Cooperativity in Amide Hydrogen Bonding Chains:  Implications for Protein-Folding Models

Kobko, Nadya; Paraskevas, Lilly-Rose; E, del Río; Jj, Dannenberg

doi:10.1021/ja004271l

Cited by 166 publications

(157 citation statements)

References 17 publications

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“…Formamide molecules align in a protein-folding array in the interlayer gallery by means of hydrogen bonding which forms between oxygen atoms in one formamide molecule www.eurjic.organd hydrogen atoms in a neighbouring formamide molecule. [34] These H-bonded formamide chains show an unusually high degree of cooperativity. Formamide cations in the interlayer gallery are arranged as in Figure 4b.…”

Section: Resultsmentioning

confidence: 99%

Designed Reversible Alkylamine Intercalation–Deintercalation in the Layered Perovskite‐Type Oxide KCa₂Nb₃O₁₀

et al. 2008

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Reactions have been designed to verify the reversibility of butylamine intercalation–deintercalation in the layered perovskite‐type oxide KCa2Nb3O10. The reactions include ion exchange to form HCa2Nb3O10·1.5H2O, butylamine intercalation for producing C4H9NH3Ca2Nb3O10, transformation of C4H9NH3Ca2Nb3O10 into HCONH3Ca2Nb3O10 by formamide substitution and conversion of HCONH3Ca2Nb3O10 into HCa2Nb3O10·1.5H2O again by ion exchange. The complete reaction cycles were monitored by XRD, Raman spectroscopy, thermogravimetric (TG) and elemental analysis, and the resulting information was used to propose the structure evolution and to determine the organic components of the products. The well‐matched powder X‐ray diffraction (XRD) patterns and Raman spectra between the initial and recovered protonated materials confirmed that they have identical structural features of a protonated triple‐layered perovskite. The C, H and N elemental analysis results and TG data indicate that the regenerated layered perovskite‐type oxides also have a high capacity for alkylamine intercalation. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)

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Section: Resultsmentioning

confidence: 99%

Designed Reversible Alkylamine Intercalation–Deintercalation in the Layered Perovskite‐Type Oxide KCa₂Nb₃O₁₀

et al. 2008

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“…The distribution of charge density of an individual molecule of water changes upon formation of a dimer, and this change results in the increased (cooperative) strength of the second hydrogen bond. [53,54] Cooperative interactions among molecules of water are observed in several systems in which hydrogen bonding is important, and include the intermolecular bonding of molecules of water, formamide, and urea, [55,56] and watermediated interactions between mono-and disaccharides. [57,58] …”

Section: The Power Of Metaphor (For Bad or Good)mentioning

confidence: 99%

Is it the shape of the cavity, or the shape of the water in the cavity?

Snyder

Lockett

Moustakas

et al. 2013

Eur. Phys. J. Spec. Top.

127

190

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“…They attributed this length dependence of Ala's helical propensity to the effect of hydrogen-bonding cooperativity, which has been observed in computational studies of hydrogen-bonded systems. 55,56 Another well-known mechanism that also induces cooperativity in helix formation is long-range electrostatic interactions among individual amide dipoles. 57 If the average helix stabilization per residue is length dependent, such dependence would affect profoundly the rate of helix formation because of the sequential nature of the elongation of the helix.…”

Section: Length-dependent T-jump Relaxation Kineticsmentioning

confidence: 99%

Length Dependent Helix−Coil Transition Kinetics of Nine Alanine-Based Peptides

et al. 2004

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It is well-known that end caps and the peptide length can dramatically influence the thermodynamics of the helix-coil transition. However, their roles in determining the kinetics of the helix-coil transition have not been studied extensively and are less well understood. Kinetic Ising models and sequential kinetic models involving barrier crossing via diffusion all predict that the helix formation time depends monotonically on the peptide length with the relaxation time increasing with respect to increasing chain length. Here, we have studied the helix-coil transition kinetics of a series of Ala-based -helical peptides of different length (19-39 residues), with and without end caps, using time-resolved infrared spectroscopy coupled with laser-induced temperature jump (T-jump) initiation method. The helical content of these peptides was kinetically monitored by probing the amide carbonyl stretching frequencies (i.e., the amide I band) of the peptide backbone. We found that the relaxation rates for peptides with efficient end caps are more rapid than those of the corresponding peptides without good end caps. These results indicate that efficient end-capping sequences can not only stabilize preexisting helices but also promote helix formation through initiation. Furthermore, we found that the relaxation times of these peptides, following a T-jump of 1-11 °C, show rather complex behaviors as a function of the peptide length, in disagreement with theoretical predications. Theses results are not readily explained by theories in which Ala is taken to have a single helical propensity (s). However, recent studies have suggested that s depends on chain length; when this factor is considered, the mean first-passage times of the coil-to-helix transition show similar dependence on the peptide length as those observed experimentally.

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Cooperativity in Amide Hydrogen Bonding Chains: Implications for Protein-Folding Models

Cited by 166 publications

References 17 publications

Designed Reversible Alkylamine Intercalation–Deintercalation in the Layered Perovskite‐Type Oxide KCa₂Nb₃O₁₀

Designed Reversible Alkylamine Intercalation–Deintercalation in the Layered Perovskite‐Type Oxide KCa₂Nb₃O₁₀

Is it the shape of the cavity, or the shape of the water in the cavity?

Length Dependent Helix−Coil Transition Kinetics of Nine Alanine-Based Peptides

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Cooperativity in Amide Hydrogen Bonding Chains: Implications for Protein-Folding Models

Cited by 166 publications

References 17 publications

Designed Reversible Alkylamine Intercalation–Deintercalation in the Layered Perovskite‐Type Oxide KCa2Nb3O10

Designed Reversible Alkylamine Intercalation–Deintercalation in the Layered Perovskite‐Type Oxide KCa2Nb3O10

Is it the shape of the cavity, or the shape of the water in the cavity?

Length Dependent Helix−Coil Transition Kinetics of Nine Alanine-Based Peptides

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Product

Resources

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Designed Reversible Alkylamine Intercalation–Deintercalation in the Layered Perovskite‐Type Oxide KCa₂Nb₃O₁₀

Designed Reversible Alkylamine Intercalation–Deintercalation in the Layered Perovskite‐Type Oxide KCa₂Nb₃O₁₀