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Related Concept Videos

Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
Structural Isomerism02:34

Structural Isomerism

Isomerism in Complexes
Isomers are different chemical species that have the same chemical formula. Structural isomerism of coordination compounds can be divided into two subcategories, the linkage isomers and coordination-sphere isomers.
Linkage isomers occur when the coordination compound contains a ligand that can bind to the transition metal center through two different atoms. For example, the CN− ligand can bind through the carbon atom or through the nitrogen atom. Similarly, SCN− can be...
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...

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Related Experiment Video

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Peptide-based Identification of Functional Motifs and their Binding Partners
14:28

Peptide-based Identification of Functional Motifs and their Binding Partners

Published on: June 30, 2013

Structural alphabet motif discovery and a structural motif database.

Shih-Yen Ku1, Yuh-Jyh Hu

  • 1Department of Computer Science, National Chiao Tung University, 1001 Tashuei Rd., Hsinchu, Taiwan.

Computers in Biology and Medicine
|November 22, 2011
PubMed
Summary

This study introduces a flexible framework for discovering structural motifs in proteins. It converts 3D structures into sequences to find conserved patterns, creating the SA-Motifbase database for structural information.

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Peptide-based Identification of Functional Motifs and their Binding Partners
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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Identifying conserved structural motifs is crucial for understanding protein function and evolution.
  • Existing methods may lack flexibility or comprehensive analysis of structural patterns.

Purpose of the Study:

  • To develop a general and adaptable framework for discovering structural motifs in proteins.
  • To create a database (SA-Motifbase) that stores and visualizes conserved structural information.

Main Methods:

  • A two-stage approach: converting protein 3D structures into structural alphabet sequences.
  • Applying sequence motif-finding tools to identify conserved motifs within these sequences.
  • Developing the SA-Motifbase to present motif 3D views, alphabet preferences, frequency distributions, and significance.

Main Results:

  • A novel framework for structural motif discovery was successfully proposed.
  • The SA-Motifbase database was established, offering detailed structural and statistical information for conserved motifs.
  • The framework demonstrated modularity, allowing for independent modification of system components.

Conclusions:

  • The proposed framework provides a versatile platform for structural motif discovery.
  • SA-Motifbase serves as a valuable resource for researchers studying protein structure and function.
  • The modular design enhances the framework's applicability across diverse biological studies.