TY  - JOUR
AU  - Grubišić, Sonja
AU  - Brancato, Giuseppe
AU  - Barone, Vincenzo
PY  - 2013
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1192
AB  - alpha,alpha-Dialkylated amino acid residues have acquired considerable importance as effective means for introducing backbone conformation constraints in synthetic peptides. The prototype of such a class of residues, namely Aib (alpha-aminoisobutyric acid), appears to play a dominant role in determining the preferred conformations of host proteins. We have recently introduced into the standard AMBER force field some new parameters, fitted against high-level quantum mechanical (QM) data, for simulating peptides containing alpha,alpha-dialkylated residues with cyclic side chains, such as TOAC (TOAC, 2,2,6,6-tetramethylpiperidine-1-oxyl4- amino-4-carboxylic acid) and Ac(6)c (Ac(6)c = 1-aminocyclohexaneacetic acid). Here, we show that in order to accurately reproduce the observed conformational geometries and structural fluctuations of linear alpha,alpha-dialkylated peptides based on Aib, further improvements of the non-bonding and side chain torsion potential parameters have to be considered, due to the expected larger structural flexibility of linear residues with respect to cyclic ones. To this end, we present an extended set of parameters, which have been optimized by fitting the energies of multiple conformations of the Aib dipeptide analogue to corresponding QM calculations that properly account for dispersion interactions (B3LYP-D3). The quality, transferability and size-consistency of the proposed force field have been assessed both by considering a series of poly-Aib peptides, modeled at the same QM level, and by performing molecular dynamics simulations in solvents with high and low polarity. As a result, the present parameters allow one to reproduce with good reliability the available QM and experimental data, thus representing a notable improvement over current force field especially in the description of the alpha/3(10)-helix conformational equilibria of alpha,alpha-dialkylated peptides with linear and cyclic side chains.
PB  - Royal Soc Chemistry, Cambridge
T2  - Physical Chemistry Chemical Physics
T1  - An improved AMBER force field for alpha,alpha-dialkylated peptides: intrinsic and solvent-induced conformational preferences of model systems
VL  - 15
IS  - 40
SP  - 17395
EP  - 17407
DO  - 10.1039/c3cp52721b
ER  - 

@article{
author = "Grubišić, Sonja and Brancato, Giuseppe and Barone, Vincenzo",
year = "2013",
abstract = "alpha,alpha-Dialkylated amino acid residues have acquired considerable importance as effective means for introducing backbone conformation constraints in synthetic peptides. The prototype of such a class of residues, namely Aib (alpha-aminoisobutyric acid), appears to play a dominant role in determining the preferred conformations of host proteins. We have recently introduced into the standard AMBER force field some new parameters, fitted against high-level quantum mechanical (QM) data, for simulating peptides containing alpha,alpha-dialkylated residues with cyclic side chains, such as TOAC (TOAC, 2,2,6,6-tetramethylpiperidine-1-oxyl4- amino-4-carboxylic acid) and Ac(6)c (Ac(6)c = 1-aminocyclohexaneacetic acid). Here, we show that in order to accurately reproduce the observed conformational geometries and structural fluctuations of linear alpha,alpha-dialkylated peptides based on Aib, further improvements of the non-bonding and side chain torsion potential parameters have to be considered, due to the expected larger structural flexibility of linear residues with respect to cyclic ones. To this end, we present an extended set of parameters, which have been optimized by fitting the energies of multiple conformations of the Aib dipeptide analogue to corresponding QM calculations that properly account for dispersion interactions (B3LYP-D3). The quality, transferability and size-consistency of the proposed force field have been assessed both by considering a series of poly-Aib peptides, modeled at the same QM level, and by performing molecular dynamics simulations in solvents with high and low polarity. As a result, the present parameters allow one to reproduce with good reliability the available QM and experimental data, thus representing a notable improvement over current force field especially in the description of the alpha/3(10)-helix conformational equilibria of alpha,alpha-dialkylated peptides with linear and cyclic side chains.",
publisher = "Royal Soc Chemistry, Cambridge",
journal = "Physical Chemistry Chemical Physics",
title = "An improved AMBER force field for alpha,alpha-dialkylated peptides: intrinsic and solvent-induced conformational preferences of model systems",
volume = "15",
number = "40",
pages = "17395-17407",
doi = "10.1039/c3cp52721b"
}

Grubišić, S., Brancato, G.,& Barone, V.. (2013). An improved AMBER force field for alpha,alpha-dialkylated peptides: intrinsic and solvent-induced conformational preferences of model systems. in Physical Chemistry Chemical Physics
Royal Soc Chemistry, Cambridge., 15(40), 17395-17407.
https://doi.org/10.1039/c3cp52721b

Grubišić S, Brancato G, Barone V. An improved AMBER force field for alpha,alpha-dialkylated peptides: intrinsic and solvent-induced conformational preferences of model systems. in Physical Chemistry Chemical Physics. 2013;15(40):17395-17407.
doi:10.1039/c3cp52721b .

Grubišić, Sonja, Brancato, Giuseppe, Barone, Vincenzo, "An improved AMBER force field for alpha,alpha-dialkylated peptides: intrinsic and solvent-induced conformational preferences of model systems" in Physical Chemistry Chemical Physics, 15, no. 40 (2013):17395-17407,
https://doi.org/10.1039/c3cp52721b . .

