A molecular dynamics approach to the structural characterization of amyloid aggregation.

A novel computational approach to the structural analysis of ordered beta-aggregation is presented and validated on three known amyloidogenic polypeptides. The strategy is based on the decomposition of the sequence into overlapping stretches and equilibrium implicit solvent molecular dynamics (MD) simulations of an oligomeric system for each stretch. The structural stability of the in-register parallel aggregates sampled in the implicit solvent runs is further evaluated using explicit water simulations for a subset of the stretches. The beta-aggregation propensity along the sequence of the Alzheimer's amyloid-beta peptide (Abeta(42)) is found to be highly heterogeneous with a maximum in the segment V(12)HHQKLVFFAE(22) and minima at S(8)G(9), G(25)S(26), G(29)A(30), and G(38)V(39), which are turn-like segments. The simulation results suggest that these sites may play a crucial role in determining the aggregation tendency and the fibrillar structure of Abeta(42). Similar findings are obtained for the human amylin, a 37-residue peptide that displays a maximal beta-aggregation propensity at Q(10)RLANFLVHSSNN(22) and two turn-like sites at G(24)A(25) and G(33)S(34). In the third application, the MD approach is used to identify beta-aggregation "hot-spots" within the N-terminal domain of the yeast prion Ure2p (Ure2p(1-94)) and to design a double-point mutant (Ure2p-N4748S(1-94)) with lower beta-aggregation propensity. The change in the aggregation propensity of Ure2p-N4748S(1-94) is verified in vitro using the thioflavin T binding assay.

[1]  S. Radford,et al.  Partially unfolded states of beta(2)-microglobulin and amyloid formation in vitro. , 2000, Biochemistry.

[2]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[3]  A. Komar,et al.  Structural Characterization of Saccharomyces cerevisiae Prion-like Protein Ure2* , 1999, The Journal of Biological Chemistry.

[4]  F. Rao,et al.  Replica exchange molecular dynamics simulations of amyloid peptide aggregation. , 2004, The Journal of chemical physics.

[5]  M. Karplus,et al.  Simulation of activation free energies in molecular systems , 1996 .

[6]  L. Serrano,et al.  Sequence dependence of amyloid fibril formation: insights from molecular dynamics simulations. , 2005, Journal of molecular biology.

[7]  D. Thirumalai,et al.  Dissecting the assembly of Abeta16-22 amyloid peptides into antiparallel beta sheets. , 2003, Structure.

[8]  T. Benzinger,et al.  Propagating structure of Alzheimer's beta-amyloid(10-35) is parallel beta-sheet with residues in exact register. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[9]  W. H. Toliver,et al.  Liquid Crystals , 1912, Nature.

[10]  T. Benzinger,et al.  Two-Dimensional Structure of β-Amyloid(10−35) Fibrils† , 2000 .

[11]  A Caflisch,et al.  Native topology or specific interactions: what is more important for protein folding? , 2001, Journal of molecular biology.

[12]  R. Riek,et al.  NMR studies in aqueous solution fail to identify significant conformational differences between the monomeric forms of two Alzheimer peptides with widely different plaque-competence, A beta(1-40)(ox) and A beta(1-42)(ox). , 2001, European journal of biochemistry.

[13]  H. King,et al.  Global Burden of Diabetes, 1995–2025: Prevalence, numerical estimates, and projections , 1998, Diabetes Care.

[14]  F. Lacroute.  Non-Mendelian Mutation Allowing Ureidosuccinic Acid Uptake in Yeast , 1971, Journal of bacteriology.

[15]  Ying Xu,et al.  Mapping abeta amyloid fibril secondary structure using scanning proline mutagenesis. , 2004, Journal of molecular biology.

[16]  R. Leapman,et al.  A structural model for Alzheimer's β-amyloid fibrils based on experimental constraints from solid state NMR , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[17]  D. M. Morgan,et al.  Structure of the β-Amyloid(10-35) Fibril , 2000 .

[18]  Max F. Perutz,et al.  Glutamine repeats and neurodegenerative diseases: molecular aspects. , 1999, Trends in biochemical sciences.

[19]  Andreas Hoenger,et al.  De novo designed peptide-based amyloid fibrils , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[20]  D. Thirumalai,et al.  Dissecting the Assembly of Aβ16–22 Amyloid Peptides into Antiparallel β Sheets , 2003 .

