Biomaterial Database

Regulating the conformation of prion protein through ligand binding. 2009

Norifumi Yamamoto, and Kazuo Kuwata

Although some antiprion compounds have been shown to interfere with the pathological conversion of prion protein into a misfolded isoform, the actual mechanism has not been elucidated. In this study, we compared different conformations of prion protein with and without ligand binding, based on molecular dynamics simulations, to clarify the role of a typical antiprion compound termed GN8. In our approach, urea-driven unfolding simulations were employed to assay whether or not GN8 prevents denaturation of prion protein. We found that urea mediates partial unfolding at helix B of the prion protein, suggesting a transition into the intermediate states of the pathological conversion. However, GN8 efficiently suppressed local fluctuations by binding to flexible spots on helix B and prevented its urea-induced denaturation. We conclude that GN8 inhibits pathological conversion by suppressing the level of the intermediate. This is the first evidence supporting the chemical chaperone hypothesis, which states that GN8 acts as a chaperone to stabilize the normal form of the prion protein. Our basic principle constitutes a promising strategy for a dynamics-based drug design of therapeutic compounds, particularly for prion diseases and other diseases related to protein misfolding.

UI	MeSH Term	Description	Entries
D008024	Ligands	A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)	Ligand
D011328	Prions	Small proteinaceous infectious particles which resist inactivation by procedures that modify NUCLEIC ACIDS and contain an abnormal isoform of a cellular protein which is a major and necessary component. The abnormal (scrapie) isoform is PrPSc (PRPSC PROTEINS) and the cellular isoform PrPC (PRPC PROTEINS). The primary amino acid sequence of the two isoforms is identical. Human diseases caused by prions include CREUTZFELDT-JAKOB SYNDROME; GERSTMANN-STRAUSSLER SYNDROME; and INSOMNIA, FATAL FAMILIAL.	Mink Encephalopathy Virus,Prion,Encephalopathy Virus, Mink
D011485	Protein Binding	The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.	Plasma Protein Binding Capacity,Binding, Protein
D011489	Protein Denaturation	Disruption of the non-covalent bonds and/or disulfide bonds responsible for maintaining the three-dimensional shape and activity of the native protein.	Denaturation, Protein,Denaturations, Protein,Protein Denaturations
D015195	Drug Design	The molecular designing of drugs for specific purposes (such as DNA-binding, enzyme inhibition, anti-cancer efficacy, etc.) based on knowledge of molecular properties such as activity of functional groups, molecular geometry, and electronic structure, and also on information cataloged on analogous molecules. Drug design is generally computer-assisted molecular modeling and does not include PHARMACOKINETICS, dosage analysis, or drug administration analysis.	Computer-Aided Drug Design,Computerized Drug Design,Drug Modeling,Pharmaceutical Design,Computer Aided Drug Design,Computer-Aided Drug Designs,Computerized Drug Designs,Design, Pharmaceutical,Drug Design, Computer-Aided,Drug Design, Computerized,Drug Designs,Drug Modelings,Pharmaceutical Designs
D017433	Protein Structure, Secondary	The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to ALPHA-HELICES; BETA-STRANDS (which align to form BETA-SHEETS), or other types of coils. This is the first folding level of protein conformation.	Secondary Protein Structure,Protein Structures, Secondary,Secondary Protein Structures,Structure, Secondary Protein,Structures, Secondary Protein
D017510	Protein Folding	Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.	Protein Folding, Globular,Folding, Globular Protein,Folding, Protein,Foldings, Globular Protein,Foldings, Protein,Globular Protein Folding,Globular Protein Foldings,Protein Foldings,Protein Foldings, Globular
D018621	PrPC Proteins	Normal cellular isoform of PRION PROTEINS encoded by a chromosomal gene and found in normal and scrapie-infected brain tissue, and other normal tissue. PrPC are protease-sensitive proteins whose function is unknown. Posttranslational modification of PrPC into PrPSC leads to infectivity.	Scrapie Amyloid Precursor Protein,Cp 33-35,Cp33-35, Scrapie,PrP-sen,PrP sen