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Results show that the water-soluble domain of the nitric oxide reductase subunit C exhibits a alpha-helical structure and contains a partially solvent-exposed heme. The heme iron is coordinated by histidine and methionine ligands in both. Data suggest that the soluble domain of subunit C interacts with the catalytic subunit B.

Research discusses the mechanism of nitric oxide reduction by nitric oxide reductase in bacteria. Data indicate a trans mechanism and involves the binuclear active site Fe(sub)B. Alternatively, nitric oxide reductase can also use a P-450-type mechanism with heme b(sub03 functioning as nitric oxide binding site.

Research illustrates the interaction of carbon monoxide with the dinuclear center of reduced bacterrial nitric oxide reductase. Results reveal that the ligand binds to iron(II) heme b(sub)3 forming a stable complex, which suggests differences in the organization of this active site from other heme-copper oxidase superfamily.

Results show that copperA-domain of cytochrome oxidase subunit II from Paracoccus denitrificans is Ph responsive exhibiting conformational changes at the copperA site with pH decrease. Data further indicate that the protein's conformational state is more stable at the 'low-pH' and the conformational transition is influenced by a slow deprotonation step.

Pleckstrin homology (PH) domains form a structurally conserved family that is associated with many regulatory pathways within the cell. Domains with a nearly identical fold are found in other families that share no sequence similarity, suggesting the existence of a stable PH superfold. The PH domains generally function as regulated membrane-binding modules that bind to inositol lipids and respond to upstream signals by targeting the host proteins to the correct cellular sites. The other domains with a similar fold, such as the phosphotyrosine binding domains, recognize protein ligands.

A unique and enhanced strategy for purifying nitric oxide reductase (NOR) form membranes of Paracoccus denitrificans was developed. The purified enzyme was identified as a cytochrome bc complex which has two subunits in a 1:1 stoichiometry. The purified NorBC complex binds 0.87 g of dodecyl maltoside/g of protein and produces a dimer in solution. The NorB subunit resembles the primary catalytic subunit of cytochrome oxidase and is believed to contain the active bimetallic center in which two NO molecules are passed on to N2O.

Recent structures of Src tyrosine kinases reveal complex mechanisms for regulation of enzymatic activity. The regulatory SH3 and SH2 domains bind to the back of the catalytic kinase domain via a linker region that joins the SH2 domain to the catalytic domain. Members of a subgroup of the Src kinase family show distinct features in this linker and in the loops that interact with it. Hydrophobicity of key residues in this region is important for intramolecular regulation. The kinases Abl, Btk and Csk seem to have the same molecular architecture as Src. Structural comparisons between serine/threonine and tyrosine kinases indicate a specific twisting mechanism involving the N- and C-terminal lobes of the catalytic domain. This motion could provide insights into the various mechanisms used to regulate kinase activity.

An investigation of the electronic and geometric structures of CuA centers through nuclear magnetic resonance spectroscopy found electron delocalization onto S atoms and proton shifts of one histidine that vary from one system to another. Data suggest that these shifts depend on the Cu-S-C-H torsion angle. The line widths of histidine proton signals indicate fast electron relaxation at room temperature arising from the close doublet levels. Results indicate that this relaxation is not sensitive to slight inequivalencies in histidine binding.

A normal coordinate analysis of the resonance Raman spectra of the CuA fragment from the cytochrome c oxidase of Paracoccus denitrificans was conducted with CuA replaced by isotopes of Cu, S and N. The Cu- and N-isotope dependencies agree with the view that the vibrational motions in CuA are mostly caused by the Cu and S atoms with much less coupling to the vibrations of the cysteinate side chain and polypeptide backbone than in the mononuclear copper-cysteinate proteins.

The WW domain of a human Yes kinase-associated protein in proline-rich peptide complex with the bound peptide GTPPPPYTVG is a slightly curved, 3-stranded, antiparallel beta-sheet. This solution structure includes two prolines that are present next to the first tryptophan, and form a hydrophobic buckle on the convex side of the sheet. The concave side comprises three hydrophobic residues which are binding sites for the ligand. A non-conserved isoleucine in the region of amino-terminal flanking covers the exposed hydrophobic residues and stabilizes the WW domain.

