Source 1primary paper2017Protein Science
Toolkit/molecular dynamics simulation
molecular dynamics simulation
Also known as: MD, MD simulation, noninvasive molecular dynamics simulation technique
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Molecular dynamics simulation is a computational method for modeling atomistic conformational dynamics of proteins and analyzing residue fluctuations and vibrational behavior. In the cited studies, it was used as a noninvasive approach to validate dynamic behavior and to compare PAS-domain dynamics across functional groups.
Usefulness & Problems
Why this is useful
This method is useful for linking protein motion to biological function without perturbing the system experimentally. In the PAS-domain study, it enabled comparison of conserved-residue fluctuations and vibrational patterns across functional groups and supported inference of function-associated dynamic signatures.
Source:
the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function
Source:
The result showed that the proteins with same function could be grouped by sequence similarity
Problem solved
It addresses the problem of characterizing protein structural dynamics and relating residue-level motion to functional divergence when static sequence or structure analysis alone is insufficient. The cited evidence specifically shows its use in distinguishing PAS functional groups by fluctuation and vibrational pattern differences.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete computational method used to design, rank, or analyze an engineered system.
Mechanisms
atomistic conformational dynamics simulationresidue fluctuation analysisvibrational pattern analysisTarget processes
No target processes tagged yet.
Implementation Constraints
The evidence indicates implementation as a noninvasive computational simulation technique applied to protein systems, including PAS domains and LOV-TAP. The supplied material does not specify software, force fields, hardware requirements, trajectory lengths, or input structure preparation details.
The supplied evidence is limited to computational analyses in PAS-domain proteins and a computer simulation study of LOV-TAP, with no direct evidence here for experimental benchmarking or broad cross-system validation. No quantitative details on simulation protocols, force fields, timescales, or predictive accuracy are provided in the supplied material.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Source 2primary paper2012Proteins Structure Function and Bioinformatics
Ranked Claims
Across the three PAS functional groups, residues conserved by sequence and structure analyses generally had lower fluctuation than other residues.
in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues
Across the three PAS functional groups, residues conserved by sequence and structure analyses generally had lower fluctuation than other residues.
in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues
Across the three PAS functional groups, residues conserved by sequence and structure analyses generally had lower fluctuation than other residues.
in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues
Across the three PAS functional groups, residues conserved by sequence and structure analyses generally had lower fluctuation than other residues.
in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues
Across the three PAS functional groups, residues conserved by sequence and structure analyses generally had lower fluctuation than other residues.
in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues
Across the three PAS functional groups, residues conserved by sequence and structure analyses generally had lower fluctuation than other residues.
in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues
Across the three PAS functional groups, residues conserved by sequence and structure analyses generally had lower fluctuation than other residues.
in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues
Different PAS functional groups displayed statistically significant differences in vibrational patterns.
proteins in different functional groups displayed statistically significant difference in their vibrational patterns
Different PAS functional groups displayed statistically significant differences in vibrational patterns.
proteins in different functional groups displayed statistically significant difference in their vibrational patterns
Different PAS functional groups displayed statistically significant differences in vibrational patterns.
proteins in different functional groups displayed statistically significant difference in their vibrational patterns
Different PAS functional groups displayed statistically significant differences in vibrational patterns.
proteins in different functional groups displayed statistically significant difference in their vibrational patterns
Different PAS functional groups displayed statistically significant differences in vibrational patterns.
proteins in different functional groups displayed statistically significant difference in their vibrational patterns
Different PAS functional groups displayed statistically significant differences in vibrational patterns.
proteins in different functional groups displayed statistically significant difference in their vibrational patterns
Different PAS functional groups displayed statistically significant differences in vibrational patterns.
proteins in different functional groups displayed statistically significant difference in their vibrational patterns
Within the PAS domain superfamily, proteins with the same function could be grouped by sequence similarity.
The result showed that the proteins with same function could be grouped by sequence similarity
Within the PAS domain superfamily, proteins with the same function could be grouped by sequence similarity.
The result showed that the proteins with same function could be grouped by sequence similarity
Within the PAS domain superfamily, proteins with the same function could be grouped by sequence similarity.
The result showed that the proteins with same function could be grouped by sequence similarity
Within the PAS domain superfamily, proteins with the same function could be grouped by sequence similarity.
The result showed that the proteins with same function could be grouped by sequence similarity
Within the PAS domain superfamily, proteins with the same function could be grouped by sequence similarity.
The result showed that the proteins with same function could be grouped by sequence similarity
Within the PAS domain superfamily, proteins with the same function could be grouped by sequence similarity.
