Protein G and protein A have developed different strategies for binding to Fc. The protein G:Fc complex involves mainly charged and polar contacts, whereas protein A and Fc are held together through non-specific hydrophobic interactions and a few polar interactions. Several residues of Fc are involved in both the protein G:Fc and the protein A:Fc interaction, which explains the competitive binding of the two proteins. The apparent differences in their Fc-binding activities result from additional unique interactions.

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Cytochrome oxidase is a membrane protein complex that catalyzes reduction of molecular oxygen to water and utilizes the free energy of this reaction to generate a transmembrane proton gradient during respiration. The electron entry site in subunit II is a mixed-valence dinuclear copper center in enzymes that oxidize cytochrome c. This center has been lost during the evolution of the quinoloxidizing branch of cytochrome oxidases but can be restored by engineering. Herein we describe the crystal structures of the periplasmic fragment from the wild-type subunit II (CyoA) of Escherichia coli quinol oxidase at 2.5-A resolution and of the mutant with the engineered dinuclear copper center (purple CyoA) at 2.3-A resolution. CyoA is folded as an 11-stranded mostly antiparallel 13-sandwich followed by three a-helices. The dinuclear copper center is located at the loops between strands 185-.16 and 189-1310. The two coppers are at a 2.5-A distance and symmetrically coordinated to the main ligands that are two bridging cysteines and two terminal histidines. The residues that are distinct in cytochrome c and quinol oxidases are around the dinuclear copper center. Structural comparison suggests a common ancestry for subunit II of cytochrome oxidase and blue copper-binding proteins.Two main branches of the cytochrome oxidase family in bacteria alternatively use cytochrome c or quinol as the electron donor (1, 2). They typically contain three subunits that are homologous to the key components of the mitochondrial enzyme. Subunit I is largely buried in the membrane and forms the core of the complex, harboring the heme-copper active site. Subunit II has been predicted to be composed of an N-terminal transmembrane helical hairpin and a hydrophilic C-terminal domain that resides in the outer side of the cytoplasmic membrane (3). In cytochrome c oxidases, this domain contains a copper center known as CUA that functions as the primary acceptor for the electron from cytochrome c (4, 5). Subunit III is a membrane protein without redox centers (3).The CUA site is a single electron acceptor and donor. It has been spectroscopically characterized as a dinuclear center with a mixed valence [Cu(1.5)-Cu(1.5)]S = 1/2 configuration (4, 6, 7), where the coppers must be in very similar chemical environments (8). The key amino acids involved in the binding site are found in the CCHM amino acid motif, which is preceded by an invariant His in all subunit II sequences of cytochrome c oxidases (Fig. 1). None of these residues are conserved in quinol oxidases lacking the metal center (9, 12, 13). The "lost" CUA site has been reengineered to subunit II of the Escherichia coli quinol oxidase (CyoA) by a simultaneous substitution of six residues that results in a protein with purple color (9) (hereafter referred to as purple CyoA). We have determined the crystal structure of CyoA and purpleThe publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance w...

DNA polymerase ɛ (Pol ɛ) is a high-fidelity polymerase that has been shown to participate in leading-strand synthesis during DNA replication in eukaryotic cells. We present here a ternary structure of the catalytic core of Pol ɛ (142 kDa) from Saccharomyces cerevisiae in complex with DNA and an incoming nucleotide. This structure provides information about the selection of the correct nucleotide and the positions of amino acids that might be critical for proofreading activity. Pol ɛ has the highest fidelity among B-family polymerases despite the absence of an extended β-hairpin loop that is required for high-fidelity replication by other B-family polymerases. Moreover, the catalytic core has a new domain that allows Pol ɛ to encircle the nascent double-stranded DNA. Altogether, the structure provides an explanation for the high processivity and high fidelity of leading-strand DNA synthesis in eukaryotes.

Alzheimer disease is a neurodegenerative disorder that is tightly linked to the self-assembly and amyloid formation of the 39 -43-residue-long amyloid-␤ (A␤) peptide. Considerable evidence suggests a correlation between Alzheimer disease development and the longer variants of the peptide, A␤-(1-42/43). Currently, a molecular understanding for this behavior is lacking. In the present study, we have investigated the hydrogen/deuterium exchange of A␤-(1-42) fibrils under physiological conditions, using solution NMR spectroscopy. Protein assemblies in the form of amyloid fibrils are today linked to a group of ϳ20 different syndromes, of which Alzheimer disease (AD), 2 as well as various forms of prion disorders, are among the most well known. Amyloids, in general, are composed of predominantly ␤-sheet structures, where the ␤-strands are arranged perpendicular to the fibrillar axis into a common so-called cross-␤ pattern (1-4). AD is a neurological disorder presenting itself as progressive dementia. The pathology is tightly linked to the aggregation of a 39 -43-residue-long peptide fragment denoted amyloid-␤ (A␤) derived as a result of proteolytic processing of the considerably larger amyloid precursor protein. Aggregated A␤ peptides are found in AD brains in the form of diffuse and senile plaques as well as in cerebrovascular tissues. Considerable experimental evidence suggests an important role of A␤-(1-42/43) in the progress of AD, because it represents the main constituent of the first deposits found in the course of disease development (5, 6) and if overproduced may result in early onset AD (7, 8) (for a recent review, see Ref.9). The mechanisms by which a cytotoxic effect is exerted in vivo and the reasons why a pathologic self-aggregation is induced in certain individuals are complex and at present not completely understood. Prevention of A␤ assembly therefore constitutes a considerable therapeutic challenge, where an increased understanding regarding the properties of amyloid, and the pathways leading to its formation, is of utmost importance.Because of the generic quaternary structure and the large size of amyloid structures, elucidation of their architecture provides a complicated problem, where traditional methods, such as crystal diffraction and solution NMR, are not readily applicable. However, two recent crystallographic studies on fibrous micro-crystals, grown from peptides with either seven or twelve residues, have revealed many interesting structural details about the cross-␤ spine of fibrils (10, 11). Solid-state NMR performed on dried fibrils provides an alternative to the above mentioned techniques and has been used extensively to investigate the structure of A␤ amyloid. Studies on A␤-(10 -35), A␤-(1-40), and A␤-(1-42) suggest an arrangement where fibrils are formed by extended parallel ␤-strands arranged into two sheets (12-14). The results suggest a fibrillar core involving residues Val 12 -Val 24 and Ala 30 -Ala 42 and a loop spanning between residues Val 24 -Ala 30 (15). The structural restrai...