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Results show that the N-terminal domain of disulfide bond protein, DsbD, functions as a versatile adaptor in electron transport and forms disulfides with other oxidized and reduced disulfide bond proteins. Crystal structure of DsbD exhibits an immunoglobulin-like fold containing cysteines in the active site.

Research has been conducted on the cytochrome c-549 and cytochrome c (sub)6. The X-ray structures of these proteins isolated from cyanobacterium Arthrospira maxima have been investigated and the results indicate that their structures are similar.

Studies of the crystal structure of human DNA polymerase beta suggest that polymerase beta may improve fidelity by an induced fit mechanism. The induced fit mechanism induces alignment of catalytic groups for catalysis when there is correct base pairing between template and incoming dNTP. Incorrect pairing between template and dNTP will not induce alignment for catalysis. Polymerase beta binds both gapped and nicked DNA with a 90 degree kink at the 5 degree phosphodiester linkage of the templating residue.

The movement of the loop and rotation of the subdomain are important for the catalytic activity of the Escherichia coli dihydrofolate reductase (ecDHFR). The enzyme cycles between five kinetic intermediates. Crystallographic analysis show that the M20 loop of ecDHFR is closed over the reactants in the holoenzyme, Michaelis and transition state complexes. The loop occupies the nicotinamide-ribose binding pocket when nicotinamide is not bound to the enzyme.

The effects of metal ions on nucleotide binding and catalysis of pol beta was analyzed by utilizing a novel experimental system which is sensitive to changes in crystal soaking solution from Mg2+ to Mn2+. Crystal soaking experiments on pol beta indicated the interaction of the sodium moiety of deoxyribonucleic acid with the backbone peptide of pol beta. The sugar and triphosphate moieties of the nucleotide also exhibited non-selective binding in solution.

The sequentially homologous helix-hairpin-helix (HhH) deoxyribonucleic acid (DNA) motifs were analyzed in the 8-kDA domain of human pol beta-DNA by metal ion soaking experiments. Short bond distances were detected between molecules that are bonded to the metal sites of the HhH motifs and the protein carbonyl atoms of the human pol beta-DNA. The DNA polymerase also exhibited tightly bound Na2+ ions that are connected to the metal sites after the metal ion soaking experiments.

The crystal structures of rat and human pol beta complexed with deoxyribonucleic acid (DNA) were analyzed to determine the mechanisms of nucleotidyl transfer and polymerase processivity and fidelity. Human and rat pol beta exhibited nucleotide differences in their 14 amino acid residues which are located in the surface molecule. Furthermore, the nucleotide selectivity and processivity of rat and human pol beta are dependent on the structure and location of the metal ions in the DNA domain.

X-ray crystallography reveals that crystal structures of Escherichia coli dihydrofolate reductase (ecDHFR) complexed with 5,10-dideazatetrahydrofolate, 5-deazafolate and folate are isomorphous with a binary complex of ecDHFR with methotrexate. In folate complex, a water molecule is hydrogen bonded to the pteridine N5 and O4, demonstrating the participation of water molecule in a vital step of the DHFR reaction. A van der Waals overlap between the nicotinamide C4 and pteridine C7 accounts for the increased acceleration of THF release by a bound NADPH.

Several studies are conducted to explain the properties and the x-ray crystallographic structure of a designed cyclic [beta]-sheet peptide dimer.

A crystal structure of human fibrinogen purified from human blood plasma was determined at approximately 3.3 [Angstrom] resolutions. The overall structure differed from that of a native fibrinogen from chicken blood and those reported for a partially proteolyzed bovine fibrinogen in the nature of twist in the coiled-coil regions which is likely due to weak forces imparted by unique crystal packing.

The tendency of different proteins to change into amyloid-like fibrils, which are found in combination with nearly 24 deadly diseases, is of great concern for protein science and structural biology in particular. A research on the structural studies was conducted and explanation to a few important queries is provided.

Many different proteins undergo misfolding and self-assemble into amyloid fibrils, resulting in a range of neurodegenerative diseases. The limitations of conventional methods of structural biology for fibril characterization have led to the use of polarized Raman spectroscopy for obtaining quantitative structural information regarding the organization of amyloid fibrils. Herein, we report the orientation of selected chemical groups and secondary structure elements in aligned insulin fibrils, including β-sheets, which possess a high level of orientation in the cross-β core, and a-helices in the disordered portions of the fibrils. Strong orientation of disulfide bonds in amyloid fibrils was also revealed, indicating their association with the fibril core. The determined orientation of chemical groups provides strong constraints for modeling the overall structure of amyloid fibrils, including the core and disordered parts. The developed methodology allows for the validation of structural models proposed in the literature for amyloid fibrils. Specifically, the polarized Raman data obtained herein strongly agreed with two insulin fibril models (Jiménez et al., Proc. Natl Acad. Sci. U. S. A. 2002, 99, 9196-9201 and Ivanova et al., Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 18990-18995) yet revealed significant qualitative and quantitative differences. This work demonstrates the great potential of polarized Raman spectroscopy for structural characterization of anisotropic biological species. [ABSTRACT FROM AUTHOR]

Protein amyloid oligomers have been strongly linked to amyloid diseases and can be intermediates to amyloid fibers. β-Sheets have been identified in amyloid oligomers. However, because of their transient and highly polymorphic properties, the details of their self-association remain elusive. Here we explore oligomer structure using a model system: macrocyclic peptides. Key amyloidogenic sequences from Aβ and tau were incorporated into macrocycles, thereby restraining them to β-strands, but limiting the growth of the oligomers so they may crystallize and cannot fibrillate. We determined the atomic structures for four such oligomers, and all four reveal tetrameric interfaces in which β-sheet dimers pair together by highly complementary, dry interfaces, analogous to steric zippers found in fibers, suggesting a common structure for amyloid oligomers and fibers. In amyloid fibers, the axes of the paired sheets are either parallel or antiparallel, whereas the oligomeric interfaces display a variety of sheet-to-sheet pairing angles, offering a structural explanation for the heterogeneity of amyloid oligomers. [ABSTRACT FROM AUTHOR]

Examines the crystal structures of cytochrome c-549 and cytochrome c[sub 6] from the cyanobacterium Arthrospira maxima. Similarity of the two structures; Oligomerization of the proteins; Potential fit of the cytochrome c-549 dimer into the model of cyanobacterial photosystem II.

This paper describes the X-ray crystallographic structure of a designed cyclic β-sheet peptide that forms a well-defined hydrogen-bonded dimer that mimics β-sheet dimers formed by proteins. The 54-membered ring macrocyclic peptide (1a) contains molecular template and turn units that induce β-sheet structure in a heptapeptide strand that forms the dimerizatiori interface. The X-ray crystallographic structure reveals the structures of the two "Hao" amino acids that help template the β-sheet structure and the two δ-linked ornithine turn units that link the Hao-containing template to the heptapeptide β-strand. The Hao amino acids adopt a conformation that resembles a tripeptide in a β-strand conformation, with one edge of the Hao unit presenting an alternating array of hydrogen-bond donor and acceptor groups in the same pattern as that of a tripeptide β-strand. The δ-linked ornithines adopt a conformation that resembles a hydrogen-bonded β-turn, in which the ornithine takes the place of the i+1 and i+2 residues. The dimers formed by macrocyclic β-sheet la resemble the dimers of many proteins, such as defensin HNP-3, the λ-Cro repressor, interleukin 8, and the ribonuclease H domain of HIV-1 reverse transcriptase. The dimers of la self-assemble in the solid state into a barrel-shaped trimer of dimers in which the three dimers are arranged in a triangular fashion. Molecular modeling in which one of the three dimers is removed and the remaining two dimers are aligned face-to-face provides a model of the dimers of dimers of closely related macrocyclic β-sheet peptides that were observed in solution. [ABSTRACT FROM AUTHOR]