Bulletin of the American Physical Society
2005 APS March Meeting
Monday–Friday, March 21–25, 2005; Los Angeles, CA
Session L22: Metalloenzymes: Structure and Function |
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Sponsoring Units: DBP Chair: Marilyn Gunner, CCNY Room: LACC 409B |
Tuesday, March 22, 2005 2:30PM - 3:06PM |
L22.00001: Experimental Studies of Structure, Function, and Coherent Oscillations in Biomolecules Invited Speaker: Femtosecond coherence spectroscopy can be used to prepare and monitor coherent states of biological samples such as heme proteins. Following laser pulse induced ligand photolysis of myoglobin, the (initially planar) heme group is left far from its final product state equilibrium geometry. This leads to coherent oscillations of those modes composing the reaction coordinate for diatomic ligand binding and dissociation. Coherence studies, along with ``white light'' continuum measurements of the spectral dynamics, show that the timescale for diatomic ligand dissociation is much shorter than the 150fs period of the Fe-histidine vibration (the Fe-histidine bond constitutes the sole covalent linkage between the heme and protein material). Recent measurements of the effects of temperature and sample condition on the coherent motions of the heme and on the ultrafast geminate rebinding of various diatomic ligands are also reported. Investigations of heme model compounds, in the absence of the protein material, show that the spectrum of low frequency heme modes can be altered by the choice of sample conditions. The studies of the heme model compounds also allow the diatomic ligand rebinding barrier to be separated into ``proximal'' and ``distal'' contributions that can be separately determined. [Preview Abstract] |
Tuesday, March 22, 2005 3:06PM - 3:18PM |
L22.00002: Investigations of the low frequency modes of Fe-porphyrin systems and perturbations induced by axial ligation Flaviu Gruia, Xiong Ye, Paul Champion We investigate the effect of a 2-methyl imidazole (2-MeIm) ligand on the low frequency ($<$250cm$^{-1})$ vibrational spectrum of iron protoporphyrin IX (Fe-PPIX). This compound is designed to mimic the active site of histidine ligated heme proteins. We use femtosecond coherence spectroscopy to probe the reduced species of Fe-PPIX with and without the 2-MeIm ligand. We notice important changes in the lowest frequency region ($<$50 cm$^{-1})$ of the spectrum, along with the expected disappearance of the 2-MeIm-Fe mode at 216cm$^{-1}$ (in the FePPIX model) when the 2-MeIm ligand is absent. Overall, these observations suggest that a low frequency mode observed near 20 cm$^{-1}$ is associated with the imidazole ligand and that the anharmonic heme doming mode, associated with the Fourier components in the power spectrum near 40 cm$^{-1}$ and 80 cm$^{-1}$, can be affected by axial ligation. [Preview Abstract] |
Tuesday, March 22, 2005 3:18PM - 3:30PM |
L22.00003: Quantitative Vibrational Dynamics of Iron in Porphyrins Bogdan M. Leu, Marek Z. Zgierski, Graeme R. A. Wyllie, Nathan Silvernail, W. Robert Scheidt, Wolfgang Sturhahn, Ercan E. Alp, Stephen M. Durbin, J. Timothy Sage We compare quantitative experimental (nuclear resonance vibrational spectroscopy - NRVS) and theoretical (density functional theory - DFT) approaches to characterize the vibrational dynamics of the $^{57}$Fe atom in CO-ligated porphyrins designed to mimic the active site of heme proteins. NRVS yields the frequencies, amplitudes, and directions of the Fe vibrations. These measurements confirm many aspects of the DFT predictions, suggesting that the latter provides a reliable description of the observed modes. We will discuss the character of normal modes for Fe(TPP)(1-MeIm)(CO), including a series of modes involving Fe motion in the plane of the heme, Fe-Im modes, Fe-ligand modes, and reactive modes. [Preview Abstract] |
Tuesday, March 22, 2005 3:30PM - 3:42PM |
L22.00004: First-Principles Hartree-Fock Investigation of Electronic Structure and Hyperfine Properties of Deoxyhemoglobin K. Ramani Lata, R. H. Scheicher (*), N. Sahoo (**), T. P. Das (***), S. Byahut The electronic structure of Deoxyhemoglobin is studied using the Unrestricted Hartree--Fock Cluster Procedure considering as representative the entity involving the porphyrin ring, the Fe$^{2+}$ ion and the proximal histidine. The positions of the atoms are taken from X-ray data. The calculated electronic structure of the spin S=2 system is used to derive the magnetic hyperfine fields, nuclear quadrupole interaction parameters and the Mossbauer isomer shifts for the $^{57m}$Fe. The results are in good agreement with experiment, providing support for the accuracy of the calculated isotropic and anisotropic components of the spin density and electronic charge density near the $^{57m}$Fe nucleus. Results for the hyperfine properties of $^{14}$N, $^{13}$C, $^{1}$H and $^{2}$H nuclei will also be discussed. (*) Present Address: Dept. of Physics, Uppsala University, Sweden (**) Present Address: M. D. Anderson Center, Houston, Texas (***) Also: Dept. of Physics, University of Central Florida, Orlando, Florida [Preview Abstract] |
Tuesday, March 22, 2005 3:42PM - 4:18PM |
