Solvent Influence on the Stability of the Peptide Hydrogen Bond: A Supramolecular Cooperative Effect

Guo, Hong; Karplus, Martin

doi:10.1021/j100080a002

Cited by 205 publications

(163 citation statements)

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“…The cooperativity effect considering the average interaction energy of each complex with respect to that observed in the corresponding dimers 43,44 is 4% in the hexamer structure in configuration A and 12% in the tetramer in configuration C, decreasing up to 5% in the hexamer. In the case of the cyclic B structure, no positive cooperativity is observed since the hexamer structure considered is not able to overcome the curvature of the interaction.…”

Section: B Clusters: Energy and Geometrymentioning

confidence: 93%

Dihydrogen bond cooperativity in (HCCBeH)n clusters

Alkorta¹,

Elguero²,

Solimannejad³

2008

The Journal of Chemical Physics

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A theoretical study has been carried out on the clusters formed by the association of ethynylhydroberyllium ͑HCϵ CBeH͒ monomers. The monomer presents a linear disposition with a dipole moment of 0.94 D. Clusters from two to six monomers have been calculated for three different configurations ͑linear, cyclic with dihydrogen bonds, and cyclic with hydrogen bonds to the -cloud͒, the third one being the most stable. The electronic properties of the clusters have been analyzed by means of the atoms in molecules and natural bond orbitals methodologies. Cooperative effects, similar to the ones described for standard hydrogen bonded clusters, are observed in those configurations where dihydrogen bonds are the main interacting force.

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Section: B Clusters: Energy and Geometrymentioning

confidence: 93%

Dihydrogen bond cooperativity in (HCCBeH)n clusters

Alkorta¹,

Elguero²,

Solimannejad³

2008

The Journal of Chemical Physics

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“…It has been suggested that this propensity for aggregation may act in coordination with their hydrophobic nature to bind with the hydrophobic residues of proteins (10,34). The hydrophobic aggregates reduce the local polarity surrounding the peptide, resulting in an increase in intramolecular hydrogen bonding (16,35,36). There is, however, limited experimental evidence of direct binding of fluorinated alcohols with hydrophobic residues (22,37).…”

Section: Construction Of Solvation Energy Of Relaxationmentioning

confidence: 99%

Solvation in protein (un)folding of melittin tetramer–monomer transition

Othon

Kwon

Lin

et al. 2009

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

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Protein structural integrity and flexibility are intimately tied to solvation. Here, we examine the effect that changes in bulk and local solvent properties have on protein structure and stability. We observe the change in solvation of an unfolding of the protein model, melittin, in the presence of a denaturant, trifluoroethanol. The peptide system displays a well defined transition in that the tetramer unfolds without disrupting the secondary or tertiary structure. In the absence of local structural perturbation, we are able to reveal exclusively the role of solvation dynamics in protein structure stabilization and the (un)folding pathway. A sudden retardation in solvent dynamics, which is coupled to the change in protein structure, is observed at a critical trifluoroethanol concentration. The large amplitude conformational changes are regulated by the local solvent hydrophobicity and bulk solvent viscosity.fluoresence spectroscopy ͉ preferential solvation ͉ protein folding ͉ ultrafast hydration

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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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Solvent Influence on the Stability of the Peptide Hydrogen Bond: A Supramolecular Cooperative Effect

Cited by 205 publications

References 0 publications

Dihydrogen bond cooperativity in (HCCBeH)n clusters

Dihydrogen bond cooperativity in (HCCBeH)n clusters

Solvation in protein (un)folding of melittin tetramer–monomer transition

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

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