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Aberrant aggregation of the Aβ protein is a hallmark of Alzheimer's disease (AD), but no complete characterization of the molecular level pathogenesis has been achieved. A promising hypothesis is that dysfunction of metal ion homeostasis, and consequently, the undesired interaction of metal ions with Aβ, may be central to the development of AD. Qualitatively, most data indicate that Cu(II) induces rapid self-assembly of both Aβ40 and Aβ42 during the initial phase of the aggregation, while at longer time scales fibrillation may occur, depending on the experimental conditions. For Aβ40 and Cu(II):Aβ ≤ 1, most data imply that low concentration of Aβ40 favors nucleation and rapid fibril elongation, while high concentration of Aβ40 favors formation of amorphous aggregates. However, there are conflicting reports on this issue. For Aβ42 and Cu(II):Aβ ≤ 1, there is consensus that the lag time is extended upon addition of Cu(II). For Cu(II):Aβ > 1, the lag time is increased upon interaction with Cu(II), and in most cases fibrillation is not observed, presumably because Cu(II) occupies a second more solvent-exposed binding site, which is more prone to form metal ion-bridged species and cause rapid formation of non-fibrillar aggregates. The interesting N-terminally truncated Aβ11-40 with high affinity for Cu(II), exhibits delay of fibrillation upon addition of 0.4 eq. Cu(II). In our view, there are still problems achieving reproducible results in this field, and we provide a shortlist of some of the pitfalls. Finally, we propose a consensus model for the effects of Cu(II) on the aggregation kinetics of Aβ.

Intracellular Cu I is controlled by the transcriptional regulator CueR, which effectively discriminates between monovalent and divalent metal ions. It is intriguing that Hg II does not activate transcription, as bis-thiolate metal sites exhibit high affinity for Hg II . Here the binding of Hg II to CueR and a truncated variant, ΔC7-CueR, without the last 7 amino acids at the C-terminus including a conserved CCHH motif is explored. ESI-MS demonstrates that up to two Hg II bind to CueR, while ΔC7-CueR accommodates only one Hg II . 199m Hg PAC and UV absorption spectroscopy indicate HgS 2 structure at both the functional and the CCHH metal site. However, at sub-equimolar concentrations of Hg II at pH 8.0, the metal binding site displays an equilibrium between HgS 2 and HgS 3 , involving cysteines from both sites. We hypothesize that the C-terminal CCHH motif provides auxiliary ligands that coordinate to Hg II and thereby prevents activation of transcription., (© 2019 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.)

Hg 2+ and Cd 2+ complexation of a short hexapeptide, Ac-DCSSCY-NH 2 (DY), was studied by pH-potentiometry, UV and NMR spectroscopy and fluorimetry in aqueous solutions and the Hg 2+ -binding ability of the ligand was also described in an immobilized form, where the peptides were anchored to a hydrophilic resin. Hg 2+ was demonstrated to form a 1 : 1 complex with the ligand even at pH = 2.0 while Cd 2+ coordination by the peptide takes place only above pH ∼ 3.5. Both metal ions form bis-ligand complexes by the coordination of four Cys-thiolates at ligand excess above pH ∼ 5.5 (Cd 2+ ) and 7.0 (Hg 2+ ). Fluorescence studies demonstrated a Hg 2+ induced concentration-dependent quenching of the Tyr fluorescence until a 1 : 1 Hg 2+  : DY ratio. The fluorescence emission intensity decreases linearly with the increasing Hg 2+ concentration in a range of over two orders of magnitude. The fact that this occurs even in the presence of 1.0 eq. of Cd 2+ per ligand reflects a complete displacement of the latter metal ion by Hg 2+ from its peptide-bound form. The immobilized peptide was also shown to bind Hg 2+ very efficiently even from samples at pH = 2.0. However, the existence of lower affinity binding sites was also demonstrated by binding of more than 1.0 eq. of Hg 2+ per immobilized DY molecule under Hg 2+ -excess conditions. Experiments performed with a mixture of four metal ions, Hg 2+ , Cd 2+ , Zn 2+ and Ni 2+ , indicate that this molecular probe may potentially be used in Hg 2+ -sensing systems under acidic conditions for the measurement of μM range concentrations.

NMR spectra of Mg2+ ions in ionic liquids were recorded using a highly sensitive variant of NMR spectroscopy known as β-NMR. The β-NMR spectra of MgCl2 in EMIM-Ac and EMIM-DCA compare favourably with conventional NMR, and exhibit linewidths of ∼3 ppm, allowing for discrimination of species with oxygen and nitrogen coordination.

We use a de Novo protein design strategy to demonstrate that the second coordination sphere of a metal site plays a key role in controlling coordination geometries of Cd(II)-tris-thiolate complexes. Specifically, we show that alteration of chirality within the core hydrophobic packing region of a three-stranded coiled coil (3SCC) can control the coordination number of Cd(II) by limiting steric encumbrance to the metal center. Within a specific class of 3SCCs [Ac-G-(LKALEEK) n -G-NH 2 ], where n = 4 is TRI and n = 5 is GRAND, one L-Leu may be substituted by L-Cys to generate a planar tris-thiolate array capable of metal binding. In the native peptide containing only the L-configuration of leucine, the three-Cys ligand site leads to a mixture of 3- and 4-coordinate Cd(II). When the L-Leu above (toward the N-terminus) the tris-Cys site is substituted with D-Leu, solely a 3-coordinate structure [Cd(II)S 3 ] was obtained. When D-Leu is located below (toward the C-terminus), a mixture of two coordination geometries, presumably Cd(II)S 3 O and Cd(II)S 3 O 2 , is observed, while substitution with D-Leu both above and below the tris-Cys plane yields a higher percentage of 4-coordinate Cd(II)S 3 O species. Thus, the use of D-amino acids around a metal's coordination sphere provides a powerful tool for controlling the properties of future designed metalloproteins.

