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Protein Organization

Protein Organization

Protein Organization

Protein Organization

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

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 Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

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.

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Updated: Jul 6, 2026

Analyzing Large Protein Complexes by Structural Mass Spectrometry

Analyzing Large Protein Complexes by Structural Mass Spectrometry

Published on: June 19, 2010

Multiple alignment tensors from a denatured protein.

Erika B Gebel¹, Ke Ruan, Joel R Tolman

¹Department of Biological Chemistry, Johns Hopkins University, School of Medicine,1915 East Madison, Baltimore, Maryland 21205, USA.

Journal of the American Chemical Society

|July 20, 2006

Summary

This summary is machine-generated.

Researchers studied the residual structure of denatured nuclease using residual dipolar couplings (RDCs). Analysis revealed at least three independent alignment tensors, indicating an asymmetric ensemble average structure in the denatured state.

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Area of Science:

Biophysics
Structural Biology
Protein Dynamics

Background:

The structural characterization of denatured protein states remains incomplete.
Residual dipolar couplings (RDCs) provide insights into protein structure under specific alignment conditions.

Purpose of the Study:

To further elucidate the residual structure of denatured nuclease.
To quantify the number of independent alignment tensors in denatured nuclease using RDC measurements.

Main Methods:

Collection of backbone amide 15N-1H RDCs from nuclease in 4 M urea across eight datasets.
Analysis of RDC data using singular value decomposition (SVD) to determine alignment tensor dimensionality.

Main Results:

SVD analysis indicated the presence of at least three independent alignment tensors.
Orthogonal linear combination (OLC)-RDC datasets confirmed the robustness of these three tensors.
The RDC data spanned three or more dimensions, suggesting asymmetry in the ensemble average structure.

Conclusions:

The denatured state of nuclease exhibits an ensemble average structure with at least three dimensions of asymmetry.
These findings are consistent with previous observations of a nativelike topology in denatured nuclease.