The role of context on α‐helix stabilization: Host‐guest analysis in a mixed background peptide model

Yang, Jinpu; Spek, Erik J.; Gong, Yanqing; Zhou, Hongxing; Kallenbach, Neville R.

doi:10.1002/pro.5560060614

Cited by 55 publications

(53 citation statements)

References 67 publications

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“…Alanine has been shown to promote helix formation in peptides and has one of the highest helix propensities, as determined from host-guest experiments (24,(26)(27)(28)(29)(30). Based on the alanine scan data, eight noncritical residues that were not part of an ion pair were substituted with alanine ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Design of helical, oligomeric HIV-1 fusion inhibitor peptides with potent activity against enfuvirtide-resistant virus

Dwyer¹,

Wilson²,

Davison³

et al. 2007

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

225

244

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Enfuvirtide (ENF), the first approved fusion inhibitor (FI) for HIV, is a 36-aa peptide that acts by binding to the heptad repeat 1 (HR1) region of gp41 and preventing the interaction of the HR1 and HR2 domains, which is required for virus-cell fusion. Treatmentacquired resistance to ENF highlights the need to create FI therapeutics with activity against ENF-resistant viruses and improved durability. Using rational design, we have made a series of oligomeric HR2 peptides with increased helical structure and with exceptionally high HR1/HR2 bundle stability. The engineered peptides are found to be as much as 3,600-fold more active than ENF against viruses that are resistant to the HR2 peptides ENF, T-1249, or T-651. Passaging experiments using one of these peptides could not generate virus with decreased sensitivity, even after >70 days in culture, suggesting superior durability as compared with ENF. In addition, the pharmacokinetic properties of the engineered peptides were improved up to 100-fold. The potent antiviral activity against resistant viruses, the difficulty in generating resistant virus, and the extended half-life in vivo make this class of fusion inhibitor peptide attractive for further development.coiled coil ͉ gp41 HIV-1 ͉ viral entry ͉ drug design

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Section: Resultsmentioning

confidence: 99%

Design of helical, oligomeric HIV-1 fusion inhibitor peptides with potent activity against enfuvirtide-resistant virus

Dwyer¹,

Wilson²,

Davison³

et al. 2007

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

225

244

View full text Add to dashboard Cite

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“…Among all natural amino acids, alanine has the greatest propensity to form α-helical segments (29,30). Therefore, we reasoned that a triple mutation of G248, L249, and S250 to alanine should hinder the bending of helix α9 upon ectoine binding; by stabilizing the open conformation of TeaA, the mutation would thus mimic the presumed allosteric effect of TeaBC, the membrane transporter.…”

Section: Simulations Indicate Complete Substrate Coordination Precedesmentioning

confidence: 99%

Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins

Marinelli

Kuhlmann

Grell

et al. 2011

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

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Numerous membrane importers rely on accessory water-soluble proteins to capture their substrates. These substrate-binding proteins (SBP) have a strong affinity for their ligands; yet, substrate release onto the low-affinity membrane transporter must occur for uptake to proceed. It is generally accepted that release is facilitated by the association of SBP and transporter, upon which the SBP adopts a conformation similar to the unliganded state, whose affinity is sufficiently reduced. Despite the appeal of this mechanism, however, direct supporting evidence is lacking. Here, we use experimental and theoretical methods to demonstrate that an allosteric mechanism of enhanced substrate release is indeed plausible. First, we report the atomic-resolution structure of apo TeaA, the SBP of the Na -coupled ectoine TRAP transporter TeaBC from Halomonas elongata DSM2581 T , and compare it with the substrate-bound structure previously reported. Conformational freeenergy landscape calculations based upon molecular dynamics simulations are then used to dissect the mechanism that couples ectoine binding to structural change in TeaA. These insights allow us to design a triple mutation that biases TeaA toward apo-like conformations without directly perturbing the binding cleft, thus mimicking the influence of the membrane transporter. Calorimetric measurements demonstrate that the ectoine affinity of the conformationally biased triple mutant is 100-fold weaker than that of the wild type. By contrast, a control mutant predicted to be conformationally unbiased displays wild-type affinity. This work thus demonstrates that substrate release from SBPs onto their membrane transporters can be facilitated by the latter through a mechanism of allosteric modulation of the former.binding thermodynamics | periplasmic binding protein | secondary transporter | ABC transporter | replica-exchange metadynamics

