Related Experiment Video

Updated: Feb 6, 2026

An Effective Inoculation Method for Phytophthora capsici on Black Pepper Plants
08:58

An Effective Inoculation Method for Phytophthora capsici on Black Pepper Plants

Published on: September 16, 2022

4.0K

Twist, grind, translocate: pepper-mill dynamics of MSPA protein pore during ssDNA transport

Priya Dey1, Brandon Meza-González1, Ganesh N Pandian1

  • 1Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8501, Japan. dpackwood@icems.kyoto-u.ac.jp.

Physical Chemistry Chemical Physics : PCCP
|February 5, 2026
PubMed

Insights

We discovered a novel "pepper-mill" motion in Mycobacterium smegmatis porin A (MSPA) during DNA translocation. This finding advances understanding of nanopore sensing and DNA sequencing technologies.

Area of Science:

  • Biophysics
  • Computational Biology
  • Nanotechnology

Background:

  • DNA translocation through protein nanopores is vital for biological processes and DNA sequencing.
  • Mycobacterium smegmatis porin A (MSPA) is a promising nanopore for single-molecule sensing due to its structure.
  • The atomic-level mechanism of DNA interaction with MSPA's dynamic motions is not well understood.

Purpose of the Study:

  • To elucidate the mechanism of single-stranded DNA (ssDNA) translocation through the MSPA nanopore.
  • To investigate the coupling between DNA and the dynamic motions of the MSPA pore at the atomic scale.

Main Methods:

  • Atomistic molecular dynamics (MD) simulations.
  • Dimensionality reduction techniques.
  • Cross-correlation analyses of simulation data.

Main Results:

  • A previously unidentified "pepper-mill"-like motion of MSPA was observed during ssDNA translocation.
  • This collective domain motion significantly influences analyte-pore interactions and DNA passage dynamics.
  • A generalizable, data-driven strategy was developed for extracting mechanistic insights from complex biomolecular simulations.

Conclusions:

  • The identified MSPA motion is critical for regulating DNA translocation.
  • Data-driven computational approaches can provide valuable insights for nanopore engineering.
  • This work accelerates the development of advanced DNA sequencing and biosensing technologies.

More Related Videos

Analysis of Effect of Compound Salt Stress on Seed Germination and Salt Tolerance Analysis of Pepper Capsicum annuum L.08:27

Analysis of Effect of Compound Salt Stress on Seed Germination and Salt Tolerance Analysis of Pepper Capsicum annuum L.

Published on: November 30, 2022

5.3K
Membrane Transport Processes Analyzed by a Highly Parallel Nanopore Chip System at Single Protein Resolution11:55

Membrane Transport Processes Analyzed by a Highly Parallel Nanopore Chip System at Single Protein Resolution

Published on: August 16, 2016

12.1K

Related Concept Videos

Pore Transport and Ion-Pair Transport01:17

Pore Transport and Ion-Pair Transport

Pore transport and ion-pair formation are critical mechanisms for the absorption and distribution of drugs in the body.
Pore transport, also known as convective transport, is a process where small molecules like urea, water, and sugars rapidly cross cell membranes as though there were channels or pores in the membrane. Although direct microscopic evidence is limited  but the concept of pores or channels is widely accepted based on physiological evidence. Despite the lack of direct...
1.3K
Cotranslational Protein Translocation01:20

Cotranslational Protein Translocation

Translocation of proteins across membranes is an ancient process that occurs even in bacteria and archaebacteria. In fact, the components of the translocation machinery are still conserved between prokaryotes and eukaryotes.
Sec61 channel partners for cotranslational translocation
During cotranslational translocation, the Sec61 channel partners with the signal recognition particle (SRP), the signal recognition particle receptor (SR), and the ribosomes to transport the nascent polypeptide chain...
9.9K
Translocation of Proteins into the Mitochondria01:19

Translocation of Proteins into the Mitochondria

Mitochondrial precursors are translocated to the internal subcompartments via independent mechanisms involving distinct protein machineries called translocases.
Sorting of outer membrane proteins:
Mitochondrial outer membrane proteins are of two types: the transmembrane, beta-barrel porins, and the membrane-anchored, alpha-helical proteins. Beta-barrel porin precursors are translocated by the TOM complex and inserted into the outer mitochondrial membrane by the SAM complex. In contrast,...
13.5K
Phloem and Sugar Transport02:02

Phloem and Sugar Transport

Like many living organisms, plants have tissues that specialize in specific plant functions. For example, shoots are well adapted to rapid growth, while roots are structured to acquire resources efficiently. However, sugar production is primarily restricted to the photosynthetic cells that reside in the leaves of angiosperm plants. Sugar and other resources are transported from photosynthetic tissues to other specialized tissues by a process called translocation.
40.1K
Bacterial Translocation and Protein Secretion01:26

Bacterial Translocation and Protein Secretion

Bacterial protein secretion involves translocation systems to ensure proteins reach their designated locations, including the plasma membrane, periplasm, outer membrane, or the external environment. These translocation systems are vital for bacterial physiology, supporting processes like membrane assembly, enzymatic activity in the periplasm, and interactions with the external environment. The division of labor between Sec and Tat pathways ensures efficiency in handling proteins with diverse...
644
Protein Translocation Machinery on the ER Membrane01:28

Protein Translocation Machinery on the ER Membrane

The translocon complex situated on the ER membrane is the main gateway for the protein secretory pathway. It facilitates the transport of nascent peptides into the ER lumen and their insertion into the ER membrane.
Sec61 protein conducting channel
In eukaryotes, the translocon complex comprises a core heterotrimeric translocator channel called the Sec61 complex. This channel includes three transmembrane proteins, Sec61α, Sec61β, and Sec61γ, and is the largest subunit of the...
6.8K