Crystal and molecular structure of putrescine DL- glutamic acid complex

The polyamines spermine, spermidine, putrescine, cadaverine, etc. have been implicated in a variety of cellular functions. However, details of their mode of interaction with other ubiquitous biomolecules is not known. We have solved a few structures of polyamine-amino acid complexes to understand the nature and mode of their interactions. Here we report the structure of a complex of putrescine with DL-glutamic acid. Comparison of the structure with the structure of putrescine-L-glutamic acid complex reveals the high degree of similarity in the mode of interaction in the two complexes. Despite the presence of a centre of symmetry in the present case, the arrangement of molecules is strikingly similar to the L-glutamic acid complex.

The crystal and molecular structure of putrescine - di-glutamic acid complexes

The polyamines spermine, spermidine, putrescine, cadaverine, etc. have been implicated in a variety of cellular functions. However, details of their mode of interaction with other ubiquitous biomolecules is not known. We have solved a few structures of polyamine-amino acid complexes to understand the nature and mode of their interactions. Here we report the structure of a complex of putrescine with DL-glutamic acid. Comparison of the structure with the structure of putrescine-L-glutamic acid complex reveals the high degree of similarity in the mode of interaction in the two complexes. Despite the presence of a centre of symmetry in the present case, the arrangement of molecules is strikingly similar to the L-glutamic acid complex.

X-ray studies on crystalline complexes involving amino acids and peptides. XXI. Structure of a (1:1) complex between L-phenylalanine and D-valine

CsHllNO2.C9HilNO2, Mr = 282.3, P1, a = 5.245 (1), b = 5.424 (1), c = 14.414 (2) A, a = 97.86 (1), fl = 93-69 (2), y = 70-48 (2) °, V= 356 A 3, Z = 1, O m = 1-32 (2), Dx = 1.32 g cm-3, h(Mo Ka) = 0-7107 A, g = 5-9 cm-1, F(000) = 158, T= 298 K, R=0.035 for 1518 observed reflections with I>2tr(I). The molecules aggregate in double layers, one ayer made up of L-phenylalanine molecules and the other of D-valine molecules. Each double layer is stabilized by interactions involving main-chain atoms of both types of molecules. The interactions include hydrogen bonds which give rise to two head-to-tail sequences. The arrangement of molecules in the complex is almost the same as that in the structure of DL-valine (and DL-leucine and DL-isoleucine) except for the change in the side chain of L molecules. The molecules in crystals containing an equal number of L and O hydrophobic amino-acid molecules thus appear to aggregate in a similar fashion, irrespective of the precise details of the side chain.

Purification of 3,5-Dichlorocatechol 1,2-Dioxygenase, a Nonheme Iron Dioxygenase and a Key Enzyme in the Biodegradation of a Herbicide, 2,4-Dichlorophenoxyacetic acid (2,4-D), from Pseudomonas cepacia CSV90

An enzyme which cleaves the benzene ring of 3,5-dichiorocatechol has been purified to homogeneity from Pseudomonas cepacia CSV90, grown with 2,4-dichlorophenoxyacetic acid (2,4-D) as the sole carbon source. The enzyme was a nonheme ferric dioxygenase and catalyzed the intradiol cleavage of all the examined catechol derivatives, 3,5-dichlorocatechol having the highest specificity constant of 7.3 μM−1 s−1 in an air-saturated buffer. No extradiol-cleaving activity was observed. Thus, the enzyme was designated as 3,5-dichlorocatechol 1,2-dioxygenase. The molecular weight of the native enzyme was ascertained to be 56,000 by light scattering method, while the Mr value of the enzyme denatured with 6 M guanidine-HCl or sodium dodecyl sulfate was 29,000 or 31,600, respectively, suggesting that the enzyme was a homodimer. The iron content was estimated to be 0.89 mol per mole of enzyme. The enzyme was deep red and exhibited a broad absorption spectrum with a maximum at around 425 nm, which was bleached by sodium dithionite, and shifted to 515 nm upon anaerobic 3,5-dichlorocatechol binding. The catalytic constant and the Km values for 3,5-dichlorocatechol and oxygen were 34.7 s−1 and 4.4 and 652 μM, respectively, at pH 8 and 25°C. Some heavy metal ions, chelating agents and sulfhydryl reagents inhibited the activity. The NH2-terminal sequence was determined up to 44 amino acid residues and compared with those of the other catechol dioxygenases previously reported.

