Molecular dynamics study of amyloid formation of two Abl-SH3 domain peptides

Journal of Peptide Science

Volumn 12, Issue 12, 2006, Pages 780-789

  Liepina, Inta ^a   Ventura, Salvador ^b   Czaplewski, Cezary ^c   Liwo, Adam ^c  

^a LATVIAN INSTITUTE OF ORGANIC SYNTHESIS   (Latvia)

^b UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^c UNIVERSITY OF GDA SK   (Poland)

Author keywords

sheet; Amyloid; Amyloid formation; Amyloid peptides; Molecular dynamics

Indexed keywords

ABELSON KINASE; AMYLOID; PROTEIN SH3;

AMYLOIDOSIS; ARTICLE; BETA SHEET; HUMAN; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RESIDUE ANALYSIS; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; AMYLOID; COMPUTER SIMULATION; HYDROGEN BONDING; MODELS, MOLECULAR; PEPTIDE FRAGMENTS; PROTEIN STRUCTURE, SECONDARY; SRC HOMOLOGY DOMAINS; TEMPERATURE; THERMODYNAMICS; WATER;

EID: 33845655561     PISSN: 10752617     EISSN: 10991387     Source Type: Journal    
DOI: 10.1002/psc.813     Document Type: Article

References (20)

1. Ventura S, Zurdo J, Naravanan S, Parreno M, Mangues R, Reif B, Chiti F, Giannoni E, Dobson CM, Axiles FX, Serrano L. Short amino acid stretches can mediate amyloid formation in globular proteins: the Src homology 3 (SH3) case. Proc. Natl. Acad. Sci. U.S.A. 2004; 101: 7258-7263.
2. Ventura S, Lacroix E, Serrano L. Insights into the origin of the tendency of the PI3-SH3 domain to form amyloid fibrils. J. Mol. Biol. 2002; 332: 1147-1158.
3. Dobson CM. Protein folding and misfolding. Nature 2003; 426: 884-890.
4. Dobson CM. Protein-misfolding disease: getting out of shape. Nature 2002; 418: 729-730.
5. Smith A. Protein misfolding. Nature 2003; 426: 883.
6. Cohen FE, Kelly JW. Therapeutic approaches to protein-misfolding diseases. Nature 2003; 426: 905-909.
7. Groot NS, Pallares I, Aviles FX, Vendrell J, Ventura S. Prediction of "hot spots" of aggregation in disease-linked polypeptides. BMC Struct. Biol. 2005; 5: 18.
8. Dobson CM. Protein misfolding, evolution and disease. Trends Biochem. Sci. 1999; 24: 329-332.
9. Linding R, Schymkowitz J, Rousseau F, Diella F, Serrano L. A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteins. J. Mol. Biol. 2004; 342: 345-353.
10. Pawar AP, Dubay KF, Zurdo J, Chiti F, Vendruscolo M, Dobson CM. Prediction of "aggregation-prone" and "aggregation-susceptible" regions in proteins associated with neurodegenerative diseases. J. Mol. Biol. 2005; 350: 379-392.
11. Fernandez-Escamilla AM, Rousseau F, Schymkowitz J, Serrano L. Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat. Biolechnol. 2004; 22: 1302-1306.
12. Zanuy D, Gunasekaran K, Lesk AM, Nussiov R. Computational study of the fibril organization of polyglutamine repeats reveals a common motif identified in β-helices. J. Mol. Biol. 2006; 358: 330-345.
13. Haspel N, Zanuy D, Ma B, Wolfson H, Nussiov R. A Comparative Study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: a single β-sheet model with a small hydrophobic core. J. Mol. Biol. 2005; 345: 1213-1227.
14. de la Paz ML, Giacomo MS, Serrano L, Colombo G. Sequence dependence of amyloid fibril formation: Insights from molecular dynamics simulations. J. Mol. Biol. 2005; 349: 583-596.
15. Zanuy D, Porat Y, Gazit E, Nussiov R. Peptide Sequence and Amyloid Formation: Molecular simulations and experimental study of a human islet amyloid polypeptide fragment and its analogues. Structure 2004; 12: 439-455.
16. Zanuy D, Nusslov R. The sequence dependence of fiber organization. A comparative molecular dynamics study of the islet amyloid polypeptide segments 22-27 and 22-29. J. Mol. Biol. 2003; 329: 565-584.
17. Klimov D, Thirumalai D. Dissecting the assembly of A β 16-22 amyloid peptides into antiparallel β-sheets. Structure 2003; 11: 295-307.
18. Ma B, Nussinov R. Stabilities and conformations of Alzheimer's β-amyloid peptide oligomers (A β 16-22, A β 16-35, and A 3 10-35): sequence effects. Proc. Natl. Acad. Sci. U.S.A. 2002; 99: 14126-14131.
19. Ma B, Nussinov R. Molecular dynamics simulation of alanine rich β-sheet oligomers: insight into amyloid formation. Protein Sci. 2002; 11: 2335-2350.
20. Liepina I, Janmey P, Czaplewski C, Liwo A. Towards gelsolin amyloid formation. Biopolym. Pept. Sci. 2004; 76: 543-548.