Insight into the conserved structural dynamics of the C-terminus of mammal PrPC identifies structural core and possible structural role of pharmacological chaperones

References

• Telling GC. The shape of things to come: structural insights into how prion proteins encipher heritable information. Nat Commun. 2022;13(1):4003. DOI:10.1038/s41467-022-31460-8.
   PubMed Web of Science ®Google Scholar
• Wang L-Q, Zhao K, Yuan H-Y, et al. Cryo-EM structure of an amyloid fibril formed by full-length human prion protein. Nat Struct Mol Biol. 2020;27(6):598–602. DOI:10.1038/s41594-020-0441-5
   PubMed Web of Science ®Google Scholar
• Glynn C, Sawaya MR, Ge P, et al. Cryo-EM structure of a human prion fibril with a hydrophobic, protease-resistant core. Nat Struct Mol Biol. 2020;27(5):417–423. DOI:10.1038/s41594-020-0403-y
   PubMed Web of Science ®Google Scholar
• Kraus A, Hoyt F, Schwartz CL, et al. High-resolution structure and strain comparison of infectious mammalian prions. Mol Cell. 2021;81(21):4540–4551.e6. DOI:10.1016/j.molcel.2021.08.011
   PubMed Web of Science ®Google Scholar
• Hoyt F, Standke HG, Artikis E, et al. Cryo-EM structure of anchorless RML prion reveals variations in shared motifs between distinct strains. Nat Commun. 2022;13(1):4005. DOI:10.1038/s41467-022-30458-6
   PubMed Web of Science ®Google Scholar
• Manka SW, Zhang W, Wenborn A, et al. 2.7 Å cryo-EM structure of ex vivo RML prion fibrils. Nat Commun. 2022;13(1):4004. DOI:10.1038/s41467-022-30457-7
   PubMed Web of Science ®Google Scholar
• Chen E-L, Kao H-W, Lee C-H, et al. 2.2 Å Cryo-EM tetra-protofilament structure of the hamster Prion 108–144 fibril reveals an ordered water channel in the center. J Am Chem Soc. 2022;144(30):13888–13894. DOI:10.1021/jacs.2c05479.
   PubMed Web of Science ®Google Scholar
• Spagnolli G, Rigoli M, Orioli S, et al. Full atomistic model of prion structure and conversion. PLOS Pathog. 2019;15(7):e1007864. DOI:10.1371/journal.ppat.1007864
   PubMed Web of Science ®Google Scholar
• Srivastava KR, Lapidus LJ. Prion protein dynamics before aggregation. Proc Natl Acad Sci. 2017;114(14):3572–3577.
   PubMed Web of Science ®Google Scholar
• Petrosyan R, Patra S, Rezajooei N, et al. Unfolded and intermediate states of PrP play a key role in the mechanism of action of an antiprion chaperone. Proc Natl Acad Sci U S A. 2021;118(9):e2010213118. DOI:10.1073/pnas.2010213118
   PubMed Web of Science ®Google Scholar
• Rigoli M, Spagnolli G, Faccioli P, et al. Ok Google, how could I design therapeutics against prion diseases? Curr Opin Pharmacol. 2019;44:39–45.
   PubMed Web of Science ®Google Scholar
• Myers R, Cembran A, Fernandez-Funez P. Insight from animals resistant to prion diseases: deciphering the genotype – morphotype – phenotype code for the Prion Protein. Front Cell Neurosci. 2020;14. DOI:10.3389/fncel.2020.00254
   PubMed Web of Science ®Google Scholar
• Mead S, Khalili-Shirazi A, Potter C, et al. Prion protein monoclonal antibody (PRN100) therapy for Creutzfeldt–Jakob disease: evaluation of a first-in-human treatment programme. Lancet Neurol. 2022;21(4):342–354. DOI:10.1016/S1474-4422(22)00082-5
   PubMed Web of Science ®Google Scholar
• Gendoo DMA, Harrison PM, Legname G. The landscape of the prion protein’s structural response to mutation revealed by principal component analysis of multiple NMR ensembles. PLoS Comput Biol. 2012;8(8):e1002646.
   PubMed Web of Science ®Google Scholar
• Soto P, Claflin IA, Bursott AL, et al. Cellular prion protein gene polymorphisms linked to differential scrapie susceptibility correlate with distinct residue connectivity between secondary structure elements. J Biomol Struct Dyn. 2021;39(1):129–139. DOI:10.1080/07391102.2019.1708794
   PubMed Web of Science ®Google Scholar
• Brooks B, Karplus M. Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci. 1983;80(21):6571–6575.
   PubMed Web of Science ®Google Scholar
• Hinsen K, Petrescu A-J, Dellerue S, et al. Harmonicity in slow protein dynamics. Chem Phys. 2000;261(1):25–37. DOI:10.1016/S0301-0104(00)00222-6
   Web of Science ®Google Scholar
• Yao X-Q, Skjærven L, Grant BJ. Rapid characterization of allosteric networks with ensemble normal mode analysis. J Phys Chem B. 2016;120(33):8276–8288.
   PubMed Web of Science ®Google Scholar
• Zhang S, Gong W, Han Z, et al. Insight into shared properties and differential dynamics and specificity of secretory phospholipase A2 family members. J Phys Chem B. 2021;125(13):3353–3363. DOI:10.1021/acs.jpcb.1c01315
   PubMed Web of Science ®Google Scholar
• David CC, Jacobs DJ. Characterizing Protein motions from structure. J Mol Graph Model. 2011;31:41–56.
   PubMed Web of Science ®Google Scholar
• Amadei A, Ceruso MA, Di Nola A. On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins’ molecular dynamics simulations. Proteins. 1999;36(4):419–424.
   PubMed Web of Science ®Google Scholar
• Viles JH, Donne D, Kroon G, et al. Local structural plasticity of the Prion Protein. Analysis of NMR Relaxation Dynamics Biochemistry. 2001;40(9):2743–2753. DOI:10.1021/bi002898a
   Google Scholar
• Romanowska J, Nowiński KS, Trylska J. Determining geometrically stable domains in molecular conformation sets. J Chem Theory Comput. 2012;8(8):2588–2599.
   PubMed Web of Science ®Google Scholar
• Grant BJ, Skjærven L, Yao X-Q. The bio3D packages for structural bioinformatics. Protein Sci. 2021;30(1):20–30.
   PubMed Web of Science ®Google Scholar
• Oldham S, Fulcher B, Parkes L, et al. Consistency and differences between centrality measures across distinct classes of networks. PLoS ONE. 2019;14(7):e0220061. DOI:10.1371/journal.pone.0220061
   PubMed Web of Science ®Google Scholar
• Foutch D, Pham B, Shen T. Protein conformational switch discerned via network centrality properties. Comput Struct Biotechnol J. 2021;19:3599–3608.
   PubMed Web of Science ®Google Scholar
• Brysbaert G, Lensink MF. Centrality measures in residue interaction networks to highlight amino acids in protein–Protein binding. Front Bioinforma. 2021;1:0.
   Google Scholar
• Negre CFA, Morzan UN, Hendrickson HP, et al. Eigenvector centrality for characterization of protein allosteric pathways. Proc Natl Acad Sci. 2018;115(52):E12201–08. DOI:10.1073/pnas.1810452115
   PubMed Web of Science ®Google Scholar
• Dima RI, Thirumalai D. Exploring the propensities of helices in PrP(C) to form beta sheet using NMR structures and sequence alignments. Biophys J. 2002;83(3):1268–1280.
   PubMed Web of Science ®Google Scholar
• Sengupta I, Udgaonkar J. Monitoring site-specific conformational changes in real-time reveals a misfolding mechanism of the prion protein. Elife. 2019;8:e44698.
   PubMed Web of Science ®Google Scholar
• Schilling KM, Tao L, Wu B, et al. Both N-Terminal and C-Terminal histidine residues of the prion protein are essential for copper coordination and neuroprotective self-regulation. J Mol Biol. 2020;432(16):4408–4425. DOI:10.1016/j.jmb.2020.05.020
   PubMed Web of Science ®Google Scholar
• Arodź T, Płonka PM. Effects of point mutations on protein structure are nonexponentially distributed. Proteins Struct Funct Bioinforma. 2012;80(7):1780–1790.
   PubMed Web of Science ®Google Scholar
• Zhou S, Shi D, Liu X, et al. PH-Induced misfolding mechanism of prion protein: insights from microsecond-accelerated molecular dynamics simulations. ACS Chem Neurosci. 2019;10(6):2718–2729. DOI:10.1021/acschemneuro.8b00582
   PubMed Web of Science ®Google Scholar
• Christen B, Hornemann S, Damberger FF, et al. Prion protein NMR structure from tammar wallaby (Macropus eugenii) shows that the beta2-alpha2 loop is modulated by long-range sequence effects. J Mol Biol. 2009;389(5):833–845. DOI:10.1016/j.jmb.2009.04.040
   PubMed Web of Science ®Google Scholar
• Sigurdson CJ, Nilsson KPR, Hornemann S, et al. A molecular switch controls interspecies prion disease transmission in mice. J Clin Invest. 2010;120(7):2590–2599. DOI:10.1172/JCI42051
   PubMed Web of Science ®Google Scholar
• Rose PW, Prlić A, Altunkaya A, et al. The RCSB protein data bank: integrative view of protein, gene and 3D structural information. Nucleic Acids Res. 2017;45(D1):D271–81. DOI:10.1093/nar/gkw1000
   PubMed Web of Science ®Google Scholar
• Wynsberghe AWV, Cui Q. Interpreting correlated motions using normal mode analysis. Structure. 2006;14(11):1647–1653.
   PubMed Web of Science ®Google Scholar
• Sethi A, Eargle J, Black AA, et al. Dynamical networks in tRna: protein complexes. Proc Natl Acad Sci. 2009;106(16):6620–6625. DOI:10.1073/pnas.0810961106
   PubMed Web of Science ®Google Scholar
• Girvan M, Newman MEJ. Community structure in social and biological networks. Proc Natl Acad Sci U S A. 2002;99(12):7821–7826.
   PubMed Web of Science ®Google Scholar
• R Core Team. R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2020. Available from: https://www.R-project.org/
   Google Scholar
• Morris GM, Huey R, Lindstrom W, et al. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem. 2009;30(16):2785–2791. DOI:10.1002/jcc.21256
   PubMed Web of Science ®Google Scholar
• National Center for Biotechnology Information. PubChem compound summary for CID 37720, pentosan polysulfate. [cited 2022 Aug 3]. Available from: https://pubchem.ncbi.nlm.nih.gov/compound/37720
   Google Scholar
• Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph. 1996;14(1): 33–38, 27–28. DOI:10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• The PyMOL Molecular Graphics System, Version 2.0; Schrödinger, LLC. https://pymol.org/2/support.html
   Google Scholar