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Related Concept Videos

Electron Transport Chains01:28

Electron Transport Chains

The final stage of cellular respiration is oxidative phosphorylation that consists of two steps: the electron transport chain and chemiosmosis. The electron transport chain is a set of proteins found in the inner mitochondrial membrane in eukaryotic cells. Its primary function is to establish a proton gradient that can be used during chemiosmosis to produce ATP and generate electron carriers, such as NAD+ and FAD, that are used in glycolysis and the citric acid cycle.
The ETC is comprised of...
Electron Behavior00:54

Electron Behavior

Overview
Electrons are negatively charged subatomic particles that are attracted to an orbit around the positively-charged nucleus of an atom. They reside in locations that are associated with energy levels called shells and are further organized into sub-shells and orbitals within each shell.
Electrons Orbit the Nucleus
Electrons are found in specific locations outside of the nucleus. The shell in which an electron resides indicates the general energy level of the electron: those closer to the...
Electron Transport Chain Components01:29

Electron Transport Chain Components

The electron transport chain (ETC) is a crucial metabolic pathway that facilitates energy conversion in prokaryotic and eukaryotic cells. In eukaryotes, the ETC comprises four membrane-associated protein complexes in the inner mitochondrial membrane. In prokaryotes, the ETC in the plasma membrane can vary in composition, with fewer or different complexes depending on the organism and environmental conditions. These complexes transfer electrons from electron donors, such as NADH and FADH2, to...
Electron Transport Chain: Complex I and II01:46

Electron Transport Chain: Complex I and II

The mitochondrial electron transport chain (ETC) is the main energy generation system in the eukaryotic cells. However, mitochondria also produce cytotoxic reactive oxygen species (ROS) due to the large electron flow during oxidative phosphorylation. While Complex I is one of the primary sources of superoxide radicals, ROS production by Complex II is uncommon and may only be observed in cancer cells with mutated complexes.
ROS generation is regulated and maintained at moderate levels necessary...
Electron Transport Chain: Complex III and IV01:43

Electron Transport Chain: Complex III and IV

During the electron transport chain, electrons from NADH and FADH2 are first transferred to complexes I and II, respectively. These two complexes then transfer the electrons to ubiquinol, which carries them further to complex III. Complex III passes the electrons across the intermembrane space to Cyt c, which carries them further to complex IV. Complex IV donates electrons to oxygen and reduces it to water. As electrons pass through complexes I, III, and IV, the energy released aids the pumping...
π Electron Effects on Chemical Shift: Overview01:27

π Electron Effects on Chemical Shift: Overview

An applied magnetic field causes loosely bound π-electrons in organic molecules to circulate, producing a local or induced diamagnetic field over a large spatial volume. As the molecules tumble in solution, the field generated by π-electrons in spherical substituents results in a zero net field. However, the net field generated by π-electrons in non-spherical substituents is not zero. The effect of this induced field depends on the orientation of the molecule with respect to B0, resulting in...

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A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Exploring biological electron transfer pathway dynamics with the Pathways plugin for VMD.

Ilya A Balabin1, Xiangqian Hu, David N Beratan

  • 1Department of Chemistry, Duke University, Durham, North Carolina 27708, USA. ilya.balabin@duke.edu

Journal of Computational Chemistry
|February 3, 2012
PubMed
Summary
This summary is machine-generated.

A new Pathways plugin for visual molecular dynamics aids in identifying and visualizing biomolecular tunneling pathways and electronic couplings. It offers unique features for analyzing atom importance and thermal motion sensitivity.

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Area of Science:

  • Computational chemistry
  • Molecular dynamics
  • Biophysics

Background:

  • Understanding electron transfer in biomolecules is crucial for various biological processes.
  • Molecular visualization tools are essential for studying complex molecular structures and dynamics.
  • Identifying tunneling pathways and electronic couplings provides insights into molecular mechanisms.

Purpose of the Study:

  • To introduce the new Pathways plugin for the visual molecular dynamics software.
  • To enable identification and visualization of tunneling pathways and pathway families in biomolecules.
  • To facilitate the calculation of relative electronic couplings and analyze their properties.

Main Methods:

  • Development of the Pathways plugin for visual molecular dynamics.
  • Implementation of algorithms for identifying and visualizing tunneling pathways.
  • Integration of methods for calculating relative electronic couplings.
  • Addition of features for analyzing atomic contributions and thermal sensitivity.

Main Results:

  • The Pathways plugin successfully identifies and visualizes tunneling pathways in biomolecules.
  • Relative electronic couplings can be calculated and analyzed using the plugin.
  • Novel features allow estimation of atomic importance and analysis of coupling sensitivity to thermal motion.
  • Visualization of pathway fluctuations provides dynamic insights.

Conclusions:

  • The Pathways plugin is a valuable addition to molecular visualization, enhancing the study of tunneling pathways and electronic couplings.
  • Its unique features offer deeper insights into the mechanisms of electron transfer in biomolecules.
  • The open-source nature of the plugin promotes accessibility and further development in the scientific community.