Biomedical subjects

Brian M Hoffman

Publications and source records attributed to Brian M Hoffman.

At least 19 recordsLinked to original sources

PubMed2006

Comparing the electronic properties of the low-spin cyano-ferric [Fe(N4)(Cys)] active sites of superoxide reductase and p450cam using ENDOR spectroscopy and DFT calculations.

Superoxide reductase (SOR) and P450 enzymes contain similar [Fe(N)4(SCys)] active sites and, although they catalyze very different reactions, are proposed to involve analogous low-spin (hydro)peroxo-Fe(III) intermediates in their respective mechanisms that can be modeled by cyanide binding. The equatorial FeN4 ligation by four histidine ligands in CN-SOR and the heme in CN-P450cam is directly compared by 14N ENDOR, while the axial Fe-CN and Fe-S bonding is probed by 13C ENDOR of the cyanide ligand and 1Hbeta ENDOR measurements to determine the spin density delocalization onto the cysteine sulfur. There are small, but notable, differences in the bonding between Fe(III) and its ligands in the two enzymes. The ENDOR measurements are complemented by DFT computations that support the semiempirical equation used to compute spin densities on metal-coordinated cysteinyl and shed light on bonding changes as the Fe-C-N linkage bends. They further indicate that H bonds to the cysteinyl thiolate sulfur ligand reduce the spin density on the sulfur in both active sites to a degree that exceeds the difference induced by the alternative sets of "in-plane" nitrogen ligands.

Binding Sites↗

PubMed2006

NMR spectroscopy can characterize proteins encapsulated in a sol-gel matrix.

Proteins encapsulated within sol-gel matrices (SG) have the potential to fill many scientific and technological roles, but these applications are hindered by the limited means of probing possible structural consequences of encapsulation. We here present the first demonstration that it is possible to obtain high-resolution, solution NMR measurements of proteins encapsulated within a SG matrix. With the aim of determining the breadth of this approach, we have encapsulated three paramagnetic proteins with different overall charges: the highly acidic human Fe3+ cytochrome b5 (cyt b5); the highly basic horse heart cytochrome c (cyt c); and the nearly neutral, sperm whale cyanomet-myoglobin. The encapsulated anionic and neutral proteins (cyt b5; myoglobin) undergo essentially free rotation, but show minor conformational perturbations as revealed by shifts of contact-shifted peaks associated with the heme and nearby amino acids.

Animals↗

PubMed2006

A methyldiazene (HN=N-CH3)-derived species bound to the nitrogenase active-site FeMo cofactor: Implications for mechanism.

Methyldiazene (HN=N-CH3) isotopomers labeled with 15N at the terminal or internal nitrogens or with 13C or 2H were used as substrates for the nitrogenase alpha-195Gln-substituted MoFe protein. Freeze quenching under turnover traps an S = (1/2) state that has been characterized by EPR and 1H-, 15N-, and 13C-electron nuclear double resonance spectroscopies. These studies disclosed the following: (i) a methyldiazene-derived species is bound to the active-site FeMo cofactor; (ii) this species binds through an [-NHx] fragment whose N derives from the methyldiazene terminal N; and (iii) the internal N from methyldiazene probably does not bind to FeMo cofactor. These results constrain possible mechanisms for reduction of methyldiazene. In the Chatt-Schrock mechanism for N2 reduction, H atoms sequentially add to the distal N before N-N bond cleavage (d-mechanism). In a d-mechanism for methyldiazene reduction, a bound [-NHx] fragment only occurs after reduction by three electrons, which leads to N-N bond cleavage and the release of the first NH3. Thus, the appearance of bound [-NHx] is compatible with the d-mechanism only if it represents a late stage in the reduction process. In contrast are mechanisms where H atoms add alternately to distal and proximal nitrogens before N-N cleavage (a-mechanism) and release of the first NH3 after reduction by five electrons. An [-NHx] fragment would be bound at every stage of methyldiazene reduction in an a-mechanism. Although current information does not rule out the d-mechanism, the a-mechanism is more attractive because proton delivery to substrate has been specifically compromised in alpha-195Gln-substituted MoFe protein.

