Related Experiment Video

Updated: Aug 8, 2025

Biophysical Characterization of Flagellar Motor Functions
06:08

Biophysical Characterization of Flagellar Motor Functions

Published on: January 18, 2017

8.3K

Molecular Simulation to Investigate Open-Close Motion of a Flagellar Export Apparatus Protein FlhAC

Akio Kitao1

  • 1School of Life Science and Technology, Tokyo Institute of Technology, Meguro, Tokyo, Japan. akitao@bio.titech.ac.jp.

Methods in Molecular Biology (Clifton, N.J.)
|February 26, 2023
PubMed

Insights

Molecular dynamics simulations, including parallel cascade selection molecular dynamics (PaCS-MD), help study protein motions. Combining PaCS-MD with Markov state models (MSM) enables free energy calculations for proteins like FlhAC.

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Molecular dynamics (MD) simulations are essential for understanding protein dynamics.
  • Investigating large-amplitude protein motions requires enhanced sampling techniques.
  • The flagellar export apparatus protein, FlhAC, plays a crucial role in flagellar assembly.

Purpose of the Study:

  • To describe protocols for investigating the open-close motion of FlhAC.
  • To detail the application of MD and PaCS-MD for conformational sampling.
  • To explain the integration of PaCS-MD with Markov state models (MSM) for free energy calculations.

Main Methods:

  • Utilized standard Molecular Dynamics (MD) simulations.
  • Employed Parallel Cascade Selection Molecular Dynamics (PaCS-MD) for enhanced conformational sampling.
  • Combined PaCS-MD with Markov State Models (MSM) for free energy calculations.

Main Results:

  • Demonstrated protocols for simulating the large-amplitude open-close motion of FlhAC.
  • Showcased the effectiveness of PaCS-MD in exploring protein conformational landscapes.
  • Successfully integrated PaCS-MD and MSM to compute free energy landscapes.

Conclusions:

  • PaCS-MD is a powerful method for enhanced sampling of protein dynamics.
  • The combination of PaCS-MD and MSM provides a robust framework for free energy calculations.
  • These methods offer valuable insights into the functional mechanisms of proteins like FlhAC.
Keywords:
Free energy profileMarkov state modelMolecular dynamics simulationOpen–close motionParallel cascade selection molecular dynamics

More Related Videos

Myosin-Specific Adaptations of In vitro Fluorescence Microscopy-Based Motility Assays08:57

Myosin-Specific Adaptations of In vitro Fluorescence Microscopy-Based Motility Assays

Published on: February 4, 2021

6.0K
Using Microfluidics and Fluorescence Microscopy to Study the Assembly Dynamics of Single Actin Filaments and Bundles08:02

Using Microfluidics and Fluorescence Microscopy to Study the Assembly Dynamics of Single Actin Filaments and Bundles

Published on: May 5, 2022

2.7K

Related Concept Videos

Flagella and Motility in Bacteria01:18

Flagella and Motility in Bacteria

Flagella are specialized, thread-like structures that extend from a bacteria's cell envelope. They play a crucial role in motility and chemotaxis. Their structural organization and functioning exemplify sophisticated biological engineering, enabling bacterial survival and adaptability in diverse environments.Structure of the FlagellumA bacterial flagellum consists of three key components: the filament, the hook, and basal body. The filament, a long, helical structure composed of repeating...
134
Mechanism of Filopodia Formation01:39

Mechanism of Filopodia Formation

Filopodia are thin, actin-rich cellular protrusions that play an important role in many fundamental cellular functions. They vary in their occurrence, length, and positioning in different cell types, suggesting their diverse roles.
Their main function is to guide migrating cells during normal tissue morphogenesis or cancer metastasis by recognizing and making initial contacts with the extracellular matrix. However, they can also act as stationary cell anchors or help to establish communication...
2.4K
Actin Polymerization and Cell Motility01:13

Actin Polymerization and Cell Motility

Actin is a family of globular proteins that are highly abundant in eukaryotic cells. It makes up approximately 1-5% of total cell protein concentration. Actin monomers polymerize to form a complex network of polarized filaments, the actin cytoskeleton, that plays a crucial role in many cellular processes, including cell motility, division, endocytosis, and metastasis of cancer cells.
Actin cytoskeleton dynamics can produce pushing, pulling, and resistance forces that help the cell to migrate....
5.3K
Studying the Cytoskeleton01:17

Studying the Cytoskeleton

The cytoskeletal architecture can be studied using different microscopic and biochemical techniques. Electron microscopy was instrumental in discovering the cytoskeletal architecture around the 1960s, which allowed obtaining structural information at a high-resolution level. However, the sample preparation procedure often limits this ability in biological samples. Several protocols have been developed over the years to optimize sample preparation. In one of the protocols known as rotary...
6.4K