Backbone chemical shift assignments for Xanthomonas campestris peroxiredoxin Q in the reduced and oxidized states: a dramatic change in backbone dynamics

Native state fluctuations in a peroxiredoxin active site match motions needed for catalysis

Peroxiredoxins are ubiquitous enzymes that detoxify peroxides and regulate redox signaling. During catalysis, a "peroxidatic" cysteine (C_P) in the conserved active site reduces peroxide while being oxidized to a C_P-sulfenate, prompting a local unfolding event that enables formation of a disulfide with a second, "resolving" cysteine. Here, we use nuclear magnetic resonance spectroscopy to probe the dynamics of the C_P-thiolate and disulfide forms of Xanthomonas campestris peroxiredoxin Q. Chemical exchange saturation transfer behavior of the resting enzyme reveals 26 residues in and around the active site exchanging at a rate of 72 s^-1 with a locally unfolded, high-energy (2.5% of the population) state. This unequivocally establishes that a catalytically relevant local unfolding equilibrium exists in the enzyme's C_P-thiolate form. Also, faster motions imply an active site instability that could promote local unfolding and, based on other work, be exacerbated by C_P-sulfenate formation so as to direct the enzyme along a functional catalytic trajectory.

Peroxiredoxins wear many hats: Factors that fashion their peroxide sensing personalities

Peroxiredoxins (Prdxs) sense and assess peroxide levels, and signal through protein interactions. Understanding the role of the multiple structural and post-translational modification (PTM) layers that tunes the peroxiredoxin specificities is still a challenge. In this review, we give a tabulated overview on what is known about human and bacterial peroxiredoxins with a focus on structure, PTMs, and protein-protein interactions. Armed with numerous cellular and atomic level experimental techniques, we look at the future and ask ourselves what is still needed to give us a clearer view on the cellular operating power of Prdxs in both stress and non-stress conditions.

Controls of nature: Secondary, tertiary, and quaternary structure of the enamel protein amelogenin in solution and on hydroxyapatite

Amelogenin, a protein critical to enamel formation, is presented as a model for understanding how the structure of biomineralization proteins orchestrate biomineral formation. Amelogenin is the predominant biomineralization protein in the early stages of enamel formation and contributes to the controlled formation of hydroxyapatite (HAP) enamel crystals. The resulting enamel mineral is one of the hardest tissues in the human body and one of the hardest biominerals in nature. Structural studies have been hindered by the lack of techniques to evaluate surface adsorbed proteins and by amelogenin's disposition to self-assemble. Recent advancements in solution and solid state nuclear magnetic resonance (NMR) spectroscopy, atomic force microscopy (AFM), and recombinant isotope labeling strategies are now enabling detailed structural studies. These recent studies, coupled with insights from techniques such as CD and IR spectroscopy and computational methodologies, are contributing to important advancements in our structural understanding of amelogenesis. In this review we focus on recent advances in solution and solid state NMR spectroscopy and in situ AFM that reveal new insights into the secondary, tertiary, and quaternary structure of amelogenin by itself and in contact with HAP. These studies have increased our understanding of the interface between amelogenin and HAP and how amelogenin controls enamel formation.

A Novel Thioredoxin-Dependent Peroxiredoxin (TPx-Q) Plays an Important Role in Defense Against Oxidative Stress and Is a Possible Drug Target in Babesia microti

Thioredoxin peroxidases (TPxs) are ubiquitous cysteine-based peroxidases that reduce peroxides as part of antioxidant defenses and redox signaling and are essential for Babesia microti protection against adverse environment agents like reactive oxygen species (ROS) and reactive nitrogen species (RNS). To better systematically understand TPxs, we identified a novel 2-Cys peroxiredoxin-Q (BmTPx-Q) of B. microti. The full-length BmTPx-Q gene is 653 bp that consists of an intact open reading frame of 594 bp that encodes a 197-amino acid protein. The predicted protein has a molecular weight of 22.3 kDa and an isoelectric point of 9.18. Moreover, BmTPx-Q showed low identity at the amino acid level to other peroxiredoxins (Prxs) among the currently known subfamilies. The recombinant BmTPx-Q protein (rBmTPx-Q) was expressed in Escherichia coli and purified with beads. The native protein BmTPx-Q was detected using mouse anti-BmTPx-Q polyclonal serum with western blotting and indirect immunofluorescence assay (IFA). In addition, enzyme activity was observed using nicotinamide adenine dinucleotide phosphate (NADPH) as substrate and triggered the NADPH-dependent reduction of the Trx/TrxR system. It was also discovered that BmTPx-Q mainly exists as a monomer whether under its native or functional states. In addition, when incubated with Chloroquine diphosphate salt for 24 h in vitro, the expression of BmTPx-Q showed a marked downward trend with the increase of drug concentration. These results suggest that B. microti uses BmTPx-Q to reduce and detoxify hydrogen peroxides to survive and proliferate inside the host. Furthermore, BmTPx-Q showed the lowest identity with host enzymes and could be a potential drug target for the development of novel strategies to control B. microti infection.