An engineered dinuclear copper center was used to describe the crystal structures of wild-type and mutant subunit II (CyoA) from the Escherichia coli respiratory quinol oxidase complex. Wild-type and mutant CyoA were studied at 2.5-Angstrom and 2.3-Angstrom resolution, respectively. The results revealed that the dinuclear copper center is inserted between strands beta5 and beta6 and beta9 and beta10, with a distance of 2.5-Angstrom in between the two coppers. It is surrounded by residues consisting of cytochrome c and quinol oxidases.

The main energy-transducing metabolic systems originated and diversified very early in the evolution of life. This makes it difficult to unravel the precise steps in the evolution of the proteins involved in these processes. Recent molecular data suggest that homologous proteins of aerobic respiratory chains can be found in Bacteria and Archaea, which points to a common ancestor that possessed these proteins. Other molecular data predict that this ancestor was unlikely to perform oxygenic photosynthesis. This evidence, that aerobic respiration has a single origin and may have evolved before oxygen was released to the atmosphere by photosynthetic organisms, is contrary to the textbook viewpoint.

The active site for the oxidation of cytochrome c by cytochrome c oxidase is the CuA domain in subunit II. A soluble form of the CuA domain of a bacterial cytochrome c oxidase was capable of oxidizing bacterial cytochrome c-550 and horse mitochondrial cytochrome c. Five amino acid residues are necessary for catalytic activity: glutamine 148, glutamate 154, aspartate 206, aspartate 221, and glutamate 246. This indicates that these residues are necessary for cytochrome c binding.

Circular dichroism, cross-linking experiments and infrared spectroscopy studies, used to examine the interactions between five SH3 domains and six distinct proline-rich peptides, provide Kd values for all the possible interactions to indicate the properties of low affinity and low specificity in the interactions. The peptides do not exhibit any binding with n-src-SH3 or spectrin-SH3 domains. The proline-rich peptides do not develop a PPII structure after binding to the SH3 domains, including Fyn-SH3 domain which is the most non-selective and Abl-SH3 which is the most selective of the peptides.

The identification of the PH domain as two repeats of approximately 100 residues of pleckstrin celebrated its first anniversary. Although the discovery is relatively new, the PH domain has been frequently seen in intracellular signalling and cytoskeletal proteins. Consequently, the PH domain has been subject of intensive research to discover its actual functions. A discussion of some of the research directions on PH domains is presented.

The three-dimensional structure of the Src-homologous SH3 domain of the cytoskeletal protein spectrin has been determined at the 1.8 angstrom level. Spectrin is important because it is the principal constituent of the cytoskeleton supporting the cell membrane. The domain is arranged as a beta-barrel consisting of five antiparallel beta-strands. This structure, with its unusual conserved residues of SH3 genetic sequences, probably functions as a binding site for the protein ligand.

Homonuclear nuclear magnetic resonance analyzes the three-dimensional structure of the pleckstrin homology domain of the cytoskeletal protein spectrin. An anti-parallel beta-sheet with seven strands forms the core of the molecule whose C-terminus winds into a long alpha-helix with another helix in a surface loop. The molecule, which is electrostatically polarized, consists of a pocket, which participates in ligand binding.

Research has been conducted on the heme-copper cbb (sub)3 cytochrome oxidase. The structural characteristics of the cbb (sub)3 binuclear center have been investigated and the results are reported.

The existence of a Cu-Cu bonding interaction in copper A is determined using far-red resonance Raman spectroscopy (RR). Genetically modified, solubilized forms of CcO subunit II from Bacillus subtilis and Paracoccus denitrificans are studied using RR with Cu isotopic substitution. Results indicate that Cu-Cu bonding in copper A applies both to the isolated subunit II and native CcO.

The intense Cu-S stretching modes at 260 and 340 nanometers in the resonance Raman spectra of Cu(sub A) in Pseudomonas aeruginosa azurin are similar to Cu(sub A) sites of cytochrome c oxidase fragments. The Cu(sub A) RR fingerprint spectrum in engineered and native Cu(sub A) supports the presence of a conserved dinuclear thiolate-bridged structure and a flexible cupredoxin-like folding motif in Cu(sub A) domain. The vibrational frequencies depend on Cu-S-Cu bond angles.