Binding Sites↗

PubMed2006

Characterization of the particulate methane monooxygenase metal centers in multiple redox states by X-ray absorption spectroscopy.

The integral membrane enzyme particulate methane monooxygenase (pMMO) converts methane, the most inert hydrocarbon, to methanol under ambient conditions. The 2.8-A resolution pMMO crystal structure revealed three metal sites: a mononuclear copper center, a dinuclear copper center, and a nonphysiological mononuclear zinc center. Although not found in the crystal structure, solution samples of pMMO also contain iron. We have used X-ray absorption spectroscopy to analyze the oxidation states and coordination environments of the pMMO metal centers in as-isolated (pMMO(iso)), chemically reduced (pMMO(red)), and chemically oxidized (pMMO(ox)) samples. X-ray absorption near-edge spectra (XANES) indicate that pMMO(iso) contains both Cu(I) and Cu(II) and that the pMMO Cu centers can undergo redox chemistry. Extended X-ray absorption fine structure (EXAFS) analysis reveals a Cu-Cu interaction in all redox forms of the enzyme. The Cu-Cu distance increases from 2.51 to 2.65 A upon reduction, concomitant with an increase in the average Cu-O/N bond lengths. Appropriate Cu2 model complexes were used to refine and validate the EXAFS fitting protocols for pMMO(iso). Analysis of Fe EXAFS data combined with electron paramagnetic resonance (EPR) spectra indicates that Fe, present as Fe(III), is consistent with heme impurities. These findings are complementary to the crystallographic data and provide new insight into the oxidation states and possible electronic structures of the pMMO Cu ions.

Copper↗

PubMed2006

Probing surface-porphyrazine reduction potentials by molecular design.

This manuscript reports electrochemical and angle-resolved X-ray photoelectron spectroscopy measurements of surface-bound porphyrazine monolayers in which the molecule-surface distance and molecular orientation of the porphyrazine are controlled through the design of the adsorbates. This system has allowed us to probe the importance of molecule-surface interaction in determining the shift in reduction potential upon binding to a gold surface. This quantity currently is in theoretical dispute, with one computation indicating that a porphyrazine/porphyrin exhibits an extremely large covalent binding energy ( approximately 10 eV) to a gold surface, whereas a more recent one finds the binding energy to be only a fraction of an electronvolt. Our study indicates that the shift in reduction potential upon surface binding is not a discontinuous function of the molecule-surface distance, as would be the case if covalent interaction of the porphyrazine core with the gold surface were controlling, but rather varies smoothly. This, therefore, rules out the possibility that the large potential shift seen for a porphyrazine whose macrocyclic core lies approximately 3.9 A above the gold surface, relative to one that lies approximately 8.9 A above the surface, DeltaDeltaE = 340 mV, is caused by direct covalent binding of the pi-system to the metal surface.

Electrochemistry↗

PubMed2006

Demonstration by 2H ENDOR spectroscopy that myo-inositol binds via an alkoxide bridge to the mixed-valent diiron center of myo-inositol oxygenase.

myo-Inositol oxygenase (MIOX) is a non-heme diiron oxygenase that cleaves cyclohexane-(1,2,3,5/4,6-hexa)-ol (myo-inositol, MI) to d-glucuronate. Here, we use 2H ENDOR spectroscopy to demonstrate that MI binds to the diiron(II/III) cofactor of MIOX via an alkoxide bridge, most likely involving O1. Analysis shows that MI adopts a symmetrical geometry in which the O-C-2H plane of the bridge is approximately orthogonal to the Fe-O-Fe plane.

Inositol↗

PubMed2006

How an enzyme tames reactive intermediates: positioning of the active-site components of lysine 2,3-aminomutase during enzymatic turnover as determined by ENDOR spectroscopy.

