Simulating the Electronic Circular Dichroism Spectra of Photoreversible Peptide Conformations
- Gattuso, H. 23
- García-Iriepa, C. 14
- Sampedro, D. 1
- Monari, A. 23
- Marazzi, M. 23
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1
Universidad de La Rioja
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2
Centre National de la Recherche Scientifique
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3
University of Lorraine
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4
Universidad de Alcalá
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ISSN: 1549-9618
Year of publication: 2017
Volume: 13
Issue: 7
Pages: 3290-3296
Type: Article
More publications in: Journal of Chemical Theory and Computation
Metrics
JCR (Journal Impact Factor)
- Year 2017
- Journal Impact Factor: 5.399
- Journal Impact Factor without self cites: 4.459
- Article influence score: 1.815
- Best Quartile: Q1
- Area: CHEMISTRY, PHYSICAL Quartile: Q1 Rank in area: 31/147 (Ranking edition: SCIE)
- Area: PHYSICS, ATOMIC, MOLECULAR & CHEMICAL Quartile: Q1 Rank in area: 5/37 (Ranking edition: SCIE)
SCImago Journal Rank
- Year 2017
- SJR Journal Impact: 2.497
- Best Quartile: Q1
- Area: Physical and Theoretical Chemistry Quartile: Q1 Rank in area: 10/174
- Area: Computer Science Applications Quartile: Q1 Rank in area: 21/2824
Scopus CiteScore
- Year 2017
- CiteScore of the Journal : 9.2
- Area: Computer Science Applications Percentile: 96
- Area: Physical and Theoretical Chemistry Percentile: 90
Journal Citation Indicator (JCI)
- Year 2017
- Journal Citation Indicator (JCI): 1.39
- Best Quartile: Q1
- Area: PHYSICS, ATOMIC, MOLECULAR & CHEMICAL Quartile: Q1 Rank in area: 3/40
- Area: CHEMISTRY, PHYSICAL Quartile: Q1 Rank in area: 21/156
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Abstract
Electronic circular dichroism (CD) spectroscopy of peptides is one of the most important experimental characterization tools to get insights regarding their structure. Nevertheless, even though highly useful, the reliable simulations of CD spectra result in a complex task. Here, we propose a combination of quantum mechanics/molecular mechanics (QM/MM) methods with a semiempirical Hamiltonian based on the Frenkel excitons theory to efficiently describe the behavior of a model 27-amino acid α-helical peptide in water. Especially, we show how the choice of the QM region, including different possible hydrogen-bonding patterns, can substantially change the final CD spectrum shape. Moreover, we prove that our approach can correctly explain the changes observed in the peptide conformation (from α-helix to α-hairpin) when covalently linked to a protonated retinal-like molecular switch and exposing the system to UVA light, as previously observed by experiment and extensive molecular dynamics. Hence our protocol may be straightforwardly exploited to characterize light-induced conformation changes in photoactive materials and more generally protein folding processes. © 2017 American Chemical Society.