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

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
Protein Folding01:22

Protein Folding

Overview
Determination of Crystal Structures01:29

Determination of Crystal Structures

In the late 1800s, the revelation that light extended beyond visible wavelengths led to the discovery of X-rays by Wilhelm Roentgen. Recognized as high-energy electromagnetic radiation with short wavelengths, X-rays prompted exploration into their interaction with crystals. Max von Laue proposed in 1912 that the periodic arrangement of atoms, ions, or molecules in crystals would cause them to diffract X-rays, a hypothesis confirmed through experiments with copper sulfate and zinc sulfide...
Conformations of Cyclohexane02:11

Conformations of Cyclohexane

Cyclohexane does not exist in a planar form due to the high angle and torsional strain it would experience in the planar structure. Instead, it adopts non-planar chair and boat conformations.
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal tetrahedral value,...

You might also read

Related Articles

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

Sort by
Same author

Insilico study to unveil the characteristics of pseudoRab GTPases in pathogenic protozoan parasites: <i>Entamoeba histolytica</i>.

In silico pharmacology·2026
Same author

ResMap: A community resource for systematic mapping of therapy-persistent residual cancer cell dependencies across contexts.

Science advances·2026
Same author

<i>In silico</i>, structural and functional characterization of Asp-175 and Phe-169 to regulate catalytic efficiency of NAD synthetase in MRSA.

Journal of biomolecular structure & dynamics·2026
Same author

Targeting bacitracin resistance-associated histidine kinase (BraS) in MRSA with isatin and indazole derivatives.

Scientific reports·2026
Same author

Influence of SmpB and ClpX interactions and interactomes on the transcription profile of Mycobacterium tuberculosis.

The Biochemical journal·2026
Same author

Macromolecular crystallography at Elettra: current and future perspectives. Corrigendum.

Journal of synchrotron radiation·2026

Related Experiment Video

Updated: May 20, 2026

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

Analysis of conformational variation in macromolecular structural models.

Sandeep Kumar Srivastava1, Savitha Gayathri, Babu A Manjasetty

  • 1Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India. sandeep@mbu.iisc.ernet.in

Plos One
|July 19, 2012
PubMed
Summary

Protein structural models vary due to experimental conditions and interacting components. Analyzing sequence and environmental factors reveals conformational selection, improving in silico dynamic information extraction.

More Related Videos

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
09:15

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

Published on: January 10, 2018

Related Experiment Videos

Last Updated: May 20, 2026

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

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
09:15

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

Published on: January 10, 2018

Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Macromolecular structural models can vary based on experimental conditions and interacting components.
  • In silico methods often overlook these factors when extracting dynamic information from protein structures.
  • Modeling large complexes from individual components is limited by context-dependent structural differences.

Purpose of the Study:

  • To analyze variations in structural models of proteins with high sequence similarity.
  • To investigate the influence of sequence features, scaffolding segments, and experimental conditions on protein structure.
  • To rationalize conformational features through conformational selection events.

Main Methods:

  • Analysis of non-redundant protein structure dataset from various SCOP classes.
  • Examination of sequence features, interacting proteins, affinity tags, and chemical components.
  • Correlation of sequence and conformational features.

Main Results:

  • Variations in protein structural models are influenced by sequence, scaffolding, and experimental conditions.
  • Conformational features can be explained by conformational selection, potentially induced by experimental settings.
  • Identified sequence-conformation correlations offer insights into protein dynamics.

Conclusions:

  • Experimental conditions and interacting components significantly impact macromolecular structural models.
  • In silico methods should incorporate sequence-conformation correlations for improved dynamic information extraction.
  • Conformational selection plays a key role in observed structural variations.