Lysine 2,3-aminomutase (LAM) utilizes a [4Fe-4S] cluster, S-adenosyl-L-methionine (SAM), and pyridoxal 5'-phosphate (PLP) to isomerize L-alpha-lysine to L-beta-lysine. LAM is a member of the radical-SAM enzyme superfamily in which a [4Fe-4S]+ cluster reductively cleaves SAM to produce the 5'-deoxyadenosyl radical, which abstracts an H-atom from substrate to form 5'-deoxyadenosine (5'-Ado) and the alpha-Lys* radical (state 3 (Lys*)). This radical isomerizes to the beta-Lys* radical (state 4(Lys*)), which then abstracts an H-atom from 5'-Ado to form beta-lysine and the 5'-deoxyadenosyl radical; the latter then regenerates SAM. We use 13C, 1,2H, 31P, and 14N ENDOR to characterize the active site of LAM in intermediate states that contain the isomeric substrate radicals or analogues. With L-alpha-lysine as substrate, we monitor the state with beta-Lys*. In parallel, we use two substrate analogues that generate stable analogues of the alpha-Lys* radical: trans-4,5-dehydro-L-lysine (DHLys) and 4-thia-L-lysine (SLys). This first glimpse of the motions of active-site components during catalytic turnover suggests a possible major movement of PLP during catalysis. However, the principal focus of this work is on the relative positions of the carbons involved in H-atom transfer. We conclude that the active site facilitates hydrogen atom transfer by enforcing van der Waals contact between radicals and their reacting partners. This constraint enables the enzyme to minimize and even eliminate side reactions of highly reactive species such as the 5'-deoxyadensosyl radical.

Binding Sites↗

PubMed2006

A Davies/Hahn multi-sequence for studies of spin relaxation in pulsed ENDOR.

We extend earlier studies of the effects of relaxation on the intensities of pulsed ENDOR signals by introducing a Davies/Hahn (D/H) pulsed ENDOR multi-sequence that corresponds to a series of Davies sequences with the preparation pulse 'turned off'. In this pulse train, the Hahn [pi/2, pi] detection pulse pair of sequence n-1 both generates the echo detected for that sequence and acts as the preparation portion of sequence n, in effect replacing the pi preparation pulse of the Davies sequence. We show both theoretically, through a master-equation approach, and with both (1)H(I=1/2) and (14)N(I=1) ENDOR experiments on the non-heme Fe enzymes, superoxide reductase (SOR) (S=1/2) and AntDO (S=3/2), that under conditions of high electron-spin polarization (high microwave frequency/low temperature) the D/H multi-sequence allows simplification of ENDOR spectra by suppression of nuclear transitions associated with the m(S)=+1/2 (alpha) manifold. As such suppression depends on the sign of A, it allows determination of this sign. The suppression as a function of the time between individual sequences is found to exhibit behaviors that can be classified into three regimes of the ratio of cross-relaxation to spin-lattice relaxation rates: strong cross-relaxation (X-case); comparable rates (XL); negligible cross relaxation (L). Interestingly, the ENDOR behavior of the S=1/2 SOR center indicates it is an L case, while the S=3/2 AntDO is an L case. Overall, the D/H protocol appears to be a robust and general tool for using relaxation effects to manipulate ENDOR spectra.

Electron Spin Resonance Spectroscopy↗

PubMed2006

Porphyrazines peripherally functionalized with hybrid ligands as molecular scaffolds for bimetallic metal-ion coordination.

