The α‐sheet: A missing‐in‐action secondary structure?

The α‐sheet has been speculated to play a role as a toxic conformer in amyloid diseases. However, except for relatively short fragments, its detection has remained elusive. Here, we present molecular dynamics simulations that support the existence of the α‐sheet as a stable, metastable, or long‐lived secondary structure in polyglutamine and, to a lesser extent, in polyasparagine aggregates. Proteins 2011. © 2010 Wiley‐Liss, Inc.

[1]  A. Esteras-Chopo,et al.  Amyloid toxicity is independent of polypeptide sequence, length and chirality. , 2008, Journal of molecular biology.

[2]  V. Daggett,et al.  Molecular mechanism for low pH triggered misfolding of the human prion protein. , 2007, Biochemistry.

[3]  T. Südhof,et al.  Bipartite Ca2+-Binding Motif in C2 Domains of Synaptotagmin and Protein Kinase C , 1996, Science.

[4]  Christopher A. Ross,et al.  Huntingtin Spheroids and Protofibrils as Precursors in Polyglutamine Fibrilization* , 2002, The Journal of Biological Chemistry.

[5]  Mehmet Sarikaya,et al.  Hsp70 and Hsp40 attenuate formation of spherical and annular polyglutamine oligomers by partitioning monomer , 2004, Nature Structural &Molecular Biology.

[6]  Ronald Wetzel,et al.  Huntington's disease age-of-onset linked to polyglutamine aggregation nucleation , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[7]  B. Chait,et al.  The structure of the potassium channel: molecular basis of K+ conduction and selectivity. , 1998, Science.

[8]  V. Daggett,et al.  Characterization of a possible amyloidogenic precursor in glutamine-repeat neurodegenerative diseases. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Hans Lehrach,et al.  Huntingtin-Encoded Polyglutamine Expansions Form Amyloid-like Protein Aggregates In Vitro and In Vivo , 1997, Cell.

[10]  Christopher M. Dobson,et al.  Experimental characterization of disordered and ordered aggregates populated during the process of amyloid fibril formation , 2009, Proceedings of the National Academy of Sciences.

[11]  V. Daggett α-Sheet: The Toxic Conformer in Amyloid Diseases? , 2006 .

[12]  S. Hayward,et al.  The geometry of α‐sheet: Implications for its possible function as amyloid precursor in proteins , 2008, Proteins.

[13]  R. Dror,et al.  Improved side-chain torsion potentials for the Amber ff99SB protein force field , 2010, Proteins.

[14]  Dmitri I Svergun,et al.  A Helical Structural Nucleus Is the Primary Elongating Unit of Insulin Amyloid Fibrils , 2007, PLoS biology.

[15]  Lauren Wickstrom,et al.  Evaluating the performance of the ff99SB force field based on NMR scalar coupling data. , 2009, Biophysical journal.

[16]  Bong-Gyoon Han,et al.  Structural basis of water-specific transport through the AQP1 water channel , 2001, Nature.

[17]  A. Young,et al.  Pharmacological promotion of inclusion formation: a therapeutic approach for Huntington's and Parkinson's diseases. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[18]  S. Hayward,et al.  Amyloid Formation May Involve α- to β Sheet Interconversion via Peptide Plane Flipping , 2006 .

[19]  G P Bates,et al.  Self-assembly of polyglutamine-containing huntingtin fragments into amyloid-like fibrils: implications for Huntington's disease pathology. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[20]  P. Lansbury,et al.  Alpha-synuclein, especially the Parkinson's disease-associated mutants, forms pore-like annular and tubular protofibrils. , 2002, Journal of molecular biology.

[21]  A. Lombardi,et al.  The crystal structure of a Dcp-containing peptide. , 2000, Biopolymers.

[22]  R. Brüschweiler,et al.  Toward quantitative interpretation of methyl side-chain dynamics from NMR by molecular dynamics simulations. , 2007, Journal of the American Chemical Society.

[23]  P. Lansbury,et al.  Annular alpha-synuclein protofibrils are produced when spherical protofibrils are incubated in solution or bound to brain-derived membranes. , 2002, Biochemistry.

[24]  P. Steinhardt,et al.  Bond-orientational order in liquids and glasses , 1983 .

[25]  T. Prangé,et al.  Structural effects of monovalent anions on polymorphic lysozyme crystals. , 1998, Acta crystallographica. Section D, Biological crystallography.

[26]  G. Hummer,et al.  Are current molecular dynamics force fields too helical? , 2008, Biophysical journal.

