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

Nucleic Acid Structure01:25

Nucleic Acid Structure

5.9K
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
5.9K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.7K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.7K
Conserved Binding Sites01:49

Conserved Binding Sites

4.1K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.1K
Molecular Geometry and Dipole Moments02:36

Molecular Geometry and Dipole Moments

12.4K
The VSEPR theory can be used to determine the electron pair geometries and molecular structures as follows:
12.4K
Molecular Structure and Acidity02:34

Molecular Structure and Acidity

16.7K
An acid can be deprotonated to form a conjugate base or an anion. If the produced anion is more stable, then the acid is stronger. On the contrary, if the anion is unstable, then the acid is weaker. Hence, to determine the acidity of the compound, the stability of its conjugate base is studied using various factors.
The size effect explains the change in atomic size on acidity. When comparing the acids formed from elements that belong to the same column in the periodic table, their atomic sizes...
16.7K
VSEPR Theory and the Basic Shapes02:52

VSEPR Theory and the Basic Shapes

67.3K
Overview of VSEPR Theory
67.3K

You might also read

Related Articles

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

Sort by
Same author

LCK-targeting molecular glues overcome resistance to inhibitor-based therapy in T-cell acute lymphoblastic leukemia.

Blood·2026
Same author

Development of a Lysine-Reactive Targeted Covalent Inhibitor for the P300/CBP-Associated Factor Bromodomain Through Structure-Based Design.

ChemMedChem·2026
Same author

Direct-to-Biology Enabled Molecular Glue Discovery.

Journal of the American Chemical Society·2025
Same author

Unfreezing structural biology for drug discovery.

Nature chemical biology·2025
Same author

An experimental proxy of water displaceability for ligand discovery.

Nature methods·2025
Same author

Development of Receptor Desolvation Scoring and Covalent Sampling in DOCK 6: Methods Evaluated on a RAS Test Set.

Journal of chemical information and modeling·2025
Same journal

Towards light-coupled sample preparation for time-resolved cryoEM studies.

IUCrJ·2026
Same journal

Cryo-EM analysis of cooperative conformational changes in the SARS-CoV-2 spike protein trimer.

IUCrJ·2026
Same journal

Towards time-resolved MicroED grid preparation using mix-and-inject gas dynamic virtual nozzles.

IUCrJ·2026
Same journal

How cryoEM has advanced our understanding of bacteriophages and bacteriocins targeting Clostridioides difficile.

IUCrJ·2026
Same journal

CryoEM structures reveal allosteric regulation of the catalytic activity of the multi-protein human MAT enzyme complexes.

IUCrJ·2026
Same journal

Cryo-EM-guided subtractive optimization of a novel VCP/p97 inhibitor.

IUCrJ·2026
See all related articles

Related Experiment Video

Updated: May 25, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

15.3K

FLEXR-MSA: electron-density map comparisons of sequence-diverse structures.

Timothy R Stachowski1, Marcus Fischer1

  • 1Department of Chemical Biology and Therapeutics, MS 1000, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.

Iucrj
|February 27, 2025
PubMed
Summary
This summary is machine-generated.

FLEXR-MSA enables comparing diverse protein structures using electron-density maps. This tool reveals unique protein dynamics and conformational differences, aiding in the design of selective ligands.

Keywords:
HSP90dynamicselectron-density samplingisoformsligand discoveryprotein conformational landscape

More Related Videos

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

1.2K
Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

20.5K

Related Experiment Videos

Last Updated: May 25, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

15.3K
Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

1.2K
Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

20.5K

Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Comparing protein crystal structures is often limited by deposited model biases.
  • Unique protein dynamics are frequently concealed within electron-density maps.
  • Current automated methods for map comparison are restricted to sequence-identical proteins.

Purpose of the Study:

  • To develop a method for unbiased electron-density map comparison of sequence-diverse protein structures.
  • To visualize and analyze unique protein dynamics and alternative conformations.
  • To aid in the design of selective ligands by revealing structural differences.

Main Methods:

  • Coupling multiple sequence alignment (MSA) with electron-density sampling.
  • Developing FLEXR-MSA for unbiased map comparisons.
  • Applying FLEXR-MSA to human HSP90 isoforms and homologs.

Main Results:

  • FLEXR-MSA enables visualization of low-occupancy features and global conformational changes.
  • The tool successfully revealed hidden differences in HSP90 variants bound to ligands.
  • Analysis highlighted protein-wide alternative conformations across different HSP90 isoforms.

Conclusions:

  • FLEXR-MSA overcomes limitations in comparing sequence-diverse protein structures.
  • The tool provides insights into conformational landscapes and structural/functional differences.
  • This facilitates the development of targeted drug design strategies for selective ligands.