Metal ions in molecular association of porphyrins

Molecular association of porphyrins and their metal derivatives has been recognized as one of the important properties for many of their biological functions. The association is classified into (i) self-aggregation, (ii) intermolecular association and (iii) intramolecular association. The presence of metal ions in the porphyrin cavity is shown to alter the magnitudes of binding constants and thermodynamic parameters of complexation. The interaction between the porphyrin unit and the acceptor is described in terms of π-π interaction. The manifestation of charge transfer states both in the ground and excited states of these complexes is shown to influence the rates of excited state electron transfer reactions. Owing to paucity of crystal structure data, the time-averaged geometries of many of these complexes have been derived from magnetic resonance data.

Effect of molecular association and reactivity on substitution in chromium(III)-salprn complexes

A new chromium(III)-Schiff base complex, [Cr(5-chlorosalprn)(H2O)(2)]ClO4, where salprn=N,N'-propylenebis(salicylideneimine) has been prepared and characterized by electrospray ionization mass spectrometric (ESIMS) analysis and other spectroscopic techniques. Single crystal X-ray data reveal that the complex assumes a trans-diaquo structure, [Cr(C17H18Cl2N2O4)]ClO4.H2O. The effect of phenyl ring substituents on the rate of formation of [O=Cr-V Schiff base](+) has been investigated. The bimolecular rate constant for the formation of O=Cr-V species by the [Cr(Schiff base)(H2O)(2)]ClO4, where the Schiff base=salprn, (1) and 5-chlorosalprn, (2) with PhOI was compared. In the case of (2) the rate was found to be faster by an order of magnitude at pH=4 compared to (1). The introduction of a chloro-substituent on the phenyl ring not only influences the rate of redox reactivity but also the pKa values of aquo ligands of the complexes, indicating the difference in the electronic environment around the metal ion in both (1) and (2).

Structural studies of analgesics and their interactions. III. The crystal and molecular structure of amidopyrine

Amidopyrine (1-phenyl-2,3-dimethyl-4-dimethylaminopyrazolone), C13HzvN30, a dimethylamino derivative of antipyrine and an important analgesic and antipyretic agent, crystallizes in the triclinic space group P1 with four molecules in a unit cell of dimensions a= 7.458 (5), b = 10.744 (5), c= 17.486 (15)/~,, e=98.6 (2),/~= 85.6 (3), y= 108-6 (2) . The structure was solved by direct methods and refined to an R value of 0.055 for 3706 photographically observed reflexions. The dimensions of the two crystallographically independent molecules are very nearly the same. The pyrazolone moiety in the molecule has dimensions comparable to those in antipyrine. Unlike antipyrine, the molecular dimensions of amidopyrine in the free state (the present structure) are close to those found in some of its hydrogenbonded complexes. Thus it appears that the presence of the dimethylamino group makes the molecule more resistant to changes in its dimensions resulting from molecular association. An attempt has also been made to correlate the polar nature of the pyrazolone moiety and the hybridization state of the hetero nitrogen atoms in antipyrine, amidopyrine and their complexes.

Optical and magnetic resonance studies of the interaction of metallo tetraphenylporphyrins with nitrobenzofuroxan

Metallo tetraphenylporphyrins form I : I molecular complexes with 4,6-dinitrobenzofuroxan. The molecular association is described in terms of T-n. interaction with porphyrins functioning as donors. The association constants and thermodynamic parameters have been evaluated using optical absorption and 'H nmr spectral methods. Based on the binding constants, the donor ability of various metalloporphyrins can be arranged in the following order: Pd(I1) > Co(I1) > Cu(I1) > Ni(I1) - VO(1V) - 2H > Zn(l1). Electron paramagnetic resonance studies of the complexes reveal that the IT-complexation results in changes in the electronic structure of the central metal ions which are reflected in the changes in the M-N 5 bonding. The dipolar contribution to the acceptor proton chemical shifts in the CoTPP complex has been partitioned from ring current contributions using the shifts observed in the ZnTPP complex. The shifts, along with the line broadening ratios observed for the CoTPP complex, are used to arrive at the possible solution structures of the complexes.

Theoretical calculations of base-base interactions in nucleic acids: I Stacking interactions in free bases

Stacking interactions in free bases were computed on the basis of molecular association. The results of the calculations were compared with the stacking patterns observed in a few single crystals of nucleic acid components as examples. The following are the conclusions: (i) there can be two types of stacking pattern classified as normal and inverted types for any two interacting bases and both can be energetically favourable (ii) in both the types the stacking interaction is a combined effect of the overlap of the interacting bases and relative positions and orientations of the atomic centres of the two bases (iii) crystal symmetry and H-bonding interaction may influence stacking patterns.

