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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...

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

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Related Experiment Video

Updated: Jul 10, 2026

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

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

Published on: July 14, 2015

A comprehensive analysis of non-sequential alignments between all protein structures.

Alexej Abyzov¹, Valentin A Ilyin

¹Department of Biology, Northeastern University 360 Huntington Avenue, Boston, MA 02115, USA. abyzov@mozart.bio.neu.edu

BMC Structural Biology

|November 17, 2007

Summary

This summary is machine-generated.

Non-sequential protein alignments are common, not rare exceptions. This study reveals they are widespread across protein structures, suggesting a fundamental organizational principle.

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Last Updated: Jul 10, 2026

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

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An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

Structural bioinformatics
Protein structure analysis
Computational biology

Background:

Most protein relationships are sequential alignments.
Non-sequential alignments with varied fragment connectivity are observed.
The frequency and distribution of non-sequential alignments are poorly understood.

Purpose of the Study:

To conduct a large-scale investigation of non-sequential protein alignments.
To determine if non-sequential alignments are frequent or sporadic.
To assess their prevalence across different protein folds.

Main Methods:

Analysis of a non-redundant set of 8,865 protein structures.
Utilized the TOPOFIT method for structural alignment.
Systematic evaluation of alignment fragment connectivity and complexity.

Main Results:

Estimated 17.4%–35.2% of alignments are non-sequential.
Non-sequential alignments occur systematically and in large numbers.
Found across over 200 protein folds, including those with different fold assignments.

Conclusions:

Non-sequential protein alignments are a widespread phenomenon.
This suggests a potentially missing organizational rule in protein structures.
Further study can improve understanding of protein stability, folding, and evolution.