Selective cleavage and modification of peptides and proteins

In silico peptide-based therapeutics against human colorectal cancer by the activation of TLR5 signaling pathways

OBJECTIVE

Colorectal cancer (CRC) is the third leading cause of cancer-related deaths in both men and women. Toll-like receptor 5 (TLR5), an autoimmune signaling receptor that plays a role in cancer, can be exploited for the suppression of human colon cancer. Salmonella flagellin protein, a novel agonist of TLR5 activating downstream signaling, could be a basis for designing anticancer peptides.

METHODS

The three-dimensional crystal structure of TLR5 (PDB ID: 3J0A, Resolution = 26.0 Å) was optimized using the AMBER force field in the YASARA suit. In silico enzymatic digestion tool, PeptideCutter, was used to identify peptides from Salmonella flagellin, an agonist against human TLR5. The 3D structure of the peptides was generated using PEP-FOLD3. These peptides were screened against human TLR5 using shape complementarity principles based on the binding affinity and interactions with the active residue of TLR5 monomer, and the selected peptides were further validated by molecular dynamic (MD) simulation.

RESULTS

In this study, we generated 42 peptides from Salmonella flagellin protein by in silico protein digestion. Then, based on a new hidden Markov model sub-optimal conformation sampling approach as well as the size of the fragments, we select 38 effective peptides from these 42 cleavages. These peptides were screened against the monomeric Xray structure of human TLR5 using shape complementarity principles. Based on the binding affinity and interactions with the active residue of TLR5 monomer (residues 294 and 366 of TLR5), nine top-scored peptides were selected for the initial molecular dynamic (MD) simulation. Among these peptides, Clv10, Clv17, and Clv28 showed high stability and less flexibility during MD simulation. A 1 μs MD simulation was performed on TLR5-Clv10, TLR-Clv17, and TLR5-Clv28 complexes to further analyze the stability, conformational changes, and binding mode (Clv10, Clv17, and Clv28). During this MD study, the peptides showed high salt bridges and ionic interactions with residue ASP294 and residue ASP366 throughout the simulation and remained in the concave of the human TLR5 monomer. The RMSD and Rg values showed that the peptide-protein complexes become stable after 200 ns of contraction and extraction.

CONCLUSION

These findings can facilitate the rational design of selected peptides as an agonist of TLR5, which have antitumor activity, suppress colorectal cancer tumors, and can be used as promising candidates and novel agonists of TLR5.

Altered inhibition of Cx26 hemichannels by pH and Zn2+ in the A40V mutation associated with keratitis-ichthyosis-deafness syndrome

Excessive opening of undocked Cx26 hemichannels in the plasma membrane is associated with disease pathogenesis in keratitis-ichthyosis-deafness (KID) syndrome. Thus far, excessive opening of KID mutant hemichannels has been attributed, almost solely, to aberrant inhibition by extracellular Ca(2+). This study presents two new possible contributing factors, pH and Zn(2+). Plasma pH levels and micromolar concentrations of Zn(2+) inhibit WT Cx26 hemichannels. However, A40V KID mutant hemichannels show substantially reduced inhibition by these factors. Using excised patches, acidification was shown to be effective from either side of the membrane, suggesting a protonation site accessible to H(+) flux through the pore. Sensitivity to pH was not dependent on extracellular aminosulfonate pH buffers. Single channel recordings showed that acidification did not affect unitary conductance or block the hemichannel but rather promoted gating to the closed state with transitions characteristic of the intrinsic loop gating mechanism. Examination of two nearby KID mutants in the E1 domain, G45E and D50N, showed no changes in modulation by pH or Zn(2+). N-bromo-succinimide, but not thiol-specific reagents, attenuated both pH and Zn(2+) responses. Individually mutating each of the five His residues in WT Cx26 did not reveal a key His residue that conferred sensitivity to pH or Zn(2+). From these data and the crystal structure of Cx26 that suggests that Ala-40 contributes to an intrasubunit hydrophobic core, the principal effect of the A40V mutation is probably a perturbation in structure that affects loop gating, thereby affecting multiple factors that act to close Cx26 hemichannels via this gating mechanism.