A prominent current hypothesis is that impaired metal ion homeostasis may contribute to Alzheimer's disease (AD). We elucidate the interaction of Cu 2+ with wild-type (WT) Aβ 1-40 and the genetic variants A2T and A2V which display increasing pathogenicity as A2T2+ significantly extends the lag phase in aggregation kinetics, in particular for the pathogenic A2V variant. Additionally, a rapid, initial, low intensity ThT response is observed, possibly reflecting formation of Cu 2+ induced amorphous aggregates, as supported by atomic force microscopy (AFM) and circular dichroism (CD) spectroscopy, again most notably for the A2V variant. Electron paramagnetic resonance (EPR) spectroscopy gives pK a values for transition between two Cu 2+ coordination geometries (component I and II) of 7.4 (A2T), 7.9 (WT), and 8.4 (A2V), that is, component I is stabilized at physiological pH in the order A2T1 H NMR relaxation exhibits the same trend for the non-coordinating aromatic residues (A2T2+ exchange for the A2V variant than for WT and A2T. We therefore hypothesize that component I of the Cu-Aβ complex is related to pathogenicity, accounting for both the pathogenic nature of the A2V variant and the protective nature of the A2T variant., (© 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Metalloproteins are essential to numerous reactions in nature, and constitute approximately one-third of all known proteins. Molecular dynamics of proteins has been elucidated with great success both by experimental and theoretical methods, revealing atomic level details of function involving the organic constituents on a broad spectrum of time scales. However, the characterization of dynamics at biomolecular metal sites on nanosecond time scales is scarce in the literature. The aqua ions of many biologically relevant metal ions exhibit exchange of water molecules on the nanosecond time scale or faster, often defining their reactivity in aqueous solution, and this is presumably also a relevant time scale for the making and breaking of coordination bonds between metal ions and ligands at protein metal sites. Ligand exchange dynamics is critical for a variety of elementary steps of reactions in metallobiochemistry, for example, association and dissociation of metal bound water, association of substrate and dissociation of product in the catalytic cycle of metalloenzymes, at regulatory metal sites which require binding and dissociation of metal ions, as well as in the transport of metal ions across cell membranes or between proteins involved in metal ion homeostasis. In Perturbed Angular Correlation of γ-rays (PAC) spectroscopy, the correlation in time and space of two γ-rays emitted successively in a nuclear decay is recorded, reflecting the hyperfine interactions of the PAC probe nucleus with the surroundings. This allows for characterization of molecular and electronic structure as well as nanosecond dynamics at the PAC probe binding site. Herein, selected examples describing the application of PAC spectroscopy in probing the dynamics at protein metal sites are presented, including (1) exchange of Cd 2+ bound water in de novo designed synthetic proteins, and the effect of remote mutations on metal site dynamics; (2) dynamics at the β-lactamase active site, where the metal ion appears to jump between the two adjacent sites; (3) structural relaxation in small blue copper proteins upon 111 Ag + to 111 Cd 2+ transformation in radioactive nuclear decay; (4) metal ion transfer between two HAH1 proteins with change in coordination number; and (5) metal ion sensor proteins with two coexisting metal site structures. With this Account, we hope to make our modest contribution to the field and perhaps spur additional interest in dynamics at protein metal sites, which we consider to be severely underexplored. Relatively little is known about detailed atomic motions at metal sites, for example, how ligand exchange processes affect protein function, and how the amino acid composition of the protein may control this facet of metal site characteristics. We also aim to provide the reader with a qualitative impression of the possibilities offered by PAC spectroscopy in bioinorganic chemistry, especially when elucidating dynamics at protein metal sites, and finally present data that may serve as benchmarks on a relevant time scale for development and tests of theoretical molecular dynamics methods applied to biomolecular metal sites.

Although metal ion binding to naturally occurring l-amino acid proteins is well documented, understanding the impact of the opposite chirality (d-)amino acids on the structure and stereochemistry of metals is in its infancy. We examine the effect of a d-configuration cysteine within a designed l-amino acid three-stranded coiled coil in order to enforce a precise coordination number on a metal center. The d chirality does not alter the native fold, but the side-chain re-orientation modifies the sterics of the metal binding pocket. l-Cys side chains within the coiled-coil structure have previously been shown to rotate substantially from their preferred positions in the apo structure to create a binding site for a tetra-coordinate metal ion. However, here we show by X-ray crystallography that d-Cys side chains are preorganized within a suitable geometry to bind such a ligand. This is confirmed by comparison of the structure of Zn II Cl(CSL16 D C) 3 2- to the published structure of Zn II (H 2 O)(GRAND-CSL12AL16 L C) 3 geometry observed by using l-Cys ligands (a mixture of three- and four-coordinate Cd - . Moreover, spectroscopic analysis indicates that the Cd II geometry observed by using l-Cys ligands (a mixture of three- and four-coordinate Cd II ) is altered to a single four-coordinate species when d-Cys is present. This work opens a new avenue for the control of the metal site environment in man-made proteins, by simply altering the binding ligand with its mirror-imaged d configuration. Thus, the use of non-coded amino acids in the coordination sphere of a metal promises to be a powerful tool for controlling the properties of future metalloproteins., (© 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Nanosecond ligand exchange dynamics at metal sites within proteins is essential in catalysis, metal ion transport, and regulatory metallobiochemistry. Herein we present direct observation of the exchange dynamics of water at a Cd 2+ binding site within two de novo designed metalloprotein constructs using 111m Cd perturbed angular correlation (PAC) of γ-rays and 113 Cd NMR spectroscopy. The residence time of the Cd 2+ -bound water molecule is tens of nanoseconds at 20 °C in both proteins. This constitutes the first direct experimental observation of the residence time of Cd 2+ coordinated water in any system, including the simple aqua ion. A Leu to Ala amino acid substitution ∼10 Å from the Cd 2+ site affects both the equilibrium constant and the residence time of water, while, surprisingly, the metal site structure, as probed by PAC spectroscopy, remains essentially unaltered. This implies that remote mutations may affect metal site dynamics, even when structure is conserved.

The formation of reactive oxygen species (ROS) is linked to the pathogenesis of neurodegenerative diseases. Here we have investigated the effect of soluble and aggregated amyloid-β (Aβ) and α-synuclein (αS), associated with Alzheimer's and Parkinson's diseases, respectively, on the Cu(2+)-catalyzed formation of ROS in vitro in the presence of a biological reductant. We find that the levels of ROS, and the rate by which ROS is generated, are significantly reduced when Cu(2+) is bound to Aβ or αS, particularly when they are in their oligomeric or fibrillar forms. This effect is attributed to a combination of radical scavenging and redox silencing mechanisms. Our findings suggest that the increase in ROS associated with the accumulation of aggregated Aβ or αS does not result from a particularly ROS-active form of these peptides, but rather from either a local increase of Cu(2+) and other ROS-active metal ions in the aggregates or as a downstream consequence of the formation of the pathological amyloid structures.

Metal-ion-responsive transcriptional regulators within the MerR family effectively discriminate between mono- and divalent metal ions. Herein we address the origin of the specificity of the CueR protein for monovalent metal ions. Several spectroscopic techniques were employed to study Ag(I) , Zn(II) , and Hg(II) binding to model systems encompassing the metal-ion-binding loop of CueR from E. coli and V. cholerae. In the presence of Ag(I) , a conserved cysteine residue displays a pKa  value for deprotonation of the thiol that is close to the physiological pH value. This property is only observed with the monovalent metal ion. Quantum chemically optimized structures of the CueR metal site with Cys 112 protonated demonstrate that the conserved Ser 77 backbone carbonyl oxygen atom from the other monomer of the homodimer is "pulled" towards the metal site. A common allosteric mechanism of the metalloregulatory members of the MerR family is proposed. For CueR, the mechanism relies on the protonation of Cys 112., (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Members of the ArsR/SmtB family of transcriptional repressors, such as CadC, regulate the intracellular levels of heavy metals like Cd(II), Hg(II), and Pb(II). These metal sensing proteins bind their target metals with high specificity and affinity, however, a lack of structural information about these proteins makes defining the coordination sphere of the target metal difficult. Lingering questions as to the identity of Cd(II) coordination in CadC are addressed via protein design techniques. Two designed peptides with tetrathiolate metal binding sites were prepared and characterized, revealing fast exchange between CdS3O and CdS4 coordination spheres. Correlation of (111m)Cd PAC spectroscopy and (113)Cd NMR spectroscopy suggests that Cd(II) coordinated to CadC is in fast exchange between CdS3O and CdS4 forms, which may provide a mechanism for rapid sensing of heavy metal contaminants by this regulatory protein.

