Reactivity Of Cysteine Residues Research Articles

First biphotochromic fluorescent protein moxSAASoti stabilized for oxidizing environment

Biphotochromic proteins simultaneously possess reversible photoswitching (on-to-off) and irreversible photoconversion (green-to-red). High photochemical reactivity of cysteine residues is one of the reasons for the development of “mox”-monomeric and oxidation resistant proteins. Based on site-saturated simultaneous two-point C105 and C117 mutagenesis, we chose C21N/C71G/C105G/C117T/C175A as the moxSAASoti variant. Since its on-to-off photoswitching rate is higher, off-to-on recovery is more complete and photoconversion rates are higher than those of mSAASoti. We analyzed the conformational behavior of the F177 side chain by classical MD simulations. The conformational flexibility of the F177 side chain is mainly responsible for the off-to-on conversion rate changes and can be further utilized as a measure of the conversion rate. Point mutations in mSAASoti mainly affect the pKa values of the red form and off-to-on switching. We demonstrate that the microscopic measure of the observed pKa value is the C–O bond length in the phenyl fragment of the neutral chromophore. According to molecular dynamics simulations with QM/MM potentials, larger C–O bond lengths are found for proteins with larger pKa. This feature can be utilized for prediction of the pKa values of red fluorescent proteins.

Global profiling of phosphorylation-dependent changes in cysteine reactivity.

Proteomics has revealed that the ~20,000 human genes engender a far greater number of proteins, or proteoforms, that are diversified in large part by post-translational modifications (PTMs). How such PTMs affect protein structure and function is an active area of research but remains technically challenging to assess on a proteome-wide scale. Here, we describe a chemical proteomic method to quantitatively relate serine/threonine phosphorylation to changes in the reactivity of cysteine residues, a parameter that can affect the potential for cysteines to be post-translationally modified or engaged by covalent drugs. Leveraging the extensive high-stoichiometry phosphorylation occurring in mitotic cells, we discover numerous cysteines that exhibit phosphorylation-dependent changes in reactivity on diverse proteins enriched in cell cycle regulatory pathways. The discovery of bidirectional changes in cysteine reactivity often occurring in proximity to serine/threonine phosphorylation events points to the broad impact of phosphorylation on the chemical reactivity of proteins and the future potential to create small-molecule probes that differentially target PTM-modified proteoforms.

The Reactivity of Cysteine in Nanopore Confined Environment

Cysteine residues on proteins are vitally important in regulating the catalysis of enzyme, maintaining structure, mediating redox states, providing the metal trafficking and etc. However, the reactivity of cysteine residues is affected by local environment including the residue contacting with the cysteine, oxidative stress and mechanical force, et al. Even though fluorescence and mass spectrometry analysis of reactive cysteine has been employed to better understand the diverse reactivity of cysteine, these methods are usually carried out in non-bionic systems, and difficult to obtain reaction dynamic or environment-dependent information to understand the activation mechanisms of related proteins. Biological nanopore provide a well-defined confined space which can accommodate a single reactant molecule. This spatial alignment of reactant within nanopore biomimics cysteine reactivity in confinement. Herein, a series of cysteine mutated aerolysin nanopore was designed to observe the reversible formation and breaking of disulfide bond between nanopore and model cysteine-contained peptides. We could hardly obtain any reaction events without oxygen. As the gradually increase of oxygen concentration, diverse types of reversible reaction events have been collected. This result help us to understand the influence of oxygen on the reaction pathway and stereoselectivity. In particular, the oxygen-dependent experiment here offered useful dynamic information regarding the aerobic sulfhydryl reaction under physiological conditions.

Gene cloning, characterization, and cytotoxic activity of methionine γ-lyase from Clostridium novyi.

