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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.

Protein and Protein Structures

Protein and Protein Structures

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 can...

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 can...

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Related Experiment Video

Updated: May 21, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

SAS-Pro: simultaneous residue assignment and structure superposition for protein structure alignment.

Shweta B Shah¹, Nikolaos V Sahinidis

¹Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.

|June 5, 2012

Summary

This summary is machine-generated.

SAS-Pro simultaneously aligns protein structures and evaluates residue assignments, improving similarity measures. This novel bilevel optimization approach enables non-sequential protein alignments, outperforming existing tools.

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Area of Science:

Computational Biology
Structural Bioinformatics
Biophysics

Background:

Protein structure alignment is crucial for understanding protein function by identifying geometric similarities.
Current methods use a two-stage approach, separating assignment evaluation and structure superposition.
This sequential decoupling limits the scope of alignment, particularly for non-sequential protein structures.

Purpose of the Study:

To introduce SAS-Pro, a novel approach for simultaneous protein structure alignment and residue assignment.
To generalize protein alignment methodology to include non-sequential alignments.
To improve the accuracy and length of protein structure alignments.

Main Methods:

Formulated protein structure alignment as a single bilevel optimization problem.
Addressed assignment evaluation and structure superposition simultaneously, removing sequentiality constraints.
Employed derivative-free optimization for the nonlinear RMSD (Root Mean Square Deviation) function.

Main Results:

SAS-Pro achieved better RMSD values and longer alignment lengths compared to existing tools.
The method successfully performed non-sequential protein alignments.
Alignments generated by SAS-Pro showed high similarity to known reference alignments for non-sequential cases.

Conclusions:

SAS-Pro offers a generalized and more effective approach to protein structure alignment.
Simultaneous optimization enhances alignment quality and extends applicability to non-sequential structures.
The source code for SAS-Pro is publicly available for further research and application.