Journal article
Conformations of phenylalanine in the tripeptides AFA and GFG probed by combining MD simulations with NMR, FTIR, polarized Raman, and VCD spectroscopy
The journal of physical chemistry. B, v 114(11), pp 3965-3978
25 Mar 2010
PMID: 20184301
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Conformational properties of small, flexible peptides are a matter of ongoing interest since they can be considered as models for unfolded proteins. However, the investigation of the conformations of small peptides is challenging as they are ensembles of rapidly interconverting conformers; moreover, the different methods used are prone to different approximations and errors. In order to obtain more reliable results, it is prudent to combine different techniques; here, molecular dynamics (MD) simulations together with nuclear magnetic resonance (NMR), Fourier transform IR (FTIR), polarized Raman, and vibrational circular dichroism (VCD) measurements were used to study the conformational propensity of phenylalanine in the tripeptides AFA and GFG, motivated by the relevance of phenylalanine for the self-aggregation of peptides. The results of this analysis indicate that the F residue predominantly populates the beta-strand (beta) and polyproline II (PPII) conformations in both AFA and GFG. However, while phenylalanine exhibits a propensity for beta-strand conformations in GFG (0.40 < or = beta population < or = 0.69 and 0.29 < or = PPII population < or = 0.42), the substitution of terminal glycines with alanine residues induces a higher population of PPII (0.31 < or = beta population < or = 0.50 and 0.37 < or = PPII population < or = 0.57).
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Details
- Title
- Conformations of phenylalanine in the tripeptides AFA and GFG probed by combining MD simulations with NMR, FTIR, polarized Raman, and VCD spectroscopy
- Creators
- Silvia Pizzanelli - Istituto per i Processi Chimico Fisici, Consiglio Nazionale delle Ricerche, Area della Ricerca di Pisa, via G. Moruzzi, 1 56124 Pisa, Italy. silvia.pizzanelli@ipcf.cnr.itClaudia ForteSusanna MontiGiorgia ZandomeneghiAndrew HagarmanThomas J MeaseyReinhard Schweitzer-Stenner
- Publication Details
- The journal of physical chemistry. B, v 114(11), pp 3965-3978
- Publisher
- American Chemical Society; Washington, DC
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Chemistry
- Web of Science ID
- WOS:000275710400028
- Scopus ID
- 2-s2.0-77949829153
- Other Identifier
- 991014878368204721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Biophysics
- Chemistry, Physical