title: New hypotheses about the structure-function of proprotein convertase subtilisin/kexin type 9: analysis of the epidermal growth factor-like repeat A docking site using WaterMap.
abstract: LDL cholesterol (LDL-C) is cleared from plasma via cellular uptake and internalization processes that are largely mediated by the low-density lipoprotein cholesterol receptor (LDL-R). LDL-R is targeted for lysosomal degradation by association with proprotein convertase subtilisin-kexin type 9 (PCSK9). Gain of function mutations in PCSK9 can result in excessive loss of receptors and dyslipidemia. On the other hand, receptor-sparing phenomena, including loss-of-function mutations or inhibition of PCSK9, can lead to enhanced clearance of plasma lipids. We hypothesize that desolvation and resolvation processes, in many cases, constitute rate-determining steps for protein-ligand association and dissociation, respectively. To test this hypothesis, we analyzed and compared the predicted desolvation properties of wild-type versus gain-of-function mutant Asp374Tyr PCSK9 using WaterMap, a new in silico method for predicting the preferred locations and thermodynamic properties of water solvating proteins ("hydration sites"). We compared these results with binding kinetics data for PCSK9, full-length LDL-R ectodomain, and isolated EGF-A repeat. We propose that the fast k(on) and entropically driven thermodynamics observed for PCSK9-EGF-A binding stem from the functional replacement of water occupying stable PCSK9 hydration sites (i.e., exchange of PCSK9 H-bonds from water to polar EGF-A groups). We further propose that the relatively fast k(off) observed for EGF-A unbinding stems from the limited displacement of solvent occupying unstable hydration sites. Conversely, the slower k(off) observed for EGF-A and LDL-R unbinding from Asp374Tyr PCSK9 stems from the destabilizing effects of this mutation on PCSK9 hydration sites, with a concomitant increase in the persistence of the bound complex.
authors.affiliation: Novartis Institutes for BioMedical Research, Global Discovery Chemistry, Cambridge, Massachusetts 02139, USA. robert.pearlstein@novartis.com
authors.forename: Robert A
authors.initials: RA
authors.lastname: Pearlstein
authors.forename: Qi-Ying
authors.initials: QY
authors.lastname: Hu
authors.forename: Jing
authors.initials: J
authors.lastname: Zhou
authors.forename: David
authors.initials: D
authors.lastname: Yowe
authors.forename: Julian
authors.initials: J
authors.lastname: Levell
authors.forename: Bethany
authors.initials: B
authors.lastname: Dale
authors.forename: Virendar K
authors.initials: VK
authors.lastname: Kaushik
authors.forename: Doug
authors.initials: D
authors.lastname: Daniels
authors.forename: Susan
authors.initials: S
authors.lastname: Hanrahan
authors.forename: Woody
authors.initials: W
authors.lastname: Sherman
authors.forename: Robert
authors.initials: R
authors.lastname: Abel
mesh_terms: D001665:Binding Sites; D002460:Cell Line; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004815:Epidermal Growth Factor / Q000737:chemistry* / Q000235:genetics; D006801:Humans; D008958:Models, Molecular; D009154:Mutation; D000071449:Proprotein Convertase 9; D043484:Proprotein Convertases; D011487:Protein Conformation; D011973:Receptors, LDL / Q000737:chemistry; D012697:Serine Endopeptidases / Q000737:chemistry* / Q000235:genetics; D012997:Solvents / Q000737:chemistry; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D011973:Receptors, LDL; D012997:Solvents; D014867:Water; D004815:Epidermal Growth Factor; C472125:PCSK9 protein, human; D000071449:Proprotein Convertase 9; D043484:Proprotein Convertases; D012697:Serine Endopeptidases