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“…This is in very good agreement with the results of O'Neil and DeGrado (44), who found a difference of 0.42 kcal/mol between serine and alanine in a coiled-coil model system. Studies in single-stranded ␣-helices have given helical propensity differences of 0.5-0.8 kcal/mol for a serine to alanine substitution (45,54,55,79). Helical propensity effects appear to be greater in single amphipathic ␣-helices than in coiled-coils presumably because of the additional stabilizing interactions available to coiled-coils (80).…”

Section: Heptads (B) Vaal 3 Heptads (C) Vaal 4 Heptads (D) Isal 3 mentioning

confidence: 99%

Designing Heterodimeric Two-stranded α-Helical Coiled-coils

Litowski¹,

Hodges²

2002

Journal of Biological Chemistry

291

236

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The E/K coil, a heterodimeric coiled-coil, has been designed as a universal peptide capture and delivery system for use in applications such as biosensors and as an expression and affinity purification tag. In this design, heterodimer formation is specified through the placement of charged residues at the e and g positions of the heptad repeat such that the E coil contains all glutamic acid residues at these positions, and the K coil contains all lysine residues at these positions. The affinity and stability of the E/K coil have been modified to allow a greater range of conditions for association and dissociation. Increasing the hydrophobicity of the coiled-coil core, by substituting isoleucine for valine, gave increases in stability of 2.81 and 3.73 kcal/mol (0.47 kcal/ mol/substitution). Increasing the ␣-helical propensity of residues outside the core, by substituting alanine for serine, yielded increases in stability of 2.68 and 3.28 kcal/mol (0.41 and 0.45 kcal/mol/substitution). These sequence changes yielded a series of heterodimeric coiledcoils whose stabilities varied from 6.8 to 11.2 kcal/mol, greatly expanding their scope for use in protein engineering and biomedical applications.The coiled-coil is an oligomerization domain found in a wide variety of proteins, including transcription factors, motor proteins, chaperone proteins, and viral fusion proteins (1-4). Recent surveys of genomic data bases suggest that up to 10% of eukaryotic proteins contain sequences predicted to be coiledcoils (5). This structural motif has been of considerable interest, both because of its diversity in structure and oligomerization state and because of its many advantages as a model system for protein design (6, 7). Coiled-coils contain a single type of secondary structure, the ␣-helix, which is easy to monitor experimentally by circular dichroism (CD) spectroscopy. Their quaternary interactions yield a structure that is folded stably in aqueous solution at neutral pH, unlike most singlestranded ␣-helices.The structural features of coiled-coils have been reviewed extensively (3,7,8). Their sequences are characterized by a heptad repeat, denoted abcdefg, in which positions a and d are occupied by hydrophobic residues. The side chains from the a and d residues pack against each other in a "knobs-intoholes" manner (9), forming a continuous hydrophobic core. Maintaining this packing along the length of the ␣-helices results in their wrapping around each other in a left-handed supercoil. The side chains of the residues in positions e and g lie alongside the hydrophobic core. These positions are typically occupied by charged residues that can participate in i to iЈϩ5 electrostatic interactions, which have been found to play an important role in specifying homo-and heteroassociation in native coiled-coils (1, 10 -13). The preference for electrostatic attractions over repulsions has been key to the de novo design of heterodimeric coiled-coils (14 -22).Despite the apparent simplicity of coiled-coils, their structures display a surpri...

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The role of context on α‐helix stabilization: Host‐guest analysis in a mixed background peptide model

Cited by 55 publications

References 67 publications

Design of helical, oligomeric HIV-1 fusion inhibitor peptides with potent activity against enfuvirtide-resistant virus

Design of helical, oligomeric HIV-1 fusion inhibitor peptides with potent activity against enfuvirtide-resistant virus

Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins

Designing Heterodimeric Two-stranded α-Helical Coiled-coils

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