The exploitation of methionine-depleting enzyme methionine γ-lyase (MGL) is a promising strategy against specific cancer cells that are strongly dependent on methionine. To identify MGL from different sources with high catalytic activity and efficient anticancer action, we have expressed and characterized MGL from Clostridium novyi and compared its catalytic efficiency with the previously studied MGL from Citrobacter freundii. The purified recombinant MGL exhibits kcat and kcat /Km for methionine γ-elimination reaction that are 2.4- and 1.36-fold higher than C. freundii enzyme, respectively, whereas absorption, fluorescence, and circular dichroism spectra are very similar, as expected on the basis of 87% sequence identity and high conservation of active site residues. The reactivity of cysteine residues with DTNB and iodoacetamide was investigated as well as the impact of their chemical modification on catalytic activity. This information is relevant because for increasing bioavailability and reducing immunogenity, MGL should be decorated with polyethylene glycol (PEG). It was found that Cys118 is a faster reacting residue, which results in a significant decrease in the γ-elimination activity. Thus, the protection of Cys118 before conjugation with cysteine-reacting PEG represents a valuable strategy to preserve MGL activity. The anticancer action of C. novyi MGL, evaluated in vitro against prostate (PC-3), chronic myelogenous leucemia (K562), and breast (MDA-MB-231 and MCF7) cancer cells, exhibits IC50 of 1.3 UmL-1 , 4.4 UmL-1 , 1.2 UmL-1 , and 3.4 UmL-1 , respectively. A higher cytotoxicity of C. novyi MGL was found against cancer cells with respect to C. freundii MGL, with the exception of PC-3, where a lower cytotoxicity was observed. © 2017 IUBMB Life, 69(9):668-676, 2017.

The oxidized thiol proteome in fission yeast—Optimization of an ICAT-based method to identify H2O2-oxidized proteins

Major intracellular disulfide formation is prevented in the cytosol by potent reducing systems. However, protein thiols can be oxidized as a consequence of redox-mediated physiological reactions or due to the unwanted toxicity of reactive oxygen species. In addition, the reactivity of cysteine residues towards peroxides is used by H(2)O(2) sensors in signal transduction pathways in a gain-of-function process to induce transcriptional antioxidant responses. Thus, the Schizosaccharomyces pombe peroxiredoxin Tpx1 and the transcription factor Pap1 are sensors of H(2)O(2) meant to promote cell survival. In an attempt to compare signaling events versus global thiol oxidation, we have optimized thiol-labeling approaches to characterize the disulfide proteome of fission yeast in response to added H(2)O(2). We propose a method based on (i) freezing the redox state of thiols with strong acids prior to cell lysis; (ii) blocking thiol groups with iodoacetamide, and reversibly oxidized thiols with heavy and light isotope-coded affinity tags (ICAT) reagents; and (iii) quantifying individual relative protein concentrations with stable-isotope dimethyl labeling. We have applied this highly sensitive strategy to provide a map of H(2)O(2)-dependent oxidized thiols in fission yeast, and found Tpx1 and Pap1 as some of the major targets.

Structural Biology by Mass Spectrometry: Mapping Protein Interaction Surfaces of Membrane Receptor Complexes with ICAT