Designed metal ion binding peptides offer a variety of applications in both basic science as model systems of more complex metalloproteins, and in biotechnology, e.g. in bioremediation of toxic metal ions, biomining or as artificial enzymes. In this work a peptide (HS: Ac-SCHGDQGSDCSI-NH2) has been specifically designed for binding of both Zn(II) and Hg(II), i.e. metal ions with different preferences in terms of coordination number, coordination geometry, and to some extent ligand composition. It is demonstrated that HS accommodates both metal ions, and the first coordination sphere, metal ion exchange between peptides, and speciation are characterized as a function of pH using UV-absorption-, synchrotron radiation CD-, (1)H-NMR-, and PAC-spectroscopy as well as potentiometry. Hg(II) binds to the peptide with very high affinity in a {HgS2} coordination geometry, bringing together the two cysteinates close to each end of the peptide in a loop structure. Despite the high affinity, Hg(II) is kinetically labile, exchanging between peptides on the subsecond timescale, as indicated by line broadening in (1)H-NMR. The Zn(II)-HS system displays more complex speciation, involving monomeric species with coordinating cysteinates, histidine, and a solvent water molecule, as well as HS-Zn(II)-HS complexes. In summary, the HS peptide displays conformational flexibility, contains many typical metal ion binding groups, and is able to accommodate metal ions with different structural and ligand preferences with high affinity. As such, the HS peptide may be a scaffold offering binding of a variety of metal ions, and potentially serve for metal ion sequestration in biotechnological applications.

Metal ions and their interaction with the amyloid beta (Aβ) peptide might be key elements in the development of Alzheimer's disease. In this work the effect of Cu(II) on the aggregation of Aβ is explored on a timescale from milliseconds to days, both at physiological pH and under mildly acidic conditions, by using stopped-flow kinetic measurements (fluorescence and light-scattering), (1) H NMR relaxation and ThT fluorescence. A minimal reaction model that relates the initial Cu(II) binding and Aβ folding with downstream aggregation is presented. We demonstrate that a highly aggregation prone Aβ⋅Cu(II) species is formed on the sub-second timescale at mildly acidic pH. This observation might be central to the molecular origin of the known detrimental effect of acidosis in Alzheimer's disease., (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Furin-dependent maturation of the BRI2 protein generates the Bri2-23 fragment that is able to arrest the aggregation of amyloidβ, the peptide implicated in Alzheimer's disease (AD). Bri2-23 contains cysteines at positions 5 and 22, which are likely to bind to metal ions such as Cu(i). Metal ions may play a role in the etiology of neurodegenerative disorders such as AD, and in this work we explore the metal ion induced folding and aggregation of Bri2-23 using Hg(ii) and Ag(i) as spectroscopic probes with structural and ligand preferences similar to those of Cu(i), while not displaying redox activity under the experimental conditions. In general, interaction of Bri2-23 with soft metal ions changes the structural properties and solution behavior of the peptide that tune to increasing metal to peptide stoichiometry. Potentiometric, (199m)Hg PAC and ESI-MS data indicate that addition of up to 0.5 equivalents of Hg(ii) to Bri2-23 yields a two-coordinated HgS2 structure at the metal site. While the free peptide is inherently unstructured, the presence of Ag(i) and Hg(ii) gives rise to β-sheet formation. NMR spectroscopy supports the formation of β-sheet structure in the presence of 0.5 equivalents of Hg(ii), and displays an interesting and marked change in the TOCSY spectra when increasing the Hg(ii) to peptide stoichiometry from 0.5 to 0.7 equivalents, indicating the equilibrium between two structural analogues of the complex. Addition of more than 0.7 equivalents of Hg(ii) gives rise to line broadening, presumably reflecting aggregation. This is further supported by ThT fluorescence studies showing that the Bri2-23 peptide does not aggregate over 24 hours, while addition of over 0.7 equivalents of Ag(i) or Hg(ii) leads to increase of fluorescence, indicating that these metal ions induce aggregation. Thus, a model integrating all data into a coherent picture is that the metal ion binding to the two thiolates gives rise to folding of the peptide into a structure that is prone to aggregation, forming aggregates with a considerable amount of β-sheets. Molecular dynamics simulations initiated with structures that agree with NMR data additionally support this model.

β-nuclear magnetic resonance (NMR) spectroscopy is highly sensitive compared to conventional NMR spectroscopy, and may be applied for several elements across the periodic table. β-NMR has previously been successfully applied in the fields of nuclear and solid-state physics. In this work, β-NMR is applied, for the first time, to record an NMR spectrum for a species in solution. (31)Mg β-NMR spectra are measured for as few as 10(7) magnesium ions in ionic liquid (EMIM-Ac) within minutes, as a prototypical test case. Resonances are observed at 3882.9 and 3887.2 kHz in an external field of 0.3 T. The key achievement of the current work is to demonstrate that β-NMR is applicable for the analysis of species in solution, and thus represents a novel spectroscopic technique for use in general chemistry and potentially in biochemistry., (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Peptide TZ1C2 can populate two distinct orientations: a staggered (out-of-register) fibril and an aligned (in-register) coiled-coil trimer. The coordination of two cadmium ions induces a registry shift that results in a reversible transition between these structural forms. This process recapitulates the self-assembly mechanism of native protein fibrils in which a ligand binding event gates a reversible conformational transition between alternate forms of a folded peptide structure.

Although metal ion homeostasis in cells is often mediated through metallochaperones, there are opportunities for toxic metals to be sequestered through the existing transport apparatus. Proper trafficking of Cu(I) in human cells is partially achieved through complexation by HAH1, the human metallochaperone responsible for copper delivery to the Wilson and Menkes ATPase located in the trans-Golgi apparatus. In addition to binding copper, HAH1 strongly complexes Hg(II), with the X-ray structure of this complex previously described. It is important to clarify the solution behavior of these systems and, therefore, the binding of Hg(II) to HAH1 was probed over the pH range 7.5 to 9.4 using (199)Hg NMR, (199m)Hg PAC and UV-visible spectroscopies. The metal-dependent protein association over this pH range was examined using analytical gel-filtration. It can be concluded that at pH 7.5, Hg(II) is bound to a monomeric HAH1 as a two coordinate, linear complex (HgS2), like the Hg(II)-Atx1 X-ray structure (PDB ID: 1CC8). At pH 9.4, Hg(II) promotes HAH1 association, leading to formation of HgS3 and HgS4 complexes, which are in exchange on the μs-ns time scale. Thus, structures that may represent central intermediates in the process of metal ion transfer, as well as their exchange kinetics have been characterized., (Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The present study aimed at examining oligosaccharides (OS) for potential stimulation of probiotic bacteria. Nineteen structurally well-defined candidate OS covering groups of β-glucosides, α-glucosides and α-galactosides with degree of polymerization 2-4 were prepared in >100 mg amounts by chemoenzymatic synthesis (i.e. reverse phosphorolysis or transglycosylation). Fourteen of the OS are not naturally occurring and five (β-D-glucosyl-fructose, β-D-glucosyl-xylitol, α-glucosyl-(1,4)-D-mannose, α-glucosyl-(1,4)-D-xylose; α-glucosyl-(1,4)-L-fucose) have recently been synthesized for the first time. These OS have not been previously tested for effects of bacterial growth and here the ability of all 19 OS to support growth of four gastrointestinal bacteria: three probiotic bacteria Bifidobacterium lactis, Bifidobacterium longum, and Lactobacillus acidophilus, and one commensal bacterium, Bacteroides vulgatus has been evaluated in monocultures. The disaccharides β-D-glucosyl-xylitol and β-D-glucosyl-(1,4)-xylose noticeably stimulated growth yields of L. acidophilus NCFM, and additionally, β-D-glucosyl-(1,4)-xylose stimulated B. longum Bl-05. α-Glucosyl-(1,4)-glucosamine and α-glucosyl-(1,4)-N-acetyl-glucosamine enhanced the growth rate of B. animalis subsp. lactis and B. longum Bl-05, whereas L. acidophilus NCFM and Bac. vulgatus did not grow on these OS. α-Galactosyl-(1,6)-α-galactosyl-(1,6)-glucose advanced the growth rate of B. animalis subsp. lactis and L. acidophilus NCFM. Thus several of the structurally well-defined OS supported growth of beneficial gut bacteria. This reflects a broad specificity of their sugar transporters for OS, including specificity for non-naturally occurring OS, hence showing promise for design of novel prebiotics.

