5 research outputs found
CHARMM Force-Fields with Modified Polyphosphate Parameters Allow Stable Simulation of the ATP-Bound Structure of Ca<sup>2+</sup>-ATPase
Adenosine triphosphate
(ATP) is an indispensable energy source
in cells. In a wide variety of biological phenomena like glycolysis,
muscle contraction/relaxation, and active ion transport, chemical
energy released from ATP hydrolysis is converted to mechanical forces
to bring about large-scale conformational changes in proteins. Investigation
of structure–function relationships in these proteins by molecular
dynamics (MD) simulations requires modeling of ATP in solution and
ATP bound to proteins with accurate force-field parameters. In this
study, we derived new force-field parameters for the triphosphate
moiety of ATP based on the high-precision quantum calculations of
methyl triphosphate. We tested our new parameters on membrane-embedded
sarcoplasmic reticulum Ca<sup>2+</sup>-ATPase and four soluble proteins.
The ATP-bound structure of Ca<sup>2+</sup>-ATPase remains stable during
MD simulations, contrary to the outcome in shorter simulations using
original parameters. Similar results were obtained with the four ATP-bound
soluble proteins. The new force-field parameters were also tested
by investigating the range of conformations sampled during replica-exchange
MD simulations of ATP in explicit water. Modified parameters allowed
a much wider range of conformational sampling compared with the bias
toward extended forms with original parameters. A diverse range of
structures agrees with the broad distribution of ATP conformations
in proteins deposited in the Protein Data Bank. These simulations
suggest that the modified parameters will be useful in studies of
ATP in solution and of the many ATP-utilizing proteins
CHARMM Force-Fields with Modified Polyphosphate Parameters Allow Stable Simulation of the ATP-Bound Structure of Ca<sup>2+</sup>-ATPase
Adenosine triphosphate
(ATP) is an indispensable energy source
in cells. In a wide variety of biological phenomena like glycolysis,
muscle contraction/relaxation, and active ion transport, chemical
energy released from ATP hydrolysis is converted to mechanical forces
to bring about large-scale conformational changes in proteins. Investigation
of structure–function relationships in these proteins by molecular
dynamics (MD) simulations requires modeling of ATP in solution and
ATP bound to proteins with accurate force-field parameters. In this
study, we derived new force-field parameters for the triphosphate
moiety of ATP based on the high-precision quantum calculations of
methyl triphosphate. We tested our new parameters on membrane-embedded
sarcoplasmic reticulum Ca<sup>2+</sup>-ATPase and four soluble proteins.
The ATP-bound structure of Ca<sup>2+</sup>-ATPase remains stable during
MD simulations, contrary to the outcome in shorter simulations using
original parameters. Similar results were obtained with the four ATP-bound
soluble proteins. The new force-field parameters were also tested
by investigating the range of conformations sampled during replica-exchange
MD simulations of ATP in explicit water. Modified parameters allowed
a much wider range of conformational sampling compared with the bias
toward extended forms with original parameters. A diverse range of
structures agrees with the broad distribution of ATP conformations
in proteins deposited in the Protein Data Bank. These simulations
suggest that the modified parameters will be useful in studies of
ATP in solution and of the many ATP-utilizing proteins
Energetics of the Presequence-Binding Poses in Mitochondrial Protein Import Through Tom20
Tom20 is located at the outer membrane
of mitochondria and functions
as a receptor for the N-terminal presequence of mitochondrial-precursor
proteins. Recently, three atomic structures of the Tom20-presequence
complex were determined using X-ray crystallography and classified
into A-, M-, and Y-poses in terms of their presequence-binding modes.
Combined with biochemical and NMR data, a dynamic-equilibrium model
between the three poses has been proposed. To investigate this mechanism
in further detail, we performed all-atom molecular dynamics (MD) simulations
and replica-exchange MD (REMD) simulations of the Tom20-presequence
complex in explicit water. In the REMD simulations, one major distribution
and another minor one were observed in the converged free-energy landscape
at 300 K. In the major distribution, structures similar to A- and
M-poses exist, whereas those similar to Y-pose are located in the
minor one, suggesting that A-pose in solution is more stable than
Y-pose. A <i>k</i>-means clustering algorithm revealed a
new pose not yet obtained by X-ray crystallography. This structure
has double salt bridges between Arg14′ in the presequence and
Glu78 or Glu79 in Tom20 and can explain the binding affinity of the
complex in previous pull-down assay experiments. Structural clustering
and analyses of contacts between Tom20 and the presequence suggest
smooth conformational changes from Y- to A-poses through low activation
barriers. M-pose lies between Y- and A-poses as a metastable state.
The REMD simulations thus provide insights into the energetics of
the multiple-binding forms and help to detail the progressive conformational
states in the dynamic-equilibrium model based on the experimental
data
Simultaneous Formation and Spatial Patterning of ZnO on ITO Surfaces by Local Laser-Induced Generation of Microbubbles in Aqueous Solutions of [Zn(NH<sub>3</sub>)<sub>4</sub>]<sup>2+</sup>
We
demonstrate the simultaneous formation and spatial patterning of ZnO
nanocrystals on an indium–tin oxide (ITO) surface upon local
heating using a laser (1064 nm) and subsequent formation of microbubbles.
Laser irradiation of an ITO surface in aqueous [ZnÂ(NH<sub>3</sub>)<sub>4</sub>]<sup>2+</sup> solution (1.0 × 10<sup>–2</sup> M at pH 12.0) under an optical microscope produced ZnO nanocrystals,
the presence of which was confirmed by X-ray diffraction analysis
and Raman microspectroscopy. Scanning the focused laser beam over
the ITO surface generated a spatial ZnO pattern (height: ∼60
nm, width: ∼1 μm) in the absence of a template or mask.
The Marangoni convection generated in the vicinity of the microbubbles
resulted in a rapid concentration/accumulation of [ZnÂ(NH<sub>3</sub>)<sub>4</sub>]<sup>2+</sup> around the microbubbles, which led to
the formation of ZnO at the solid–bubble–solution three-phase
contact line around the bubbles and thus afforded ZnO nanocrystals
on the ITO surface upon local heating with a laser
Formation of M‑Like Intermediates in Proteorhodopsin in Alkali Solutions (pH ≥ ∼8.5) Where the Proton Release Occurs First in Contrast to the Sequence at Lower pH
Proteorhodopsin (PR) is an outward
light-driven proton pump observed
in marine eubacteria. Despite many structural and functional similarities
to bacteriorhodopsin (BR) in archaea, which also acts as an outward
proton pump, the mechanism of the photoinduced proton release and
uptake is different between two H<sup>+</sup>-pumps. In this study,
we investigated the pH dependence of the photocycle and proton transfer
in PR reconstituted with the phospholipid membrane under alkaline
conditions. Under these conditions, as the medium pH increased, a
blue-shifted photoproduct (defined as M<sub>a</sub>), which is different
from M, with a p<i>K</i><sub>a</sub> of ca. 9.2 was produced.
The sequence of the photoinduced proton uptake and release during
the photocycle was inverted with the increase in pH. A p<i>K</i><sub>a</sub> value of ca. 9.5 was estimated for this inversion and
was in good agreement with the p<i>K</i><sub>a</sub> value
of the formation of M<sub>a</sub> (∼9.2). In addition, we measured
the photoelectric current generated by PRs attached to a thin polymer
film at varying pH. Interestingly, increases in the medium pH evoked
bidirectional photocurrents, which may imply a possible reversal of
the direction of the proton movement at alkaline pH. On the basis
of these findings, a putative photocycle and proton transfer scheme
in PR under alkaline pH conditions was proposed