tert-Butyl (6S)-4-hydroxy-6-isobutyl-2-oxo-1,2,5,6-tetrahydropyridine-1-carboxylate and tert-butyl (4R,6S)-4-hydroxy-6-isobutyl-2-oxopiperidine-1-carboxylate

X-ray studies reveal that tert-butyl (6S)-6-isobutyl-2,4-dioxopiperidine-1-carboxylate occurs in the 4-enol form, viz. tert-butyl (6S)-4-hydroxy-6-isobutyl-2-oxo-1,2,5,6-tetrahydropyridine-1-carboxylate, C14H23NO4, when crystals are grown from a mixture of dichloromethane and pentane, and has an axial orientation of the isobutyl side chain at the 6-position of the piperidine ring. Reduction of the keto functionality leads predominantly to the corresponding beta-hydroxylated delta-lactam, tert-butyl (4R,6S)-4-hydroxy-6-isobutyl-2-oxopiperidine-1-carboxylate, C14H25NO4, with a cis configuration of the 4-hydroxy and 6-isobutyl groups. The two compounds show similar molecular packing driven by strong O-H...O=C hydrogen bonds, leading to infinite chains in the crystal structure.

(6S)-6-Isobutylpiperidine-2,4-dione and (4R,6S)/(4S,6S)-4-hydroxy-6-isobutylpiperidin-2-one

The crystal structure of (6S)-6-isobutylpiperidine-2,4-dione, C9H15NO2, shows that the keto tautomer is favoured in the solid state. The reduction of the keto functionality leads to the corresponding 4-hydroxy-6-isobutylpiperidin-2-one, C9H17NO2, with an 84:16 cis/trans ratio, containing the 4R,6S and 4S,6S isomers; the ratio of the two isomers was determined by NMR analysis of the reaction mixture. Crystals obtained from the mixture of both isomers have been studied and shown to contain the isomers in a 86:14 ratio. Hence, both X-ray and NMR analyses show that crystallization does not select the major diastereomer formed by the reduction. In both crystal structures, the two independent molecules dimerize through an R2(2)(8) hydrogen-bond motif between adjacent amide groups.

Purification, crystallization and preliminary X-ray diffraction data of L7Ae sRNP core protein from Pyrococcus abyssii

The L7Ae sRNP core protein from Pyrococcus abyssii was crystallized using the sitting-drop vapour-diffusion method. Crystals were obtained in the presence of MgCl(2), PEG 2000 MME and acetate buffer at pH 4.0. A native data set has been collected at 2.9 A resolution using a rotating-anode generator at room temperature. Crystals belong to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 70.7, b = 112.9, c = 34.8 A. There are two monomers of MW 14 200 Da per asymmetric unit and the packing density V(M) is 2.45 A(3) Da(-1). A molecular-replacement analysis gave solutions for the rotation and translation functions.

Synthesis of Enantiopure 4-Hydroxypipecolate and 4-Hydroxylysine Derivatives from a Common 4,6-Dioxopiperidinecarboxylate Precursor

tert-Butyl 2-substituted 4,6-dioxo-1-piperidinecarboxylates 4 have been prepared in good yield starting from Boc-Asp-O(t)Bu and other beta-amino acids. By analogy with chiral tetramic acids, their reduction by NaBH(4) in CH(2)Cl(2)/AcOH afforded the corresponding cis-4-hydroxy delta-lactams in good yield and stereoselectivity (68-98% de). In the absence of the A(1,3) strain (reduction of 6-substituted 2,4-dioxo-1-piperidines 7), the cis-4-hydroxy isomer was still obtained as the major product but the de values were consistently lower. 4-Hydroxy-6-oxo-1,2-piperidinedicarboxylate 2a, readily accessible from Boc-Asp-O(t)Bu (three steps, 63% overall yield), has proven to be an excellent building block for the synthesis of cis- and trans-4-hydroxypipecolates 17 and 24 (52 and 36% overall yield, respectively) and for the synthesis of a protected 4-hydroxylysine derivative 29 (41% overall yield).

The `Octopus' plate for protein crystallization under an electric field

A piece of equipment, adapted to a vapour-diffusion plate, has been designed to apply an external electrical field during the crystallization of protein samples.

