Chemical Modification Of Cysteine Residues Research Articles

Multimerization of small G-protein H-Ras induced by chemical modification at hyper variable region with caged compound.

The lipid-anchored small G protein Ras is a central regulator of cellular signal transduction processes, thereby functioning as a molecular switch. Ras forms a nanocluster on the plasma membrane by modifying lipids in the hypervariable region (HVR) at the C-terminus to exhibit physiological functions. In this study, we demonstrated that chemical modification of cysteine residues in HVR with caged compounds (instead of lipidation) induces multimerization of H-Ras. The sulfhydryl-reactive caged compound, 2-nitrobenzyl bromide, was stoichiometrically incorporated into the cysteine residue of HVR and induced the formation of the Ras multimer. Light irradiation induced the elimination of the 2-nitrobenzyl group, resulting in the conversion of the multimer to a monomer. Size-exclusion chromatography coupled with high-performance liquid chromatography and small-angle x-ray scattering analysis revealed that H-Ras forms a pentamer. Electron microscopic observation of the multimer showed a circular ring shape, which is consistent with the structure estimated from x-ray scattering. The shape of the multimer may reflect the physiological state of Ras. It was suggested that the multimerization and monomerization of H-Ras were controlled by modification with a caged compound in HVR under light irradiation.

Interrogating permeation and gating of Orai channels using chemical modification of cysteine residues.

Chemical modification of ion channels using the substituted cysteine accessibility method has a rich and successful history in elucidating the structural basis of ion channel function. In this approach, cysteine residues are introduced in regions of interest into the protein and their accessibility to water soluble thiol-reactive reagents is determined by monitoring ion channel activity. Because a wide range of these reagents are available with differing size, charge, and membrane solubility, the physio-chemical environment of the introduced cysteine residue and therefore the protein domain of interest can be probed with great precision. The approach has been widely employed for determining the secondary structure of specific ion channel domains, the location and nature of the channel gate, and the conformational rearrangements in the channel pore that underlie the opening/closing of the pore. In this chapter, we describe the use of these and related approaches to probe the functional architecture and gating of store-operated Orai1 channels.

Isolation of Cysteine-Rich Peptides from Citrullus colocynthis.

The plant Citrullus colocynthis, a member of the squash (Cucurbitaceae) family, has a long history in traditional medicine. Based on the ancient knowledge about the healing properties of herbal preparations, plant-derived small molecules, e.g., salicylic acid, or quinine, have been integral to modern drug discovery. Additionally, many plant families, such as Cucurbitaceae, are known as a rich source for cysteine-rich peptides, which are gaining importance as valuable pharmaceuticals. In this study, we characterized the C. colocynthis peptidome using chemical modification of cysteine residues, and mass shift analysis via matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. We identified the presence of at least 23 cysteine-rich peptides in this plant, and eight novel peptides, named citcol-1 to -8, with a molecular weight between ~3650 and 4160 Da, were purified using reversed-phase high performance liquid chromatography (HPLC), and their amino acid sequences were determined by de novo assignment of b- and y-ion series of proteolytic peptide fragments. In silico analysis of citcol peptides revealed a high sequence similarity to trypsin inhibitor peptides from Cucumis sativus, Momordica cochinchinensis, Momordica macrophylla and Momordica sphaeroidea. Using genome/transcriptome mining it was possible to identify precursor sequences of this peptide family in related Cucurbitaceae species that cluster into trypsin inhibitor and antimicrobial peptides. Based on our analysis, the presence or absence of a crucial Arg/Lys residue at the putative P1 position may be used to classify these common cysteine-rich peptides by functional properties. Despite sequence homology and the common classification into the inhibitor cysteine knot family, these peptides appear to have diverse and additional bioactivities yet to be revealed.

Regioselective Chemical Modification of Cysteine Residues on Protein Surfaces Focusing on Local Environment around the Conjugation Site.

For chemical modification of cysteines in a protein, the regioselectivity among cysteine residues on the protein surface is an issue to be considered. To elucidate the determinants of cysteine reactivities on protein surfaces, we have investigated the chemical modification of the adenylate kinase A55C/C77S/V169C mutant as an experimental model. Although Cys55 and Cys169 are commonly located on the protein surface, Cys55 showed the ca. 3-6-fold higher reactivity compared to Cys169 in a reaction with a pyrene derivative. By a further conjugation of a phenanthroline derivative into the vacant Cys thiol, fluorescence quenching was attained by a pyrene-phenanthroline interaction that occurred by the conformational change of the protein. The K50A mutation further enhanced the regioselectivity of pyrene conjugation in Cys55, which is attributed to the effects of structural flexibility in the vicinity of Cys55 on its reactivity. To regioselectively conjugate different types of synthetic molecules onto the surface of a protein, perturbation in the local structural flexibility around the conjugation sites will be a useful strategy.

