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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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...

Protein and Protein Structure

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...

Conserved Binding Sites

Conserved Binding Sites

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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Conservation of Protein Domains

Conservation of Protein Domains

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...

What is Conservation Biology?

What is Conservation Biology?

Conservation biology is a scientific field that focuses on the preservation of biodiversity in order to protect ecosystems while meeting the needs of the human population. Humans require properly functioning ecosystems to maintain our supply of natural resources, including food, medicines, and building materials.

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Related Experiment Video

Updated: Jan 31, 2026

Optimized Negative Staining: a High-throughput Protocol for Examining Small and Asymmetric Protein Structure by Electron Microscopy

Optimized Negative Staining: a High-throughput Protocol for Examining Small and Asymmetric Protein Structure by Electron Microscopy

Published on: August 15, 2014

Asymmetric protein design from conserved supersecondary structures.

Mohammad ElGamacy¹, Murray Coles¹, Andrei Lupas¹

¹Dept. of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany.

Journal of Structural Biology

|December 19, 2018

Summary

Scientists designed a novel globular protein using an interface-driven strategy, not just repeating structures. This method successfully created a dRP lyase domain with high structural accuracy, demonstrating new protein design possibilities.

Keywords:

Computational protein design Conserved motifs Globular protein design Interface-driven strategy

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Last Updated: Jan 31, 2026

Optimized Negative Staining: a High-throughput Protocol for Examining Small and Asymmetric Protein Structure by Electron Microscopy

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Published on: August 15, 2014

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Published on: July 16, 2017

Area of Science:

Protein engineering
Computational biology
Structural biology

Background:

Computational protein design often uses supersecondary structures as building blocks.
Previous methods relied on fragment amplification and self-compatible folding propensities.

Purpose of the Study:

To explore an interface-driven strategy for designing novel globular proteins.
To move beyond repeat-based designs by using heterologous supersecondary structures.

Main Methods:

Designed an asymmetric, globular protein domain using an interface-driven approach.
Utilized conserved fragments and interface-directed sampling for protein construction.
Determined the protein structure using Nuclear Magnetic Resonance (NMR) spectroscopy.

Main Results:

Successfully designed a dRP lyase domain with a novel sequence.
The experimental NMR structure closely matched the computational design (backbone RMSD of 0.94 Å).
Demonstrated that residual folding information and interface-directed sampling yield functional globular proteins.

Conclusions:

An interface-driven strategy can successfully construct novel globular proteins from heterologous supersecondary structures.
This approach offers an alternative to repeat-based protein design.
The designed protein exhibits desired biophysical properties and high structural fidelity.