The result showed that the proteins with same function could be grouped by sequence similarity
Within the PAS domain superfamily, proteins with the same function could be grouped by sequence similarity.
The result showed that the proteins with same function could be grouped by sequence similarity
In each PAS biological function group, fluctuation of conserved residues was strongly correlated with the corresponding biological function.
the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function
In each PAS biological function group, fluctuation of conserved residues was strongly correlated with the corresponding biological function.
the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function
In each PAS biological function group, fluctuation of conserved residues was strongly correlated with the corresponding biological function.
the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function
In each PAS biological function group, fluctuation of conserved residues was strongly correlated with the corresponding biological function.
the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function
In each PAS biological function group, fluctuation of conserved residues was strongly correlated with the corresponding biological function.
the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function
In each PAS biological function group, fluctuation of conserved residues was strongly correlated with the corresponding biological function.
the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function
In each PAS biological function group, fluctuation of conserved residues was strongly correlated with the corresponding biological function.
the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
LOV-TAP is an artificial protein construct in which AsLOV2-Jα is ligated to TrpR.
the artificial protein construct light-oxygen-voltage (LOV)-tryptophan-activated protein (TAP), in which the LOV-2-Jα photoswitch of phototropin1 from Avena sativa (AsLOV2-Jα) has been ligated to the tryptophan-repressor (TrpR) protein from Escherichia coli
LOV-TAP is an artificial protein construct in which AsLOV2-Jα is ligated to TrpR.
the artificial protein construct light-oxygen-voltage (LOV)-tryptophan-activated protein (TAP), in which the LOV-2-Jα photoswitch of phototropin1 from Avena sativa (AsLOV2-Jα) has been ligated to the tryptophan-repressor (TrpR) protein from Escherichia coli
LOV-TAP is an artificial protein construct in which AsLOV2-Jα is ligated to TrpR.
the artificial protein construct light-oxygen-voltage (LOV)-tryptophan-activated protein (TAP), in which the LOV-2-Jα photoswitch of phototropin1 from Avena sativa (AsLOV2-Jα) has been ligated to the tryptophan-repressor (TrpR) protein from Escherichia coli
LOV-TAP is an artificial protein construct in which AsLOV2-Jα is ligated to TrpR.
the artificial protein construct light-oxygen-voltage (LOV)-tryptophan-activated protein (TAP), in which the LOV-2-Jα photoswitch of phototropin1 from Avena sativa (AsLOV2-Jα) has been ligated to the tryptophan-repressor (TrpR) protein from Escherichia coli
LOV-TAP is an artificial protein construct in which AsLOV2-Jα is ligated to TrpR.
the artificial protein construct light-oxygen-voltage (LOV)-tryptophan-activated protein (TAP), in which the LOV-2-Jα photoswitch of phototropin1 from Avena sativa (AsLOV2-Jα) has been ligated to the tryptophan-repressor (TrpR) protein from Escherichia coli
LOV-TAP is an artificial protein construct in which AsLOV2-Jα is ligated to TrpR.
the artificial protein construct light-oxygen-voltage (LOV)-tryptophan-activated protein (TAP), in which the LOV-2-Jα photoswitch of phototropin1 from Avena sativa (AsLOV2-Jα) has been ligated to the tryptophan-repressor (TrpR) protein from Escherichia coli
LOV-TAP is an artificial protein construct in which AsLOV2-Jα is ligated to TrpR.
the artificial protein construct light-oxygen-voltage (LOV)-tryptophan-activated protein (TAP), in which the LOV-2-Jα photoswitch of phototropin1 from Avena sativa (AsLOV2-Jα) has been ligated to the tryptophan-repressor (TrpR) protein from Escherichia coli
After photoexcitation, Cys450-FMN adduct formation in the AsLOV2-Jα binding pocket induces cleavage of the peripheral Jα-helix from the LOV core.
Cys450-FMN-adduct formation in the AsLOV2-Jα-binding pocket after photoexcitation induces the cleavage of the peripheral Jα-helix from the LOV core
After photoexcitation, Cys450-FMN adduct formation in the AsLOV2-Jα binding pocket induces cleavage of the peripheral Jα-helix from the LOV core.
Cys450-FMN-adduct formation in the AsLOV2-Jα-binding pocket after photoexcitation induces the cleavage of the peripheral Jα-helix from the LOV core
After photoexcitation, Cys450-FMN adduct formation in the AsLOV2-Jα binding pocket induces cleavage of the peripheral Jα-helix from the LOV core.
