Crystal structure of Hsp33 chaperone (TM1394) from Thermotoga maritima at 2.20 Å resolution

Near diffusion-controlled reaction of a Zn(Cys)4 zinc finger with hypochlorous acid

Reaction rate constants of HOCl with zinc-bound cysteines are determined, demonstrating that zinc fingers are potent targets for HOCl and may serve as HOCl sensors.

Hypochlorous acid (HOCl) is one of the strongest oxidants produced in mammals to kill invading microorganisms. The bacterial response to HOCl involves proteins that are able to sense HOCl using methionine, free cysteines or zinc-bound cysteines of zinc finger sites. Although the reactivity of methionine or free cysteine with HOCl is well documented at the molecular level, this is not the case for zinc-bound cysteines. We present here a study that aims at filling this gap. Using a model peptide of the Zn(Cys)₄ zinc finger site of the chaperone Hsp33, a protein involved in the defence against HOCl in bacteria, we show that HOCl oxidation of this model leads to the formation of two disulfides. A detailed mechanistic and kinetic study of this reaction, relying on stopped-flow measurements and competitive oxidation with methionine, reveals very high rate constants: the absolute second-order rate constants for the reaction of the model zinc finger with HOCl and its conjugated base ClO^– are (9.3 ± 0.8) × 10⁸ M^–1 s^–1 and (1.2 ± 0.2) × 10⁴ M^–1 s^–1, the former approaching the diffusion limit. Revised values of the second-order rate constants for the reaction of methionine with HOCl and ClO^– were also determined to be (5.5 ± 0.8) × 10⁸ M^–1 s^–1 and (7 ± 5) × 10² M^–1 s^–1, respectively. At physiological pH, the zinc finger site reacts faster with HOCl than methionine and glutathione or cysteine. This study demonstrates that zinc fingers are potent targets for HOCl and confirms that they may serve as HOCl sensors as proposed for Hsp33.

Theoretical insights into the mechanism of redox switch in heat shock protein Hsp33

Heat shock protein 33 (Hsp33) is activated in the presence of H2O2 by a very interesting redox switch based on a tetra-coordinated zinc-cysteine complex present in the fully reduced and inactive protein form. The oxidation of this zinc center by H2O2 induces formation of two S-S bridges and the zinc release followed by the protein unfolding. We report here a theoretical study of the step-by-step sequence of the overall process starting with the oxidation of the first cysteine residue and ending with the zinc release. Each reaction step is characterized by its Gibbs free energy barrier (∆G (‡)). It is predicted that the first reaction step consists in the oxidation of Cys263 by H2O2 which is by far the most reactive cysteine (∆G (‡) = 15.4 kcal mol(-1)). The next two reaction steps are the formation of the first S-S bridge between Cys263 and Cys266 (∆G (‡) = 13.6 kcal mol(-1)) and the oxidation of Cys231 by H2O2 (∆G (‡) = 20.4 kcal mol(-1)). It is then shown that the formation of the second S-S bridge (Cys231-Cys233) before the zinc release is most unlikely (∆G (‡) = 34.8 kcal mol(-1)). Instead, the release of zinc just after the oxidation of the third cysteine (Cys231) is shown to be thermodynamically (dissociation Gibbs free energy ∆G d = 6.0 kcal mol(-1)) and kinetically (reaction rate constant k d ≈ 10(6) s(-1)) favored. This result is in good agreement with the experimental data on the oxidation mechanism of Hsp33 zinc center available to date.

