Development of the multiple sequence approximation within the AGADIR model of α-helix formation: Comparison with Zimm-Bragg and Lifson-Roig formalisms

Muñoz, Víctor; Serrano, Luís

doi:10.1002/(sici)1097-0282(19970415)41:5<495::aid-bip2>3.0.co;2-h

Cited by 399 publications

(244 citation statements)

References 27 publications

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“…For EnHD, the stability of the HTH motif is exceptionally high with the measured helical propensity of H1, H2, and H3 at approximately 30%, 15%, and 25% and predicted at approximately 70%, 30%, and 2% (4) by the program Agadir (25). In contrast, the predicted values for Pit1 are approximately 8%, 8%, and 1% (Fig.…”

Section: Discussionmentioning

confidence: 78%

Malleability of folding intermediates in the homeodomain superfamily

Banachewicz

Religa

Schaeffer

et al. 2011

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

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Members of the homeodomain superfamily are three-helix bundle proteins whose second and third helices form a helix-turn-helix motif (HTH). Their folding mechanism slides from the ultrafast, three-state framework mechanism for the engrailed homeodomain (EnHD), in which the HTH motif is independently stable, to an apparent two-state nucleation-condensation model for family members with an unstable HTH motif. The folding intermediate of EnHD has nearly native HTH structure, but it is not docked with helix1. The determinant of whether two-or three-state folding was hypothesized to be the stability of the HTH substructure. Here, we describe a detailed Φ-value analysis of the folding of the Pit1 homeodomain, which has similar ultrafast kinetics to that of EnHD. Formation of helix1 was strongly coupled with formation of HTH, which was initially surprising because they are uncoupled in the EnHD folding intermediate. However, we found a key difference between Pit1 and EnHD: The isolated peptide corresponding to the HTH motif in Pit1 was not folded in the absence of H1. Independent molecular dynamics simulations of Pit1 unfolding found an intermediate with H1 misfolded onto the HTH motif. The Pit1 folding pathway is the connection between that of EnHD and the slower folding homeodomains and provides a link in the transition of mechanisms from two-to three-state folding in this superfamily. The malleability of folding intermediates can lead to unstable substructures being stabilized by a variety of nonnative interactions, adding to the continuum of folding mechanisms.protein folding | temperature jump | diffusion collision | transition state T he nucleation-condensation mechanism was proposed from a Φ-value analysis of the folding of the protein chymotrypsin inhibitor 2 (CI2) (1, 2). The individual elements of secondary structure in CI2 are not independently stable, leading to highly cooperative formation of structure in the transition state (TS) for folding in which the helix is the best-formed region, stabilized by long-range interactions. No element of secondary structure is fully formed in the TS and its folding is kinetically two-state (3). It was hypothesized that multistate folding requires independently stable elements of structure or an unstable element of structure being stabilized by interacting with other elements. At the other extreme, the three-helix engrailed homeodomain, EnHD, is a small protein that folds ultrafast via a stable intermediate in line with the framework mechanism, whereby secondary structure forms first followed by docking of the helices (4, 5). Its folding intermediate consists of helix1 (H1) being helical but not docked on to the helix2-turn-helix3 (HTH) DNA binding motif (5, 6). The HTH motif is independently stable in the on-pathway intermediate (7). Studies of other members of the homoedomain superfamily show a slide from this multistate framework folding mechanism to two-state folding and nucleation condensation for members with less stable HTH motifs, consistent with our earlier hypoth...

