Amino Acid Based MOFs: Synthesis, Structure, Single Crystal to Single Crystal Transformation, Magnetic and Related Studies in a Family of Cobalt and Nickel Aminoisophthales

Four new 5-aminoisophthalates of cobalt and nickel have been prepared employing hydro/solvothermal methods: [Co2(C8H5NO4)2(C4H4N2)(H2O)2]·3H2O (I), [Ni2(C8H5NO4)2(C4H4N2)(H2O)2]·3H2O (II), [Co2(H2O)(μ3-OH)2(C8H5NO4)] (III), and [Ni2(H2O)(μ3-OH)2(C8H5NO4)] (IV). Compounds I and II are isostructural, having anion-deficient CdCl2 related layers bridged by a pyrazine ligand, giving rise to a bilayer arrangement. Compounds III and IV have one-dimensional M−O(H)−M chains connected by the 5-aminoisophthalate units forming a three-dimensional structure. The coordinated as well as the lattice water molecules of I and II could be removed and inserted by simple heating−cooling cycles under the atmospheric conditions. The removal of the coordinated water molecule is accompanied by changes in the coordination environment around the M2+ (M = Co, Ni) and color of the samples (purple to blue, Co; green to dark yellow, Ni). This change has been examined by a variety of techniques that include in situ single crystal to single crystal transformation studies and in situ IR and UV−vis spectroscopic studies. Magnetic studies indicate antiferromagnetic behavior in I and II, a field-induced magnetism in III, and a canted antiferromagnetic behavior in IV.

Hybrid peptide design. Hydrogen bonded conformations in peptides containing the stereochemically constrained gamma-amino acid residue, gabapentin

he crystal structure of 12 peptides containing the conformationally constrained 1-(aminomethyl)cyclohexaneacetic acid, gabapentin (Gpn), are reported. In all the 39 Gpn residues conformationally characterized so far, the torsion angles about the C-alpha-C-beta and C-beta-C-gamma bonds are restricted to the gauche conformation (+/- 60 degrees). The Gpn residue is constrained to adopt folded conformations resulting in the formation of intramolecularly hydrogen-bonded structures even in short peptides. The peptides Boc-Ac(6)c-Gpn-OMe 1 and Boc-Gpn-Aib-Gpn-Aib-OMe 2 provide examples of C-7 conformation; peptides Boc-Gpn-Aib-OH 3, Boc-Ac(6)c-Gpn-OH 4, Boc-Val-Pro-Gpn-OH 5, Piv-Pro-Gpn-Val-OMe 6, and Boc-Gpn-Gpn-Leu-OMe 7 provide examples of C-9 conformation; peptide Boc-Ala-Aib-Gpn-Aib-Ala-OMe 8 provides an example of C-12 conformation and peptides Boc-beta Leu-Gpn-Val-OMe 9 and Boc-beta Phe-Gpn-Phe-OMe 10 provide examples of C-13 conformation. Gpn peptides provide examples of backbone expanded mimetics for canonical alpha-peptide turns like the gamma (C-7) and the beta (C-10) turns. The hybrid beta gamma sequences provide an example of a mimetic of the C-13 alpha-turn formed by three contiguous alpha-amino acid residues. Two examples of folded tripeptide structures, Boc-Gpn-beta Phe-Leu-OMe 11 and Boc-Aib-Gpn-beta Phg-NHMe 12, lacking internal hydrogen bonds are also presented. An analysis of available Gpn residue conformations provides the basis for future design of folded hybrid peptides.

Rationalizing the effects of amino acid side chain, pyridine, and imidazole on the assembly and reversible disassembly of a octanuclear Cu(III) complex

This paper reports the observation of a reversible disassembly process for a previously reported octanuclear Cu(II) complex with imidazole. To identify the factors responsible for the process, five Cu(II) complexes of different nuclearity with different amino acid-derived tetradentate ligands were structurally characterized. The results show that the coordination geometry preference of Cu(II), the tendency of imidazole to act as in-plane ligand, and H-bonding played important role in the formation and disassembly of the octanuclear complex. A general scheme describing the effect of different amino acid side arms, solvents, and exogenous ligands on the nuclearity of the Cu(II) complexes has been presented. The crystals of the complexes also showed formation of multifaceted networks in the resulting complexes.