The zinc finger domain of RING finger protein 141 reveals a unique RING fold.

Human RING finger protein 141 (RFP141) is a germ cell-specific transcription factor during spermatogenesis. We synthesized a compact construct encoding the C-terminal zinc finger of RFP141 (RFP141C peptide). Herein we determined the solution structure of the RFP141C peptide by nuclear magnetic resonance (NMR). Moreover, NMR data and the chemical modification of cysteine residues demonstrated that the RFP141C peptide binds to two zinc atoms in a cross-brace arrangement. The Simple Modular Architecture Research Tool database predicted the structure of RFP141C as a RING finger. However, the actual structure of the RFP141C peptide adopts an atypical compact C3 HC4 -type RING fold. The position and range of the helical active site of the RFP141C structure were elucidated at the atomic level. Therefore, structural analysis may allow RFP141C to be used for designing an artificial RING finger possessing specific ubiquitin-conjugating enzyme (E2)-binding capabilities.

Diverse functionalization of Aurora-A kinase at specified surface and buried sites by native chemical modification.

The ability to obtain a homogeneous sample of protein is invaluable when studying the effect of alterations such as post-translational modifications (PTMs). Selective functionalization of a protein to investigate the effect of PTMs on its structure or activity can be achieved by chemical modification of cysteine residues. We demonstrate here that one such technique, which involves conversion of cysteine to dehydroalanine followed by thiol nucleophile addition, is suitable for the site-specific installation of a wide range of chemical mimics of PTMs, including acetylated and dimethylated lysine, and other unnatural amino acids. These reactions, optimized for the clinically relevant kinase Aurora-A, readily proceed to completion as revealed by intact protein mass spectrometry. Moreover, these reactions proceed under non-denaturing conditions, which is desirable when working with large protein substrates. We have determined reactivity trends for a diverse range of thiol nucleophile addition reactions at two separate sites on Aurora-A, and we also highlight limitations when using thiol nucleophiles that contain basic functional groups. We show that chemical modification of cysteine residues is possible not only on a flexible surface-exposed loop, but also within a deep active site pocket at the conserved DFG motif, which reveals the potential use of this method in exploring enzyme function through modification of catalytic site residues.

Primary sequence determination of a monoclonal antibody against α-synuclein using a novel mass spectrometry-based approach

A novel mass spectrometry-based workflow for de novo sequencing of a full-length monoclonal antibody (LB509) against α-synuclein is presented. This approach combines chemical modification of cysteine residues, multiple enzymatic digestion, stable isotope labeled amino acids in cell culture (SILAC), liquid chromatography coupled tandem mass spectrometry (LC/MS/MS) analysis including collision-induced dissociation (CID), higher energy collision-induced dissociation (HCD), and de novo sequencing software for data interpretation. The introduction of aminoethyl-8 (A-8) reagent which renders cysteine residues in the antibody to become substrates for trypsin digestion significantly increases the sequence coverage of the antibody, especially in the complementarity determining regions (CDRs). Incorporation of SILAC helps to distinguish minor sequence variations between original and deduced sequences. Methods in obtaining detailed sequence characterization are described, highlighting the advantage of using multiple fragmentation schemes, CID in ion trap and HCD in C-trap. Complete primary sequence for LB509 has been construed and the antibody generated exhibits specific binding to α-synuclein. The development and implementation of this technology enables an alternative approach for generating therapeutic candidate and reagent antibodies.

Protein Modification, Bioconjugation, and Disulfide Bridging Using Bromomaleimides

The maleimide motif is widely used for the selective chemical modification of cysteine residues in proteins. Despite widespread utilization, there are some potential limitations, including the irreversible nature of the reaction and, hence, the modification and the number of attachment positions. We conceived of a new class of maleimide which would address some of these limitations and provide new opportunities for protein modification. We report herein the use of mono- and dibromomaleimides for reversible cysteine modification and illustrate this on the SH2 domain of the Grb2 adaptor protein (L111C). After initial modification of a protein with a bromo- or dibromomaleimide, it is possible to add an equivalent of a second thiol to give further bioconjugation, demonstrating that bromomaleimides offer opportunities for up to three points of attachment. The resultant protein−maleimide products can be cleaved to regenerate the unmodified protein by addition of a phosphine or a large excess of a thiol. Furthermore, dibromomaleimide can insert into a disulfide bond, forming a maleimide bridge, and this is illustrated on the peptide hormone somatostatin. Fluorescein-labeled dibromomaleimide is synthesized and inserted into the disulfide to construct a fluorescent somatostatin analogue. These results highlight the significant potential for this new class of reagents in protein modification.