Heat-induced Antigen Retrieval in Conventionally Processed Epon-embedded Specimens: Procedures and Mechanisms

We studied the effectiveness of heat-induced antigen retrieval (HIAR) in conventionally processed, epon-embedded specimens and the mechanisms of HIAR in the specimens. Frozen sections were first immunostained to examine the possibility of using HIAR for 18 antigens to avoid the effects of epoxy resin embedment. The antigenicity of 7 out of 18 antigens was retrieved with glutaraldehyde fixation followed by osmium tetroxide treatment whereas none were retrieved with glutaraldehyde fixation without post-osmication. Six antigens also exhibited positive immunostaining in semi-thin epon sections when the sections were deplasticized with sodium ethoxide followed by autoclaving. In the immunoelectron microscopy with the post-embedding method, positive reactions with fine ultrastructures were obtained using HIAR without deplasticization. These results suggested that osmium tetroxide binds to ethylene double bonds (which are introduced into protein crosslinks by glutaraldehyde) and forms an extremely stable resonance interaction with the Schiff bases, thus destabilizing the protein crosslinks. Heating also further degrades these crosslinks. The present study demonstrated that archival epon blocks can be useful resources for immunohistochemical studies for both light and electron microscopy.

Enzymatic and chemical cleavage of fusion proteins

This unit provides protocols for some commonly used methods of site-specific cleavage of fusion proteins. The first three protocols describe enzymatic cleavage of proteins using proteases (factor Xa, thrombin, and enterokinase) that display highly restricted specificities, which greatly decrease the likelihood that unwanted secondary cuts will occur. Three additional protocols describe specific cleavage of fusion proteins with chemical reagents (cyanogen bromide, hydroxylamine, and low pH) as an alternative to enzymatic cleavage.

Chemical and Photochemical Modification of Colicin E1 and Gramicidin A in Bilayer Lipid Membranes

Chemical modification and photodynamic treatment of the colicin E1 channel-forming domain (P178) in vesicular and planar bilayer lipid membranes (BLMs) was used to elucidate the role of tryptophan residues in colicin E1 channel activity. Modification of colicin tryptophan residues by N-bromosuccinimide (NBS), as judged by the loss of tryptophan fluorescence, resulted in complete suppression of wild-type P178 channel activity in BLMs formed from fully saturated (diphytanoyl) phospholipids, both at the macroscopic-current and single-channel levels. The similar effect on both the tryptophan fluorescence and the electric current across BLM was observed also after NBS treatment of gramicidin channels. Of the single-tryptophan P178 mutants studied, W460 showed the highest sensitivity to NBS treatment, pointing to the importance of the water-exposed Trp460 in colicin channel activity. In line with previous work, the photodynamic treatment (illumination with visible light in the presence of a photosensitizer) led to suppression of P178 channel activity in diphytanoyl-phospholipid membranes concomitant with the damage to tryptophan residues detected here by a decrease in tryptophan fluorescence. The present work revealed novel effects: activation of P178 channels as a result of both NBS and photodynamic treatments was observed with BLMs formed from unsaturated (dioleoyl) phospholipids. These phenomena are ascribed to the effect of oxidative modification of double-bond-containing lipids on P178 channel formation. The pronounced stimulation of the colicin-mediated ionic current observed after both pretreatment with NBS and sensitized photomodification of the BLMs support the idea that distortion of membrane structure can facilitate channel formation.

Determination of endogenous peptides in the porcine brain: possible construction of peptidome, a fact database for endogenous peptides

Peptides play crucial roles in many physiological events. However, a database for endogenous peptides has not yet been developed, because the peptides are easily degraded by proteolytic enzymes during extraction and purification. In this study, we demonstrated that the data for endogenous peptides could be collected by minimizing the proteolytic degradation. We separated porcine brain peptides into 5250 fractions by 2-dimensional chromatography (first ion-exchange and second reversed-phase high-performance liquid chromatography), and 75 fractions of average peptide contents were analyzed in detail by mass spectrometers and a protein sequencer. Based on the analysis data obtained in this study, more than 10000 peptides were deduced to be detected, and more than 1000 peptides to be identified starting from 2 g of brain tissue. Thus, we deduce that it is possible to construct a database for endogenous peptides starting from a gram level of tissue by using 2-dimensional high-performance liquid chromatography coupled with a mass spectrometer.