TY  - JOUR
AU  - Grubišić, Sonja
AU  - Brancato, Giuseppe
AU  - Pedone, Alfonso
AU  - Barone, Vincenzo
PY  - 2012
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1127
AB  - The popular biomolecular AMBER (ff99SB) force field (FF) has been extended with new parameters for the simulations of peptides containing alpha, alpha dialkylated residues with cyclic side chains. Together with the recent set of nitroxide parameters [E. Stendardo, A. Pedone, P. Cimino, M. C. Menziani, O. Crescenzi and V. Barone, Phys. Chem. Chem. Phys., 2010, 12, 11697] this extension allows treating the TOAC residue (TOAC, 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) widely used as a spin label in protein studies. All the conformational minima of the Ac-Ac6C-NMe (Ac = acetyl, Ac6C = 1-aminocyclohexaneacetic acid, NMe = methylamino) and Ac-TOAC-NMe dipeptides have been examined in terms of geometry and relative energy stability by Quantum Mechanical (QM) computations employing an hybrid density functional (PBE0) for an extended training set of conformers with various folds. A very good agreement between QM and MM (molecular mechanics) data has been obtained in most of the investigated properties, including solvent effects. Finally, the new set of parameters has been validated by comparing the conformational and dynamical behavior of TOAC-labeled polypeptides investigated by means of classical molecular dynamics (MD) simulations with QM data and experimental evidence. The new FF accurately describes the tuning of conformational and dynamical behavior of the Ac-TOAC-NMe dipeptide and double spin-labeled heptapeptide Fmoc-(Aib-Aib-TOAC)(2)-Aib-OMe (Fmoc, fluorenyl-9-methoxycarbonyl; Aib, alpha-aminoisobutyric acid; OMe, methoxy) by solvents with different polarity. In particular, we found that the 3(10) helical structure of heptapeptide is the most stable one in vacuo, with a geometry very similar to the X-ray crystallographic structure, whereas a conformational equilibrium between the 3(10)- and alpha-helical structures is established in aqueous solution, in agreement with EPR data.
PB  - Royal Soc Chemistry, Cambridge
T2  - Physical Chemistry Chemical Physics
T1  - Extension of the AMBER force field to cyclic alpha,alpha dialkylated peptides
VL  - 14
IS  - 44
SP  - 15308
EP  - 15320
DO  - 10.1039/c2cp42713c
ER  - 

@article{
author = "Grubišić, Sonja and Brancato, Giuseppe and Pedone, Alfonso and Barone, Vincenzo",
year = "2012",
abstract = "The popular biomolecular AMBER (ff99SB) force field (FF) has been extended with new parameters for the simulations of peptides containing alpha, alpha dialkylated residues with cyclic side chains. Together with the recent set of nitroxide parameters [E. Stendardo, A. Pedone, P. Cimino, M. C. Menziani, O. Crescenzi and V. Barone, Phys. Chem. Chem. Phys., 2010, 12, 11697] this extension allows treating the TOAC residue (TOAC, 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) widely used as a spin label in protein studies. All the conformational minima of the Ac-Ac6C-NMe (Ac = acetyl, Ac6C = 1-aminocyclohexaneacetic acid, NMe = methylamino) and Ac-TOAC-NMe dipeptides have been examined in terms of geometry and relative energy stability by Quantum Mechanical (QM) computations employing an hybrid density functional (PBE0) for an extended training set of conformers with various folds. A very good agreement between QM and MM (molecular mechanics) data has been obtained in most of the investigated properties, including solvent effects. Finally, the new set of parameters has been validated by comparing the conformational and dynamical behavior of TOAC-labeled polypeptides investigated by means of classical molecular dynamics (MD) simulations with QM data and experimental evidence. The new FF accurately describes the tuning of conformational and dynamical behavior of the Ac-TOAC-NMe dipeptide and double spin-labeled heptapeptide Fmoc-(Aib-Aib-TOAC)(2)-Aib-OMe (Fmoc, fluorenyl-9-methoxycarbonyl; Aib, alpha-aminoisobutyric acid; OMe, methoxy) by solvents with different polarity. In particular, we found that the 3(10) helical structure of heptapeptide is the most stable one in vacuo, with a geometry very similar to the X-ray crystallographic structure, whereas a conformational equilibrium between the 3(10)- and alpha-helical structures is established in aqueous solution, in agreement with EPR data.",
publisher = "Royal Soc Chemistry, Cambridge",
journal = "Physical Chemistry Chemical Physics",
title = "Extension of the AMBER force field to cyclic alpha,alpha dialkylated peptides",
volume = "14",
number = "44",
pages = "15308-15320",
doi = "10.1039/c2cp42713c"
}

Grubišić, S., Brancato, G., Pedone, A.,& Barone, V.. (2012). Extension of the AMBER force field to cyclic alpha,alpha dialkylated peptides. in Physical Chemistry Chemical Physics
Royal Soc Chemistry, Cambridge., 14(44), 15308-15320.
https://doi.org/10.1039/c2cp42713c

Grubišić S, Brancato G, Pedone A, Barone V. Extension of the AMBER force field to cyclic alpha,alpha dialkylated peptides. in Physical Chemistry Chemical Physics. 2012;14(44):15308-15320.
doi:10.1039/c2cp42713c .

Grubišić, Sonja, Brancato, Giuseppe, Pedone, Alfonso, Barone, Vincenzo, "Extension of the AMBER force field to cyclic alpha,alpha dialkylated peptides" in Physical Chemistry Chemical Physics, 14, no. 44 (2012):15308-15320,
https://doi.org/10.1039/c2cp42713c . .