The fast and the slow: folding and trapping of λ6-85.

@article{Prigozhin2011TheFA,
  title={The fast and the slow: folding and trapping of $\lambda$6-85.},
  author={Maxim B. Prigozhin and Martin Gruebele},
  journal={Journal of the American Chemical Society},
  year={2011},
  volume={133 48},
  pages={
          19338-41
        }
}
Molecular dynamics simulations combining many microsecond trajectories have recently predicted that a very fast folding protein like lambda repressor fragment λ(6-85) D14A could have a slow millisecond kinetic phase. We investigated this possibility by detecting temperature-jump relaxation to 5 ms. While λ(6-85) D14A has no significant slow phase, two even more stable mutants do. A slow phase of λ(6-85) D14A does appear in mild denaturant. The experimental data and computational modeling… 
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References

SHOWING 1-10 OF 21 REFERENCES

Folding λ-repressor at its speed limit

We show that the five-helix bundle λ6–85 can be engineered and solvent-tuned to make the transition from activated two-state folding to downhill folding. The transition manifests itself as the…

Reducing lambda repressor to the core.

This work hypothesized that removal of three out of five helices of λ(*)(6-85) would further reduce this protein to its smallest folding core, and found the most stable two-helix bundle, λ(blue1), is a cooperatively folding miniprotein with the same melting temperature and folding rate as the full-length λ (*)(6) pseudo wild type and a well-defined computed structure.

Direct observation of downhill folding of lambda-repressor in a microfluidic mixer.

A survey of lambda repressor fragments from two-state to downhill folding.

Folding at the speed limit

Very rapidly folding mutants of the five-helix bundle protein λ6–85, whose activated state is significantly populated during folding, are studied, showing that the molecular timescale represents the natural pre-factor for transition state models of folding.

Rate−Temperature Relationships in λ-Repressor Fragment λ6-85 Folding†

Two classes of λ6-85 mutants (those richer in alanine, and those richer in glycine) have very similar slopes in an Arrhenius plot of the unfolding rates but very different temperature dependencies of…

Structure and stability of monomeric lambda repressor: NMR evidence for two-state folding.

This study investigates a new form of the N-terminal domain of bacteriophage lambda repressor consisting of residues 6-85 (lambda 6- 85) using nuclear magnetic resonance (NMR) and circular dichroism (CD) and provides strong evidence for two-state folding.

Computational design and experimental testing of the fastest-folding β-sheet protein.

Atomistic folding simulations of the five-helix bundle protein λ(6−85).

An atomistic model of the folding of an 80-residue fragment of the λ repressor protein with explicit solvent that captures dynamics on a 10 milliseconds time scale is reported.

Backbone Dynamics of the Monomeric λ Repressor Denatured State Ensemble under Nondenaturing Conditions

It is concluded that conformational restriction of the backbone MetO-lambdaLS is due to nascent helix formation in the region corresponding to native helix 1 and the bulkiness of amino acid residues in the C-terminal third leads to the potential for hydrophobic interactions.