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

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...

Newman Projections

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.

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...

2D NMR: Overview of Homonuclear Correlation Techniques

2D NMR: Overview of Homonuclear Correlation Techniques

Homonuclear correlation spectroscopy (COSY) is a powerful technique used in Nuclear Magnetic Resonance (NMR) spectroscopy to study the correlations between nuclei of the same type within a molecule. It provides information about scalar couplings between adjacent nuclei, which helps determine connectivity and structural information. There are several COSY variants, each with its unique strengths and experimental parameters.
COSY90 is the standard two-dimensional (2D) COSY experiment that...

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.

Protein Folding

Protein Folding

You might also read

Related Articles

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

Sort by

Same author

ProMeta: a meta-learning framework for robust disease diagnosis and prediction from plasma proteomics.

Bioinformatics (Oxford, England)·2026

Same author

Towards the construction of a virtual yeast.

Nature·2026

Same author

How is agentic AI changing how we do science?

Cell systems·2026

Same author

Atlas of predicted protein complex structures across kingdoms.

Nature communications·2026

Same author

DeepRCI: predicting RNA-chromatin interactions via deep learning with multi-omics data.

Quantitative biology (Beijing, China)·2026

Same author

<i>CCK</i> * (Convex Closure <i>K</i> *): A Suite of Algorithms for the De Novo Design of L- and D-peptide Binders.

bioRxiv : the preprint server for biology·2025

Search research articles

Related Experiment Video

Updated: Jun 21, 2026

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

A Hausdorff-based NOE assignment algorithm using protein backbone determined from residual dipolar couplings and

Jianyang Zeng¹, Chittaranjan Tripathy, Pei Zhou

¹Department of Computer Science, Duke University, Durham, NC 27708, USA.

Computational Systems Bioinformatics. Computational Systems Bioinformatics Conference

|August 1, 2009

Summary

This study introduces HANA, a novel algorithm for Nuclear Magnetic Resonance (NMR) data analysis. HANA improves automated NOE assignment, overcoming spectral noise to achieve high accuracy in protein structure determination.

More Related Videos

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D ¹H NMR

Published on: December 16, 2013

Related Experiment Videos

Last Updated: Jun 21, 2026

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D ¹H NMR

Published on: December 16, 2013

Area of Science:

Biophysics
Structural Biology
Computational Biology

Background:

High-throughput protein structure determination using Nuclear Magnetic Resonance (NMR) spectroscopy is crucial for structural genomics.
Automated assignment of Nuclear Overhauser Effect (NOE) spectral peaks is a major bottleneck due to resonance degeneracy and experimental uncertainties.
Accurate NOE assignment is essential for deriving distance restraints and determining protein structures.

Purpose of the Study:

To develop a novel algorithm for automated NOE assignment in NMR spectroscopy.
To address challenges posed by spectral noise and resonance degeneracy in NOE assignment.
To improve the accuracy and efficiency of protein structure determination using NMR data.

Main Methods:

Introduced the HAusdorff-based NOE Assignment (HANA) algorithm.
Utilized a Hausdorff-based pattern matching technique for NOE spectral similarity analysis.
Integrated residual dipolar couplings (RDCs) for initial protein backbone computation and rotamer selection for filtering assignments.

Main Results:

Achieved over 90% NOE assignment accuracy on biological NMR data for human ubiquitin, pol eta, and hSRI.
The HANA algorithm effectively overcomes spectral noise.
Final protein structures determined using HANA showed low RMSD values (<1.7 Å backbone, <2.5 Å all-heavy-atom) compared to reference structures.

Conclusions:

The HANA algorithm significantly enhances automated NOE assignment in NMR spectroscopy.
It enables the determination of high-quality protein structures from noisy spectral data.
HANA represents a valuable tool for structural genomics and protein structure determination.