Solution structure for an Encephalitozoon cuniculi adrenodoxin-like protein in the oxidized state

Encephalitozoon cuniculi is a unicellular, obligate intracellular eukaryotic parasite in the Microsporidia family and one of the agents responsible for microsporidosis infections in humans. Like most Microsporidia, the genome of E. cuniculi is markedly reduced and the organism contains mitochondria-like organelles called mitosomes instead of mitochondria. Here we report the solution NMR structure for a protein physically associated with mitosome-like organelles in E. cuniculi, the 128-residue, adrenodoxin-like protein Ec-Adx (UniProt ID Q8SV19) in the [2Fe-2S] ferredoxin superfamily. Oxidized Ec-Adx contains a mixed four-strand β-sheet, β2-β1-β4-β3 (↓↑↑↓), loosely encircled by three α-helices and two 3₁₀ -helices. This fold is similar to the structure observed in other adrenodoxin and adrenodoxin-like proteins except for the absence of a fifth anti-parallel β-strand next to β3 and the position of α3. Cross peaks are missing or cannot be unambiguously assigned for 20 amide resonances in the ¹ H-¹⁵ N HSQC spectrum of Ec-Adx. These missing residues are clustered primarily in two regions, G48-V61 and L94-L98, containing the four cysteine residues predicted to ligate the paramagnetic [2Fe-2S] cluster. Missing amide resonances in ¹ H-¹⁵ N HSQC spectra are detrimental to NMR-based solution structure calculations because ¹ H-¹ H NOE restraints are absent (glass half-empty) and this may account for the absent β-strand (β5) and the position of α3 in oxidized Ec-Adx. On the other hand, the missing amide resonances unambiguously identify the presence, and immediate environment, of the paramagnetic [2Fe-2S] cluster in oxidized Ec-Adx (glass half-full).

Exploring the conformational transition between the fully folded and locally unfolded substates of Escherichia coli thiol peroxidase

Temporal acquisition of the fully folded conformational substate of the Escherichia coli thiol peroxidase by accelerated molecular dynamics simulations.

Solution NMR structures of oxidized and reduced Ehrlichia chaffeensis thioredoxin: NMR-invisible structure owing to backbone dynamics

Thioredoxins are small ubiquitous proteins that participate in a diverse variety of redox reactions via the reversible oxidation of two cysteine thiol groups in a structurally conserved active site. Here, the NMR solution structures of a reduced and oxidized thioredoxin from Ehrlichia chaffeensis (Ec-Trx, ECH_0218), the etiological agent responsible for human monocytic ehrlichiosis, are described. The overall topology of the calculated structures is similar in both redox states and is similar to those of other thioredoxins: a five-stranded, mixed β-sheet (β1-β3-β2-β4-β5) surrounded by four α-helices. Unlike other thioredoxins studied by NMR in both redox states, the 1H-15N HSQC spectrum of reduced Ec-Trx was missing eight additional amide cross peaks relative to the spectrum of oxidized Ec-Trx. These missing amides correspond to residues Cys35-Glu39 in the active-site-containing helix (α2) and Ser72-Ile75 in a loop near the active site, and suggest a change in backbone dynamics on the millisecond-to-microsecond timescale associated with the breakage of an intramolecular Cys32-Cys35 disulfide bond in a thioredoxin. A consequence of the missing amide resonances is the absence of observable or unambiguous NOEs to provide the distance restraints necessary to define the N-terminal end of the α-helix containing the CPGC active site in the reduced state. This region adopts a well defined α-helical structure in other reported reduced thioredoxin structures, is mostly helical in oxidized Ec-Trx and CD studies of Ec-Trx in both redox states suggests there is no significant difference in the secondary structure of the protein. The NMR solution structure of reduced Ec-Trx illustrates that the absence of canonical structure in a region of a protein may be owing to unfavorable dynamics prohibiting NOE observations or unambiguous NOE assignments.

Backbone chemical shift assignments and secondary structure analysis of the U1 protein from the Bas-Congo virus

The Bas-Congo virus (BASV) is the first rhabdovirus associated with a human outbreak of acute hemorrhagic fever. The single-stranded, negative-sense RNA genome of BASV contains the five core genes present in all rhabdoviral genomes plus an additional three genes, annotated U1, U2, and U3, with weak (<21%) sequence similarity only to a handful of genes observed in a few other rhabdoviral genomes. The function of the rhabdoviral U proteins is unknown, but, they are hypothesized to play a role in viral infection or replication. To better understand this unique family of proteins, a construct containing residues 27-203 of the 216-residue U1 protein (BASV-U1*) was prepared. By collecting data in 0.5 M urea it was possible to eliminate transient association enough to enable the assignment of most of the observable ¹H^N, ¹Hα, ¹⁵N, ¹³Cα, ¹³Cβ, and ¹³C´ chemical shifts for BASV-U1* that will provide a foundation to study its solution properties. The analyses of these chemical shifts along with ¹⁵N-edited NOESY data enabled the identification of the elements of secondary structure present in BASV-U1*.

Peroxiredoxin Catalysis at Atomic Resolution

Peroxiredoxins (Prxs) are ubiquitous cysteine-based peroxidases that guard cells against oxidative damage, are virulence factors for pathogens, and are involved in eukaryotic redox regulatory pathways. We have analyzed catalytically active crystals to capture atomic resolution snapshots of a PrxQ subfamily enzyme (from Xanthomonas campestris) proceeding through thiolate, sulfenate, and sulfinate species. These analyses provide structures of unprecedented accuracy for seeding theoretical studies, and reveal conformational intermediates giving insight into the reaction pathway. Based on a highly non-standard geometry seen for the sulfenate intermediate, we infer that the sulfenate formation itself can strongly promote local unfolding of the active site to enhance productive catalysis. Further, these structures reveal that preventing local unfolding, in this case via crystal contacts, results in facile hyperoxidative inactivation even for Prxs normally resistant to such inactivation. This supports previous proposals that conformation-specific inhibitors may be useful for achieving selective inhibition of Prxs that are drug targets.