Biomedical subjects

Wei Yuan Yang

Publications and source records attributed to Wei Yuan Yang.

6 recordsLinked to original sources

PubMed2004

Rate-temperature relationships in lambda-repressor fragment lambda 6-85 folding.

Two classes of lambda(6-85) 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 the folding rates. Temperature-dependent interactions (e.g., hydrophobicity) play a large role in the initial stages of folding but not in the initial stages of unfolding of lambda(6-85). Placement of the transition state in terms of its surface exposure and entropy shows that at least two reaction coordinates are required to describe folding of all mutants over the full temperature range. The unusual Arrhenius plots of the very fastest mutant provide an additional kinetic signature for downhill folding.

Alanine↗

PubMed2004

Detection-dependent kinetics as a probe of folding landscape microstructure.

The folding landscapes of polypeptides and proteins exhibit a hierarchy of local minima. The causes range from proline isomerization all the way down to microstructure in the free energy caused by residual frustration inherent in even the best 20 amino acid design. The corresponding time scales range from hours to submicroseconds. The smallest microstructures are difficult to detect. We have measured the folding/unfolding kinetics of the engineered trpzip2 peptide at different tryptophan fluorescence wavelengths, each yielding a different rate. Wavelength-dependent folding kinetics on 0.1-2 mus time scales show that different microstructures with a range of solvent exposure and local dynamics are populated. We estimate a lower limit for the roughness of the free energy surface based on the range of rates observed.

Animals↗

PubMed2004

Heterogeneous folding of the trpzip hairpin: full atom simulation and experiment.

The beta-hairpin trpzip2 can be tuned continuously from a two-state folder to folding on a rough energy landscape without a dominant refolding barrier. At high denaturant concentration, this extremely stable peptide exhibits a single apparent "two-state" transition temperature when monitored by different spectroscopic techniques. However, under optimal folding conditions the hairpin undergoes an unusual folding process with three clusters of melting transitions ranging from 15 degrees C to 160 degrees C, as monitored by 12 different experimental and computational observables. We explain this behavior in terms of a rough free energy landscape of the unfolded peptide caused by multiple tryptophan interactions and alternative backbone conformations. The landscape is mapped out by potentials of mean force derived from replica-exchange molecular dynamics simulations. Implications for deducing cooperativity from denaturant titrations, for the origin of folding cooperativity, and for the folding of thermophilic proteins are pointed out. trpzip is an excellent small tunable model system for the glass-like folding transitions predicted by landscape theory.

Circular Dichroism↗

PubMed2004

Folding lambda-repressor at its speed limit.

We show that the five-helix bundle lambda(6-85) can be engineered and solvent-tuned to make the transition from activated two-state folding to downhill folding. The transition manifests itself as the appearance of additional dynamics faster than the activated kinetics, followed by the disappearance of the activated kinetics when the bias toward the native state is increased. Our fastest value of 1 micros for the "speed" limit of lambda(6-85) is measured at low concentrations of a denaturant that smooths the free-energy surface. Complete disappearance of the activated phase is obtained in stabilizing glucose buffer. Langevin dynamics on a rough free-energy surface with variable bias toward the native state provides a robust and quantitative description of the transition from activated to downhill folding. Based on our simulation, we estimate the residual energetic frustration of lambda(6-85) to be delta(2) G approximately 0.64 k(2)T(2). We show that lambda(6-86), as well as very fast folding proteins or folding intermediates estimated to lie near the speed limit, provide a better rate-topology correlation than proteins with larger energetic frustration. A limit of beta > or = 0.7 on any stretching of lambda(6-85) barrier-free dynamics suggests that a low-dimensional free-energy surface is sufficient to describe folding.

Circular Dichroism↗

PubMed2003

On the extended beta-conformation propensity of polypeptides at high temperature.

At room temperature, natural polypeptides exposed to high concentrations of a strong denaturant nearly attain the circular dichroism spectra characteristic of random coils. As temperature is increased, the spectra begin to show the signature of a substantial fraction of extended chain, the structure common in beta-sheets. This structural propensity at high temperature is not altered by concentration changes over a greater than 1000-fold range, so it is not caused by aggregation. Four proteins with different folds and varying amounts of alpha-helical and beta-sheet secondary structure, in the presence or absence of denaturant, all were subject to extended chain formation upon heating. This effect arises naturally from the steric constraints associated with polypeptides and is probably counteracted, not enhanced, by hydrophobic interactions. Molecular dynamics simulations in the 298-1000 K range reveal an attractive potential of mean force in the extended chain region of the Ramachandran diagram, which broadens as the temperature is raised. We also demonstrate a direct correlation between extended structure content and the rate of aggregation kinetics. Thus pre-existing extended structure could funnel proteins into aggregates.

Circular Dichroism↗

PubMed2003

Folding at the speed limit.

Many small proteins seem to fold by a simple process explicable by conventional chemical kinetics and transition-state theory. This assumes an instant equilibrium between reactants and a high-energy activated state. In reality, equilibration occurs on timescales dependent on the molecules involved, below which such analyses break down. The molecular timescale, normally too short to be seen in experiments, can be of a significant length for proteins. To probe it directly, we studied very rapidly folding mutants of the five-helix bundle protein lambda(6-85), whose activated state is significantly populated during folding. A time-dependent rate coefficient below 2 micro s signals the onset of the molecular timescale, and hence the ultimate speed limit for folding. A simple model shows that the molecular timescale represents the natural pre-factor for transition state models of folding.

Circular Dichroism↗