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Protein Organization01:24

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 Organization01:13

Protein Organization

Overview
Protein Organization01:13

Protein Organization

Overview
Protein Organization01:24

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 Proteins02:26

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 and Protein Structure02:15

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: Jun 20, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

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

Published on: July 14, 2015

Algorithms for optimal protein structure alignment.

Aleksandar Poleksic1

  • 1Department of Computer Science, University of Northern Iowa, Cedar Falls, IA 50614, USA. poleksic@cs.uni.edu

Bioinformatics (Oxford, England)
|September 8, 2009
PubMed
Summary

This study introduces a novel method to optimize protein structural similarity measures, proving it

Area of Science:

  • Computational Biology
  • Structural Bioinformatics

Background:

  • Protein structural alignment is crucial for evolutionary relationship analysis.
  • The structural alignment problem is computationally challenging due to infinite superposition possibilities.
  • Unlike sequence alignment, structural alignment's solvability remains unclassified.

Purpose of the Study:

  • To optimize a widely used measure of protein structural similarity.
  • To develop algorithms for optimizing other structure similarity measures.
  • To present a polynomial time algorithm for near-optimal protein superposition.

Main Methods:

  • Investigated a similarity measure based on superimposed residue pairs within a distance cutoff.
  • Proved that this measure is optimizable for most distance cutoffs.

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Related Experiment Videos

Last Updated: Jun 20, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

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

Published on: July 14, 2015

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

  • Developed a polynomial time algorithm for near-optimal superposition with provable quality.

    • Main Results:

    • Demonstrated that a key protein structural similarity measure can be optimized for any two proteins.
    • The proposed method yields algorithms for various structure similarity measures.
    • A near-optimal superposition algorithm with guaranteed quality was developed.

    Conclusions:

    • The study provides a significant advancement in optimizing protein structural similarity.
    • The developed algorithms can enhance protein structure prediction experiments.
    • The near-optimal algorithm offers a practical solution with verifiable accuracy.