Peptide sequence and amyloid formation; molecular simulations and experimental study of a human islet amyloid polypeptide fragment and its analogs.

We present a combined experimental and theoretical investigation of the tendencies to form amyloid fibrils by a hexapeptide derivative of the human islet amyloid polypeptide, the NFGAIL (22-27) fragment and its mutants. We performed a complete alanine scan of this fragment and studied the capability of the wild-type and its mutant analogs to form ordered fibrils by ultrastructural and biophysical analyses. In parallel, we conducted a meticulous characterization of each sequence-complex at an atomistic level by performing nine independent molecular dynamics simulations for a total of 36 ns. These allowed us to rationalize the experimental observations and to establish the role of every residue in the fibrillogenesis. The main factor that determines the formation of regular fibrils is a coherent organization of the intersheet space. In particular, phenylalanine side chains cement the macromolecular assemblies due to their aromatic chemical character and restricted conformational flexibility when interacting with aliphatic residues.

[1]  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.

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

[3]  H. Mulder,et al.  Islet amyloid polypeptide in the islets of Langerhans: friend or foe? , 2000, Diabetologia.

[4]  R. Nussinov,et al.  Molecular dynamics simulations of alanine rich β‐sheet oligomers: Insight into amyloid formation , 2002, Protein science : a publication of the Protein Society.

[5]  C. Blake,et al.  From the globular to the fibrous state: protein structure and structural conversion in amyloid formation , 1998, Quarterly Reviews of Biophysics.

[6]  R. Kisilevsky.  Review: amyloidogenesis-unquestioned answers and unanswered questions. , 2000, Journal of structural biology.

[7]  R. Nussinov,et al.  Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL. , 2003, Biophysical journal.

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

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

[10]  C. Brooks,et al.  Folding Free Energy Surface of a Three-Stranded β-Sheet Protein , 1999 .

[11]  J. Rothbard,et al.  Amylin found in amyloid deposits in human type 2 diabetes mellitus may be a hormone that regulates glycogen metabolism in skeletal muscle. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[12]  T. Benzinger,et al.  Propagating structure of Alzheimer’s β-amyloid(10–35) is parallel β-sheet with residues in exact register , 1998 .

[13]  P. Lansbury,et al.  Amyloid fibrillogenesis: themes and variations. , 2000, Current opinion in structural biology.

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

[15]  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.

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

[17]  Ehud Gazit,et al.  Analysis of the Minimal Amyloid-forming Fragment of the Islet Amyloid Polypeptide , 2001, The Journal of Biological Chemistry.

[18]  A. Miranker,et al.  Islet amyloid: phase partitioning and secondary nucleation are central to the mechanism of fibrillogenesis. , 2002, Biochemistry.

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

[20]  M. Kirkitadze,et al.  Identification and characterization of key kinetic intermediates in amyloid beta-protein fibrillogenesis. , 2001, Journal of molecular biology.

[21]  R. Leapman,et al.  Amyloid Fibril Formation by Aβ16-22, a Seven-Residue Fragment of the Alzheimer's β-Amyloid Peptide, and Structural Characterization by Solid State NMR† , 2000 .

[22]  W. Atkins,et al.  Self-assembly and gelation of oxidized glutathione in organic solvents. , 2001, Journal of the American Chemical Society.

[23]  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.

[24]  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.

[25]  C. Betsholtz,et al.  Islet amyloid polypeptide: pinpointing amino acid residues linked to amyloid fibril formation. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[26]  L. Serpell,et al.  Structure and texture of fibrous crystals formed by Alzheimer's abeta(11-25) peptide fragment. , 2003, Structure.

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

[28]  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.

[29]  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.

[30]  U. Aebi,et al.  Full-length rat amylin forms fibrils following substitution of single residues from human amylin. , 2003, Journal of molecular biology.

[31]  P. Selvin.  Lighting up single ion channels. , 2003, Biophysical journal.

[32]  R. Nussinov,et al.  The sequence dependence of fiber organization. A comparative molecular dynamics study of the islet amyloid polypeptide segments 22-27 and 22-29. , 2003, Journal of molecular biology.

[33]  Christopher M Dobson,et al.  The behaviour of polyamino acids reveals an inverse side chain effect in amyloid structure formation , 2002, The EMBO journal.

[34]  P. Fraser,et al.  Design of peptide-based inhibitors of human islet amyloid polypeptide fibrillogenesis. , 2002, Journal of molecular biology.

[35]  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.

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