Pathways of electron transfer and proton translocation in the action of superoxide dismutase dimer.

Superoxide dismutase, known to gain large rate enhancement on dimerization, forms a homodimer stabilized by hydrogen bonding between a number of internal water molecules and a few amino acid residues at the interface. Within each subunit the ß-sheets provide a sequence of delocalized π-electron units of peptide bonds alternating with hydrogen bonds referred as π-H pathway. These pathways in the two subunits in the dimer are interlinked through a chain of four water molecules bridged by hydrogen bonds at the interface. Connecting the two Cu-centers this π-H pathway can enable rapid electron transfer from one superoxide molecule to the other, crucial for the catalytic reaction and the high rate in the dimer. A proton relay of hydrogen-bonded water molecules in the dimer translocates protons to form the product, hydrogen peroxide.

Connecting CuA with metal centers of heme a, heme a3, CuB and Zn by pathways with hydrogen bond as the bridging element in cytochrome c oxidase.

Pathways formed of delocalized π-electron systems and polar groups of polypeptide chains bridged by hydrogen bonds are referred as π-H pathways. Suitable for electron transfer, these pathways in cytochrome c oxidase connect CuA, the source of electrons distributed in cytochrome c oxidase, with the metal centers, heme a, heme a3, CuB, the constituents of the catalytic binuclear center. The unusually rapid electron transfer between heme a and heme a3 would have been facilitated by the link pathway of a long sequence of alternate peptide unit and hydrogen bond spanning Pro336-Val374, referred as suprahelix, between these hemes. Two pathways between CuA center and zinc center, share some portions with purported proton-translocating channels, designated "K" and "D".

Hydrogen bond-linked pathways of peptide units and polar groups of amino acid residues suitable for electron transfer in cytochrome c proteins.

Electron transfer occurs through heme-Fe across the cytochrome c protein. The current models of long range electron transfer pathways in proteins include covalent σ-bonds, van der Waals forces, and through space jump. Hydrogen-bond-linked pathways of delocalized electron units in peptide units and polar side chains of amino acid residues in proteins and internal water molecules are better suited for intramolecular atom-to-atom electron transfer in proteins. Crystal structures of cytochrome c proteins from horse (1HRC), tuna (3CYT), rice (1CCR), and yeast (3CX5) were analyzed using pymol software for 'Hydrogen Bonds' marking the polar atoms within the distance of 2.6-3.3 Å and tracing the atom-to-atom pathways linked by hydrogen bonds. Pathways of hydrogen-bond-linked peptide units, polar side chains of the amino acid residues, and buried water molecules connect heme-Fe through axially coordinated Met80-S and His18-N have been traced in cytochrome c proteins obtained from horse, tuna, rice and yeast with an identical hydrogen-bonded sequence around the heme-Fe: Asn-N-water-O-Tyr-O-Met-S-heme-Fe-His (HN-C=N)-Pro-Asn-Pro-Gly (peptide unit, HN-C=O)-water-O. More than half of the amino acid residues in these pathways are among the conserved list and delocalized electron units, internal water molecules and hydrogen bonds are conspicuous by their presence.

Alternative pathway linked by hydrogen bonds connects heme-Fe of cytochrome c with subunit II-CuA of cytochrome a.

The bridging element for electron transfer in proteins is the hydrogen bond according to the new experimental perspective in preference to carbon-carbon σ-bond presently used. The purpose of this study is to identify an alternative pathway linked by hydrogen bonds suitable for electron transfer from heme-Fe of cytochrome c to subunit II-CuA of cytochrome a. A pathway consisting of 15 delocalized electron systems including peptide bonds, 5 polar groups of side chains of amino acid residues and 8 water molecules, linked by 27 hydrogen bonds, exists between the two metal electron centers of heme-Fe of cytochrome c, cytochrome c and of subunit II-CuA of cytochrome a. Pathways built of delocalized π-electron systems, polar groups and water molecules linked by hydrogen bonds may be considered for intramolecular and intermolecular electron transfer in proteins.

Genetic characterization of Toxoplasma gondii from autopsy proven cases of AIDS associated cerebral toxoplasmosis in South India.

Toxoplasma gondii (T.gondii) infection can be devastating in the immunodeficient causing high morbidity and mortality. Due to limited availability of both diagnostic facilities and Highly Active Antiretroviral Therapy (HAART), toxoplasmosis continues to be a significant problem amongst Acquired Immuno Deficiency Syndrome (AIDS) patients in India. While scanty literature is available on T. gondii isolates in animals in India, little is known about the genetic diversity of the parasite in humans. Therefore, the present study investigated the genetic diversity of T. gondii in 25 confirmed cases of cerebral toxoplasmosis developing on the background of human immunodeficiency virus (HIV) infection/AIDS. PCR DNA sequencing was performed at four important genetic loci of T. gondii: BTUB, GRA6, alternative SAG2 (alt SAG2) and SAG3 on DNA from tissues obtained at postmortem. The amplified products from all the cases were successfully sequenced except at one locus for one case. Results of the present study suggest that majority of the patients (22/25; 88%) in South India are infected with strains that are recombinants of type II/III and/or strains representing T. gondii different from the archetypal lineages I, II, and III. In addition, clonal types III, MAS, and MAS variant genotypes were encountered. No clonal type I or II was seen in the present study. In addition, variants were observed at alt SAG2 and SAG3 but BTUB and GRA6 were highly conserved. Single nucleotide polymorphisms were observed mainly at two loci which are coding for surface antigens at alt SAG2 and SAG3. In conclusion, the present study reveals genetic diversity in India amongst strains of T. gondii from clinical cases of toxoplasmosis which is in accordance with other recent studies showing a high rate of genetic diversity in this parasite across the globe. There is a need to genotype T. gondii from different forms of toxoplasmosis in humans in India.

A novel mutation in the transglutaminase-1 gene in an autosomal recessive congenital ichthyosis patient.

Structure-function implication on a novel homozygous Trp250/Gly mutation of transglutaminase-1 (TGM1) observed in a patient of autosomal recessive congenital ichthyosis is invoked from a bioinformatics analysis. Structural consequences of this mutation are hypothesized in comparison to homologous enzyme human factor XIIIA accepted as valid in similar structural analysis and are projected as guidelines for future studies at an experimental level on TGM1 thus mutated.