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Molecular dynamics simulations of coordination in protein binding sites
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Image of FIG. 1.
FIG. 1.

Depiction of the native zinc binding in HLADH. The amino acids with polar side chains are marked with cyan/red for , respectively. The N-terminus corresponds to Phe and the C-terminus to Asp.

Image of FIG. 2.
FIG. 2.

Representative structures of the zinc binding site of four peptides. (a) The native peptide (CCCC) with four sulfurs coordinating the zinc. (b) The peptide CCCA with three sulfurs and three waters coordinating the zinc. (c) The peptide CAAC with two sulfurs, one carbonyl oxygen and two waters coordinating the zinc. (d) The peptide AAAC with one sulfur, three carbonyl oxygens, and two waters coordinating the zinc.

Image of FIG. 3.
FIG. 3.

coordination function for the AAAC peptide, where denotes carbonyl oxygen.

Image of FIG. 4.
FIG. 4.

polarization function for some representative polypeptides.

Image of FIG. 5.
FIG. 5.

Simulated EXAFS spectra (left side) and their Fourier transform (right side). ACCC O/N denotes the ACCC peptide with one of its carbonyl oxygens replaced with nitrogen. 1N8K(S) is the structural site. 1N8K(C) is the catalytic site.


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Table I.

Residue 93-115 in ADH and mutants. The charge of the side chain is marked with italic for , plain for 0 and underline for . The N-terminus is positively charged while the C-terminus is negative. The net charge of the peptides ranges from for CCCC to for AAAA. The numbering of the residues corresponds to that of the protein structure 1n8k.

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Table II.

Quantum and classical binding energies for clusters . R denotes mean Zn–S or Zn–O distances (Å).

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Table III.

Number of different atoms in first coordination shell. Plateau values for the first coordination sphere with mean distances (in Å) to water and carbonyl oxygens and sulfurs. Underline and italic correspond to positive and negative residue charges, respectively. is the one letter amino acid residue code for the coordinating carbonyls.

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Table IV.

rms deviations and fluctuations. rms (D) distances and (F) fluctuations for the peptides in nm.

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Table V.

Fourier transformed EXAFS data from Fig. 5. FWHM denotes full width half maximum and PP denotes peak position.

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Table VI.

Zinc-ligand QM and MD binding energy (kJ/mol) comparison for model clusters using with zero point energies (ZPEs), where Nr specifies the amount of ligand molecule in the first coordination shell.

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Table VII.

Zinc-ligand energies E and G in kJ/mol. Calculations using with ZPE included and where is the minimal mean distance (Å) to ligand X in the QM cluster. . is the protonation state correction energy. is the classical free energy integration energy. . and are the theoretical and experimental binding energies, respectively.


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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Molecular dynamics simulations of Zn2+ coordination in protein binding sites