Side-chain Functional Groups Research Articles

The β-Sheet Structure-Stabilizing Potential of Twenty Kinds of Amino Acid Residues in Protected Peptides

Abstract A host–guest approach was devised to investigate the β-sheet structure-stabilizing potential of the 20 common amino acid residues in protected peptides where functional groups in side chains were protected by suitable groups commonly used in peptide synthesis. The potential was evaluated using solvent-titration curves for the disruption of the β-sheet structure of cross-linked polystyrene resin-bound host–guest hexa- and octapeptides in CH2Cl2 by HFIP. The β-sheet structure of host–guest hexapeptides, Boc–Val–Ile–X2–Val–Ile-NHCH2–resins, in which X stands for guest amino acid residues, was disrupted in CH2Cl2 by adding increasing amounts of HFIP; the disrupted behaviors were strongly dependent on the nature of guest amino acid residues. A scale for the β-sheet structure-stabilizing potential of the 20 kinds of amino acid residues in CH2Cl2 could be derived at 0.25 M of HFIP concentration as follows: Ile, Val>>Asn>His(Tos) or His, Gln, Cys(Bzl), Tyr(Bzl)>Phe, Gly, Lys(Z), Arg(Tos), Leu>Thr(Bzl), Ala, Met(O), Glu(OBzl), Trp(CHO)>>Ser(Bzl), Asp(OBzl)>>Pro. To confirm the scale, their β-sheet structure-stabilizing potential was further examined using host–guest octapeptides, Boc–X2–Val–Ile–X2–Val–Ile–NHCH2–resins. The disrupted behaviors of the octapeptides having Gly, Ala, and Thr(Bzl) residues as guests were remarkably different from those of the corresponding hexapeptides; the β-sheet structure-stabilizing potential of the Gly, Ala, and Thr(Bzl) residues became significantly high with an increase in their ratios to host residues. The potential of the Gly, Ala, and Thr(Bzl) residues appears to reflect the ratios of guest amino acid residues to hosts, the repeated sequence, and/or neighbor interactions in the sequence. The significance of the present study in the design of synthetic routes for peptides and proteins is briefly discussed.

Reactivity of side chain functional groups in macrocyclic Cu2+ complexes

Abstract

Total synthesis of urogastrone (human epidermal growth factor, h-EGF). Part 2. Synthesis of urogastrone having the structure proposed for the natural compound

Deprotection of the fully protected urogastrone was carried out by a two-step deprotection strategy. In the first step the protecting groups of all side-chain functional groups except for the cysteine thiol were removed by treatment with HF and the resulting (S-Acm)6-urogastrone was purified by ion-exchange chromatography prior to the disulphide bond formation. In the second step the six Acm groups of the purified (S-Acm)6-urogastrone were removed by Hg(OAc)2. After formation of disulphide bonds by air oxidation, the synthetic urogastrone was purified by ion-exchange chromatography and gel filtration. The structure of the synthetic urogastrone was further characterized by amino acid analysis, tryptic peptide mapping, thermolytic peptide mapping, and fast atom bombardment mass spectroscopy.

Synthesis of a docosapeptide comprising the hydrophobic membrane spanning region of glycophorin A.

The docosapeptide which constitutes the membrane spanning region (amino acid residues 73-94) of the human red blood cell protein glycophorin A has been synthesized. This may be the first example of the synthesis of the entire membrane embedded domain of a membrane spanning protein. Three fully protected fragments were prepared by stepwise elongation using dicyclohexylcarbodiimide and p-nitrophenyl ester activation of N alpha-tert.-butyloxycarbonyl amino acids. The three fragments represent amino acid residues 73-79, 80-86, and 87-94 in the sequence of glycophorin A and contain a large proportion of valine, leucine, and isoleucine residues but contain no amino acids with ionizable side chain functional groups. The three fragments were condensed using both the azide method and the dicyclohexylcarbodiimide method to give fully protected docosapeptide. Benzyl groups protecting the side chains of the docosapeptide were removed by prolonged hydrogenolysis to give the desired product N alpha-tert.-butyloxycarbonyldocosapeptide ethyl ester. High resolution proton n.m.r. spectra of the protected fragments in 100% deuterochloroform showed all resonances to be broadened with the amide resonances broadened beyond recognition. In perdeuterodimethylsulfoxide all resonances were relatively sharp with all amide resonances visible and showing coupling constants of 7-8 Hz. Solvent titration of the proton spectra of two of the fragments from 100% perdeuterodimethylsulfoxide to 100% deuterochloroform demonstrated a transition to the broadened spectrum, accompanied by a decrease in the coupling constant of the amide protons (JNH-CH alpha) suggesting solvent dependent onset of intramolecular secondary structure, possibly accompanied by aggregation. A proton n.m.r. spectrum of the docosapeptide in perdeuterodimethylsulfoxide shows a few resolved amide resonances with coupling constants of 7-9 Hz. Solvent titration with perdeuterochloroform again suggests a transition to a rigid intramolecular secondary structure.

ChemInform Abstract: (((AMINOMETHYL)ARYL)OXY)ACETIC ACID ESTERS. A NEW CLASS OF HIGH‐CEILING DIURETICS. 2. MODIFICATIONS OF THE OXYACETIC SIDE CHAIN

AbstractDargestellt werden die Verbindungen (IV)‐(VII), von denen (VII) die höchste saluretische Wirkung aufweist.

Synthesis of a decapeptide with the sequence 1?10 of human calcitonin with minimum protection of the amino acids

A decapeptide with sequence 1–10 of human calcitonin has been synthesized by a 5+5 scheme with the minimum protection of the side-chain functional groups of the amino acid.

Irreversible inhibition of phosphotransacetylase by S-dimethylarsino-CoA

S-Dimethylarsino-CoA was synthesized by acylation of CoA with dimethylchloroarsine. The new analogue of acetyl-CoA was tested as an active-site-directed irreversible inhibitor of phosphotrasacetylase (EC. 2.3.1.8), carnitine acetyltransferase (EC 2.3.1.7) and citrate synthase (EC 4.1.3.7). Irreversible inhibition was observed only with phosphotransacetylase, which was derivatized via a simple bimolecular process ( k 2 = 197 ± 15 min −1· M −1 ). Acetyl-CoA provided complete substrate protection against the inactivation, while phosphate (a substrate) and desulfo-CoA (a competitive inhibitor) provided a partial protection. The inactivation was not reversed by dithiothreitol. The new reagent was a linear competitive inhibitor versus acetyl-CoA with both carnitine acetyltransferase ( K i = 41 μM) and citrate synthase ( K i = 20 μM). Chemical studies showed that S-dimethylarsino-CoA reacts with the thiol of N α -acetylcysteine but not with the side-chain functional groups of histidine and lysine. The nature of the chemical modification of cysteine was determined by investigating a model system. Thus the chemical reaction between the thioarsenite linkage of S-dimethylarsinobenzylmercaptan and the thiol of cysteine was shown to involve transesterification of the dimethylarsino group.

Estimation of peptide hormone noncovalent binding site functionality from frequencies of interaction of amino acid side chains in proteins.

A method is described for estimating the amino acid side chain functional groups most likely to occur at a receptor site (or other protein-type binding site) given a particular peptide hormone sequence. The predictions are based on mutual affinities of amino acid side chains, as manifested in the frequencies of side chain contacts occurring in proteins. The relative merits of various measures of these affinities are discussed, and a new set of contact frequency data based on 36 proteins (coordinate data taken from the Brookhaven Protein Data Bank) is presented. Evaluation of predictions was carried out using subunit-subunit interfaces as models for peptide-receptor association; accuracy of guesses was found to be 3-4 times better than random, according to this measure. Computer programs for carrying out all requisite data manipulations are described.

Reduction of Trichloromethyl Compounds by Hydrogen Donors Induced by Transition Metal Carbonyls, their Complexes, or their Salts

A new method of selective reduction of various trichloromethyl derivatives is described. The method may be applied to reduce α,α, α-trichloro-, α,α,α,β,β-pentachloro-, α,α,α,ω-tetrachloro-, and α,α,α,γ-tetrachloroalkanes as well as for gem-trichloroalkanes containing aromatic or functional groups in side chains, to the corresponding α,α-dichloromethyl compounds. Secondary alcohols, mercaptans, silicon hydrides, amines, and amides are employed as reducing agents. The reaction is initiated by transition metal carbonyls, their complexes, or their salts. 1. Introduction 2. Structural Effects of the Substrate 2.1. Tetrachloromethane and Trichloromethane 2.2. α,α,α-Tri- , α,α,α,ω-Tetra-, and α,α,α,γ- Tetrachloroalkanes 2.3. α,α,α,β-Tetrachloro- and α,α,α, β,β-Pentachloroalkanes 2.4. 2,2-Bis[4-chlorophenyl]-1,1,1-trichloroethane (DDT), its Analogues, and Related Compounds 2.5. Trichloromethyl Compounds Containing Functional Groups as Substituents 3. Conclusions

New arenemanganese dicarbonyl cyanides with ?-functional groups in side chain

New arenemanganese dicarbonyl cyanides with ω-functional substituents in the side chain were prepared, and a principally new possibility for nitrogen of the CN group coordinated with manganese in arenemanganese dicarbonyl cyanides to enter into additional complex formation with an atom of a transition metal was shown.

Amino acids and peptides. VI. Curtius rearrangement of acyl amino acid and peptide azides and reactivity of the isocyanates.

Studies on the rate of Curtius rearrangement of acyl amino acid and peptide azides were carried out by means of IR (infrared) spectrophotometry at 25°. It was found that Z-Gly-N3 and Z-Pro-N3 were more stable than the other acyl amino acid azides. The reactivity of isocyanates derived from azides with side chain functional groups of various amino acids or additives was also studied. It was found that isocyanates thus obtained were decomposed in the presence of triethylamine, its hydrochloride or 1-hydroxy-benzotriazole at 25°.

Phosphinyl- and Phosphinothioylamino Acids and Peptides. IV. Further Examples of Use of the Diphenylphosphinothioyl Group for the Protection of Amino Acids

Abstract The preparation and purification of diphenylphosphinothioyl(Ppt)-amino acids were studied. The side-chain functional groups of tyrosine and cysteine were found to react also with diphenylphosphinothioyl chloride to form O-Ppt and S-Ppt derivatives. Acidic reagents for the removal of N-Ppt group were examined by using N,O-bis-Ppt-tyrosine ethyl ester (III) as the most difficult model, HCl in HCO2H–CH2Cl2 being found to be most preferable. The O- and S-Ppt bonds were stable during the course of acidic treatments, but could be removed by alkaline hydrolysis. An application of Ppt-amino acids to the solid phase peptide synthesis is given.

Use of random copolymers to determine the helix-coil stability constants of the naturally occurring amino acids

Abstract Short-range interactions dominate in determining the conformational preferences of the amino acid residues in proteins, and a variety of procedures (based on this concept) have been developed to predict the conformational states of the residues of a protein molecule. This paper is concerned with two such conformational states, helical and non-helical (or coil) states; the relative preferences of each of the twenty naturally occurring amino acids for these two states can be expressed in terms of the Zimm-Bragg parameters s and σ. In principle, these parameters can be determined from experimental studies of the thermally-induced helix-coil transition in homopolymers of amino acids in water. However, since most homopolyamino acids are insoluble in water, or are not helical, or (if helical) do not melt between 0 and 100°C in water, resort is had to the host-guest technique in which a random copolymer of a water-soluble host residue and a small amount of a guest residue is prepared. Using the helix-coil transition curves of such a copolymer, and the values of s and σ for the host homopolymer, it is possible to compute the values of s and σ over the temperature range of 0 – 70°C for the guest residue which is, in turn, each of the twenty naturally occurring amino acids. In most cases, the random copolymers are prepared from their N-carboxyan-hydrides, using suitable blocking groups to protect otherwise-reactive side-chain functional groups. The water-soluble copolymers are checked for the absence of racemization, α → β shifts, etc., and for the required degree of randomness. For example, for methionine as a guest residue, cyanogen bromide cleavage of the polymer chain yields a series of oligopeptides which indicates that the methionine was incorporated randomly in the chain. When the resulting values of s and σ are compared to the frequencies of occurrence of helical and non-helical conformations in proteins, a good correlation is obtained in most cases. In those cases where the correlation breaks down, the discrepancy provides information about the influence of specific long-range (e.g., electrostatic) interactions on the helical preferences of the given amino acid residues. The statistical weights deduced from the one-dimensional short-range interaction model are then incorporated with medium- and long-range interactions into a model to try to predict the three-dimensional structures of globular proteins.

Cd spectra of DNP derivatives of aromatic α-amino acids and related compounds: DNP-aromatic rule as a method for determining absolute configuration of chiral amines of RCH(NH 2)XAr type

Introduction of an aromatic group to the side-chain functional group or to the α-car☐yl group of aliphatic DNP-α-amino acids gives compounds which can be regarded as analogs of aromatic DNP-α-amino acids. DNP-aromatic rule 1 has been proved applicable to these compounds and also to the derivatives of DNP-phenylalanine homologs in which the car☐yl group is modified variously. By summarizing the compiled data extension of the DNP-aromatic rule to the DNP-derivatives of chiral amines with a general formula R-CH(NH 2)-XAr is proposed.

Conformational analysis of Methionine-Enkephalin and some analogs

Conformational energy calculations on Methionine-Enkephalin and on several of its analogues indicate that the calculated lowest energy conformation of the native enkephalin may not be the conformer which interacts at the opioid active site. Substitution at the end groups and various D and L-Alanine analogs were examined and a low energy conformation which differs from the native low energy conformer was found for the very active analog, [D-Ala 2]-Met-Enkephalin-NH 2. The stereopositions of side-chain functional groups are discussed and compared to the structure of morphine.

Kinetic Studies on the Reactivity of Three Side-chain Functional Groups on Triesters of lsocyanuric Acid

The three step alkaline hydrolysis of tris(2-acetoxyethyl)isocyanurate (TAEIC), tris(methoxycarbonylmethyl)isocyanurate (TMCMIC) and tris(2-methoxycarbonylenthyl)isocyangrurate (TMCEIC), and the three step reaction of tris(2, 3-epoxypropyl)isocyanurate (TEPIC) with either substituted benzoic acids or sodium thiosulfate have been investigated under various conditions.The three rate constants have been determined by use of the general method of calculating the rate constants for a three-step consecutive-competitive second-order reaction of the type A+B → C+F, A+C → D+F, A+D → E+FIt was observed that in the hydrolysis of TAEIC and in the reaction between TEPIC apd substituted benzoic acids, the ratio of k1/k3 and k2/k3 were 3 and 2, respectively, whereas in the hydrolysis of TMCMIC and TMCEIC and in the reaction of TEPIC with sodium thiosulfate, the ratio were as follows; k1/k3> 3 and k2/k3> 2. The experimental observantion can be explained on the basis of the isocyanurate-ions or neutral molecules in the several steps.

Solid-phase synthesis with attachment of peptide to resin through an amino acid side chain: (8-lysine)-vasopressin.

It is proposed that the scope of solid-phase peptide synthesis could be considerably broadened by attaching peptides to the solid-phase through functional side-chain groups rather than through the commonly used alpha-carboxyl groups. Side-chain attachment offers the use of a large variety of chemical linkages to solid supports. Attachment through the epsilon-amino group of the lysine residue to a polystyrene resin has been applied to a solid-phase synthesis of lysine-vasopressin. N(alpha)-tert-butyl-oxycarbonyl-L-lysyl-glycinamide was condensed with chloroformoxymethyl polystyrene-2% divinylbenzene resin. After removal of the N(alpha)-protecting tert-butyloxycarbonyl group, the peptide chain was elongated by standard Merrifield procedures to give Tos-Cys(Bzl)-Tyr-Phe-Glu-(NH(2)) - Asp(NH(2)) - Cys(Bzl) - Pro - Lys(Z - resin) - Gly-NH(2). Cleavage from the resin with HBr in dioxane or trifluoroacetic acid gave a partially protected nonapeptide hydrobromide. For purification, it was converted into a fully protected peptide by treatment with benzyl p-nitro-phenyl carbonate and crystallized. Deprotection by sodium in liquid ammonia, oxidative cyclization, IRC-50 desalting, and ion-exchange chromatography gave lysinevasopressin with high potency in a rat-pressor assay.