PMID: 21424227;PMCID: PMC3229278;Abstract:
A method based on the Carr-Purcell-Meiboom- Gill relaxation dispersion experiment is presented for measuring the temperature coefficients of amide proton chemical shifts of low populated 'invisible' protein states that exchange with a 'visible' ground state on the millisecond time-scale. The utility of the approach is demonstrated with an application to an I58D mutant of the Pfl6 Cro protein that undergoes exchange between the native, folded state and a cold denatured, unfolded conformational ensemble that is populated at a level of 6% at 2.5°C. A wide distribution of amide temperature coefficients is measured for the unfolded state. The distribution is centered about -5.6 ppb/K, consistent with an absence of intra-molecular hydrogen bonds, on average. However, the large range of values (standard deviation of 2.1 ppb/K) strongly supports the notion that the unfolded state of the protein is not a true random coil polypeptide chain. © Springer Science+Business Media B.V. 2011.
Abstract:
The synthesis of the two stereoisomers of spiro(bicyclo[2.2.1]heptane-2,1'-cyclopropan)-2'-one, 3a and 4a, from diazomethane and the ketene 2-carbonylylbicyclo[2.2.1]heptane in ether at 195 K yields a ~1.6 to 1 ratio. At 245 K, the ratio changes in a first-order manner, with an observed rate constant of 1.7 x 10-4 s-1, to an equilibrium ratio of 0.8 to 1. The temperature dependence of the interconversion of 3a and 4a (GC method) and that of their dideuterio derivatives 3b and 4b (NMR method) have been determined and yield activation parameters E(a) = 16.3 ± 1.4 kcal/mol and log A = 10.4 ± 1.4 (A in s-1) (GC method) and E(a) = 15.3 ± 1.4 and log A = 9.6 ± 1.4 (NMR method). The free energies of activation at 239 K have been determined in four solvents: dichloromethane (16.1 kcal/mol), acetone (17.7), hexane (17.9), and ether (19.1). The solvent dependence does not correlate well with commonly used measures of solvent polarity, and the reaction is unexpectedly slow in acetone and ether. This deceleration is explained in terms of nucleophilic association of these solvents with the carbonyl groups in the cyclopropanones, leading to a ground state stabilization.
PMID: 17376085;Abstract:
The gene regulatory circuitry of phage λ is among the best-understood circuits. Much of the circuitry centres around the immunity region, which includes genes for two repressors, CI and Cro, and their cis-acting sites. Related phages, termed lambdoid phages, have different immunity regions, but similar regulatory circuitry and genome organization to that of λ, and show a mosaic organization, arising by recombination between lambdoid phages. We sequenced the immunity regions of several wild phages with the immunity specificity of λ, both to determine whether natural variation exists in regulation, and to analyse conservation and variability in a region rich in well-studied regulatory elements. CI, Cro and their cis-acting sites are almost identical to those in λ, implying that regulatory mechanisms controlled by the immunity region are conserved. A segment adjacent to one of the operator regions is also conserved, and may be a novel regulatory element. In most isolates, different alleles of two regulatory proteins (N and CII) flank the immunity region; possibly the lysis-lysogeny decision is more variable among isolates. Extensive mosaicism was observed for several elements flanking the immunity region. Very short sequence elements or microhomologies were also identified. Our findings suggest mechanisms by which fine-scale mosaicism arises. © 2007 The Authors.
Previously reported crystal structures of free and DNA-bound dimers of lambda Cro differ strongly (about 4 A backbone rmsd), suggesting both flexibility of the dimer interface and induced-fit protein structure changes caused by sequence-specific DNA binding. Here, we present two crystal structures, in space groups P3(2)21 and C2 at 1.35 and 1.40 A resolution, respectively, of a variant of lambda Cro with three mutations in its recognition helix (Q27P/A29S/K32Q, or PSQ for short). One dimer structure (P3(2)21; PSQ form 1) resembles the DNA-bound wild-type Cro dimer (1.0 A backbone rmsd), while the other (C2; PSQ form 2) resembles neither unbound (3.6 A) nor bound (2.4 A) wild-type Cro. Both PSQ form 2 and unbound wild-type dimer crystals have a similar interdimer beta-sheet interaction between the beta1 strands at the edges of the dimer. In the former, an infinite, open beta-structure along one crystal axis results, while in the latter, a closed tetrameric barrel is formed. Neither the DNA-bound wild-type structure nor PSQ form 1 contains these interdimer interactions. We propose that beta-sheet superstructures resulting from crystal contact interactions distort Cro dimers from their preferred solution conformation, which actually resembles the DNA-bound structure. These results highlight the remarkable flexibility of lambda Cro but also suggest that sequence-specific DNA binding may not induce large changes in the protein structure.
A "switch" mutant of the Arc repressor homodimer was constructed by interchanging the sequence positions of a hydrophobic core residue, leucine 12, and an adjacent surface polar residue, asparagine 11, in each strand of an intersubunit beta sheet. The mutant protein adopts a fold in which each beta strand is replaced by a right-handed helix and side chains in this region undergo significant repacking. The observed structural changes allow the protein to maintain solvent exposure of polar side chains and optimal burial of hydrophobic side chains. These results suggest that new protein folds can evolve from existing folds without drastic or large-scale mutagenesis.
