The DOI matches its Crossref record; 31 of the 32 references it cites were found in a registry or an index.
Rationally designed mutations convert de novo amyloid-like fibrils into monomeric β-sheet proteins
Open accessAbstract
Amyloid fibrils are associated with a variety of neurodegenerative maladies including Alzheimer's disease and the prion diseases. The structures of amyloid fibrils are composed of β-strands oriented orthogonal to the fibril axis (“cross β” structure). We previously reported the design and characterization of a combinatorial library of de novo β-sheet proteins that self-assemble into fibrillar structures resembling amyloid. The libraries were designed by using a “binary code” strategy, in which the locations of polar and nonpolar residues are specified explicitly, but the identities of these residues are not specified and are varied combinatorially. The initial libraries were designed to encode proteins containing amphiphilic β-strands separated by reverse turns. Each β-strand was designed to be seven residues long, with polar (○) and nonpolar (●) amino acids arranged with an alternating periodicity (○●○●○●○). The initial design specified the identical polar/nonpolar pattern for all of the β-strands; no strand was explicitly designated to form the edges of the resulting β-sheets. With all β-strands preferring to occupy interior (as opposed to edge) locations, intermolecular oligomerization was favored, and the proteins assembled into amyloid-like fibrils. To assess whether explicit design of edge-favoring strands might tip the balance in favor of monomeric β-sheet proteins, we have now redesigned the first and/or last β-strands of several sequences from the original library. In the redesigned β-strands, the binary pattern is changed from ○●○●○●○ to ○●○K○●○ (K denotes lysine). The presence of a lysine on the nonpolar face of a β-strand should disfavor fibrillar structures because such structures would bury an uncompensated charge. The nonpolar → lysine mutations, therefore, would be expected to favor monomeric structures in which the ○●○K○●○ sequences form edge strands with the charged lysine side chain accessible to solvent. To test this hypothesis, we constructed several second generation sequences in which the central nonpolar residue of either the N-terminal β-strand or the C-terminal β-strand (or both) is changed to lysine. Characterization of the redesigned proteins shows that they form monomeric β-sheet proteins.
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“Related to these findings, inward-pointing charged side chains in edge strands are known to be a common negative design principle that prevents aggregation of soluble β-sandwich proteins (68) and has been employed to convert de novo amyloid fibrils into monomeric β-sheet proteins (69).”
From MAP2 caps tau fibrils and inhibits aggregation (2023) · cites this paper as [69]
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Cites
Proteins: Structures and Molecular Properties
Creighton, T. E. (1986) · Medical Entomology and Zoology · Cited by 2,645
Proteins. Structures and molecular properties
(1984) · Analytical Biochemistry · doi:10.1016/0003-2697(84)90583-9 · Cited by 1,308
Spontaneous assembly of a self-complementary oligopeptide to form a stable macroscopic membrane.
Zhang, S., Holmes, T. C., Lockshin, C., & Rich, A. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.8.3334 · Cited by 1,304
De Novo Protein Design: Fully Automated Sequence Selection
Dahiyat, B. I., & Mayo, S. L. (1997) · Science · doi:10.1126/science.278.5335.82 · Cited by 1,156
The Structure of Amyloid Fibrils by Electron Microscopy and X-Ray Diffraction
Sunde, M., & BLAKE, C. (1997) · Advances in protein chemistry · doi:10.1016/s0065-3233(08)60320-4 · Cited by 780
Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation
Richardson, J. S., & Richardson, D. C. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.052706099 · Cited by 753
Protein Design by Binary Patterning of Polar and Nonpolar Amino Acids
Kamtekar, S., Schiffer, J. M., Xiong, H., Babik, J. M., & Hecht, M. H. (1993) · Science · doi:10.1126/science.8259512 · Cited by 731
Self-citationHecht, M. H., Richardson, J. S., Richardson, D. C., & Ogden, R. C. (1990) · Science · doi:10.1126/science.2392678 · Cited by 391
Self-citationDesign of a 20-Amino Acid, Three-Stranded β-Sheet Protein
Kortemme, T., Ramı́rez-Alvarado, M., & Serrano, L. G. (1998) · Science · doi:10.1126/science.281.5374.253 · Cited by 325
De novo amyloid proteins from designed combinatorial libraries
West, M. W., Wang, W., Patterson, J., Mancias, J. D., Beasley, J. R., & Hecht, M. H. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.20.11211 · Cited by 321
Self-citation
Research works printed but not linked: 6
- M W West Ph.D. dissertation (Princeton Univ., Princeton, 1997).
- W Wang Ph.D. dissertation (Princeton Univ., Princeton, 2001).
- 10.1021/ja973984 · DOI
- , ed W F Degrado Chem Rev (Protein Design) 101, 3025–3232 (2001).
- J S Richardson, D C Richardson Protein Engineering, eds D L Oxander, C F Fox (Liss, New York), pp. 149–163 (1987).
- S Roy Ph.D. dissertation (Princeton Univ., Princeton, 1998).
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Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation
Richardson, J. S., & Richardson, D. C. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.052706099 · Cited by 753
Pawar, A. P., DuBay, K. F., Zurdo, J., Chiti, F., Vendruscolo, M., & Dobson, C. M. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.04.016 · Cited by 593
Peptide‐Based Nanotubes and Their Applications in Bionanotechnology
Gao, X., & Matsui, H. (2005) · Advanced Materials · doi:10.1002/adma.200401849 · Cited by 478
Prediction of the Absolute Aggregation Rates of Amyloidogenic Polypeptide Chains
DuBay, K. F., Pawar, A. P., Chiti, F., Zurdo, J., Dobson, C. M., & Vendruscolo, M. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.06.043 · Cited by 320
Emerging ideas on the molecular basis of protein and peptide aggregation
Thirumalai, D. (2003) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(03)00032-0 · Cited by 314
Metadata
- Authors
- Wang, W., & Hecht, M. H.
- Affiliations
- Princeton University (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2002-03-05
- Volume
- 99
- Issue
- 5
- Pages
- 2760-2765
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC122421
- OpenAlex
- W2118038132
- Cited by
- 159
- References
- 32
- Citations by year
- 2026: 3 · 2025: 1 · 2023: 2 · 2022: 1 · 2021: 2 · 2020: 3 · 2019: 2 · 2018: 2 · 2017: 3 · 2016: 4 · 2015: 5 · 2014: 7 · 2013: 4 · 2012: 2
- FWCI
- 12.21
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Alzheimer's disease research and treatments
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Organic Chemistry › Chemical Synthesis and Analysis
- Keywords
- amyloid fibrils, cross-β structure, combinatorial protein libraries, lysine mutations, protein self-assembly, neurodegenerative diseases, Alzheimer's disease, prion disease
- MeSH terms
- Amino Acid Sequence, Amyloid, Models, Molecular, Molecular Sequence Data, Oligopeptides, Solubility, Mutagenesis, Protein Structure, Secondary
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