Strategy for the study of paramagnetic proteins with slow electronic relaxation rates by nmr spectroscopy: application to oxidized human [2Fe-2S] ferredoxin

NMR studies of paramagnetic proteins are hampered by the rapid relaxation of nuclei near the paramagnetic center, which prevents the application of conventional methods to investigations of the most interesting regions of such molecules. This problem is particularly acute in systems with slow electronic relaxation rates. We present a strategy that can be used with a protein with slow electronic relaxation to identify and assign resonances from nuclei near the paramagnetic center. Oxidized human [2Fe-2S] ferredoxin (adrenodoxin) was used to test the approach. The strategy involves six steps: (1) NMR signals from (1)H, (13)C, and (15)N nuclei unaffected or minimally affected by paramagnetic effects are assigned by standard multinuclear two- and three-dimensional (2D and 3D) spectroscopic methods with protein samples labeled uniformly with (13)C and (15)N. (2) The very broad, hyperfine-shifted signals from carbons in the residues that ligate the metal center are classified by amino acid and atom type by selective (13)C labeling and one-dimensional (1D) (13)C NMR spectroscopy. (3) Spin systems involving carbons near the paramagnetic center that are broadened but not hyperfine-shifted are elucidated by (13)C[(13)C] constant time correlation spectroscopy (CT-COSY). (4) Signals from amide nitrogens affected by the paramagnetic center are assigned to amino acid type by selective (15)N labeling and 1D (15)N NMR spectroscopy. (5) Sequence-specific assignments of these carbon and nitrogen signals are determined by 1D (13)C[(15)N] difference decoupling experiments. (6) Signals from (1)H nuclei in these spin systems are assigned by paramagnetic-optimized 2D and 3D (1)H[(13)C] experiments. For oxidized human ferredoxin, this strategy led to assignments (to amino acid and atom type) for 88% of the carbons in the [2Fe-2S] cluster-binding loops (residues 43-58 and 89-94). These included complete carbon spin-system assignments for eight of the 22 residues and partial assignments for each of the others. Sequence-specific assignments were determined for the backbone (15)N signals from nine of the 22 residues and ambiguous assignments for five of the others.     

Links between microscopic and macroscopic fluid mechanics

The microscopic and macroscopic versions of fluid mechanics differ qualitatively. Microscopic particles obey time-reversible ordinary differential equations. The resulting particle trajectories {q(t)} may be time-averaged or ensemble-averaged so as to generate field quantities corresponding to macroscopic variables. On the other hand, the macroscopic continuum fields described by fluid mechanics follow irreversible partial differential equations. Smooth particle methods bridge the gap separating these two views of fluids by solving the macroscopic field equations with particle dynamics that resemble molecular dynamics. Recently, nonlinear dynamics have provided some useful tools for understanding the relationship between the microscopic and macroscopic points of view. Chaos and fractals play key roles in this new understanding. Non-equilibrium phase-space averages look very different from their equilibrium counterparts. Away from equilibrium the smooth phase-space distributions are replaced by fractional-dimensional singular distributions that exhibit time irreversibility.     

Gaussian Property of the Rings R(X) and R〈X〉

The content of a polynomial f over a commutative ring R is the ideal c(f) of R generated by the coefficients of f. A commutative ring R is said to be Gaussian if c(fg) = c(f)c(g) for every polynomials f and g in R[X]. A number of authors have formulated necessary and sufficient conditions for R(X) (respectively, R?X?) to be semihereditary, have weak global dimension at most one, be arithmetical, or be Prüfer. An open question raised by Glaz is to formulate necessary and sufficient conditions that R(X) (respectively, R?X?) have the Gaussian property. We give a necessary and sufficient condition for the rings R(X) and R?X? in terms of the ring R in case the square of the nilradical of R is zero.     

DCAP: a broad-spectrum antibiotic that targets the cytoplasmic membrane of bacteria

Persistent infections are frequently caused by dormant and biofilm-associated bacteria, which often display characteristically slow growth. Antibiotics that require rapid cell growth may be ineffective against these organisms and thus fail to prevent reoccurring infections. In contrast to growth-based antimicrobial agents, membrane-targeting drugs effectively kill slow-growing bacteria. Herein we introduce 2-((3-(3,6-dichloro-9H-carbazol-9-yl)-2-hydroxypropyl)amino)-2-(hydroxymethyl)propane-1,3-diol (DCAP), a potent broad-spectrum antibiotic that reduces the transmembrane potential of Gram-positive and Gram-negative bacteria and causes mislocalization of essential membrane-associated proteins, including MinD and FtsA. Importantly, DCAP kills nutrient-deprived microbes and sterilizes bacterial biofilms. DCAP is lethal against bacterial cells, has no effect on red blood cell membranes, and only decreases the viability of mammalian cells after ≥6 h. We conclude that membrane-active compounds are a promising solution for treating persistent infections. DCAP expands the limited number of compounds in this class of therapeutic small molecules and provides new opportunities for the development of potent broad-spectrum antimicrobial agents.     

Natural J-coupling analysis: interpretation of scalar J-couplings in terms of natural bond orbitals.

