Biomedical subjects

Jens Antony

Publications and source records attributed to Jens Antony.

5 recordsLinked to original sources

PubMed2005

Anharmonic midinfrared vibrational spectra of benzoic acid monomer and dimer.

Anharmonic vibrational calculations for the benzoic acid monomer and dimer in the mid-IR regime (500-1800 cm(-1)) are reported. Harmonic frequencies and intensities are obtained at the DFT/B3LYP level of theory employing D95(d,p) and cc-pVTZ basis sets. Anharmonic corrections obtained from standard perturbation theory lead to redshifts of 1%-3%. In almost all cases, the resulting frequencies deviate by less than 1% from previous measurements [Bakker et al., J. Chem. Phys. 119, 11180 (2003)]. Calculated intensities are in qualitative agreement with the absorption experiment, with the cc-pVTZ values being superior to the D95(d,p) ones for a few modes of the dimer. The antisymmetric out-of-plane bending mode of the dimer, which is strongly blueshifted with respect to the monomer frequency, represents a remarkable exception: The harmonic frequencies obtained for the two basis sets differ notably from each other, and the anharmonically corrected frequencies deviate from the experimental value by 8% [D95(d,p)] or 3% (cc-pVTZ). Nonperturbative calculations in reduced dimensionality reveal that the relatively small total anharmonic shift (few tens of cm(-1)) comprises of partly much larger contributions (few hundreds of cm(-1)) which are mostly canceling each other. Many of the individual anharmonic couplings are beyond the validity of second-order perturbation theory based on cubic and semidiagonal quartic force constants only. This emphasizes the need for high-dimensional, nonperturbative anharmonic calculations at high quantum-chemical level when accurate frequencies of H-atom vibrations in double hydrogen bonds are sought for.

Journal Article↗

PubMed2005

Nonadiabatic effects on peptide vibrational dynamics induced by conformational changes.

Quantum dynamical simulations of vibrational spectroscopy have been carried out for glycine dipeptide (CH(3)-CO-NH-CH(2)-CO-NH-CH(3)). Conformational structure and dynamics are modeled in terms of the two Ramachandran dihedral angles of the molecular backbone. Potential energy surfaces and harmonic frequencies are obtained from electronic structure calculations at the density functional theory (DFT) [B3LYP/6-31+G(d)] level. The ordering of the energetically most stable isomers (C(7) and C(5)) is reversed upon inclusion of the quantum mechanical zero point vibrational energy. Vibrational spectra of various isomers show distinct differences, mainly in the region of the amide modes, thereby relating conformational structures and vibrational spectra. Conformational dynamics is modeled by propagation of quantum mechanical wave packets. Assuming a directed energy transfer to the torsional degrees of freedom, transitions between the C(7) and C(5) minimum energy structures occur on a sub-picosecond time scale (700...800 fs). Vibrationally nonadiabatic effects are investigated for the case of the coupled, fundamentally excited amide I states. Using a two state-two mode model, the resulting wave packet dynamics is found to be strongly nonadiabatic due to the presence of a seam of the two potential energy surfaces. Initially prepared adiabatic vibrational states decay upon conformational change on a time scale of 200...500 fs with population transfer of more than 50% between the coupled amide I states. Also the vibrational energy transport between localized (excitonic) amide I vibrational states is strongly influenced by torsional dynamics of the molecular backbone where both enhanced and reduced decay rates are found. All these observations should allow the detection of conformational changes by means of time-dependent vibrational spectroscopy.

Computer Simulation↗

PubMed2005

Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-beta-lactamase by polarizable molecular mechanics. Validation on model binding sites by quantum chemistry.

Using the polarizable molecular mechanics method SIBFA, we have performed a search for the most stable binding modes of D- and L-thiomandelate to a 104-residue model of the metallo-beta-lactamase from B. fragilis, an enzyme involved in the acquired resistance of bacteria to antibiotics. Energy balances taking into account solvation effects computed with a continuum reaction field procedure indicated the D-isomer to be more stably bound than the L-one, conform to the experimental result. The most stably bound complex has the S(-) ligand bridging monodentately the two Zn(II) cations and one carboxylate O(-) H-bonded to the Asn193 side chain. We have validated the SIBFA energy results by performing additional SIBFA as well as quantum chemical (QC) calculations on small (88 atoms) model complexes extracted from the 104-residue complexes, which include the residues involved in inhibitor binding. Computations were done in parallel using uncorrelated (HF) as well as correlated (DFT, LMP2, MP2) computations, and the comparisons extended to corresponding captopril complexes (Antony et al., J Comput Chem 2002, 23, 1281). The magnitudes of the SIBFA intermolecular interaction energies were found to correctly reproduce their QC counterparts and their trends for a total of twenty complexes.

Algorithms↗

PubMed2004

First principle calculations of (113)Cd chemical shifts for proteins and model systems.

113Cd isotropic NMR shieldings are calculated for a number of metal ion binding sites in proteins, using the GIAO-B3LYP and GIAO-HF methods with the uncontracted (19s15p9d4f) polarized basis set of Kellö and Sadlej on cadmium and 6-31G(d) on the ligands. The results compare favorably with experimental data, indicating that first principle calculations are a useful tool for structural interpretation of (113)Cd chemical shift data from metal ion containing proteins. The effect of different ligand types (thiolate, imidazole, water, and monodentate carboxylate), coordination number, and deviations of the coordination geometry from ideal structures is evaluated. In particular, the ligand type and coordination number are important factors, but also changes in cadmium-ligand bond lengths may cause significant changes of the chemical shift.

Binding Sites↗

PubMed2002

Binding of D- and L-captopril inhibitors to metallo-beta-lactamase studied by polarizable molecular mechanics and quantum mechanics.

The bacterial Zn2+ metallo-beta-lactamase from B. fragilis is a zinc-enzyme with two potential metal ion binding sites. It cleaves the lactam ring of antibiotics, thus contributing to the acquired resistance of bacteria against antibiotics. The present study bears on the binuclear form of the enzyme. We compare several possible binding modes of captopril, a mercaptocarboxamide inhibitor of several zinc-metalloenzymes. Two diastereoisomers of captopril were considered, with either a D- or an L-proline residue. We have used the polarizable molecular mechanics procedure SIBFA (Sum of Interactions Between Fragments ab initio computed). Two beta-lactamase models were considered, encompassing 104 and 188 residues, respectively. The energy balances included the inter and intramolecular interaction energies as well as the contribution from solvation computed using a continuum reaction field procedure. The thiolate ion of the inhibitor is binding to both metal ions, expelling the bridging solvent molecule from the uncomplexed enzyme. Different competing binding modes of captopril were considered, either where the inhibitor binds in a monodentate mode to the zinc cations only with its thiolate ion, or in bidentate modes involving additional zinc binding by its carboxylate or ketone carbonyl groups. The additional coordination by the inhibitor's carboxylate or carbonyl group always occurs at the zinc ion, which is bound by a histidine, a cysteine, and an aspartate side chain. For both diastereomers, the energy balances favor monodentate binding of captopril via S-. The preference over bidentate binding is small. The interaction energies were recomputed in model sites restricted to captopril, the Zn2+ cations, and their coordinating end side chains from beta-lactamase (98 atoms). The interaction energies and their ranking among competing arrangements were consistent with those computed by ab initio HF and DFT procedures.

Algorithms↗