Bulletin of the American Physical Society
2007 APS March Meeting
Volume 52, Number 1
Monday–Friday, March 5–9, 2007; Denver, Colorado
Session L35: Metalloproteins: Theory and Experiment |
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Sponsoring Units: DPB DCP DCOMP Chair: Sergei Savikhin, Purdue University Room: Colorado Convention Center 405 |
Tuesday, March 6, 2007 2:30PM - 2:42PM |
L35.00001: Hartree - Fock study of the Heme Unit of deoxy-hemoglobin for Hyperfine Interactions and Vibrational Properties. T.P. Das, K. Ramani Lata, R.H. Pink, Dip N. Mahato, Archana Dubey, H.P. Saha, A.F. Schulte, Lee Chow, R.H. Scheicher, N.B. Maharjan, N. Sahu The electronic structure of the Heme Unit of deoxy- Hemoglobin has been studied by the Hartree- Fock - Roothaan procedure for understanding the hyperfine interaction properties of the $^{57m}$Fe nucleus and vibrational properties associated with Fe and proximal imidazole. Results will be presented for the $^{57m}$Fe nucleus, including the isomer shift in Mossbauer spectroscopy, magnetic hyperfine and nuclear quadrupole interactions and for the Fe-N$_{\varepsilon }$ vibrational frequency. Comparisons will be made with available experimental data and possible further investigations will be discussed. [Preview Abstract] |
Tuesday, March 6, 2007 2:42PM - 2:54PM |
L35.00002: DFT Studies of NO Activation of Heme Proteins. A. Barabanschikov, J.T. Sage, N.J. Silvernail, W.R. Scheidt, J. Zhao, Wolfgang Sturhahn, E.E. Alp Many important cardiovascular and neural system processes are triggered by activation of the enzyme soluble guanylate cyclase (sGC), a sensor of NO widely thought to be activated through binding of NO to heme. Our understanding of these processes will remain incomplete without knowing why NO activates sGC more effectively than other diatomic ligands. We report DFT calculations on various porphyrins and heme protein active sites to test the hypothesis that activation of sGC is associated with disruption of the Fe-histidine bond to the protein. We demonstrate that NO binding significantly weakens this bond. Also, comparing the predicted vibrational spectra of these compounds with nuclear resonance vibrational spectroscopy (NRVS) measurements allows us to identify the Fe- histidine stretching mode, a reaction coordinate for histidine dissociation in NO-ligated heme proteins. Comparison of 5-coordinate and 6-coordinate NO and CO compounds provides additional tests of the hypothesis. [Preview Abstract] |
Tuesday, March 6, 2007 2:54PM - 3:06PM |
L35.00003: Ab-Initio-Based Approach to Study Complete Metalloproteins: Divide and Conquer Geometry Optimization of Nitric-Oxide Reductase Yutao Yue, Teepanis Chachiyo, Jorge H. Rodriguez The direct application of ab-initio methods (Hartree-Fock or density functional theory) to study complete biomolecules has been impossible due to the huge computational cost of fully quantum mechanical calculations. As an initial step towards overcoming this problem, we implemented an ab-initio-based method to predict geometric structures of large metalloproteins using the principle of ``divide and conquer.'' The method has been applied to small test systems showing satisfactory agreement with all-atom ab initio calculations. We have successfully applied the divide and conquer approach to partially optimize the geometry of a ligand-enzyme system, namely NO binding to nitric-oxide reductases (NOR, P450nor). NOR is a metalloenzyme that catalyzes the reduction of NO to N$_2$O. To compare our results with all atom calculations we studied a biochemically relevant subsystem (375 atoms) of the ligand-enzyme complex. The deviation between the divide and conquer geometry and the all atom partial geometry optimization is minor, on order of 10$^-1$ {\AA} for bond lengths. The computational cost of the method is moderately expensive making its application to large (bio) molecules plausible. Supported by NSF CAREER Award CHE-0349189 (JHR). [Preview Abstract] |
Tuesday, March 6, 2007 3:06PM - 3:18PM |
