Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder.

Recent evidence suggests that amyloidogenic oligomers may be the toxic species in cell cultures. Thus, it is crucial to understand their structure and oligomerization mechanism in atomistic detail. By employing tens of fast central processing units and an advanced phase-space sampling algorithm, parallel-tempering molecular dynamics, we have explored the energy landscape of amyloidogenic peptide oligomerization in explicit water. A pentapeptide, DFNKF, derived from human calcitonin and its mutant, DFAKF, was simulated with a total simulation time of approximately 500 ns. The detailed oligomerization process of a DFNKF parallel beta-sheet formation at 300 K has been characterized. The assembly of a parallel beta-sheet from the amorphous state mainly occurs via a "bottleneck" channel where the interstrand Asn-Asn stacking is the major interaction. The interactions of Asn-Asn stacking include both backbone and side-chain hydrogen bonds. The Asn-Asn interactions work like "glue" by sticking the DFNKF strands together and assist the "on-pathway" oligomerization. The Asn-Asn stacking observed here is similar to the Asn ladder commonly found in globular beta-helix proteins. A control run shows that when Asn is mutated to Ala, the stability and population of the DFAKF parallel beta-sheet is decreased. Furthermore, our in vitro mutagenesis experiments show that the ability of DFAKF peptides to form amyloid fibrils is significantly reduced, in agreement with the simulations. Knowledge of the energy landscape of oligomerization may provide hints for rational drug design, preventing amyloid-associated diseases.

[1]  S Gnanakaran,et al.  Peptide folding simulations. , 2003, Current opinion in structural biology.

[2]  F. Rao,et al.  Replica exchange molecular dynamics simulations of reversible folding , 2003 .

[3]  Meital Reches,et al.  Amyloid Fibril Formation by Pentapeptide and Tetrapeptide Fragments of Human Calcitonin* , 2002, The Journal of Biological Chemistry.

[4]  D. Thirumalai,et al.  Dissecting the assembly of A β 16-22 amyloid peptides into antiparallel β-sheets , 2002 .

[5]  J. Straub,et al.  Aqueous urea solution destabilizes Aβ16–22 oligomers , 2004 .

[6]  R. Nussinov,et al.  Stabilities and conformations of Alzheimer's β-amyloid peptide oligomers (Aβ16–22, Aβ16–35, and Aβ10–35): Sequence effects , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Michael R. Shirts,et al.  Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. , 2003, Biopolymers.

[8]  C. Maury,et al.  Creation of amyloid fibrils from mutant Asn187 gelsolin peptides. , 1992, Biochemical and biophysical research communications.

[9]  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.

[10]  Meital Reches,et al.  Amyloidogenic hexapeptide fragment of medin: homology to functional islet amyloid polypeptide fragments , 2004, Amyloid : the international journal of experimental and clinical investigation : the official journal of the International Society of Amyloidosis.

[11]  Anthony K. Felts,et al.  Free Energy Surfaces of -Hairpin and -Helical Peptides Generated by Replica Exchange Molecular Dynamics with the AGBNP Implicit Solvent Model , 2004 .

[12]  Tohru Terada,et al.  A method for evaluating multicanonical potential function without iterative refinement: Application to conformational sampling of a globular protein in water , 2003 .

[13]  Meital Reches,et al.  Casting Metal Nanowires Within Discrete Self-Assembled Peptide Nanotubes , 2003, Science.

[14]  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.

[15]  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.

[16]  P. Argos,et al.  Knowledge‐based protein secondary structure assignment , 1995, Proteins.

[17]  S. Santini,et al.  Pathway Complexity of Alzheimer's β-Amyloid Aβ16-22 Peptide Assembly , 2004 .

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

[19]  P. Loll,et al.  An expanded glutamine repeat destabilizes native ataxin-3 structure and mediates formation of parallel β-fibrils , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[20]  J. Weissman,et al.  A census of glutamine/asparagine-rich regions: implications for their conserved function and the prediction of novel prions. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[21]  R. Tycko.  Progress towards a molecular-level structural understanding of amyloid fibrils. , 2004, Current opinion in structural biology.

[22]  R. Kamm,et al.  Supramolecular structure of helical ribbons self-assembled from a β-sheet peptide , 2003 .

[23]  J. Hardy,et al.  The Amyloid Hypothesis of Alzheimer ’ s Disease : Progress and Problems on the Road to Therapeutics , 2009 .

[24]  Fred E. Cohen,et al.  Evidence for assembly of prions with left-handed β-helices into trimers , 2004 .

[25]  J T Finch,et al.  Amyloid fibers are water-filled nanotubes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[26]  B. Berne,et al.  Novel methods of sampling phase space in the simulation of biological systems. , 1997, Current opinion in structural biology.

[27]  R. Nussinov,et al.  The stability and dynamics of the human calcitonin amyloid peptide DFNKF. , 2004, Biophysical journal.

[28]  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.

[29]  J. Onuchic,et al.  Folding a protein in a computer: An atomic description of the folding/unfolding of protein A , 2003, Proceedings of the National Academy of Sciences of the United States of America.

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

[31]  R. Zhou.  Trp-cage: Folding free energy landscape in explicit water , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[32]  H. Scheraga,et al.  Monte Carlo-minimization approach to the multiple-minima problem in protein folding. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[33]  A. Drake,et al.  The structure and mechanism of formation of human calcitonin fibrils. , 1993, The Journal of biological chemistry.

[34]  L. Serpell,et al.  Alzheimer's amyloid fibrils: structure and assembly. , 2000, Biochimica et biophysica acta.

[35]  Pawel Sikorski,et al.  Molecular basis for amyloid fibril formation and stability. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[36]  Ruth Nussinov,et al.  A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: a single beta-sheet model with a small hydrophobic core. , 2005, Journal of molecular biology.

[37]  William Swope,et al.  Understanding folding and design: Replica-exchange simulations of ``Trp-cage'' miniproteins , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[38]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[39]  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.

[40]  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.

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

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

[43]  Jun-tao Guo,et al.  Molecular modeling of the core of Aβ amyloid fibrils , 2004 .

[44]  R. Pickersgill,et al.  The architecture of parallel β-helices and related folds , 2001 .

[45]  R. Wetzel.  Ideas of order for amyloid fibril structure. , 2002, Structure.

[46]  B. Berne,et al.  The free energy landscape for β hairpin folding in explicit water , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[47]  Yuji Sugita,et al.  Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape , 2000, cond-mat/0009119.

[48]  Eric D. Ross,et al.  Scrambled Prion Domains Form Prions and Amyloid , 2004, Molecular and Cellular Biology.

[49]  Michael R. Shirts,et al.  Mathematical analysis of coupled parallel simulations. , 2001, Physical review letters.

[50]  A. Naito,et al.  Structural diversity of amyloid fibril formed in human calcitonin as revealed by site‐directed 13C solid‐state NMR spectroscopy , 2004, Magnetic resonance in chemistry : MRC.