Ab Initio and QM/MM Study of Electron Addition on the Disulfide Bond in Thioredoxin

n→π* Interactions Modulate the Properties of Cysteine Residues and Disulfide Bonds in Proteins

Noncovalent interactions are ubiquitous in biology, taking on roles that include stabilizing the conformation of and assembling biomolecules, and providing an optimal environment for enzymatic catalysis. Here, we describe a noncovalent interaction that engages the sulfur atoms of cysteine residues and disulfide bonds in proteins-their donation of electron density into an antibonding orbital of proximal amide carbonyl groups. This n→ π* interaction tunes the reactivity of the CXXC motif, which is the critical feature of thioredoxin and other enzymes involved in redox homeostasis. In particular, an n→ π* interaction lowers the p K_a value of the N-terminal cysteine residue of the motif, which is the nucleophile that initiates catalysis. In addition, the interplay between disulfide n→ π* interactions and C5 hydrogen bonds leads to hyperstable β-strands. Finally, n→ π* interactions stabilize vicinal disulfide bonds, which are naturally diverse in function. These previously unappreciated n→ π* interactions are strong and underlie the ability of cysteine residues and disulfide bonds to engage in the structure and function of proteins.

Simple MD-based model for oxidative folding of peptides and proteins

Significant strides have been recently made to fold peptides and small proteins in silico using MD simulations. However, facilities are currently lacking to include disulfide bonding in the MD models of protein folding. To address this problem, we have developed a simple empirical protocol to model formation of disulfides, which is perturbation-free, retains the same speed as conventional MD simulations and allows one to control the reaction rate. The new protocol has been tested on 15-aminoacid peptide guanylin containing four cysteine residues; the net simulation time using Amber ff14SB force field was 61 μs. The resulting isomer distribution is in qualitative agreement with experiment, suggesting that oxidative folding of guanylin in vitro occurs under kinetic control. The highly stable conformation of the so-called isomer 2(B) has been obtained for full-length guanylin, which is significantly different from the poorly ordered structure of the truncated peptide PDB ID 1GNB. In addition, we have simulated oxidative folding of guanylin within the 94-aminoacid prohormone proguanylin. The obtained structure is in good agreement with the NMR coordinates 1O8R. The proposed modeling strategy can help to explore certain fundamental aspects of protein folding and is potentially relevant for manufacturing of synthetic peptides and recombinant proteins.

Tuning of thioredoxin redox properties by intramolecular hydrogen bonds

Thioredoxin-like proteins contain a characteristic C-x-x-C active site motif and are involved in a large number of biological processes ranging from electron transfer, cellular redox level maintenance, and regulation of cellular processes. The mechanism for deprotonation of the buried C-terminal active site cysteine in thioredoxin, necessary for dissociation of the mixed-disulfide intermediate that occurs under thiol/disulfide mediated electron transfer, is not well understood for all thioredoxin superfamily members. Here we have characterized a 8.7 kD thioredoxin (BC3987) from Bacillus cereus that unlike the typical thioredoxin appears to use the conserved Thr8 side chain near the unusual C-P-P-C active site to increase enzymatic activity by forming a hydrogen bond to the buried cysteine. Our hypothesis is based on biochemical assays and thiolate pKa titrations where the wild type and T8A mutant are compared, phylogenetic analysis of related thioredoxins, and QM/MM calculations with the BC3987 crystal structure as a precursor for modeling of reduced active sites. We suggest that our model applies to other thioredoxin subclasses with similar active site arrangements.

The one-electron reduction potential of methionine-containing peptides depends on the sequence

The protein residue methionine (Met) is one of the main targets of oxidizing free radicals produced in oxidative stress. Despite its biological importance, the mechanism of the oxidation of this residue is still partly unknown. In particular the one-electron redox potentials of the couple Met(•+)/Met have not been measured. In this work, two approaches, experimental as well as theoretical, were applied for three dipeptides L-Met L-Gly, L-Gly L-Met and L-Met L-Met. Measurements by electrochemistry indicated differences in the ease of oxidation. Two DFT methods (BH&HLYP and PBE0) with two basis sets (6-31G(d) and 6-311+G(2d,2p)) were used to determine the redox potentials of Met in these peptides present in different conformations. In agreement with experimental results, we show that they vary with the sequence and the spatial structure of the peptide, most of the values being higher than 1 V (up to 2 V) vs NHE.

Reactions of CH3SH and CH3SSCH3 with gas-phase hydrated radical anions (H2O)n(•-), CO2(•-)(H2O)n, and O2(•-)(H2O)n

The chemistry of (H(2)O)(n)(•-), CO(2)(•-)(H(2)O)(n), and O(2)(•-)(H(2)O)(n) with small sulfur-containing molecules was studied in the gas phase by Fourier transform ion cyclotron resonance mass spectrometry. With hydrated electrons and hydrated carbon dioxide radical anions, two reactions with relevance for biological radiation damage were observed, cleavage of the disulfide bond of CH(3)SSCH(3) and activation of the thiol group of CH(3)SH. No reactions were observed with CH(3)SCH(3). The hydrated superoxide radical anion, usually viewed as major source of oxidative stress, did not react with any of the compounds. Nanocalorimetry and quantum chemical calculations give a consistent picture of the reaction mechanism. The results indicate that the conversion of e(-) and CO(2)(•-) to O(2)(•-) deactivates highly reactive species and may actually reduce oxidative stress. For reactions of (H(2)O)(n)(•-) with CH(3)SH as well as CO(2)(•-)(H(2)O)(n) with CH(3)SSCH(3), the reaction products in the gas phase are different from those reported in the literature from pulse radiolysis studies. This observation is rationalized with the reduced cage effect in reactions of gas-phase clusters.