L35.00004: Ab-Initio Based Computation of Rate Constants for Spin Forbidden Metalloprotein-Substrate Reactions Abdullah Ozkanlar, Jorge H. Rodriguez Some chemical and biochemical reactions are non-adiabatic processes whereby the total spin angular momentum, before and after the reaction, is not conserved. These are named spin- forbidden reactions. The application of ab-initio methods, such as spin density functional theory (SDFT), to the prediction of rate constants is a challenging task of fundamental and practical importance. We apply non-adiabatic transition state theory (NA-TST) in conjuntion with SDFT to predict the rate constant of the spin- forbidden recombination of carbon monoxide with iron tetracarbonyl. To model the surface hopping probability between singlet and triplet states, the Landau-Zener formalism is used. The lowest energy point for singlet-triplet crossing, known as minimum energy crossing point (MECP), was located and used to compute, in a semi-quantum approach, reaction rate constants at 300 K. The predicted rates are in very good agreement with experiment. In addition, we present results for the spin- forbidden ligand binding reactions of iron-containing heme proteins such as myoglobin. [Preview Abstract] |
Tuesday, March 6, 2007 3:18PM - 3:30PM |
L35.00005: Dependence of Localized Electronic Structure on Ligand Configuration in the [2Fe] Hydrogenase Catalytic Core$^{\ast}$ Christopher H. Chang, Kwiseon Kim The [FeFe] hydrogenase enzyme is found in a variety of organisms, including Archaea, Eubacteria, and green algae$^{1,2}$, and crystallographically determined atomic position data is available for two examples. The biologically unusual catalytic H-cluster, responsible for proton reduction to H$_{2}$ \textit{in vivo}, is conserved in the known structures and includes two \textit{bis}-thiolato bridged iron ions with extensive cyano- and carbonyl ligation. To address the configurational specificity of the diatomic ligand ligation, density functional theoretical calculations were done on [2Fe] core models of the active center, with varying CO and CN$^{-}$ ligation patterns. Bonding in each complex has been characterized within the Natural Bond Orbital formalism. The effect of ligand configuration on bonding and charge distribution as well as Kohn-Sham orbital structure will be presented. [1] M. Forestier, P. King, L. Zhang, M. Posewitz, S. Schwarzer, T. Happe, M.L. Ghirardi, and M. Seibert, Eur. J. Biochem. \textbf{270, }2750 (2003). [2] Posewitz, M.C., P.W. King, S.L. Smolinski, R.D. Smith, II, A.R. Ginley, M.L. Ghirardi, and M. Seibert, Biochem. Soc. Trans. \textbf{33, }102 (2005). \newline $^{\ast}$This work was supported by the US DOE-SC-BES Hydrogen Fuels Initiative, and done in collaboration with the NREL Chemical and Biosciences Center. [Preview Abstract] |
Tuesday, March 6, 2007 3:30PM - 3:42PM |
L35.00006: Ab Initio Computation of Spin Orbit Coupling Effects on Magnetic Properties of Iron-Containing Complexes and Proteins Fredy Aquino, Jorge H. Rodriguez Zero-Field Splittings (ZFS) in metalloproteins and other metal complexes arise from the combined action of crystalline fields acting on the metal valence electrons and spin-orbit coupling (SOC), a relativistic effect. The ab-initio calculation of ZFS parameters of metal-containing (bio)molecules is a challenging computational problem of practical relevance to metalloenzyme biochemistry, inorganic chemistry, and molecular-based bio- nanotechnology. We have implemented a methodology which treats the nonrelativistic electronic structure of magnetic (bio) molecules within the framework of spin density functional theory (SDFT) and adds the relativistic effects of SOC via perturbation theory (PT). This combined SDFT-PT approach allowed us to compute the ZFS parameters of iron-containing complexes and non-heme iron proteins with a good degree of accuracy. We also developed a semiquantitative approach to elucidate the physico-chemical origin of the magnitudes of ZFS parameters. We present results for biochemically relevant iron complexes and for nitric oxide-containing non-heme iron proteins, such as isopenicillin N synthase, which have unusually large ZFS. The computed ZFS parameters are in good agreement with experiment. Supported by NSF CAREER Award CHE- 0349189 (JHR). [Preview Abstract] |
Tuesday, March 6, 2007 3:42PM - 3:54PM |
L35.00007: F\"{o}rster-type mechanism of the redox-driven proton pump Lev Mourokh, Anatoly Smirnov, Franco Nori We propose a model to describe an electronically-driven proton pump in the \textit{cytochrome c oxidase} (\textit{CcO}). We examine the situation when the electron transport between the two sites embedded into the inner membrane of the mitochondrion occurs in parallel with the proton transfer from the protonable site that is close to the negative (inner) side of the membrane to the other protonable site located nearby the positive (outer) surface of the membrane. In addition to the conventional electron and proton tunnelings between the sites, the Coulomb interaction