We report the synthesis and physical characterization of a new family of peripherally functionalized porphyrazine (pz) compounds, denoted 1[M1, M2], where metal ion M1 is incorporated into the pz core and metal ion M2 is bound to a salicylidene/picolinamide "hybrid" chelate built onto two nitrogen atoms attached to the pz periphery. The complexes 1[MnCl, Cu], 1[VO, Cu], and 1[Cu, Cu] have been prepared, and crystal structures show 1[MnCl, Cu] and 1[VO, Cu] to be isostructural. These complexes have been subjected to electron paramagnetic resonance and temperature-dependent magnetic susceptibility measurements. The variation of the ligand-mediated exchange splittings (delta) in these complexes is striking: delta/k(B) values for 1[MnCl, Cu] and 1[VO, Cu] are 22 and 40 K, respectively, while delta/k(B) for 1[Cu, Cu] is only 1 K. These coupling results are explained in terms of the relative orientation of the M1 and M2 orbitals and reflect the fact that the ligand set of M2 in the periphery is rotated in-plane by 45 degrees relative to the effectively coplanar pz ligand set of M1. The exchange couplings are essentially the same as those we determined for the Schiff base porphyrazines (pzs). Thus, the hybrid ligand has eliminated the dimerization found to occur when Cu(II) is bound to the periphery of bis(picolinamido) pzs and has created a more robust ligand system than the Schiff base pzs while retaining the ability they show to promote spin coupling between M1 and M2.

Crystallography, X-Ray↗

PubMed2006

Rapid freeze-quench ENDOR study of chloroperoxidase compound I: the site of the radical.

The classical heme-monooxygenase active intermediate, compound I (Cpd-I), incorporates a heme which is oxidized by two equivalents above the resting ferric state, one equivalent associated with a ferryl center, [Fe=O]2+ (FeS = 1), and the other with an active-site radical (RS = 1/2). Theoretical calculations on models of a Cpd-I with a thiolato axial ligand have presented divergent views about its electronic structure. In one picture, the radical is on the porphyrin; in the other, it is on the sulfur. In this report, ENDOR spectroscopy answers the question, does Cpd-I of the enzyme chloroperoxidase contain a porphyrin pi-cation radical or an iron-bound cysteinyl radical: the radical is predominantly on the porphyrin, with spin density on sulfur having an upper bound, rhoS </= rhoSmax approximately 0.23. We further suggest that the same answer applies to Cpd-I of cytochromes P450.

Chloride Peroxidase↗

PubMed2006

Porphyrazines as molecular scaffolds: flexible syntheses of novel multimetallic complexes.

Reductive deselenation of selenodiazole-fused porphyrazines, followed by acylation of the resultant labile porphyrazinediamines, was used to prepare macrocycles bearing two Collins ligands, two oxamido residues, or two quinoline-2-carboxamido units. Peripheral coordination of copper(II) to the di-(quinoline-2-carboxamido)-porphyrazine gave a metal-linked face-to-face porphyrazine dimer array. Sequential derivatization of the two amino groups in the porphyrazinediamines was used to prepare mixed peripheral ligand systems including a dimetallic picolinamido-Schiff base porphyrazine. Such systems exhibit strong metal-metal spin coupling and are anticipated to be of value in the synthesis of novel electronic and magnetic materials.

Journal Article↗

PubMed2006

Breaking the N2 triple bond: insights into the nitrogenase mechanism.

Nitrogenase is the metalloenzyme that performs biological nitrogen fixation by catalyzing the reduction of N2 to ammonia. Understanding how the nitrogenase active site metal cofactor (FeMo-cofactor) catalyzes the cleavage of the N2 triple bond has been the focus of intense study for more than 50 years. Goals have included the determination of where and how substrates interact with the FeMo-cofactor, and the nature of reaction intermediates along the reduction pathway. Progress has included the trapping of intermediates formed during turnover of non-physiological substrates (e.g., alkynes, CS2) providing insights into how these molecules interact with the nitrogenase FeMo-cofactor active site. More recently, substrate-derived species have been trapped at high concentrations during the reduction of N2, a diazene, and hydrazine, providing the first insights into binding modes and possible mechanisms for N2 reduction. A comparison of the current state of knowledge of the trapped species arising from non-physiological substrates and nitrogenous substrates is beginning to reveal some of the intricacies of how nitrogenase breaks the N2 triple bond.