We examine the performance of Density Functional Theory (DFT) approaches based on the Zeroth-Order Regular Approximation (ZORA) Hamiltonian (with and without inclusion of spin-orbit coupling) for predictions of electric field gradients (EFGs) at the heavy atom Hg nucleus. This is achieved by comparing with benchmark DFT and CCSD-T data (Arcisauskaite et al., Phys. Chem. Chem. Phys., 2012, 14, 2651-2657) obtained from 4-component Dirac-Coulomb Hamiltonian calculations. The investigated set of molecules comprises linear HgL(2) (L = Cl, Br, I, CH(3)) and bent HgCl(2) mercury compounds as well as the trigonal planar [HgCl(3)](-) system. In 4-component calculations we used the dyall.cv3z basis set for Hg, Br, I and the cc-pCVTZ basis set for H, C, Cl, whereas in ZORA calculations we used the QZ4P basis set for all the atoms. ZORA-4 reproduces the fully relativistic 4-component DFT reference values within 6% for all studied Hg compounds and employed functionals (BH&H, BP86, PBE0), whereas scalar relativistic (SR)-ZORA-4 results show deviations of up to 15%. Compared to our 4-component CCSD-T benchmark the BH&H functional performs best at both 4-component and ZORA levels. We furthermore observe that changes in the largest component of the diagonalised EFG tensor, V(zz), of linear HgCl(2) show a slightly stronger dependence than the r(-3) scaling upon bond length r(Hg-Cl) alterations. The 4-component/BH&H V(zz) value of -9.26 a.u. for a bent HgCl(2) (∠Cl-Hg-Cl = 120°) is close to -9.60 a.u. obtained for the linear HgCl(2) structure. Thus a point charge model for EFG calculations completely fails in this case. By means of a projection analysis of molecular orbital (MO) contributions to V(zz) in terms of the atomic constituents, we conclude that this is due to the increased importance of the Hg 5d orbitals upon bending HgCl(2) compared to the linear HgCl(2) structure. Changing ligand leads to only minor changes in V(zz) (from -9.60 a.u. (HgCl(2)) to -8.85 a.u. (HgI(2)) at the 4-component/BH&H level). This appears to be due to cancellation of contributions with opposite signs to V(zz) arising from: (i) increasing electron donation from occupied ligand orbitals to the formally empty Hg 6p orbitals and (ii) an increasing bond length and a decreasing negative charge on the ligand along the series.

A four amino acid peptide containing the β-turn template dPro-Pro in the middle and two cysteines (Cys) in the terminal positions (CdPPC) has been synthesized and its mercury(II) coordination properties studied using different spectroscopic methods. The UV-vis, CD, (199m)Hg PAC, and Raman spectroscopic studies indicate the binding of Hg(II) to the two Cys, forming the dithiolatemercury(II) complex Hg(CdPPC). Electrospray ionization mass spectrometry corroborates the 1:1 complex formation. A log K = 40.0 was determined for the formation constant of the Hg(CdPPC) complex using competition potentiometric studies. Replacement of the dPro-Pro motif by a Pro-Pro unit generated a peptide (CPPC) capable of forming a similar species [Hg(CPPC)] but showing a lower affinity for Hg(II) (at least 3-3.5 orders of magnitude lower). The introduction of the dPro-Pro motif is crucial to induce the folding of the CdPPC peptide into a β-turn, preorganizing the two Cys for mercury(II) coordination. While the simple dPro-Pro unit mimics the overall preorganization achieved by the protein scaffold in metalloproteins containing the conserved metal ion chelation unit CXXC, the high thiophilicity of this metal stabilizes the final complex in a wide pH range (1.1-10). Using computational modeling, the structures of two conformers for Hg(CdPPC) have been optimized that differ mainly in the orientation of the plane containing S-Hg-S with respect to the anchoring C atoms.

Aim: Total mesorectal excision (TME) has been shown to improve the outcome for patients with rectal cancer. In contrast, there are fewer data on complete mesocolic excision (CME) for colonic cancer., Method: Data from the National Colorectal Cancer Database were analysed. This includes about 95% of all patients with colorectal cancer in Denmark. Only patients having elective surgery for colonic cancer in the period 2001-2008 were included. Overall and relative survival analyses were carried out. The study period was divided into the periods 2001-2004 and 2005-2008., Results: 9149 patients were included for the final analysis. The overall 5-year survival rates were 0.65 in 2001-2004 and 0.66 in 2005-2008. The relative 5-year survival rates were also within 1% of each other. None of these comparisons was statistically significant., Conclusion: Survival following elective colon cancer surgery has been almost unchanged since 2001., (© 2011 The Authors. Colorectal Disease © 2011 The Association of Coloproctology of Great Britain and Ireland.)

Introduction: We have developed a one-hour standardised, accelerated diagnostic investigation programme to evaluate women with urinary incontinence (UI). The purpose of the study was to record how many patients followed the programme and had a diagnosis and a treatment plan after a one-hour visit and to describe the causes of deviation from the programme. A second purpose was to monitor patient satisfaction., Methods: In this retrospective cohort study, 276 women with the diagnosis UI participated. All patients completed a standardised investigation programme that included their medical history and an evaluation of the fluid/urination schedule. Before patients left the clinic, they were given a diagnosis and a treatment plan., Results: A total of 91% of the patients underwent examination and had a treatment plan after one consultation; 9% made multiple visits. The median patient age was 59 years (range 17-99 years); body mass index was 27 kg/m² (range 18-50 kg/m²); and the number of childbirths was 2.4; no significant difference were observed between the two groups. In the multiple-visits group, the number of previous gynaecological surgical procedures was significantly larger (67% versus 32%). These patients had significantly more chronic diseases (88% versus 58%). A total of 81 patients completed a post-examination questionnaire and (99%) were satisfied with the accelerated programme., Conclusion: A total of 91% of the patients underwent an examination and received a treatment plan after one consultation; 9% paid several visits due to chronic diseases and previous gynaecological surgery. The patients expressed great satisfaction with the accelerated investigation programme., Funding: not relevant., Trial Registration: not relevant.

Metal ions, especially Zn(2+) and Cu(2+), are implemented in the neuropathogenesis of Alzheimer's disease (AD) by modulating the aggregation of amyloid-β peptides (Aβ). Also, Cu(2+) may promote AD neurotoxicity through production of reactive oxygen species (ROS). Impaired metal ion homeostasis is most likely the underlying cause of aberrant metal-Aβ interaction. Thus, focusing on the body's natural protective mechanisms is an attractive therapeutic strategy for AD. The metalloprotein metallothionein-3 (MT-3) prevents Cu-Aβ-mediated cytotoxicity by a Zn-Cu exchange that terminates ROS production. Key questions about the metal exchange mechanisms remain unanswered, e.g., whether an Aβ-metal-MT-3 complex is formed. We studied the exchange of metal between Aβ and Zn(7)-MT-3 by a combination of spectroscopy (absorption, fluorescence, thioflavin T assay, and nuclear magnetic resonance) and transmission electron microscopy. We found that the metal exchange occurs via free Cu(2+) and that an Aβ-metal-MT-3 complex is not formed. This means that the metal exchange does not require specific recognition between Aβ and Zn(7)-MT-3. Also, we found that the metal exchange caused amyloid-related structural and morphological changes in the resulting Zn-Aβ aggregates. A detailed model of the metal exchange mechanism is presented. This model could potentially be important in developing therapeutics with metal-protein attenuating properties in AD.

