Conformational aspects of polypeptide structure. XLI. Crystal structure of S-thiazolidine-4-carboxylic acid and helical structure of poly((S)-thiazolidine-4-carboxylic acid)

The helical structures of poly[(S)-thiazolidine-4-carboxylic acid], in the cis and trans forms, were redetermined by using the new sets of bond angles and bond lengths established by X-ray diffraction analysis of L -thioproline. Calculations of the helical structures of poly-L -proline and poly[(S)-oxazolidine-4-carboxylic acid] were also repeated. As a result of these energy calculations, it is suggested that, in contrast to poly-L -proline and poly[(S)-oxazolidine-4-carboxylic acid], poly[(S)-thiazolidine-4-carboxylic acid] should not mutarotate from the trans to the cis form. This result is due to the fact that the energy barrier for the conversion is most likely too high. Previous experimental work is consistent with this finding.     

The x ray structure of thiazolidine-4-carboxylic acid

The X ray crystal structure of thiazolidine-4-carboxylic acid has been determined. It appears that the anomalously low basicity of this compound in comparison with that of its non-sulfur-containing analogue, proline, is due to the resonance stabilization of the unprotonated form of thiazolidine-4-carboxylic acid. This stabilization is conferred through an increased interaction of the sulfur atom with the thiazolidine-4-carboxylic acid ring that is only possible when the nitrogen atom maintains a trigonal geometry. This effect seems also to account for the greater instability of N-hydroxymethylamines formed from thiazolidine-4-carboxylic acid as compared to those formed from proline. The crystal structure shows, in addition, an intramolecular hydrogen bond in combination with a bifurcated hydrogen bond.     

Crystal structure of L-2-oxothiazolidine-4-carboxylic acid

Crystals of the title compound, L-2-oxothiazolidine-4-carboxylic acid, OTC (C4H5NO3S), grown from an aqueous solution are orthorhombic, space group P2(1)2(1)2(1) with the following cell parameters at 22 +/- 3 degrees: a = 5.381(1), b = 5.961(1), c = 17.929(3)A, V = 575.1A(3), Mr = 146.2, Dc = 1.688 g.cm-3, mu = 43.9 cm-1 and Z = 4. The crystal structure was solved by the application of direct methods and refined to an R value of 0.032 for 596 reflections with I greater than 3 sigma(I). The thiazolidine ring adopts a "twist" conformation. This structure contains a short (2.619(3)A) intermolecular hydrogen bond between the carboxyl OH and the oxygen of the 2-oxo moiety, a feature common to most acyl amino acids and acyl peptides.     

Conformational studies of peptides. The crystal structures of N-acetyl-L-prolinamide and N-acetyl-(S)-thiazolidine-4-carboxamide

The crystal structure of N′-acetyl-L -prolinamide and its isomorphous alalog N′-acetyl-(S)-thiazolidine-4-carboxamide was determined using highly accurate parameters obtained by room- and low-temperature data-collecting systems. Both crystals are orthorhombic, space group P2₁2₁2₁, with four molecules per unit cell held together by a hydrogen-bond system that extends in all directions. Both molecules exhibit the following conformational features: the acetyl group is in the trans configuration in respect to the tertiary amide. The primary amide is almost at right angles with respect to the mean plane of the ring and the –NH₂ group is over the ring. The pyrrolidine and thiazolidine rings were found to be rather flexible with C^β puckering in the former and sulfur in the latter.     

Conformational aspect of polypeptide structure. XLIV. Conformational transitions of poly(N-methyl-alanines) induced by trifluoroacetic acid

The synthesis of poly(N-methyl-L -alanine) and poly (N-methyl-DL -alanine) are described. The polymers were examined by 220 MHz high-resolution nuclear magnetic resonance (nmr) and circular dichroism (CD). The results demonstrate that poly(N-methyl-L -alanine) exists as an ordered helical structure with all the amide bonds in the trans configuration in appropriate solvents. As trifluoroacetic acid (TFA) is added to the solutions of the polymer in helix-supporting solvents, resonances corresponding to both trans and cis amide conformations of N-methyl, C-methyl, and α-CH are observed. The presence of both the trans and the cis peptide bonds in a polymer chain disrupts the ordered structures. Our conclusions from CD data are in agreement with the nmr results. Ultracentrifugation shows that degradation of the polymer chain does not occur during the TFA treatment.     

