H, Weissig H, Shindyalov IN, Shindyalov IN, Bourne PE, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235-242
3. Blaber M, Zhang XJ, Matthews BW (1993) Structural basis of amino acid alpha helix propensity. Science 260:1637-1640
4. Bowie JU (1997) Helix packing in membrane proteins. J Mol Biol 272:780-789
5. Bywater RP, Thomas D, Vriend G (2001) A sequence and structural study of transmembrane helices. J Comput Aided Mol Des 15:533-552
6. Cordes FS, Bright JN, Sansom MSP (2002) Proline-induced distortions of transmembrane helices. J Mol Biol 323:951-960
7. Eilers M, Patel AB, Liu W, Smith SO (2002) Comparison of helix interactions in membrane and soluble alpha-bundle proteins. Biophys J 82:2720-2736
8. Engel DE, DeGrado WF (2004) Amino acid propensities are position-dependent throughout the length of alpha-helices. J Mol Biol 337:1195-1205
9. Hessa T, Kim H, Bihlmaier K, Lundin C, Boekel J, Andersson H, Nilsson I, White SH, von Heijne G (2005) Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature 433:377-381
10. Hessa T, Meindl-Beinker NM, Bernsel A, Kim H, Sato Y, Lerch-Bader M, Nilsson I, White SH, von Heijne G (2007) Molecular code for transmembrane-helix recognition by the Sec61 translocon. Nature 450:1026-1030
11. Holt A, Killian JA (2009) Orientation and dynamics of transmembrane peptides: the power of simple models. Eur Biophys J 39:609-621
12. Huang Y, Huang Y, Niu B, Niu B, Gao Y, Gao Y, Fu L, Fu L, Li W, Li W (2010) CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 26:680-682. Available at: http://eutils.ncbi.nlm.nih. gov/entrez/eutils/elink.fcgi?dbfrom=pubmedandid=20053844andretmode=refandcmd= prlinks
13. Illergård K, Kauko A, Elofsson A (2011) Why are polar residues within the membrane core evolutionary conserved? Proteins 79:79-91
14. Jayasinghe S, Hristova K, White SH (2001a) Energetics, stability, and prediction of transmembrane helices. J Mol Biol 312:927-934
15. Jayasinghe S, Jayasinghe S, Hristova K, Hristova K, White SH, White SH (2001b) MPtopo: a database of membrane protein topology. Protein Sci 10:455-458
16. Johansson ACV, Lindahl E (2007) Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations. Proteins 70:1332-1344
17. Lerch-Bader M, Lundin C, Kim H, Nilsson I, von Heijne G (2008) Contribution of positively charged flanking residues to the insertion of transmembrane helices into the endoplasmic reticulum. Proc Natl Acad Sci USA 105:4127-4132
18. Li SC, Deber CM (1994) A measure of helical propensity for amino acids in membrane environments. Nat Struct Biol 1:558
19. Lomize MA, Pogozheva ID, Joo H, Mosberg HI, Lomize AL (2012) OPM database and PPM web server: resources for positioning of proteins in membranes. Nucleic Acids Res 40:370-376
20. MacCallum JL, Bennett WFD, Tieleman DP (2008) Distribution of amino acids in a lipid bilayer from computer simulations. Biophys J 94:3393-3404
21. Martínez-Gil L, Saurí A, Marti-Renom MA, Mingarro I (2011) Membrane protein integration into the endoplasmic reticulum. FEBS J 278:3846-3858
22. Nilsson I, von Heijne G (1990) Fine-tuning the topology of a polytopic membrane protein: role of positively and negatively charged amino acids. Cell 62:1135-1141
23. Nilsson I, Johnson AE, von Heijne G (2003) How hydrophobic is alanine? J Biol Chem 278:29389-29393
24. Nilsson J, Persson B, von Heijne G (2005) Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes. Proteins 60:606-616
25. Orzáez M, Salgado J, Giménez-Giner A, Pérez- Payá E, Mingarro I (2004) Influence of proline residues in transmembrane helix packing. J Mol Biol 335:631-640
26. Pal L, Chakrabarti P, Basu G (2003) Sequence and structure patterns in proteins from an analysis of the shortest helices: implications for helix nucleation. J Mol Biol 326:273-291
27. Saurí A, Tamborero S, Martínez-Gil L, Johnson AE, Mingarro I (2009) Viral membrane protein topology is dictated by multiple determinants in its sequence. J Mol Biol 387:113-128
28. Senes A, Gerstein M, Engelman DM (2000) Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions. J Mol Biol 296:921-936
29. Sharpe HJ, Stevens TJ, Munro S (2010) A comprehensive comparison of transmembrane domains reveals organelle-specific properties. Cell 142:158-169
30. Ulmschneider MB, Sansom MS (2001) Amino acid distributions in integral membrane protein structures. Biochim Biophys Acta 1512:1-14
31. Ulmschneider MB, Sansom MSP, Di Nola A (2005) Properties of integral membrane protein structures: derivation of an implicit membrane potential. Proteins 59:252-265
32. von Heijne G (1992) Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J Mol Biol 225:487-494
33. Wallin E, von Heijne G (1998) Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 7:1029-1038
34. White SH (2004) The progress of membrane protein structure determination. Protein Sci 13:1948-1949
35. White SH (2009) Biophysical dissection of membrane proteins. Nature 459:344-346
36. White SH, Wimley WC (1999) Membrane protein folding and stability: physical principles. Annu Rev Biophys Biomol Struct 28:319-365
37. Williams RW, Chang A, Juretić D, Loughran S (1987) Secondary structure predictions and medium range interactions. Biochim Biophys Acta 916:200-204