Snorkeling Preferences Foster an Amino Acid Composition Bias in Transmembrane Helices

Chamberlain, Aaron K.; Lee, Yohan; Kim, Sanguk; Bowie, James U.

doi:10.1016/j.jmb.2004.03.072

Cited by 73 publications

(53 citation statements)

References 54 publications

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“…54 In addition, burial of Trp and Tyr residues within helix-helix interfaces may be competed for by snorkelling of their partially hydrophilic side-chains to the lipid head-group region of the membrane. [55][56][57] In other studies, Phe as well as Trp and Tyr have been reported to contribute to TMD-TMD interactions. 58,59 Phe is an abundant amino acid in TMDs.…”

Section: The Fxxgxxxg Motif In Natural Tmdsmentioning

confidence: 85%

Phenylalanine Promotes Interaction of Transmembrane Domains via GxxxG Motifs

Unterreitmeier

Fuchs

Schäffler

et al. 2007

Journal of Molecular Biology

101

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Section: The Fxxgxxxg Motif In Natural Tmdsmentioning

confidence: 85%

Phenylalanine Promotes Interaction of Transmembrane Domains via GxxxG Motifs

Unterreitmeier

Fuchs

Schäffler

et al. 2007

Journal of Molecular Biology

101

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“…Ideally, we would consider the cytoplasmic and extracellular ends of the helix differently, and would additionally discriminate the N-terminal ends from the C-terminal ends of the helices (because the residues have different rotamer distributions on either end of the helix). 15,16 However, to maximize the signal-to-noise ratio, these features were not differentiated, and the distance of the residues C β (C α for Gly) from the bilayer center was measured. Figure 1 illustrates the propensity for the sidechains to occupy consecutive 2 Å regions beginning at the center of the bilayer, and extending to 30 Å along a line that is normal to the bilayer plane.…”

Section: Resultsmentioning

confidence: 99%

Ez, a Depth-dependent Potential for Assessing the Energies of Insertion of Amino Acid Side-chains into Membranes: Derivation and Applications to Determining the Orientation of Transmembrane and Interfacial Helices

Senes¹,

Chadi²,

Law³

et al. 2007

Journal of Molecular Biology

146

177

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“…An explanation of these somewhat surprising observations could be reflected in the complexity of interactions that exist in natural systems. The basic amino acids, arginine and lysine, due to the long aliphatic linker between the ␣-carbon and charged head group often play steric roles in concert with the role of a component in a salt bridge (42,43). Therefore, it may not be a coincidence that these two residues are arginine, and it could be possible that removal of these large side chains is permitting rearrangement of the interface to maximize stability.…”

Section: Discussionmentioning

confidence: 99%

Alanine-shaving Mutagenesis to Determine Key Interfacial Residues Governing the Assembly of a Nano-cage Maxi-ferritin

Zhang

Raudah

Teo

et al. 2010

Journal of Biological Chemistry

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The fundamental process of protein self-assembly is governed by protein-protein interactions between subunits, which combine to form structures that are often on the nano-scale. The nano-cage protein, bacterioferritin from Escherichia coli, a maxi-ferritin made up of 24 subunits, was chosen as the basis for an alanine-shaving mutagenesis study to discover key amino acid residues at symmetry-related protein-protein interfaces that control protein stability and self-assembly. By inspection of these interfaces and "virtual alanine scanning," nine mutants were designed, expressed, purified, and characterized using transmission electron microscopy, size exclusion chromatography, dynamic light scattering, native PAGE, and temperaturedependent CD. Many of the selected amino acids act as hot spot residues. Four of these (Arg-30, which is located at the two-fold axis, and Arg-61, Tyr-114, and Glu-128, which are located at the three-fold axis), when individually mutated to alanine, completely shut down detectable solution formation of 24-mer, favoring a cooperatively folded dimer, suggesting that they may be oligomerization "switch residues." Furthermore, two residues, Arg-30 and Arg-61, when changed to alanine form mutants that are more thermodynamically stable than the native protein. This investigation into the structure and energetics of this self-assembling nano-cage protein not only can act as a jumping off point for the eventual design of novel protein nanostructures but can also help to understand the role that structure plays on the function of this important class of proteins.

show abstract

Snorkeling Preferences Foster an Amino Acid Composition Bias in Transmembrane Helices

Cited by 73 publications

References 54 publications

Phenylalanine Promotes Interaction of Transmembrane Domains via GxxxG Motifs

Phenylalanine Promotes Interaction of Transmembrane Domains via GxxxG Motifs

Ez, a Depth-dependent Potential for Assessing the Energies of Insertion of Amino Acid Side-chains into Membranes: Derivation and Applications to Determining the Orientation of Transmembrane and Interfacial Helices

Alanine-shaving Mutagenesis to Determine Key Interfacial Residues Governing the Assembly of a Nano-cage Maxi-ferritin

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