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Vincent L Pecoraro

Publications and source records attributed to Vincent L Pecoraro.

At least 19 recordsLinked to original sources
PubMed2006

Assessing the integrity of designed homomeric parallel three-stranded coiled coils in the presence of metal ions.

De novo design of alpha-helical peptides that self-assemble to form helical coiled coils is a powerful tool for studying molecular recognition between peptides/proteins and determining the fundamental forces involved in their folding and structure. These amphipathic helices assemble in aqueous solution to generate the final coiled coil motif, with the hydrophobic residues in the interior and the polar/hydrophilic groups on the exterior. Considerable effort has been devoted to investigate the forces that determine the overall stability and final three-dimensional structure of the coiled coils. One of the major challenges in coiled coil design is the achievement of specificity in terms of the oligomeric state, with respect to number (two, three, four, or higher), nature (homomers vs heteromers), and strand orientation (parallel vs antiparallel). As seen in nature, metal ions play an important role in this self-organization process, and the overall structure of metalloproteins is primarily the result of two driving forces: the metal coordination preference and the fold of the polypeptide backbone. Previous work in our group has shown that metal ions such as As(III) and Hg(II) can be used to enforce different aggregation states in the Cys derivatives of the designed homotrimeric coiled-coil TRI family [Ac-G(LKALEEK)4G-CONH2]. We are now interested in studying the interplay between the metal ion and peptide preferences in controlling the specificity and relative orientation of the alpha-helices in coiled coils. For this objective, two derivatives of the TRI family, TRi L2WL9C and TRi L2WL23C, have been synthesized. Along with those two peptides, two derivatives of Coil-Ser, CSL9C and CSL19C (CS = Ac-EWEALEKKLAALESKLQALEKKLEALEHG-CONH2), a similar de novo designed three-stranded coiled coil that has the potential to form antiparallel coiled coils, have also been used. Circular dichroism, UV-vis, and 199Hg and 113Cd NMR spectroscopy results reveal that the addition of Hg(II) and Cd(II) to the different mixtures of these peptides forms preferentially homotrimeric coiled coils, over a statistical population of heterotrimeric parallel and antiparallel coiled coils.

Cations↗
PubMed2006

Insight into the catalytic mechanism of vanadium haloperoxidases. DFT investigation of vanadium cofactor reactivity.

Density functional theory (DFT) has been used to investigate the catalytic properties of the isolated vanadium cofactor found in vanadium haloperoxidases, with a particular emphasis on the steps going from the resting form of the cofactor to the peroxo complex. Computation of transition states, intermediate species, and UV-vis spectra, as well as comparison of reaction energies, demonstrated the important role of protonation in cofactor activation. This illustrates that the resting form of the vanadium cofactor reacts with hydrogen peroxide according to a mechanism that implies formation of an aqua complex, release of the apical water molecule according to a dissociative pathway, and binding of hydrogen peroxide to vanadium. This process leads to a side-on peroxo species corresponding to the peroxo form observed in the enzyme. In addition, it appears that an acid-base catalysts strongly accelerates the conversion to the side-on peroxo form. The comparison of computed and experimental UV-vis spectra corroborated the proposed reaction pathway and allowed us to explain the effects of the vanadium ligands on the electronic properties of the cofactor.

Catalysis↗
PubMed2006

Peptidic models for the binding of Pb(II), Bi(III) and Cd(II) to mononuclear thiolate binding sites.

