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To understand the structural and molecular conformational differences between the members of the rice ALDH protein superfamily as well as their protein-protein interaction characteristics and ligand-protein interaction properties, the 21 deduced ALDH protein sequences were modeled using the top ten PDB closed template structures by I-Tasser [62].
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To rationalize the observed functional contributions of amino acid changes in these three locations (positions 55, 130, and 191), we performed molecular dynamics simulations to sample conformational differences in protein structure in the presence of d- or l-Thy.
We attempted to evaluate whether or not the striking alterations predicted by the molecular dynamics simulations corresponded to actual conformational differences between peptide-free and peptide loaded proteins, using conformation-specfic superantigen and antibody probes of DR1 structure.
Compound binding is captured in complex with representative LpxC orthologs, and structural analysis reveals large conformational differences that mostly reflect inherent molecular features of distinct LpxC orthologs, whereas ligand-induced structural adaptations occur at a smaller scale.
On the other hand, when the same experiment is performed on a pure biotin-KKKKC SAM no difference in binding events is observed (see Supporting Information), indicating that despite the different potentials applied no molecular conformational changes are occurring.
Detailed αS molecular analyses using an ELISA approach revealed striking differences in immunoreactivity with different antibodies in sick mice, questioning their possible relationship with conformational differences between the disease-associated αS and its normal counterpart.
Thus, several variants were not sensitive to the conformational differences.
Conformational differences between picrotoxin- (closed/resting) and picrotoxin/GABA-bound (pre-active) human α1β3γ2L GABAAR structures.
Consequently, conformational differences must impact particle association with cellular receptors or membranes and subsequent intracellular sorting.
Chemical evaluation of conformational differences in native and chemically modified proteins.
Conformational differences between picrotoxin- (closed/resting) and alprazolam/GABA-bound (desensitized) human α1β3γ2L GABAAR structures.
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