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Related Concept Videos

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 and Protein Structures02:15

Protein and Protein Structures

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 can...
Protein and Protein Structure02:15

Protein and Protein Structure

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 can...
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...
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...
Electron Microscope Tomography and Single-particle Reconstruction01:07

Electron Microscope Tomography and Single-particle Reconstruction

Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
Electron tomography can be performed either in TEM or STEM (scanning transmission...

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method.

Chesley M Leslin1, Alexej Abyzov, Valentin A Ilyin

  • 1Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA.

Nucleic Acids Research
|October 27, 2006
PubMed
Summary

TOPOFIT-DB (T-DB) offers a public database for protein structural alignment using the TOPOFIT method. This tool objectively identifies common and variable protein regions, aiding in comparative analysis and functional annotation.

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Area of Science:

  • Structural Bioinformatics
  • Computational Biology
  • Protein Science

Background:

  • Comparative analysis of protein structures is crucial for understanding function and evolution.
  • Existing methods may lack objective criteria for distinguishing conserved and variable regions.
  • Identifying non-sequential relationships between protein structures remains a challenge.

Purpose of the Study:

  • To introduce TOPOFIT-DB (T-DB), a public web-based database for protein structural alignments.
  • To provide a resource for objective identification of common and variable protein structural regions.
  • To facilitate the detection of non-sequential structural relationships and aid in functional annotation.

Main Methods:

  • Utilizes the TOPOFIT method, identifying a saturation point (topomax point) on the alignment curve.
  • Develops TOPOFIT-DB (T-DB) as a comprehensive database of protein structural alignments.
  • Implements T-Server for one-to-all structure comparisons and T-Pair for pair-wise analysis.

Main Results:

  • TOPOFIT-DB provides objective identification of borders between common and variable protein structural parts.
  • The TOPOFIT method effectively detects non-sequential relationships between protein structures.
  • T-DB enables retrieval and analysis of structural neighbors, facilitating detailed studies of protein variability.

Conclusions:

  • TOPOFIT-DB serves as a valuable resource for researchers studying protein structure variability and function.
  • The TOPOFIT method offers an objective approach to protein structural comparison and annotation.
  • The database supports comprehensive analysis through integrated tools and visualization options.