Herein, we evaluate the binding of Pb(II) and Bi(III) to cysteine-substituted versions of the TRI peptides [AcG-(LKALEEK)4G-NH2] which have previously been shown to bind Hg(II) and Cd(II) in unusual geometries as compared with small-molecule thiol ligands in aqueous solutions. Studies of Pb(II) and Bi(III) with the peptides give rise to complexes consistent with the metal ions bound to three sulfur atoms with M-S distances of 2.63 and 2.54 A, respectively. Competition experiments between the metal ions Pb(II), Cd(II), Hg(II) and Bi(III) for the peptides show that Hg(II) has the highest affinity, owing to the initial formation of the extremely strong HgS2 bond. Cd(II) and Pb(II) have comparable binding affinities at pH > 8, while Bi(III) displays the weakest affinity, following the model, M(II) + (TRI LXC)3(3-) --> M(II)(TRI LXC)3(-). While the relevant equilibria for Hg(II) binding to the TRI peptides corresponds to a strong first step forming Hg(TRI LXC)2(HTRI LXC), followed by a single deprotonation to give Hg(TRI LXC)3(-), the binding of Cd(II) and Pb(II) is consistent with initial formation of M(II)(TRI LXC)(HTRI LXC)2 (+) at pH < 5 followed by a two-proton dissociation step (pK(a2)) yielding M(II)(TRI LXC)3(-). Pb(II)(TRI LXC)(HTRI LXC)2(+) converts to Pb(II)(TRI LXC)3(-) at slightly lower pH values than the corresponding Cd(II)-peptide complexes. In addition, Pb(II) displays a lower pK (a) of binding to the "d"-substituted peptide, (TRI L12C, pK(a2) = 12.0) compared with the "a"-substituted peptide, (TRI L16C, pK (a2) = 12.6), the reverse of the order seen for Hg(II) and Cd(II). Pb(II) also showed a stronger binding affinity for TRI L12C (K(bind) = 3.2 x 10(7) M(-1)) compared with that with TRI L16C (K(bind) = 1.2 x 10(7) M(-1)) at pH > 8.

Amino Acid Sequence↗
PubMed2005

Site-selective metal binding by designed alpha-helical peptides.

It is known that the designed alpha-helical peptide family TRI [(Ac-G(LKALEEK)4G-CONH2)], containing single site substitution of a cysteine for a leucine, is capable of binding Cd(II) within a three-stranded coiled coil. The binding affinity of cadmium is dependent upon the site of substitution, with cysteine incorporated at the a site leading to cadmium complexes of higher affinity than when a d site was modified. In this work we have examined whether this differential binding affinity can be expressed in a di-cysteine-substituted peptide in order to develop site specificity within a designed system. The peptide TRI L9CL19C was used to determine whether significant differences in binding affinities at nearly proximal sites could be achieved in a short designed peptide. On the basis of 113Cd, 1H NMR, and circular dichroic spectroscopies, we have shown that 1 equiv of Cd(II) binds exclusively at the a site. Only after that position is filled does the second site become populated. Thus, the TRI system represents the first example where stoichiometrically equivalent peptides with different sequences form the framework for designing molecular assemblies that show site-specific ion recognition. We propose that the distinct metal affinities are due to the cysteine conformers at different substitution points along the peptide. Furthermore, we have shown that site selectivity in biomolecules can be encoded into relatively short peptides with helical sequences and, therefore, do not necessarily require the extensive protein scaffolds found in natural systems.

Amino Acid Sequence↗
PubMed2005

Metallacryptate single-molecule magnets: effect of lower molecular symmetry on blocking temperature.

The structural characterization of complexes [Mn(II)4Mn(III)22(pdol)12(OCH3)12(O)16(N3)6] (1) and [Mn(II)4Mn(III)22(pdol)12(OCH3)12(O)16(OH)2(H3O)(OCH3)3].ClO4.5CH3OH (2), where pdol(2-) is di-2-pyridyl methanediol, reveals that each has a metallacryptand shell that encapsulates a manganese oxide core. Variable-temperature direct current magnetic susceptibility measurements on 2 indicate a paramagnetic ground state that results from an overall antiferromagnetic interaction in the cluster, with chiT values decreasing from 300 K (51.2 cm3 K mol(-1)) to 2 K (19.8 cm3 K mol(-1)). Variable-temperature alternating current magnetic susceptibility measurements imply that both 1 and 2 behave as single-molecule magnets. Fitting the frequency-dependent out-of-phase magnetic susceptibility to the Arrhenius equation yields an effective energy barrier, Ueff, to magnetization relaxation of 16.5 +/- 0.7 K (11.5 +/- 0.5 cm(-1)) for 1 and 36.2 +/- 2.0 K (25.1 +/- 1.4 cm(-1)) for 2. The larger value for 2 is in agreement with the lower molecular symmetry, larger magnetoanisotropy, and higher ground spin state of 2 compared to those of 1. This observation suggests a new strategy for increasing the blocking temperatures in high-nuclearity manganese clusters.

Crystallography, X-Ray↗
PubMed2005

Linear free-energy analysis of mercury(II) and cadmium(II) binding to three-stranded coiled coils.