Succination of Protein Thiols during Adipocyte Maturation

Although obesity is a risk factor for development of type 2 diabetes and chemical modification of proteins by advanced glycoxidation and lipoxidation end products is implicated in the development of diabetic complications, little is known about the chemical modification of proteins in adipocytes or adipose tissue. In this study we show that S-(2-succinyl)cysteine (2SC), the product of chemical modification of proteins by the Krebs cycle intermediate, fumarate, is significantly increased during maturation of 3T3-L1 fibroblasts to adipocytes. Fumarate concentration increased > or =5-fold during adipogenesis in medium containing 30 mm glucose, producing a > or =10-fold increase in 2SC-proteins in adipocytes compared with undifferentiated fibroblasts grown in the same high glucose medium. The elevated glucose concentration in the medium during adipocyte maturation correlated with the increase in 2SC, whereas the concentration of the advanced glycoxidation and lipoxidation end products, N(epsilon)-(carboxymethyl)lysine and N(epsilon)-(carboxyethyl)lysine, was unchanged under these conditions. Adipocyte proteins were separated by one- and two-dimensional electrophoresis and approximately 60 2SC-proteins were detected using an anti-2SC polyclonal antibody. Several of the prominent and well resolved proteins were identified by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry. These include cytoskeletal proteins, enzymes, heat shock and chaperone proteins, regulatory proteins, and a fatty acid-binding protein. We propose that the increase in fumarate and 2SC is the result of mitochondrial stress in the adipocyte during adipogenesis and that 2SC may be a useful biomarker of mitochondrial stress in obesity, insulin resistance, and diabetes.

Regioselective Cysteine Bioconjugation by Appending a Labeled Cystein Tag to a Protein by Using Protein Splicing in trans

Orthogonal cysteines: The chemical modification of cysteine residues is one of the most important methods for the chemoselective bioconjugation of proteins; however, it lacks regioselectivity. By assembling the protein from two pieces using protein trans-splicing, regioselectivity can be achieved. This reaction can even be performed in complex mixtures such as cell extracts.

Methyllysine analogs: rewriting the code

Lysine methylation has been implicated in gene transcription and epigenetic control. Chemical modification of cysteine residues results in a highly similar structural and functional analog of methylated lysine and provides a means to study this important modification in nucleosomes.

Different redox states of metallothionein/thionein in biological tissue

Mammalian metallothioneins are redox-active metalloproteins. In the case of zinc metallothioneins, the redox activity resides in the cysteine sulfur ligands of zinc. Oxidation releases zinc, whereas reduction re-generates zinc-binding capacity. Attempts to demonstrate the presence of the apoprotein (thionein) and the oxidized protein (thionin) in tissues posed tremendous analytical challenges. One emerging strategy is differential chemical modification of cysteine residues in the protein. Chemical modification distinguishes three states of the cysteine ligands (reduced, oxidized and metal-bound) based on (i) quenched reactivity of the thiolates when bound to metal ions and restoration of thiol reactivity in the presence of metal-ion-chelating agents, and (ii) modification of free thiols with alkylating agents and subsequent reduction of disulfides to yield reactive thiols. Under normal physiological conditions, metallothionein exists in three states in rat liver and in cell lines. Ras-mediated oncogenic transformation of normal HOSE (human ovarian surface epithelial) cells induces oxidative stress and increases the amount of thionin and the availability of cellular zinc. These experiments support the notion that metallothionein is a dynamic protein in terms of its redox state and metal content and functions at a juncture of redox and zinc metabolism. Thus redox control of zinc availability from this protein establishes multiple methods of zinc-dependent cellular regulation, while the presence of both oxidized and reduced states of the apoprotein suggest that they serve as a redox couple, the generation of which is controlled by metal ion release from metallothionein.