The solvent in CNBr cleavage reactions determines the fragmentation efficiency of ketosteroid isomerase fusion proteins used in the production of recombinant peptides

Abnormal fragmentation during cyanogen bromide polypeptide cleavage rarely occurs, although parallel side reactions are known to typically accompany normal cleavage. We have observed that cyanogen bromide cleavage of highly hydrophobic fusion proteins utilized for production of recombinant peptides results in almost complete abolishment of the expected reaction products when the reaction is carried out in 70% trifluoroacetic acid. On the basis of mass spectrometric analysis of the reaction products, we have identified a number of fragments whose origin can be attributed to incomplete fragmentation of the fusion protein, and to unspecific degradation affecting the carrier protein. Substituting the solvent in the reaction media with 70% formic acid or with a matrix composed of 6M guanidinium hydrochloride in 0.1M HCl, however, was found to alleviate polypeptide cleavage. We have attributed the poor yields of the CNBr cleavage carried out in 70% TFA to the increased hydrophobicity of our particular fusion proteins, and to the poor solubilizing ability of this reaction medium. We propose the utilization of chaotropic agents in the presence of diluted acids as the preferred cyanogen bromide cleavage medium of fusion proteins in order to maximize cleavage efficiency of hydrophobic sequences and to prevent deleterious degradation and structural modifications of the target peptides.

Presentation of epitopes on genetically engineered peptides and selection of lymphoma-targeting moieties based on epitope biorecognition

A His-tagged coiled coil stem loop peptide with stable secondary structure was designed and biosynthesized. A series of oligopeptides related to the EBV envelope glycoprotein 350/220 N-terminal nonapeptide as potential CD21 receptor-binding epitopes were engineered into the loop region of the peptide scaffold. It was shown that these peptides had a stable alpha-helical coiled coil structure and assumed a monomeric form in PBS. Biorecognition of the epitopes was studied by immobilizing the epitope-containing peptides on complexed Ni2+-containing surfaces through His-Ni2+ chelation and incubating with purified soluble CD21 receptor or CD21+ cells. The results showed that the potential epitopes bound to CD21 and CD21+ cells at different affinities depending on oligopeptide structures. This approach allows for the evaluation of epitope biorecognizabilities and the selection of optimal oligopeptides among sequences for use as targeting moieties in the design of new lymphoma-targeting polymeric drug carriers.

Exposure of Mn and FeSODs, but not Cu/ZnSOD, to NO leads to nitrosonium and nitroxyl ions generation which cause enzyme modification and inactivation: an in vitro study

The effect of NO treatment in vitro on structural and functional alterations of Cu/Zn, Mn, and Fe type of SODs was studied. Significant difference in response to NO of Cu/ZnSOD compared to the Mn and Fe types was demonstrated. Cu/ZnSOD was shown to be stable with respect to NO: even on prolonged exposure, NO produced negligible effect on its structure and activity. In contrast, both Mn and Fe types were found to be NO-sensitive: exposure to NO led to their fast and extensive inactivation, which was accompanied by extensive structural alterations, including (in some of the samples tested) the cleavage of enzyme polypeptide chains, presumably at His residues of the enzyme metal binding sites. The generation of nitrosonium (NO+) and nitroxyl (NO-) ions in NO treated Mn and FeSODs, which produce enzyme modifications and inactivation, was demonstrated. The physiological and biomedical significance of described findings is briefly discussed.

Effects of physico-chemical treatments on haemagglutination activity of Anopheles gambiae haemolymph and midgut extract

Anopheles gambiae midgut extracts and haemolymph possessed agglutinins, titre 1:16 to 1:256, against human red blood cells (RBCs). Subjection of both tissues to protein precipitation reagents, organic chemical and selected protease, neuraminidase and other glycosidic hydrolase treatments revealed the haemagglutinins to be protein, most likely glycoprotein, in nature--not lipoprotein, lipid, glycolipid or nucleic acid. An.gambiae agglutinins were thermo-labile > 40 degrees C, affected by freezing and thawing treatments, and contained disulphide and hydrogen bonds on the basis of sensitivity following exposure to dithiothreitol and urea respectively. Optimum haemagglutination depended generally on slightly acid to neutral pH conditions and agglutinin activity was Ca2+ ion, albeit to a lesser extent Mg2+ ion, dependent. The midgut extract agglutinin subunit molecule had a relative molecular weight (M(r)) of 65 kDa whilst that of haemolymph was 40 kDa. This study presents the first report on selected physico-chemical properties, the glycoproteinaceous nature and tentative subunit M(r) of mosquito midgut extract and haemolymph anti-RBC agglutinin(s).