Investigators have studied how proteins enforce nonstandard geometries on metal centers to assess the question of how protein structures can define the coordination geometry and binding affinity of an active-site metal cofactor. We have shown that cysteine-substituted versions of the TRI peptide series [AcG-(LKALEEK)(4)G-NH(2)] bind Hg(II) and Cd(II) in geometries that are different from what is normally found with thiol ligands in aqueous solution. A fundamental question has been whether this structural perturbation is due to protein influence or a change in the metal geometry preference. To address this question, we have completed linear free-energy analyses that correlate the association of three-stranded coiled coils in the absence of a metal with the binding affinity of the peptides to the heavy metals, Hg(II) and Cd(II). In this paper, six new members of this family have been synthesized, replacing core leucine residues with smaller and less hydrophobic residues, consequently leading to varying degrees of self-association affinities. At the same time, studies with some smaller and longer sequenced peptides have also been examined. All of these peptides are seen to sequester Hg(II) and Cd(II) in an uncommon trigonal environment. For both metals, the binding is strong with micromolar dissociation constants. For binding of Hg(II) to the peptides, the dissociation constants range from 2.4 x 10(-)(5) M for Baby L12C to 2.5 x 10(-)(9) M for Grand L9C for binding of the third thiolate to a linear Hg(II)(pep)(2) species. The binding of Hg(II) to the peptide Grand L9C is similar in energetics for metal binding in the metalloregulatory protein, mercury responsive (merR), displaying approximately 50% trigonal Hg(II) formation at nanomolar metal concentrations. Approximately, 11 kcal/mol of the Hg(II)(Grand L9C)(3)(-) stability is due to peptide interactions, whereas only 1-4 kcal/mol stabilization results from Hg(II)(RS)(2) binding the third thiolate ligand. This further validates the hypothesis that the favorable tertiary interactions in protein systems such as merR go a long way in stabilizing nonnatural coordination environments in biological systems. Similarly, for the binding of Cd(II) to the TRI family, the dissociation constants range from 1.3 x 10(-)(6) M for Baby L9C to 8.3 x 10(-)(9) M for TRI L9C, showing a similar nature of stable aggregate formation.

Amino Acid Sequence↗
PubMed2005

Corroborative models of the cobalt(II) inhibited Fe/Mn superoxide dismutases.

Attempting to model superoxide dismutase (SOD) enzymes, we designed two new N3O-donor ligands to provide the same set of donor atoms observed in the active site of these enzymes: K(i)Pr2TCMA (potassium 1,4-diisopropyl-1,4,7-triazacyclononane-N-acetate) and KBPZG (potassium N,N-bis(3,5-dimethylpyrazolylmethyl) glycinate). Five new Co(II) complexes (1-5) were obtained and characterized by X-ray crystallography, mass spectrometry, electrochemistry, magnetochemistry, UV-vis, and electron paramagnetic resonance (EPR) spectroscopies. The crystal structures of 1 and 3-5 revealed five-coordinate complexes, whereas complex 2 is six-coordinate. The EPR data of complexes 3 and 4 agree with those of the Co(II)-substituted SOD, which strongly support the proposition that the active site of the enzyme structurally resembles these models. The redox behavior of complexes 1-5 clearly demonstrates the stabilization of the Co(II) state in the ligand field provided by these ligands. The irreversibility displayed by all of the complexes is probably related to an electron-transfer process followed by a rearrangement of the geometry around the metal center for complexes 1 and 3-5 that probably changes from a trigonal bipyramidal (high spin, d7) to octahedral (low spin, d6) as Co(II) is oxidized to Co(III), which is also expected to be accompanied by a spin-state conversion. As the redox potentials to convert the Co(II) to Co(III) are high, it can be inferred that the redox potential of the Co(II)-substituted SOD may be outside the range required to convert the superoxide radical (O2*-) to hydrogen peroxide, and this is sufficient to explain the inactivity of the enzyme. Finally, the complexes reported here are the first corroborative structural models of the Co(II)-substituted SOD.

Binding Sites↗
PubMed2005

Multinuclear Fe(III) complexes with polydentate ligands of the family of dicarboxyimidazoles: nuclearity- and topology-controlled syntheses and Magneto-structural correlations.

