Related Experiment Video
Updated: Feb 15, 2026
06:37
Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
Published on: September 17, 2021
5.1K
Two-step relaxation mode analysis with multiple evolution times applied to all-atom molecular dynamics protein
N Karasawa1, A Mitsutake1, H Takano1
1Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan.
Physical Review. E
|January 20, 2018
Summary
This study refines protein dynamics analysis using a two-step relaxation mode analysis (RMA) method. The enhanced technique improves the accuracy of estimating protein structural fluctuations and relaxation times.
Area of Science:
- Biophysics
- Computational Biology
- Protein Dynamics
Background:
- Protein function is intrinsically linked to its 3D structure and dynamic behavior.
- Relaxation mode analysis (RMA) has been used to study protein dynamics and structural fluctuations.
- Previous RMA methods provided approximate estimations of slow relaxation modes and times.
Purpose of the Study:
- To enhance the accuracy of estimating protein relaxation modes and times.
- To apply an improved two-step RMA method to complex protein systems.
- To investigate the dynamic properties of hen egg-white lysozyme.
Main Methods:
- Principal Component Analysis (PCA) applied to a 2-μs molecular dynamics simulation of hen egg-white lysozyme.
- Two-step Relaxation Mode Analysis (RMA) with multiple evolution times applied to PCA results.
- Iterative refinement of slow relaxation modes and their corresponding times.
Main Results:
- The two-step RMA method significantly improved the accuracy of estimating relaxation modes and times for protein principal components.
- The refined analysis provided a more precise characterization of the slow dynamic motions within the protein.
- Application to hen egg-white lysozyme demonstrated the method's effectiveness on complex heteropolymer systems.
Conclusions:
- The two-step RMA with multiple evolution times offers a more accurate approach for analyzing protein dynamics.
- This enhanced method is suitable for complex heteropolymer systems, including proteins.
- Improved understanding of protein dynamics can be achieved through this refined computational technique.
More Related Videos
Related Concept Videos
01:28Atomic Nuclei: Types of Nuclear Relaxation
1.0K
Nuclear relaxation restores the equilibrium population imbalance and can occur via spin–lattice or spin–spin mechanisms, which are first-order exponential decay processes.
In spin–lattice or longitudinal relaxation, the excited spins exchange energy with the surrounding lattice as they return to the lower energy level. Among several mechanisms that contribute to spin–lattice relaxation, magnetic dipolar interactions are significant. Here, the excited nucleus transfers...
In spin–lattice or longitudinal relaxation, the excited spins exchange energy with the surrounding lattice as they return to the lower energy level. Among several mechanisms that contribute to spin–lattice relaxation, magnetic dipolar interactions are significant. Here, the excited nucleus transfers...
1.0K
01:23Atomic Nuclei: Nuclear Relaxation Processes
1.3K
In the absence of an external magnetic field, nuclear spin states are degenerate and randomly oriented. When a magnetic field is applied, the spins begin to precess and orient themselves along (lower energy) or against (higher energy) the direction of the field. At equilibrium, a slight excess population of spins exists in the lower energy state. Because the direction of the magnetic field is fixed as the z-axis, the precessing magnetic moments are randomly oriented around the z-axis.
1.3K
02:24Regulation of Expression Occurs at Multiple Steps
26.6K
Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
26.6K
02:24Regulation of Expression Occurs at Multiple Steps
4.0K
4.0K
01:23Regulation of Expression at Multiple Steps
1.4K
The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
1.4K
01:54Convergent Evolution
33.1K
Evolution shapes the features of organisms over time, ensuring that they are suited for the environments in which they live. Sometimes, selection pressure leads to the rise of similar but unrelated adaptations in organisms with no recent common ancestors, a process known as convergent evolution.
33.1K