Comparison of helix interactions in membrane and soluble alpha-bundle proteins
- PMID: 11964258
- PMCID: PMC1302060
- DOI: 10.1016/S0006-3495(02)75613-0
Comparison of helix interactions in membrane and soluble alpha-bundle proteins
Abstract
Helix-helix interactions are important for the folding, stability, and function of membrane proteins. Here, two independent and complementary methods are used to investigate the nature and distribution of amino acids that mediate helix-helix interactions in membrane and soluble alpha-bundle proteins. The first method characterizes the packing density of individual amino acids in helical proteins based on the van der Waals surface area occluded by surrounding atoms. We have recently used this method to show that transmembrane helices pack more tightly, on average, than helices in soluble proteins. These studies are extended here to characterize the packing of interfacial and noninterfacial amino acids and the packing of amino acids in the interfaces of helices that have either right- or left-handed crossing angles, and either parallel or antiparallel orientations. We show that the most abundant tightly packed interfacial residues in membrane proteins are Gly, Ala, and Ser, and that helices with left-handed crossing angles are more tightly packed on average than helices with right-handed crossing angles. The second method used to characterize helix-helix interactions involves the use of helix contact plots. We find that helices in membrane proteins exhibit a broader distribution of interhelical contacts than helices in soluble proteins. Both helical membrane and soluble proteins make use of a general motif for helix interactions that relies mainly on four residues (Leu, Ala, Ile, Val) to mediate helix interactions in a fashion characteristic of left-handed helical coiled coils. However, a second motif for mediating helix interactions is revealed by the high occurrence and high average packing values of small and polar residues (Ala, Gly, Ser, Thr) in the helix interfaces of membrane proteins. Finally, we show that there is a strong linear correlation between the occurrence of residues in helix-helix interfaces and their packing values, and discuss these results with respect to membrane protein structure prediction and membrane protein stability.
Similar articles
-
Helix packing moments reveal diversity and conservation in membrane protein structure.J Mol Biol. 2004 Mar 26;337(3):713-29. doi: 10.1016/j.jmb.2004.02.001. J Mol Biol. 2004. PMID: 15019789
-
Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins.J Mol Biol. 2001 Aug 24;311(4):891-907. doi: 10.1006/jmbi.2001.4908. J Mol Biol. 2001. PMID: 11518538
-
Helix packing in membrane proteins.J Mol Biol. 1997 Oct 10;272(5):780-9. doi: 10.1006/jmbi.1997.1279. J Mol Biol. 1997. PMID: 9368657
-
Ca2+ -ATPase structure in the E1 and E2 conformations: mechanism, helix-helix and helix-lipid interactions.Biochim Biophys Acta. 2002 Oct 11;1565(2):246-66. doi: 10.1016/s0005-2736(02)00573-4. Biochim Biophys Acta. 2002. PMID: 12409199 Review.
-
From interactions of single transmembrane helices to folding of alpha-helical membrane proteins: analyzing transmembrane helix-helix interactions in bacteria.Curr Protein Pept Sci. 2007 Feb;8(1):45-61. doi: 10.2174/138920307779941578. Curr Protein Pept Sci. 2007. PMID: 17305560 Review.
Cited by
-
Computational design and experimental characterization of peptides intended for pH-dependent membrane insertion and pore formation.ACS Chem Biol. 2015 Apr 17;10(4):1082-93. doi: 10.1021/cb500759p. Epub 2015 Jan 28. ACS Chem Biol. 2015. PMID: 25630033 Free PMC article.
-
Mouse Models of Human Pathogenic Variants of TBC1D24 Associated with Non-Syndromic Deafness DFNB86 and DFNA65 and Syndromes Involving Deafness.Genes (Basel). 2020 Sep 24;11(10):1122. doi: 10.3390/genes11101122. Genes (Basel). 2020. PMID: 32987832 Free PMC article.
-
Developing a high-quality scoring function for membrane protein structures based on specific inter-residue interactions.J Comput Aided Mol Des. 2012 Mar;26(3):301-9. doi: 10.1007/s10822-012-9556-z. Epub 2012 Mar 1. J Comput Aided Mol Des. 2012. PMID: 22395902 Free PMC article.
-
Transmembrane domain V plays a stabilizing role in the function of human bile acid transporter SLC10A2.Biochemistry. 2013 Jul 30;52(30):5117-24. doi: 10.1021/bi400028q. Epub 2013 Jul 16. Biochemistry. 2013. PMID: 23815591 Free PMC article.
-
Association of transmembrane helices: what determines assembling of a dimer?J Comput Aided Mol Des. 2006 Jan;20(1):27-45. doi: 10.1007/s10822-006-9034-6. Epub 2006 May 19. J Comput Aided Mol Des. 2006. PMID: 16775778
References
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources