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      Prion protein with a mutant N-terminal octarepeat region undergoes cobalamin-dependent assembly into high–molecular weight complexes

      research-article
      1 , 1 , 2 , 1 , 1 , 1 , 3 , 1 , 4 , 3 , 1 ,
      The Journal of Biological Chemistry
      American Society for Biochemistry and Molecular Biology
      prion, oligomer, conformational change, glycoprotein, plasma membrane, cobalamin, vitamin B12, sporadic disease, Al, aluminum, Ca, calcium, Cbl, cobalamin, CJD, Creutzfeldt–Jakob disease, Co, cobalt, Cr, chromium, Cu, copper, CV, coefficient of variation, DEPC, diethylpyrocarbonate, DMEM, Dulbecco's modified Eagle's medium, Fe, iron, GPI, glycosylphosphatidylinositol, GSS, Gerstmann–Sträussler syndrome, HMW, high–molecular weight, LLPS, liquid–liquid phase separation, MD, molecular dynamics, Mg, magnesium, Mn, manganese, mPrP, mouse PrP, MS, mass spectrometry, Ni, nickel, OR, octarepeat, PDB, Protein Data Bank, PK, proteinase K, PNGase F, peptide-N-glycosidase F, PrPC, cellular prion protein, PrPSc, scrapie-associated prior protein, recPrP, recombinant PrP, RIPA, radioimmunoprecipitation assay, Tg, transgenic, Zn, zinc

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          Abstract

          The cellular prion protein (PrP C) has a C-terminal globular domain and a disordered N-terminal region encompassing five octarepeats (ORs). Encounters between Cu(II) ions and four OR sites produce interchangeable binding geometries; however, the significance of Cu(II) binding to ORs in different combinations is unclear. To understand the impact of specific binding geometries, OR variants were designed that interact with multiple or single Cu(II) ions in specific locked coordinations. Unexpectedly, we found that one mutant produced detergent-insoluble, protease-resistant species in cells in the absence of exposure to the infectious prion protein isoform, scrapie-associated prion protein (PrP Sc). Formation of these assemblies, visible as puncta, was reversible and dependent upon medium formulation. Cobalamin (Cbl), a dietary cofactor containing a corrin ring that coordinates a Co 3+ ion, was identified as a key medium component, and its effect was validated by reconstitution experiments. Although we failed to find evidence that Cbl interacts with Cu-binding OR regions, we instead noted interactions of Cbl with the PrP C C-terminal domain. We found that some interactions occurred at a binding site of planar tetrapyrrole compounds on the isolated globular domain, but others did not, and N-terminal sequences additionally had a marked effect on their presence and position. Our studies define a conditional effect of Cbl wherein a mutant OR region can act in cis to destabilize a globular domain with a wild type sequence. The unexpected intersection between the properties of PrP Sc's disordered region, Cbl, and conformational remodeling events may have implications for understanding sporadic prion disease that does not involve exposure to PrP Sc.

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          UCSF Chimera--a visualization system for exploratory research and analysis.

          The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/. Copyright 2004 Wiley Periodicals, Inc.
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            AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.

            AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed-up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user. Copyright 2009 Wiley Periodicals, Inc.
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              Considerations and Challenges in Studying Liquid-Liquid Phase Separation and Biomolecular Condensates

              Evidence is now mounting that liquid-liquid phase separation (LLPS) underlies the formation of membraneless compartments in cells. This realization has motivated major efforts to delineate the function of such biomolecular condensates in normal cells and their roles in contexts ranging from development to age-related disease. There is great interest in understanding the underlying biophysical principles and the specific properties of biological condensates with the goal of bringing insights into a wide range of biological processes and systems. The explosion of physiological and pathological contexts involving LLPS requires clear standards for their study. Here, we propose guidelines for rigorous experimental characterization of LLPS processes in vitro and in cells, discuss the caveats of common experimental approaches, and point out experimental and theoretical gaps in the field.
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                Author and article information

                Contributors
                Journal
                J Biol Chem
                J Biol Chem
                The Journal of Biological Chemistry
                American Society for Biochemistry and Molecular Biology
                0021-9258
                1083-351X
                07 March 2022
                April 2022
                07 March 2022
                : 298
                : 4
                : 101770
                Affiliations
                [1 ]Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada
                [2 ]Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
                [3 ]Faculty of Engineering - Electrical & Computer Engineering Department, University of Alberta, Edmonton, Canada
                [4 ]Department of Biochemistry, University of Alberta, Edmonton, Canada
                Author notes
                []For correspondence: David Westaway david.westaway@ 123456ualberta.ca
                Article
                S0021-9258(22)00210-1 101770
                10.1016/j.jbc.2022.101770
                9010764
                35271850
                c57f322e-ea9d-4696-bd34-0f99c58b4586
                © 2022 The Authors

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 22 December 2021
                : 16 February 2022
                Categories
                Research Article

                Biochemistry
                prion,oligomer,conformational change,glycoprotein,plasma membrane,cobalamin,vitamin b12,sporadic disease,al, aluminum,ca, calcium,cbl, cobalamin,cjd, creutzfeldt–jakob disease,co, cobalt,cr, chromium,cu, copper,cv, coefficient of variation,depc, diethylpyrocarbonate,dmem, dulbecco's modified eagle's medium,fe, iron,gpi, glycosylphosphatidylinositol,gss, gerstmann–sträussler syndrome,hmw, high–molecular weight,llps, liquid–liquid phase separation,md, molecular dynamics,mg, magnesium,mn, manganese,mprp, mouse prp,ms, mass spectrometry,ni, nickel,or, octarepeat,pdb, protein data bank,pk, proteinase k,pngase f, peptide-n-glycosidase f,prpc, cellular prion protein,prpsc, scrapie-associated prior protein,recprp, recombinant prp,ripa, radioimmunoprecipitation assay,tg, transgenic,zn, zinc

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