The NMR spectra of naturally occurring iron-sulfur proteins have been studied for some 15 years by now1"4 and yet are not fully understood because there is disagreement between the reported spectra and those expected on a theoretical basis. We have investigated the NMR spectra of a reduced 2Fe-2S protein over a quite extended spectral width and detected some more signals that may provide the key for the assignment of the NMR spectra of every kind of ironsulfur cluster. Six to eight signals had been detected1•4"10 *in several reduced 2Fe-2S ferredoxins (one iron(III) and one iron(II)) in the range from 45 ppm downfield to 5 ppm upfield from DSS, four of them showing an anti-Curie type temperature dependence and the remaining a Curie type temperature dependence. The first idea was to assign the isotropically shifted signals to /3-CH2's of the four bound cysteines.1 7•6 Subsequently, the four signals showing anti-Curie behavior were assigned to the ß-CH2's of the cysteines coordinated to the iron(II) center.4•5

Many diseases cause significant changes to the concentrations of small molecules (a.k.a. metabolites) that appear in a person’s biofluids, which means such diseases can often be readily detected from a person’s “metabolic profile"—i.e., the list of concentrations of those metabolites. This information can be extracted from a biofluids Nuclear Magnetic Resonance (NMR) spectrum. However, due to its complexity, NMR spectral profiling has remained manual, resulting in slow, expensive and error-prone procedures that have hindered clinical and industrial adoption of metabolomics via NMR. This paper presents a system, BAYESIL, which can quickly, accurately, and autonomously produce a person’s metabolic profile. Given a 1D 1 H NMR spectrum of a complex biofluid (specifically serum or cerebrospinal fluid), BAYESIL can automatically determine the metabolic profile. This requires first performing several spectral processing steps, then matching the resulting spectrum against a reference compound library, which contains the “signatures” of each relevant metabolite. BAYESIL views spectral matching as an inference problem within a probabilistic graphical model that rapidly approximates the most probable metabolic profile. Our extensive studies on a diverse set of complex mixtures including real biological samples (serum and CSF), defined mixtures and realistic computer generated spectra; involving > 50 compounds, show that BAYESIL can autonomously find the concentration of NMR-detectable metabolites accurately (~ 90% correct identification and ~ 10% quantification error), in less than 5 minutes on a single CPU. These results demonstrate that BAYESIL is the first fully-automatic publicly-accessible system that provides quantitative NMR spectral profiling effectively—with an accuracy on these biofluids that meets or exceeds the performance of trained experts. We anticipate this tool will usher in high-throughput metabolomics and enable a wealth of new applications of NMR in clinical settings. BAYESIL is accessible at http://www.bayesil.ca.

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Oxidized ferredoxin from Clostridium acidi urici, containing two [Fe4S4I2+ clusters, has been investigated through 1H NOESY and TOCSY spectroscopies. The protons of coordinated cysteines have been identified and assigned to each cluster with use of a procedure based on the assignment of two spatially close @CH2 pairs and on the shift ratios of each PCH2 proton in oxidized, half-reduced, and reduced forms; each cysteine proton has been then sequence-specifically and stereospecifically assigned by looking for dipolar connectivities with amino acid residues in the vicinity of the cluster. By comparing the present data with the available spectra of the analogous protein from Clostridium pasteurianum, the sequence-specific and stereospecific assignments of cysteine protons have been obtained also for the latter protein. The natural abundance 13C signals of the cysteine protons have been also sequencespecifically assigned. By taking advantage of the X-ray structure of a similar protein, the lH and I3C hyperfine shifts have been related to the dihedral angle between the iron-sulfur-0-carbon plane and the sulfur-fl-carbon-@-proton or sulfur-/3-carbon-a-carbon planes. A parametric equation is proposed. The spin delocalization mechanism has been found to be largely dependent on unpaired spin density on the pz orbital of the sulfur atom. Through EXSY spectroscopy, the proton signals of the [Fe&]+ clusters in the reduced protein have been assigned. Their temperature dependence is compared with that of the [Fe&I3+ clusters present in oxidized HiPIPs and discussed in terms of the Heisenberg model for the magnetic exchange coupling within the clusters.

In the frame of a broad study on the structural differences between the two redox forms of cytochromes to be related to the electron transfer process, the NMR solution structure of horse heart cytochrome c in the reduced form has been determined. The structural data obtained in the present work are compared to those already available in the literature on the same protein and the presence of conformational differences is discussed in the light of the experimental method employed for the structure determination. Redox-state dependent changes are analyzed and in particular they are related to the role of propionate-7 of the heme. Also some hydrogen bonds are changed upon reduction of the heme iron. A substantial similarity is observed for the backbone fold, independently of the oxidation state. At variance, some meaningful differences are observed in the orientation of a few side chains. These changes are related to those found in the case of the highly homologous cytochrome c from Saccharomyces cerevisiae. The exchangeability of the NH protons has been investigated and found to be smaller than in the case of the oxidized protein. We think that this is a characteristic of reduced cytochromes and that mobility is a medium for molecular recognition in vivo.