The functional glycosyltransferase signature sequence of the human beta 1,3-glucuronosyltransferase is a XDD motif

The human beta 1,3-glucuronosyltransferase I (GlcAT-I) is the key enzyme responsible for the completion of glycosaminoglycan-protein linkage tetrasaccharide of proteoglycans (GlcA beta 1,3Gal beta 1,3Gal beta 1,4Xyl beta 1-O-serine). We have investigated the role of aspartate residues Asp194-Asp195-Asp196 corresponding to the glycosyltransferase DXD signature motif, in GlcAT-I function by UDP binding experiments, kinetic analyses, and site-directed mutagenesis. We presented the first evidence that Mn2+ is not only essential for GlcAT-I activity but is also required for cosubstrate binding. In agreement, kinetic studies were consistent with a metal-activated enzyme model whereby activation probably occurs via binding of a Mn2+.UDP-GlcA complex to the enzyme. Mutational analysis showed that the Asp194-Asp195-Asp196 motif is a major element of the UDP/Mn2+ binding site. Furthermore, determination of the individual role of each aspartate showed that substitution of Asp195 as well as Asp196 to alanine strongly impaired GlcAT-I activity, whereas Asp194 replacement produced only a moderate alteration of the enzyme activity. These findings along with molecular modeling and three-dimensional structure comparison of the GlcAT-I catalytic center with that of the Bacillus subtilis glycosyltransferase SpsA provided evidence that the interactions of Asp195 with the ribose moiety of UDP and of Asp196 with the metal cation Mn2+ were crucial for GlcAT-I function. Altogether, these results indicated that, similarly to the SpsA enzyme, the nucleotide binding site of GlcAT-I contains a XDD motif rather than a DXD motif.

Crystallization and preliminary X-ray studies of the glutaredoxin from poplar in complex with glutathione

A monocysteinic mutant of poplar glutaredoxin (C30S) has been overproduced and purified. The protein has been crystallized in complex with glutathione using the hanging-drop vapour-diffusion technique in the presence of PEG 4000 as a precipitating agent. A native data set was collected at 1.55 A resolution. The crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 45.7, b = 49.1, c = 104.8 A. Isomorphous crystals of a selenomethionine derivative were grown under the same conditions. Three data sets were collected at 1.73 A using the FIP synchrotron beamline at the ESRF. The positions of the Se atoms were determined and model rebuilding and refinement are in progress.

Crystal structure of two ternary complexes of phosphorylating glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus with NAD and D-glyceraldehyde 3-phosphate

The crystal structure of the phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Bacillus stearothermophilus was solved in complex with its cofactor, NAD, and its physiological substrate, D-glyceraldehyde 3-phosphate (D-G3P). To isolate a stable ternary complex, the nucleophilic residue of the active site, Cys(149), was substituted with alanine or serine. The C149A and C149S GAPDH ternary complexes were obtained by soaking the crystals of the corresponding binary complexes (enzyme.NAD) in a solution containing G3P. The structures of the two binary and the two ternary complexes are presented. The D-G3P adopts the same conformation in the two ternary complexes. It is bound in a non-covalent way, in the free aldehyde form, its C-3 phosphate group being positioned in the P(s) site and not in the P(i) site. Its C-1 carbonyl oxygen points toward the essential His(176), which supports the role proposed for this residue along the two steps of the catalytic pathway. Arguments are provided that the structures reported here are representative of a productive enzyme.NAD.D-G3P complex in the ground state (Michaelis complex).

Diastereoselective hydroxylation of 6-substituted piperidin-2-ones. An efficient synthesis of (2S,5R)-5-hydroxylysine and related alpha-amino acids

The synthesis of (2S,5R)-5-hydroxy-6-oxo-1,2-piperidinedicarboxylates (5) and related (3S,6R)-3-hydroxy-6-alkyl-2-oxo-1-piperidinecarboxylates has been developed. The approach is based on the asymmetric hydroxylation of enolates generated from the corresponding N-protected-6-substituted piperidin-2-ones. The utility of 5a as a precursor in the synthesis of (2S,5R)-5-hydroxylysine (1), an amino acid unique to collagen and collagen-like proteins, has also been demonstrated. (2S)-6-oxo-1,2-piperidinedicarboxylates (6) required for hydroxylation studies were prepared in 38-74% yield, starting from conveniently protected aspartic acid as inexpensive chiral adduct. Hydroxylation of 6 to 5 proceeds in high yield and excellent diastereoselectivity by treatment of their Li-enolate with (+)-camphorsulfonyloxaziridine at -78 degrees C. Ring opening of di-tert-butyl (2S,5R)-6-oxo-1,2-piperidinedicarboxylate ((5R)-5a) under reductive conditions afforded the corresponding 1,2-diol (17) in 91%, which was further transformed to (2S,5R)-5-hydroxylysine in four steps (84%). 17 is also a versatile intermediate in the preparation of tert-butyl (2S,5R)-2-[(tert-butoxycarbonyl)amino]-5-hydroxy-6-iodohexanoate (3) and tert-butyl (2S)-2-[(tert-butoxycarbonyl)amino]-4-[(2R)-oxiranyl]butanoate (4), two amino acid derivatives used in the total synthesis of the bone collagen cross-link (+)-pyridinoline (2a).