We investigate the magnitude and interplay of relativistic and electron correlation effects on the electric field gradient (EFG) at the position of Hg in linear and bent HgL(2) (L = CH(3), Cl, Br, I) and trigonal planar [HgCl(3)](-) compounds using four-component relativistic Dirac-Coulomb (DC) and non-relativistic (NR) calculations at the Hartree-Fock (HF), DFT, MP2 and coupled cluster (CC) levels. The relativistic and electron correlation contributions to EFG have opposite signs and are not additive, demonstrating the importance of taking into account relativistic and electron correlation contributions on an equal footing. DC-MP2 overestimates the electron correlation correction by 0.48-0.56 a.u. for Hg-halides and by 0.8 a.u. for Hg(CH(3))(2), respectively, while DC-CCSD underestimates the correlation correction by 0.57-0.66 a.u. compared to the reference DC-CCSD-T data. EFGs obtained at the DC-DFT level vary considerably with the functional; DC-CAMB3LYP and DC-BH&H reproduce DC-CCSD-T results within 0.08-0.24 a.u. (1%-3%) for Hg(CH(3))(2) and Hg-halides, respectively. An updated value of the nuclear quadrupole moment of the I = 5/2 excited state of (199)Hg, Q((199)Hg) = 0.675(12) b is derived from the literature. This value compares well with that derived from our calculated EFG at the DC-CCSD-T level and the experimental data for Hg(CH(3))(2); Q((199)Hg) = 0.650 b.

(204m)Pb perturbed angular correlation of γ-rays (PAC) spectroscopy has been applied successfully for the first time to detect the nuclear quadrupole interaction in a lead(II) coordination compound in a molecular crystal [tetraphenylarsonium lead(II) isomaleonitriledithiolate ([AsPh(4)](4)[Pb(2)(i-mnt)(4)])]. The recorded parameters from a powder crystalline sample are ν(Q) = 0.178(1) GHz and η = 0.970(7). The electric field gradient (EFG) was determined at the PW91/QZ4P level including relativistic effects using the two-component zeroth-order regular approximation method for both the [Pb(i-mnt)(2)](2-) monomer and the [Pb(2)(i-mnt)(4)](4-) dimer. Only the EFG for the latter compares favorably with the experimental data, indicating that the picture of this complex as a prototypical hemidirected coordination geometry with a stereochemically active lone pair on lead(II) is inadequate. Advantages and limitations of (204m)Pb PAC spectroscopy as a novel technique to elucidate the electronic and molecular structures of lead-containing complexes and biomolecules are presented.

In Staphylococcus aureus, ClpP proteases were previously shown to be essential for virulence and stress tolerance in strains derived from NCTC8325. Because these strains exhibit a severely reduced activity of the alternative sigma factor, SigB, we here reassessed the role of ClpP in SigB-proficient clinical strains. To this end, clpP was deleted in strains COL, Newman, and SA564, and the strains were characterized phenotypically. The proteomic changes accomplished by the clpP deletion in the different strains were analyzed using the 2-D DIGE technique. The proteomic analyses revealed mostly conserved changes in the protein profiles of the ClpP-deficient strains. Among the strain-specific changes were the up-regulation of prophage proteins that coincided with an increased spontaneous release of prophages and the relatively poorer growth of the clpP mutants in some strain backgrounds. Interestingly, the effect of ClpP on the expression of selected virulence genes was strain-dependent despite the fact that the expression of the global virulence regulators RNAIII, mgrA, sarZ, sarR, and arlRS was similarly changed in all clpP mutants. ClpP affected the expression of sarS in a strain-dependent manner, and we propose that the differential expression of sarS is central to the strain-dependent effect of ClpP on the expression of virulence genes.

A de novo designed dodecapeptide (HS), inspired by the metal binding loops of metal-responsive transcriptional activators, was synthesized. The aim was to create a model system for structurally promiscuous and intrinsically unstructured proteins, and explore the effect of metal ions on their structure and dynamics. The interaction with Cd(II) was investigated by UV, synchrotron radiation CD, (1)H NMR, and perturbed angular correlation (PAC) of γ-rays spectroscopy, pH-potentiometry, and molecular modelling. The peptide mainly displays characteristics of random coil in the CD spectra, and the molecular dynamics simulations demonstrate that it is unstructured with transient and varying helical content. The spectroscopic studies revealed the formation of loop structures with the coordination of the two Cys-thiolates close to each end of the HS peptide, in the presence of one equivalent of Cd(II) per ligand. The imidazole moiety from histidine is also bound to Cd(II) at neutral pH and above. In the presence of 0.5 equivalent of Cd(II) per HS metal bridged structures with e.g. CdS(2)N(2) and possibly CdS(4) coordination geometries are formed above pH ~6. In an equilibrium of several co-existing species the peptide is exchanging between a number of structures also in its metal ion bound state(s), as indicated by NMR and PAC data.

We investigate the importance of relativistic effects on NMR shielding constants and chemical shifts of linear HgL(2) (L = Cl, Br, I, CH(3)) compounds using three different relativistic methods: the fully relativistic four-component approach and the two-component approximations, linear response elimination of small component (LR-ESC) and zeroth-order regular approximation (ZORA). LR-ESC reproduces successfully the four-component results for the C shielding constant in Hg(CH(3))(2) within 6 ppm, but fails to reproduce the Hg shielding constants and chemical shifts. The latter is mainly due to an underestimation of the change in spin-orbit contribution. Even though ZORA underestimates the absolute Hg NMR shielding constants by ∼2100 ppm, the differences between Hg chemical shift values obtained using ZORA and the four-component approach without spin-density contribution to the exchange-correlation (XC) kernel are less than 60 ppm for all compounds using three different functionals, BP86, B3LYP, and PBE0. However, larger deviations (up to 366 ppm) occur for Hg chemical shifts in HgBr(2) and HgI(2) when ZORA results are compared with four-component calculations with non-collinear spin-density contribution to the XC kernel. For the ZORA calculations it is necessary to use large basis sets (QZ4P) and the TZ2P basis set may give errors of ∼500 ppm for the Hg chemical shifts, despite deceivingly good agreement with experimental data. A Gaussian nucleus model for the Coulomb potential reduces the Hg shielding constants by ∼100-500 ppm and the Hg chemical shifts by 1-143 ppm compared to the point nucleus model depending on the atomic number Z of the coordinating atom and the level of theory. The effect on the shielding constants of the lighter nuclei (C, Cl, Br, I) is, however, negligible., (© 2011 American Institute of Physics)

