Divalent Metal Binding Properties of the Methionyl Aminopeptidase from \u3cem\u3eEscherichia coli\u3c/em\u3e

The metal-binding properties of the methionyl aminopeptidase from Escherichia coli (MetAP) were investigated. Measurements of catalytic activity as a function of added Co(II) and Fe(II) revealed that maximal enzymatic activity is observed after the addition of only 1 equiv of divalent metal ion. Based on these studies, metal binding constants for the first metal binding event were found to be 0.3 ± 0.2 μM and 0.2 ± 0.2 μM for Co(II)- and Fe(II)-substituted MetAP, respectively. Binding of excess metal ions (\u3e50 equiv) resulted in the loss of ∼50% of the catalytic activity. Electronic absorption spectral titration of a 1 mM sample of MetAP with Co(II) provided a binding constant of 2.5 ± 0.5 mM for the second metal binding site. Furthermore, the electronic absorption spectra of Co(II)-loaded MetAP indicated that both metal ions reside in a pentacoordinate geometry. Consistent with the absorption data, electron paramagnetic resonance (EPR) spectra of [CoCo(MetAP)] also indicated that the Co(II) geometries are not highly constrained, suggesting that each Co(II) ion in MetAP resides in a pentacoordinate geometry. EPR studies on [CoCo(MetAP)] also revealed that at pH 7.5 there is no significant spin-coupling between the two Co(II) ions, though a small proportion (∼5%) of the sample exhibited detectable spin−spin interactions at pH values \u3e 9.6. EPR studies on [Fe(III)_(MetAP)] and [Fe(III)Fe(III)(MetAP)] also suggested no spin-coupling between the two metal ions. 1H nuclear magnetic resonance (NMR) spectra of [Co(II)_(MetAP)] in both H2O and D2O buffer indicated that the first metal binding site contains the only active-site histidine residue, His171. Mechanistic implications of the observed binding properties of divalent metal ions to the MetAP from E. coli are discussed

Mutagenic and Spectroscopic Investigation of pH Dependent CooA DNA Binding

The carbon monoxide (CO) sensing heme protein, CooA, is a transcription factor which exists in several bacteria that utilize CO as an energy source. CooA positively regulates the expression of coo genes in the presence of CO such that the corresponding proteins may metabolize CO. The present studies have yielded the unexpected result that Fe(III) CooA binds DNA tightly at pH \u3c 7, deviating from all previously reported work which indicate that CooA DNA binding is initiated only when the exogenous CO effector reacts with the Fe(II) CooA heme. This observation suggests that the disruption of one or more salt bridges upon effector binding may be a critical feature of the normal CooA activation mechanism. To test this possibility, several protein variants that eliminated a selected salt bridge for the CooA homolog from Rhodospirillum rubrum were prepared via site-directed mutagenesis. Samples of these variant proteins, which were overexpressed in Escherichia coli, were then characterized by spectroscopic methods and functional assays to investigate the impact these mutations had on CooA heme coordination structure and DNA-binding activity. Results of this work are presented in light of the accepted CooA activation mechanism

Converting CooA from a Carbon Monoxide to an Oxygen-Sensing Heme Protein Transcription Factor: Investigations into the Structure and Mechanism of Gas Binding

CooA is a carbon monoxide-sensing (CO-sensing) heme protein transcription factor that regulates gene activation in several bacteria and, importantly, is a convenient model for studying analogous proteins in the human body. In the present study, the specificity and mechanism of gas-binding of CooA have been investigated by efforts to convert CooA from a CO to an oxygen (O2) sensor through site directed mutagenesis of residues in the gas binding pocket of the heme group. The resulting mutated proteins were then isolated and characterized with spectroscopy. The results of this research project will provide further insight into the current model for the specificity and mechanisms of gas binding in heme proteins

CO adsorption on (111) and (100) surfaces of the Pt sub 3 Ti alloy. Evidence for parallel binding and strong activation of CO

The CO adsorption on a 40 atom cluster model of the (111) surface and a 36 atom cluster model of the (100) surface of the Pt3Ti alloy was studied. Parallel binding to high coordinate sites associated with Ti and low CO bond scission barriers are predicted for both surfaces. The binding of CO to Pt sites occurs in an upright orientation. These orientations are a consequence of the nature of the CO pi donation interactions with the surface. On the Ti sites the orbitals donate to the nearly empty Ti 3d band and the antibonding counterpart orbitals are empty. On the Pt sites, however, they are in the filled Pt 5d region of the alloy band, which causes CO to bond in a vertical orientation by 5 delta donation from the carbon end

