Sentence examples for the loop motion from inspiring English sources

Two out of the six binary and ternary MD simulations were meaningful for describing this step: 1fdtB-NADPH-E1 (C3), which confirmed the loop motion with subsequent opening of gate 1 and the drift of E2 toward gate 3; and 1fdtA-NADPH (B1), which showed the egress path of the cofactor due to gate 1 enlargement.

The MD of the ternary complex C3 best described step 4 with an ΔG of −8.31 kcal/mol for the first 10 ns (ΔGbind −28.3 kcal/mol): E1 maintained its hydrogen bonds to Ser142/Tyr155 for the first 10 ns, until being pushed toward gate 3 and out of the SUB in the following 7 ns due to the loop motion toward the αG'-helix (Figure 7) and the inward rotation of Phe192 and Phe226.

On the other hand, as can be seen from the rmsd and the traces following the loop motion, the βII−βIII loop is likely to be more disordered without the peptide bound.

Four mutation sites are carefully selected, Trp184 and M185 which are deeply buried in the helix 2 region and Gln155 and Glu159 which regulate the loop motion at the MHR region.

Here we describe the loop motions in two chains comprising the dimer along the first three eigenvectors, which account for 44% and 42% of the overall motion of chains D and E respectively.

The reasons therefore could be the presence of E1 in the SUB, influencing the loop motions, but also because a much longer simulation time would be required to sample such marked conformational changes.

The progression of E1 to the end of the tunnel was favoured by the loop motions, the rotation of the apolar residues Phe192, Met193 and Phe226 into the SUB (Figure 7), and by the edging out of His221 and Glu282 and the consequent enlargement of gate 3. Interestingly, a decrease of ΔG from −8.31 (after ca. 10 ns) to −6.36 kcal/mol (after 17 ns) was observed.

Given the caveats above, how do the loop motions highlighted in Table 1 and Figure 1 influence the structure and chemistry of the antigen-binding sites?

Furthermore, for most of the results in Table 1, we simply do not know whether any of the loop motions are readily sampled by free TCRs or whether they are induced by binding and, if they are induced, we do not have estimates of the associated energetic penalties.

Huang et al. (2011) successfully simulated the looping motion observed in Typhoon Krosa (2007) with a fine resolution, realistic topography, although their simulated vortex turned northward after looping, but the observed one moved northwestward.

The complex stability of B2 was also reflected by a good free energy ΔG (−9.35 kcal/mol) with respect to the positive values of B1 and B3 (Table 2), which substantiated our structural hypothesis for catalytic step 2. The MD of the ternary complex 1i5r-NADPH-E1 (C2) described very well the expected loop motion from cluster cl3, shielding the COF, to cluster cl2 (Figure 5).