Role of Aromatic Side Chains in the Folding and Thermodynamic Stability of Integral Membrane Proteins

Hong, Heedeok; Park, Sang-Ho; Jiménez, Ricardo H. Flores; Rinehart, Dennis; Tamm, Lukas K.

doi:10.1021/ja068849o

Cited by 157 publications

(225 citation statements)

References 42 publications

(79 reference statements)

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“…In addition to stabilizing the concentration of monomer in aqueous solutions, inclusion of any C-terminal aromatic residue provided a lipid/water interfacial anchor. As was seen with W, F residues are commonly present (and Y to a lesser extent) at the hydrophobic/hydrophilic interface for TM segments of membrane proteins (Braun and von Heijne, 1999;Mall et al, 2000;Demmers et al, 2001;de Planque et al, 2003;Granseth et al, 2005;van der Wel et al, 2007;Hong et al, 2007 Comparing all of the summarized data in Tables 3 and 4 and the profiles shown in Figs. 16 and 17, the sequences displaying the highest ion transport activity and the second and third most left-shifted k 1/2 values are both W containing peptide sequences, NK 4 -M2GlyR-p22 T19R, S22W and NK 4 -M2GlyR-p22 Q21W, S22R.…”

Section: Wt S22wmentioning

confidence: 55%

“…A propensity for tryptophans residing at the aqueous/lipid interface also had been observed and tested by others (Braun and von Heijne, 1999;Mall et al, 2000;Demmers et al, 2001;de Planque et al, 2003;Granseth et al, 2005;van der Wel et al, 2007;Hong et al, 2007). Placing a W at the Cterminus sets the registry of the TM segment that spans the bilayer.…”

Section: M2glyr Studiesmentioning

confidence: 90%

See 1 more Smart Citation

Channel Replacement Therapy for Cystic Fibrosis

Tomich¹,

Bukovnik²,

Layman³

et al. 2012

Cystic Fibrosis - Renewed Hopes Through Research

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Section: Wt S22wmentioning

confidence: 55%

Section: M2glyr Studiesmentioning

confidence: 90%

Channel Replacement Therapy for Cystic Fibrosis

Tomich¹,

Bukovnik²,

Layman³

et al. 2012

Cystic Fibrosis - Renewed Hopes Through Research

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“…For example, tyrosine has been thought to be a particularly suitable amino acid for β-barrel aromatic girdles. Its amphiphilic character is ideal for the interfacial environment, it is statistically overrepresented and highly conserved in aromatic girdles, and it has been experimentally observed to make a larger contribution to β-barrel stability than would be predicted from hydrophobicity scales (59). In natural β-barrels, tyrosine is predominantly found at the C-terminal ends of β-strands (60); at this end the available χ 1 dihedral angles better position the sidechain to "snorkel" into the lipid headgroup region.…”

Section: Discussionmentioning

confidence: 99%

Computational redesign of the lipid-facing surface of the outer membrane protein OmpA

Stapleton

Whitehead

Nanda

2015

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

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Advances in computational design methods have made possible extensive engineering of soluble proteins, but designed β-barrel membrane proteins await improvements in our understanding of the sequence determinants of folding and stability. A subset of the amino acid residues of membrane proteins interact with the cell membrane, and the design rules that govern this lipid-facing surface are poorly understood. We applied a residue-level depth potential for β-barrel membrane proteins to the complete redesign of the lipid-facing surface of Escherichia coli OmpA. Initial designs failed to fold correctly, but reversion of a small number of mutations indicated by backcross experiments yielded designs with substitutions to up to 60% of the surface that did support folding and membrane insertion. T he β-barrel membrane proteins comprise one of the two structural classes of integral membrane proteins. They are found within the outer membranes of bacteria, mitochondria, and chloroplasts, where they perform a range of structural, transport, and catalytic functions (1). In addition to their biological interest they are increasingly relevant to biotechnology, serving as scaffolds for bacterial surface display (2, 3) and atomically precise pores for nanopore-based DNA sequencing. Although the suitability of natural β-barrel membrane proteins for biotechnology has been improved by protein engineering (3-10), the ability to design membrane proteins de novo would deliver tools customized to meet the demands of each application.De novo design provides a stringent test of our understanding of the determinants of protein folding and stability. Protein design software [e.g., Rosetta (11,12)] has made tremendous strides in addressing the design problem for small water-soluble proteins (13-15), and design of simplified model α-helical membrane proteins including single transmembrane helices and small bundles (16)(17)(18)(19)(20) has also been accomplished. In contrast, a designed β-barrel membrane protein has yet to be reported, perhaps as a consequence of the unique design challenges presented by the folding pathway and architecture of these proteins. Unlike the α-helical membrane proteins, nascent β-barrel membrane proteins must transit the periplasm to the outer membrane, where folding and membrane insertion are thought to occur in concert (21,22). An extensive network of chaperones maintains the solubility of the unfolded barrel and guides membrane insertion. The C-terminal β-strand is known to interact with the BAM chaperone complex (23-25), which assists the folding of all β-barrel membrane proteins. However, despite recent progress (26-30), we do not fully understand how interactions between chaperones and transiting membrane proteins are directed by sequence-encoded information.Further complicating design is the inside-out architecture of β-barrel membrane proteins. In place of a hydrophobic core is either a central water-filled pore or a solid core composed of polar side chains. The lipid bilayer becomes increasingly hydrophobic...

