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Related Experiment Video

Updated: May 25, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Inter-domain movements in polyketide synthases: a molecular dynamics study.

Swadha Anand¹, Debasisa Mohanty

¹National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India.

Molecular Biosystems

|January 28, 2012

Summary

Modular polyketide synthases (PKS) are crucial for producing pharmaceuticals. Molecular dynamics simulations show limited domain movement, suggesting intrinsically disordered linkers may facilitate substrate transfer in polyketide biosynthesis.

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Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

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Published on: January 16, 2016

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Last Updated: May 25, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

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Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

Published on: January 16, 2016

Area of Science:

Biochemistry
Structural Biology
Computational Chemistry

Background:

Modular polyketide synthases (PKS) are vital for synthesizing pharmaceutically important secondary metabolites.
Understanding PKS structure and dynamics is key to elucidating polyketide biosynthesis mechanisms.

Purpose of the Study:

Investigate inter-domain movements in KS-AT di-domains of PKS.
Clarify the role of these movements in substrate channeling during polyketide biosynthesis.

Main Methods:

Performed explicit solvent molecular dynamics (MD) simulations (10-15 ns) on KS-AT di-domains and sub-fragments.
Analyzed MD trajectories to assess domain flexibility and inter-domain interface dynamics.

Main Results:

Catalytic domains and linker regions showed limited movement from starting structures.
Inter-domain movements occurred around hinge regions, with the KS-linker interface being more flexible than linker-AT.
Simulated movements did not significantly reduce the distance between KS and AT catalytic centers for substrate channeling.

Conclusions:

Inter-domain movements alone may not facilitate efficient substrate channeling in the studied PKS domains.
Intrinsically unstructured linkers preceding the ACP domain are proposed to facilitate ACP domain movement to catalytic centers.