Cross-strand disulfides in the hydrogen bonding site of antiparallel ß-sheet (aCSDhs): Forbidden disulfides that are highly strained, easily broken.

Some disulfide bonds perform important structural roles in proteins, but another group has functional roles via redox reactions. Forbidden disulfides are stressed disulfides found in recognizable protein contexts, which currently constitute more than 10% of all disulfides in the PDB. They likely have functional redox roles and constitute a major subset of all redox-active disulfides. The torsional strain of forbidden disulfides is typically higher than for structural disulfides, but not so high as to render them immediately susceptible to reduction under physionormal conditions. Previously we characterized the most abundant forbidden disulfide in the Protein Data Bank, the aCSDn: a canonical motif in which disulfide-bonded cysteine residues are positioned directly opposite each other on adjacent anti-parallel ß-strands such that the backbone hydrogen-bonded moieties are directed away from each other. Here we perform a similar analysis for the aCSDh, a less common motif in which the opposed cysteine residues are backbone hydrogen bonded. Oxidation of two Cys in this context places significant strain on the protein system, with the ß-chains tilting toward each other to allow disulfide formation. Only left-handed aCSDh conformations are compatible with the inherent right-handed twist of ß-sheets. aCSDhs tend to be more highly strained than aCSDns, particularly when both hydrogen bonds are formed. We discuss characterized roles of aCSDh motifs in proteins of the dataset, which include catalytic disulfides in ribonucleotide reductase and ahpC peroxidase as well as a redox-active disulfide in P1 lysozyme, involved in a major conformation change. The dataset also includes many binding proteins.

Probing the correlation between insulin activity and structural stability through introduction of the rigid A6-A11 bond.

The development of fast-acting and highly stable insulin analogues is challenging. Insulin undergoes structural transitions essential for binding and activation of the insulin receptor (IR), but these conformational changes can also affect insulin stability. Previously, we substituted the insulin A6-A11 cystine with a rigid, non-reducible C=C linkage ("dicarba" linkage). A cis-alkene permitted the conformational flexibility of the A-chain N-terminal helix necessary for high-affinity IR binding, resulting in surprisingly rapid activity in vivo Here, we show that, unlike the rapidly acting LysB28ProB29 insulin analogue (KP insulin), cis-dicarba insulin is not inherently monomeric. We also show that cis-dicarba KP insulin lowers blood glucose levels even more rapidly than KP insulin, suggesting that an inability to oligomerize is not responsible for the observed rapid activity onset of cis-dicarba analogues. Although rapid-acting, neither dicarba species is stable, as assessed by fibrillation and thermodynamics assays. MALDI analyses and molecular dynamics simulations of cis-dicarba insulin revealed a previously unidentified role of the A6-A11 linkage in insulin conformational dynamics. By controlling the conformational flexibility of the insulin B-chain helix, this linkage affects overall insulin structural stability. This effect is independent of its regulation of the A-chain N-terminal helix flexibility necessary for IR engagement. We conclude that high-affinity IR binding, rapid in vivo activity, and insulin stability can be regulated by the specific conformational arrangement of the A6-A11 linkage. This detailed understanding of insulin's structural dynamics may aid in the future design of rapid-acting insulin analogues with improved stability.

Insulin in motion: The A6-A11 disulfide bond allosterically modulates structural transitions required for insulin activity.

The structural transitions required for insulin to activate its receptor and initiate regulation of glucose homeostasis are only partly understood. Here, using ring-closing metathesis, we substitute the A6-A11 disulfide bond of insulin with a rigid, non-reducible dicarba linkage, yielding two distinct stereo-isomers (cis and trans). Remarkably, only the cis isomer displays full insulin potency, rapidly lowering blood glucose in mice (even under insulin-resistant conditions). It also posseses reduced mitogenic activity in vitro. Further biophysical, crystallographic and molecular-dynamics analyses reveal that the A6-A11 bond configuration directly affects the conformational flexibility of insulin A-chain N-terminal helix, dictating insulin's ability to engage its receptor. We reveal that in native insulin, contraction of the Cα-Cα distance of the flexible A6-A11 cystine allows the A-chain N-terminal helix to unwind to a conformation that allows receptor engagement. This motion is also permitted in the cis isomer, with its shorter Cα-Cα distance, but prevented in the extended trans analogue. These findings thus illuminate for the first time the allosteric role of the A6-A11 bond in mediating the transition of the hormone to an active conformation, significantly advancing our understanding of insulin action and opening up new avenues for the design of improved therapeutic analogues.

