Single-atom test of all-atom empirical potentials: Fe in myoglobin

Protein and water confined in nanometer-scale reverse micelles studied by near infrared, terahertz, and ultrafast visible spectroscopies

Protein-containing reverse (PCR) micelles are suitable systems to study the properties of proteins and waters in a cell-like environment. A model for determining the structural parameters of PCR micelles, such as the aqueous cavity size and molecule number of water within the reverse micelle, is presented. The model is based on an important hypothesis that the structural parameters of the protein-unfilled reverse micelle do not change after solubilization of protein. I describe a procedure using near infrared spectroscopy of OH stretching vibration band of water to verify the hypothesis. Further, the terahertz (THz) absorption spectrum of myoglobin is derived from THz time-domain spectroscopy of the PCR micellar solution, and the states of waters in reverse micelles with and without protein are discussed on the basis of the structural parameters. The last topic is on internal dynamics of PCR micelles on timescales from femtoseconds to nanoseconds studied by femtosecond time-resolved fluorescence spectroscopy.

Predicting Nuclear Resonance Vibrational Spectra of [Fe(OEP)(NO)]

Nuclear Resonance Vibrational Spectroscopy (NRVS) is a sensitive vibrational probe for biologically important heme complexes. The exquisite sensitivity of the NRVS data to the electronic structure provides detailed insights into the nature of these interesting compounds, but requires highly accurate computational methods for the mode assignments. To determine the best combinations of density functionals and basis sets, a series of benchmark DFT calculations on the previously characterized complex [Fe(OEP)NO] (OEP(2-)=octaethylporphyrinatio dianion) were performed. A test set of 21 methodology combinations including 8 functionals (BP86, mPWPW91, B3LYP, PBE1PBE, M062X, M06L, LC-BP86 and ωB97X-D) and 5 basis set (VTZ, TZVP, Lanl2DZ for iron and 6-31G*, 6-31+G* for other atoms) was carried out to calculate electronic structures and vibrational frequencies. We also implemented the conversion of frequency calculations into orientation-selective mode composition factors (e(2)), which can used to simulate the Vibrational Density Of States (VDOS) using Gaussian normal distribution functions. These use a series of user-friendly scripts for their application to NRVS. The structures as well as the isotropic and anisotropic NRVS of [Fe(OEP)NO] obtained with the M06L functional with a variety of basis sets are found to best reproduce the available experimental data, followed by B3LYP/LanL2DZ calculations. Other density functionals and basis sets do not produce the same level of accuracy. The noticeably worse agreement between theory and experiment for the out-plane NRVS compared with the excellent performance of the M06L functional for the in-plane prediction is attributed to deficiencies of the physical model rather than the computational methodology.

Dynamical transition in proteins and non-Gaussian behavior of low-frequency modes in self-consistent normal mode analysis

Self-consistent normal mode analysis (SCNMA) is applied to heme c type cytochrome f to study temperature-dependent protein motion. Classical normal mode analysis assumes harmonic behavior and the protein mean-square displacement has a linear dependence on temperature. This is only consistent with low-temperature experimental results. To connect the protein vibrational motions between low and physiological temperatures, we have incorporated a fitted set of anharmonic potentials into SCNMA. In addition, quantum harmonic-oscillator theory has been used to calculate the displacement distribution for individual vibrational modes. We find that the modes involving soft bonds exhibit significant non-Gaussian dynamics at physiological temperature, which suggests that it may be the cause of the non-Gaussian behavior of the protein motions probed by elastic incoherent neutron scattering. The combined theory displays a dynamical transition caused by the softening of few "torsional" modes in the low-frequency regime ( <50 cm(-1) or <6 meV or >0.6 ps). These modes change from Gaussian to a classical distribution upon heating. Our theory provides an alternative way to understand the microscopic origin of the protein dynamical transition.

Resilience of the iron environment in heme proteins

Conformational flexibility is essential to the functional behavior of proteins. We use an effective force constant introduced by Zaccai, the resilience, to quantify this flexibility. Site-selective experimental and computational methods allow us to determine the resilience of heme protein active sites. The vibrational density of states of the heme Fe determined using nuclear resonance vibrational spectroscopy provides a direct experimental measure of the resilience of the Fe environment, which we compare quantitatively with values derived from the temperature dependence of atomic mean-squared displacements in molecular dynamics simulations. Vibrational normal modes in the THz frequency range dominate the resilience. Both experimental and computational methods find a higher resilience for cytochrome c than for myoglobin, which we attribute to the increased number of covalent links to the peptide in the former protein. For myoglobin, the resilience of the iron environment is larger than the average resilience previously determined for hydrogen sites using neutron scattering. Experimental results suggest a slightly reduced resilience for cytochrome c upon oxidation, although the change is smaller than reported in previous Mössbauer investigations on a bacterial cytochrome c, and is not reproduced by the simulations. Oxidation state also has no significant influence on the compressibility calculated for cyt c, although a slightly larger compressibility is predicted for myoglobin.

Vibrational spectroscopy and normal-mode analysis of Fe(II) octaethylporphyrin

The normal-mode spectrum for the four-coordinated heme compound Fe(II) octaethylporphyrin, Fe(OEP), has been determined by refining force constants to the experimental Fe vibrational density of states measured with nuclear resonance vibrational spectroscopy (NRVS). Convergence of the calculated spectrum to the data was achieved by first imposing D4 symmetry on the model structure as well as the force constants, progressively including different internal coordinates of motion, then allowing the true Ci (or S2) point group symmetry of the C(i)1 Fe(OEP) crystal structure. The NRVS-refined normal modes are in good agreement with Raman and IR spectra at high frequencies. Prior density functional theory predictions for a model porphyrin are similar to the core modes computed with the best-fit force field, but significant differences between D4 and Ci modes underline the sensitivity of porphyrin Fe normal modes to structural details. Some differences between the Ci best fit and the NRVS data can be attributed to intermolecular contacts not included in the normal-mode analysis.