Detection of neuronal growth inhibitory factor (metallothionein-3) in polyacrylamide gels and by Western blot analysis

Neuronal growth inhibitory factor (GIF) is a small cysteine-rich metal binding protein downregulated in Alzheimer's disease. The protein belongs to the superfamily of metallothioneins (MTs) and was classified as MT-3. Although first identified as a brain specific protein, several reports now indicate a substantially broader expression pattern. However, currently available detection methods for MT-3 show low sensitivity in gel electrophoresis and Western blot. We have developed a fast and sensitive method for MT-3 detection in SDS–PAGE (detection limit ∼10 ng) and Western blot (detection limit ∼1 ng). The method is based on the chemical modification of cysteine residues with the dye monobromobimane and an improved blotting protocol.

Identification of a membrane-localized cysteine cluster near the substrate-binding sites of the Streptococcus equisimilis hyaluronan synthase

The membrane-bound hyaluronan synthase (HAS) from Streptococcus equisimilis (seHAS), which is the smallest Class I HAS, has four cysteine residues (positions 226, 262, 281, and 367) that are generally conserved within this family. Although Cys-null seHAS is still active, chemical modification of cysteine residues causes inhibition of wild-type enzyme. Here we studied the effects of N-ethylmaleimide (NEM) treatment on a panel of seHAS Cys-mutants to examine the structural and functional roles of the four cysteine residues in the activity of the enzyme. We found that Cys226, Cys262, and Cys281 are reactive with NEM, but Cys367 is not. Substrate protection studies of wild-type seHAS and a variety of Cys-mutants revealed that binding of UDP-GlcUA, UDP-GlcNAc, or UDP can protect Cys226 and Cys262 from NEM inhibition. Inhibition of the six double Cys-mutants of seHAS by sodium arsenite, which can cross-link vicinyl sulfhydryl groups, also supported the conclusion that Cys262 and Cys281 are close enough to be cross-linked. Similar results indicated that Cys281 and Cys367 are also very close in the active enzyme. We conclude that three of the four Cys residues in seHAS (Cys262, Cys281, and Cys367) are clustered very close together, that these Cys residues and Cys226 are located at the inner surface of the cell membrane, and that Cys226 and Cys262 are located in or near a UDP binding site.

Surface topography of phytochrome A deduced from specific chemical modification with iodoacetamide.

Phytochromes are a photoreversible photochromic light switch for photomorphogenesis in plants. The molecular structure and functional mechanism of phytochromes are not fully understood. On the basis of complete mapping of total tryptic digest of the iodoacetamide-modified oat phytochrome A (phyA), the molecular surface topography of phyA was probed by specific chemical modification of cysteine residues with [14C]iodoacetamide. Under native conditions, only two cysteines (Cys-158 and Cys-311) of eleven half-cystines of the N-terminal chromophore binding domain were modified to a significant extent. In the C-terminal domain, six cysteine residues (Cys-715, Cys-774, Cys-809, Cys-869, Cys-961, Cys-995) were readily accessible to iodoacetamide. Among the reactive cysteine residues, only cysteine-311 displayed reactivity that was dependent on the photochromic form (Pr left arrow over right arrow Pfr) of the photoreceptor. Surprisingly, the modification of Cys-311 in the vicinity of the chromophore attachment site (Cys-321) did not have any detectable effect on spectral properties of phyA. Most of the cysteines of the N-terminal domain (Cys-83, Cys-175, Cys-291, Cys-370, Cys-386, Cys-445, Cys-506) are deeply buried in the core of the chromophore binding domain, as they can be modified only after denaturation of the chromoprotein. In the C-terminal domain, modification of only one cysteine residue (Cys-939) required protein denaturation. Since all 22 half-cystines can be modified with iodoacetamide without reduction of the chromoprotein, it follows that oat phyA does not have any disulfide bonds. We found that Cys-311, Cys-774, Cys-961, and Cys-995 could be easily partially oxidized under the conditions used for phytochrome isolation. The surface topography/conformation of oat phyA and its role in protein-protein recognition in phytochrome-mediated signal transduction are discussed in terms of the relative reactivity of cysteine residues.

Improvement in the solution stability of porcine somatotropin by chemical modification of cysteine residues

Improvement in the solution stability of porcine somatotropin by chemical modification of cysteine residues

Structural studies of the contractile tail sheath protein of bacteriophage T4. 1. Conformational change of the tail sheath upon contraction as probed by differential chemical modification