Cys450-FMN-adduct formation in the AsLOV2-Jα-binding pocket after photoexcitation induces the cleavage of the peripheral Jα-helix from the LOV core
After photoexcitation, Cys450-FMN adduct formation in the AsLOV2-Jα binding pocket induces cleavage of the peripheral Jα-helix from the LOV core.
Cys450-FMN-adduct formation in the AsLOV2-Jα-binding pocket after photoexcitation induces the cleavage of the peripheral Jα-helix from the LOV core
After photoexcitation, Cys450-FMN adduct formation in the AsLOV2-Jα binding pocket induces cleavage of the peripheral Jα-helix from the LOV core.
Cys450-FMN-adduct formation in the AsLOV2-Jα-binding pocket after photoexcitation induces the cleavage of the peripheral Jα-helix from the LOV core
After photoexcitation, Cys450-FMN adduct formation in the AsLOV2-Jα binding pocket induces cleavage of the peripheral Jα-helix from the LOV core.
Cys450-FMN-adduct formation in the AsLOV2-Jα-binding pocket after photoexcitation induces the cleavage of the peripheral Jα-helix from the LOV core
After photoexcitation, Cys450-FMN adduct formation in the AsLOV2-Jα binding pocket induces cleavage of the peripheral Jα-helix from the LOV core.
Cys450-FMN-adduct formation in the AsLOV2-Jα-binding pocket after photoexcitation induces the cleavage of the peripheral Jα-helix from the LOV core
In the dark state, the AsLOV2-Jα photoswitch exerts a repulsive electrostatic force on the DNA surface, leading to distortion of the hairpin region and disruption of LOV-TAP from DNA.
in the dark state the AsLOV2-Jα photoswitch remains inactive and exerts a repulsive electrostatic force on the DNA surface. This leads to a distortion of the hairpin region, which finally relieves its tension by causing the disruption of LOV-TAP from the DNA.
In the dark state, the AsLOV2-Jα photoswitch exerts a repulsive electrostatic force on the DNA surface, leading to distortion of the hairpin region and disruption of LOV-TAP from DNA.
in the dark state the AsLOV2-Jα photoswitch remains inactive and exerts a repulsive electrostatic force on the DNA surface. This leads to a distortion of the hairpin region, which finally relieves its tension by causing the disruption of LOV-TAP from the DNA.
In the dark state, the AsLOV2-Jα photoswitch exerts a repulsive electrostatic force on the DNA surface, leading to distortion of the hairpin region and disruption of LOV-TAP from DNA.
in the dark state the AsLOV2-Jα photoswitch remains inactive and exerts a repulsive electrostatic force on the DNA surface. This leads to a distortion of the hairpin region, which finally relieves its tension by causing the disruption of LOV-TAP from the DNA.
In the dark state, the AsLOV2-Jα photoswitch exerts a repulsive electrostatic force on the DNA surface, leading to distortion of the hairpin region and disruption of LOV-TAP from DNA.
in the dark state the AsLOV2-Jα photoswitch remains inactive and exerts a repulsive electrostatic force on the DNA surface. This leads to a distortion of the hairpin region, which finally relieves its tension by causing the disruption of LOV-TAP from the DNA.
In the dark state, the AsLOV2-Jα photoswitch exerts a repulsive electrostatic force on the DNA surface, leading to distortion of the hairpin region and disruption of LOV-TAP from DNA.
in the dark state the AsLOV2-Jα photoswitch remains inactive and exerts a repulsive electrostatic force on the DNA surface. This leads to a distortion of the hairpin region, which finally relieves its tension by causing the disruption of LOV-TAP from the DNA.
In the dark state, the AsLOV2-Jα photoswitch exerts a repulsive electrostatic force on the DNA surface, leading to distortion of the hairpin region and disruption of LOV-TAP from DNA.
in the dark state the AsLOV2-Jα photoswitch remains inactive and exerts a repulsive electrostatic force on the DNA surface. This leads to a distortion of the hairpin region, which finally relieves its tension by causing the disruption of LOV-TAP from the DNA.
In the dark state, the AsLOV2-Jα photoswitch exerts a repulsive electrostatic force on the DNA surface, leading to distortion of the hairpin region and disruption of LOV-TAP from DNA.
in the dark state the AsLOV2-Jα photoswitch remains inactive and exerts a repulsive electrostatic force on the DNA surface. This leads to a distortion of the hairpin region, which finally relieves its tension by causing the disruption of LOV-TAP from the DNA.