Comparative analysis of thermoadaptation within the archaeal glyceraldehyde-3-phosphate dehydrogenases from mesophilic Methanobacterium bryantii and thermophilic Methanothermus fervidus

To gain insight into the molecular determinants of thermoadaptation within the family of archaeal glyceraldehyde-3-phosphate dehydrogenases (GAPDH), a homology-based 3-D model of the mesophilic GAPDH from Methanobacterium bryantii was built and compared with the crystal structure of the thermophilic GAPDH from Methanothermus fervidus. The homotetrameric model of the holoenzyme was initially assembled from identical subunits completed with NADP molecules. The structure was then refined by energy minimization and simulated-annealing procedures. PROCHECK and the 3-D profile method were used to appraise the model reliability. Striking molecular features underlying the difference in stability between the enzymes were deduced from their structural comparison. First, both the increase in hydrophobic contacts and the decrease in accessibility to the protein core were shown to discriminate in favor of the thermophilic enzyme. Besides, but to a lesser degree, the number of ion pairs involved in cooperative clusters appeared to correlate with thermostability. Finally, the decreased stability of the mesophilic enzyme was also predicted to proceed from both the lack of charge-dipole interactions within alpha-helices and the enhanced entropy of unfolding due to an increase in chain flexibility. Thus, archaeal GAPDHs appear to be governed by thermoadaptation rules that differ in some aspects from those previously observed within their eubacterial counterparts.

Disulphide dimerised peptide creates a crystal contact in an anti-peptide antibody

Although many Fab derived from human and murine antibodies have been crystallized, several such fragments, including anti-peptide Fab 4 x 11, remain problematic for crystallisation. Diffracting crystals have been obtained for this Fab only in complex with a cysteine containing peptide CGGIRGERA. The IRGERA portion contained in the C-terminus of histone H3 is recognised by the monoclonal antibody and the CGG portion is an essential spacer. Crystallisation experiments and seeding studies show that disulphide bond formation is essential for obtaining crystals. Data has been collected to 2.7 A resolution, and the structure solved by molecular replacement. The asymmetric unit contains two antibodies whose binding sites are face-to-face in an non-crystallographic approximate two-fold rotational axis. We find two Fab in the asymmetric unit with the two antigen combining sites facing each other. This result was unexpected since it has been common practice to avoid the cysteine-containing peptides because of heterogeneity, since the peptide solution is likely to contain both dimeric and monomeric peptides. This result suggests that the cysteine containing peptides used in immunisation for coupling them to a carrier protein could also be used to screen for crystals. Structural data obtained for the same peptides as those used in the immunisation is valuable to evaluate to what extent the linker to the carrier protein may have contributed to the shaping of the antibody binding site. The introduction of exposed cysteines on the surface of proteins by site directed mutagenesis could help resolve difficult crystallisation cases. Should these not form a disulphide bridge in the crystal but nonetheless crystallize, the free cysteine could be used to make a heavy atom derivative for isomorphous replacement.

Crystallization and preliminary X-ray diffraction studies of the peptide methionine sulfoxide reductase B domain of Neisseria meningitidis PILB

Peptide methionine sulfoxide reductases (Msr) are ubiquitous enzymes that catalyse the reduction of free and protein-bound methionine sulfoxide back to methionine via sulfenic acid chemistry. Two classes of Msrs, MsrA and MsrB, have been described. The fact that the two Msrs display opposite stereoselectivities and have no sequence identity suggests that there is no structural similarity between the two classes. No three-dimensional structure of a MsrB is known. In the present report, the MsrB subdomain of Neisseria meningitidis PILB was used to grow orthorhombic crystals by the hanging-drop vapour-diffusion technique. The crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 44.0, b = 118.6, c = 138.5 A. Crystals of selenomethionine-substituted MsrB were grown under the same conditions in order to use the MAD method for structure determination. Three diffraction data sets at 1.8 A resolution were collected. The positions of the Se atoms were determined and should result in a full structure determination.

Thioredoxins and related proteins in photosynthetic organisms: molecular basis for thiol dependent regulation

Thioredoxins are small molecular weight disulfide oxidoreductases specialized in the reduction of disulfide bonds on other proteins. Generally, the enzymes which are selectively and reversibly reduced by these proteins oscillate between an oxidized and inactive conformation and a reduced and active conformation. Thioredoxin constitutes the archetype of a family of protein disulfide oxidoreductases which comprises glutaredoxin and protein disulfide isomerase. Thioredoxin and glutaredoxin serve many roles in the cell, including the redox regulation of target enzymes and transcription factors. They can also serve as hydrogen donors to peroxiredoxins, recently discovered heme free peroxidases, the function of which is to get rid of hydroperoxides in the cell. This review describes the molecular basis for the functioning and interaction between these enzymes in photosynthetic organisms.

