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

Unrealistic Optimism Bias01:30

Unrealistic Optimism Bias

239
Unrealistic optimism bias is the tendency to overestimate the likelihood of positive outcomes. This cognitive bias makes individuals believe they are less likely to experience failures, setbacks, or risks and more likely to succeed than others. For example, people may assume they are less prone to health issues, accidents, or financial struggles than their peers, even when they share similar risk factors.One key component of this bias is the above-average effect, where individuals perceive...
239
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

8.8K
Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
8.8K
Conformity01:20

Conformity

48.2K
Conformity is the change in a person’s behavior to go along with the group, even if that person does not agree with the group.
48.2K
Properties of Transition Metals02:58

Properties of Transition Metals

29.9K
Transition metals are defined as those elements that have partially filled d orbitals. As shown in Figure 1, the d-block elements in groups 3–12 are transition elements. The f-block elements, also called inner transition metals (the lanthanides and actinides), also meet this criterion because the d orbital is partially occupied before the f orbitals.
29.9K
Confirmation Biases01:31

Confirmation Biases

8.2K
The confirmation bias is the tendency to focus on information that confirms our existing beliefs and ignore information that is inconsistent with our expectations. For example, if you think that your professor is not very nice, you notice all of the instances of rude behavior exhibited by the professor while ignoring the countless pleasant interactions he is involved in on a daily basis. Have you ever fallen prey to the confirmation bias, either as the source or target of such bias?
8.2K
Mean free path and Mean free time01:22

Mean free path and Mean free time

5.2K
Consider the gas molecules in a cylinder. They move in a random motion as they collide with each other and change speed and direction. The average of all the path lengths between collisions is known as the "mean free path."
5.2K

You might also read

Related Articles

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

Sort by
Same author

Deep Receptor Scanning Reveals General Sequence Constraints on GPCR Biosynthesis.

bioRxiv : the preprint server for biology·2025
Same author

NMR-Guided Studies to Establish the Binding Interaction between a Peptoid and Protein.

Journal of the American Chemical Society·2025
Same author

An electrostatic network with strong connectivity is a phospho-sensor for regulating affinity of Syk-receptor association.

Proceedings of the National Academy of Sciences of the United States of America·2025
Same author

Protein-Sequence-Based Search of Nonreceptor ITAM-Like Regions to Identify Cytosolic Syk-Recruiting Proteins.

The journal of physical chemistry. B·2024
Same author

CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.

The journal of physical chemistry. B·2024
Same author

Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases.

Nature communications·2024

Related Experiment Video

Updated: Feb 5, 2026

High-Pressure NMR Experiments for Detecting Protein Low-Lying Conformational States
04:37

High-Pressure NMR Experiments for Detecting Protein Low-Lying Conformational States

Published on: June 29, 2021

3.2K

Protein Conformational Transitions from All-Atom Adaptively Biased Path Optimization.

Heng Wu1, Carol Beth Post1

  • 1Department of Medicinal Chemistry and Molecular Pharmacology, Markey Center for Structural Biology, Purdue Center for Cancer Research , Purdue University , West Lafayette , Indiana 47907 , United States.

Journal of Chemical Theory and Computation
|September 18, 2018
PubMed
Summary
This summary is machine-generated.

Adaptively biased path optimization (ABPO) now successfully maps all-atom protein conformational transitions. This computational method efficiently identifies optimal pathways, advancing our understanding of protein dynamics.

More Related Videos

Monitoring Conformational Dynamics of Single Unmodified Proteins using Plasmonic Nanotweezers
09:33

Monitoring Conformational Dynamics of Single Unmodified Proteins using Plasmonic Nanotweezers

Published on: March 21, 2025

1.4K
Differential Scanning Calorimetry — A Method for Assessing the Thermal Stability and Conformation of Protein Antigen
08:13

Differential Scanning Calorimetry — A Method for Assessing the Thermal Stability and Conformation of Protein Antigen

Published on: March 4, 2017

40.3K

Related Experiment Videos

Last Updated: Feb 5, 2026

High-Pressure NMR Experiments for Detecting Protein Low-Lying Conformational States
04:37

High-Pressure NMR Experiments for Detecting Protein Low-Lying Conformational States

Published on: June 29, 2021

3.2K
Monitoring Conformational Dynamics of Single Unmodified Proteins using Plasmonic Nanotweezers
09:33

Monitoring Conformational Dynamics of Single Unmodified Proteins using Plasmonic Nanotweezers

Published on: March 21, 2025

1.4K
Differential Scanning Calorimetry — A Method for Assessing the Thermal Stability and Conformation of Protein Antigen
08:13

Differential Scanning Calorimetry — A Method for Assessing the Thermal Stability and Conformation of Protein Antigen

Published on: March 4, 2017

40.3K

Area of Science:

  • Computational Biology
  • Biophysics
  • Structural Biology

Background:

  • Protein conformational transitions are crucial for function but experimentally challenging to capture.
  • High free energy barriers necessitate specialized computational algorithms for studying these transitions.
  • Adaptively biased path optimization (ABPO) is a method designed to overcome these barriers.

Purpose of the Study:

  • To evaluate the effectiveness of ABPO at an all-atom resolution for protein conformational transitions.
  • To explore the conformational changes in three distinct protein systems using ABPO.

Main Methods:

  • Utilized Adaptively Biased Path Optimization (ABPO) with an all-atom model.
  • Identified reduced variables (distance-based or torsion-angle) from unbiased trajectories for each protein.
  • Computed ABPO within the identified reduced variable space to determine transition paths.

Main Results:

  • Successfully constructed all-atom conformational transition paths for triose phosphate isomerase, dihydrofolate reductase, and estrogen receptor α ligand binding domain.
  • Demonstrated ABPO's capability to converge optimal transition paths for proteins with loop flipping and helix conformational changes.
  • Validated the application of ABPO at higher resolution for exploring complex protein dynamics.

Conclusions:

  • All-atom ABPO is a robust methodology for elucidating protein conformational transitions.
  • The study successfully mapped transition paths for diverse protein systems, including those involved in ligand binding and receptor activation.
  • This approach significantly advances the computational study of protein dynamics and functional mechanisms.