Disallowed Ramachandran Conformations of Amino Acid Residues in Protein Structures

An analysis of the nature and distribution of disallowed Ramachandran conformations of amino acid residues observed in high resolution protein crystal structures has been carried out. A data set consisting of 110 high resolution, non-homologous, protein crystal structures from the Brookhaven Protein Data Bank was examined. The data set consisted of a total of 18,708 non-Gly residues, which were characterized on the basis of their backbone dihedral angles (φ, ψ). Residues falling outside the defined “broad allowed limits” on the Ramachandran map were chosen and the reportedB-factor value of the α-carbon atom was used to further select well defined disallowed conformations. The conformations of the selected 66 disallowed residues clustered in distinct regions of the Ramachandran map indicating that specific φ, ψ angle distortions are preferred under compulsions imposed by local constraints. The distribution of various amino acid residues in the disallowed residue data set showed a predominance of small polar/charged residues, with bulky hydrophobic residues being infrequent. As a further check, for all the 66 cases non-hydrogen van der Waals short contacts in the protein structures were evaluated and compared with the ideal “Ala-dipeptide” constructed using disallowed dihedral angle (φ, ψ) values. The analysis reveals that short contacts are eliminated in most cases by local distortions of bond angles. An analysis of the conformation of the identified disallowed residues in related protein structures reveals instances of conservation of unusual stereochemistry.

Protein content and amino acid composition of some varieties of grain sorghum

Determination of the protein content and lysine levels of a number of nonhybrid varieties of grain sorghum indicates large variations in the protein content. Statistical analysis of data on amounts of lysine shows that a negative correlation exists between per cent lysine in the protein and per cent protein in the seed. The proportion of various protein fractions in endosperm of five varieties of grain sorghum of both low- and high-protein type has been determined. Results show that prolamine and glutelin are the principal protein fractions, and increased protein levels in sorghum varieties are correlated with an increase mainly in the prolamine fraction. Nine high- and low-protein varieties of grain sorghum have been analyzed for their amino acid composition by ion exchange procedures. One of the high-protein genetic varieties of sorghum has a high concentration of lysine in the seed. Amino acid composition of the protein fractions of two varieties is also reported. These data permit an evaluation of the nutritional quality of sorghum protein and factors that influence the quality of the protein.

Detection,amplification and sequence homology of sodC in clinical isolates of Salmonella sp

Background & objectives: Periplasmic copper and zinc superoxide dismutase (Cu,Zn-SOD or SodC) is an important component of the antioxidant shield which protects bacteria from the phagocytic oxidative burst. Cu,Zn-SODs protect Gram-negative bacteria against oxygen damage which have also been shown to contribute to the pathogenicity of these bacterial species. We report the presence of SodC in drug resistant Salmonella sp. isolated from patients suffering from enteric fever. Further sodC was amplified, cloned into Escherichia coli and the nucleotide sequence and amino acid sequence homology were compared with the standard strain Salmonella Typhimurium 14028. Methods: Salmonella enterica serovar Typhi (S. Typhi) and Salmonellaenterica serovar Paratyphi (S. Paratyphi) were isolated and identified from blood samples of the patients. The isolates were screened for the presence of Cu, Zn-SOD by PAGE using KCN as inhibitor of Cu,Zn-SOD. The gene (sodC) was amplified by PCR, cloned and sequenced. The nucleotide and amino acid sequences of sodC were compared using CLUSTAL X.Results: SodC was detected in 35 per cent of the Salmonella isolates. Amplification of the genomic DNA of S. Typhi and S. Paratyphi with sodC specific primers resulted in 519 and 515 bp amplicons respectively. Single mutational difference at position 489 was observed between thesodC of S. Typhi and S. Paratyphi while they differed at 6 positions with the sodC of S. Typhimurium 14028. The SodC amino acid sequences of the two isolates were homologous but 3 amino acid difference was observed with that of standard strain S. Typhimurium 14028.Interpretation & conclusions: The presence of SodC in pathogenic bacteria could be a novel candidate as phylogenetic marker.

Biochemical Characterization Of Β-N-Oxalyl-L-Α,Β-Diaminopropionic Acid, The Lathyrus Sativus Neurotoxin As An Excitant Amino Acid

Abstract—β-N-Oxalyl-l-α,β-diaminopropionic acid (ODAP), the toxin isolated from the seeds of Luthyrus sativus produces head retraction, tremors and convulsions when injected into a variety of experimental animals. In 12-day-old rats, it has been found that the convulsive behaviour is accompanied by profound biochemical changes in the brain. The brain homogenates prepared from ODAP injected animals show a higher rate of respiration. There is a decrease in the brain glucose, glycogen, ATP, phosphocreatine and acetylcholine levels of the convulsing animals. The inorganic phosphate, lactic acid and acetylcholineesterase levels increase. These results establish that ODAP is a typical convulsant.

Studies in the polarographic behaviour of zinc-amino acid complexes

1. The polarographic behaviour of amino-acid complexes of zinc has been studied using seven amino acids as complexing agents. 2. The effect of varying the pH of the base solution and the concentration of amino-acid anion on the polarographic behaviour of zinc in these solutions have indi cated the formation of twelve amino-acid complexes. The stability constants could not be calculated due to the irreversible nature of the waves. 3. The effect of sodium hydroxide, sodium carbonate, and ammonia on the polarographic behaviour of zinc has been investigated. The results can be interpreted as due to the formation of mixed complexes in many systems. 4. Amino-acid base solutions have been found to be suitable for the polarographic estimation of zinc.

