Related Experiment Video
Updated: Apr 19, 2026
07:08
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
7.8K
Identifying tandem Ankyrin repeats in protein structures
Broto Chakrabarty1, Nita Parekh2
1Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India. broto.chakrabarty@research.iiit.ac.in.
BMC Bioinformatics
|December 31, 2014
Summary
This study introduces AnkPred, a novel graph spectral approach for identifying Ankyrin repeat proteins. The method accurately detects repeat types and copy numbers, aiding in disease-associated protein analysis.
Area of Science:
- Structural bioinformatics
- Computational biology
- Protein repeat analysis
Background:
- Tandemly repeated structural motifs are common in proteins, crucial for diverse functions.
- Identifying these repeats, like Ankyrin repeats, is challenging due to sequence variability.
- Defects in repeat proteins are linked to various diseases, necessitating accurate identification methods.
Purpose of the Study:
- To develop a structure-based computational method for accurately identifying Ankyrin repeat proteins.
- To determine the repeat type and copy number within protein structures.
- To provide a tool for discovering novel Ankyrin repeat-containing proteins.
Main Methods:
- Representing protein structures as graphs and analyzing their spectral properties (eigen spectra).
- Developing rules for Ankyrin repeat detection using a non-redundant set of known Ankyrin proteins.
- Evaluating the graph spectral approach against existing methods and annotations.
Main Results:
- The graph spectral approach effectively captures protein 3D topology for repeat detection.
- Unique eigen spectra profiles were identified for Ankyrin repeat motifs.
- The method identified 641 previously unrecognized Ankyrin repeat proteins in the PDB database.
- The approach demonstrated high accuracy compared to sequence-based and other structure-based methods.
Conclusions:
- AnkPred offers an efficient and accurate graph-based method for detecting Ankyrin structural repeats.
- The method leverages protein structure graph eigen spectra and secondary structure information.
- AnkPred is particularly valuable for identifying new members of known repeat families.
Related Concept Videos
01:13Cytoskeletal Accessory Proteins
4.4K
The cytoskeleton is an essential cell component that plays several structural and functional roles. However, the filaments that make up the cytoskeleton cannot function independently and depend on the accessory or ancillary proteins to effectively carry out their function. Accessory proteins associate with cytoskeletal filaments and their monomers, aiding filament formation and function. They also help in the cross-communication among cytoskeletal filaments. Cytoskeletal accessory proteins are...
4.4K
01:18Assembly of Cytoskeletal Filaments
28.5K
Cytoskeletal filaments are polymeric forms of smaller protein subunits. However, individual cytoskeletal filaments may easily disassemble or associate with other similar filaments to form rigid structures. Microfilaments, made of actin monomers, rely on actin-binding proteins to form bundles and create networks of individual actin filaments. Microtubules rely on microtubule-associated proteins (MAPs) to form sturdy cylindrical structures. However, the proteins involved in forming complex...
28.5K
02:15Protein and Protein Structure
93.7K
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
A protein's shape is critical to its function. For example, an enzyme...
93.7K
01:19The Structure of Intermediate Filaments
6.1K
The intermediate filaments are one of three widely studied cytoskeletal filaments. They are so named as their diameter (10 nm) is in between that of microfilaments (7 nm) and the microtubules (25 nm). These filaments are highly stable and can remain intact when exposed to high salt concentrations and detergents. These filaments are responsible for providing stability and mechanical support to the cells. They also help in cell adhesion and maintaining tissue integrity.
Intermediate...
Intermediate...
6.1K
01:23Catenins
3.3K
Catenins are characterized by multiple binding domains and dynamic structures that allow them to function as linker proteins in cell junction complexes. All catenins, except α-catenin, contain a characteristic protein sequence called the armadillo repeat and are therefore also called armadillo proteins.
Catenins in Cell Junctions
Catenins bind to cell adhesion molecules such as cadherins and link them to different cytoskeletal proteins depending on the type of cell junction. At the...
Catenins in Cell Junctions
Catenins bind to cell adhesion molecules such as cadherins and link them to different cytoskeletal proteins depending on the type of cell junction. At the...
3.3K
01:45Tail-anchoring of Proteins in the ER Membrane
4.1K
Tail-anchored, or TA, proteins are estimated to make up to 3-5% of membrane proteins found in the eukaryotic cell. Such proteins have a single transmembrane domain located approximately 30 amino acid residues upstream from the C-terminal end. As a result, the signal recognition particle (SRP) cannot guide a TA protein to the ER membrane for cotranslational insertion. Hence, they are integrated into the ER membrane post-translationally using their C-terminal end as the anchor. TA proteins...
4.1K