Mechanical Stretching-Induced Electron-Transfer Reactions and Conductance Switching in Single Molecules.

A central idea in electron-transfer theories is the coupling of the electronic state of a molecule to its structure. Here we show experimentally that fine changes to molecular structures by mechanically stretching a single metal complex molecule via changing the metal-ligand bond length can shift its electronic energy levels and predictably guide electron-transfer reactions, leading to the changes in redox state. We monitor the redox state of the molecule by tracking its characteristic conductance, determine the shift in the redox potential due to mechanical stretching of the metal-ligand bond, and perform model calculations to provide insights into the observations. The work reveals that a mechanical force can shift the redox potential of a molecule, change its redox state, and thus allow the manipulation of single molecule conductance.

Modeling Flexible Molecules in Solution: A pKa Case Study.

Continuum solvation models have been incredibly successful for the computationally efficient study of chemical reactions in solution. However, their development and application has generally been on focused on investigations of small, rigid molecules. Additional factors must be considered when studying large, flexible and multiply ionizable species. These include whether the use of thermocycle or entirely solution-phase approaches are more appropriate for the calculation of solution-phase free energies, which metrics can be used to reliably identify the conformation(s) adopted by flexible molecules in solution, and how errors due to inaccuracies in the prediction of low energy vibrational frequencies can be avoided. Here we explore these issues using the calculation of pKas for a diverse set of amine-containing species as a case study. We show that thermocycle-based approaches should only be applied where there are relatively small structural changes between the gas- and solution-phase molecular geometries, and that these methods are generally not appropriate for conformational searching. Using gas- or solution-phase energies or gas-phase free energies can also lead to errors in the identification of the most stable molecular conformation(s). Scaling of low energy vibrational modes (i.e., use of the quasi-harmonic oscillator approximation) is helpful, however care must be taken to ensure modes that change as part of the reaction are not disregarded. Entirely solution-phase approaches to the Gibbs free energy and hence pKa calculations were found to yield accurate pKa values for the amine test set studied when each charged site is complexed with an explicit water molecule and a proton exchange scheme is applied with an appropriately chosen reference acid.

Electrostatic catalysis of a Diels-Alder reaction.

It is often thought that the ability to control reaction rates with an applied electrical potential gradient is unique to redox systems. However, recent theoretical studies suggest that oriented electric fields could affect the outcomes of a range of chemical reactions, regardless of whether a redox system is involved. This possibility arises because many formally covalent species can be stabilized via minor charge-separated resonance contributors. When an applied electric field is aligned in such a way as to electrostatically stabilize one of these minor forms, the degree of resonance increases, resulting in the overall stabilization of the molecule or transition state. This means that it should be possible to manipulate the kinetics and thermodynamics of non-redox processes using an external electric field, as long as the orientation of the approaching reactants with respect to the field stimulus can be controlled. Here, we provide experimental evidence that the formation of carbon-carbon bonds is accelerated by an electric field. We have designed a surface model system to probe the Diels-Alder reaction, and coupled it with a scanning tunnelling microscopy break-junction approach. This technique, performed at the single-molecule level, is perfectly suited to deliver an electric-field stimulus across approaching reactants. We find a fivefold increase in the frequency of formation of single-molecule junctions, resulting from the reaction that occurs when the electric field is present and aligned so as to favour electron flow from the dienophile to the diene. Our results are qualitatively consistent with those predicted by quantum-chemical calculations in a theoretical model of this system, and herald a new approach to chemical catalysis.

Quantitative Analysis of Step-Growth Polymers by Size Exclusion Chromatography.

We report an advanced analysis protocol that allows to quantitatively study the course of step-growth reactions by size exclusion chromatography on the example of the depolymerization of a Diels-Alder polymer based on a furane/maleimide couple at elevated temperatures. Frequently occurring issues of molar mass calibrations and overlap of monomer with solvent signals are addressed for determining reliable molar masses. Thereby, even kinetic parameters (e.g., rate coefficients) can be derived that otherwise would require performing additional spectroscopic experiments. Our results confirm first-order behavior of the rDA reaction with an activation energy of 33 kJ mol-1.

