The TCR integrates forces in its triggering process upon interaction with pMHC. Force elicits TCR catch-slip bonds with strong pMHCs but slip-only bonds with weak pMHCs. We develop two models and apply them to analyze 55 datasets, demonstrating the models’ ability to quantitatively integrate and...
group has to rotate from the majorsynto the minorantiisomer prior to hybridization (Fig.2a). However, becauseantiis the preferred isomer in the canonical duplex, and because hybridization is rate-limiting under our experimental conditions (see below), the apparentkoffwould remain equivalent to that...
The residues involved in each interaction layer are depicted by stick models and colored following the same scheme. See also Figure S3. The exit of substrates to the extracellular side is blocked by a number of gating residues mainly in TM1 and TM7 (Figure 3, E1–E3). At the extracellular...
Due to approximations in the empirical potential energy functions for the folding simulations, most simulated τs reported to date have been much longer than the corresponding experimental τs. For example, early molecular dynamics (MD) simulations of fast-folding proteins using a distributed computing...
Cardiovascular disease (CVD) is one of the major causes of deaths in the world. Epidemiological analyses have identified multiple risk factors responsible for CVD. Out of these factors, high level of low-density lipoprotein (LDL), which supplies cholesterol in an uncontrolled manner to artery-wall...
Owing to this very strong interaction and the high protein concentrations required in the NMR experiments, we employed fluorescence spectroscopy to avoid ligand depletion effects and to ultimately determine the dissociation constant, Kd, of albicidin binding to AlbAS and AlbAL. The experimental read-...
in front of a T. Its crystal structure at 1.5 Å resolution confirms that there is no structural element in the active site that could lead to the rejection of A in front of T. To resolve this contradiction, we show that a nearby gene is a triphosphohydolase specific of dATP (Dat...
The use of the ML approach in NNScore 2.0 does not automatically allow it to account for specific interaction terms in a proper way. For instance, the hydrogen bond-related descriptors showed that the influence of the hydrogen bond acceptors (HBA) was overestimated, whereas the influence of ...
VHS-RNase binds to the cap structure of stable host mRNAs via its interaction with eIF4H. HSV-1 RNase acts differently on stress response RNAs that carry AU-rich elements (ARE) in their 31-ends. These RNAs undergo cleavage in their 31 UTRs, but the capped 51-end of the RNA is ...
. Some IDPs are fully disordered and contain only one IDR from the N- to C-terminus. Other IDPs comprise a mixture of IDRs and structural domains. Some long IDRs contain functional regions that conditionally fold into specific structures upon binding to interaction partners. This disorder-to-...