Related Experiment Video
Updated: Jun 25, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
The SAAPdb web resource: a large-scale structural analysis of mutant proteins
Jacob M Hurst1, Lisa E M McMillan, Craig T Porter
1Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom.
Human Mutation
|February 5, 2009
Summary
The Single Amino Acid Polymorphism database (SAAPdb) analyzes mutations, mapping single nucleotide polymorphisms (SNPs) and pathogenic deviations (PDs) to protein structures. This resource helps explain deleterious phenotypes by identifying structural effects of mutations.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Understanding the structural impact of genetic variations is crucial for disease research.
- Existing databases may not comprehensively link mutations to structural data for phenotype explanation.
Purpose of the Study:
- To introduce SAAPdb, a novel resource for analyzing and visualizing the structural effects of mutations.
- To investigate differences between SNPs and PDs using structural mapping.
Main Methods:
- Mapping single nucleotide polymorphisms (SNPs) and pathogenic deviations (PDs) to protein structural data from the Protein Data Bank.
- Analyzing sequence and structural characteristics of mapped mutations.
Main Results:
- SAAPdb successfully maps mutations onto protein structures to hypothesize local structural effects.
- Significant differences in sequence and structural characteristics were observed between SNPs and PDs.
- Pathogenic deviations (PDs) were more frequently explained by structural analysis.
Conclusions:
- SAAPdb provides a valuable resource for the mutation research community.
- Structural analysis of mutations aids in explaining deleterious phenotypes.
- The database is publicly accessible for broader scientific use.
Related Concept Videos
02:47Protein 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...
01:24Protein 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.
The primary structure of a protein is its amino acid sequence.
01:57Gene Families
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
02:21Globular 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...
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...
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...