Crystallization and preliminary X-ray data of a bifunctional peroxiredoxin from poplar

Two variants (wild type and V152C mutant) of a bifunctional poplar peroxiredoxin have been overexpressed in Escherichia coli cells. The two recombinant enzymes were purified and crystallized using the hanging-drop vapour-diffusion technique. Data sets were collected to 1.62 and 2.48 A resolution using X-ray synchrotron-source radiation from two crystal forms of wild-type peroxiredoxin which belonged to the monoclinic space group P2(1) (with unit-cell parameters a = 59.26, b = 68.80, c = 75.71 A, beta = 93.45 degrees ) and to the orthorhombic space group P2(1)2(1)2 (with unit-cell parameters a = 64.70, b = 130.73, c = 35.59 A), respectively. Data were also collected to 2.17 A resolution using a home X-ray source from a V152C peroxiredoxin crystal which belongs to the triclinic space group (P1), with unit-cell parameters a = 36.65, b = 41.53, c = 58.06 A, alpha = 70.52, beta = 93.45, gamma = 64.31 degrees. Phases have been obtained using molecular replacement with the structure of human peroxiredoxin V (PDB code 1hd2) as a search model. Refinement of the structures is in progress.

Extractable polysaccharides of Panax quinquefolius L. (North American ginseng) root stimulate TNFalpha production by alveolar macrophages

We have investigated the immunostimulatory activity of the medicinal plant Panax quinquefolius L. (North American ginseng). Rat alveolar macrophages were treated with different extracts from 4-year old roots, and tumour necrosis factor alpha (TNF) production was used as a measure of immunostimulatory activity. Aqueous extracts of P. quinquefolius root (1-100 microg/ml) were found to significantly stimulate alveolar macrophage TNF release. Both a P. quinquefolius methanol extract containing ginsenosides (but no polysaccharides), and pure ginsenoside-Rb1, the major ginsenoside present in P. quinquefolius, were found to be inactive as TNF-stimulating agents. Significant TNF-stimulating activity was found in the extractable polysaccharide fraction, which was hydrolyzed and found to contain glucose, galactose, arabinose, rhamnose, and mannose. This represents the first evidence that North American ginseng exerts cytokine-stimulating activity on macrophages.

A pipecolic acid (Pip)-containing dipeptide, Boc-D-Ala-L-Pip-NH(i)Pr

The title dipeptide, 1-(tert-butoxycarbonyl-D-alanyl)-N-isopropyl-L-pipecolamide or Boc-D-Ala-L-Pip-NH(i)Pr (H-Pip-OH is pipecolic acid or piperidine-2-carboxylic acid), C(17)H(31)N(3)O(4), with a D-L heterochiral sequence, adopts a type II' beta-turn conformation, with all-trans amide functions, where the C-terminal amide NH group interacts with the Boc carbonyl O atom to form a classical i+3 --> i intramolecular hydrogen bond. The C(alpha) substituent takes an axial position [H(alpha) (Pip) equatorial] and the trans pipecolamide function is nearly planar.

Influence of silaproline on peptide conformation and bioactivity

The analogue gamma-(dimethylsila)-proline, denoted silaproline (Sip), was synthesized in both enantiomerically pure forms by diastereoselective alkylation of a chiral glycine equivalent with use of Schöllkopf's bis-lactim ether method. The effect of replacing a proline residue in model peptides by this new proline surrogate has been examined in the crystal state by X-ray diffraction and in solution by IR absorption and NMR techniques. Silaproline and proline-containing sequences exhibit very similar conformational properties. Silaproline was also substituted for proline in a neurotensin (8-13) analogue that retained biological activity and exhibited enhanced resistance to biodegradation.

Crystal structure of the W35A mutant thioredoxin h from Chlamydomonas reinhardtii: the substitution of the conserved active site Trp leads to modifications in the environment of the two catalytic cysteines

The conformational analysis of W35A thioredoxin h from the eukaryotic green alga Chlamydomonas reinhardtii in the solid state has been carried out by x-ray diffraction, with the aim to clarify the role of Trp in the catalysis. Comparative analysis of W35A mutant with wild-type (WT) thioredoxin shows that, even if the structural motif of thioredoxin is not perturbed, the substitution of Trp35 by an Ala leads to significant changes in protein conformation near the active site. This rearrangement increases its solvent exposure and explains the change of the pKa values of the catalytic cysteines. The substitution of the Trp residue also influences the crystal packing as well as the recognition ability of thioredoxin. The solid state analysis suggests that the Trp residue has a structural function both to force the active site in the bioactive conformation, and to mediate the protein-protein recognition.