Structure and molecular dynamics simulation of archaeal prefoldin: the molecular mechanism for binding and recognition of nonnative substrate proteins.
Prefoldin (PFD) is a heterohexameric molecular chaperone complex in the eukaryotic cytosol and archaea with a jellyfish-like structure containing six long coiled-coil tentacles. PFDs capture protein folding intermediates or unfolded polypeptides and transfer them to group II chaperonins for facilitated folding. Although detailed studies on the mechanisms for interaction with unfolded proteins or cooperation with chaperonins of archaeal PFD have been performed, it is still unclear how PFD captures the unfolded protein. In this study, we determined the X-ray structure of Pyrococcus horikoshii OT3 PFD (PhPFD) at 3.0 A resolution and examined the molecular mechanism for binding and recognition of nonnative substrate proteins by molecular dynamics (MD) simulation and mutation analyses. PhPFD has a jellyfish-like structure with six long coiled-coil tentacles and a large central cavity. Each subunit has a hydrophobic groove at the distal region where an unfolded substrate protein is bound. During MD simulation at 330 K, each coiled coil was highly flexible, enabling it to widen its central cavity and capture various nonnative proteins. Docking MD simulation of PhPFD with unfolded insulin showed that the beta subunit is essentially involved in substrate binding and that the alpha subunit modulates the shape and width of the central cavity. Analyses of mutant PhPFDs with amino acid replacement of the hydrophobic residues of the beta subunit in the hydrophobic groove have shown that beta Ile107 has a critical role in forming the hydrophobic groove.
Ohtaki
Akashi
A
Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
Kida
Hiroshi
H
Miyata
Yusuke
Y
Ide
Naoki
N
Yonezawa
Akihiro
A
Arakawa
Takatoshi
T
Iizuka
Ryo
R
Noguchi
Keiichi
K
Kita
Akiko
A
Odaka
Masafumi
M
Miki
Kunio
K
Yohda
Masafumi
M
D019943:Amino Acid Substitution; D002950:Citrate (si)-Synthase / Q000737:chemistry; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D049452:Green Fluorescent Proteins / Q000737:chemistry; D057927:Hydrophobic and Hydrophilic Interactions; D007328:Insulin; D008958:Models, Molecular; D018832:Molecular Chaperones / Q000737:chemistry*; D050505:Mutant Proteins / Q000737:chemistry; D009154:Mutation / Q000235:genetics; D011485:Protein Binding; D017510:Protein Folding; D017433:Protein Structure, Secondary; D021122:Protein Subunits / Q000737:chemistry; D043902:Pyrococcus horikoshii / Q000737:chemistry*; D013696:Temperature
D007328:Insulin; D018832:Molecular Chaperones; D050505:Mutant Proteins; D021122:Protein Subunits; C112806:prefoldin; D049452:Green Fluorescent Proteins; D002950:Citrate (si)-Synthase