between electrons and protons localized on the corresponding sites leads to so-called F\"{o}rster transfer, i.e. to the process when the simultaneous electron and proton tunnelings are accompanied by the resonant energy transfer between the electrons and protons. Our calculations based on reasonable parameters have demonstrated that the F\"{o}rster process facilitates the proton pump at physiological temperatures. We have examined the effects of an electron voltage build-up, external temperature, and molecular electrostatics driving the electron and proton energies to the resonant conditions, and have shown that these parameters can control the proton pump operation. [Preview Abstract] |
Tuesday, March 6, 2007 3:54PM - 4:06PM |
L35.00008: Investigation of copper(II) binding to the protein precursor of Non-Amyloid-Beta Component of Alzheimer Disease Amyloid Plaque Francis Rose, Miroslav Hodak, Jerry Bernholc The Non-Amyloid-Beta Component Precursor (NACP) is a natively unfolded synaptic protein that is implicated in Alzheimers and Parkinsons diseases. Its aggregation into fibrillar structures is accelerated by the binding of copper(II). Experimental studies suggest that the dominant copper binding site is located at the histidine residue in NACP. Based on this evidence we assembled a model fragment of the binding site and used DFT to analyze the conformational details of the most probable binding motifs. We investigated the overall conformational effects with classical MD by constraining the copper binding site to the most energetically favorable geometry obtained from the DFT calculations. These results are compared and contrasted with those of the unbound NACP. [Preview Abstract] |
Tuesday, March 6, 2007 4:06PM - 4:18PM |
L35.00009: Cooperative binding modes of Cu(II) in prion protein Miroslav Hodak, Robin Chisnell, Wenchang Lu, Jerry Bernholc The misfolding of the prion protein, PrP, is responsible for a group of neurodegenerative diseases including mad cow disease and Creutzfeldt-Jakob disease. It is known that the PrP can efficiently bind copper ions; four high-affinity binding sites located in the octarepeat region of PrP are now well known. Recent experiments suggest that at low copper concentrations new binding modes, in which one copper ion is shared between two or more binding sites, are possible. Using our hybrid Thomas-Fermi/DFT computational scheme, which is well suited for simulations of biomolecules in solution, we investigate the geometries and energetics of two, three and four binding sites cooperatively binding one copper ion. These geometries are then used as inputs for classical molecular dynamics simulations. We find that copper binding affects the secondary structure of the PrP and that it stabilizes the unstructured (unfolded) part of the protein. [Preview Abstract] |
Tuesday, March 6, 2007 4:18PM - 4:30PM |
L35.00010: Studies of myoglobin dynamics by dielectric relaxation spectroscopy Guo Chen, I. Mihut, B. H. McMahon, A. Migliori, P. W. Fenimore Proteins are dynamic molecules and their motions are intimately linked to the fluctuations of their solvent environment. In this work we studied the protein-solvent interactions by measuring the dielectric response of horse myoglobin (Mb) in glycerol/H$_2$O mixtures over a frequency range of 40Hz-110MHz. Two relaxation processes were observed at temperatures above 220K. The high frequency process corresponds to the $\alpha$-fluctuations of the glycerol/H$_2$O solvent and its rates were found to increase slightly at the presence of the Mb protein. The low frequency process, slower by roughly four orders of magnitude, is relevant to Mb motions and absent for the samples without Mb. The temperature dependence of the two processes can be approximated with the same Vogel-Tammann-Fulcher temperature dependence. Preliminary analyses suggest that the Mb-related process is associated with the conformational fluctuations of the whole Mb protein. Such fluctuations require the coordinated motions of surrounding solvent molecules and are thus an example of protein slaving to the solvent fluctuations. [Preview Abstract] |
Tuesday, March 6, 2007 4:30PM - 4:42PM |