The natural J-coupling (NJC) method presented here analyzes the Fermi contact portion of J-coupling in the framework of finite perturbation theory applied to ab initio/density function theory (DFT) wave functions, to compute individual and pairwise orbital contributions to the net J-coupling. The approach is based on the concepts and formalisms of natural bond orbital (NBO) methods. Computed coupling contributions can be classified as Lewis (individual orbital contributions corresponding to the natural Lewis structure of the molecule), delocalization (resulting from pairwise donor-acceptor interactions), and residual repolarization (corresponding to correlation-like interactions). This approach is illustrated by an analysis of the angular and distance dependences of the contributions to vicinal (3)J(HH) couplings in ethane and to the long-range (6)J(HH) couplings in pentane. The results indicate that approximately 70% or more of the net J-coupling is propagated by steric exchange antisymmetry interactions between Lewis orbitals (predominantly sigma bonding orbitals). Hyperconjugative sigma to sigma delocalization interactions account for the remainder of the coupling. Calculated pairwise-steric and hyperconjugative-delocalization energies provide a means for relating coupling mechanisms to molecular energetics. In this way, J-coupling contributions can be related directly to the localized features of the molecular electronic structure in order to explain measured J-coupling patterns and to predict J-coupling trends that have yet to be measured.     

Rieske protein from Thermus thermophilus: 15N NMR titration study demonstrates the role of iron-ligated histidines in the pH dependence of the reduction potential

A unique feature of Rieske proteins is the pH dependence of their reduction potentials. It has been proposed that protonation of the Nepsilon2 atoms of the two histidine rings ligated to the iron-sulfur cluster is coupled with cluster reduction (electron transfer). We have incorporated [15Ndelta1, 15Nepsilon2]-histidine into the Rieske protein from Thermus thermophilis and have used 15N NMR spectroscopy to determine the pKa values of the histidine residues in the oxidized state of the protein. As expected from studies of a Rieske-type ferredoxin, the signals from the 15Ndelta1 atoms directly bound to iron were too broad to be detected, but broad signals could be detected from the 15Nepsilon2 atom of each of the ligated histidine rings. We measured the chemical shifts of these signals as a function of pH between pH 6 and pH 12 and fitted them to theoretical titration curves. The results yielded well-separated pKa values for the two histidines (7.46 and 9.24), with Hill coefficients close to unity. The pKa values are in excellent agreement with values predicted from the pH dependence of the reduction potentials (7.85 and 9.65).     

Paramagnetic NMR spectroscopy and density functional calculations in the analysis of the geometric and electronic structures of iron-sulfur proteins

Paramagnetic NMR spectroscopy has been underutilized in the study of metalloproteins. One difficulty of the technique is that paramagnetic relaxation broadens signals from nuclei near paramagnetic centers. In systems with low electronic relaxation rates, this makes such signals difficult to observe or impossible to assign by traditional methods. We show how the challenges of detecting and assigning signals from nuclei near the metal center can be overcome through the combination of uniform and selective 2H, 13C, and 15N isotopic labeling with NMR experiments that utilize direct one-dimensional (2H, 13C, and 15N) and two-dimensional (13C-X) detection. We have developed methods for calculating NMR chemical shifts and relaxation rates by density functional theory (DFT) approaches. We use the correspondence between experimental NMR parameters and those calculated from structural models of iron-sulfur clusters derived from X-ray crystallography to validate the computational approach and to investigate how structural differences are manifested in these values. We have applied this strategy to three iron-sulfur proteins: Clostridium pasteurianum rubredoxin, Anabaena [2Fe-2S] ferredoxin, and human [2Fe-2S] ferredoxin. Provided that an accurate structural model of the iron-sulfur cluster and surrounding residues is available from diffraction data, our results show that DFT calculations can return NMR observables with excellent accuracy. This suggests that it might be possible to use calculations to refine structures or to generate structural models of active sites when crystal structures are unavailable. The approach has yielded insights into the electronic structures of these iron-sulfur proteins. In rubredoxin, the results show that substantial unpaired electron spin is delocalized across NH...S hydrogen bonds and that the reduction potential can be changed by 77 mV simply by altering the strength of one of these hydrogen bonds. In reduced [2Fe-2S] ferredoxins, hyperfine shift data have provided quantitative information on the degree of valence trapping. The approach described here for iron-sulfur proteins offers new avenues for detailed studies of these and other metalloprotein systems.     

Mixing apparatus for preparing NMR samples under pressure

The size limit for protein NMR spectroscopy in solution arises in large part from line broadening caused by slow molecular tumbling. One way to alleviate this problem is to increase the effective tumbling rate by reducing the viscosity of the solvent. Because proteins generally require an aqueous environment to remain folded, one approach has been to encapsulate hydrated proteins in reverse micelles formed by a detergent and to dissolve the encapsulated protein in a low-viscosity fluid. The high volatility of suitable low-viscosity fluids requires that the samples be prepared and maintained under pressure. We describe a novel apparatus used for the preparation of such samples. The apparatus includes a chamber for mixing the detergent with the low-viscosity solvent, a second chamber for mixing this with hydrated protein, and a 5-mm (o.d.) zirconium oxide NMR sample tube with shut-off valves designed to contain pressures on the order of 10 bar, sufficient for liquid propane. Liquids are moved from one location to another by introducing minor pressure differentials between two pressurization vessels. We discuss the operation of this apparatus and illustrate this with data on a 30-kDa protein complex (chymotrypsin:turkey ovomucoid third domain) encapsulated in reverse micelles of the detergent, sodium bis (2-ethylhexyl) sulfosuccinate, aerosol-ot (AOT), dissolved in liquid propane.