Quaternary association in beta-prism I fold plant lectins: Insights from X-ray crystallography, modelling and molecular dynamics

Dimeric banana lectin and calsepa, tetrameric artocarpin and octameric heltuba are mannose-specific beta-prism I fold lectins of nearly the same tertiary structure. MD simulations on individual subunits and the oligomers provide insights into the changes in the structure brought about in the protomers on oligomerization, including swapping of the N-terminal stretch in one instance. The regions that undergo changes also tend to exhibit dynamic flexibility during MD simulations. The internal symmetries of individual oligomers are substantially retained during the calculations. Energy minimization and simulations were also carried out on models using all possible oligomers by employing the four different protomers. The unique dimerization pattern observed in calsepa could be traced to unique substitutions in a peptide stretch involved in dimerization. The impossibility of a specific mode of oligomerization involving a particular protomer is often expressed in terms of unacceptable steric contacts or dissociation of the oligomer during simulations. The calculations also led to a rationale for the observation of a heltuba tetramer in solution although the lectin exists as an octamer in the crystal, in addition to providing insights into relations among evolution, oligomerization and ligand binding.

Molecular complexes of metallo tetraphenyl porphyrins with 2,4,5,7-tetranitro fluorenone

The interactions of mesotetraphenyl porphyrin and its metallo derivatives with 2,4,5,7-tetra nitrofluorenone have been studied using spectroscopic methods. The association constants (K) for 1:1 complexes in Ch2Cl2Cl2 follow the order Pd+2>Co+2> Cu+2>VO+2>Ni+2>Zn+2. The values of K are accounted in terms of stereochemistry of MTPPs and the electronic configuration of the metal ions. The magnitude and direction of the proton NMR shifts of the acceptor and donor in the complexes and their ESR parameter furnish information as to the possible structures of these complexes in solution.

Intra and Inter-Molecular Communications Through Protein Structure Network

Communication within and across proteins is crucial for the biological functioning of proteins. Experiments such as mutational studies on proteins provide important information on the amino acids, which are crucial for their function. However, the protein structures are complex and it is unlikely that the entire responsibility of the function rests on only a few amino acids. A large fraction of the protein is expected to participate in its function at some level or other. Thus, it is relevant to consider the protein structures as a completely connected network and then deduce the properties, which are related to the global network features. In this direction, our laboratory has been engaged in representing the protein structure as a network of non-covalent connections and we have investigated a variety of problems in structural biology, such as the identification of functional and folding clusters, determinants of quaternary association and characterization of the network properties of protein structures. We have also addressed a few important issues related to protein dynamics, such as the process of oligomerization in multimers, mechanism on protein folding, and ligand induced communications (allosteric effect). In this review we highlight some of the investigations which we have carried out in the recent past. A review on protein structure graphs was presented earlier, in which the focus was on the graphs and graph spectral properties and their implementation in the study of protein structure graphs/networks (PSN). In this article, we briefly summarize the relevant parts of the methodology and the focus is on the advancement brought out in the understanding of protein structure-function relationships through structure networks. The investigations of structural/biological problems are divided into two parts, in which the first part deals with the analysis of PSNs based on static structures obtained from x-ray crystallography. The second part highlights the changes in the network, associated with biological functions, which are deduced from the network analysis on the structures obtained from molecular dynamics simulations.

Molecular-complexes of metallo tetraphenyl porphyrins with 2,4,5,7-tetranitro fluorenone

The interactions of mesotetraphenyl porphyrin and its metallo derivatives with 2,4,5,7-tetra nitrofluorenone have been studied using spectroscopic methods. The association constants (K) for 1:1 complexes in Ch2Cl2Cl2 follow the order Pd+2>Co+2> Cu+2>VO+2>Ni+2>Zn+2. The values of K are accounted in terms of stereochemistry of MTPPs and the electronic configuration of the metal ions. The magnitude and direction of the proton NMR shifts of the acceptor and donor in the complexes and their ESR parameter furnish information as to the possible structures of these complexes in solution.

Molecular complexes of macrocyclic polyethers with 1, 3, 5-trinitrobenzene

The interaction of six macrocyclic polyethers with 1, 3, 5-trinitrobenzene has been studied by spectroscopic methods. The association constants have been evaluated by1HMR chemical shift method. There is evidence that major contribution to the interaction isvia n andπ electrons. The donor strengths of the polyethers have been evaluated.

New structural insights and molecular-modelling studies of 4-methyl-5-beta-hydroxyethylthiazole kinase from Pyrococcus horikoshii OT3 (PhThiK)

4-Methyl-5-beta-hydroxyethylthiazole kinase (ThiK) catalyses the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole. This work reports the first crystal structure of an archaeal ThiK: that from Pyrococcus horikoshii OT3 (PhThiK) at 1.85 angstrom resolution with a phosphate ion occupying the position of the beta-phosphate of the nucleotide. The topology of this enzyme shows the typical ribokinase fold of an alpha/beta protein. The overall structure of PhThiK is similar to those of Bacillus subtilis ThiK (BsThiK) and Enterococcus faecalis V583 ThiK (EfThiK). Sequence analysis of ThiK enzymes from various sources indicated that three-quarters of the residues involved in interfacial regions are conserved. It also revealed that the amino-acid residues in the nucleotide-binding, magnesium ion-binding and substrate-binding sites are conserved. Binding of the nucleotide and substrate to the ThiK enzyme do not influence the quaternary association (trimer) as revealed by the crystal structure of PhThiK.

