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
(b) Poisson-Boltzmann electrostatic-potential surface (color bar range ± 5 kT/e) generated by PyMOL APBS tool79 for side α4α5 (top) and side α6 (bottom) of the R2 repeat. Full size image In a further effort to solve the three-dimensional structure of the full-length domain,...
To understand the functional importance of rare mutations in VRC34 lineage maturation, we analyzed SHMs of VRC34 lineage variants, their frequencies of occurrence, and their potential contacts with Env (Figures 4A and 4B). VRC34.01 had 23 and 12 amino acid mutations on heavy- and light-chain...
domestica CHS2 with Gly342 in HaBPS. As a result, BIS and BPS create a hydrophobic surface for the interaction with the small hydrophobic CoA thioesters of benzoates. Interestingly, the size of the active-site cavity of MdBIS3 is dramatically reduced by the replacement of Thr197 in CHS ...
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-...
which is exposed to the solvent. Either D87 is able to come back to its canonical position once all the substrates and ions are in place, or its position is conserved in the complex: to resolve this point, we investigate below with molecular dynamics its flexibility and potential to stabilis...
To probe this process of perturbation in more detail, we present here a study of the interaction of B2088 with model membranes using atomistic molecular dynamics (MD) simulations. 2. Methods The structure of the model branched peptide B2088 (RGRKVVRR)2KK is shown in Fig. 1. B2088 was ...
right images show the close-up views of the intracellular gating interactions seen from the intracellular side. N- and C-domain helices are colored yellow and light blue, respectively. The residues involved in each interaction layer are depicted by stick models and colored following the same ...
we show that m6A pairs with uridine with the methylamino group in theanticonformation to form a Watson-Crick base pair that transiently exchanges on the millisecond timescale with a singly hydrogen-bonded low-populated (1%) mismatch-like conformation in which the methylamino group issyn. This abil...
Based on the primary structures of TbCet1 and TcCet1, the kinetoplastid enzymes contain all the putative counterparts of β-strands that comprise the yeast Cet1 triphosphate tunnel but lack extra domains appended to the N-terminal region that are essential for homodimerization and interaction with ...