Cis-regulatory module detection using constraint programming

We propose a method for finding CRMs in a set of co-regulated genes. Each CRM consists of a set of binding sites of transcription factors. We wish to find CRMs involving the same transcription factors in multiple sequences. Finding such a combination of transcription factors is inherently a combinatorial problem. We solve this problem by combining the principles of itemset mining and constraint programming. The constraints involve the putative binding sites of transcription factors, the number of sequences in which they co-occur and the proximity of the binding sites. Genomic background sequences are used to assess the significance of the modules. We experimentally validate our approach and compare it with state-of-the-art techniques

Electronic structures of Zn1−x_{1-x}Cox_xO using photoemission and x-ray absorption spectroscopy

Electronic structures of Zn$_{1-x}$Co$_x$O have been investigated using photoemission spectroscopy (PES) and x-ray absorption spectroscopy (XAS). The Co 3d states are found to lie near the top of the O $2p$ valence band, with a peak around $\sim 3$ eV binding energy. The Co $2p$ XAS spectrum provides evidence that the Co ions in Zn$_{1-x}$Co$_{x}$O are in the divalent Co$^{2+}$ ($d^7$) states under the tetrahedral symmetry. Our finding indicates that the properly substituted Co ions for Zn sites will not produce the diluted ferromagnetic semiconductor property.Comment: 3 pages, 2 figure

Structural Plasticity and Noncovalent Substrate Binding in the GroEL Apical Domain. A study using electrospray ionization mass spectrometry and fluorescence binding studies

Advances in understanding how GroEL binds to non-native proteins are reported. Conformational flexibility in the GroEL apical domain, which could account for the variety of substrates that GroEL binds, is illustrated by comparison of several independent crystallographic structures of apical domain constructs that show conformational plasticity in helices H and I. Additionally, ESI-MS indicates that apical domain constructs have co-populated conformations at neutral pH. To assess the ability of different apical domain conformers to bind co-chaperone and substrate, model peptides corresponding to the mobile loop of GroES and to helix D from rhodanese were studied. Analysis of apical domain-peptide complexes by ESI-MS indicates that only the folded or partially folded apical domain conformations form complexes that survive gas phase conditions. Fluorescence binding studies show that the apical domain can fully bind both peptides independently. No competition for binding was observed, suggesting the peptides have distinct apical domain-binding sites. Blocking the GroES-apical domain-binding site in GroEL rendered the chaperonin inactive in binding GroES and in assisting the folding of denatured rhodanese, but still capable of binding non-native proteins, supporting the conclusion that GroES and substrate proteins have, at least partially, distinct binding sites even in the intact GroEL tetradecamer

To Bind or not to Bind: Understanding how CooA Activates

CooA, a gas-sensing heme protein found in several organisms, binds to DNA in the presence of carbon monoxide (CO) to regulate important metabolic functions. CO binding to a heme, an iron-containing entity of the protein, initiates a series of structural changes of CooA that enables it to bind a specific DNA target. The broader goal of this research is to understand the key steps that take place as CooA is activated for DNA binding. Previously and surprisingly, data suggested CooA appeared to bind DNA under non-native conditions: without CO and at low pH values. This observation was potentially important because it suggested the breaking of a CooA salt-bridge (a pair of oppositely-charged amino acids that are attracted to one another) may be a key step that allows the protein to change shape into its “active” form. Current research definitely refuted one key aspect of this hypothesis as experiments revealed this apparent low pH DNA binding is not an attribute unique to CooA; specifically results of fluorescence anisotropy assays showed that several proteins without hemes and having a range of properties also showed apparent binding activity at low pH to a DNA target specifically tailored for CooA. Although low pH binding is not supported by these experiments, this does not rule out the importance of the breaking of the salt bridge as a critical part of CooA activation. To further investigate this idea, variants of CooA with mutated salt-bridge amino acids were made and purified. Analysis of these CooA variant proteins are underway and experimental results will be presented in light of the proposed CooA activation mechanism