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Protein Organization

Protein Organization

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 Organization

Protein Organization

Protein Organization

Protein Organization

Protein and Protein Structure

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...

RNA Structure

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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Related Experiment Video

Updated: Apr 14, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Tertiary structural propensities reveal fundamental sequence/structure relationships.

Fan Zheng¹, Jian Zhang², Gevorg Grigoryan³

¹Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA.

Structure (London, England : 1993)

|April 28, 2015

Summary

This summary is machine-generated.

This study introduces a novel "structure score" to assess protein model accuracy using local tertiary structural motifs (TERMs). This method effectively identifies poorly predicted regions and offers insights into protein structures.

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Area of Science:

Structural biology
Computational biology
Biophysics

Background:

The Protein Data Bank (PDB) is a vast resource for understanding protein structures.
Extracting quantitative generalizations from the PDB is crucial for advancing structural biology.
Local tertiary structural motifs (TERMs) represent fundamental building blocks of protein architecture.

Purpose of the Study:

To investigate the potential of TERMs within the PDB for quantitative analysis.
To develop a novel metric, the "structure score," for evaluating protein structure compatibility with amino acid sequences.
To assess the utility of TERM-based analysis for predicting protein model accuracy and gaining structural insights.

Main Methods:

Decomposition of protein structures into constituent TERMs.
Querying the PDB to characterize natural ensembles corresponding to each TERM.
Calculating a "structure score" based on TERM compatibility with a given amino acid sequence.
Validation using data from Critical Assessment of Structure Prediction (CASP) experiments.

Main Results:

A strong correlation (R = 0.69) was observed between the "structure score" and model accuracy in CASP predictions.
Poorly predicted regions in protein models were readily identifiable using this metric.
TERM-based analysis provided rapid structural insights for multi-state proteins, consistent with experimental data.
The performance of the "structure score" surpassed leading atomistic statistical energy functions.

Conclusions:

TERM-based analysis offers a valuable approach for extracting quantitative information from the PDB.
The "structure score" is a promising metric for assessing protein model quality and identifying inaccuracies.
This methodology has considerable utility for protein structural biology research and applications.