Mechanical force can fine-tune redox potentials of disulfide bonds

Mechanical force applied along a disulfide bond alters its rate of reduction. We here aimed at quantifying the direct effect of force onto the chemical reactivity of a sulfur-sulfur bond in contrast to indirect, e.g., steric or mechanistic, influences. To this end, we evaluated the dependency of a disulfide bond's redox potential on a pulling force applied along the system. Our QM/MM simulations of cystine as a model system take conformational dynamics and explicit solvation into account and show that redox potentials increase over the whole range of forces probed here (30-3320 pN), and thus even in the absence of a significant disulfide bond elongation (<500 pN). Instead, at low forces, dihedrals and angles, as the softer degrees of freedom are stretched, contribute to the destabilization of the oxidized state. We find physiological forces to be likely to tune the disulfide's redox potentials to an extent similar to the tuning within proteins by point mutations.

X-ray-induced deterioration of disulfide bridges at atomic resolution

Overall and site-specific X-ray-induced damage to porcine pancreatic elastase was studied at atomic resolution at temperatures of 100 and 15 K. The experiments confirmed that irradiation causes small movements of protein domains and bound water molecules in protein crystals. These structural changes occur not only at 100 K but also at temperatures as low as 15 K. An investigation of the deterioration of disulfide bridges demonstrated the following. (i) A decrease in the occupancy of S(γ) atoms and the appearance of new cysteine rotamers occur simultaneously. (ii) The occupancy decrease is observed for all S(γ) atoms, while new rotamers arise for some of the cysteine residues; the appearance of new conformations correlates with the accessibility to solvent. (iii) The sum of the occupancies of the initial and new conformations of a cysteine residue is approximately equal to the occupancy of the second cysteine residue in the bridge. (iv) The most pronounced changes occur at doses below 1.4 × 10(7) Gy, with only small changes occurring at higher doses. Comparison of the radiation-induced changes in an elastase crystal at 100 and 15 K suggested that the dose needed to induce a similar level of deterioration of the disulfide bonds and atomic displacements at 15 K to those seen at 100 K is more than two times higher.

The assessment of density functionals for DNA–protein stacked and T-shaped complexes

The present work uses 129 nucleobase – amino acid CCSD(T)/CBS stacking and T-shaped interaction energies as reference data to test the ability of various density functionals with double-zeta quality basis sets, as well as some semi-empirical and molecular mechanics methods, to accurately describe noncovalent DNA–protein π–π and π+–π interactions. The goal of this work is to identify methods that can be used in hybrid approaches (QM/MM, ONIOM) for large-scale modeling of enzymatic systems involving active-site (substrate) π–π contacts. Our results indicate that AMBER is a more appropriate choice for the lower-level method in hybrid techniques than popular semi-empirical methods (AM1, PM3), and suggest that AMBER accurately describes the π–π interactions found throughout DNA–protein complexes. The M06–2X and PBE-D density functionals were found to provide very promising descriptions of the 129 nucleobase – amino acid interaction energies, which suggests that these may be the most suitable methods for describing high-level regions. Therefore, M06–2X and PBE-D with both the 6–31G(d) and 6–31+G(d,p) basis sets were further examined through potential-energy surface scans to better understand how these techniques describe DNA–protein π–π interactions in both minimum and nonminimum regions of the potential-energy surfaces, which is critical information when modeling enzymatic reaction pathways. Our results suggest that studies of stacked nucleobase – amino acid systems should implement the PBE-D/6–31+G(d,p) method. However, if T-shaped contacts are involved and (or) smaller basis sets must be considered due to limitations in computational resources, then M06–2X/6–31G(d) provides an overall excellent description of both nucleobase – amino acid stacking and T-shaped interactions for a range of DNA–protein π–π and π+–π interactions.

Factors governing electron capture by small disulfide loops in two-cysteine peptides

Integrated molecular orbital-molecular orbital (IMOMO) calculations on 17 short disulfide-bridged peptides (up to 16 residues, with at most five intraloop residues) were performed to elucidate some factors controlling their electron capture. These illustrative systems display contrasted behaviors, shedding light on several criteria of differentiation: size, shape, and rigidity of the disulfide-linking loop, intramolecular hydrogen bonds, etc. The geometrical malleability of disulfide radical anions, whose existence and role as intermediate have been evidenced, is discussed. The disulfide elongation (by ca. 0.7 A) upon electron capture induces "soft" structural damages for these turn structures, with a weakening or cleavage of vicinal hydrogen bond(s). On the basis of a series of six Cys-Alan-Cys peptides, it is proposed that electron affinity reflects the topological frustration of these short and highly constrained structures. Results for a series of amino acid mutations are analyzed for the Cys-Xxx-Yyy-Cys motif, common to redox enzymes of the thioredoxin superfamily.