Paramagnetic 'H-NMR spectra of Co(II)-substituted Cysll2Asp azurin from Pseudomonas aeruginosa have been analyzed and compared with those of the Co(II) wild-type (WT) protein. Hyperfine-shifted signals (including Aspl 12 /3-CHi signals in the mutant as well as previously unobserved Cysl 12 /I-CH2 signals in WT) from all the metal-coordinated residues have been detected and unambiguously assigned. Notably, the spectra indicate that very little if any unpaired spin density is located on the Metl21 protons in the Cysl 12Asp protein. A computergenerated model of the mutant Co(II) structure consistent with electronic absorption as well as the NMR data includes a Gly45 carbonyl, His46, an unusually coordinated Aspl 12, and Hisll7 in the ligation sphere.

Static zero field splitting effects on the electronic relaxation of paramagnetic metal ion complexes in solution A low-field paramagnetic nuclear spin relaxation theory Electron spin relaxation for an Sϭ1 system and its field dependence in the presence of static zero-field splitting ͑ZFS͒ has been described and incorporated in a model for nuclear spin-lattice relaxation in paramagnetic complexes in solution, proposed earlier by the group in Florence. Slow reorientation is assumed and the electron spin energy level structure ͑at any orientation of the molecule with respect to the laboratory frame͒ is described in terms of the Zeeman interaction and of the static ZFS. The electron spin relaxation is assumed to be caused by a transient ZFS modulated by the deformation of the complex described as a distortional ͑or pseudorotational͒ motion and the Redfield theory is used to derive the electron spin relaxation matrices. In the description of the electron spin relaxation we neglect any contribution from mechanisms involving modulation by reorientation, such as those of the static ZFS and the less important Zeeman interaction, as we limit ourselves to the slow-rotation limit ͑i.e., R ӷ S ͒. This in general covers the behavior of proteins and macromolecules. The decomposition ͑DC͒ approximation is used, which means that the reorientational motion and electron spin dynamics are assumed to be uncorrelated. This is not a serious problem, due to the slow-rotation condition, since reorientational and distortional motions are time-scale separated. The resulting nuclear magnetic relaxation dispersion ͑NMRD͒ profiles obtained using the Florence model are calculated and compared with the calculations of the Swedish approach, which can be considered essentially exact within the given set of assumed interactions and dynamic processes. That theory is not restricted by the Redfield limit and can thus handle electron spin relaxation in the slow-motion regime, which is a consequence of not explicitly defining any electron spin relaxation times. Furthermore, the DC approximation is not invoked, and in addition, the electron spin relaxation is described by reorientationally modulated static ZFS and Zeeman interaction besides the distortionally modulated transient ZFS. The curves computed with the Florence model show a satisfactory agreement with these more accurate calculations of the Swedish approach, in particular for the axially symmetric static ZFS tensor, providing confidence in the adequacy of the electron spin relaxation model under the condition of slow rotation. The comparison is also quite instructive as far as the physical meaning of the electron spin relaxation and of its interplay with the nuclear spin system are concerned.

Effective cancer therapy largely depends on inducing apoptosis in cancer cells via chemotherapy and/or radiation. Monitoring apoptosis in real-time provides invaluable information for evaluating cancer therapy response and screening preclinical anticancer drugs. In this work, we describe the design, synthesis, characterization and in vitro evaluation of caspase probe 1 (CP1), a bimodal fluorescence-magnetic resonance (FL-MR) probe that exhibits simultaneous FL-MR turn-on response to caspase-3/7. Both caspases exist as inactive zymogens in normal cells but are activated during apoptosis and are unique biomarkers for this process. CP1 has three distinct components: a DOTA-Gd(III) chelate that provides the MR signal enhancement, tetraphenylethylene as the aggregation induced emission luminogen (AIEgen), and DEVD peptide which is a substrate for caspase-3/7. In response to caspase-3/7, the water-soluble peptide DEVD is cleaved and the remaining Gd(III)-AIEgen (Gad-AIE) conjugate aggregates leading to increased FL-MR signals. CP1 exhibited sensitive and selective dual FL-MR turn-on response to caspase-3/7 in vitro and was successfully tested by fluorescence imaging of apoptotic cells. Remarkably, we were able to use the FL response of CP1 to quantify the exact concentrations of inactive and active agents and accurately predict the MR signal in vitro. We have demonstrated that the aggregation-driven FL-MR probe design is a unique method for MR signal quantification. This probe design platform can be adapted for a variety of different imaging targets, opening new and exciting avenues for multimodal molecular imaging.