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. 2023 Aug 30;13:14179. doi: 10.1038/s41598-023-40818-x

Table 3.

List of some known members of Dynamozone.

Structure Dynamozones Proteins Role or Function References
Loop Flap

• HIV protease

• Plasmepsins

• Beta-secretase

• Cathepsin

• Pepsins

These regions control the entrance and stabilization of ligands in the active site 6770
Loop Loop (Residues 166–176) • Triosephosphate isomerase In the ligand-bound state, the loop moves for ∼7 Å as a rigid lid toward the active site and accepts a “closed” conformation. These motions of the rigid lid close to the active site are essential for the catalytic mechanism of the enzyme 7173
Loop Loop

• Enolases

• Aldolases

Movements of the loop permit the catalytic residues to be oriented in a suitable position for catalysis 7476
Loop WPD loop • Protein tyrosine phosphatases (PTPs) This loop closes over the active site upon binding of the substrate, and loop closure permits the correct orientation of catalytic residues around the ligand 77,78
Loop Met20 loop (Active site loop ( • Dihydrofolate reductase (DHFR) This loop acts as a lid that closes on the cofactor, thereby allowing DHFR to adopt occluded and closed conformations 7981
Loop Helical loop • Lipases This loop is important for the enzyme function, acting as a lid to open or close the hydrophobic active site 82,83
Loop Long loop • β1,4-galactosyl transferase A displacement of more than 20 Å this long loop in protein provides binding sites for various ligands 84
Loop Omega loop • Cdc34-like E2 enzymes This loop can act as a lid that regulates the accessibility of the catalytic site and disturbs the charging activity of ubiquitin until a conformational change toward an open state is promoted by phosphorylation 8587
Linker Flexible linker • Calmodulin (CaM) CaM has two globular domains connected by a short and flexible linker that permits the protein to accept a wide variety of extended and compact conformations 8890

Hinge

Loop

Linker

• Hinge region

• P-loop

• hydrophobic “spines”

• A-loop

• αC helix

• DFG motif

• αB helix

• Protein kinases (PKs)

• Tyrosin kinase

• Src protein kinase

Hinge region: The hinge motion is necessary for the opening and closure of the kinase catalytic domain (CD)

P-loop (β1-β2 loop or G-loop or Gly-rich loop): This flexible loop is very important for the coordination of ATP phosphates

Hydrophobic “spines”: Two hydrophobic “spines” link the two lobes of protein kinase and dynamically connect all the elements important for catalysis

A-loop (Activation loop): In the inactive state of the enzyme, the A-loop is folded onto itself, and its opening is required to create the catalytically active form

αC helix: This helix in the “in” active conformation forms a hydrogen bond with the β3 strand for creating the catalytically active form of the enzyme

DFG motif: This motif in the active site switches from an inactive (DFG-out) conformation to an active (DFG-in) conformation, which is necessary to create the catalytically active form of the enzyme

αB helix: This helix creates a cavity, the so-called PIF pocket, which is very important for allosteric regulation of the protein kinases belonging to the AGC family

9196
Hinge Hinge region • Lactoferrin The hinge motions permit the formation of the complete iron-binding site in the closed states of lactoferrin 97100
Hinge Hinge region • Immunoglobulins The hinge region is connecting the Fab (Fragment antigen binding) region to the Fc (Fragment crystallizable) region 101,102