Design of Redox/Radical Sensing Molecules via Nitrile Imine-Mediated Tetrazole-ene Cycloaddition (NITEC).

The current study introduces a novel synthetic avenue for the preparation of profluorescent nitroxides via nitrile imine-mediated tetrazole-ene cycloaddition (NITEC). The photoinduced cycloaddition was performed under metal-free, mild conditions allowing the preparation of a library of the nitroxide functionalized pyrazolines and corresponding methoxyamines. High reaction rates and full conversion were observed, with the presence of the nitroxide having no significant impact on the cycloaddition performance. The formed products were investigated with respect to their photophysical properties in order to quantify their "switch on/off" behavior. The fluorescence quenching performance is strongly dependent on the distance between the chromophore and the free radical spin as demonstrated theoretically and experimentally. Highest levels of fluorescence quenching were achieved for pyrazolines with the nitroxide directly fused to the chromophore. Importantly, the pyrazoline profluorescent nitroxides were shown to efficiently act as sensors for redox/radical processes.

Potential role of glutathione in evolution of thiol-based redox signaling sites in proteins.

Cysteine is susceptible to a variety of modifications by reactive oxygen and nitrogen oxide species, including glutathionylation; and when two cysteines are involved, disulfide formation. Glutathione-cysteine adducts may be removed from proteins by glutaredoxin, whereas disulfides may be reduced by thioredoxin. Glutaredoxin is homologous to the disulfide-reducing thioredoxin and shares similar binding modes of the protein substrate. The evolution of these systems is not well characterized. When a single Cys is present in a protein, conjugation of the redox buffer glutathione may induce conformational changes, resulting in a simple redox switch that effects a signaling cascade. If a second cysteine is introduced into the sequence, the potential for disulfide formation exists. In favorable protein contexts, a bistable redox switch may be formed. Because of glutaredoxin's similarities to thioredoxin, the mutated protein may be immediately exapted into the thioredoxin-dependent redox cycle upon addition of the second cysteine. Here we searched for examples of protein substrates where the number of redox-active cysteine residues has changed throughout evolution. We focused on cross-strand disulfides (CSDs), the most common type of forbidden disulfide. We searched for proteins where the CSD is present, absent and also found as a single cysteine in protein orthologs. Three different proteins were selected for detailed study-CD4, ERO1, and AKT. We created phylogenetic trees, examining when the CSD residues were mutated during protein evolution. We posit that the primordial cysteine is likely to be the cysteine of the CSD which undergoes nucleophilic attack by thioredoxin. Thus, a redox-active disulfide may be introduced into a protein structure by stepwise mutation of two residues in the native sequence to Cys. By extension, evolutionary acquisition of structural disulfides in proteins can potentially occur via transition through a redox-active disulfide state.

Decoloration rates of a photomerocyanine dye as a visual probe into hydrogen bonding interactions.

We have developed a visual marker for the investigation of hydrogen bonding (HB) effects. The decoloration rate of a photochromic dye that incorporates a latent intra-molecular HB feature can be linked to the HB character of the media. Kinetic and thermodynamic parameters of this simple decoloration approach for HB sensing are investigated both experimentally and by high level theoretical studies. This principle has been applied for the detection of changes in the HB character of stationary and fluidic systems. A major finding is the observation of a shear-related perturbation of the balance between intra- and inter-molecular HB within a dynamic thin film.

The effect of leaving radical on the formation of tetrahydroselenophene by SHi ring closure: an experimental and computational study.

Competition kinetic studies augmented with laser-flash photolysis and high-level computational techniques [G3(MP2)-RAD], with [COSMO-RS, SMD] and without solvent correction, provide kinetic parameters for the ring closures of a series of 4-(alkylseleno)butyl radicals 1. At 22 °C rate constants (kc) that lie between 10(4)-10(7) s(-1) were determined experimentally and correlate with expectations based on leaving group ability. Activation energies (Eact) were determined to lie between 10.6 (R = Ph2CH) and 28.0 (R = n-Bu) kJ mol(-1), while log(A/s(-1)) values were generally between 9 and 10 in benzene. Computationally determined rate constants were in good-to-excellent agreement with those determined experimentally, with the COSMO-RS solvation model providing values that more closely resemble those from experiment than SMD.