[27]  Pawel Sikorski,et al.  The common architecture of cross-beta amyloid. , 2010, Journal of molecular biology.

[28]  E. Žerovnik,et al.  Similar toxicity of the oligomeric molten globule state and the prefibrillar oligomers , 2008, FEBS letters.

[29]  Valerie Daggett,et al.  Anatomy of an Amyloidogenic Intermediate: Conversion of β-Sheet to α-Sheet Structure in Transthyretin at Acidic pH , 2004 .

[30]  R. Wetzel,et al.  Mutational analysis of the structural organization of polyglutamine aggregates , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[31]  V. Hornak,et al.  Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.

[32]  Richard Leapman,et al.  Peptide conformation and supramolecular organization in amylin fibrils: constraints from solid-state NMR. , 2007, Biochemistry.

[33]  R. Kayed,et al.  Common structure and toxic function of amyloid oligomers implies a common mechanism of pathogenesis , 2006, Neurology.

[34]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[35]  R. Riek,et al.  3D structure of Alzheimer's amyloid-β(1–42) fibrils , 2005 .

[36]  M. Biancalana,et al.  Minimalist design of water-soluble cross-β architecture , 2010, Proceedings of the National Academy of Sciences.

[37]  Paul J Muchowski,et al.  Polyglutamine dances the conformational cha-cha-cha. , 2009, Structure.

[38]  Dalaver H. Anjum,et al.  Polyglutamine disruption of the huntingtin exon1 N-terminus triggers a complex aggregation mechanism , 2009, Nature Structural &Molecular Biology.

[39]  R. Dror,et al.  Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins. , 2008, The journal of physical chemistry. B.

[40]  Zbyszek Otwinowski,et al.  Secondary structure of Huntingtin amino-terminal region. , 2009, Structure.

[41]  R. MacKinnon,et al.  Chemistry of ion coordination and hydration revealed by a K+ channel–Fab complex at 2.0 Å resolution , 2001, Nature.

[42]  J T Finch,et al.  Glutamine repeats as polar zippers: their possible role in inherited neurodegenerative diseases. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[43]  L. Pauling,et al.  The pleated sheet, a new layer configuration of polypeptide chains. , 1951, Proceedings of the National Academy of Sciences of the United States of America.

[44]  Ronald Wetzel,et al.  Amyloid-like features of polyglutamine aggregates and their assembly kinetics. , 2002, Biochemistry.

[45]  Carl W. Cotman,et al.  Common Structure of Soluble Amyloid Oligomers Implies Common Mechanism of Pathogenesis , 2003, Science.

[46]  S. Sprang,et al.  Structure of the first C2 domain of synaptotagmin I: A novel Ca2+/phospholipid-binding fold , 1995, Cell.

[47]  A. Lombardi,et al.  A crystal structure with features of an antiparallel α‐pleated sheet , 1994, Biopolymers.

[48]  A. Lombardi,et al.  Conformational behaviour of Cα,α‐diphenylglycine: folded vs. extended structures in DϕG‐containing tripeptides , 1998 .

[49]  Mark Turmaine,et al.  Formation of Neuronal Intranuclear Inclusions Underlies the Neurological Dysfunction in Mice Transgenic for the HD Mutation , 1997, Cell.

[50]  Harald Schwalbe,et al.  Starting structure dependence of NMR order parameters derived from MD simulations: implications for judging force-field quality. , 2008, Biophysical journal.

[51]  R. Wetzel,et al.  Polyglutamine aggregation behavior in vitro supports a recruitment mechanism of cytotoxicity. , 2001, Journal of molecular biology.

[52]  Y. Urade,et al.  A toxic monomeric conformer of the polyglutamine protein , 2007, Nature Structural &Molecular Biology.

[53]  H. Zoghbi,et al.  Glutamine repeats and neurodegeneration. , 2000, Annual review of neuroscience.

[54]  F. Vovelle,et al.  Sheet structures in alternating poly(D,L-peptides) , 1981 .

[55]  H. G. Nagendra,et al.  Role of water in plasticity, stability, and action of proteins: The crystal structures of lysozyme at very low levels of hydration , 1998, Proteins.

[56]  Christine Van Broeckhoven,et al.  Pathogenesis of polyglutamine disorders: aggregation revisited. , 2003, Human molecular genetics.

[57]  Pawel Sikorski,et al.  New model for crystalline polyglutamine assemblies and their connection with amyloid fibrils. , 2005, Biomacromolecules.