Herein we report how de novo designed peptides can be used to investigate whether the position of a metal site along a linear sequence that folds into a three-stranded α-helical coiled coil defines the physical properties of Cd(II) ions in either CdS(3) or CdS(3)O (O-being an exogenous water molecule) coordination environments. Peptides are presented that bind Cd(II) into two identical coordination sites that are located at different topological positions at the interior of these constructs. The peptide GRANDL16PenL19IL23PenL26I binds two Cd(II) as trigonal planar 3-coordinate CdS(3) structures whereas GRANDL12AL16CL26AL30C sequesters two Cd(II) as pseudotetrahedral 4-coordinate CdS(3)O structures. We demonstrate how for the first peptide, having a more rigid structure, the location of the identical binding sites along the linear sequence does not affect the physical properties of the two bound Cd(II). However, the sites are not completely independent as Cd(II) bound to one of the sites ((113)Cd NMR chemical shift of 681 ppm) is perturbed by the metalation state (apo or [Cd(pep)(Hpep)(2)](+) or [Cd(pep)(3)](-)) of the second center ((113)Cd NMR chemical shift of 686 ppm). GRANDL12AL16CL26AL30C shows a completely different behavior. The physical properties of the two bound Cd(II) ions indeed depend on the position of the metal center, having pK(a2) values for the equilibrium [Cd(pep)(Hpep)(2)](+) → [Cd(pep)(3)](-) + 2H(+) (corresponding to deprotonation and coordination of cysteine thiols) that range from 9.9 to 13.9. In addition, the L26AL30C site shows dynamic behavior, which is not observed for the L12AL16C site. These results indicate that for these systems one cannot simply assign a "4-coordinate structure" and assume certain physical properties for that site since important factors such as packing of the adjacent Leu, size of the intended cavity (endo vs exo) and location of the metal site play crucial roles in determining the final properties of the bound Cd(II).

Current models for global virulence regulation in Staphylococcus aureus are mainly based on studies performed with only a limited number of laboratory strains derived from NCTC8325. In these strains the small regulatory RNA, RNAIII, has a central role in virulence gene regulation. Recently, RNAIII was suggested to control transcription of target genes partly by inhibiting translation of the transcriptional regulator Rot. The present study was undertaken to examine if the model for RNAIII/Rot-dependent virulence regulation is conserved among clinical strains. To this end, we used Rot antibodies to directly assess the amount of Rot protein in 4 well-characterized S. aureus laboratory strains (8325-4, COL, Newman, and UAMS-1) and in 9 strains of clinical origin (encompassing USA300 and Mu50). Additionally, the cellular amount of RNAIII and rot mRNA was determined in all strains. The experiments revealed considerable variation in the Rot and RNAIII levels between strains. However, in the majority of strains the cellular amount of Rot was inversely correlated to the RNAIII level. As we demonstrate that Rot is a stable protein and that the level of rot transcript appeared similar in all strains, our data support that the model for RNAIII-mediated inhibition of rot mRNA translation is conserved among clinical strains. Assessment of Rot-dependent regulation of target genes revealed that Rot is a positive regulator of spa (protein A) transcription in all strains examined. In contrast, Rot repression of sspA (serine protease) and hlb (beta-hemolysin) transcription was not conserved between strains. From this study, we conclude that while the paradigm for understanding RNAIII-dependent regulation of Rot is well-conserved, regulation of single genes is subject to considerable strain variation. We propose that variation in global regulatory networks contribute considerably to the phenotypic variation observed between S. aureus isolates., ((c) 2009 Elsevier GmbH. All rights reserved.)

Metallo-beta-lactamases (MbetaLs) stand as one of the main mechanisms of bacterial resistance toward carbapenems. The rational design of an inhibitor for MbetaLs has been limited by an incomplete knowledge of their catalytic mechanism and by the structural diversity of their active sites. Here we show that the MbetaL GOB from Elizabethkingia meningoseptica is active as a monometallic enzyme by using different divalent transition metal ions as surrogates of the native Zn(II) ion. Of the metal derivatives in which Zn(II) is replaced, Co(II) and Cd(II) give rise to the most active enzymes and are shown to occupy the same binding site as the native ion. However, Zn(II) is the only metal ion capable of stabilizing an anionic intermediate that accumulates during nitrocefin hydrolysis, in which the C-N bond has already been cleaved. This finding demonstrates that the catalytic role of the metal ion in GOB is to stabilize the formation of this intermediate prior to nitrogen protonation. This role may be general to all MbetaLs, whereas nucleophile activation by a Zn(II) ion is not a conserved mechanistic feature.

Experimental and calculated (B3LYP/6-31G(d)) vibrational circular dichroism (VCD) and IR spectra are compared, illustrating that the structure and absolute configuration of ginkgolide B (GB) may be characterized directly in solution. A conformational search for GB using MacroModel and subsequent DFT optimizations (B3LYP/6-31G(d)) provides a structure for the lowest energy conformer which agrees well with the structure determined by X-ray diffraction. In addition, a conformer at an energy of 7 kJ mol(-1) (B3LYP/6-311+G(2d,2p)) with respect to the lowest energy conformer is predicted, displaying different intramolecular hydrogen bonding. Differences between measured and calculated IR and VCD spectra for GB at certain wavenumbers are rationalized in terms of interactions with solvent, intermolecular GB-GB interactions, and the potential presence of more than one conformer. This is the first detailed investigation of the spectroscopic fingerprint region (850-1300 cm(-1)) of the natural product GB employing infrared absorption and VCD spectroscopy., (2009 Wiley-Liss, Inc.)

The present study demonstrates that both the nature (Zn(II), Cd(II) or Hg(II)) and supply of metal ions determine whether zinc fingers fold into the well-known, fully loaded structures or alternatively populate a variety of structural states under substoichiometric conditions. Metal-bridged species are observed by perturbed angular correlation (PAC), EXAFS, UV spectroscopy, and stopped-flow kinetics. Transitions between structural states as adaptive reactions to changed metal-ion supply might represent intelligent system changes in zinc homeostasis, trafficking and signalling, and reflect features of heavy-metal toxicity at the molecular level. Because the zinc fingers exist in structural states that are different from the metal-free and fully loaded species, the prevailing view on metal-mediated molecular regulation in terms of "on and off control" might be oversimplified.

The reversible unfolding of metallo-beta-lactamase from Chryseobacterium meningosepticum (BlaB) by guanidinium hydrochloride is best described by a three-state model including folded, intermediate, and unfolded states. The transformation of the folded apoenzyme into the intermediate state requires only very low denaturant concentrations, in contrast to the Zn2-enzyme. Similarly, circular dichroism spectra of both BlaB and metallo-beta-lactamase from Bacillus cereus 569/H/9 (BcII) display distinct differences between metal-free and Zn2-enzymes, indicating that the zinc ions affect the folding of the proteins, giving a larger alpha-helix content. To identify the regions of the protein involved in this zinc ion-induced change, a hydrogen deuterium exchange study with matrix-assisted laser desorption ionization tandem time of flight mass spectrometry on metal-free and Zn1- and Zn2-BcII was carried out. The region spanning the metal binding metallo-beta-lactamases (MBL) superfamily consensus sequence His-X-His-X-Asp motif and the loop connecting the N- and C-terminal domains of the protein undergoes a zinc ion-dependent structural change between intrinsically disordered and ordered states. The inherent flexibility even appears to allow for the formation of metal ion-bridged protein-protein complexes which may account for both electrospray ionization-mass spectroscopy results obtained upon variation of the zinc/protein ratio and stoichiometry-dependent variations of 199mHg-perturbed angular correlation of gamma-rays spectroscopic data. We suggest that this flexible "zinc arm" motif, present in all the MBL subclasses, is disordered in metal-free MBLs and may be involved in metal ion acquisition from zinc-carrying molecules different from MBL in an "activation on demand" regulation of enzyme activity.