Inhibition of human and murine cytosolic epoxide hydrolase by group-selective reagents

1. Human and murine cytosolic epoxide hydrolase were inhibited by thiol-, imidazole- and carboxyl-selective reagents. They were not inhibited by amino-, guanido- or activated serine-selective reagents. 2. Murine, but not human, cytosolic epoxide hydrolase was inhibited by N-bromosuccinimide, a tryptophan selective reagent. 3. Based on sequence data from peptides isolated from CNBr digests, human and murine CEH share areas of sequence homology. Of the five unique human CEH CNBr peptides sequenced, three shared common sequences with one of the unique murine CEH CNBr peptides. The human and murine CEH peptides with common sequences had between 64 and 78% sequence identity. 4. A cysteine important for the activity of murine CEH appears not to be in the active site as judged by N-phenylmaleimide inhibition in the presence and absence of either (2S,3S)-2,3-epoxy-3-(4-nitrophenyl)glycidol, a competitive inhibitor, or trans-stilbene oxide, a substrate.

Selective photochemical modification by trichloroethanol of tryptophan residues in proteins with a high tyrosine-to-tryptophan ratio

We present an improved procedure for the selective modification of tryptophan residues in proteins. A simple, low-cost set-up allows rapid tryptophan photoreaction upon ultraviolet irradiation in the presence of 2,2,2-trichloroethanol. This photochemical reaction is carried out under native conditions, occurs only in the excited state of tryptophan, and yields a single, as yet unidentified, photoproduct. Except for tyrosine, no reaction with other amino acid side chains are known. Stringent photoselection of tryptophan, ensuring that tyrosine residues are not affected, is achieved in situ without the need for an elaborate system of optical filters or lenses. Illumination with a medium-wave uv lamp of samples placed in disposable, dual pathlength, polystyrene fluorescence cuvettes allows treatment of small sample volumes (greater than or equal to 100 microliters) of various optical density. Chromophore accessibility in oligomeric assemblies or protein-nucleic acid complexes can be assessed by this reaction since the integrity of these structures is preserved. Moreover, this technique can be used to evaluate the involvement of tryptophan residues in catalytic or ligand binding processes.

DNA sequencing of four bases using three lanes

A three-lane DNA sequencing strategy is described which is based on redundant binary coding principles from communications theory. Three-lane sequencing is an efficient, accurate, and flexible strategy, suitable for large-scale automated DNA sequencing. Communications theory and algebraic coding principles can also be applied to sequencing other informational macromolecules.

Studies on the biotin-binding site of avidin. Minimized fragments that bind biotin

The object of this study was to define minimized biotin-binding fragments, or 'prorecognition sites', of either the egg-white glycoprotein avidin or its bacterial analogue streptavidin. Because of the extreme stability to enzymic hydrolysis, fragments of avidin were prepared by chemical means and examined for their individual biotin-binding capacity. Treatment of avidin with hydroxylamine was shown to result in new cleavage sites in addition to the known Asn-Gly cleavage site (position 88-89 in avidin). Notably, the Asn-Glu and Asp-Lys peptide bonds (positions 42-43 and 57-58 respectively) were readily cleaved; in addition, lesser levels of hydrolysis of the Gln-Pro (61-62) and Asn-Asp (12-13 and 104-105) bonds could be detected. The smallest biotin-binding peptide fragment, derived from hydroxylamine cleavage of either native or non-glycosylated avidin, was identified to comprise residues 1-42. CNBr cleavage resulted in a 78-amino acid-residue fragment (residues 19-96) that still retained activity. The data ascribe an important biotin-binding function to the overlapping region (residues 19-42) of avidin, which bears the single tyrosine moiety. This contention was corroborated by synthesizing a tridecapeptide corresponding to residues 26-38 of avidin; this peptide was shown to recognize biotin. Streptavidin was not susceptible to either enzymic or chemical cleavage methods used in this work. The approach taken in this study enabled the experimental distinction between the chemical and structural elements of the binding site. The capacity to assign biotin-binding activity to the tyrosine-containing domain of avidin underscores its primary chemical contribution to the binding of biotin by avidin.

