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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 Folding

Protein Folding

Protein Folding

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

Protein Folding

Protein Folding

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

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Related Experiment Video

Updated: May 17, 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

Inferences from structural comparison: flexibility, secondary structure wobble and sequence alignment optimization.

Gaihua Zhang¹, Zhen Su

¹State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100094, People's Republic of China.

BMC Bioinformatics

|October 11, 2012

Summary

This summary is machine-generated.

Protein structures are not rigid and exhibit flexibility, impacting their reliability as a gold standard for evaluating protein structure prediction methods. Optimization of derived data is crucial for accurate assessment.

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Last Updated: May 17, 2026

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

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Published on: July 14, 2015

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

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

Published on: July 16, 2017

Area of Science:

Structural biology
Computational biology
Biophysics

Background:

Protein structure prediction is vital for biological research.
Experimental structures are the gold standard for evaluating prediction accuracy.
Protein flexibility challenges the reliability of this gold standard.

Purpose of the Study:

To investigate the influence of protein structure flexibility on the reliability of experimental structures as a gold standard.
To assess the variability in protein structures and derived data.

Main Methods:

Analysis of 3,652 protein structures from 137 unique sequences across 24 protein families.
Calculation of root-mean-square deviation (RMSD) for backbone Cα atoms.
Evaluation of secondary structure wobble and sequence alignment variability.

Main Results:

Protein structures are not rigid, with an average maximum RMSD of 1.06 Å for identical sequences.
Derived structural data is not constant; secondary structure wobble can reach 60.69%.
Sequence alignments from structural comparisons of proteins within the same family can differ significantly.

Conclusions:

Proteins can adopt multiple stable conformations.
Data derived from resolved structures require optimization before use as a gold standard for evaluating prediction methods.
Helix/beta-sheet transitions and coil ratios influence X-ray crystallography resolution.