The mutation Gly328Glu required limited loop sampling to resolve main-chain clashes resulting from the insertion of a larger side chain.
The resulting structures are subsequently "relaxed" to improve the local backbone and side-chain orientations and to minimize side-chain clashes.
Crystal lattices were constructed in PyMOL using the unit cell determined by Clearer [ 30], and these were minimized to remove side-chain clashing and unfavourable conformations.
These amino acid side chains would clash with the second phosphate of MVAPP (5 ).
This may be explained by the structural observation that the side chain of Leu56 clashes with a PA Tyr688 in our putative PA-TEM8 complex model (Figure 3E).
In both models, the side chain of Met311 clashes with residues in HP2, suggesting that the conformational changes in HP2 and the NMD motif must be concerted.
A close up of the model is shown in the right hand panel with side chains involved in clashes shown as sticks.
Ser20 adopts a normal backbone geometry, and the side chain makes no steric clashes in models of IAPP amyloid fibers, suggesting that the increased rate of amyloid formation by the mutant does not result from the relief of steric incompatibility in the fiber state.
Streaking through the al fresco venue, music clashing, chains at the neck, metal bangles above the elbows, hair whooshed up in 1980s tough chic, this was a different woman from the gentler (dare we say older?) creature using Missoni as a cover up.
The evening began slowly, like any karaoke night, with mostly older white males singing Creedence, Alice in Chains, and the Clash, each taking his song as seriously as a book report.
Structural modeling suggests the branched-chain residues would clash with the DNA and interfere with CarD function.