Multi-component protein complexes underlie most high-order cellular functions. Elucidating the structures of these complexes and understanding how the interactions that bind them change under perturbation is a major goal of structural biology. To help in this effort, Underbakke et al provide a new twist on the proteomics technique of isotope coded affinity tagging (ICAT). In proteomics, ICAT allows relative quantification of proteins in comparable samples by reacting their exposed cysteine thiols with alkylating agents that contain either a heavy (13C) or light (12C) isotope and an affinity tag1; 2. One sample/condition is modified with the heavy tag, the other with the light, they are mixed, proteolytically cleaved into peptides, affinity purified and analyzed by mass spectrometry. Relative signals from the two mass tags report on the availability of the cysteine for modification in the two conditions. This availability reflects how much of a given cysteine residue (and its cognate protein) is there to be labeled, or in the present example, how reactive the cysteine residue is under the condition tested. Originally, the tag employed was a biotin moiety1, but this has been adapted to smaller, glucanime-based labels that can be enriched on a boronate matrix3; 4. Silverman and Harbury applied this method to the foot printing of protein accessibility and interaction surfaces4, in a manner that parallels the logic of hydrogen exchange mass spectrometery5. The current report was predicated by the author’s development of new ICAT reagents based on the glucamine backbone that are more water soluble, but have varying degrees of electrophilicity6. By measuring rates of alklyation (not just total amounts of product), the relative reactivity of cysteine residues that were specifically targeted to a protein surface could be better quantified. Here, the authors extend these studies to mapping interactions within the receptor kinase complexes that compose the bacterial chemotaxis transmembrane signaling system. Bacterial chemotaxis relys on polar clusters of transmembrane chemoreceptors coupled to the histidine kinase CheA through an adaptor protein CheW. There is great interest in the detailed architecture of the receptor arrays and how CheA activity is regulated by ligands7. Biochemical protection assays8; 9, genetic studies10; 11; 12; 13 and structural work14; 15 have probed functional interfaces in this ultrastable complex16, making it an ideal subject for testing new mapping techniques. The authors target the CheW coupling protein because it interacts with both CheA and the receptors. By substituting surface residues for cysteine and evaluating ICAT reactivity in the absence and presence of the other components they identify CheA and receptor binding regions of CheW that are largely consistent with the previous studies mentioned above. Unlike the proteomics application, careful work must be done to target the Cys residues appropriately and verify that substitution and subsequent modification does not alter activity; however, the affinity purification is a big advantage in avoiding background labeling in the complex mixture of native bacterial membranes. Importantly, the resolution of the technique is at the residue level, and has the potential to reveal how interactions between the components change subtly as they switch among activity states.

ミトコンドリア内膜のADP/ATP透過担体のC末端領域の構造特性と機能

Mitochondrial ADP/ATP carrier (AAC) is a protein catalyzing the transport of adenine nucleotides across inner mitochondrial membrane. In this review article, we first briefly introduce structural and functional properties of this protein. Next, we describe the results of our recent studies on the difference in the C-terminal region between yeast type 2 AAC isoform and bovine type 1 AAC isoform. Furthermore, based on the reactivities of cysteine residues that replaced amino acids in the sixth transmembrane segment, the probable structural features of the C-terminal region of this carrier are discussed.

Cysteine reactivity and oligomeric structures of phospholamban and its mutants.

To test models for the pentameric structure of phospholamban (PLB) and study its structure and molecular dynamics in SDS solution, we characterized recombinant PLB and several of its mutants by (a) reactivity of cysteine residues toward DTNB [5, 5'-dithiobis(2-nitrobenzoic acid)] and a thiol-reactive spin label, (b) oligomeric state on SDS-PAGE, and (c) EPR of the spin-labeled proteins. WT-PLB has three cysteine residues (36, 41, and 46), all located in the hydrophobic C-terminal transmembrane region. In SDS at pH 7.5, exhaustive reaction with either sulfhydryl reagent resulted in essentially 2 mol of cysteine reacted/mol of WT-PLB, with only slight destabilization of the native pentameric structure. When WT-PLB was denatured in guanidine at pH 8.1, all three cysteines reacted, disrupting the pentamer, which was restored upon cleavage of the disulfide bonds with DTT. In the tetrameric mutant C41L-PLB, the two remaining cysteine residues reacted, reversibly destabilizing the tetramer. In the monomeric mutant L37A-PLB, all three cysteines reacted. The pentameric double cysteine replacement mutant C36,46A-PLB showed negligible reactivity. We conclude that Cys-41 is the unreactive cysteine in PLB and is located at a crucial site for the maintenance of the pentameric structure. EPR spectra in SDS of spin-labeled WT-PLB and mutants correlate with the oligomeric state on SDS-PAGE; oligomeric proteins show decreased spin-label mobility compared with monomers. Molecular dynamics calculations were used to construct an atomic model for the transmembrane region of the PLB pentamer, constrained by previous mutagenesis results and the results of the present study. We conclude that (a) the mobilities of spin-labels attached to PLB and its mutants are sensitive to oligomeric state and (b) the pattern of cysteine reactivity, spin-label mobility, and oligomeric state supports a structural model for the PLB pentamer in which interactions between each pair of subunits are stabilized by a leucine-isoleucine zipper.

