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Journal Issue - Volume 7 Issue 3 (March 1998)

Abstract We have investigated the mechanism and the evolutionary pathway of protein dimerization through analysis of experimental structures of dimers. We propose that the evolution of dimers may have multiple pathways, including (1) formation of a functional dimer directly without going through an ancestor monomer, (2) formation of a stable monomer as an intermediate followed by mutations of its surface residues, and (3), a domain...

Abstract The X‐ray crystal structure of a human copper/zinc superoxide dismutase mutant (G37R CuZnSOD) found in some patients with the inherited form of Lou Gehrig's disease (FALS) has been determined to 1.9 Å resolution. The two SOD subunits have distinct environments in the crystal and are different in structure at their copper binding sites. One subunit (subunitintact) shows a four‐coordinate ligand geometry of the copper ion, whereas the...

Abstract Carbonic anhydrase IV (CAIV) is a membrane‐associated enzyme anchored to plasma membrane surfaces by a phosphatidylinositol glycan linkage. We have determined the 2.8‐Å resolution crystal structure of a truncated, soluble form of recombinant murine CAIV. We have also determined the structure of its complex with a drug used for glaucoma therapy, the sulfonamide inhibitor brinzolamide (Azopt™). The overall structure of murine...

Abstract Alteromonas haloplanctis is a bacterium that flourishes in Antarctic sea‐water and it is considered as an extreme psychrophile. We have determined the crystal structures of the α‐amylase (AHA) secreted by this bacterium, in its native state to 2.0 Å resolution as well as in complex with Tris to 1.85 Å resolution. The structure of AHA, which is the first experimentally determined three‐dimensional structure of a...

Abstract We examine the water solvation of the complex of the inhibitors DMP323 and A76928 bound to HIV‐1 protease through grand canonical Monte Carlo simulations, and demonstrate the ability of this method to reproduce crystal waters and effectively predict water positions not seen in the DMP323 or A76928 structures. The simulation method is useful for identifying structurally important waters that may not be resolved in the...

Abstract Phycoerythrin 545 from the cryptomonad alga, Rhodomonas lens, has been crystallized under a wide variety of conditions. Although this type of photosynthetic light‐harvesting protein is water soluble, detergents were always required for crystallization. The crystals were typically poorly ordered, or ordered in only two dimensions. However, crystals that were well‐ordered in three dimensions could be obtained under two different ...

Abstract The enzyme cholesterol lecithin acyl transferase (LCAT) shares the Ser/Asp‐Glu/His triad with lipases, esterases and proteases, but the low level of sequence homology between LCAT and these enzymes did not allow for the LCAT fold to be identified yet. We, therefore, relied upon structural homology calculations using threading methods based on alignment of the sequence against a library of solved three‐dimensional protein...

Abstract To further investigate favorable effects of divalent cations on the formation of protein crystals, three complexes of Salmonella typhimurium histidine‐binding protein were crystallized with varying concentrations of cadmium salts. For each of the three histidine‐binding protein complexes, cadmium cations were found to promote or improve crystallization. The optimal cadmium concentration is ligand specific and falls within a narrow...

Abstract Three helicase structures have been determined recently: that of the DNA helicase PcrA, that of the hepatitis C virus RNA helicase, and that of the Escherichia coli DNA helicase Rep. PcrA and Rep belong to the same super‐family of helicases (SF1) and are structurally very similar. In contrast, the HCV helicase belongs to a different super‐family of helicases, SF2, and shows little sequence homology with the PcrA/Rep ...

Abstract γB‐crystallin consists of two domains each comprising two “Greek key” motifs. Both domains fold independently, and domain interactions contribute significantly to the stability of the C‐terminal domain. In a previous study (Palme S et al., 1996, Protein Sci 6:1529‐1636) it was shown that Phe56 from the N‐terminal domain, a residue involved in forming a hydrophobic core at the domain interface, effects the interaction of the...

Abstract The third component of complement, C3, plays a central role in activation of the classical, alternative, and lectin pathways of complement activation. Recently, we have identified a 13‐residue cyclic peptide (named Compstatin) that specifically binds to C3 and inhibits complement activation. To investigate the topology and the contribution of each critical residue to the binding of Compstatin to C3, we have now determined...

Abstract Human deoxyribonuclease I (DNase I), an enzyme used to treat cystic fibrosis patients, has been systematically analyzed by site‐directed mutagenesis of residues at the DNA binding interface. Crystal structures of bovine DNase I complexed with two different oligonucleotides have implicated the participation of over 20 amino acids in catalysis or DNA recognition. These residues have been classified into four groups based on...

Abstract The mechanism whereby fragments of streptokinase (SK) derived from its N terminus (e.g., SK1‐59 or SK1‐63) enhance the low plasminogen (PG)‐activating ability of other fragments, namely SK64‐386, SK60‐414, SK60‐387, and SK60‐333 (reported previously), has been investigated using a synthetic peptide approach. The addition of either natural SK1‐59, or chemically synthesized SK16‐59, at saturation (about 500‐fold molar excess)...

Abstract Multiple molecular dynamics (MD) simulations of crambin with different initial atomic velocities are used to sample conformations in the vicinity of the native structure. Individual trajectories of length up to 5 ns sample only a fraction of the conformational distribution generated by ten independent 120 ps trajectories at 300 K. The backbone atom conformational space distribution is analyzed using principal components...

Abstract Spider minor ampullate silk is a strong non‐elastic deformably stretchable silk used in web formation. This silk from Nephila clavipes is composed of two proteins, MiSp 1 and 2, whose transcripts are 9.5 and 7.5 kb, respectively, as determined by northern blots. Both MiSp proteins are organized into a predominantly repetitive region and a small nonrepetitive carboxy terminal region. These highly repetitive regions are composed mainly...

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