Amino acid sequence of a soybean (Glycine max) seed polypeptide having a poly(L-aspartic acid) structure

A polypeptide of Mr 4400 was isolated from soybean (Glycine max) seeds by extraction with 60% ethanol followed by ion-exchange and reverse-phase chromatography. The peptide contains an unusually high amount of aspartic acid residues (approximately 25%, and hence is designated as soybean aspartic acid-rich peptide). Its complete primary structure was determined by conventional methods to be the following. Ser-Lys-Trp-Gln-His-Gln-Gln-Asp-Ser-Cys-Arg-Lys-Gln-Leu-Gln-Gly-Val-Asn- Leu-Thr-Pro-Cys-Glu-Lys-His-Ile-Met-Glu-Lys-Ile-Gln-Gly-Arg-Gly-Asp-Asp- Asp-Asp-Asp-Asp-Asp-Asp-Asp A striking features of this primary structure is the presence of a poly(L-aspartic acid) sequence at the carboxyl terminus, and this polyaspartyl segment was found to precipitate bovine trypsin. The presence of the putative cell attachment sequence Arg-Gly-Asp was also noted.     

Polynucleotides. XL. Synthesis and properties of poly 2''-azido-2''-deoxyadenylic acid.

Poly 2'-azido-2'-deoxyadenylic acid (Poly Az) was synthesized from 2'-azido-2'-deoxyadenosine diphosphate by polynucleotide phosphorylase. Poly (Az) has U.V. absorption properties similar to poly (A) and hypochromicity of 40% at 0.1 M Na+ and neutrality. CD curve also resembled to that of poly (A), but has smaller ellipticity. Titration of poly (Az) with HCl gave a transition at pH 5.5, but exact structure of the acid-form complex was not elucidated. Upon mixing with poly (U), poly (Az) forms a 1:1 and 1:2 complexes having Tm's somewhat higher than that of poly (A)- poly (U) complex in the same condition.     

Peptides containing 4-amino-1,2-dithiolane-4-carboxylic acid (Adt): conformation of Boc-Adt-Adt-NHMe and NH...S interactions.

To study the conformational preferences induced by the insertion of the 4-amino-1,2-dithiolane-4-carboxylic acid (Adt) residue into a peptide backbone, the achiral N-protected dipeptide methylamide Boc-Adt-Adt-NHMe (1) was synthesized and its crystal state and solution conformation studied and compared with that exhibited by its carba-analogue Boc-Ac5c-Ac5c-NHMe containing two residues of 1-aminocyclopentane-1-carboxylic acid (Ac5c). Compound 1 in the crystal adopts a type-III beta-turn conformation and an analogous structure is that preferred in chloroform solution as established by 1H-NMR and NOE information. In the crystal packing three different Adt rings form a cavity and the involved sulphur atoms give rise to unusual multiple interactions with one NH group. The chemical nature of these intermolecular and intramolecular main-chain...side-chain NH...S interactions are discussed in terms of quantum chemical calculations.     

The effect of the L-azetidine-2-carboxylic acid residue on protein conformation. III. Collagen-like poly(tripeptide)s

The chemical and biological properties of collagen are altered by the biosynthetic substitution of the L-azetidine-2-carboxylic acid(Aze) residue in the place of proline. The reasons for this alteration have been studied by means of conformational energy computations on single- and triple-stranded structures formed by poly(Gly-X-Y) poly(tripeptide)s, where X and Y can be Pro or Aze. The most stable triple helix formed by Poly(Gly-Pro-Aze) is collagen-like, but all low-energy triple helices that can be formed by poly(Gly-Aze-Pro) and poly(Gly-Aze-Aze) are very different from collagen. Thus, the regular substitution of Aze for Pro in position X is not compatible with the collagen structure. In the absence of solvent effects, all of these triple helices are stable, relative to the statistical coil, but the substitutions reduce the stability of the collagen-like triple helix, as compared with poly(Gly-Pro-Pro).     

Mechanistic crystallography. Mechanism of inactivation of gamma-aminobutyric acid aminotransferase by (1R,3S,4S)-3-amino-4-fluorocyclopentane-1-carboxylic acid as elucidated by crystallography

(1R,3S,4S)-3-Amino-4-fluorocyclopentane-1-carboxylic acid (7) was previously shown to be a mechanism-based inactivator of gamma-aminobutyric acid aminotransferase (GABA-AT) [Qiu, J. and Silverman, R. B. (2000) J. Med. Chem. 43, 706-720]. Two mechanisms were considered as reasonable possibilities, a Michael addition mechanism and an enamine mechanism. On the basis of a variety of chemical studies, including tedious radiolabeling experiments, it was concluded that inactivation by 7 proceeds by a Michael addition mechanism. Here, a crystal structure of 7 bound to pig liver GABA-AT is reported, which clearly demonstrates that the adduct formed is derived from an enamine mechanism. This represents another example of how crystallography is an important tool for elucidation of inactivation mechanisms.     

