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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 Organization

Protein Organization

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.

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...

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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Related Experiment Video

Updated: Jul 10, 2026

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

Topology independent protein structural alignment.

Joe Dundas¹, T A Binkowski, Bhaskar DasGupta

¹Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607-7053, USA. jdunda1@uic.edu

BMC Bioinformatics

|October 17, 2007

Summary

This summary is machine-generated.

This study introduces a novel algorithm for protein structure alignment, enabling the discovery of previously unknown circular and non-cyclic permutations. The method accurately identifies structurally similar proteins despite topological differences and sequence order variations.

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Last Updated: Jul 10, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

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Published on: November 3, 2011

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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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

Area of Science:

* Structural bioinformatics
* Computational biology
* Protein structure analysis

Background:

* Identifying proteins with similar structures but different topologies is crucial for understanding protein folding, evolution, and design.
* Existing methods struggle with complex topological rearrangements like circular permutations and non-cyclic permutations.
* Sequence-order independent alignment is needed to overcome limitations of traditional structural alignment methods.

Purpose of the Study:

* To develop an approximation algorithm for sequence-order independent protein structure alignment.
* To identify novel instances of circular and non-cyclic permutations in protein structures.
* To create a method robust to insertions, deletions, gaps, and topological variations.

Main Methods:

* Formulated protein structure alignment as a maximum-weight independent set problem.
* Employed an approximation algorithm by iteratively solving relaxations of an integer programming problem.
* Utilized a novel similarity score and statistical model for p-value significance.

Main Results:

* Discovered novel circular permutations between nucleoplasmin-core and auxin binding proteins, and aspartate racemase and 3-dehydrogenate dehydratase.
* Identified circular permutation with strand-swapping between migration inhibition factor and arginine repressor.
* Found naturally occurring non-cyclic permuted protein structures between AML1/core binding factor and riboflavin synthase.

Conclusions:

* The approximation algorithm effectively solves protein structure alignment problems, even with topological differences.
* The method successfully detected structural similarities despite significant spatial rearrangement, as shown in the MIF-arginine repressor alignment.
* The discovery of previously unknown circular and non-cyclic permutations validates the algorithm's effectiveness for large-scale, topology-agnostic protein structure alignment.