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“…The structure contains two aromatic side chains, Phe 9 and Trp 14 , that point toward each other in the kink region and that face the hydrophobic interior of the lipid membrane (3). Because aromatic side chains are well known to anchor membrane proteins in the membrane interface (16,17), it was reasonable to hypothesize that Phe 9 and Trp 14 would also stabilize the active conformation of the HA fusion domain in membranes. However, recent data were not entirely consistent with this hypothesis.…”

Section: Discussionmentioning

confidence: 99%

“…Therefore, additional factors must contribute to the formation of the active boomerang conformation of the HA fusion domain in membranes. Trp contributes Ϫ2.0 kcal/mol more energy to the stability of membrane proteins than Ala, but Phe contributes only Ϫ1.2 kcal/mol more (17,18). Because Ile 10 is located right next to Phe 9 in the hydrophobic pocket of the boomerang structure (3) and because Ile is expected to contribute another Ϫ0.5 kcal/mol over Ala (18), we suspected that both Phe 9 and Ile 10 were needed to stabilize the N-terminal arm of the boomerang structure in the membrane interface.…”

Section: Discussionmentioning

confidence: 99%

Locking the Kink in the Influenza Hemagglutinin Fusion Domain Structure

Lai

Tamm

2007

Journal of Biological Chemistry

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We have previously identified Trp 14 as a critical residue that stabilizes the kink in the boomerang structure of the influenza fusion domain and found that cells expressing hemagglutinin with a Trp 14 to Ala mutation cannot fuse with red blood cells. However, mutating another aromatic residue, Phe 9 , on the other side of the kink did not have a significant effect on fusion or the ability of the mutant fusion peptide to bind to or perturb the bilayer structure of lipid model membranes. We reasoned that Phe is not as potent to contribute to the kink as the larger Trp and that the cooperation of Phe 9 and Ile 10 might be needed to elicit the same effect. Indeed, the double mutant F9A/I10A diminished cell-cell fusion and the ability of the fusion domain to bind to and perturb lipid bilayers in a similar fashion as the W14A mutant. A structure determination of F9A in lipid micelles by solution NMR shows that F9A adopts a similarly kinked structure as wild type. Distances between the two arms of the boomerang structure of wild type, F9A, W14A, and F9A/I10A in lipid bilayers were measured by double electron-electron resonance spectroscopy and showed that the kinks of W14A and F9A/I10A are more flexible than those of wild type and F9A. These results underscore the importance of large hydrophobic residues on both sides of the kink region of the influenza hemagglutinin fusion domain to fix the angle of the boomerang structure and thereby confer fusion function to this critical domain.Enveloped viruses enter host cells by membrane fusion. Influenza virus, as an example, first attaches to the plasma membrane of the host cell, and the virus is then taken up by the host cell by receptor-mediated endocytosis. When the pH in the endosome decreases to around 5, influenza hemagglutinin (HA) 2 on the viral envelope undergoes a dramatic conformational change, which triggers fusion of the viral and endosome membranes. Each monomer of the HA homotrimer consists of two subunits, HA1 and HA2. While HA1 is responsible for receptor recognition, HA2, which also anchors HA in the viral membrane, is responsible for membrane fusion. The fusion domain or fusion peptide of HA consists of a relatively hydrophobic sequence located at the N terminus of the HA2 subunit.Under resting condition at neutral pH, the fusion domains are buried in hydrophobic pockets at the interfaces between monomers in the HA trimer. However, under acidic conditions, the fusion domains become exposed and insert into the endosomal target membrane of the host cell, where they initiate fusion. A single fusion site is thought to consist of several HA trimers. Thus, multiple fusion domains are suggested to work cooperatively to merge the two membranes. In addition to these fusion domain-lipid interactions, the pH-induced conformational change also tilts the coiled-coil rods of HA2 relative to the two membranes and thereby drags them into close proximity (1). Some current models of HA-mediated membrane fusion suggest that there are interactions between the transmembrane and...

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Role of Aromatic Side Chains in the Folding and Thermodynamic Stability of Integral Membrane Proteins

Cited by 157 publications

References 42 publications

Channel Replacement Therapy for Cystic Fibrosis

Channel Replacement Therapy for Cystic Fibrosis

Computational redesign of the lipid-facing surface of the outer membrane protein OmpA

Locking the Kink in the Influenza Hemagglutinin Fusion Domain Structure

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