Crystal structures of (2R,4R)-2-(polyhydroxyalkyl)-1,3-thiazolidine-4-carboxylic acids: condensation products of l-cysteine with d-hexoses

We report herein the first crystal structures of (4-carboxy-1,3-thiazolidin-2-yl)pentitols [2-(polyhydroxyalkyl)thiazolidine-4-carboxylic acids], condensation products of l-cysteine with d-galactose and d-mannose: 2-(d-galacto-pentahydroxypentyl)thiazolidine-4-carboxylic acid hydrate, Gal-Cys·H(2)O (1), and 2-(d-manno-pentahydroxypentyl)thiazolidine-4-carboxylic acid hydrate, Man-Cys·H(2)O (2). In 1 and 2 the compounds crystallize as zwitterions, with the carboxylic groups deprotonated and the thiazolidine N atoms protonated. The sugar moiety and carboxylate group are in a cis configuration relative to the thiazolidinium ring, which adopts different conformation: twisted (T) on C(β)-S in 1, and S-puckered envelope (E) in 2. The carbon chain of the galactosyl/mannosyl moiety remains in an extended zig-zag conformation. The orientation of the sugar O2 atom with respect to the thiazolidinium S and N atoms is trans-gauche in 1 and gauche-gauche in 2. The molecular conformation is stabilized by the intramolecular N-H?O(Cys) contacts in both 1 and 2 and by the additional N-H?O(Man) interaction in 2. The crystal packing of orthorhombic 1 and monoclinic 2 is determined mainly by N/O/C-H?O hydrogen bonds forming ribbons linked to each other by direct and water-mediated O/C-H?O/S contacts.     

Involvement of 30S ribosomal protein S1 in poly(U)-directed polyphenylalanine synthesis.

The effect of 30S ribosomal protein S1 on poly(U)-directed polyphenylalanine synthesis was studied using a highly purified cell-free system which was devoid of endogenous S1. The system consisted of homogeneous preparations of EF-Tu, EF-Ts, and EF-G, and 70S ribosomes from which protein S1 had been removed by poly(U)-cellulose column chromatography. It was found that protein S1 was indispensable for translation of poly(U) by an S1-depleted system at low concentrations of poly(U). On the other hand, at higher concentrations of poly(U), a considerable amount of polyphenylalanine was synthesized in the absence of added S1. The stimulatory effect of S1 was observed at all Mg2+ concentrations examined but was most pronounced at 10 mM Mg2+. Some physicochemical properties of the protein were also studied. It was demonstrated that the protein has an elongated shape with an axial ratio of approximately 8.5.     

Synthesis of L-2-oxothiazolidine-4-carboxylic acid

An improved synthesis of L-2- oxothiazolidine -4-carboxylic acid is described. The new procedure, which leads to excellent yields of product, does not require the use of phosgene. The new method is thus less hazardous than the original one, and is readily adaptable to the preparation of 35S-labeled product.     

The site of 1-aminocyclopropane-1-carboxylic acid synthesis in senescing carnation petals

To study the cause of the uneven production of ethylene by upper and basal portions of detached petals of carnation ( Dianthus caryophyllus L. cv. White Sim), the petals were divided and exposed to ethylene (30 μl 1^-1 for 16 h). The treatment induced rapid wilting and autocatalytic ethylene production in the basal portion similar to that induced in entire petals. In contrast to the response in entire petals and the basal portions, the upper portions responded to ethylene by delayed wilting and much lower ethylene production. Aminocyclopropane carboxylic acid (ACC)-synthase activity in the basal portion of the petals was 38 to 400 times that in the upper portion. In untreated detached petal pieces from senescing carnation flowers, ethylene production by the upper portion declined after 6 h while the basal portion was still producing ethylene at a steady rate 18 h later. Application of ACC to the upper portion of senescing petals increased their ethylene production. α-Aminooxyacetic acid (0.5 m M ), reduced the ethylene production of the senescing basal portion more than that of the upper portion. Endogenous ACC content in basal portions of senescing carnation petals was 3 to 4 times higher than in the upper parts. When detached senescing petals were divided immediately after detaching, the endogenous ACC levels in upper portions remained steady or declined during 24 h after division, while in the basal portions the ACC level rose steadily as in the intact petals. There was no change in the conjugated ACC in either portion after 24 h. Benzyladenine (BA) applied as a pretreatment to entire preclimacteric petals greatly reduced the development of ACC-synthase activity of the basal portion, but had little effect on the activity in the upper portion of the petal. In both portions, however, BA effectively reduced the conversion of ACC to ethylene.     

Activation of nuclear polypeptide synthesis in rat liver cells after inhibition of template protein synthesis. The role of nuclear polypeptide synthesis in the changes of the chromatin structure

The correlation between the rates of nuclear polypeptide synthesis (NPS) and matrix protein synthesis in rat liver cells was investigated. It was shown that NPS is activated under conditions of protein synthesis inhibition in the cytoplasm. Model experiments revealed that the NPS and ADP ribosylation systems compete for chromatin structure: ADP ribosylation induces condensation, while NPS--decondensation of chromatin.