Studies in the polarography of metal-amino acid complexes - Part I. Cadmium

1. A detailed polarographic study of cadmium has been made employing glycine, α-alanine, β-alanine, valine, aspartic acid, glutamic acid and asparagine as complexing agents at various pH values. The effect of incorporating sodium hydroxide, sodium carbonate and ammonium nitrate + ammonium hydroxide, on the polarographic behaviour of amino acid complexes of cadmium has also been investigated. 2. The reduction process has been found to be reversible in all systems. 3. The small shifts in the half-wave potentials noticed due to increase in the concentration of sodium hydroxide and sodium carbonate in presence of amino acids have been explained on the basis of formation of mixtures of pure and mixed amino acid complexes of cadmium. Mixed complexes have also been noticed in presence of ammonium hydroxide and ammonium nitrate and amino acids. 4. Polarographic evidence has been obtained for the formation of over 30 pure and mixed complexes. The dissociation constant Kd, the Δ F° value for the dissociation, and standard potential value for the formation, of each complex have been computed. 5. It has been found that cadmium can be polarographically estimated in amino acid solutions.

Studies in the polarography of metal-amino acid complexes -Part II. Lead

1. The polarographic behaviour of glycine, α-alanine, β-alanine, valine, aspartic acid, glutamic acid and asparagine complexes of lead has been studied at various pH values and in presence of (1) NaOH, (2) Na2CO3 and (3) NH4 NO3+NH4OH. All the polarographic waves have been found to be reversible. 2. Experiments conducted on the effect of variation of pH, i.e., 7amino-acid have indicated the formation of Pb A and Pb A2. The data have been analysed employing the equations developed by DeFord and Hume as modified by McKenzie and Mellor. 3. Only pure complexes are produced below pH 11·2 in the case of aspartic acid, glutamic acid and glycine, while mono hydroxy complexes are produced in α-alanine, valine and asparagine systems. 4. It has been found that no mixed hydroxy and mixed ammonia complexes are produced in presence of sodium hydroxide and ammonia-ammonium nitrate, respectively. However evidence is obtained for the formation of mixed carbonate complexes in glycine and aspartic acid systems in presence of sodium carbonate. 5. Thermodynamic data have been calculated from polarographic measurements for 18 complexes. 6. The suitability of incorporating amino acids in base solutions for the polarographic estimation of lead has been tested.

Empirical torsional potential functions from protein structure data. Phi- and psi-potentials for non-glycyl amino acid residues.

The torsional potential functions Vt(phi) and Vt(psi) around single bonds N--C alpha and C alpha--C, which can be used in conformational studies of oligopeptides, polypeptides and proteins, have been derived, using crystal structure data of 22 globular proteins, fitting the observed distribution in the (phi, psi)-plane with the value of Vtot(phi, psi), using the Boltzmann distribution. The averaged torsional potential functions, obtained from various amino acid residues in L-configuration, are Vt(phi) = 1.0 cos (phi + 60 degrees); Vt(psi) = 0.5 cos (psi + 60 degrees) - 1.0 cos (2 psi + 30 degrees) - 0.5 cos (3 psi + 30 degrees). The dipeptide energy maps Vtot(phi, psi) obtained using these functions, instead of the normally accepted torsional functions, were found to explain various observations, such as the absence of the left-handed alpha helix and the C7 conformation, and the relatively high density of points near the line psi = 0 degrees. These functions derived from observational data on protein structures, will, it is hoped, explain various previously unexplained facts in polypeptide conformation.

A novel approach to design of cis-acting DNA structural element for regulation of gene expression in vivo

Taking advantage of the degeneracy of the genetic code we have developed a novel approach to introduce, within a gene, DNA sequences capable of adopting unusual structures and to investigate the role of such sequences in regulation of gene expression in vivo. We used a computer program that generates alternative codon sequences for the same amino-acid sequence to convert a stretch of nucleotides into an inverted-repeat sequence with the potential to adopt cruciform structure. This approach was used to replace a 51-base-pair EcoRI-HindIII segment in the N-terminal region of the beta-galactosidase gene in plasmid pUC19 with a 51-bp synthetic oligonucleotide sequence with the potential to adopt a cruciform structure with 18 bp in the stem region. In selecting the 51-bp sequence, care was taken to include those codons that are preferred in E. coli. E. coli DH5-alpha cells harbouring the plasmid containing the redesigned sequence showed drastic reduction in expression of the beta-galactosidase gene compared to cells harbouring the plasmid with the native sequence. This approach demonstrates the possibility of introducing DNA secondary-structure elements to alter regulation of gene expression in vivo.