L22.00005: Time-resolved heme protein intermediates Invited Speaker: To determine the enzymatic mechanisms of heme proteins, it is necessary to identify the intermediates along the catalytic pathway and measure the times of their formation and decay. Resonance Raman scattering spectra are especially powerful for obtaining such information as the electronic structure of the heme group and the nature of the ligand coordinated to the heme iron atom may be monitored. The oxygen intermediates of two physiologically important enzymes will be presented. Nitric oxide synthase (NOS) uses oxygen to convert arginine to NO and citrulline; and cytochrome c oxidase (CcO) reduces oxygen to water to support oxidative phosphorylation. The fate or the oxygen in each of these enzymes has been followed by resonance Raman scattering. In NOS the oxygen is slowly converted to an activated species that then reacts fast, whereas in CcO the oxygen is rapidly converted to a reactive species that subsequently reacts slowly. The properties of the intermediates and the origin of the differences between these enzymes will be discussed. [Preview Abstract] |
Tuesday, March 22, 2005 4:18PM - 4:30PM |
L22.00006: Density Functional Theory / Nudged Elastic Band Investigation of the Hydroxylation Reaction Mechanism Catalyzed by P450cam Montiago LaBute, Graeme Henkelman, Benjamin McMahon We have calculated the complete minimum-energy reaction path for the hydroxylation of camphor by the P450 enzyme from Pseudomonas putida using the nudged elastic band method of Jonsson and co-workers[1]. Single-point force and energy calculations on pathway images were performed at the hybrid density functional level of theory (B3LYP) with large basis sets for the iron atom (6-311+G) and O$_{2}$ ligand (6-31+G*) on a ~100 atom active site extracted from a recent high-resolution crystal structure[2]. Our model includes the heme group liganded to both Cys357 and dioxygen and we also include Thr251 and Asp252, which have been shown to significantly affect product yield by mutational studies[3]. We find that, upon transfer of the 2nd electron to the active site, the Fe-O$_{2}$ moiety is unstable and decays to a Fe-OOH- intermediate via a Asp252-H$_{2}$O proton transfer chain. The barrier for dioxygen cleavage and the identity of the reactive species will be discussed. [1] H. Jonsson, G. Mills, K.W. Jacobsen, in Classical and Quantum Dynamics in Condensed Phase Simulation, World Scientific (1998). [2] I. Schlichting, et al., Science 287, no. 5458, p. 1615-1622 (2000). [3] R. Davydov, et al., J. Am. Chem. Soc., 123: 1403-1415 (2001). [Preview Abstract] |
Tuesday, March 22, 2005 4:30PM - 4:42PM |
L22.00007: Models of the photosynthetic oxygen-evolving centerand electronic structure of Mn clusters Gabriel Drobny, Michal Bajdich, Lubos Mitas It is known that the oxidation of water to O$_2$ in green plants is associated with a tetramanganese complex of the photosystem II (PSII) protein-cofactor complex but the exact structure of the oxygen-evolving center (OEC) remains unknown. The recent X-ray spectroscopic studies suggest that the OEC contains a cubane-like Mn$_3$CaO$_4$ center linked to a forth Mn by an oxo-bridge. Using ab-initio methods we carry out geometry optimizations for a few models of the OEC and study their electronic properties. We consider the cubane-like Mn$_3$CaO$_4$ center, a funnel-like Mn4 core with Ca ligand and a synthetic Mn$_4$O$_6$ core structure. Possibilities for binding sites and eventual reaction paths of the water splitting are explored. Manganese clusters are recognized also as single-molecule magnets. Therefore we investigate spin properties of ground and excited states of these clusters. High spin ground states of Mn$_2$O$_2$ and Mn$_4$ compared to a low spin ground state of Mn$_4$O$_4$ illustrate a competition between ferromagnetic and antiferromagnetic ordering. [Preview Abstract] |
Tuesday, March 22, 2005 4:42PM - 4:54PM |
L22.00008: Pre-Crystallization State of Ferritin at Low Temperature Sebastien Boutet, Ian Robinson In the course of a systematic exploration of the crystallization kinetics and conditions of the protein ferritin using x-rays, we discovered an unexpected new state of aggregation of the protein at low temperature. This new state was found to form reversibly below the freezing point of the solution. Using Small Angle X-ray Scattering (SAXS), we studied the properties of solutions of ferritin upon cooling and found that ferritin molecules form clusters of varying size and structures depending on the temperature and the thermal history of the sample. Simulations of the SAXS patterns were made using various cluster structures and these show that clusters of roughly 50 molecules form upon freezing. The structure was found to be similar to the FCC structure of macroscopic ferritin crystals which leads us to the conclusion that these clusters may be precursor states to the crystallization of ferritin. [Preview Abstract] |
Tuesday, March 22, 2005 4:54PM - 5:06PM |
L22.00009: Ab initio studies of [Fe$_{4}$S$_{4}$]$ ^{2+/3+}$ clusters in metalloprotein MutY Jong-Chin Lin, Daniel Cox, Rajiv Singh Iron sulfur clusters are present in the DNA repair protein MutY in a region highly homologous in species as diverse as E. Coli and Homo Sapiens, yet their function remains unknown. In MutY, this mixed valence cluster exists in two oxidation states, [Fe$_ {4}$S$_{4}$]$^{2+/3+}$, with the stability depending upon the presence of DNA. We have studied the electronic structure and stability of these clusters using density functional theory, in particular the local orbital based SIESTA program. Our calculation shows that the energy difference between 2+ and 3+ forms is within the range of 0.1eV, which suggests that the redox process is reversible. We use this to propose a possible redox mechanism for modulating the rate for scanning for oxidized G-A mismatches in DNA by MutY \footnote{M. Slutsky and L.A. Mirny, preprint q-bio.BM/0402005 at http://arxiv.org.}. We note that this redox modulation mechanism for site recognition scanning may have broader generality. [Preview Abstract] |
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