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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: Oct 26, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

An automated iterative approach for protein structure refinement using pseudocontact shifts.

Stefano Cucuzza¹, Peter Güntert^2,3,4, Andreas Plückthun⁵

¹Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.

Journal of Biomolecular NMR

|August 2, 2021

Summary

This study introduces an automated method for protein structure refinement using limited backbone amide pseudocontact shifts (PCSs). This approach enables accurate structure calculation for complex proteins where sidechain assignments are challenging.

Keywords:

Armadillo repeat protein NMR Pseudocontact shift Structure refinement

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Last Updated: Oct 26, 2025

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Published on: July 14, 2015

Area of Science:

Biochemistry
Structural Biology
Nuclear Magnetic Resonance (NMR) Spectroscopy

Background:

NMR structure calculation traditionally relies on Nuclear Overhauser Effect (NOE) distance restraints, demanding extensive backbone and sidechain resonance assignments.
Pseudocontact shifts (PCSs) are valuable for NMR protein structure calculation, often augmenting NOE data.
Existing PCS-based refinement protocols frequently require numerous sidechain assignments or additional experimental restraints.

Purpose of the Study:

To develop an automated iterative procedure for backbone protein structure refinement.
To reduce the reliance on extensive sidechain assignments in NMR structure determination.
To enable structure calculation for proteins where traditional methods are difficult.

Main Methods:

An automated iterative procedure was developed for backbone protein structure refinement.
The method utilizes a limited set of backbone amide PCSs.
Known structural features from homology models are incorporated into a scaffold refined by experimental PCSs.

Main Results:

The procedure successfully refines protein structures using only limited backbone amide PCSs.
The method was applied to designed Armadillo repeat proteins (dArmRPs), where sidechain assignments are difficult.
The solution NMR structure of YM4A, a dArmRP, was calculated with high convergence to a single structure.

Conclusions:

This automated approach is particularly useful for refining structures when approximate folds are known from other techniques like X-ray crystallography.
It avoids potential artifacts associated with crystal packing.
The method offers a robust alternative for determining structures of challenging protein systems.