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

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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...

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

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.

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

Protein Folding

Protein Folding

Protein Folding

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

You might also read

Related Articles

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

Sort by

Same author

RNA-binding protein transcripts reflect composition of target mRNAs.

Nucleic acids research·2026

Same author

Dynamic yet well-defined organization of the FUS RGG3 dense phase.

Communications chemistry·2026

Same author

Translon: a single term for translated regions.

Nature methods·2025

Same author

PHLPP2 is a pseudophosphatase that lost activity in the metazoan ancestor.

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

Same author

A new view of missense mutations in α-mannosidosis using molecular dynamics conformational ensembles.

Protein science : a publication of the Protein Society·2025

Same author

CFAP410 has a bimodular architecture with a conserved surface patch on its N-terminal leucine-rich repeat motif for binding interaction partners.

Frontiers in cell and developmental biology·2025

Search research articles

Related Experiment Video

Updated: Jun 17, 2026

Averaging of Viral Envelope Glycoprotein Spikes from Electron Cryotomography Reconstructions using Jsubtomo

Averaging of Viral Envelope Glycoprotein Spikes from Electron Cryotomography Reconstructions using Jsubtomo

Published on: October 21, 2014

Conformational averaging in structural biology: issues, challenges and computational solutions.

Daniela Kruschel¹, Bojan Zagrovic

¹Laboratory of Computational Biophysics, Mediterranean Institute for Life Sciences, Mestrovicevo setaliste bb, Split, HR-21000, Croatia.

Molecular Biosystems

|December 22, 2009

Summary

Structural biology experiments often yield averaged data, creating idealized models. This review questions how well these models reflect reality and the impact of averaging artifacts on understanding molecular function.

More Related Videos

Optimized Negative Staining: a High-throughput Protocol for Examining Small and Asymmetric Protein Structure by Electron Microscopy

Optimized Negative Staining: a High-throughput Protocol for Examining Small and Asymmetric Protein Structure by Electron Microscopy

Published on: August 15, 2014

Related Experiment Videos

Last Updated: Jun 17, 2026

Averaging of Viral Envelope Glycoprotein Spikes from Electron Cryotomography Reconstructions using Jsubtomo

Averaging of Viral Envelope Glycoprotein Spikes from Electron Cryotomography Reconstructions using Jsubtomo

Published on: October 21, 2014

Optimized Negative Staining: a High-throughput Protocol for Examining Small and Asymmetric Protein Structure by Electron Microscopy

Optimized Negative Staining: a High-throughput Protocol for Examining Small and Asymmetric Protein Structure by Electron Microscopy

Published on: August 15, 2014

Area of Science:

Structural Biology
Biophysics
Computational Biology

Background:

Experimental methods in structural biology typically provide time- and ensemble-averaged signals.
This averaging leads to molecular structures that often display idealized, average features rather than true dynamic states.
Experimental signals are indirectly related to molecular geometries, and structure determination can lack uniqueness.

Purpose of the Study:

To critically assess the accuracy of conformationally-averaged structural models derived from experimental data.
To investigate whether averaging artifacts can artificially bias the observation of certain structural motifs.
To explore the practical consequences of ignoring averaging effects on functional and mechanistic interpretations.

Main Methods:

Review of common structural biology experimental techniques (NMR, X-ray crystallography, spectroscopy).
Analysis of the susceptibility of these methods to conformational (motional) averaging.
Discussion of theoretical approaches, particularly molecular dynamics simulations, for interpreting experimental data.

Main Results:

Experimental methods inherently average structural and dynamic information.
Averaging can lead to misrepresentation of true molecular conformations and potentially introduce artifacts.
Molecular dynamics simulations are valuable tools for dissecting averaging effects and improving structural model interpretation.

Conclusions:

Conformationally-averaged models may not fully represent microscopic reality in structural biology.
Ignoring averaging effects can have significant consequences for understanding molecular mechanisms and function.
Integrating computational methods like molecular dynamics is crucial for accurate interpretation of experimental structural data.