On the design of zinc-finger models with cyclic peptides bearing a linear tail

Cyclic peptides with a linear tail (CPLT) have been successfully used to model two zinc fingers (ZFs) adopting the treble-clef- and loosened zinc-ribbon folds. In this article, we examine the factors that may influence the design of such ZF models: mutations in the sequence, size of the cycle, and size of the tail. For this purpose, several peptides derived from the CPLT-based models of the treble-clef- and loosened zinc-ribbon ZF were synthesized and studied. CPLT-based models appear to be robust toward mutations, accommodate various cycle sizes, and are sensible to the size of the linking region of the tail located between the cycle and the coordinating amino acids. Based on these criteria, we describe the design of a new CPLT-based model for the zinc-ribbon ZFs, LZR , and compare it to a linear analogue, LZR(lin) . The model complex Zn⋅LZR is able to fold correctly around the metal ion contrary to Zn⋅LZR(lin) , suggesting that CPLT-based models are more likely to yield structurally meaningful models of ZF sites than linear peptide models. Finally, we draw some rules that could allow the design of new CPLT-based metallopeptides with a controlled fold.

The RCSB Protein Data Bank: new resources for research and education

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) develops tools and resources that provide a structural view of biology for research and education. The RCSB PDB web site (http://www.rcsb.org) uses the curated 3D macromolecular data contained in the PDB archive to offer unique methods to access, report and visualize data. Recent activities have focused on improving methods for simple and complex searches of PDB data, creating specialized access to chemical component data and providing domain-based structural alignments. New educational resources are offered at the PDB-101 educational view of the main web site such as Author Profiles that display a researcher’s PDB entries in a timeline. To promote different kinds of access to the RCSB PDB, Web Services have been expanded, and an RCSB PDB Mobile application for the iPhone/iPad has been released. These improvements enable new opportunities for analyzing and understanding structure data.

Crystal structure of constitutively monomeric E. coli Hsp33 mutant with chaperone activity

Heat shock protein 33 (Hsp33) from Escherichia coli is a redox-regulated molecular chaperone that protects cells from oxidative stress. To understand the molecular basis for the monomer-dimer switch in the functional regulation of E. coli Hsp33, we generated a constitutively monomeric Hsp33 by introducing the Q151E mutation in the dimeric interface and determined its crystal structure. The overall scaffold of the monomeric Hsp33(1-235) (Q151E) mutant is virtually the same as that of the dimeric form, except that there is no domain swapping. The measurement of chaperone activity to thermally denatured luciferase showed that the constitutively monomeric Hsp33 mutant still retains chaperone activity similar to that of wild-type Hsp33(1-235), suggesting that a Hsp33 monomer is sufficient to interact with slowly unfolded substrate.

Archease from Pyrococcus abyssi improves substrate specificity and solubility of a tRNA m5C methyltransferase

Members of the archease superfamily of proteins are represented in all three domains of life. Archease genes are generally located adjacent to genes encoding proteins involved in DNA or RNA processing. Archease have therefore been predicted to play a modulator or chaperone role in selected steps of DNA or RNA metabolism, although the roles of archeases remain to be established experimentally. Here we report the function of one of these archeases from the hyperthermophile Pyrococcus abyssi. The corresponding gene (PAB1946) is located in a bicistronic operon immediately upstream from a second open reading frame (PAB1947), which is shown here to encode a tRNA m(5)C methyltransferase. In vitro, the purified recombinant methyltransferase catalyzes m(5)C formation at several cytosines within tRNAs with preference for C49. The specificity of the methyltransferase is increased by the archease. In solution, the archease exists as a monomer, trimer, and hexamer. Only the oligomeric states bind the methyltransferase and prevent its aggregation, in addition to hindering dimerization of the methyltransferase-tRNA complex. This P. abyssi system possibly reflects the general function of archeases in preventing protein aggregation and modulating the function of their accompanying proteins.

Zinc center as redox switch--new function for an old motif

Oxidative stress affects a wide variety of different cellular processes. Now, an increasing number of proteins have been identified that use the presence of reactive oxygen species or alterations in the cellular thiol-disulfide state as regulators of their protein function. This review focuses on two members of this growing group of redox-regulated proteins that utilize a cysteine-containing zinc center as the redox switch: Hsp33, the first molecular chaperone, whose ability to protect cells against stress-induced protein unfolding depends on the presence of reactive oxygen species and RsrA, the first anti-sigma factor that uses a cysteine-containing zinc center to sense and respond to cellular disulfide stress.