Light activation changes the polarity of the LOV photoswitch and promotes electrostatic attraction of LOV-TAP onto the DNA surface.
causing a change of its polarity and electrostatic attraction of the photoswitch onto the DNA surface
Light activation changes the polarity of the LOV photoswitch and promotes electrostatic attraction of LOV-TAP onto the DNA surface.
causing a change of its polarity and electrostatic attraction of the photoswitch onto the DNA surface
Light activation changes the polarity of the LOV photoswitch and promotes electrostatic attraction of LOV-TAP onto the DNA surface.
causing a change of its polarity and electrostatic attraction of the photoswitch onto the DNA surface
Light activation changes the polarity of the LOV photoswitch and promotes electrostatic attraction of LOV-TAP onto the DNA surface.
causing a change of its polarity and electrostatic attraction of the photoswitch onto the DNA surface
Light activation changes the polarity of the LOV photoswitch and promotes electrostatic attraction of LOV-TAP onto the DNA surface.
causing a change of its polarity and electrostatic attraction of the photoswitch onto the DNA surface
Light activation changes the polarity of the LOV photoswitch and promotes electrostatic attraction of LOV-TAP onto the DNA surface.
causing a change of its polarity and electrostatic attraction of the photoswitch onto the DNA surface
Light activation changes the polarity of the LOV photoswitch and promotes electrostatic attraction of LOV-TAP onto the DNA surface.
causing a change of its polarity and electrostatic attraction of the photoswitch onto the DNA surface
Unfolding and flexibilization of the interdomain hairpin-like helix-loop-helix region enables condensation of LOV-TAP onto the DNA surface.
This goes along with the flexibilization through unfolding of a hairpin-like helix-loop-helix region interlinking the AsLOV2-Jα- and TrpR-domains, ultimately enabling the condensation of LOV-TAP onto the DNA surface.
Unfolding and flexibilization of the interdomain hairpin-like helix-loop-helix region enables condensation of LOV-TAP onto the DNA surface.
This goes along with the flexibilization through unfolding of a hairpin-like helix-loop-helix region interlinking the AsLOV2-Jα- and TrpR-domains, ultimately enabling the condensation of LOV-TAP onto the DNA surface.
Unfolding and flexibilization of the interdomain hairpin-like helix-loop-helix region enables condensation of LOV-TAP onto the DNA surface.
This goes along with the flexibilization through unfolding of a hairpin-like helix-loop-helix region interlinking the AsLOV2-Jα- and TrpR-domains, ultimately enabling the condensation of LOV-TAP onto the DNA surface.
Unfolding and flexibilization of the interdomain hairpin-like helix-loop-helix region enables condensation of LOV-TAP onto the DNA surface.
This goes along with the flexibilization through unfolding of a hairpin-like helix-loop-helix region interlinking the AsLOV2-Jα- and TrpR-domains, ultimately enabling the condensation of LOV-TAP onto the DNA surface.
Unfolding and flexibilization of the interdomain hairpin-like helix-loop-helix region enables condensation of LOV-TAP onto the DNA surface.
This goes along with the flexibilization through unfolding of a hairpin-like helix-loop-helix region interlinking the AsLOV2-Jα- and TrpR-domains, ultimately enabling the condensation of LOV-TAP onto the DNA surface.
Unfolding and flexibilization of the interdomain hairpin-like helix-loop-helix region enables condensation of LOV-TAP onto the DNA surface.
This goes along with the flexibilization through unfolding of a hairpin-like helix-loop-helix region interlinking the AsLOV2-Jα- and TrpR-domains, ultimately enabling the condensation of LOV-TAP onto the DNA surface.
Unfolding and flexibilization of the interdomain hairpin-like helix-loop-helix region enables condensation of LOV-TAP onto the DNA surface.
This goes along with the flexibilization through unfolding of a hairpin-like helix-loop-helix region interlinking the AsLOV2-Jα- and TrpR-domains, ultimately enabling the condensation of LOV-TAP onto the DNA surface.
Approval Evidence
2 sources1 linked approval claimfirst-pass slug molecular-dynamics-simulation
validated by molecular dynamics (MD) simulation
Source:
using the noninvasive molecular dynamics simulation technique
Source:
sequence structure dynamics function connectionsupports
The study suggests a direct connection in which protein sequences are related to functions through structural dynamics.
This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics
Source:
Comparisons
Source-backed strengths
The cited literature supports that MD can detect lower fluctuations in residues conserved by sequence and structure analyses and identify statistically significant differences in vibrational patterns among PAS functional groups. It also supported a strong correlation between conserved-residue fluctuation and biological function within each PAS function group.
Ranked Citations
- 1.
- 2.