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Protein Families

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...

Protein Families

Protein Families

Structural Protein Function

Structural Protein Function

Structural Protein Function

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...

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.
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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.
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Author Spotlight: Characterizing DNA Replication of Pathogenic Repeats to Uncover Mechanisms of Replication Fork Stalling and Expansion

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DbStRiPs: Database of structural repeats in proteins.

Broto Chakrabarty¹, Nita Parekh¹

¹Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India.

Protein Science : a Publication of the Protein Society

|February 28, 2021

Summary

We developed DbStRiPs, a database for classifying protein structural repeats. It integrates sequence and structure data, aiding in the discovery of new protein repeat families and improving annotations for 16,472 repeat entries.

Keywords:

protein repeat database proteins repeats structural repeat proteins tandem repeats

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Identification of Functional Protein Regions Through Chimeric Protein Construction

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Published on: January 8, 2019

Area of Science:

Structural biology
Bioinformatics
Protein science

Background:

Repeat proteins are crucial due to their stable structures, conservation, and diverse functions.
High sequence variation complicates the identification and classification of these repeats.
Structure-based methods are needed for accurate characterization.

Purpose of the Study:

To develop a comprehensive database for classifying tandem structural repeats in proteins.
To integrate sequence and structure-based classification for refined protein annotation.
To facilitate the discovery of novel protein repeat families and clusters.

Main Methods:

Utilized a network-based pipeline and manual curation.
Employed Kajava's structure-based classification schema.
Mapped the Pfam sequence classification scheme onto the structural classification.

Main Results:

Created the Database of Structural Repeats in Proteins (DbStRiPs).
Identified 16,472 repeat annotations across 15,141 protein chains.
Discovered one novel protein repeat family (left-handed beta helix) and 33 protein repeat clusters.
Classified ~79% of repeat proteins into defined families or clusters.

Conclusions:

DbStRiPs provides high-quality annotations, including boundaries, copy number, structure, disease association, and cross-references.
The database aids in identifying functional groups within structural subclasses.
DbStRiPs offers valuable search and download functionalities for researchers.