Mechanism of gallic acid biosynthesis in bacteria (Escherichia coli) and walnut (Juglans regia)

Gallic acid (GA), a key intermediate in the synthesis of plant hydrolysable tannins, is also a primary anti-inflammatory, cardio-protective agent found in wine, tea, and cocoa. In this publication, we reveal the identity of a gene and encoded protein essential for GA synthesis. Although it has long been recognized that plants, bacteria, and fungi synthesize and accumulate GA, the pathway leading to its synthesis was largely unknown. Here we provide evidence that shikimate dehydrogenase (SDH), a shikimate pathway enzyme essential for aromatic amino acid synthesis, is also required for GA production. Escherichia coli (E. coli) aroE mutants lacking a functional SDH can be complemented with the plant enzyme such that they grew on media lacking aromatic amino acids and produced GA in vitro. Transgenic Nicotiana tabacum lines expressing a Juglans regia SDH exhibited a 500% increase in GA accumulation. The J. regia and E. coli SDH was purified via overexpression in E. coli and used to measure substrate and cofactor kinetics, following reduction of NADP(+) to NADPH. Reversed-phase liquid chromatography coupled to electrospray mass spectrometry (RP-LC/ESI-MS) was used to quantify and validate GA production through dehydrogenation of 3-dehydroshikimate (3-DHS) by purified E. coli and J. regia SDH when shikimic acid (SA) or 3-DHS were used as substrates and NADP(+) as cofactor. Finally, we show that purified E. coli and J. regia SDH produced GA in vitro.

Redox regulation of protein tyrosine phosphatase 1B (PTP1B): Importance of steric and electronic effects on the unusual cyclization of the sulfenic acid intermediate to a sulfenyl amide

The redox regulation of protein tyrosine phosphatase 1B (PTP1B) via the unusual transformation of its sulfenic acid (PTP1B-SOH) to a cyclic sulfenyl amide intermediate is studied by using small molecule chemical models. These studies suggest that the sulfenic acids derived from the H2O2-mediated reactions o-amido thiophenols do not efficiently cyclize to sulfenyl amides and the sulfenic acids produced in situ can be trapped by using methyl iodide. Theoretical calculations suggest that the most stable conformer of such sulfenic acids are stabilized by n(O) -> sigma* (S-OH) orbital interactions, which force the -OH group to adopt a position trans to the S center dot center dot center dot O interaction, leading to an almost linear arrangement of the O center dot center dot center dot S-O moiety and this may be the reason for the slow cyclization of such sulfenic acids to their corresponding sulfenyl amides. On the other hand, additional substituents at the 6-position of o-amido phenylsulfenic acids that can induce steric environment and alter the electronic properties around the sulfenic acid moiety by S center dot center dot center dot N or S center dot center dot center dot O nonbonded interactions destabilize the sulfenic acids by inducing strain in the molecule. This may lead to efficient the cyclization of such sulfenic acids. This model study suggests that the amino acid residues in the close proximity of the sulfenic acid moiety in PTP1B may play an important role in the cyclization of PTP1B-SOH to produce the corresponding sulfenyl amide.

Ab Initio Molecular Dynamics Simulations of Amino Acids in Aqueous Solutions: Estimating pK(a) Values from Metadynamics Sampling

Changes in the protonation and deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. Here, we report calculations of the free-energy profile for the protonation deprotonation reaction of the 20 canonical alpha amino acids in aqueous solutions using ab initio Car-Parrinello molecular dynamics simulations coupled with metad-ynamics sampling. We show here that the calculated change in free energy of the dissociation reaction provides estimates of the multiple pK(a) values of the amino acids that are in good agreement with experiment. We use the bond-length-dependent number of the protons coordinated to the hydroxyl oxygen of the carboxylic and the amine groups as the collective variables to explore the free-energy profiles of the Bronsted acid-base chemistry of amino acids in aqueous solutions. We ensure that the amino acid undergoing dissociation is solvated by at least three hydrations shells with all water molecules included in the simulations. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pK(a) values with a mean relative error, with respect to experimental results, of 0.2 pK(a) units.

Hydrogelation of bile acid-peptide conjugates and in situ synthesis of silver and gold nanoparticles in the hydrogel matrix

Fabricating supramolecular hydrogels with embedded metal nanostructures is important for the design of novel hybrid nanocomposite materials for diverse applications such as biosensing and chemosensing platforms, catalytic and antibacterial functional materials etc. Supramolecular self-assembly of bile acid-dipeptide conjugates has led to the formation of new supramolecular hydrogels. Gelation of these molecules depends strongly on the hydrophobic character of the bile acids. The possibility of in situ fabrication of Ag and Au NPs in these supramolecular hydrogels by incorporating Ag+ and Au3+ salts was investigated via photoreduction. Chemical reductions of Ag+ and Au3+ salts in the hydrogels were performed without adding any external stabilizing agents. In this report we have shown that the color, size and shape of silver nanoparticles formed by photoreduction depend on the amino acid residue of the side chain.