Two polydentate ligands of the family of dicarboxyimidazoles, H(2)MeDCBI (= 4,5-dicarboxy-1-methyl-1H-imidazole) and H(3)DCBI (= 4,5-dicarboxyimidazole), have been used in reactions with the [Fe(3,5-(t)()Bu(2)salpn)](+) species {3,5-(t)Bu(2)salpn = the dianion of 1,3-bis-[(3,5-di-tert-butylsalicylidene)amino]propane} to synthesize selectively complexes of different nuclearities. Four complexes have been synthesized: the mononuclear complex [Fe(3,5-(t)Bu(2)salpn)(HMeDCBI)] (1), the two binuclear but topologically different complexes [Fe(3,5-(t)Bu(2)salpn)(MeDCBI)Fe(3,5-(t)Bu(2)salpn)] (2) and {[Fe(3,5-(t)Bu(2)salpn)](2)(HDCBI)} (3), and the trinuclear complex {[Fe(3,5-(t)Bu(2)salpn)](2)(DCBI)Fe(3,5-(t)Bu(2)salpn)} (4). The structures of these complexes have been determined by X-ray crystallography. Variable-temperature direct-current magnetic susceptibility measurements were conducted for all compounds to obtain information about their electronic structure and to investigate the extent of magnetic communication among the Fe(III) centers. The results of these measurements allowed us to correlate the different structural motifs with the possible magnetic interactions that arise in multinuclear complexes of dicarboxyimidazoles. For 1, the room-temperature chi(M)T value reveals an S = (5)/(2) ground state. The data for the binuclear but topologically different complexes 2 and 3, and the trinuclear complex 4 suggest that weak intramolecular antiferromagnetic interactions are present, with interaction parameters ranging from -3.6 to -5.1 cm(-1). Differences in the extent of the magnetic communication between the metal centers through the two different interaction pathways of the ligands MeDCBI and DCBI (either through the imidazole ring or through the carboxylate groups) have been observed in complexes 2-4 that can be explained by the structural differences observed in the crystal structures of these compounds (the separation of the metal centers and the coplanarity of the metal ion orbitals with the pi system of the ligands). Cyclic voltammetry measurements for the mononuclear compound 1 show an irreversible reduction wave that is attributed to Fe(3+) + e(-) --> Fe(2+). The electrochemical behavior of the multinuclear complexes 2-4 is more complicated; however, it indicates that there is a degree of electronic communication between the Fe(III) centers.

Algorithms↗
PubMed2005

Reactivity of peroxo forms of the vanadium haloperoxidase cofactor. A DFT investigation.

Density functional theory has been used to investigate structural, electronic and reactivity properties of complexes related to the peroxo forms of vanadium haloperoxidases (VHPO). In particular, the reactivity of the cofactor as a function of protonation state and environment, which are two factors thought to be crucial in modulating the activity of the enzyme, has been examined. In full agreement with experimental data, results highlight the role of protonation in the activation of the peroxo-vanadium complexes and show that the oxo-transfer step involves the unprotonated axial peroxo oxygen atom, which is easily accessible to substrates in the peroxo form of the enzyme. The role of Lys353, which in the X-ray structure of the peroxide-bound form of vanadium chloroperoxidase is hydrogen bonded to the equatorial oxygen atom of the peroxo group, has been also explored. It is concluded that Lys353 can play a role similar to a H+ in the activation of the peroxo form of the cofactor.

Ascomycota↗
PubMed2005

Probing metal-protein interactions using a de novo design approach.

De novo design of metalloproteins provides a valuable tool for understanding the structural constraints and functional attributes of natural biological systems using first principles. This review focuses on recent research aimed primarily at probing the subtle interactions between metals and proteins in designed systems. Considerable attention has focussed on redefining novel design methods used in mimicking natural hemeproteins, mononuclear and dinuclear metallopeptides and functional biological electron-transfer proteins. The present results indicate that the field of metalloprotein design is contributing significantly to the understanding of metals in biology.

Binding Sites↗
PubMed2005

Ternary complexes of gentamicin with iron and lipid catalyze formation of reactive oxygen species.