Electron Spin Resonance Spectroscopy↗

PubMed2006

Compound I of heme oxygenase cannot hydroxylate its heme meso-carbon.

Heme oxygenase (HO) catalyzes heme catabolism through three successive oxygenation steps where the substrate heme itself activates O2. It has been thought that the reactive species responsible for the first heme oxygenation, meso-hydroxylation, is the hydroperoxy-ferric heme intermediate (Fe-OOH) rather than an oxo ferryl porphyrin cation radical, so-called compound I. A recent theoretical study (Kamachi, T.; Yoshizawa, K. J. Am. Chem. Soc. 2005, 127, 10686), however, proposed that compound I can oxidize its meso-carbon atom with the assistance of a bridging water molecule. In this communication, we report the first direct observation of compound I of a heme-HO-1 complex, generated by reaction of ferric-HO-1 with m-chloroperbenzoic acid. HO compound I slowly decays to compound II without producing any meso-hydroxylated products. It does react with guaiacol and thioanisole, however. Our findings unambiguously rule out involvement of compound I in the HO catalysis.

Animals↗

PubMed2006

Ring-opening metathesis polymer sphere-supported seco-porphyrazines: efficient and recyclable photooxygenation catalysts.

[reaction: see text] Crossover Linstead macrocyclization of norbornenyl-tagged diaminomaleonitrile with dipropylmaleonitrile gave the corresponding magnesium diaminohexapropylporphyrazine, which was subsequently converted into its zinc seco-derivative. Polymerization gave the corresponding ROMPgel and ROMPsphere (ROMP = ring-opening metathesis polymer) reagents, the latter of which proved efficient as an immobilized catalyst for the sensitized production of singlet oxygen for the purification-minimized parallel synthesis of endoperoxides and ene adducts.

Catalysis↗

PubMed2006

Geometries and electronic structures of cyanide adducts of the non-heme iron active site of superoxide reductases: vibrational and ENDOR studies.

We have added cyanide to oxidized 1Fe and 2Fe superoxide reductase (SOR) as a surrogate for the putative ferric-(hydro)peroxo intermediate in the reaction of the enzymes with superoxide and have used vibrational and ENDOR spectroscopies to study the properties of the active site paramagnetic iron center. Addition of cyanide changes the active site iron center in oxidized SOR from rhombic high-spin ferric (S = 5/2) to axial-like low-spin ferric (S = 1/2). Low-temperature resonance Raman and ENDOR data show that the bound cyanide adopts three distinct conformations in Fe(III)-CN SOR. On the basis of 13CN, C15N, and 13C15N isotope shifts of the Fe-CN stretching/Fe-C-N bending modes, resonance Raman studies of 1Fe-SOR indicate one near-linear conformation (Fe-C-N angle approximately 175 degrees) and two distinct bent conformations (Fe-C-N angles <140 degrees). FTIR studies of 1Fe-SOR at ambient temperatures reveals three bound C-N stretching frequencies in the oxidized (ferric) state and one in the reduced (ferrous) state, indicating that the conformational heterogeneity in cyanide binding is a characteristic of the ferric state and is not caused by freezing-in of conformational substates at low temperature. 13C-ENDOR spectra for the 13CN-bound ferric active sites in both 1Fe- and 2Fe-SORs also show three well-resolved Fe-C-N conformations. Analysis of the 13C hyperfine tensors for the three substates of the 2Fe-SOR within a simple heuristic model for the Fe-C bonding gives values for the Fe-C-N angles in the three substates of ca. 123 degrees (C3) and 133 degrees (C2), taking a reference value from vibrational studies of 175 degrees (C1 species). Resonance Raman and ENDOR studies of SOR variants, in which the conserved glutamate and lysine residues in a flexible loop above the substrate binding pocket have been individually replaced by alanine, indicate that the side chains of these two residues are not involved in direct interaction with bound cyanide. The implications of these results for understanding the mechanism of SOR are discussed.

