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A Monte Carlo method is presented which can obtain the correct tertiary fold of a protein given the secondary structure and as few as three interactions between each secondary structure unit. This method was used to fold hemerythrin, flavodoxin, bovine pancreatic trypsin inhibitor and a variable light domain from an immunoglobulin using the known secondary structures of these proteins. Each of ...

The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. Here, we report an atomistic model o...

The crystal structure of the oxidized form of flavodoxin from Desulfovibrio vulgaris has been studied at 2.0-A resolution, and a detailed description of the region around the flavin mononucleotide binding site is now available. The flavin is between a tyrosine group, roughly parallel to it on one side, and a tryptophan, about 45 degrees from being parallel, on the other side. The two carbonyl g...

The cytochrome P450 enzymes are major catalysts involved in the oxidations of xenobiotic chemicals in microorganisms as well as higher animals and plants. Because of their functional roles, they offer potential in biodegradation technology. A number of microbial P450s have already been characterized and offer advantages in terms of their high catalytic rates and facile expression in microorgani...

Analysis of the crystal structure of NifF from Rhodobacter capsulatus and its homologues reported so far reflects the existence of unique structural features in nif flavodoxins: a leucine at the re face of the isoalloxazine, an eight-residue insertion at the C-terminus of the 50's loop and a remarkable difference in the electrostatic potential surface with respect to non-nif flavodoxins. A phyl...

The crystal structure of the complex between the heme- and FMN-binding domains of bacterial cytochrome P450BM-3, a prototype for the complex between eukaryotic microsomal P450s and P450 reductase, has been determined at 2.03 A resolution. The flavodoxin-like flavin domain is positioned at the proximal face of the heme domain with the FMN 4.0 and 18.4 A from the peptide that precedes the heme-bi...