Differential chemical modifications of tyrosine residues of the tail sheath protein, gp18, were performed to elucidate the structural change of the tail sheath upon contraction. Tyrosine residues of monomeric gp18, extended tail sheath, and contracted tail sheath were nitrated by tetranitromethane, and the modified tyrosine residues in each state of the sheath protein were identified by peptide mapping and amino acid sequence analyses of the isolated peptides. Of 31 tyrosine residues in gp18 monomer or in the extended sheath, 12 or 13 residues (Tyr63 and/or -73, -225, -254, -270, -304, -455, -460, -493, -532, -535, -569, and -590) were modified. When photo-CIDNP difference spectra were measured with monomeric gp18, two peaks, which are due to highly exposed tyrosine residues on the molecular surface of gp18, were observed. These two peaks disappeared when the monomeric gp18 was nitrated. With contracted sheath, however, only eight tyrosine residues (Tyr225, -254, -270, -455, -460, -493, -532, and -535) were nitrated on the contracted sheath. Chemical modification of cysteine residues by sulfhydryl group specific reagent ABD-F [(4-aminosulfonyl)-7-fluoro-2,1,3-benzoxadiazole] revealed that, among five cysteine residues, Cys377, Cys477, and Cys607 have a sulfhydryl group. Cys402 and Cys406 were modified only under reducing conditions, which strongly suggested the presence of a disulfide bond between these two residues.

Properties of myosin light chain kinase prepared from rabbit skeletal muscle by an improved method.

Myosin light chain kinase was prepared from rabbit skeletal muscle. DEAE-Sephadex, calmodulin-Sepharose 4B affinity gel and Ultrogel AcA 34 were used for the purification. It took 3 days for the preparation, and 6.2 mg of myosin light chain kinase was isolated from 600 g of frozen muscle. The molecular weight of the myosin light chain kinase estimated by sedimentation equilibrium analysis was 103,000 +/- 4,100. The isoelectric point was 5.0. Chemical modification of cysteine residues did not affect the catalytic activity, but modification of tyrosine residues diminished the activity. In order to activate myosin light chain kinase, it was necessary to bind calmodulin in an equimolar ratio and the dissociation constant was estimated to be 3.6 nM. The optimum pH for the catalytic activity was 7.5, and the activity was inhibited by NaCl and KCl. In the presence of 2.74 mg/ml myosin light chain and 75 mM KCl, the catalytic activity was found to be 88 s-1. The Vm and Km at 0.14 M KCl were 100 s-1 and 53 microM, respectively, for the isolated light chain as substrate and 70-80 s-1 and 19 microM for myosin as substrate.

Rat alpha-foetoprotein. Purification, physicochemical characterization, oestrogen-binding properties and chemical modification of the thiol group.

1. Rat alpha-foetoprotein, an oestrogen-binding foetal globulin, was isolated in large quantities from amniotic fluid and serum by preparative electrophoresis on polyacrylamide slab gels or by chromatography on an immunoadsorbent column. Subsequently the two electrophoretic forms of this protein were separated by electrophoresis on the same medium. 2. Both forms were found to show identical binding with oestradiol. From the extrinsic fluorescence of the bound dye 8-anilinonaphthalene-1-sulphonic acid it was shown that the polarity of the binding site is practically identical for both forms. One residue of tryptophan was determined for both forms. The two electrophoretic variants display the same amount of secondary structure as demonstrated by circular dichroism. 3. The affinity of total alpha-foetoprotein for oestradiol as a function of pH was studied by using a Sephadex G-25 gel-equilibration method. Maximal binding occurred at pH8.5. Only a fractional number of binding sites per molecule could be measured at pH7.4, whereas at higher pH the number of sites was very close to unity. There was no significant effect of pH on the value of the association constant (K(a)=4.3x10(7)+/-1.2x10(7)m(-1)). 4. Displacement experiments of bound labelled oestradiol with various steroids have permitted investigation of the specificity of alpha-foetoprotein. This foetal globulin binds rather strongly compounds that display the rigid structure of the oestratriene skeleton (oestradiol, oestrone). Diminished binding for diethylstilboestrol and a diethylstilboestrol affinity label was observed. No binding was measured with a more flexible structure such as hexoestrol [4,4'-(1,2-diethylethane-1,2-diyl)bisphenol]. 5. Chemical modification of cysteine residues of alpha-foetoprotein with two alkylating reagents [iodoacetic acid and 8-[N-(iodoacetylaminoethyl)amino]naphthalene-1-sulphonic acid] has very little effect on the oestrogen binding. It is suggested that the oestrogen-binding site does not contain a cysteine residue. From the kinetics of alkylation and from the fluorescence properties of the chemically bound thiol reagent 8-[N-(iodoacetylaminoethyl)amino]naphthalene-1-sulphonic acid], it was demonstrated that the very-slow-reacting thiol group is probably located in a non-polar region of the molecule.