Design of parallel đ˝âsheet nanofibrils using Monte Carlo search, coarseâgrained simulations, and experimental testing Article Swipe
Sudeep Sarma
,
Tarunya Rao Sudarshan
,
Van Thuan Nguyen
,
Alicia S. Robang
,
Xingqing Xiao
,
Justin V. Le
,
Michael E. Helmicki
,
Anant K. Paravastu
,
Carol K. Hall
¡
YOU?
¡
¡ 2024
¡ Open Access
¡
¡ DOI: https://doi.org/10.1002/pro.5102
YOU?
¡
¡ 2024
¡ Open Access
¡
¡ DOI: https://doi.org/10.1002/pro.5102
Peptide selfâassembly into amyloid fibrils provides numerous applications in drug delivery and biomedical engineering applications. We augment our previouslyâestablished computational screening technique along with experimental biophysical characterization to discover 7âmer peptides that selfâassemble into âparallel β âsheetsâ, that is, β âsheets with NâterminusâtoâCâterminus đ˝âstrand vectors oriented in parallel. To accomplish the desired β âstrand organization, we applied the PepAD amino acid sequence design software to the Classâ1 crossâ β spine defined by Sawaya et al. This molecular configuration includes two layers of parallel β âsheets stacked such that NâterminusâtoâCâterminus vectors are oriented antiparallel for molecules on adjacent β âsheets. The first cohort of PepAD identified peptides were examined for their fibrillation behavior in DMD/PRIME20 simulations, and the top performing sequence was selected as a prototype for a subsequent round of sequence refinement. The two rounds of design resulted in a library of eight 7âmer peptides. In DMD/PRIME20 simulations, five of these peptides spontaneously formed fibrilâlike structures with a predominantly parallel đ˝âsheet arrangement, two formed fibrilâlike structure with <50% in parallel đ˝âsheet arrangement and one remained a random coil. Among the eight candidate peptides produced by PepAD and DMD/PRIME20, five were synthesized and purified. All five assembled into amyloid fibrils composed of parallel β âsheets based on Fourier transform infrared spectroscopy, circular dichroism, electron microscopy, and thioflavinâT fluorescence spectroscopy measurements.
Related Topics
Concepts
Antiparallel (mathematics)
Beta sheet
Thioflavin
Random coil
Fibril
Peptide sequence
Peptide
Circular dichroism
Protein secondary structure
Sequence (biology)
Chemistry
Crystallography
Materials science
Biophysics
Physics
Biochemistry
Biology
Disease
Quantum mechanics
Alzheimer's disease
Magnetic field
Pathology
Medicine
Gene
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1002/pro.5102
- https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pro.5102
- OA Status
- hybrid
- Cited By
- 4
- References
- 52
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4400886670
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
-
https://openalex.org/W4400886670Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1002/pro.5102Digital Object Identifier
- Title
-
Design of parallel đ˝âsheet nanofibrils using Monte Carlo search, coarseâgrained simulations, and experimental testingWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2024Year of publication
- Publication date
-
2024-07-22Full publication date if available
- Authors
-
Sudeep Sarma, Tarunya Rao Sudarshan, Van Thuan Nguyen, Alicia S. Robang, Xingqing Xiao, Justin V. Le, Michael E. Helmicki, Anant K. Paravastu, Carol K. HallList of authors in order
- Landing page
-
https://doi.org/10.1002/pro.5102Publisher landing page
- PDF URL
-
https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pro.5102Direct link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
hybridOpen access status per OpenAlex
- OA URL
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https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pro.5102Direct OA link when available
- Concepts
-
Antiparallel (mathematics), Beta sheet, Thioflavin, Random coil, Fibril, Peptide sequence, Peptide, Circular dichroism, Protein secondary structure, Sequence (biology), Chemistry, Crystallography, Materials science, Biophysics, Physics, Biochemistry, Biology, Disease, Quantum mechanics, Alzheimer's disease, Magnetic field, Pathology, Medicine, GeneTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
4Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 3, 2024: 1Per-year citation counts (last 5 years)
- References (count)
-
52Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.antiparallel | 93 |
| abstract_inverted_index.applications | 8 |
| abstract_inverted_index.arrangement, | 162 |
| abstract_inverted_index.experimental | 25 |
| abstract_inverted_index.fibrillation | 111 |
| abstract_inverted_index.fluorescence | 217 |
| abstract_inverted_index.simulations, | 115, 148 |
| abstract_inverted_index.spectroscopy | 218 |
| abstract_inverted_index.đ˝âsheet | 161, 171 |
| abstract_inverted_index.applications. | 15 |
| abstract_inverted_index.computational | 20 |
| abstract_inverted_index.configuration | 78 |
| abstract_inverted_index.fibrilâlike | 155, 165 |
| abstract_inverted_index.measurements. | 219 |
| abstract_inverted_index.organization, | 55 |
| abstract_inverted_index.predominantly | 159 |
| abstract_inverted_index.spectroscopy, | 210 |
| abstract_inverted_index.spontaneously | 153 |
| abstract_inverted_index.âsheetsâ, | 37 |
| abstract_inverted_index.đ˝âstrand | 44 |
| abstract_inverted_index.thioflavinâT | 216 |
| abstract_inverted_index.selfâassemble | 33 |
| abstract_inverted_index.selfâassembly | 2 |
| abstract_inverted_index.characterization | 27 |
| abstract_inverted_index.previouslyâestablished | 19 |
| abstract_inverted_index.NâterminusâtoâCâterminus | 43, 89 |
| cited_by_percentile_year.max | 97 |
| cited_by_percentile_year.min | 90 |
| corresponding_author_ids | https://openalex.org/A5062697029, https://openalex.org/A5057051008 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 9 |
| corresponding_institution_ids | https://openalex.org/I130701444, https://openalex.org/I137902535 |
| citation_normalized_percentile.value | 0.72139688 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |