Quantitative numerical analysis of g strain in the EPR of distributed systems and its importance for multicenter metalloproteins

A method for simulation of inhomogeneously broadened EPR of metallo-proteins based on recent theoretical advances is surveyed critically in terms of efficiency and accuracy. From the quality of the experimental spectrum, minimal boundary conditions are established for the spatial integration over the g-strained polycrystal. Computational efficiency is achieved by generating the spectrum as an absorption in g space, reducing the number of molecular orientations computed by filtering mosaic artifacts from the Fourier-transformed spectrum, and generating the lineshape due to g strain from a tabulated distribution function. These techniques provide a reduction in computation time by some two orders of magnitude and make the data analysis of EPR of metalloproteins by minimization practical. The resulting simulation program is superior to current approaches in that it does not introduce artifactual multiplicities, and it is expected to require a smaller number of fitting parameters for the quantitative analysis of most cases. To illustrate its potential, the method is applied to EPR data from the iron-sulfur centers in NADH:Q oxidoreductase and in QH2:ferricytochrome c oxidoreductase, clarifying existing controversies on the stoichiometries of these centers.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/25873/1/0000436.pd

Quarter field resonance and integer-spin/half-spin interaction in the EPR of Thermus thermophilus ferrodoxin. Possible new fingerprints for three iron clusters

We describe two new characteristics of the EPR of the seven-iron containing ferrodoxin from Thermus thermophilus. First, the reduced state of the 3Fe center, which has traditionally been considered to be EPR-silent, has been found to exhibit [Delta]m = 4 transition, which is unique for Fe-S centers. This signal is similar to that of high-spin Fe2+-EDTA and supports the suggestion that the ground electronic state of the 3Fe cluster is S = 2. Second, we have recorded the EPR spectrum of the fully reduced protein at 9 and 15 GHz and found that changes occur in the signal which are consistent with a weak electronic spin-spin interaction between the [4Fe-4S]+ (S = 1/2) and the reduced 3Fe center. A theoretical explanation is given for the observation of interaction signals with constant effective g values.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/25700/1/0000254.pd

A statistical theory for powder EPR in distributed systems

A statistical interpretation is presented for "g strain," the dominant broadening in the EPR spectra of metallo-proteins. The direct cause of g strain is described by a three-dimensional tensor p, whose principal elements are random variables. The p and g tensors are not necessarily colinear. The observed EPR linewidth results from a distribution in the effective g value as a function of (a) the joint distribution function of the elements of the p tensor and (b) the spatial relationship between the two principal axis systems involved. The theory is reformulated in terms of matrices that facilitate a direct comparison with earlier work. Two previous theories of g strain represent different subsets of the general theory, namely, the case of zero rotation between axis systems and the case with nonzero rotation and full correlation between elements of the p tensor.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/25870/1/0000433.pd

An investigation of Chromatium vinosum high-potential irondashsulfur protein by EPR and Mossbauer spectroscopy; evidence for a freezing-induced dimerization in NaCl solutions

The high-potential irondashsulfur protein (HiPIP) from Chromatium vinosum contains a cubane prosthetic group that shuttles between the [4Fe-4S]3+,2+ states. We find that the EPR spectra from this protein can be explained as a sum of two components, a major one with g=2.02; 2.04; 2.12, and a minor one with g=2.04; 2.07; ~2.13. In the presence of 0.1-2.0 M NaCl, freezing induces polymerization of the protein (presumably dimers), which is detected as intercluster spindashspin interaction in the EPR. The observed spindashspin interactions are interpreted as being due to two very similar dimeric structures in an approx. 1:2 ratio. Computer simulation of the X- and Q-band EPR spectra shows that the z-components of the g-tensors in each dimer pair must be co-linear, with center-to-center distances between the clusters of ~ 13 A and ~ 16 A. Inspection of possible dimeric structures of C. vinosum HiPIP by standard molecular graphics procedures revealed that the Fe/S cluster is exposed toward a flattened surface and is accessible to solvent. Moreover, the Fe/S clusters in two HiPIP molecules can easily achieve a center-to-center distance of ~ 14 A when approaching along a common 3-fold axis that extends through the S4 sulfur atom of the cubane; the z-component of the EPR g-tensor is co-linear with this symmetry axis.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/29129/1/0000168.pd

