253
8 Molecular Dynamics Simulations of Lipid Bilayers with Incorporated Peptides
similarly like I 24 , but in DPPC/gel phase fluctuates even more because it is longer
due to additional amino acid. But for example the fluctuations of I 24 in DMPC/LC
can be increased also by bending and unbending of peptide, which increase standard
deviation from average structure.
The differences in fluctuations of I 24 , A 24 , V 24 and L 24 are presented on Fig. 8.6,
where root mean square fluctuations (RMSF) of C
β
, C
γ
and C
δ
atoms are compared.
The fluctuation depends also on temperature and position of C atom in side chain.
Because of temperature dependence it is possible only to compare fluctuations from
simulations made by same conditions of atoms with same parameters. The Leu side
chains are most stable, while the Ile side chains are the most fluctuating. The fluctuation of Val side chains are between that of Leu and Ile. This instability of amino
acids side chains affect also surrounding lipids (see below). The fluctuations are affected also by distortions in helical structure—for example C
δ
in DPPC/gel. In this
case in C end of the peptide the fluctuations are similar in Leu and Ile. But the L 24
peptide formed a kink at this position (aprox. one turn from C end). The stability of
side chains has been studied also by Pace et al. [87] and Johanson and Lindahl [54]
(determined enthalpy and entropy of exchanging Ala with different amino acids in
poly-Ala transmembrane chain) and Barlow et al. [86] (studied entropy of χ angles).
Fig. 8.4 Bended peptide
during simulation (I 24 in
DMPC/LC)
8 Molecular Dynamics Simulations of Lipid Bilayers with Incorporated Peptides
similarly like I 24 , but in DPPC/gel phase fluctuates even more because it is longer
due to additional amino acid. But for example the fluctuations of I 24 in DMPC/LC
can be increased also by bending and unbending of peptide, which increase standard
deviation from average structure.
The differences in fluctuations of I 24 , A 24 , V 24 and L 24 are presented on Fig. 8.6,
where root mean square fluctuations (RMSF) of C
β
, C
γ
and C
δ
atoms are compared.
The fluctuation depends also on temperature and position of C atom in side chain.
Because of temperature dependence it is possible only to compare fluctuations from
simulations made by same conditions of atoms with same parameters. The Leu side
chains are most stable, while the Ile side chains are the most fluctuating. The fluctuation of Val side chains are between that of Leu and Ile. This instability of amino
acids side chains affect also surrounding lipids (see below). The fluctuations are affected also by distortions in helical structure—for example C
δ
in DPPC/gel. In this
case in C end of the peptide the fluctuations are similar in Leu and Ile. But the L 24
peptide formed a kink at this position (aprox. one turn from C end). The stability of
side chains has been studied also by Pace et al. [87] and Johanson and Lindahl [54]
(determined enthalpy and entropy of exchanging Ala with different amino acids in
poly-Ala transmembrane chain) and Barlow et al. [86] (studied entropy of χ angles).
Fig. 8.4 Bended peptide
during simulation (I 24 in
DMPC/LC)