α-Helix nucleation by a calcium-binding peptide loop

Siedlecka, Monika; Goch, Grażyna; Ejchart, Andrzej; Sticht, Heinrich; Bierzyński, Andrzej

doi:10.1073/pnas.96.3.903

Cited by 85 publications

(80 citation statements)

References 39 publications

(39 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…1-3) to those observed when the helix is initiated by a helical template or an actual fixed helical nucleus (4)(5)(6)(7). The first results obtained by using a synthetic template to initiate helix formation (4)(5)(6) showed little relation to the results found with standard peptides.…”

mentioning

confidence: 68%

Circular dichroism spectra of short, fixed-nucleus alanine helices

Chin

Woody

Rohl

et al. 2002

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

120

View full text Add to dashboard Cite

Very short alanine peptide helices can be studied in a fixed-nucleus, helix-forming system [Siedlicka, M., Goch, G., Ejchart, A., Sticht, H. & Bierzynski, A. (1999) Proc. Natl. Acad. Sci. USA 96, 903-908]. In a 12-residue sequence taken from an EF-hand protein, the four C-terminal peptide units become helical when the peptide binds La 3؉ , and somewhat longer helices may be made by adding alanine residues at the C terminus. The helices studied here contain 4, 8, or 11 peptide units. Surprisingly, these short fixed-nucleus helices remain almost fully helical from 4 to 65°C, according to circular dichroism results reported here, and in agreement with titration calorimetry results reported recently. These peptides are used here to define the circular dichroism properties of short helices, which are needed for accurate measurement of helix propensities. Two striking properties are: (i) the temperature coefficient of mean peptide ellipticity depends strongly on helix length; and (ii) the intensity of the signal decreases much less rapidly with helix length, for very short helices, than supposed in the past. The circular dichroism spectra of the short helices are compared with new theoretical calculations, based on the experimentally determined direction of the NV 1 transition moment.A long-standing goal in the study of peptide helices has been to relate the properties of helix formation in standard peptides (for example, in alanine-based peptides; refs. 1-3) to those observed when the helix is initiated by a helical template or an actual fixed helical nucleus (4-7). The first results obtained by using a synthetic template to initiate helix formation (4-6) showed little relation to the results found with standard peptides. In particular, alanine residues added to the synthetic template were reported (4-6) to have a lower helix propensity than in alanine-based peptides. The synthetic template used in these initial studies was acetyl-L-Pro-L-Pro, only one of whose three conformers is productive in initiating a helix (4-6). Bierzynski and coworkers (7) succeeded in nucleating short alanine-rich helices with a helical nucleus obtained by binding La 3ϩ to a 12-residue peptide (P1) modeled on an EF-hand protein. The four C-terminal peptide units become helical when P1 binds La 3ϩ , and longer helices can be made by adding residues at the C terminus of P1. The NMR structure (7) of a second peptide P2, with four additional residues (A 3 Q) added to, P1 defines the structure of the fixed helical nucleus, and agrees with earlier work (8) on the ligands that coordinate La 3ϩ . All but one of the participating ligands lie outside the helix in the N-terminal direction; the side-chain -COOH group of Glu 12, inside the helix, participates in binding La 3ϩ . Recently, Bierzynski and coworkers made an extensive study of helix propagation in this system (to be published), and they found a helix propensity for alanine in good agreement with results from standard alaninebased peptides (A. Bierzynski, personal communication).Circular dich...

show abstract

mentioning

confidence: 68%

Circular dichroism spectra of short, fixed-nucleus alanine helices

Chin

Woody

Rohl

et al. 2002

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

120

View full text Add to dashboard Cite

show abstract

“…NMR study shows that upon La 3ϩ binding, the P2A peptide folds into a structure in which the last eight residues are helical (24). These changes in the structure induced by La 3ϩ binding can also be monitored by CD spectroscopy (26,27).…”

Section: Design Of the Guest Position In Peptidesmentioning

confidence: 99%

“…3. (24,26,32). Because La 3ϩ binding leads to the folding of the P2X peptides, the La 3ϩ -binding affinities of the peptides will include contribution from the helix formation, thus allowing estimates of the thermodynamic helix propensity scale.…”

Section: Design Of the Guest Position In Peptidesmentioning

confidence: 99%

“…Because the P2X peptides have certain helical structure in the absence of La 3ϩ (24), the difference in the F ␣ Ϫ (P2X) should be taken into account as…”

Section: ]mentioning

confidence: 99%

“…Most of these shortcomings have been overcome recently by using a model system in which metal binding induces helix formation in a short helical peptide (24,25), thus allowing the use of isothermal titration calorimetry (ITC) to monitor the enthalpy of helix-coil transition (26). By using different peptides, it was found that the enthalpy of the helix-coil transition for alanine is Ϫ0.9 Ϯ 0.1 kcal͞mol, and is independent of peptide length (26).…”

mentioning

confidence: 99%

See 2 more Smart Citations

Enthalpy of helix–coil transition: Missing link in rationalizing the thermodynamics of helix-forming propensities of the amino acid residues

Richardson

López

Makhatadze

2005

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

View full text Add to dashboard Cite

It is known that different amino acid residues have effects on the thermodynamic stability of an ␣-helix. The underlying mechanism for the thermodynamic helical propensity is not well understood. The major accepted hypothesis is the difference in the side-chain configurational entropy loss upon helix formation. However, the changes in the side-chain configurational entropy explain only part of the thermodynamic helical propensity, thus implying that there must be a difference in the enthalpy of helix-coil transition for different residues. This work provides an experimental test to this hypothesis. Direct calorimetric measurements of folding of a model host peptide in which the helix formation is induced by metal binding is applied to a wide range of residue types, both naturally occurring and nonnatural, at the guest site. Based on the calorimetric results for 12 peptides, it was found that indeed there is a difference in the enthalpy of helix-coil transition for different amino acid residues, and simple empirical rules that define these differences are presented. The obtained difference in the enthalpies of helix-coil transition complement the differences in configurational entropies and provide the complete thermodynamic characterization of the helix-forming tendencies.protein stability ͉ thermodynamics ͉ calorimetry T he structure of the ␣-helix in polypeptides was proposed more than a half-century ago (1). Nevertheless, some details of the thermodynamics of the helix-coil transition remain to be deciphered (see reviews in refs. 2-7 and references therein). From the basic consideration of the structure of an ␣-helix, the arrangement of the i to i ϩ 4 hydrogen-bonding pattern by the peptide backbone is the driving force for helix formation, and is enthalpically favorable (8,9). It is also known that, entropically, helix formation restricts the configurational freedom of the side chain (10-17). For example, the loss in configurational entropy for alanine will be very small because it has a very small side chain, while valine, because of the ␤-branching of the side chain, will have a large decrease in conformational entropy upon helix formation (14). Based on these observations, it was proposed that the loss in configurational entropy is a major factor that defines the helix-forming propensities of different amino acid residues (17). Later, it was noticed that the loss in configurational entropy explains only 50-70% of the difference in the thermodynamic propensity as measured by the difference in the Gibbs energy. This finding suggests that there is unaccounted entropy change or there is also a difference in the enthalpy of a helix-coil transition for different amino acid residues (18)(19)(20). Indirect estimates of the enthalpy of helix-coil transitions for just four amino acid residues further suggests the sequence dependence of the enthalpy (18,19).Direct calorimetric measurements of the enthalpy of helixcoil transition are very difficult, for numerous reasons, including the small absolute values, low coope...

show abstract

α‐Helices propagating from stable nucleators exhibit unconventional thermal folding

2021

View full text Add to dashboard Cite

Although the effect of thermal perturbations on protein structure has long been modeled in helical peptides, several details, such as the relation between the thermal stabilities of the propagating and nucleating segments of helices, remain elusive. We had earlier reported on the helix‐nucleating propensities of covalent H‐bond surrogate‐constrained α‐turns. Here, we analyze the thermal stabilities of helices that propagate along peptides appended to these α‐helix nucleators using their NMR and far‐UV CD spectra. Unconventional thermal folding of these helix models reveals that the helical fold in propagating backbones resists thermal perturbations as long as their nucleating template is intact. The threshold temperature of such resistance is also influenced by the extent of similarity between the natures of helical folds in the nucleating and propagating segments. Correlations between helicities and rigidities of helix‐nucleating and helix‐propagating segments reveal subtle interdependence, which explains cooperativity and residual helix formation during protein folding.

show abstract

α-Helix nucleation by a calcium-binding peptide loop

Cited by 85 publications

References 39 publications

Circular dichroism spectra of short, fixed-nucleus alanine helices

Circular dichroism spectra of short, fixed-nucleus alanine helices

Enthalpy of helix–coil transition: Missing link in rationalizing the thermodynamics of helix-forming propensities of the amino acid residues

α‐Helices propagating from stable nucleators exhibit unconventional thermal folding

Contact Info

Product

Resources

About