What best characterizes cryptic binding pockets in proteins?

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Question restatement: What best characterizes cryptic binding pockets in proteins?

Option 1: They are pockets that appear in some protein conformations, often only upon ligand binding. 
This option highlights a hallmark of cryptic pockets: they are not evident in all conformations and may become accessible or form when a ligand binds or when the protein adopts a particular conformation. This aligns with the concept of cryptic or inducible pockets that are hidden in the unbound structure and revealed upon structural rearrangements.

Option 2: They are parts of the protein that are filtered out during clustering due to high RMSD. 
This statement describes a data-processing artifact rather than a biological feature of cryptic pockets. High RMSD clustering might separate conformations, but it does not define cryptic pockets themselves, which are about the existence and inducibility of binding sites, not about exclusion during analysis.

Option 3: They are rigid cavities on the protein surface that are always solvent-accessible. 
If a pocket were rigid and always solvent-accessible, it would be a static feature of a protein structure. Cryptic pockets, by contrast, are typically not visible in every conformation and often are not permanently solvent-accessible; they emerge through conformational changes, not as always-present rigid, readily accessible cavities.

Option 4: They are hydrophobic regions that generally bind lipids instead of small-molecule drugs. 
While hydrophobic regions can participate in ligand binding, cryptic pockets are defined by their inducible nature and conditional exposure, not by a predisposition to bind lipids specifically. This description mischaracterizes the general concept, which applies to small-molecule binding possibilities as well, not exclusively to lipid interactions.

In summary, option 1 correctly captures the defining feature of cryptic pockets: their appearance is conditional, often dependent on specific protein conformations or ligand-induced rearrangements, rather than being always present or defined by a particular chemical property alone. The other options describe scenarios unrelated to the cryptic, inducible nature of these pockets or mix in concepts (clustering artifacts, always-open cavities, lipid preference) that do not characterize cryptic pockets across typical protein structures.

2254 BIOSC 1544 SEC1000 Quiz #22: CADD and Protein Flexibility

What best characterizes cryptic binding pockets in proteins?

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