[21]  Y. Lyubchenko,et al.  Residues 17–20 and 30–35 of beta‐amyloid play critical roles in aggregation , 2004, Journal of neuroscience research.

[22]  Y. Duan,et al.  The role of Phe in the formation of well-ordered oligomers of amyloidogenic hexapeptide (NFGAIL) observed in molecular dynamics simulations with explicit solvent. , 2005, Biophysical journal.

[23]  Christopher M. Dobson,et al.  Amyloid fibrils from muscle myoglobin , 2001, Nature.

[24]  Akhlesh Lakhtakia,et al.  The physics of liquid crystals, 2nd edition: P.G. De Gennes and J. Prost, Published in 1993 by Oxford University Press, Oxford, UK, pp 7,597 + xvi, ISBN: 0-19-852024 , 1995 .

[25]  R. Leapman,et al.  Multiple quantum solid-state NMR indicates a parallel, not antiparallel, organization of β-sheets in Alzheimer's β-amyloid fibrils , 2000 .

[26]  M. Hecht,et al.  De novo amyloid proteins from designed combinatorial libraries. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[27]  K. Higuchi,et al.  Amyloid fibril proteins , 2002, Mechanisms of Ageing and Development.

[28]  A Caflisch,et al.  Role of native topology investigated by multiple unfolding simulations of four SH3 domains. , 2001, Journal of molecular biology.

[29]  Roger D Kamm,et al.  Kinetic control of dimer structure formation in amyloid fibrillogenesis. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Robert A. Grothe,et al.  An amyloid-forming peptide from the yeast prion Sup35 reveals a dehydrated β-sheet structure for amyloid , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[31]  T. Yeates,et al.  Identification of a subunit interface in transthyretin amyloid fibrils: evidence for self-assembly from oligomeric building blocks. , 2001, Biochemistry.

[32]  C. Dobson,et al.  High-resolution molecular structure of a peptide in an amyloid fibril determined by magic angle spinning NMR spectroscopy. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[33]  R. Leapman,et al.  Multiple quantum solid-state NMR indicates a parallel, not antiparallel, organization of beta-sheets in Alzheimer's beta-amyloid fibrils. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[34]  C. Masters,et al.  Amyloid Fibril Protein Nomenclature - 2002 , 2002, Amyloid : the international journal of experimental and clinical investigation : the official journal of the International Society of Amyloidosis.

[35]  P. Axelsen,et al.  β Sheet Structure in Amyloid β Fibrils and Vibrational Dipolar Coupling , 2005 .

[36]  A. Kishimoto,et al.  beta-Helix is a likely core structure of yeast prion Sup35 amyloid fibers. , 2004, Biochemical and biophysical research communications.

[37]  Randomness in nanoscopic liquid-crystal droplets—How small is too small? , 2002 .

[38]  Sharon Gilead,et al.  Identification and characterization of a novel molecular-recognition and self-assembly domain within the islet amyloid polypeptide. , 2002, Journal of molecular biology.

[39]  Ronald Wetzel,et al.  Seeding Specificity in Amyloid Growth Induced by Heterologous Fibrils* , 2004, Journal of Biological Chemistry.

[40]  R. Wickner,et al.  [URE3] as an altered URE2 protein: evidence for a prion analog in Saccharomyces cerevisiae. , 1994, Science.

[41]  J. Straub,et al.  Charge states rather than propensity for β‐structure determine enhanced fibrillogenesis in wild‐type Alzheimer's β‐amyloid peptide compared to E22Q Dutch mutant , 2002 .

[42]  C. Dobson.  Protein folding and misfolding , 2003, Nature.

[43]  E. Wilander,et al.  The influence of amyloid deposits on the islet volume in maturity onset diabetes mellitus , 1978, Diabetologia.

[44]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[45]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[46]  M. Perutz,et al.  Aggregation of proteins with expanded glutamine and alanine repeats of the glutamine-rich and asparagine-rich domains of Sup35 and of the amyloid β-peptide of amyloid plaques , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[47]  L. Serpell,et al.  Structural characterisation of islet amyloid polypeptide fibrils. , 2004, Journal of molecular biology.

[48]  P. Pedersen,et al.  Defective protein folding as a basis of human disease. , 1995, Trends in biochemical sciences.

[49]  J. Bernhagen,et al.  Identification of a penta- and hexapeptide of islet amyloid polypeptide (IAPP) with amyloidogenic and cytotoxic properties. , 2000, Journal of molecular biology.

[50]  Jörg Gsponer,et al.  Molecular dynamics simulations of protein folding from the transition state , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[51]  Amedeo Caflisch,et al.  Free Energy Surface of the Helical Peptide Y(MEARA)6 , 2000 .

[52]  A. Cavalli,et al.  The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates , 2004, Protein science : a publication of the Protein Society.

[53]  Richard D. Leapman,et al.  Self-Propagating, Molecular-Level Polymorphism in Alzheimer's ß-Amyloid Fibrils , 2005, Science.

[54]  Robert A. Grothe,et al.  Structure of the cross-beta spine of amyloid-like fibrils. , 2005, Nature.

[55]  Ueli Aebi,et al.  The parallel superpleated beta-structure as a model for amyloid fibrils of human amylin. , 2005, Journal of molecular biology.

[56]  J. Banavar,et al.  Computer Simulation of Liquids , 1988 .

[57]  R. Wickner,et al.  Prion domain initiation of amyloid formation in vitro from native Ure2p. , 1999, Science.

[58]  P. Gennes,et al.  The physics of liquid crystals , 1974 .

[59]  B. Magasanik,et al.  Regulation of nitrogen assimilation in Saccharomyces cerevisiae: roles of the URE2 and GLN3 genes , 1988, Journal of bacteriology.

[60]  R. Wickner,et al.  The prion model for [URE3] of yeast: spontaneous generation and requirements for propagation. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[61]  R. Leapman,et al.  Supramolecular structural constraints on Alzheimer's beta-amyloid fibrils from electron microscopy and solid-state nuclear magnetic resonance. , 2002, Biochemistry.

[62]  S. Younkin,et al.  The 'Arctic' APP mutation (E693G) causes Alzheimer's disease by enhanced Aβ protofibril formation , 2001, Nature Neuroscience.

[63]  Gerhard Hummer,et al.  Molecular dynamics simulations of Alzheimer's β-amyloid protofilaments , 2005 .

[64]  Lars Terenius,et al.  A Molecular Model of Alzheimer Amyloid β-Peptide Fibril Formation* , 1999, The Journal of Biological Chemistry.

[65]  Sarah Tomlin,et al.  Microtechnology: Laying it on thick , 1999, Nature.

[66]  K. Murata,et al.  Amyloid‐like aggregates of a plant protein: a case of a sweet‐tasting protein, monellin , 1999, FEBS letters.

[67]  J. J. Balbach,et al.  Supramolecular Structure in Full-Length Alzheimer's β-Amyloid Fibrils: Evidence for a Parallel β-Sheet Organization from Solid-State Nuclear Magnetic Resonance , 2002 .

[68]  Michele Vendruscolo,et al.  Prediction of the absolute aggregation rates of amyloidogenic polypeptide chains. , 2004, Journal of molecular biology.

[69]  J. M. Griffiths,et al.  Rotational Resonance Solid-State NMR Elucidates a Structural Model of Pancreatic Amyloid , 1995 .

[70]  I D Campbell,et al.  Amyloid fibril formation by an SH3 domain. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[71]  L. Serrano,et al.  Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins , 2004, Nature Biotechnology.

[72]  Hoover,et al.  Canonical dynamics: Equilibrium phase-space distributions. , 1985, Physical review. A, General physics.

[73]  Ralf Langen,et al.  Structural and Dynamic Features of Alzheimer's Aβ Peptide in Amyloid Fibrils Studied by Site-directed Spin Labeling* , 2002, The Journal of Biological Chemistry.

[74]  Gerhard Hummer,et al.  Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments. , 2005, Journal of molecular biology.

[75]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[76]  Andrey V Kajava,et al.  A model for Ure2p prion filaments and other amyloids: the parallel superpleated beta-structure. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[77]  Ehud Gazit,et al.  A possible role for π‐stacking in the self‐assembly of amyloid fibrils , 2002, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[78]  A. Caflisch,et al.  Folding simulations of a three-stranded antiparallel beta -sheet peptide. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[79]  C. A. Andersen,et al.  Continuum secondary structure captures protein flexibility. , 2002, Structure.

[80]  T. Benzinger,et al.  Two-dimensional structure of beta-amyloid(10-35) fibrils. , 2000, Biochemistry.

[81]  T. Darden,et al.  An Atomic Model for the Pleated β-Sheet Structure of Aβ Amyloid Protofilaments , 1999 .

[82]  M. Citron.  Beta-secretase inhibition for the treatment of Alzheimer's disease--promise and challenge. , 2004, Trends in pharmacological sciences.

[83]  J. Apostolakis,et al.  Evaluation of a fast implicit solvent model for molecular dynamics simulations , 2002, Proteins.

[84]  P. Decottignies,et al.  Structural characterization of the fibrillar form of the yeast Saccharomyces cerevisiae prion Ure2p. , 2004, Biochemistry.

[85]  Y. Sugita,et al.  Replica-exchange molecular dynamics method for protein folding , 1999 .

[86]  Claudio Zannoni,et al.  Molecular design and computer simulations of novel mesophases , 2001 .

[87]  J. Kelly,et al.  Sequence-dependent denaturation energetics: A major determinant in amyloid disease diversity , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[88]  Laxmikant V. Kale,et al.  NAMD2: Greater Scalability for Parallel Molecular Dynamics , 1999 .

[89]  J. Brewer,et al.  Solution NMR Studies of the Aβ(1−40) and Aβ(1−42) Peptides Establish that the Met35 Oxidation State Affects the Mechanism of Amyloid Formation , 2004 .

[90]  L. Tjernberg,et al.  Arrest of -Amyloid Fibril Formation by a Pentapeptide Ligand (*) , 1996, The Journal of Biological Chemistry.

[91]  A. Cavalli,et al.  Fast protein folding on downhill energy landscape , 2003, Protein science : a publication of the Protein Society.

[92]  D. Selkoe,et al.  Translating cell biology into therapeutic advances in Alzheimer's disease , 1999, Nature.

[93]  A. Horwich.  Protein aggregation in disease: a role for folding intermediates forming specific multimeric interactions. , 2002, The Journal of clinical investigation.

[94]  Louise C. Serpell,et al.  Synchrotron X-ray studies suggest that the core of the transthyretin amyloid fibril is a continuous β-sheet helix , 1996 .

[95]  C. Dobson.  The structural basis of protein folding and its links with human disease. , 2001, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[96]  Christine Wurth,et al.  Mutations that reduce aggregation of the Alzheimer's Abeta42 peptide: an unbiased search for the sequence determinants of Abeta amyloidogenesis. , 2002, Journal of molecular biology.

[97]  L. Lannfelt,et al.  Unique physicochemical profile of beta-amyloid peptide variant Abeta1-40E22G protofibrils: conceivable neuropathogen in arctic mutant carriers. , 2004, Journal of molecular biology.

[98]  Ralf Langen,et al.  Identifying Structural Features of Fibrillar Islet Amyloid Polypeptide Using Site-directed Spin Labeling* , 2004, Journal of Biological Chemistry.

[99]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[100]  D. Kirschner,et al.  Structural analysis of Alzheimer's beta(1-40) amyloid: protofilament assembly of tubular fibrils. , 1998, Biophysical journal.

[101]  L. Serpell,et al.  Synchrotron X-ray studies suggest that the core of the transthyretin amyloid fibril is a continuous beta-sheet helix. , 1996, Structure.

[102]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[103]  Elena Orlova,et al.  Cryo‐electron microscopy structure of an SH3 amyloid fibril and model of the molecular packing , 1999, The EMBO journal.

[104]  A. Caflisch,et al.  The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35 , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[105]  C. Dobson.  Protein misfolding, evolution and disease. , 1999, Trends in biochemical sciences.

[106]  C. Dobson,et al.  Rationalization of the effects of mutations on peptide andprotein aggregation rates , 2003, Nature.

[107]  Amedeo Caflisch,et al.  Prediction of aggregation rate and aggregation‐prone segments in polypeptide sequences , 2005, Protein science : a publication of the Protein Society.

[108]  C. Blake,et al.  The structure of amyloid fibrils by electron microscopy and X-ray diffraction. , 1997, Advances in protein chemistry.