EPR analysis of multiple forms of [4Fe–4S] 3+ clusters in HiPIPs

The electron paramagnetic resonance (EPR) spectrum from the [4Fe–4S] 3+ cluster in several high-potential iron–sulfur proteins (HiPIPs) is complex: it is not the pattern of a single, isolated S =1/2 system. Multifrequency EPR from 9 to 130 GHz reveals that the apparent peak positions ( g values) are frequency-independent: the spectrum is dominated by the Zeeman interaction plus g -strain broadening. The spectra taken at frequencies above the X-band are increasingly sensitive to rapid-passage effects; therefore, the X-band data, which are slightly additionally broadened by dipolar interaction, were used for quantitative spectral analysis. For a single geometrical [4Fe–4S] 3+ structure the (Fe–Fe) 5+ mixed-valence dimer can be assigned in six different ways to a pair of iron ions, and this defines six valence isomers. Systematic multicomponent g -strain simulation shows that the [4Fe–4S] 3+ paramagnets in seven HiPIPs from different bacteria each consist of three to four discernible species, and these are assigned to valence isomers of the clusters. This interpretation builds on previous EPR analyzes of [4Fe–4S] 3+ model compounds, and it constitutes a high-resolution extension of the current literature model, proposed from paramagnetic NMR studies.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47867/1/775_2005_Article_656.pd

The Isl1/Ldb1 complex orchestrates heart-specific chromatin organization and transcriptional regulation

Cardiac stem/progenitor cells hold great potential for regenerative therapies however the mechanisms regulating their expansion and differentiation remain insufficiently defined. Here we show that the multi-adaptor protein Ldb1 is a central regulator of cardiac progenitor cell differentiation and second heart field (SHF) development. Mechanistically, we demonstrate that Ldb1 binds to the key regulator of SHF progenitors Isl1 and protects it from proteasomal degradation. Furthermore, the Isl1/Ldb1 complex promotes long-range promoter-enhancer interactions at the loci of the core cardiac transcription factors Mef2c and Hand2. Chromosome conformation capture followed by sequencing identified surprisingly specific, Ldb1-mediated interactions of the Isl1/Ldb1 responsive Mef2c anterior heart field enhancer with genes which play key roles in cardiac progenitor cell function and cardiovascular development. Importantly, the expression of these genes was downregulated upon Ldb1 depletion and Isl1/Ldb1 haplodeficiency. In conclusion, the Isl1/Ldb1 complex orchestrates a network for heart-specific transcriptional regulation and coordination in three-dimensional space during cardiogenesis

Radical-SAM dependent nucleotide dehydratase (SAND), rectification of the names of an ancient iron-sulfur enzyme using NC-IUBMB recommendations

In 1789, the influential French chemist Antoine-Laurent Lavoisier described his view of science and its langague in his book Traité élémentaire de chimie. According to the Robert Kerr’s translation it states (Lavoisier, 1790): “As ideas are preserved and communicated by means of words, it necessarily follows that we cannot improve the language of any science without at the same time improving the science itself; neither can we, on the other hand, improve a science without improving the language or nomenclature which belongs to it.” This view reminds us of Confucius’s earlier doctrine, the rectification of names (Steinkraus, 1980; Lau, 2000). Confucius believed that rectification of names is imperative. He explained (Steinkraus, 1980; Lau, 2000): “If language is incorrect, then what is said does not concord with what was meant, what is to be done cannot be affected. If what is to be done cannot be affected, then rites and music will not flourish. If rites and music do not flourish, then mutilations and lesser punishments will go astray. And if mutilations and lesser punishments go astray, then the people have nowhere to put hand or foot. Therefore the gentleman uses only such language as is proper for speech, and only speaks of what it would be proper to carry into effect. The gentleman in what he says leaves nothing to mere chance.” Inspired by these views, we make the analogy that the progress of science and the language used to describe it are two entangled electrons. This entanglement highlights the importance of introducing systemic names for enzymes using EC classification and the ever-growing problem of protein names (McDonald and Tipton, 2021). Here, we tackle one specific case of iron-sulfur ([FeS]) enzymes. We show that the language used to describe a conserved [FeS] enzyme of the innate immune system, i.e., viperin or RSAD2, is now inadequate and disentangled from its science. We discuss that the enzyme has cellular functions beyond its antiviral activity and that eukaryotic and prokaryotic enzymes catalyse the same chemical reactions. To prevent bias towards antiviral activity while studying various biochemical activities of the enzyme and using scientifically incorrect terms like “prokaryotic viperins,” we rectify the language describing the enzyme. Based on NC-IUBMB recommendations, we introduce the nomenclature S-adenosylmethionine (SAM) dependent Nucleotide Dehydratase (SAND)