9 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
National trends in the outcomes of subarachnoid haemorrhage and the prognostic influence of stroke centre capability in Japan: retrospective cohort study
Objectives To examine the national, 6-year trends in in-hospital clinical outcomes of patients with subarachnoid haemorrhage (SAH) who underwent clipping or coiling and the prognostic influence of temporal trends in the Comprehensive Stroke Center (CSC) capabilities on patient outcomes in Japan.Design Retrospective study.Setting Six hundred and thirty-one primary care institutions in Japan.Participants Forty-five thousand and eleven patients with SAH who were urgently hospitalised, identified using the J-ASPECT Diagnosis Procedure Combination database.Primary and secondary outcome measures Annual number of patients with SAH who remained untreated, or who received clipping or coiling, in-hospital mortality and poor functional outcomes (modified Rankin Scale: 3–6) at discharge. Each CSC was assessed using a validated scoring system (CSC score: 1–25 points).Results In the overall cohort, in-hospital mortality decreased (year for trend, OR (95% CI): 0.97 (0.96 to 0.99)), while the proportion of poor functional outcomes remained unchanged (1.00 (0.98 to 1.02)). The proportion of patients who underwent clipping gradually decreased from 46.6% to 38.5%, while that of those who received coiling and those left untreated gradually increased from 16.9% to 22.6% and 35.4% to 38%, respectively. In-hospital mortality of coiled (0.94 (0.89 to 0.98)) and untreated (0.93 (0.90 to 0.96)) patients decreased, whereas that of clipped patients remained stable. CSC score improvement was associated with increased use of coiling (per 1-point increase, 1.14 (1.08 to 1.20)) but not with short-term patient outcomes regardless of treatment modality.Conclusions The 6-year trends indicated lower in-hospital mortality for patients with SAH (attributable to better outcomes), increased use of coiling and multidisciplinary care for untreated patients. Further increasing CSC capabilities may improve overall outcomes, mainly by increasing the use of coiling. Additional studies are necessary to determine the effect of confounders such as aneurysm complexity on outcomes of clipped patients in the modern endovascular era