Folding kinetics of phage T4 thioredoxin

A reexamination of the conformational transitions of T4 thioredoxin

The unfolding and refolding of T4 thioredoxin was observed by equilibrium and kinetic size exclusion chromatographic measurements in guanidine hydrochloride at 4 degrees C and pH 7.0. All the observed chromatographic profiles can be simulated by a cubic mechanism using a consistent set of equilibrium and kinetic parameters describing each of the coupled transitions. The four components in the folded protein and in the unfolded protein are interrelated by configurational transitions having parameters characteristic for proline peptide isomerizations. Only two of the four folded conformations are significantly populated at equilibrium. Each of the four unfolded components can refold by a unique conformational transition. No transiently populated folding intermediates are detected having hydrodynamic volumes intermediate between those characteristics for the folded and unfolded protein.

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.

Structure and fluctuations of bacteriophage T4 glutaredoxin modelled by molecular dynamics

A 120 ps molecular dynamics (MD) trajectory for bacteriophage T4 glutaredoxin was calculated including non-inertial solvent effects. The potential energy attains an equilibrated regime after the first 20 ps. The r.m.s. difference of all non-hydrogen atoms between X-ray and average MD structures for the regular secondary structure is 0.99A which shows that the MD simulation reproduces the essentials of the structure with high accuracy. Loop displacements are detected, shown by the larger full structure all non-hydrogen atom r.m.s. difference of 1.2A. The fluctuation pattern derived from MD agrees fairly well with that derived from X-ray isotropic temperature factors. The active site is a stable structural region in this MD modellization. Structural changes are put in context with the protein's function.

Folding of the reduced form of the thioredoxin from bacteriophage T4

The folding pattern for bacteriophage T4 thioredoxin is similar to that of the oxidized form [Borden, K. L. B., & Richards, F. M. (1990) Biochemistry 29, 3071-3077]. Equilibrium and kinetic studies were carried out by fluorescence and circular dichroism techniques. The same box model proposed for the oxidized form, with four identifiable states, can accommodate most of the data: N----Uc----Ut----It----N, where N is the native state, Uc is the unfolded species with Pro 66 in the cis form, Ut is the unfolded species with Pro 66 in the trans form, and It is a trans-Pro 66 intermediate with a volume comparable to that of N. However, the relative importance of the different components is shifted between the oxidized and reduced proteins. In spite of the small size of the disulfide loop, the Cys 14-Cys 17 bond appears to be important in stabilizing It. The tertiary structure as monitored by near-UV CD and fluorescence indicates that the reduced form is significantly less stable than its oxidized counterpart; however, the two secondary structures, as seen by far-UV CD, are very similar. The intermediate It behaves as though it is cold denaturated at 4 degrees C.