Introduction and Hypothesis: We compared cure rates of tension-free vaginal tape (TVT) with intravaginal slingplasty (IVS) and evaluated changes in cure rates over time., Methods: One hundred three underwent TVT and 213 underwent IVS. Follow-ups were done at 3 months, 1 year, and 5 years., Results: The following results were found: objective cure for TVT 98-95-94% vs. IVS 86-86-80% (p < 0.03); subjective cure for TVT 82-79-74% vs. IVS 79-81-71% (NS). In IVS, a significant decline in subjective cure took place. Vaginal erosions were found in 11.8% of women in the IVS group and none in the TVT group., Conclusions: TVT is an effective and stable treatment, whereas IVS has a significant inferior objective cure rate, and a significant decline in subjective cure rate occurred over time. A high rate of vaginal erosions was found in the IVS group. We cannot recommend the use of multifilament polypropylene tape (IVS) for surgical treatment of stress urinary incontinence.

Cd(II) has been used as a probe of zinc metalloenzymes and proteins because of the spectroscopic silence of Zn(II). One of the most commonly used spectroscopic techniques is (113)Cd NMR; however, in recent years (111m)Cd Perturbed Angular Correlation spectroscopy ((111m)Cd PAC) has also been shown to provide useful structural, speciation and dynamics information on Cd(II) complexes and biomolecules. In this article, we show how the joint use of (113)Cd NMR and (111m)Cd PAC spectroscopies can provide detailed information about the Cd(II) environment in thiolate-rich proteins. Specifically we show that the (113)Cd NMR chemical shifts observed for Cd(II) in the designed TRI series (TRI = Ac-G(LKALEEK)(4)G-NH(2)) of peptides vary depending on the proportion of trigonal planar CdS(3) and pseudotetrahedral CdS(3)O species present in the equilibrium mixture. PAC spectra are able to quantify these mixtures. When one compares the chemical shift range for these peptides (from delta = 570 to 700 ppm), it is observed that CdS(3) species have delta 675-700 ppm, CdS(3)O complexes fall in the range delta 570-600 ppm and mixtures of these forms fall linearly between these extremes. If one then determines the pK(a2) values for Cd(II) complexation [pK(a2) is for the reaction Cd[(peptide-H)(2)(peptide)](+)-->Cd(peptide)(3)(-) + 2H(+)] and compares these to the observed chemical shift for the Cd(peptide)(3)(-) complexes, one finds that there is also a direct linear correlation. Thus, by determining the chemical shift value of these species, one can directly assess the metal-binding affinity of the construct. This illustrates how proteins may be able to fine tune metal-binding affinity by destabilizing one metallospecies with respect to another. More important, these studies demonstrate that one may have a broad (113)Cd NMR chemical shift range for a chemical species (e.g., CdS(3)O) which is not necessarily a reflection of the structural diversity within such a four-coordinate species, but rather a consequence of a fast exchange equilibrium between two related species (e.g., CdS(3)O and CdS(3)). This could lead to reinterpretation of the assignments of cadmium-protein complexes and may impact the application of Cd(II) as a probe of Zn(II) sites in biology.

A de novo protein design strategy provides a powerful tool to elucidate how heavy metals interact with proteins.Cysteine derivatives of the TRI peptide family (Ac-G(LKALEEK)4G-NH2) have been shown to bind heavy metals in an unusual trigonal geometry. Our present objective was to design binding sites in R-helical scaffolds that are able to form higher coordination number complexes with Cd(II) and Hg(II). Herein, we evaluate the binding of Cd(II) and Hg(II) to double cysteine substituted TRI peptides lacking intervening leucines between sulfurs in the heptads. We compare a -Cysd-X-X-X-Cysa- binding motif found in TRIL12CL16C to the more common -Cysa-X-X-Cysd- sequence of native proteins found in TRIL9CL12C. Compared to TRI, these substitutions destabilize the helical aggregates,leading to mixtures of two- and three-stranded bundles. The three-stranded coiled coils are stabilized by the addition of metals. TRIL9CL12C forms distorted tetrahedral complexes with both Cd(II) and Hg(II), as supported by UV-vis,CD, 113Cd NMR, 199Hg NMR and 111mCd PAC spectroscopy. Additionally, these signatures are very similar to those found for heavy metal substituted rubredoxin. These results suggest that in terms of Hg(II) binding, TRIL9CL12Ccan be considered as a good mimic of the metallochaperone HAH1, that has previously been shown to form protein dimers. TRIL12CL16C has limited ability to generate homoleptic tetrahedral complexes (Cd(SR)42-). These type of complexes were identified only for Hg(II). However, the spectroscopic signatures suggest a different geometry around the metal ion, demonstrating that effective metal sequestration into the hydrophobic interior of the bundle requires more than simply adding two sulfur residues in adjacent layers of the peptide core. Thus, proper design of metal binding sites must also consider the orientation of cysteine sidechains in a vs d positions of the heptads.

Here, we report a previously undescribed approach for controlling metal ion coordination geometry in biomolecules by reorientating amino acid side chains through substitution of L- to D-amino acids. These diastereopeptides allow us to manipulate the spatial orientation of amino acid side chains to alter the sterics of metal binding pockets. We have used this approach to design the de novo metallopeptide, Cd(TRIL12L(D)L16C)(3)(-), which is an example of Cd(II) bound to 3 L-Cys as exclusively trigonal CdS(3), as characterized by a combination of (113)Cd NMR and (111m)Cd PAC spectroscopy. We subsequently show that the physical properties of such a site, such as the high pK(a2) for Cd(II) binding of 15.1, is due to the nature of the coordination number and not the ligating group. Further more this approach allowed for the design of a construct, GRANDL12L(D)L16CL26AL30C, capable of independently binding 2 equivalents of Cd(II) to 2 very similar Cys sites as exclusively 3- and 4-, CdS(3) and CdS(3)O, respectively. Demonstrating that we are capable of controlling the Cd(II) coordination number in these 2 sites solely by varying the nature of a noncoordinating second coordination sphere amino acid, with D-leucine and L-alanine resulting in exclusively 3- and 4-coordinate structures, respectively. Cd(II) was found to selectively bind to the 4-coordinate CdS(3)O site, demonstrating that a protein can be designed that displays metal-binding selectivity based solely on coordination number control and not on the chemical identity of coordinating ligands.

ArsR (or ArsR/SmtB) family metalloregulatory homodimeric repressors collectively respond to a wide range of metal ion inducers in regulating homeostasis and resistance of essential and nonessential metal ions in bacteria. BxmR from the cyanobacterium Osciliatoria brevis is the first characterized ArsR protein that senses both Cu (I)/Ag (I) and divalent metals Zn (II)/Cd (II) in cells by regulating the expression of a P-type ATPase efflux pump (Bxa1) and an intracellular metallothionein (BmtA). We show here that both pairs of predicted alpha3N and alpha5 sites bind metal ions, but with distinct physicochemical and functional metal specificities. Inactivation of the thiophilic alpha3N site via mutation (C77S) abolishes regulation by both Cd (II) and Cu (I), while Zn (II) remains a potent allosteric negative effector of operator/promoter binding (Delta G c >or= +3.2 kcal mol (-1)). In contrast, alpha5 site mutant retains regulation by all four metal ions, albeit with a smaller coupling free energy (Delta G c approximately +1.7 (+/-0.1) kcal mol (-1)). Unlike the other metals ions, the BxmR dimer binds 4 mol equiv of Cu (I) to form an alpha3N binuclear Cu (I) 2S 4 cluster by X-ray absorption spectroscopy. BxmR is thus distinguishable from other closely related ArsR family sensors, in having evolved a metalloregulatory alpha3N site that can adopt an expanded range of coordination chemistries while maintaining redundancy in the response to Zn (II). The evolutionary implications of these findings for the ArsR metal sensor family are discussed.