The environments of Trp-248 and Trp-330 in tryptophan indole-lyase from Escherichia coli

The two tryptophan residues, Trp-248 and Trp-330, in tryptophan indole-lyase (tryptophanase) from E. coli have been separately mutated to phenylalanine using site-directed mutagenesis. Both single tryptophan mutant enzymes have full catalytic activity, but exhibit different fluorescence and near-UV circular dichroism spectra. These results indicate that Trp-330 is more deeply buried than is Trp-248, and is in a more asymmetric environment. Neither residue reacts with N-bromosuccinimide (NBS), although tryptophan indole-lyase is inactivated by NBS. These results demonstrate that the tryptophan residues in tryptophan indole-lyase are not catalytically essential.

Type 2-depleted fungal laccase

Although copper is quantitatively removed from fungal laccase (Polyporus versicolor) by extended dialysis against high concentrations of cyanide, we have been unable to reconstitute the protein by addition of Cu(I) ions. However, two new methods for reversibly removing the type 2 Cu centre have been developed. The visible absorption at 610 nm, which is attributable to type 1 Cu, is unaffected by the procedure, but the absorbance of the type 3 Cu at 330 nm is decreased by 60 +/- 10%. The decrease is due, at least in part, to partial reduction of the binuclear type 3 centre, although there may be some change in the molar absorptivity of the oxidized chromophore as well. The change in the c.d. spectrum that occurs at approx. 350 nm may be explained in the same way, but it may also reflect the loss of a signal due to the type 2 Cu. Upon removal of the type 2 Cu an absorbance increase appears at approx. 435 nm, and it is assigned to the semi-reduced form of the type 3 pair. In the e.p.r. spectrum of the type 2-depleted enzyme the type 1 Cu signal exhibits well-resolved ligand hyperfine splitting, which can be simulated on the basis of contributions from two N and two H nuclei (AH congruent to AN congruent to 25 MHz). The H atoms are assumed to be attached to the beta-carbon of the covalently bonded cysteine ligand. A signal from a semi-reduced form(s) of the type 3 site can also be resolved in the spectrum of the type 2-depleted enzyme, and on the basis of the second integral of the e.p.r. spectrum 40% of the type 3 pairs are believed to be in a partially reduced state. The semi-reduced type 3 site is remarkably stable and is not readily oxidized by H2O2 or IrCl6(2-) or reduced by Fe(CN)6(4-). Intramolecular electron transfer is apparently quite slow in at least some forms of the type 2-depleted enzyme, and this may explain why the activity is at best 5% of that of the native enzyme. Full activity returns when type 2 copper is restored.

Radioiodination of proteins and lipoproteins using N-bromosuccinimide as oxidizing agent

In an attempt to improve conditions for radioiodination of sensitive proteins we used N-bromosuccinimide as a mild oxidizing agent. Under gentle conditions we increased the average labeling efficiency of a wide variety of proteins to above 97%. There was no loss of binding activity of low density lipoprotein particles, which are most sensitive to oxidation. Depending on high labeling efficiency, our method reduces preparation time as well as radioactive waste, costs, and irradiation exposure to personnel.

Purification and characterisation of a non-specific lipid transfer protein from goat liver

A non-specific lipid transfer protein has been purified from the pH 5.1 supernatant of goat liver by DEAE-cellulose, CM-cellulose and Sephadex G-75 column chromatography. The protein shows a single band on polyacrylamide gel electrophoresis and transfers 450 nmol of phosphatidylcholine per min per mg of protein under the present assay condition. This protein has a subunit molecular weight of 12,000 and an isoelectric point of 8.65. Amino acid analysis reveals the absence of methionine. Histidine has been identified as the only N-terminal amino acid. Besides phosphatidylcholine, the protein transfers phosphatidylinositol, phosphatidylethanolamine, phosphatidylserine and cholesterol. Chemical modification studies showed the involvement of free amino and thiol groups in the maintenance of the transfer activity of the goat liver protein.

Structure-stability relationship in proteins: fundamental tasks and strategy for the development of stabilized enzyme catalysts for biotechnology

The problem of relationships between the protein structure and its stability comprises two major questions. First, how to elucidate the peculiarities of the protein structure responsible for its stability. Second, knowing the general molecular basis of protein stability, how to change the structure of a given protein in order to increase its stability. This review is an attempt to show the modern state of the first (fundamental) and the second (applied) aspects of the problem.

