The reason for this could be a conformational averaging around the dihedral C4′-C5′, which nevertheless does not change the conclusion that conformer 11 was determined as the main conformation, because only dihedrals of C3′-C4′, C2′-C3′ and C2′-N define the conformation for the configurational analysis of C2′ and C3′.
In the chagasin cathepsin L complex, T31 contacts the peptidase active site cysteine via a water mediated hydrogen bond and helps to define the conformation of L6 such that it cannot be attacked by the peptidase [15].
Without arbitrary parameters to pre-define the conformation of the chromosome chain (i.e., no conformation parameters), the models allow a direct examination of how chromosome conformations emerge from different modes of condensin interactions (i.e., stochastic pairwise interactions and higher order condensing assemblies for the Type I and II models, respectively).
In contrast, removal of the hydroxyl group in T32V caused a significant increase in the K i. T32 has well defined roles satisfying intra-molecular hydrogen bonds and defining the conformation of L2.
While we could not find intra-molecular cross peak connecting the two caffeoyl arms (at least judging from the signals of the double bond, as the aromatic are to close to the diagonal to be resolved if present), some other intra-molecular NOEs are useful in defining the conformation of the caffeoyl arms.
Single-molecule fluorescence measurements define the clamp conformation during transcription initiation and elongation.
This approach allows us to define the phrase "conformation" in terms of the dynamical behavior of the molecular system and to characterize the dynamical stability of conformations.
In contrast to the intermolecular distance restraints, the intraprotein restraints used to define the open conformation of cNTnC·Ca2+(3), though well-validated by a subsequently determined crystal structure (31), are only approximately valid when applied toward a cNTnC·Ca2+·W7 complex.
As W7 binding induced conformational changes in cNTnC·Ca2+ that were similar (as monitored by NMR) to those induced by the binding of Sp (9, 10), we investigate the assumption that the distance restraints used to define the protein conformation can be reused from the study defining the structure of the cNTnC·Ca2+·Sp complex.
We define the new neighborhood conformation, tabu object and acceptance criteria of current conformation based on the original TS algorithm and put forward an improved TS algorithm.
Glycan receptors have been defined according to their overall conformation, via a parameter called the θ angle, which defines the form of the nonreducing end of the glycan receptors.