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Section: Discussionmentioning

confidence: 78%

Malleability of folding intermediates in the homeodomain superfamily

Banachewicz

Religa

Schaeffer

et al. 2011

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

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“…Not surprisingly, these electrostatically complementary residues are essentially conserved in all known c-Myb and CBP/p300 sequences (28). Table S1 reports the top six point mutant candidates that were predicted from AGADIR (68)(69)(70)(71)(72) to increase the helical propensity of the α 3 helix and therefore can potentially affect cooperative binding (SI Text). Out of all of the C-terminal residues located in the α 3 helix that make no intermolecular native contacts with either c-Myb or MLL, only six point mutations at either Lys667 or Ser670 caused a significant increase in the predicted helicity of α 3 (∼3.5-12.7%) relative to the wild-type sequence.…”

Section: Discussionmentioning

confidence: 99%

Prepaying the entropic cost for allosteric regulation in KIX

Law¹,

Gagnon²,

Mapp

et al. 2014

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

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The kinase-inducible domain interacting (KIX) domain of the CREB binding protein (CBP) is capable of simultaneously binding two intrinsically disordered transcription factors, such as the mixedlineage leukemia (MLL) and c-Myb peptides, at isolated interaction sites. In vitro, the affinity for binding c-Myb is approximately doubled when KIX is in complex with MLL, which suggests a positive cooperative binding mechanism, and the affinity for MLL is also slightly increased when KIX is first bound by c-Myb. Expanding the scope of recent NMR and computational studies, we explore the allosteric mechanism at a detailed molecular level that directly connects the microscopic structural dynamics to the macroscopic shift in binding affinities. To this end, we have performed molecular dynamics simulations of free KIX, KIX-c-Myb, MLL-KIX, and MLL-KIX-c-Myb using a topology-based Go-like model. Our results capture an increase in affinity for the peptide in the allosteric site when KIX is prebound by a complementary effector and both peptides follow an effector-independent folding-and-binding mechanism. More importantly, we discover that MLL binding lowers the entropic cost for c-Myb binding, and vice versa, by stabilizing the L 12 -G 2 loop and the C-terminal region of the α 3 helix on KIX. This work demonstrates the importance of entropy in allosteric signaling between promiscuous molecular recognition sites and can inform the rational design of small molecule stabilizers to target important regions of conformationally dynamic proteins.

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“…Helical Prediction-The entire intracellular C-terminal tail of D6 (from four species) and human CCR1-5 were analyzed for putative helical content using AGADIR software (35).…”

Section: D6-k142rmentioning

confidence: 99%

Multiple Roles for the C-terminal Tail of the Chemokine Scavenger D6

McCulloch¹,

Morrow²,

Milasta

et al. 2008

Journal of Biological Chemistry

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D6 is a heptahelical receptor that suppresses inflammation and tumorigenesis by scavenging extracellular pro-inflammatory CC chemokines. Previous studies suggested this is dependent on constitutive trafficking of stable D6 protein to and from the cell surface via recycling endosomes. By internalizing chemokine each time it transits the cell surface, D6 can, over time, remove large quantities of these inflammatory mediators. We have investigated the role of the conserved 58-amino acid C terminus of human D6, which, unlike the rest of the protein, shows no clear homology to other heptahelical receptors. We show that, in human HEK293 cells, a serine cluster in this region controls the constitutive phosphorylation, high stability, and intracellular trafficking itinerary of the receptor and drives green fluorescent protein-tagged ␤-arrestins to membranes at, and near, the cell surface. Unexpectedly, however, these properties, and the last 44 amino acids of the C terminus, are dispensable for D6 internalization and effective scavenging of the chemokine CCL3. Even in the absence of the last 58 amino acids, D6 still initially internalizes CCL3 but, surprisingly, exposure to ligand inhibits subsequent CCL3 uptake by this mutant. Progressive scavenging is therefore abrogated. We conclude that the heptahelical body of D6 on its own can engage the endocytotic machinery of HEK293 cells but that the C terminus is indispensable for scavenging because it prevents initial chemokine engagement of D6 from inhibiting subsequent chemokine uptake.

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Development of the multiple sequence approximation within the AGADIR model of α-helix formation: Comparison with Zimm-Bragg and Lifson-Roig formalisms

Cited by 399 publications

References 27 publications

Malleability of folding intermediates in the homeodomain superfamily

Malleability of folding intermediates in the homeodomain superfamily

Prepaying the entropic cost for allosteric regulation in KIX

Multiple Roles for the C-terminal Tail of the Chemokine Scavenger D6

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