L35.00011: Vibrational Characterization of Myoglobin Compound II W. Zeng, A. Barabanschikov, Y. Zhang, J.T. Sage, E.E. Alp, W. Sturhahn, J. Zhao Compound II intermediates are essential to oxygen activation by heme proteins. The protonation status of the Fe$^{IV}$ oxo fragment is controversial. EXAFS and Raman spectroscopy have long suggested an Fe$^{IV}$=O group, but recent crystal structures show a long Fe-O distance more consistent with a protonated Fe-OH. We use nuclear resonance vibrational spectroscopy (NRVS) to probe the motion of $^{57}$Fe in compound II of horse heart myoglobin(Mb II). Although the NRVS signal is weaker than expected, we clearly identify the Fe-O stretch at 805 cm$^{-1}$, in addition to previously unobserved in-plane Fe vibrations near 360 cm$^{-1}$. Cryogenic Raman measurement on isotopically labeled Mb II reveals that the kinetic energy distribution (KED) of the Fe-O stretch is localized on the Fe-O fragment, with no significant involvement from the putative proton. Comparison with DFT vibrational predictions provide further insight into the character of the observed normal modes. We conclude that the oxo group is not protonated in Mb II. [Preview Abstract] |
Tuesday, March 6, 2007 4:42PM - 4:54PM |
L35.00012: Investigations of the 40cm$^{-1}$ mode in hexacoordinated ferric heme systems Flaviu Gruia, Xiong Ye, Paul Champion The 40cm$^{-1}$ mode dominates the low frequency spectra of most hexacoordinated ferric heme systems investigated to date. For a better understanding and assignment of this mode we have measured the FCS excitation profile of cyanide bound myoglobin, which shows this feature particularly well. We observe a very interesting behavior of the initial phase and the amplitude of this mode which do not fit within the existent theoretical models. The experimental results could be explained if we postulate the existence of a fast non-radiative transition between the nuclear excited and the ground states. There are also arguments that support the existence of a charge transfer band that underlies the Soret band. [Preview Abstract] |
Tuesday, March 6, 2007 4:54PM - 5:06PM |
L35.00013: Novel photo-protection mechanism in strongly coupled chlorophyll complexes: triplet excitons in chlorosomes and in artificial chlorophyll aggregates. Sergei Savikhin, Hanyoup Kim, Hui Li, Julia Maresca, Donald Bryant Bacteriochlorophyll (BChl) and chlorophyll (Chl) molecules are known to produce highly toxic singlet oxygen due to energy transfer from their excited triplet states to oxygen molecules. The monomeric (B)Chl molecules in a solution photo-degrade within minutes under sunlight. In (B)Chl pigment-protein complexes of photosynthesis, a carotenoid is typically positioned within a distance of 4 {\AA} of individual (B)Chl or antenna arrays, allowing rapid triplet energy transfer from (B)Chl to the carotenoid. Our time resolved and steady state optical experiments reveal that strongly coupled BChl arrays of pigments are inherently protected due to the formation of triplet excitonic states. According to model simulations, the energy of the triplet exciton is substantially lower than that of the triplet state of an individual BChl, dropping below that of singlet oxygen, and blocking the triplet energy transfer to both carotenoid and to oxygen. This effect is observed experimentally in photosynthetic chlorosomes and in artificial BChl complexes. [Preview Abstract] |
Tuesday, March 6, 2007 5:06PM - 5:18PM |
L35.00014: Transport dynamics in membranes of photosynthetic purple bacteria Felipe Caycedo, Ferney Rodriguez, Luis Quiroga, Francesca Fassioli, Neil Johnson Photo-Syntethic Unit (PSU) of purple bacteria is conformed by three basic constituents: Light Harvesting Complex 2 (LH2) antenna complexes, where chromophores are distributed in a ring in close contact with caroteniods with a function of collecting light; LH1s, ring shaped structures of chromophores which harvest and funnel excitations to the Reaction Centre (RC), where phtosynthesis takes place. Studies concerning a single PSU have been capable of reproducing experimental transfer times, but incapable of explaining the fact that architecture LH2-LH1-RC of phototosynthetic membranes changes as light intensity conditions vary. The organization of antenna complexes in the membranes that support PSU seems to have its own functionality. A hopping model where excitations are transferred within a membrane is used, and populations of RC, LH1 and LH2 are investigated. Different statistics concerning arrival times of excitations that excite a single PSU are considered and compared with the global model where coordinates of a great portion of a membrane are included. The model permits in a classical basis to understand which parameters make photosynthesis in purple bateria efficient and reliable. [Preview Abstract] |
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