The binding site dependence of binding energy in both metalated and protonated diglycine and triglycine peptides

Ai, Hongqi; Li, Yun; Zhang, Chong; Feng, Jiwen

doi:10.1016/j.chemphys.2007.02.015

Cited by 2 publications

(2 citation statements)

References 43 publications

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“…For the reactions of P 2 H + + M + → P 2 H + M x + , two kinds of P 2 H + M x + complexes (P 2 H + M1 + and P 2 H + M2 + ) should be produced when one M + attacks the bare carboxyl oxygens of P 2 H + species, respectively. , Each P 2 H + M x + isomer has one PBE value …”

Section: Calculation Schemesmentioning

confidence: 99%

“…The binding energy (or affinity energy) of either proton was negative in the diprotonized glycine systems except for some water-molecule assistant cases . Interestingly, for the double ion-involved (at least a M + ) peptides, such a PBE rule was found to be greatly influenced by the length of the main chains, and its value would become negative when n ≥ 4 for G n H + Li + , n ≥ 5 for G n H + Na + , and n ≥ 6 for G n H + K + systems . The “ n ” denotes the number of glycine residues (G) between two cations (H + and M + ).…”

Section: Introductionmentioning

confidence: 99%

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Dependence of Positive Binding Energies on Side ChainsA Theoretical Prediction on the Origin of Regular Ordering for the Amino Acid Residues in the Selectivity Filter

Zhang

et al. 2007

J. Phys. Chem. B

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The side-chain effects of metalated and protonated dipeptides, including GGH(+)M(+), GAH(+)M(+), AGH(+)M(+), AAH(+)M(+), GWH(+)M(+), GSH(+)M(+), GTH(+)M(+), GFH(+)M(+), GYH(+)M(+), and GVH(+)M(+) (G = glycine, A = alanine, W = tryptophan, S = serine, T = threonine, F = phenylalanine, and V = valine; M = Li, Na, and K), are theoretically explored in this paper on their positive binding energies (PBEs), which are derived from interactions of M+ with the carboxyl oxygen(s). The B3LYP/6-311++G(**)// B3LYP/6-31G(*) calculations suggest that the PBEs of dipeptides with side chain(s) are much smaller than those with no side chain (GGH(+)M(+)). Generally, larger side chains and smaller M(+) radii would lead to fewer PBEs for the M(+) involved systems. On the basis of the direct dependence of PBE on the electrostatic repulsion between two kinds of cations (H(+) and M(+)) in these dipeptide models, it could be reasonably expected that the side-chain effect on the electrostatic repulsion and consequently on the PBEs could offer one good insight, on a chemical-physical basis, into the origin of regular ordering of the amino acids when they form a filter in the K(+) channel protein (MacKinnon, et al. Science 1998, 280, 106).

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Section: Calculation Schemesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Dependence of Positive Binding Energies on Side ChainsA Theoretical Prediction on the Origin of Regular Ordering for the Amino Acid Residues in the Selectivity Filter

Zhang

et al. 2007

J. Phys. Chem. B

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Solvation counteracts coulombic repulsion in the binding of two cations to a model hexapeptide

Zhang

et al. 2011

J Mol Model

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In the present paper we employ a series of dicationized (K(+)& C(+); C = H, Li, Na, or K) hexapeptide (G(6)C(+)K(+)(x), x = 1, 2, … or 5) complexes in gas phase (GP) and aqueous phase (AP) as models to mimic the key characteristics of the real biosystems. An interesting phenomenon is observed that the binding properties of K(+)(x) to G(6)C(+) species change in the two phases, i.e., those positive binding energies in the GP become negative ones in the AP. Then we probe the origin of property change of the binding energies in the two different phases and associate these changes with some biological phenomena.

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The binding site dependence of binding energy in both metalated and protonated diglycine and triglycine peptides

Cited by 2 publications

References 43 publications

Dependence of Positive Binding Energies on Side ChainsA Theoretical Prediction on the Origin of Regular Ordering for the Amino Acid Residues in the Selectivity Filter

Dependence of Positive Binding Energies on Side ChainsA Theoretical Prediction on the Origin of Regular Ordering for the Amino Acid Residues in the Selectivity Filter

Solvation counteracts coulombic repulsion in the binding of two cations to a model hexapeptide

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