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A Theoretical Investigation of the Octapeptide Region in the Human Prion Protein

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A Theoretical Investigation of the Octapeptide Region in the Human Prion Protein A Theoretical Investigation of the Octapeptide Region in the Human Prion Protein Eva-Stina Riihimäki Doctoral Thesis in Chemistry Stockholm, Sweden 2007 Department of Chemistry Royal Institute of Technology Stockholm, Sweden, 2007 ISBN 978-91-7178-719-4 ISSN 1654-1081 TRITA-CHE-Report 2007:40 Akademisk avhandling som med tillstånd av Kungliga Tekniska högskolan i Stockholm framlägges till offentlig granskning för avläggande av teknologie doktorsexamen i kemi fredagen den 15 juni 2007, klockan 10.00 i Sydvästra galleriet, KTH Biblioteket, Plan 3, Osquars backe 31, Stockholm. © Eva-Stina Riihimäki, Maj 2007 Universitetsservice US AB, Stockholm 2007 Abstract The copper-binding ability of the prion protein is thought to be closely related to its function. The human prion protein contains a copper-binding octapeptide region, where the octapeptide PHGGGWGQ is repeated four times consecutively. This work focuses on investigation of the structure and the dynamics of the octapeptide region by means of theoretical methods. Quantum chemical structural optimization allowed a detailed comparison of the interaction of several cations at the copper coordination site. These calculations identified rhodium(III) as a potent substitute for copper(II) that could be used to study the coordination site with NMR-spectroscopic methods. Solvation models that could be used in molecular dynamics simulations as an alternative to periodic boundary conditions were evaluated. Periodic boundary conditions are the best method for modeling the aqueous bulk in the kind of systems that are studied in this work. Molecular dynamics simulations were used to compare the behavior of the octapeptide region in the absence and presence of copper ions. Interaction between nonpolar rings strongly influences the structure of the region in the absence of copper ions. Four different non-bonded and bonded models for describing the interaction between copper and the protein were evaluated. Theoretical EXAFS spectra were calculated from the simulated structures. The results obtained for the bonded model are nearly identical with experimental data, which validates the use of the bonded model. This work thus shows strong evidence for copper(II) ions interacting with the octapeptide region through the histidine imidazole Nδ, the deprotonated nitrogen atoms of the following two glycine residues and the carbonyl oxygen atom of the second glycine residue. Notably, the simulations show that the axial sites of the copper ion do not stably coordinate water molecules in solution, as opposed to the crystal structure reported for the coordination site. Instead, the tryptophan indole ring interacted directly with the copper ion through stabilizing cation-π interaction without water mediation. The interaction of the indole ring with the copper ion was well-defined and was observed to occur on both sides of the coordination plane. The investigations of the interaction between copper ions and the octapeptide region with molecular dynamics simulations show how the presence of copper ions results in a more structured octapeptide region. iii Sammanfattning Den kopparbindande egenskapen hos prionproteiner är sannolikt kopplad till proteinets funtion. Det mänskliga prionproteinet innehåller ett kopparbindande oktapeptidområde, där PHGGGWGQ-sekvensen upprepas fyra gånger i följd. Syftet med detta arbete är att undersöka strukturen och dynamiken i oktapeptidområdet genom att använda teoretiska metoder. Med kvantkemisk strukturoptimering genomfördes en detaljerad jämförelse av växelverkan mellan flera katjoner och det kopparbindande området. Enligt dessa beräkningar är rodium(III) en möjlig ersättare för koppar(II) i NMR- specktroskopiska koordinationsstudier. Alternativa solvatiseringsmodeller i molekyldynamiksimuleringar har också jämförts. Periodiska randvillkor är mest lämpade för användning i de system som undersöks i detta arbete. Molekyldynamiksimuleringar användes för att jämföra oktapeptidområdets struktur och dynamik med och utan kopparjoner. Växelverkan mellan aminosyrornas ringar påverkar starkt strukturen i detta område i frånvaro av kopparjoner. Fyra olika icke-bindande och bindande modeller har studerats, vilka skiljer i sin beskrivning av växelverkan mellan koppar och proteinet. Teoretiska EXAFS spektra beräknades från dem simulerade strukturerna. Spektra som genererats för den bindande modellen är nästan identiska med experimentiella resultat, vilket stöder användandet av den bindande modellen. Detta arbete visar att kopparjoner interagerar med histidin imidazolringens Nδ, deprotonerade amidkväven hos de därpå följande glycinerna samt karbonylsyret hos den andra glycinen. Simuleringarna kunde visa att kopparjonen inte stabilt binder några axiella vattenmolekyler i lösning, till skillnad från en kristallstruktur av koordinationsstrukturen. Indolringen hos tryptofan interagerar direkt med kopparjonen genom stabiliserande katjon-π växelverkan utan direkt medverkan av någon vattenmolekyl. Växelverkan mellan indolringen och kopparjonen var väldefinierad och observerades kunna ske på båda sidor av koordinationsplanet. Molekyldynamiksimuleringarna med kopparjoner och oktapeptidområdet visade hur närvaron av kopparjoner ledde till ett mer strukturerat oktapeptidområde. iv This thesis is based on the following publications: Paper I E.