Removal of an N-terminal peptide from mitochondrial aspartate aminotransferase abolishes its interactions with mitochondria in vitro.

Treatment of mitochondrial aspartate aminotransferase from rat liver with trypsin leads to specific cleavage of the bonds between residues 26 and 27, and residues 31 and 32. The proteolysed enzyme has only a small residual catalytic activity, but retains a conformation similar to that of the native form as judged by accessibility and reactivity of cysteine residues. Proteolysis abolishes the ability of the enzyme either to bind to mitochondria or to be imported into the organelles. This suggests that the N-terminal segment of the native enzyme is essential for both of these functions, at least in the model system used to study the import process.

Structure and reactivity of cysteine residues in mitochondrial serine hydroxymethyltransferase.

Six cysteine-containing tryptic peptides were isolated and sequenced from rabbit liver mitochondrial serine hydroxymethyltransferase. 2 of the 6 cysteine residues were located on the surface of the enzyme. These 2 cysteine residues are sufficiently close to each other that they form a disulfide bond when oxidized by periodate. Another of the cysteine residues is exposed upon removal of the active site pyridoxal phosphate. The remaining three cysteines are buried and react with sulfhydryl reagents only when the enzyme is denatured. Blocking of one of the surface sulfhydryls with any of several sulfhydryl reagents results in increased catalytic activity when allothreonine is the substrate but decreased activity when serine and tetrahydrofolate are the substrates. The activation and inhibition effects are on Vmax and not on the affinity of the enzyme for its substrates. Of the six cysteine peptides from the mitochondrial enzyme, three show substantial homology with cysteine-containing peptides from the cytosolic form of the enzyme. For both enzyme forms, one of these homologous pairs is a cysteine residue on the surface of the enzyme. These results suggest that the mitochondrial and cytosolic forms of rabbit liver serine hydroxymethyltransferases are the products of separate genes.

Ca2+-induced conformational changes of 20,000 dalton light chain of vertebrate striated muscle myosins.

The 20,000 dalton light chain (L2) was isolated from rabbit and chicken striated muscle myosins, and the Ca2+-induced conformational changes of these proteins were investigated. 1) The reaction of thiol groups of L2 with dithiobisnitrobenzoic acid (DTNB), 2) measurements of the UV difference absorption spectrum, 3) measurements of Stokes radius (Rs) by gel filtration and 4) measurements of the ESR spectrum of L2 whose cysteine or tyrosine residues were spin-labeled were used for the structural studies. The effect of Ca2+ on phosphorylated L2 was also investigated. The long axis of chicken L2 was calculated as 136A from the Stokes radius, suggesting that the L2 is an asymmetrical molecule. After the addition of Ca2+ the long axis was reduced to 104 A. The same effect of Ca2+ has been reported with rabbit L2 (Alexis, N.M. & Gratzer, W.B. (1978) Biochemistry 17, 2319-2325). Besides this large shape change, the addition of Ca2+ to L2 induced environmental changes around tyrosine residues and also changes in the reactivity of cysteine residues with DTNB. Ca2+ is supposed to be bound to the N-terminal region of the molecule, while the tyrosine and cysteine residues are located at the C-terminal region, which is probably sterically remote from the N-terminal region. The reason for the remote effect of Ca2+ may be related to the structural rigidity of the L2 molecule. The functions of two properties of L2, Ca2+-binding and phosphorylation, are discussed in relation to muscle contraction.