Evaluating the stability of general proteins using distance-dependant statistical potential based on <i>general protein library</i>.

<p>RAPDF (general) represents the statistical RAPDF scores calculated using the general protein database [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119417#pone.0119417.ref017" target="_blank">17</a>]. RAPDF (Composite) represents the statistical RAPDF scores calculated using the composite protein database composed of α-, β- and α+β proteins <b><i>(2566 proteins)</i></b>.</p

Predicted stability of designed repeat proteins using distance-dependant statistical potential based on TPR (light blue) or AR (blue) protein libraries.

<p>Predicted stability of designed repeat proteins using distance-dependant statistical potential based on TPR (light blue) or AR (blue) protein libraries.</p

Comparison of kinetic energies and RAPDF scores of TPR proteins.

<p>Comparison of kinetic energies and RAPDF scores of TPR proteins.</p

PRIDE2 structure comparison of non-redundant repeat proteins (Drawtree).

<p>The repeat proteins are divided into branches, which are shown as groups (A) AR (B) TPR.</p

Evaluating the stability of β proteins using distance-dependant statistical potential based on β protein library (288 proteins).

<p>RAPDF (β) represents the statistical RAPDF scores calculated using the β- database. First 4 sets were single misfold decoy sets and the rest 16 sets were from multiple decoy sets with a representative decoy selected.</p

Correlation between the RAPDF scores of CTPRa<i>n</i> and the equilibrium unfolding free energies.

<p>(A) RAPDF scores versus ΔG_D-N(kcal/mol), the thermal unfolding free energies (B) RAPDF scores versus ΔG_0-j(kcal/mol), the folding free energies calculated from fitting the Ising model.</p

Evaluating the stability of α proteins using distance-dependant statistical potential based on α protein library (1007 proteins).

<p>RAPDF (α) represents the statistical RAPDF scores calculated using the α- database. First 6 sets were single misfold decoy sets and the rest 14 sets were from multiple decoy sets with a representative decoy selected.</p

Distance-dependant statistical potential based on <i>ankyrin repeat protein library (33 proteins)</i>.

<p>Homology models were used as decoys. RAPDF (Ankyrin) represents the statistical RAPDF scores calculated using the Ankyrin database.</p

Switchable DNA Catalysts for Proximity Labeling at Sites of Protein–Protein Interactions

Proximity labeling (PL) has emerged as a powerful approach to elucidate proteomes within a defined radius around a protein of interest (POI). In PL, a catalyst is attached to the POI and tags nearby endogenous proteins, which are then isolated by affinity purification and identified by mass spectrometry. Although existing PL methods have yielded numerous biological insights, proteomes with greater spatial resolution could be obtained if PL catalysts could be activated at more specific subcellular locations, such as sites where both the POI and a chemical stimulus are present or sites of protein–protein interactions (PPIs). Here, we report DNA-based switchable PL catalysts that are attached to a POI and become activated only when a secondary molecular trigger is present. The DNA catalysts consist of a photocatalyst and a spectral quencher tethered to a DNA oligomer. They are catalytically inactive by default but undergo a conformational change in response to a specific molecular trigger, thus activating PL. We designed a system in which the DNA catalyst becomes activated on living mammalian cells specifically at sites of Her2–Her3 heterodimers and c-Met homodimers, PPIs known to increase the invasion and growth of certain cancers. While this study employs a Ru(bpy)3-type complex for tagging proteins with biotin phenol, the switchable DNA catalyst design is compatible with diverse synthetic PL photocatalysts. Furthermore, the switchable DNA PL catalysts can be constructed from conformation-switching DNA aptamers that respond to small molecules, ions, and proteins, opening future opportunities for PL in highly specific subcellular locations

Legislative Documents

Also, variously referred to as: House bills; House documents; House legislative documents; legislative documents; General Court documents