-S. Riihimäki, J. M. Martínez, and L. Kloo, “An evaluation of non-periodic boundary condition models in molecular dynamics simulations using prion octapeptides as probes”, Journal of Molecular Structure: THEOCHEM 2006, 760, 91-98. Paper II E.-S. Riihimäki and L. Kloo, “Computational Comparison of Cation Coordination to Human Prion Peptide Models”, Inorganic Chemistry 2006, 45, 8509-8516. Paper III E.-S. Riihimäki, J. M. Martínez, and L. Kloo, “Molecular Dynamics Simulations of Cu(II) and the PHGGGWGQ- Octapeptide” Submitted for publication in Journal of Physical Chemistry B. Paper IV E.-S. Riihimäki, J. M. Martínez, and L. Kloo, “Structural Effects of Cu(II)-Coordination in the Octapeptide Region of the Human Prion Protein” Manuscript. Paper V E.-S. Riihimäki, L. Kloo, E. Sánchez Marcos, and J. M. Martínez, “Theoretical EXAFS Studies of the Cu(II)-Octapeptide Complex” Manuscript. v vi Abbreviations B3LYP A quantum chemical method BSE Bovine Spongiform Encephalopathy CJD Creutzfeldt-Jakob Disease DFT Density Functional Theory ECP Effective Core Potential ESR Electron Spin Resonance EXAFS Extended X-ray Absorption Fine Structure FFI Fatal Familial Insomnia FTIR Fourier-Transform Infrared spectroscopy GGGTH Peptide consisting of glycine, glycine, glycine, tryptophan and histidine GPI Glycosylphosphatidylinisotol HGGG Peptide consisting of histidine, glycine, glycine and glycine HGGGW Peptide consisting of proline, histidine, glycine, glycine, glycine and tryptophan MDF A pseudopotential MWB A pseudopotential NMR Nuclear Magnetic Resonance vCJD variant Creutzfeldt-Jakob Disease PBC Periodic Boundary Conditions PCM Polarizable Continuum Model PES Potential Energy Surface PGTO Primitive Gaussian-Type Orbital PHGGGWGQ Peptide consisting of proline, histidine, glycine, glycine, glycine, tryptophan, glycine and glutamine PrPC Prion protein, cellular form (healthy) PrPSc Prion protein, scrapies form (misfolded) RESP Restrained Electrostatic Potential SCRF Self-Consistent Reaction Field SOD Superoxide Dismutase SPC Simple Point Charge, a water model SPC/E Extended Simple Point Charge, a water model SPME Smooth Particle Mesh Ewald TIP3P Transferable Intermolecular Potential 3P, a water model UAHF United Atom Topological Model vii viii Table of Contents 1 Introduction.................................................................................................. 1 1.1 Different Prion Diseases ........................................................................................ 1 1.2 The Prion Protein.................................................................................................... 2 1.3 Possible Functions of the Prion Protein.............................................................. 4 1.4 The Role of Copper in Biochemistry ................................................................... 5 2 Computational Methods...............................................................................7 2.1 Molecular Dynamics Simulations.......................................................................... 7 2.1.1 Modeling Solvent Effects............................................................................... 8 2.1.2 Appropriate Choice of Simulation Conditions ........................................10 2.2 Quantum Chemistry Methods.............................................................................11 2.2.1 Choice of Basis Set and Level of Theory..................................................12 2.2.2 Polarizable Continuum Model ....................................................................13 2.3 RESP Calculations.................................................................................................13 2.4 EXAFS Calculations..............................................................................................15 2.5 Programs and Software Packages........................................................................16 3 The Octapeptide Region in the Absence of Cations ................................. 17 3.1 Comparison of Solvation Models .......................................................................17 3.2 Longer Peptides of the Octapeptide Region.....................................................23
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