Role of water in the dynamic disproportionation of Zn-based TCNQ(F4) coordination polymers (TCNQ = tetracyanoquinodimethane).

Intriguingly, coordination polymers containing TCNQ(2­) and TCNQF4(2­) (TCNQ = 7,7,8,8-tetracyanoquinodimethane, TCNQF4 = 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane, both designated as TCNQ(F4)(2­)) may be generated from reaction of metal ions with TCNQ(F4)•­. An explanation is now provided in terms of a solvent-dependent dynamic disproportionation reaction. A systematic study of reactions associated with TCNQ(F4) and electrochemically generated TCNQ(F4)MeCN•­ and TCNQ(F4)MeCN(2­) revealed that disproportionation of TCNQ(F4)MeCN•­ radical anions in acetonitrile containing a low concentration of water is facilitated by the presence of ZnMeCN(2+). Thus, while the disproportionation reaction 2TCNQ(F4)MeCN•­ TCNQ(F4)MeCN + TCNQ(F4)MeCN(2­) is thermodynamically very unfavorable in this medium (Keq ≈ 9 × 10(­10); TCNQF4), the preferential precipitation of ZnTCNQ(F4)(s) drives the reaction: ZnMeCN(2+) + 2 TCNQ(F4)MeCN•­ ZnTCNQ(F4)(s) + TCNQ(F4)MeCN. The concomitant formation of soluble TCNQ(F4)MeCN and insoluble ZnTCNQ(F4)(s) and the loss of TCNQ(F4)MeCN•­ were verified by UV­visible and infrared spectroscopy and steady-state voltammetry. Importantly, the reverse reaction of comproportionation rather than disproportionation becomes the favored process in the presence of ≥3% (v/v) water, due to the increased solubility of solid ZnTCNQ(F4)(s). Thus, in this "wet" environment, ZnMeCN(2+) and TCNQ(F4)MeCN•­ are produced from a mixture of ZnTCNQ(F4)(s) and TCNQ(F4)MeCN and with the addition of water provides a medium for synthesis of [Zn(TCNQ(F4))2(H2O)2]. An important conclusion from this work is that the redox level of TCNQ(F4)-based materials, synthesized from a mixture of metal cations and TCNQ(F4)•­, is controlled by a solvent-dependent disproportionation/comproportionation reaction that may be tuned to favor formation of solids containing the monoanion radical, the dianion, or even a mixture of both.

Thiol-based redox signalling: rust never sleeps.

Cysteine residues in proteins are covalently modified under conditions of oxidative and nitrosative stress by oxidation, nitrosation, glutathionylation and disulfide formation. Modifications induce conformational changes in substrate proteins, effecting signal cascades that evoke a biological response. A growing number of structures with modified cysteines are allowing a piecemeal understanding of the mechanistic aspects of these signalling pathways to emerge. Conformational changes upon conjugation of nitric oxide and glutathione are generally small and often accompanied by a local increase in protein disorder. Burial of nitric oxide is also apparent, which may increase the timeframe of signalling. Conformational changes upon disulfide formation/reduction range from the small to the spectacular. They include order/disorder transitions; oxidation of disulfides following expulsion of metals such as Zn; major reorganisation or "morphing" of portions of the polypeptide backbone; and changes in quaternary structure including domain swapping.

Disulfides as redox switches: from molecular mechanisms to functional significance.

The molecular mechanisms underlying thiol-based redox control are poorly defined. Disulfide bonds between Cys residues are commonly thought to confer extra rigidity and stability to their resident protein, forming a type of proteinaceous spot weld. Redox biologists have been redefining the role of disulfides over the last 30-40 years. Disulfides are now known to form in the cytosol under conditions of oxidative stress. Isomerization of extracellular disulfides is also emerging as an important regulator of protein function. The current paradigm is that the disulfide proteome consists of two subproteomes: a structural group and a redox-sensitive group. The redox-sensitive group is less stable and often associated with regions of stress in protein structures. Some characterized redox-active disulfides are the helical CXXC motif, often associated with thioredoxin-fold proteins; and forbidden disulfides, a group of metastable disulfides that disobey elucidated rules of protein stereochemistry. Here we discuss the role of redox-active disulfides as switches in proteins.