Molecular characterisation of ABC transporter type FtsE and FtsX proteins of Mycobacterium tuberculosis.

Elicitation of drug resistance and various survival strategies inside host macrophages have been the hallmarks of Mycobacterium tuberculosis as a successful pathogen. ATP Binding Cassette (ABC) transporter type proteins are known to be involved in the efflux of drugs in bacterial and mammalian systems. FtsE, an ABC transporter type protein, in association with the integral membrane protein FtsX, is involved in the assembly of potassium ion transport proteins and probably of cell division proteins as well, both of which being relevant to tubercle bacillus. In this study, we cloned ftsE gene of M. tuberculosis, overexpressed and purified. The recombinant MtFtsE-6xHis protein and the native MtFtsE protein were found localized on the membrane of E. coli and M. tuberculosis cells, respectively. MtFtsE-6xHis protein showed ATP binding in vitro, for which the K42 residue in the Walker A motif was found essential. While MtFtsE-6xHis protein could partially complement growth defect of E. coli ftsE temperature-sensitive strain MFT1181, co-expression of MtFtsE and MtFtsX efficiently complemented the growth defect, indicating that the MtFtsE and MtFtsX proteins might be performing an associated function. MtFtsE and MtFtsX-6xHis proteins were found to exist as a complex on the membrane of E. coli cells co-expressing the two proteins.

Characterization of single-stranded DNA-binding proteins from Mycobacteria. The carboxyl-terminal of domain of SSB is essential for stable association with its cognate RecA protein

Single-stranded DNA-binding proteins (SSB) play an important role in most aspects of DNA metabolism including DNA replication, repair, and recombination. We report here the identification and characterization of SSB proteins of Mycobacterium smegmatis and Mycobacterium tuberculosis. Sequence comparison of M. smegmatis SSB revealed that it is homologous to M. tuberculosis SSB, except for a small spacer connecting the larger amino-terminal domain with the extreme carboxyl-terminal tail. The purified SSB proteins of mycobacteria bound single-stranded DNA with high affinity, and the association and dissociation constants were similar to that of the prototype SSB. The proteolytic signatures of free and bound forms of SSB proteins disclosed that DNA binding was associated with structural changes at the carboxyl-terminal domain. Significantly, SSB proteins from mycobacteria displayed high affinity for cognate RecA, whereas Escherichia coli SSB did not under comparable experimental conditions. Accordingly, SSB and RecA were coimmunoprecipitated from cell lysates, further supporting an interaction between these proteins in vivo. The carboxyl-terminal domain of M. smegmatis SSB, which is not essential for interaction with ssDNA, is the site of binding of its cognate RecA. These studies provide the first evidence for stable association of eubacterial SSB proteins with their cognate RecA, suggesting that these two proteins might function together during DNA repair and/or recombination.

Evidence for an association with type 2 diabetes mellitus at the PPARG locus in a South Indian population

Peroxisome proliferator activated receptor-gamma 2 (PPARG2) is a nuclear hormone receptor of ligand-dependent ranscription factor involved in adipogenesis and a molecular target of the insulin sensitizers thiazolidinediones. We addressed the question of whether the 3 variants (-1279G/A, Pro12Ala, and His478His) in the PPARG2 gene are associated with type 2 diabetes mellitus and its related traits in a South Indian population. The study subjects (1000 type 2 diabetes mellitus and 1000 normal glucose-tolerant subjects) were chosen randomly from the Chennai Urban Rural Epidemiology Study, an ongoing population-based study in southern India. The variants were screened by single-stranded conformational variant, direct sequencing, and restriction fragment length polymorphism. Linkage disequilibrium was estimated from the estimates of haplotypic frequencies. The -1279G/A, Pro12Ala, and His478His variants of the PPARG2 gene were not associated with type 2 diabetes mellitus. However, the 2-loci analyses showed that, in the presence of Pro/Pro genotype of the Pro12Ala variant, the -1279G/A promoter variant showed increased susceptibility to type 2 diabetes mellitus (odds ratio, 2.092; 95% confidence interval, 1.22-3.59; P = .008), whereas in the presence of 12Ala allele, the -1279G/A showed a protective effect against type 2 diabetes mellitus (odds ratio, 0.270; 95% confidence interval, 0.15-0.49; P < .0001). The 3-loci haplotype analysis showed that the A-Ala-T (-1279G/A-Pro12Ala-His478His) haplotype was associated with a reduced risk of type 2 diabetes mellitus (P < .0001). Although our data indicate that the PPARG2 gene variants, independently, have no association with type 2 diabetes mellitus, the 2-loci genotype analysis involving -1279G/A and Pro12Ala variants and the 3-loci haplotype analysis have shown a significant association with type 2 diabetes mellitus in this South Indian population. (C) 2010 Elsevier Inc. All rights reserved.