Internal packing of helical membrane proteins

Eilers, Markus; Shekar, S. Chandra; Shieh, Ted; Smith, Steven O.; Fleming, Patrick

doi:10.1073/pnas.97.11.5796

Cited by 245 publications

(248 citation statements)

References 47 publications

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“…However, despite the predominance of hydrophobic residues within the lipid bilayer, analyses of TM domains reveal that about 25% of all TM domains from single-spanning membrane proteins contain a strongly polar residue. [32][33][34] Our results are consistent with previous studies that polar residues could provide stability and specificity to TM-TM helix association; for example, mutations at polar residues Gln129 and His139 dramatically decrease CAT activities in the TOXCAT assay. The ability of a polar residue to promote helix association appears to be related to the side chain's potential to be both a good hydrogen bond (H-bond) donor and acceptor.…”

Section: Discussionsupporting

confidence: 91%

The dimerization interface of the glycoprotein Ibβ transmembrane domain corresponds to polar residues within a leucine zipper motif

Wei

Liu

et al. 2011

Protein Science

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Experiments with the transmembrane (TM) domains of the glycoprotein (GP) Ib-IX complex have indicated that the associations between the TM domains of these subunits play an important role in the proper assembly of the complex. As a first step toward understanding these associations, we previously found that the Ibb TM domain dimerized strongly in Escherichia coli cell membranes and led to Ibb TM-CYTO (cytoplasmic domain) dimerization in the SDS-PAGE assay, while neither Iba nor IX TM-CYTO was able to dimerize. In this study, we used the TOXCAT assay to probe the Ibb TM domain dimerization interface by Ala-and Leu-scanning mutagenesis. Our results show that this interface is based on a leucine zipper-like heptad repeat pattern of amino acids. Mutating either one of polar residues Gln129 or His139 to Leu or Ala disrupted Ibb TM dimerization dramatically, indicating that polar residues might form part of the leucine zipperbased dimerization interface. Furthermore, these specific mutational effects in the TOXCAT assay were confirmed in the thiol-disulfide exchange and SDS-PAGE assays. The computational modeling studies further revealed that the most likely leucine zipper interface involves hydrogen bonding of Gln129 and electrostatic interaction of the His139 side chain. Correlation of computer modeling results with experimental mutagenesis studies on the Ibb TM domain may provide insights for understanding the role of the association of TM domains on the assembly of GP Ib-IX complex.

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Section: Discussionsupporting

confidence: 91%

The dimerization interface of the glycoprotein Ibβ transmembrane domain corresponds to polar residues within a leucine zipper motif

Wei

Liu

et al. 2011

Protein Science

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“…1B). We note that the average surface area buried per residue is similar in membrane and soluble ␣-helices, because transmembrane segments bury smaller residues on average (13,14) (supporting information (SI) Fig. S1).…”

Section: Resultsmentioning

confidence: 95%

“…The hydrophobic effect is a dominant contributor to the structure stabilization of soluble proteins and the extramembrane regions of membrane proteins (7,20), but water is essentially absent in the hydrocarbon core of the bilayer, where membrane proteins must operate. Consequently, the relative importance of other forces, such as van der Waals packing and hydrogen bonds, must increase in the apolar environment of the membrane core (13). To make good use of dispersion forces and polar interactions, membrane proteins therefore may need to pack a larger fraction of their surface area to maintain a stable structure.…”

Section: Resultsmentioning

confidence: 99%

Structural imperatives impose diverse evolutionary constraints on helical membrane proteins

