Electric Field Effects on 13C and 17O Chemical Shifts and CO Stretching Frequency of Carbon Monoxide Bound to Fe2+

Strategy for Modeling the Electrostatic Responses of the Spectroscopic Properties of Proteins

For better understanding and more efficient use of the spectroscopic probes (vibrational and NMR) of the local electrostatic situations inside proteins, appropriate modeling of the properties of those probes is essential. The present study is devoted to examining the strategy for constructing such models. A more well-founded derivation than the ones in previous studies is given in constructing the models. Theoretical analyses are conducted on two representative example cases related to proteins, i.e., the peptide group of the main chains and the CO and NO ligands to the Fe²⁺ ion of heme, with careful treatment of the behavior of electrons in the electrostatic responses and with verification of consistency with observable quantities. It is shown that, for the stretching frequencies and NMR chemical shifts, it is possible to construct reasonable electrostatic interaction models that encompass the situations of hydration and uniform electric field environment and thus are applicable also to the cases of nonuniform electrostatic situations, which are highly expected for inside of proteins.

NMR, IR, Mössbauer and quantum chemical investigations of metalloporphyrins and metalloproteins

We review contributions made towards the elucidation of CO and O2binding geometries in respiratory proteins. Nuclear magnetic resonance, infrared spectroscopy, Mössbauer spectroscopy, X-ray crystallography and quantum chemistry have all been used to investigate the Fe –ligand interactions. Early experimental results showed linear correlations between17O chemical shifts and the infrared stretching frequency (νCO) of the CO ligand in carbonmonoxyheme proteins and between the17O chemical shift and the13CO shift. These correlations led to early theoretical investigations of the vibrational frequency of carbon monoxide and of the13C and17O NMR chemical shifts in the presence of uniform and non-uniform electric fields. Early success in modeling these spectroscopic observables then led to the use of computational methods, in conjunction with experiment, to evaluate ligand-binding geometries in heme proteins. Density functional theory results are described which predict57Fe chemical shifts and Mössbauer electric field gradient tensors,17O NMR isotropic chemical shifts, chemical shift tensors and nuclear quadrupole coupling constants (e2qQ/h) as well as13C isotropic chemical shifts and chemical shift tensors in organometallic clusters, heme model metalloporphyrins and in metalloproteins. A principal result is that CO in most heme proteins has an essentially linear and untilted geometry (τ = 4 °, β = 7 °) which is in extremely good agreement with a recently published X-ray synchrotron structure. CO / O2discrimination is thus attributable to polar interactions with the distal histidine residue, rather than major Fe–C–O geometric distortions.

A new model for mapping the peptide backbone: predicting proton chemical shifts in proteins

This paper describes a methodology that correlates experimental chemical shifts (at the alpha proton) of proteins with their geometrical data (both dihedral angles and distances) obtained from 13 representative proteins, which are taken from the Protein Data Bank (PDB) and the BioMagRes Data Bank (BMRB). To this end, the experimentally measured proton chemical shifts of simple amides have been correlated with DFT-based calculated structures, at the B3PW91/6-31G* level. This results in a series of mathematical relationships, which are extrapolated to the above-mentioned proteins giving rise to a modified equation for such skeleta. It is relevant to note that the equation is also supported by a clear comparison with NMR data of a protein beyond the chosen set, such as insulin, even with lower errors. The model also relates the dependence of chemical shifts on hydrophobic and anisotropic effects at the amino acid residues.

Modeling heme proteins using atomistic simulations

Heme proteins are found in all living organisms, and perform a wide variety of tasks ranging from electron transport, to the oxidation of organic compounds, to the sensing and transport of small molecules. In this work we review the application of classical and quantum-mechanical atomistic simulation tools to the investigation of several relevant issues in heme proteins chemistry: (i) conformational analysis, ligand migration, and solvation effects studied using classical molecular dynamics simulations; (ii) electronic structure and spin state energetics of the active sites explored using quantum-mechanics (QM) methods; (iii) the interaction of heme proteins with small ligands studied through hybrid quantum mechanics-molecular mechanics (QM-MM) techniques; (iv) and finally chemical reactivity and catalysis tackled by a combination of quantum and classical tools.

Chemical shifts in amino acids, peptides, and proteins: from quantum chemistry to drug design

This chapter discusses recent progress in the investigation and use of (13)C, (15)N, and (19)F nuclear magnetic resonance (NMR) chemical shifts and chemical shift tensors in proteins and model systems primarily using quantum chemical (ab initio Hartree-Fock and density functional theory) techniques. Correlations between spectra and structure are made and the techniques applied to other spectroscopic and electrostatic properties as well, including hydrogen bonding, ligand binding to heme proteins, J-couplings, electric field gradients, and atoms-in-molecules theory, together with a brief review of the use of NMR chemical shifts in drug design.