Binding Sites↗

PubMed2006

Developing a structure-function relationship for anionic porphyrazines exhibiting selective anti-tumor activity.

The porphyrazines (pzs) are a class of porphyrin derivatives being studied for their use as optical imaging agents and photodynamic therapy (PDT) anti-tumor agents. A previous study revealed that the anionic pz, 18--of the form H2[pz(An;B4-n)], where A is [S(CH2)3CO2-], B is a fused beta',beta'-diisopropyloxy benzo group, with n=2 (trans)--selectively killed tumor cells, while analogous neutral and positively charged pzs lacked this property. In this report, we compare the properties of a suite of three H2[pz(An;B4-n)] pzs containing the same A and B groups as 18, but differing in their values of n: pzs 4 (n=4) and 11 (n=3), and 18 (n=2, trans) exhibit a progressive variation in charge due to the carboxylates, balance between hydrophobic/hydrophilic character, as well as a progressive variation in the singlet oxygen quantum yield (PhiDelta): PhiDelta (18)>PhiDelta (11)>PhiDelta (4). The biological activity of the pzs was tested in human lung carcinoma (A549) and SV40 transformed embryonic (WI-38 VA13) cell lines. Pzs 4 and 11 exhibited significant toxicity in both tumor and normal cells, while 18 showed selective anti-tumor cell activity in a dose-dependent manner. As the number of net negative charges decreased, the compounds became less toxic to normal cells, and the killing effect observed with these compounds was light independent. These observations indicate that the toxicity may have little to do with singlet oxygen quantum yields, but rather is more dependent on the net number of negative charges a pz contains. The study reported herein presents an example of how the porphyrazines can be easily modified to vary their biological behavior and specifically suggest that anionic porphyrazines pzs with lower n (fewer carboxylates, larger hydrophobic core) are more specific tumor killers, while those with larger n (increased net negative charge) are more potent tumor killers.

Antineoplastic Agents↗

PubMed2005

Charge dependence of cellular uptake and selective antitumor activity of porphyrazines.

Porphyrazines (pzs), or tetraazaporphyrins, can be viewed as porphyrinic macrocycles in which the porphyrin meso (CH) groups are replaced by nitrogen atoms; as such, it can be anticipated that pzs would show similar biocompatibility and biodistribution to those of porphyrins. However, distinctive chemical and physical features of the pzs differentiate them from either the porphyrins or phthalocyanines, in particular making them excellent candidates as optical imaging/therapeutic agents. The novelty of the pzs requires that we first determine how specific structures selectively alter biological function, leading to the development of "rules" that will be used to predict future biologically functional pzs. In the first of these studies, we present here a correlation of pz charge with biocompatibility for a suite of three pzs-neutral, negative, and positive. Confocal fluorescence microscopy and proliferation/viability measurements disclose that the three pzs differ in their toxicity, uptake, and localization in A549 human lung adenocarcinoma cells and WI-38 VA13 normal cells. Interestingly, the negatively charged pz exhibits selective dark toxicity in pulmonary adenocarcinoma cells.

Antineoplastic Agents↗

PubMed2005

The copper chelator methanobactin from Methylosinus trichosporium OB3b binds copper(I).

The oxidation state of copper bound to methanobactin, a small siderophore-like molecule from the methanotroph Methylosinus trichosporium OB3b, was investigated. Purified methanobactin loaded with Cu(II) exhibits a weak EPR signal probably due to adventitious Cu(II). The EPR signal intensity increases significantly upon addition of the strong oxidant nitric acid. Features of the X-ray absorption near edge spectrum, including a 1s --> 4p transition at 8985 eV, further indicate the presence of Cu(I). EXAFS data were best fit using a multiple scattering model generated from previously reported crystallographic parameters. These results establish definitively that M. trichosporium OB3b methanobactin binds Cu(I) and suggest that methanobactin itself reduces Cu(II) to Cu(I).

Absorptiometry, Photon↗