Oberai

Joh

Pettit

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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The amino acid sequences of transmembrane regions of helical membrane proteins are highly constrained, diverging at slower rates than their extramembrane regions and than water-soluble proteins. Moreover, helical membrane proteins seem to fall into fewer families than water-soluble proteins. The reason for the differential restrictions on sequence remains unexplained. Here, we show that the evolution of transmembrane regions is slowed by a previously unrecognized structural constraint: Transmembrane regions bury more residues than extramembrane regions and soluble proteins. This fundamental feature of membrane protein structure is an important contributor to the differences in evolutionary rate and to an increased susceptibility of the transmembrane regions to disease-causing single-nucleotide polymorphisms.disease mutation ͉ potassium channel ͉ protein folding ͉ protein stability ͉ single nucleotide polymorphisms E volutionary rates vary considerably in different cellular compartments (1). Membrane proteins have been found to diverge faster overall than soluble proteins (2, 3), but this increased rate is confined entirely to the rapidly evolving extramembrane regions. Transmembrane regions, on average, diverge much more slowly than the extramembrane regions more slowly than soluble proteins (1, 4-6).A major factor controlling protein sequence divergence is the need to preserve protein function by maintaining a folded structure (7). Because the physical forces that drive folding can change with environment, proteins in different cellular locations can be subject to distinct evolutionary constraints. Membrane proteins, in particular, must accommodate to a dramatically varied environment, ranging from hydrocarbon chains in the bilayer core to water as they emerge from the membrane (8, 9). It therefore seems possible that distinct structural imperatives found in different environments could be an important contributor to evolutionary rates. An obvious sequence adaptation is the hydrophobic matching of the protein exterior, reflected in an apolar transmembrane amino acid composition. Although amino acid diversity is more limited in the transmembrane segments, simple compositional differences do not explain the slower divergence rates of transmembrane regions (1, 4, 5).Here, we find that the transmembrane regions of membrane proteins bury more residues on average than soluble proteins and much more than extramembrane regions, a possible mechanism for increasing stabilization in the absence of the hydrophobic effect. Because buried residues evolve at slower rates than surface residues (10-12), the higher level of residue burial in the transmembrane regions leads to slower sequence divergence. Moreover, we find that higher residue burial may explain a higher prevalence of disease-causing mutations in the transmembrane region of membrane proteins compared with the extramembrane regions. Results and DiscussionTransmembrane Regions Bury More Residues. Fig. 1A shows plots of the fractional surface area buried per residue v...

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“…For example, it has become possible to identify sequence motifs and patterns of interactions that seem important for the folding of membrane proteins (3,4). Furthermore, systematic mutagenesis experiments of a few natural helical membrane proteins (5,6) as well as model transmembrane helices (7,8) have contributed insight into interactions important for the association of transmembrane helices.…”

mentioning

confidence: 99%

Sequence determinants of the energetics of folding of a transmembrane four-helix-bundle protein

Howard

Lear²,

DeGrado³

2002

Proc. Natl. Acad. Sci. U.S.A.

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Although previous studies are beginning to point to the specific types of helix-helix interactions that stabilize the folds of membrane-bound helical proteins, quantitative thermodynamic data on natural membrane proteins has been very limited. Here the database is expanded substantially by adding thermodynamic data for a series of sequence variants of M2 protein from influenza A virus. The M2 protein has a single transmembrane helix that homotetramerizes to form proton-selective channels that are essential to virus function. To determine the contributions of specific residues to the folding of this protein, a series of transmembrane peptides with single-site changes near the core of the protein were studied by using sedimentation equilibrium analytical ultracentrifugation. Remarkably, a large number of the mutations increased the stability of the protein. The free energies of tetramerization of the variants can be understood in terms of current models for the structure of the protein. In general, the energetic consequences of the mutations are smaller than those observed for similar mutations in water-soluble proteins. This observation is consistent with previous studies and hence may represent a general phenomenon.

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Internal packing of helical membrane proteins

Cited by 245 publications

References 47 publications

The dimerization interface of the glycoprotein Ibβ transmembrane domain corresponds to polar residues within a leucine zipper motif

The dimerization interface of the glycoprotein Ibβ transmembrane domain corresponds to polar residues within a leucine zipper motif

Structural imperatives impose diverse evolutionary constraints on helical membrane proteins

Sequence determinants of the energetics of folding of a transmembrane four-helix-bundle protein

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