Effect of Direct and Water-Mediated Interactions on the Identification of Hotspots in Biomolecular Complexes with Multiple Subsystems
Journal of Chemical Information and Modeling,
Journal Year:
2024,
Volume and Issue:
64(19), P. 7602 - 7615
Published: Sept. 16, 2024
Identification
of
important
residues
in
biochemical
complexes
is
often
a
crucial
step
for
many
problems
molecular
biology
and
biochemistry.
A
method
proposed
to
identify
hotspots
biomolecular
based
on
new
metric,
derived
from
networks
representing
subunits
(residues,
bridging
solvent
molecules,
ligands
etc.)
connected
by
interactions.
singular
value
decomposition
the
weighted
adjacency
matrix
used
construct
scalar
rank
each
subunit
that
reflects
its
importance
residue
interaction
network.
This
metric
called
centrality.
In
addition,
formalism
account
water-mediated
interactions
ranking
residues.
Interactions
network
can
be
provided
various
computational
methods.
this
work
are
obtained
full
quantum-mechanical
calculations
protein-protein
using
fragment
orbital
method.
The
results
shown
good
agreement
with
earlier
experimental
studies.
developed
gain
deeper
insight
into
role
complex
systems.
Language: Английский
Partition analysis of dipole moments in solution applied to functional groups in polypeptide motifs
Physical Chemistry Chemical Physics,
Journal Year:
2024,
Volume and Issue:
26(27), P. 18614 - 18628
Published: Jan. 1, 2024
A
decomposition
analysis
of
dipole
moments
is
developed
for
density
functional
theory.
Dipole
groups
polypeptides
in
solution
reveal
the
importance
concerted
contributions
carbonyls
α-helices.
Language: Английский
Fragmentation of disulfide bonds in the fragment molecular orbital method
Computational and Theoretical Chemistry,
Journal Year:
2024,
Volume and Issue:
unknown, P. 114885 - 114885
Published: Sept. 1, 2024
Language: Английский
Importance of Charge Balance for the Embedding of Zwitterionic Solutes in the Fragment Molecular Orbital Method
The Journal of Physical Chemistry A,
Journal Year:
2024,
Volume and Issue:
unknown
Published: Dec. 12, 2024
Three
new
schemes
of
induced
solvent
charges
for
the
auxiliary
polarization
formulation
fragment
molecular
orbital
method
are
proposed
and
compared
to
original
approach.
It
is
found
that
charge
balance
solute
embeddings
crucial
maintaining
a
proper
gap
between
occupied
virtual
orbitals
fragments
zwitterionic
systems
in
solution.
The
instability
eliminated
with
scheme
fragment-specific
charges.
developed
stable
embedding
applied
perform
MP2/aug-cc-pVTZ
calculations
protein–ligand
complex
containing
1102
amino
acid
residues.
Language: Английский