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Related Concept Videos

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...
Conserved Binding Sites01:49

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...
Conserved Binding Sites01:49

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...
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 Organization01:24

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.

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Related Experiment Video

Updated: May 23, 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

Evolutionary information hidden in a single protein structure.

Chien-Hua Shih1, Chih-Min Chang, Yeong-Shin Lin

  • 1Institute of Bioinformatics, National Chiao Tung University, HsinChu 30050, Taiwan, Republic of China.

Proteins
|March 29, 2012
PubMed
Summary
This summary is machine-generated.

Protein structure

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Last Updated: May 23, 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

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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Published on: July 16, 2017

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Conserved sequences in proteins are crucial for identifying functionally or structurally important residues.
  • Generating sequence conservation profiles typically requires aligning homologous sequences and understanding evolutionary relationships.

Purpose of the Study:

  • To investigate if protein sequence conservation profiles can be quantitatively derived from a single protein structure.
  • To explore the relationship between structural characteristics and sequence conservation.

Main Methods:

  • Utilizing only backbone information from a single protein structure.
  • Calculating reciprocal packing density profiles.
  • Comparing structural profiles with sequence conservation profiles.

Main Results:

  • Reciprocal packing density profiles closely resemble sequence conservation profiles.
  • For 74% of 554 nonhomologous enzymes, the correlation coefficient between these profiles exceeded 0.5.
  • Protein structure significantly influences evolutionary constraints on residues.

Conclusions:

  • Quantitative derivation of residue-level conservation profiles is possible from a single protein structure.
  • Protein three-dimensional structure imposes strong evolutionary constraints, reflecting structural characteristics in sequence conservation.
  • Structural information offers a novel approach to understanding protein evolution and function.