Computational study of the free energy landscape of the miniprotein CLN025 in explicit and implicit solvent
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Tipus de documentArticle
Data publicació2010-02-17
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Abstract
The prediction capabilities of atomistic simulations of peptides
are hampered by different difficulties, including the reliability of force fields, the
treatment of the solvent or the adequate sampling of the conformational space.
In this work, we have studied the conformational profile of the 10 residue
miniprotein CLN025 known to exhibit a β-hairpin in its native state to
understand the limitations of implicit methods to describe solvent effects and
how these may be compensated by using different force fields. For this purpose,
we carried out a thorough sampling of the conformational space of CLN025 in
explicit solvent using the replica exchange molecular dynamics method as a
sampling technique and compared the results with simulations of the system
modeled using the analytical linearized Poisson-Boltzmann (ALPB) method
with three different AMBER force fields: parm94, parm96, and parm99SB. The
results show the peptide to exhibit a funnel-like free energy landscape with two
minima in explicit solvent. In contrast, the higher minimum nearly disappears
from the energy surface when the system is studied with an implicit representation
of the solvent. Moreover, the different force fields used in combination with the ALPB method do not describe the system in the
same manner. The results of this work suggest that the balance between intra- and intermolecular interactions is the cause of the
differences between implicit and explicit solvent simulations in this system, stressing the role of the environment to define properly the
conformational profile of a peptide in solution.
CitacióRodríguez, A. [et al.]. Computational study of the free energy landscape of the miniprotein CLN025 in explicit and implicit solvent. "Journal of physical chemistry B", 17 Febrer 2010, vol. 115, núm. 6, p. 1440-1449.
ISSN1520-6106
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