Rotamerically Induced Perturbations

RIP: Large Local Perturbations

In these simulations, RIP is applied with a a rotational temperature of 300K to a protein that has been pre-equilibrated to 300K. A rotational temperature of 300K should reproduce the rotational velocities of sidechains at ~ 5000K.

These perturbations can kick out α-helices and loops that are not tightly bound to the body of the protein.

The flexibility of different regions of a structure can be calculated from an analysis of the trajectories generated by applying RIP to all residues in a protein.
Third PDZ domain of PSD95
Adregenic Receptor
Par6 PDZ domain [with ligand]
Estrogen-Related Receptor ligand-binding domain
Androgen Receptor ligand-binding domain
Estrogen Receptor ligand-binding domain
Second PDZ domain of Protein Tyrosine Phosphotase
Third PDZ domain of PSD95 [with ligand]
InaD fifth PDZ domain
α-lytic Protease
Ubiquitin
Second PDZ domain of Protein Tyrosine Phosphotase [with ligand]
N-terminal domain of HSP90
Chymotrypsin
WW domain [with ligand]
NtrC
Protein G
NtrC [phosphorylated]
Dihydrofolase Reductase [open]
Protein A
Glucocorticoid Receptor ligand-binding domain
Carbonic Anhydrase
WW domain
Triosephosphate Isomerase [closed]
InaD fifth PDZ domain [reduced form]
Thyroid Receptor ligand-binding domain
Kinesin ATP binding domain
Ebola Envelope Glyco Protein 2
Interleukin-2 [with inhibitor]
Zinc-finger mimic
Par6 PDZ domain
Sex-lethal developmental splicing factor
Triosephosphate Isomerase [open]
SGPB
Trypsin
Dihydrofolase Reductase [occluded]
Interleukin-2