Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Allosteric Proteins-ATCase

Allosteric Proteins-ATCase

Binding sites linkages can regulate a protein's function. For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...

Amino Acid Catabolism

Amino Acid Catabolism

Microorganisms rely on proteins as an essential carbon and energy source, particularly in environments with limited polysaccharides or lipids. However, proteins are too large to cross the plasma membrane unaided, necessitating enzymatic degradation. Microbes secrete extracellular proteases and peptidases that hydrolyze proteins into peptides, which can then be transported across the membrane. Once inside the cell, intracellular proteases degrade these peptides into free amino acids, which...

Transition State Theory

Transition State Theory

Transition-state theory, also known as activated-complex theory, provides a molecular-level explanation of reaction rates in both gas-phase and solution-phase reactions. It extends earlier kinetic models by considering the formation of a short-lived, high-energy configuration during a reaction.The progress of a chemical reaction can be represented using a reaction profile, which plots potential energy against the reaction coordinate. As two reactant molecules approach one another, their...

ATP Synthase: Mechanism

ATP Synthase: Mechanism

In animals, the mitochondrial F1F0 ATP synthase is the key protein that synthesizes ATP molecules through a complex catalytic mechanism. While the nuclear genome encodes the majority of ATP synthase subunits, the mitochondrial genome encodes some of the enzyme's most critical components. The formation of this multi-subunit enzyme is a complex multi-step process regulated at the level of transcription, translation, and assembly. Defects in one or more of these steps can result in decreased ATP...

The ADP/ATP Carrier Protein

The ADP/ATP Carrier Protein

ADP/ATP carrier or AAC protein is the most abundant carrier protein in the inner mitochondrial membrane. It transports large quantities of ADP and ATP, equivalent to the average human body weight, every day. Among other transporters, ACC protein is one of the best-studied members of the mitochondrial carrier protein family. The ADP/ATP carrier protein comprises two transmembrane helices connected to a loop and a single alpha-helix on the matrix side. It switches between two conformational...

tRNA Activation

tRNA Activation

Aminoacyl-tRNA synthetases are present in both eukaryotes and bacteria. Though eukaryotes have 20 different aminoacyl-tRNA synthetases to couple to 20 amino acids, many bacteria do not have genes for all of these aminoacyl-tRNA synthetases. Despite this, they still use all 20 amino acids to synthesize their proteins. For instance, some bacteria do not have the gene encoding the enzyme that couples glutamine with its partner tRNA. In these organisms, one enzyme adds glutamic acid to all of the...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

hexABC seeking the physical code of DNA.

Nature communications·2026

Same author

Decoding Cancer-Associated Mutations in DNA Polymerase η through Atomistic Simulations.

Journal of chemical theory and computation·2026

Same author

Structural and functional role of the magnesium ion in the human oxytocin receptor.

Journal of inorganic biochemistry·2026

Same author

pH-dependent structural dynamics of neuropeptide Y in aqueous solution.

PloS one·2026

Same author

Protonation-dependent substrate release in a bacterial homolog of vesicular glutamate.

Biophysical journal·2026

Same author

Exploring elastin-like polypeptide tags and mini-intein for recombinant protein purification in Leishmaniatarentolae.

Protein expression and purification·2026

Search research articles

Related Experiment Video

Updated: Jul 17, 2026

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

Catabolite activator protein in aqueous solution: a molecular simulation study.

Marco Berrera¹, Sergio Pantano, Paolo Carloni

¹Scuola Internazionale Superiore di Studi Avanzati (SISSA) and INFM, Democritos Modeling Center for Research In Atomistic Simulation, via Beirut 4, 34014 Trieste, Italy.

The Journal of Physical Chemistry. B

|January 25, 2007

Summary

The catabolite activator protein (CAP) in solution adopts a symmetric structure, differing from its X-ray conformation. This symmetric form may be crucial for DNA binding and transcription regulation in bacteria.

More Related Videos

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Published on: May 20, 2020

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations

Published on: April 26, 2024

Related Experiment Videos

Last Updated: Jul 17, 2026

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

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Published on: May 20, 2020

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations

Published on: April 26, 2024

Area of Science:

Molecular Biology
Structural Biology
Biophysics

Background:

Catabolite activator protein (CAP) is a crucial bacterial transcription regulator.
CAP activity is modulated by cyclic adenosine monophosphate (cAMP) binding.
Each CAP subunit comprises cyclic nucleotide and DNA-binding domains.

Purpose of the Study:

To investigate the structural features of ligand-bound CAP in aqueous solution.
To compare the solution structure with available X-ray crystallographic data.
To elucidate the role of CAP's solution conformation in DNA recognition.

Main Methods:

Molecular dynamics simulations.
Utilized existing X-ray crystallographic structures as a basis.
Electrostatics calculations.

Main Results:

Simulations suggest a symmetric arrangement of the homodimeric CAP in solution.
This symmetric conformation features separated DNA-binding and cyclic nucleotide-binding domains.
The solution structure contrasts with the asymmetric conformation observed in X-ray crystallography.

Conclusions:

The symmetric structure of CAP in solution may be essential for effective DNA molecular recognition.
This finding offers insights into the mechanism of transcription regulation by CAP.
Highlights the importance of considering solution dynamics in structural biology.