Conformational changes in redox pairs of protein structures.

Disulfides are conventionally viewed as structurally stabilizing elements in proteins but emerging evidence suggests two disulfide subproteomes exist. One group mediates the well known role of structural stabilization. A second redox-active group are best known for their catalytic functions but are increasingly being recognized for their roles in regulation of protein function. Redox-active disulfides are, by their very nature, more susceptible to reduction than structural disulfides; and conversely, the Cys pairs that form them are more susceptible to oxidation. In this study, we searched for potentially redox-active Cys Pairs by scanning the Protein Data Bank for structures of proteins in alternate redox states. The PDB contains over 1134 unique redox pairs of proteins, many of which exhibit conformational differences between alternate redox states. Several classes of structural changes were observed, proteins that exhibit: disulfide oxidation following expulsion of metals such as zinc; major reorganisation of the polypeptide backbone in association with disulfide redox-activity; order/disorder transitions; and changes in quaternary structure. Based on evidence gathered supporting disulfide redox activity, we propose disulfides present in alternate redox states are likely to have physiologically relevant redox activity.

High torsional energy disulfides: relationship between cross-strand disulfides and right-handed staples.

Redox-active disulfides are capable of being oxidized and reduced under physiological conditions. The enzymatic role of redox-active disulfides in thiol-disulfide reductases is well-known, but redox-active disulfides are also present in non-enzymatic protein structures where they may act as switches of protein function. Here, we examine disulfides linking adjacent beta-strands (cross-strand disulfides), which have been reported to be redox-active. Our previous work has established that these cross-strand disulfides have high torsional energies, a quantity likely to be related to the ease with which the disulfide is reduced. We examine the relationship between conformations of disulfides and their location in protein secondary structures. By identifying the overlap between cross-strand disulfides and various conformations, we wish to address whether the high torsional energy of a cross-strand disulfide is sufficient to confer redox activity or whether other factors, such as the presence of the cross-strand disulfide in a strained beta-sheet, are required.

Structures and thermochemistry of calcium-containing molecules.

A variety of theoretical procedures, including the high-level ab initio methods G3, G3[CC](dir,full), and W2C//ACQ, have been used to predict the structures and heats of formation of several small calcium-containing molecules (CaH, CaH2, CaO, CaOH, Ca(OH)2, CaF, CaF2, CaS, CaCl, and CaCl2). B3-LYP and CCSD(T) with both the (aug-)cc-pWCVQZ and (aug-)cc-pWCVQ+dZ basis sets are found to give molecular geometries that agree well with the experimental results. The CCSD(T)(riv)/(aug-)cc-pWCVQ+dZ results are found to be the most accurate, with a mean absolute deviation from experiment of just 0.008 angstroms. Zero-point vibrational energies (ZPVEs) and thermochemical corrections are found to be relatively insensitive to the level of theory, except in the case of molecules with highly anharmonic calcium-centered bending modes (CaH2, Ca(OH)2, CaF2, CaCl2), where special procedures need to be employed in order to obtain satisfactory results. Several potential improvements to the W2C method were investigated, most of which do not produce significant changes in the heats of formation. It was observed, however, that for CaO and CaS the scalar relativistic corrections are unexpectedly large and highly basis set dependent. In these cases, Douglas-Kroll CCSD(T)/(aug-)cc-pWCV5Z calculations appear to give a converged result. The G3[CC](dir,full) and best W2C-type heats of formation are both found generally to agree well with experimental values recommended in recent critical compendia. However, in some cases (CaO, Ca(OH)2, and CaF2), they differ from one another by more than their predicted error margins. The available experimental data are not sufficiently precise to distinguish definitively between the two sets of results although, in general, when discrepancies exist the W2C heats of formation are lower in energy and tend to be in better agreement with experiment. In the case of CaO, the W2C heat of formation (20.7 kJ mol(-1)) is approximately 20 kJ mol(-1) lower than the G3[CC](dir, full) result and most of the experimental data. Extensive investigation of possible refinements of the W2C method has failed to reveal any weaknesses that could account for this discrepancy. We therefore believe that the heat of formation of CaO is likely to lie closer to the more recent direct experimental determination of 27 kJ mol(-1) than to the value of approximately 40 kJ mol(-1) recommended in recent thermochemical reviews.