Internal chain cleavage and product heterogeneity during Edman degradation of isosteric peptide analogs lacking the alpha-carbonyl function

A synthetic peptide analog, with one peptide carbonyl group replaced by a methylene bridge, was submitted to structural analysis by Edman degradation. Multiple cleavages were obtained in the first cycle, due to phenylthiocarbamylation of the internal secondary amine as well as spontaneous alkaline cyclization and subsequent recoupling with the Edman reagent. Three fragments from cleavage of the peptide analog after a single Edman cycle were purified by reverse-phase high-performance liquid chromatography. The results support previous observations in a novel combination. The reactions may also be important with native polypeptides since non-quantitative alkaline cyclization now encountered can mimic apparent N-terminal heterogeneity in agreement with earlier data, while quantitative cyclization can mimic loss of N-terminal residues.

Cleavage at acyl-proline bonds with sodium in liquid ammonia: application with nanomolar amounts of peptides and separation of products by high-performance liquid chromatography for structural analysis

Cleavage of X-Pro bonds with metallic sodium in liquid ammonia is a little-used method due to difficulties with handling of reagents, variable cleavage yields, and separation of peptides from salt byproducts. Construction of a small distillation/reaction apparatus permitted peptide incubations at the nanomole scale. Reverse-phase high-performance liquid chromatography (HPLC) of the residue after removal of NH3 allows separation of the salts and fractionation of the cleaved peptides which may be taken directly for sequence analysis. HPLC also allows rapid assessment of the degree of cleavage before structural analysis. Cleavage of some peptides proceeded in high yield while others were cleaved poorly or not at all, modifying earlier generalizations on factors influencing cleavage.

The bacterial phosphoenolpyruvate-dependent phosphotransferase system. Isolation of active site peptides by reversed-phase high-performance liquid chromatography and determination of their primary structure

Using reversed-phase high-performance liquid chromatography (HPLC) it was possible to isolate 32P-labelled active-site regions of various proteins from the bacterial phosphoenolpyruvate-dependent phosphotransferase system. The purified peptides obtained by proteolytic cleavage with Lys-C protease and trypsin were sequenced by the gas phase method. The fragments derived from enzyme I (MW 70 000) of two streptococcal species show 100% homology. The analogous peptide of Staphylococcus aureus Enzyme I differs in the N-terminal region. A labelled peptide from the glucose-specific enzyme III protein of Escherichia coli obtained by cleavage with alkaline protease was isolated and sequenced. It could be fitted into the primary structure of this protein, which was derived from DNA sequence data. The active-site histidine residue of this protein is therefore localized at position 91. The HPLC separation method described is suitable for the isolation of peptides derived from active sites containing labile amino acid derivatives such as phosphohistidines.

Reductive cleavage of Xaa-proline peptide bonds by mild alkaline borohydride treatment employed to release O-glycosidically linked carbohydrate units of glycoproteins

During the deglycosylation reaction of fish egg polysialoglycoproteins under the conditions of 1 M NaBH4 in 0.1 M NaOH at 37 degrees C for 48 h, a marked loss of the glycine content has been encountered, besides the serine and threonine residues to which the carbohydrate units are linked. The chemical basis behind this phenomenon has been elucidated by amino acid analysis first of the major glycopeptides (carbohydrate-(O)Thr-Gly-Pro-Ser) derived from desialylated polysialoglycoproteins and subsequently six proline-containing peptides before and after treatment under similar conditions. It has thus been established that -Xaa-Pro- sequences are remarkably susceptible to reductive cleavage under such mild aqueous conditions. In view of the finding that the reductive cleavage of insulin B-chain, which contains a single proline residue adjacent and C-terminal to a threonine residue, led to about 80% loss of the threonine residue, deglycosylation with alkaline borohydride reagents warrants a special comment. The decreased amounts of serine or threonine residues cannot be related simply to the degree of glycosylation of these residues. The above results are therefore discussed in the relation to other work.

Ethoxyformylation and guanidination of snake venom phospholipases A2: effects on enzymatic activity, lethality and some pharmacological properties

Lysine residues in the basic and relatively toxic N. nigricollis phospholipase A2 and in the acidic and relatively nontoxic N. n. atra phospholipase A2 were modified by acylation with ethoxyformic anhydride (in the presence or absence of the substrate dihexanoyl lecithin) or guanidination with O-methylisourea. Ethoxyformylation gave rise to some protein fractions in which enzymatic activity was preserved to a greater degree than intraventricular lethality. Guanidination had little effect on the isoelectric point or catalytic activity of either enzyme or on the lethal potency of the N. n. atra enzyme. However, the intraventricular lethality of the N. nigricollis enzyme was decreased much more than was its intravenous lethality, direct hemolytic potency, anticoagulant activity or cardiotoxic action on rat atrium. These results are compared to those previously obtained when the lysines in these two enzymes were carbamylated with potassium cyanate, a procedure which markedly decreased the isoelectric point of the enzymes. It is concluded that charge alone does not account for differences in toxicity. The data also indicate that there are at least two distinct active sites in both enzymes, one being primarily responsible for enzymatic activity and the other(s) associated with lethal and pharmacological effects of the protein. Modification of lysines affects the latter site(s), while having little or no effect on enzymatic activity.