Molecular dynamics simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (NPT) ensemble give highly ordered, gel-like bilayers with an area per lipid of approximately 48 A(2). To obtain fluid (L(alpha)) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid headgroup and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential fitting method. We tested the derived charges in molecular dynamics simulations of a fully hydrated DPPC bilayer. Only the simulation with the new restricted electrostatic potential charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 +/- 0.1 A(2). Compared to the 48 A(2), the new value of 60.4 A(2) is in fair agreement with the experimental value of 64 A(2). In addition, the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the NPT ensemble by employing our modified CHARMM27 force field.

The use of de novo designed peptides is a powerful strategy to elucidate Hg(II)-protein interactions and to gain insight into the chemistry of Hg(II) in biological systems. Cysteine derivatives of the designed alpha-helical peptides of the TRI family [Ac-G-(L(a)K(b)A(c)L(d)E(e)E(f)K(g))(4)-G-NH(2)] bind Hg(II) at high pH values and at peptide/Hg(II) ratios of 3:1 with an unusual trigonal thiolate coordination mode. The resulting Hg(II) complexes are good water-soluble models for Hg(II) binding to the protein MerR. We have carried out a parallel study using (199)Hg NMR and (199m)Hg perturbed angular correlation (PAC) spectroscopy to characterize the distinct species that are generated under different pH conditions and peptide TRI L9C/Hg(II) ratios. These studies prove for the first time the formation of [Hg{(TRI L9C)(2)-(TRI L9C-H)}], a dithiolate-Hg(II) complex in the hydrophobic interior of the three-stranded coiled coil (TRI L9C)(3). (199)Hg NMR and (199m)Hg PAC data demonstrate that this dithiolate-Hg(II) complex is different from the dithiolate [Hg(TRI L9C)(2)], and that the presence of third alpha-helix, containing a protonated cysteine, breaks the symmetry of the coordination environment present in the complex [Hg(TRI L9C)(2)]. As the pH is raised, the deprotonation of this third cysteine generates the trigonal thiolate-Hg(II) complex Hg(TRI L9C)(3)(-) on a timescale that is slower than the NMR timescale (0.01-10 ms). The formation of the species [Hg{(TRI L9C)(2)(TRI L9C-H)}] is the result of a compromise between the high affinity of Hg(II) to form dithiolate complexes and the preference of the peptide to form a three-stranded coiled coil.

Perturbed angular correlation of gamma-rays (PAC) spectroscopy of cadmium substituted plastocyanin shows one dominant metal site configuration at pH 7.5. Lowering the pH to 4.8 a fraction of the molecules undergoes structural change and loses the bound cadmium ion. At pH 4.4 all plastocyanin is in the apo-form. Increasing the pH back to neutral pH values two distinct metal site coordination geometries were observed. One of the two signals is the same as that found initially at pH 7.5; the other form is stable for hours at 1 degrees C, indicating the existence of a long lived intermediate metal site structure. The cadmium ion is surrounded by the same ligands (His37, Cys84, His87 and Met92) in both forms, however the metal center in the long lived intermediate metal site structure can be best described by a larger His-metal-His angle.

The effect of cadmium on the photosynthetic activity of Synechocystis PCC 6803 was monitored in this study. The oxygen evolving capacity of Synechocystis treated with 40 muM CdCl(2) was depressed to 10% of the maximum in 15 min, indicating that Cd(2+) penetrated rapidly into the cells and blocked the photosynthetic activity. However, neither photosystem II (PSII) nor photosystem I (PSI) activity showed a significant short-term decrease which would explain this fast decrease in the whole-chain electron transport. Thermoluminescence measurements have shown that the charge separation and stabilization in PSII remains essentially unchanged during the first few hours following the Cd(2+) treatment. The electron flow through PSI was monitored by following the redox changes of the P700 reaction centers of PSI. Alterations in the oxidation kinetics of P700 in the Cd(2+)-treated cells indicated that Cd(2+) treatment might affect the available electron acceptor pool of P700, including the CO(2) reduction and accumulation in the cells. Perturbed angular correlation of gamma-rays (PAC) using the radioactive (111m)Cd isotope was used to follow the Cd(2+) uptake at a molecular level. The most plausible interpretation of the PAC data is that Cd(2+) is taken up by one or more Zn proteins replacing Zn(2+) in Synechocystis PCC 6803. Using the radioactive (109)Cd isotope, a protein of approximately 30 kDa that binds Cd(2+) could be observed in sodium dodecyl sulfate polyacrylamide gel electrophoresis. The results indicate that Cd(2+) might inactivate different metal-containing enzymes, including carbonic anhydrase, by replacing the zinc ion, which would explain the rapid and almost full inhibition of the photosynthetic activity in cyanobacteria.

Three possible methyl-substituted phenyloxiranes have been synthesized in enantioenriched form (89-99% enantiomeric excess (ee)), and their vibrational absorption (VA) and vibrational circular dichroism (VCD) spectra have been recorded. The experimental spectra are compared to theoretical spectra obtained from quantum mechanical calculations (density functional theory with the B3LYP hybrid exchange correlation functional with 6-31++G*, aug-cc-pVDZ, or aug-cc-pVTZ basis set) and related to the physical structure of the compounds. The absolute configuration could be established directly in each case by comparing experimental and theoretical spectra. In addition, we have been able to document the changes that occur both in structures and in the VA and VCD spectra due to substituent effects on the oxirane ring.

In this study the pH-dependent structural changes of reduced spinach plastocyanin were investigated using perturbed angular correlation (PAC) of gamma-rays and dynamic light scattering (DLS). PAC data of Ag-substituted plastocyanin indicated that the coordinating ligands are two histidine residues (His37, His87) and a cysteine residue (Cys84) in a planar configuration, whereas the methionine (Met92) found perpendicular to this plane is not a coordinating ligand at neutral pH. Two slightly different conformations with differences in the Cys-metal ion-His angles could be observed with PAC spectroscopy. At pH 5.3 a third coordination geometry appears which can be explained as the absence of the His87 residue and the coordination of Met92 as a ligand. With DLS the aggregation of reduced plastocyanin could be observed below pH 5.3, indicating that not only the metal binding site but also the aggregation properties of the protein change upon pH reduction. Both the structural changes at the metal binding site and the aggregation are shown to be reversible. These results support the hypothesis that the pH of the thylakoid lumen has to remain moderate during steady-state photosynthesis and indicate that low pH induced aggregation of plastocyanin might serve as a regulatory switch for photosynthesis.

We have applied pharmacophore generation, database searching, docking methodologies, and experimental enzyme kinetics to discover new structures for design of di-zinc metallo-beta-lactamase inhibitors. Based on crystal structures of class B1 metallo-beta-lactamases with a succinic acid and a mercapto-carboxylic acid inhibitor bound to the enzyme, two pharmacophore models were constructed. With the Catalyst program, these pharmacophores were used to search the ACD database, which provided a total of 74 hits representing four different chemical classes of compounds: Dicarboxylic acids, phosphonic and sulfonic acid derivatives, and mercapto-carboxylic acids. All hits were docked into different metallo-beta-lactamases (from classes B1 and B3) using the GOLD docking program. A selection scheme based on the GOLD scores, the Catalyst fit and shape values, and the size of the compounds (molecular weight, surface area, and number of rotatable bonds) was developed and thirteen compounds representing all four chemical classes were selected for experimental studies. Three compounds with new scaffolds hitherto not present in metallo-beta-lactamase inhibitors have IC50 values less than 15 microM and may serve as starting points in the design of metallo-beta-lactamase inhibitors.