This study was designed to elucidate the mechanisms underlying the formation of reactive oxygen species (ROS) by aminoglycoside antibiotics which may be causally related to the toxic side effects of these drugs to the kidney and the inner ear. ROS formation by aminoglycosides in vitro requires iron and the presence of polyunsaturated lipids as electron donors. Electron spray ionization mass spectrometry (ESI-MS) confirmed earlier observations that gentamicin strongly binds to L-alpha-phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2), a membrane lipid rich in arachidonic acid. Studies using lipid-coated membranes (PIP strips) further indicated that iron ions and gentamicin can simultaneously bind to phosphoinositides with at least one phosphate group on the inositol ring, suggesting the existence of ternary complexes among gentamicin, iron, and phospholipids. Peroxidation of PtdIns(4,5)P2 by ferrous ions significantly increased in the presence of gentamicin, and EI-MS measurements indicated that oxidative damage to PtdIns(4,5)P2 was accompanied by the release of arachidonic acid. Arachidonic acid also forms a ternary complex with Fe(2+/3+)-gentamicin, confirmed by ESI-MS, that reacts with lipid peroxides and molecular oxygen, leading to the propagation of arachidonic acid peroxidation.

Arachidonic Acid↗
PubMed2004

Understanding metalloprotein folding using a de novo design strategy.

Metal ions play significant roles in most biological systems. Over the past two decades, there has been significant interest in the redesign of existing metal binding sites in proteins/peptides and the introduction of metals into folded proteins/peptides. Recent research has focused on the effects of metal binding on the overall secondary and tertiary conformations of unstructured peptides/proteins. In this context, de novo design of metallopeptides has become a valuable approach for studying the consequence of metal binding. It has been seen that metal ions not only direct folding of partially folded peptides but have at times also been the elixir for properly folding random-coil-like structures in stable secondary conformations. Work in our group has focused on binding of heavy metal ions such as Hg(II) to de novo designed alpha-helical three stranded coiled coil peptides with sequences based on the heptad repeat motif. Removal from or addition of a heptad to the parent 30-residue TRI peptide with the amino acid sequence Ac-G(LKALEEK)(4)G-NH(2) generated peptides whose self-aggregation affinities were seen to be dependent on their lengths. It was noted that adjustment in the position of the thiol from an "a" position in the case of the shorter BabyL9C to a "d" position for BabyL12C resulted in a peptide with low association affinities for itself, weaker binding with Hg(II), and a considerably faster kinetic profile for metal insertion. Similar differences in thermodynamic and kinetic parameters were also noted for the longer TRI peptides. At the same time, metal insertion into the prefolded and longer TRI and Grand peptides has clearly demonstrated that the metal binding is both thermodynamically as well kinetically different from that to unassociated peptides.

Amino Acid Sequence↗
PubMed2004

The electronic structure of Mn in oxides, coordination complexes, and the oxygen-evolving complex of photosystem II studied by resonant inelastic X-ray scattering.

Resonant inelastic X-ray scattering (RIXS) was used to collect Mn K pre-edge spectra and to study the electronic structure in oxides, molecular coordination complexes, as well as the S1 and S2 states of the oxygen-evolving complex (OEC) of photosystem II (PS II). The RIXS data yield two-dimensional plots that can be interpreted along the incident (absorption) energy or the energy transfer axis. The second energy dimension separates the pre-edge (predominantly 1s to 3d transitions) from the main K-edge, and a detailed analysis is thus possible. The 1s2p RIXS final-state electron configuration along the energy transfer axis is identical to conventional L-edge absorption spectroscopy, and the RIXS spectra are therefore sensitive to the Mn spin state. This new technique thus yields information on the electronic structure that is not accessible in conventional K-edge absorption spectroscopy. The line splittings can be understood within a ligand field multiplet model, i.e., (3d,3d) and (2p,3d) two-electron interactions are crucial to describe the spectral shapes in all systems. We propose to explain the shift of the K pre-edge absorption energy upon Mn oxidation in terms of the effective number of 3d electrons (fractional 3d orbital population). The spectral changes in the Mn 1s2p(3/2) RIXS spectra between the PS II S1 and S2 states are small compared to that of the oxides and two of the coordination complexes (Mn(III)(acac)3 and Mn(IV)(sal)2(bipy)). We conclude that the electron in the step from S1 to S2 is transferred from a strongly delocalized orbital.

Electrons↗
PubMed2004

Control of metal coordination number in de novo designed peptides through subtle sequence modifications.

Substitution of an alanine for leucine (shown in light blue) in the hydrophobic interior of designed three-stranded coiled coils allows for the control of metal ion coordination number and geometry. The influence of this perturbation by a noncoordinating residue can be monitored by the dramatic impact on the 113Cd NMR spectrum. The structural effect occurs even when the residue substitution is as much as 7 A from the metal binding site.

Amino Acid Sequence↗