Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Regulation of Nuclear Protein Sorting01:45

Regulation of Nuclear Protein Sorting

2.3K
Nuclear protein sorting regulates nucleus composition and gene expression, crucial for determining the fate of a eukaryotic cell. Hence, the entry and exit of molecules across the nuclear envelope is a tightly controlled process. Nuclear protein sorting can be inhibited by one of the following ways: 1) masking cargo signal sequences, 2) modifying the nuclear receptor's affinity for cargo, 3) controlling the nuclear pore size, 4) retaining the cargo during its transit to the cytosol or the...
2.3K
Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

5.7K
Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
5.7K
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

1.6K
1.6K
GPCRs Regulate Adenylyl Cylase Activity01:09

GPCRs Regulate Adenylyl Cylase Activity

5.1K
Some GPCRs transmit signals through adenylyl cyclase (AC), a transmembrane enzyme. AC helps synthesize second messenger cyclic adenosine monophosphate (cAMP). AC catalyzes cyclization reaction and converts ATP to cAMP by releasing a pyrophosphate. The pyrophosphate is further hydrolyzed to phosphate by the enzyme pyrophosphatase, which drives cAMP synthesis to completion. However, cAMP is rapidly degraded to 5′ AMP by the enzymes phosphodiesterase (PDE), preventing overstimulation of...
5.1K
Regulation of the Unfolded Protein Response01:31

Regulation of the Unfolded Protein Response

2.4K
Inositol-requiring kinase one or IRE1 is the most conserved eukaryotic unfolded protein response (UPR) receptor. It is a type I transmembrane protein kinase receptor with a distinctive site-specific RNase activity. As the binding mechanics of the misfolded proteins with the N-terminal domain of IRE-1 are unclear, three binding models — direct, indirect, and allosteric -- are proposed for receptor activation. Nevertheless, it is known that once a misfolded protein associates with IRE1, it...
2.4K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

9.6K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
9.6K

You might also read

Related Articles

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

Sort by
Same author

Discovery, Structural Characterization, and Preclinical Evaluation of Monoclonal Antibodies against Xylazine Poisoning.

ACS pharmacology & translational science·2026
Same author

Selective targeting of human TREX1 exonuclease by small molecule inhibitors is mediated by a conformational switch.

NAR molecular medicine·2026
Same author

Polarity and anti-distortive polarons in WO<sub>3</sub> through epitaxial shear strain.

Nature communications·2026
Same author

Collapsing retroviruses for efficient delivery of viro-toxic cargoes.

bioRxiv : the preprint server for biology·2026
Same author

Structural and Functional Characterization of Heterologous Nitrogenase Complexes.

Biochemistry·2026
Same author

Full-length structure of the anti-viral and pro-tumor DNA deaminase APOBEC3B.

bioRxiv : the preprint server for biology·2026

Related Experiment Video

Updated: May 21, 2025

Analysis of SCAP N-glycosylation and Trafficking in Human Cells
11:27

Analysis of SCAP N-glycosylation and Trafficking in Human Cells

Published on: November 8, 2016

8.6K

Regulatory Interactions between APOBEC3B N- and C-Terminal Domains.

Mac Kevin E Braza1, Özlem Demir1, Surl-Hee Ahn2

  • 1Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States.

Journal of Chemical Information and Modeling
|March 19, 2025
PubMed
Summary

Full-length APOBEC3B (A3B) dynamics were modeled, revealing that NTD-CTD interactions promote active site opening. This structural insight into A3B offers potential cancer therapeutic targets.

More Related Videos

Identifying Protein-protein Interaction Sites Using Peptide Arrays
07:44

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

17.9K
Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

6.6K

Related Experiment Videos

Last Updated: May 21, 2025

Analysis of SCAP N-glycosylation and Trafficking in Human Cells
11:27

Analysis of SCAP N-glycosylation and Trafficking in Human Cells

Published on: November 8, 2016

8.6K
Identifying Protein-protein Interaction Sites Using Peptide Arrays
07:44

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

17.9K
Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

6.6K

Area of Science:

  • Biochemistry
  • Structural Biology
  • Cancer Research

Background:

  • APOBEC3B (A3B) contributes to DNA mutations driving tumor evolution.
  • While individual domains of A3B are structurally characterized, the full-length protein's (fl-A3B) structure and dynamics remain unclear.
  • The C-terminal domain (A3Bctd) is often depicted in a closed conformation.

Purpose of the Study:

  • To elucidate the structural dynamics of full-length APOBEC3B (fl-A3B).
  • To investigate the mechanism of fl-A3B active site opening.
  • To identify potential druggable sites on fl-A3B for cancer therapy.

Main Methods:

  • Integrative structural biology for fl-A3B modeling.
  • Conventional and Gaussian accelerated molecular dynamics (MD) simulations.
  • Weighted ensemble methods to study active site dynamics.

Main Results:

  • A top model of fl-A3B was generated and analyzed for dynamics.
  • Comparison of A3Bctd and fl-A3B dynamics revealed distinct behaviors.
  • NTD-CTD interface interactions were found to increase fl-A3B active site opening frequency.

Conclusions:

  • The study provides insights into the dynamic mechanisms of fl-A3B.
  • Observed active and allosteric sites suggest potential for therapeutic targeting.
  • Understanding A3B dynamics may open new avenues for cancer treatment.