2 research outputs found
Hydration Behavior along the Folding Pathways of Trpzip4, Trpzip5 and Trpzip6
The
microscopic properties of water confined within different segments
of Trpzip4 (TZ4), Trpzip5 (TZ5), and Trzpip6 (TZ6) have been compared
for all the states characterized along their folding pathways. In
particular, structural ordering, energetics, and dynamics of water
have been examined as the peptide unfolds along the free energy landscape.
It is observed that the structuring of tetrahedral network as well
as translational and rotational motions of hydration waters confined
within the strands and the turn regions are very different, revealing
motional heterogeneity in small 16-residue trpzips. The polar and
charged groups present at the peptide surface anchor to water molecules
through hydrogen bonds and are responsible for differential hydration
among various segments of the peptide, which is found to be correlated
to their hydropathy values. The coherent collective dynamics of water
is strongly coupled with conformational changes in the peptide since
the trends observed in most of the computed quantities are in accordance
with the folded and unfolded states classified along the folding pathway
for all trpzips. The hydration behavior conform to the heterogeneity
observed in the free energy landscape of stable TZ4 with four unfolded
states as compared to more flexible TZ5 and TZ6 with two unfolded
states each, in addition to the folded state. The hydration waters
are observed to regulate the protein dynamics by continuous fluctuations
in hydrogen bond network involving lateral side chains that inject
conformational motions in the peptide to facilitate its unfolding.
The implications of mutations on various aspects of hydration water
dynamics including their impact on structural and dynamic organization
of hydrogen bonds are also highlighted. Our studies affirm that topology
of the free energy landscape is shaped by both spatial organization
and dynamic transitions in hydration waters in addition to the conformational
fluctuations in the peptide along the folding pathway
Understanding the Nature of Amino Acid Interactions with Pd(111) or Pd–Au Bimetallic Catalysts in the Aqueous Phase
The
interaction of methionine (Met) with different bimetallic-segregated
surfaces comprising a uniform distribution of strips and islands of
Au on the Pd(111) surface was examined using molecular dynamics (MD)
simulations. Out of all the segregated and uniformly doped surfaces
studied, the design of Pd–Au islands showed some reduction
in the interaction energy (<i>E</i><sub>int</sub> = −43.7
kJ/mol) as compared to that of the pure Pd(111) surface (<i>E</i><sub>int</sub> = −50 kJ/mol) for a single Met molecule. However,
at a higher coverage of 9 Met molecules/simulation cell, none of the
Pd–Au alloy surfaces showed any improvement as compared to
the Pd(111) surface. In order to develop a comprehensive understanding
of the nature of the nonbonded interaction of aqueous biogenic impurities
with the Pd catalyst surface, the MD study was extended to include
a variety of aliphatic, S-containing, aromatic, and polar amino acids.
The potential of mean force (PMF) profiles were observed to be distinct
for each class of amino acids with substantial differences among amino
acids with acidic and basic side chains. The side chains of all the
polar and aromatic amino acids showed direct contact with the surface
while aliphatic amino acids had their hydrophobic side chain aligned
away from the surface. Interestingly, lysine (Lys) and tyrosine (Tyr)
were the only two amino acids which interacted preferentially via
the distant backbone nitrogen and backbone oxygen, respectively, despite
their side chains being in direct contact with the metal surface.
The strength of interaction was correlated with the size of the amino
acid; the interaction energies were observed to be the maximum for
large molecules such as arginine (Arg, <i>E</i><sub>int</sub> = −87.7 kJ/mol) and tryptophan (Trp, <i>E</i><sub>int</sub> = −73.4 kJ/mol), while it was a minimum for aliphatic
amino acids such as alanine (Ala, <i>E</i><sub>int</sub> = −10.9 kJ/mol). The study is focused on examining the sensitivity
of the choice of the preferential interaction site, conformational
preferences, and interaction energies to the side-chain specificity