Thioredoxin induced by bacteriophage T4: crystallization and preliminary crystallographic data

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

BACKGROUND

An elastic network model is proposed for the interactions between closely (< or = 7.0 A) located alpha-carbon pairs in folded proteins. A single-parameter harmonic potential is adopted for the fluctuations of residues about their mean positions in the crystal structure. The model is based on writing the Kirchhoff adjacency matrix for a protein defining the proximity of residues in space. The elements of the inverse of the Kirchhoff matrix give directly the auto-correlations or cross-correlations of atomic fluctuations.

RESULTS

The temperature factors of the C alpha atoms of 12 X-ray structures, ranging from a 41 residue subunit to a 633 residue dimer, are accurately predicted. Cross-correlations are also efficiently characterized, in close agreement with results obtained with a normal mode analysis coupled with energy minimization.

CONCLUSIONS

The simple model and method proposed here provide a satisfactory description of the correlations between atomic fluctuations. Furthermore, this is achieved within computation times at least one order of magnitude shorter than commonly used molecular approaches.

Structure of oxidized bacteriophage T4 glutaredoxin (thioredoxin). Refinement of native and mutant proteins

The structure of wild-type bacteriophage T4 glutaredoxin (earlier called thioredoxin) in its oxidized form has been refined in a monoclinic crystal form at 2.0 A resolution to a crystallographic R-factor of 0.209. A mutant T4 glutaredoxin gives orthorhombic crystals of better quality. The structure of this mutant has been solved by molecular replacement methods and refined at 1.45 A to an R-value of 0.175. In this mutant glutaredoxin, the active site residues Val15 and Tyr16 have been substituted by Gly and Pro, respectively, to mimic that of Escherichia coli thioredoxin. The main-chain conformation of the wild-type protein is similar in the two independently determined molecules in the asymmetric unit of the monoclinic crystals. On the other hand, side-chain conformations differ considerably between the two molecules due to heterologous packing interactions in the crystals. The structure of the mutant protein is very similar to the wild-type protein, except at mutated positions and at parts involved in crystal contacts. The active site disulfide bridge between Cys14 and Cys17 is located at the first turn of helix alpha 1. The torsion angles of these residues are similar to those of Escherichia coli thioredoxin. The torsion angle around the S-S bond is smaller than that normally observed for disulfides: 58 degrees, 67 degrees and 67 degrees for wild-type glutaredoxin molecule A and B and mutant glutaredoxin, respectively. Each sulfur atom of the disulfide cysteines in T4 glutaredoxin forms a hydrogen bond to one main-chain nitrogen atom. The active site is shielded from solvent on one side by the beta-carbon atoms of the cysteine residues plus side-chains of residues 7, 9, 21 and 33. From the opposite side, there is a cleft where the sulfur atom of Cys14 is accessible and can be attacked by a nucleophilic thiolate ion in the initial step of the reduction reaction.