Chain length, temperature and solvent effects on the structural properties of alpha-aminoisobutyric acid homooligopeptides
Само за регистроване кориснике
2016
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Non-coded alpha-amino acids, originally exploited by nature, have been successfully reproduced by recent synthetic strategies to confer special structural and functional properties to small peptides. The most known and well-studied atypical residue is alpha-aminoisobutyric acid (Aib), which is contained in a fairly large number of peptides with known antibiotic effects. Here, we report on a molecular dynamics (MD) study of a series of homooligopeptides based on alpha-aminoisobutyric acid (Aib) with increasing length (Ac-(Aib)(n)-NMe, n = 5, 6, 7 and 10) and at various temperatures, employing a recent extension of the AMBER force field tailored for the Aib residue. Solvent effects have been analyzed by comparative MD simulations of a heptapeptide in water and dimethylsulfoxide at different temperatures. Our results show that the preference for the 3(10)- and/or alpha-helix structures, which typically characterize Aib based peptides, is finely tuned by several factors including the chain... length, temperature and solvent nature. While the transitions between intra-molecular i -> i + 3 and i -> i + 4 hydrogen bonds characterizing 3(10) and alpha-helices, respectively, are rather fast in small peptides (in the picosecond timescale), our analysis shows that the above physical and chemical factors modulate the relative equilibrium populations of the two helical structures. The obtained results nicely agree with available experimental data and support the use of the new force field for modeling Aib containing peptides.
Извор:
Physical Chemistry Chemical Physics, 2016, 18, 30, 20389-20398Издавач:
- Royal Soc Chemistry, Cambridge
Финансирање / пројекти:
- MIUR through the PRIN program - 2012SK7ASN
- Рационални дизајн и синтеза биолошки активних и координационих једињења и функционалних материјала, релевантних у (био)нанотехнологији (RS-MESTD-Basic Research (BR or ON)-172035)
- COST CMST-Action Molecules in Motion (MOLIM) - CM1405
- Bilateral Serbian-Italian project - 680-00-566/2013-09/07
DOI: 10.1039/c6cp01120a
ISSN: 1463-9076
PubMed: 27402118
WoS: 000381428600043
Scopus: 2-s2.0-84979918092
Институција/група
IHTMTY - JOUR AU - Grubišić, Sonja AU - Chandramouli, Balasubramanian AU - Barone, Vincenzo AU - Brancato, Giuseppe PY - 2016 UR - https://cer.ihtm.bg.ac.rs/handle/123456789/1843 AB - Non-coded alpha-amino acids, originally exploited by nature, have been successfully reproduced by recent synthetic strategies to confer special structural and functional properties to small peptides. The most known and well-studied atypical residue is alpha-aminoisobutyric acid (Aib), which is contained in a fairly large number of peptides with known antibiotic effects. Here, we report on a molecular dynamics (MD) study of a series of homooligopeptides based on alpha-aminoisobutyric acid (Aib) with increasing length (Ac-(Aib)(n)-NMe, n = 5, 6, 7 and 10) and at various temperatures, employing a recent extension of the AMBER force field tailored for the Aib residue. Solvent effects have been analyzed by comparative MD simulations of a heptapeptide in water and dimethylsulfoxide at different temperatures. Our results show that the preference for the 3(10)- and/or alpha-helix structures, which typically characterize Aib based peptides, is finely tuned by several factors including the chain length, temperature and solvent nature. While the transitions between intra-molecular i -> i + 3 and i -> i + 4 hydrogen bonds characterizing 3(10) and alpha-helices, respectively, are rather fast in small peptides (in the picosecond timescale), our analysis shows that the above physical and chemical factors modulate the relative equilibrium populations of the two helical structures. The obtained results nicely agree with available experimental data and support the use of the new force field for modeling Aib containing peptides. PB - Royal Soc Chemistry, Cambridge T2 - Physical Chemistry Chemical Physics T1 - Chain length, temperature and solvent effects on the structural properties of alpha-aminoisobutyric acid homooligopeptides VL - 18 IS - 30 SP - 20389 EP - 20398 DO - 10.1039/c6cp01120a ER -
@article{ author = "Grubišić, Sonja and Chandramouli, Balasubramanian and Barone, Vincenzo and Brancato, Giuseppe", year = "2016", abstract = "Non-coded alpha-amino acids, originally exploited by nature, have been successfully reproduced by recent synthetic strategies to confer special structural and functional properties to small peptides. The most known and well-studied atypical residue is alpha-aminoisobutyric acid (Aib), which is contained in a fairly large number of peptides with known antibiotic effects. Here, we report on a molecular dynamics (MD) study of a series of homooligopeptides based on alpha-aminoisobutyric acid (Aib) with increasing length (Ac-(Aib)(n)-NMe, n = 5, 6, 7 and 10) and at various temperatures, employing a recent extension of the AMBER force field tailored for the Aib residue. Solvent effects have been analyzed by comparative MD simulations of a heptapeptide in water and dimethylsulfoxide at different temperatures. Our results show that the preference for the 3(10)- and/or alpha-helix structures, which typically characterize Aib based peptides, is finely tuned by several factors including the chain length, temperature and solvent nature. While the transitions between intra-molecular i -> i + 3 and i -> i + 4 hydrogen bonds characterizing 3(10) and alpha-helices, respectively, are rather fast in small peptides (in the picosecond timescale), our analysis shows that the above physical and chemical factors modulate the relative equilibrium populations of the two helical structures. The obtained results nicely agree with available experimental data and support the use of the new force field for modeling Aib containing peptides.", publisher = "Royal Soc Chemistry, Cambridge", journal = "Physical Chemistry Chemical Physics", title = "Chain length, temperature and solvent effects on the structural properties of alpha-aminoisobutyric acid homooligopeptides", volume = "18", number = "30", pages = "20389-20398", doi = "10.1039/c6cp01120a" }
Grubišić, S., Chandramouli, B., Barone, V.,& Brancato, G.. (2016). Chain length, temperature and solvent effects on the structural properties of alpha-aminoisobutyric acid homooligopeptides. in Physical Chemistry Chemical Physics Royal Soc Chemistry, Cambridge., 18(30), 20389-20398. https://doi.org/10.1039/c6cp01120a
Grubišić S, Chandramouli B, Barone V, Brancato G. Chain length, temperature and solvent effects on the structural properties of alpha-aminoisobutyric acid homooligopeptides. in Physical Chemistry Chemical Physics. 2016;18(30):20389-20398. doi:10.1039/c6cp01120a .
Grubišić, Sonja, Chandramouli, Balasubramanian, Barone, Vincenzo, Brancato, Giuseppe, "Chain length, temperature and solvent effects on the structural properties of alpha-aminoisobutyric acid homooligopeptides" in Physical Chemistry Chemical Physics, 18, no. 30 (2016):20389-20398, https://doi.org/10.1039/c6cp01120a . .