Cleavage of dehydroalanine-containing peptides with mercuric acetate

The dehydroalanine containing peptides glycyldehydroalanine and t-butyloxy-carbonyl-L-alanyldehydroalanyl-beta-methyl-D, L-aspartic acid methyl ester were synthesized, respectively, from chloroacetamide and pyruvate and from t-butyloxycarbonyl-L-alanyl-S-methyl-L-cysteinyl-beta-methyl-D, L-aspartic acid methyl ester. They were reacted with mercuric acetate in water, 50% methanol and dimethylformamide at 25 degrees and at 80 degrees for various time periods. Reaction proceeded to yield an amino acid amide from the N-terminal side of the unsaturated residue and pyruvate from the C-terminal side. Yields of amino acid amides were 76% for the dipeptide and 40% for the tripeptide. The applicability of the neutral reaction conditions employed to the cleavage of glycoproteins containing both O- and N-glycosidically-linked carbohydrate chains following beta-elimination of the serine and threonine linked oligosaccharides is pointed out.

Reaction of osmium reagents with amino acids and proteins. Reactivity of amino acid residues and peptide bond cleavage

We report a study of the relative reactivity of the common amino acids and of their residues in lysozyme with osmium tetroxide, the osmium tetroxide-pyridine reagent, and with the oxo-osmium(VI)-pyridine reagent. With free amino acids, the osmium(VIII) reagents are most reactive with Met, Cys, His, Thr, Ser, Trp, Lys, and Pro; the osmium(VI) reagent only reacts significantly with His, Met, Cys, Thr, and Ser. In lysozyme, only Cys, Met, and Trp react extensively with the osmium(VIII) reagents; with the osmium(VI) reagent, Cys and Met are most reactive. We also note evidence both for cross-linking of proteins and for peptide bond cleavage, which appears to have considerable specificity for tryptophanyl residues.

Mitochondria and sarcoplasmic reticulum as model targets for neurotoxic and myotoxic phospholipases A2

Certain neurotoxins and myotoxins from snake venoms have phospholipase A(2) activity (phosphatide 2-acylhydrolase, EC 3.1.1.4), which appears to be necessary for their toxicity. Several of these toxins inhibit the net uptake of Ca(2+) into sarcoplasmic reticulum vesicles and brain mitochondria. We have obtained evidence that the ability to inhibit this Ca(2+) uptake is a mechanistically relevant correlate of the toxicity of these proteins rather than being just a nonspecific consequence of their phospholipase A(2) activity. Two of the toxins, beta-bungarotoxin and notexin, had 5% and 50%, respectively, of the phospholipase A(2) activity of IVa phospholipase A(2)(a nontoxic enzyme), but beta-bungarotoxin was as effective as IVa in inhibiting Ca(2+) uptake into brain mitochondria and notexin was more effective. Each of the myotoxic enzymes substantially inhibited Ca(2+) uptake into sarcoplasmic reticulum, notexin being the most effective in this regard. This ability correlated better with their myotoxic potency than with their phospholipase A(2) activity. beta-Bungarotoxin lost its toxicity but not its measurable phospholipase A(2) activity after modification with ethoxyformic anhydride in the presence of dihexanoylphosphatidylcholine. The modified toxin also lost most of its ability to inhibit Ca(2+) uptake into sarcoplasmic reticulum and brain mitochondria. Sarcoplasmic reticulum vesicles reconstituted from solubilized sarcoplasmic reticulum retained their sensitivity to notexin.

Oxidation of tryptophan to oxindolylalanine by dimethyl sulfoxide-hydrochloric acid. Selective modification of tryptophan containing peptides

Tryptophan is readily oxidized to oxindolylalanine (2-hydroxytryptophan) in good yield on treatment in acetic acid solution with a mixture of dimethyl sulfoxide (DMSO) and concentrated aqueous HCl at room temperature. Other sulfoxides can be used in combination with HCl; for example, methionine sulfoxide reacts with an equimolar amount of tryptophan to give high yields of methionine and oxindolylalanine. Methionine and cysteine are quantitatively oxidized by DMSO/HCl to methionine sulfoxide and cystine, respectively. The tryptophan containing peptides LRF (luteinizing hormone-releasing factor), somatostatin, valine-gramicidin A and ACTH 1-24 were each treated with the DMSO/HCl reagent in acetic acid solution and the corresponding oxindolylalanine-derivatives isolated in over 90% yield after chromatography. The identity and purity of the derivatives were established on the basis of ultraviolet spectral characteristics and quantitative amino acid analysis of the oxindolylalanine content of acid hydrolyzates of the oxidized peptides with 3N-p-toluenesulfonic acid at 110 degrees for 24 h. The results indicate that modification of tryptophan peptides with DMSO/HCl provides a useful procedure, which seems superior to previously used reagents. In addition, the method could be well applied to other indoles of biological and pharmacological interest.

The reactivity of tryptophan residues in proteins. Stopped-flow kinetics of fluorescence quenching

The quenching of tryptophan fluorescence by N-bromosuccinamide, studied by the fluorescence stopped-flow technique, was used to compare the reactivities of tryptophan residues in protein molecules. The reaction of N-bromosuccinamide with the indole group of N-acetyltryptophanamide, a model compound for bound tryptophan, followed second-order kinetics with a rate constant of (7.8 +/- 0.8) . 10(5) dm3 . mol-1 . s-1 at 23 degrees C. The rate does not depend on ionic strength or on the pH near neutrality. The non-fluorescent intermediate formed from N-acetyltryptophanamide on the reaction with N-bromosuccinamide appears to be a bromohydrin compound. The second-order rate constant for fluorescence quenching of tryptophan in Gly-Trp-Gly by N-bromosuccinamide was very similar, (8.8 +/- 0.8) . 10(5) dm3 . mol-1 . s-1. Apocytochrome c has the conformation of a random coil with the single tryptophan largely exposed to the solvent. The rate constant for the fluorescence quenching of the tryptophan in apocytochrome c by N-bromosuccinamide was (3.7 +/- 0.3) . 10(5) dm3 . mol-1 . s-1. The fluorescence quenching by N-bromosuccinamide of the tryptophan residues incorporated in alpha-chymotrypsin at pH 7.0 showed three exponential terms from which the following rate constants were derived: 1.74 . 10(5), 0.56 . 10(5) and 0.11 . 10(5) dm3 . mol-1 . s-1. This protein is known to have eight tryptophan residues in the native state, six residues at the surface, and two buried. Three of the surface tryptophans have the indole rings protruding out of the molecule and may account for the fastest kinetic phase of the quenching process. The intermediate phase may be due to three surface tryptophans whose indole rings point inwards, and the slowest to the two interior tryptophan residues.

Improved preparation and structural elucidation of the tryptophan cleavage reagent 2-(2'-nitro-phenylsulfenyl)-3-methyl-3-bromoindolenine (BNPS-skatole)

Methods are described for a high yield preparation (overall yield greater than 90%) of analytically pure 2-(2'-nitrophenylsulfenyl)-3-methyl-3-bromoindolenine (BNPS-skatole). The chromatographic and spectroscopic data are given. The yield of tryptophan cleavage is considerably dependent on the degree of purity of the BNPS-skatole.

Quantitation of methionyl peptides in nanomole quantities by a fluorometric method

A quantitative and highly specific method to determine low concentrations of methionyl peptides, which do not contain tryptophan or cysteine residues, has been developed. The method is based on the stoichiometry and selectivity of N-chlorosuccinimide (NCS) towards methionine and N-acetyltryptophan. N-Chlorosuccinimide reacts with N-acetyltryptophan in a 1:1 ratio to produce the N-acetyl-2-oxindolealanine--a derivative essentially devoid of fluorescence. The decrease in fluorescence intensity is approximately linear with respect to the NCS concentration. Preincubation of NCS with methionine or methionyl peptide consumes a stoichiometric amount of the reagent and the unreacted NCS is quantitated by the decrease in fluorescence intensity resulting upon incubation of the mixture with 1 eq of N-acetyltryptophan. Less than 1 nmol of methionyl peptide can be accurately quantitated by this method.