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Despite their different function and architecture the proteins are found to employ common mechanisms for substrate selectivity: an induced geometrical fit by structurally homologous binding sites and an induced rapid dipole moment reversal.
Although these enzymes use different mechanisms for substrate deamination, all form a keto-product.
In spite of their high physiological and pharmaceutical importance, the molecular recognition by these transporters of the amino acid side chains of short peptides and thus the mechanisms for substrate binding and specificity are far from being understood.
In addition, the recent structural analysis of the binding surfaces for the 19S regulator both of the immuno- and constitutive 20S proteasome shows high similarity, such that the gating mechanisms for substrate entry are unlikely to differ (Huber et al., 2012).
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We used this docked model to postulate a mechanism for substrate transport and inhibitor binding for VAChT.
It is possible that XylC uses a different mechanism for substrate recognition and catalysis compared to other xylanases.
All these evidence and results provided the possible mechanism for substrate transportation inside the enzyme-MOF composites.
These substitutions may reduce the hydrophobic interactions for aromatic aldehydes in KmGRE2, which suggests that the molecular mechanism for substrate recognition differs between KmGRE2 and GRE2.
Comparison of the apo and inhibitor-bound structures reveals conformational changes in a flexible cap that allows the substrate to access the relatively buried active site, providing new insight into the mechanism for substrate recognition.
The pathway determined from the SMD simulations for the exit of substrate from the S1 site corresponds exactly to a water channel (Table 4), thus identifying a specific mechanism for substrate binding in the S2 site to trigger permeation.
HECT domain architecture for ubiquitin ligation suggests mechanism for substrate lysine prioritization.
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