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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...

Conservation of Protein Domains

Conservation of Protein Domains

Protein Diffusion in the Membrane

Protein Diffusion in the Membrane

Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...

Cotranslational Protein Translocation

Cotranslational Protein Translocation

Translocation of proteins across membranes is an ancient process that occurs even in bacteria and archaebacteria. In fact, the components of the translocation machinery are still conserved between prokaryotes and eukaryotes.
Sec61 channel partners for cotranslational translocation
During cotranslational translocation, the Sec61 channel partners with the signal recognition particle (SRP), the signal recognition particle receptor (SR), and the ribosomes to transport the nascent polypeptide chain...

Protein Networks

Protein 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,...

Protein Networks

Protein Networks

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Related Experiment Video

Updated: Feb 16, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Percolation in protein sequence space.

Patrick C F Buchholz¹, Silvia Fademrecht¹, Jürgen Pleiss¹

¹Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany.

|December 21, 2017

Summary

Protein sequence space is a connected network, not isolated clusters. This interconnectedness supports efficient evolution and reveals potential enzyme candidates for biotechnology.

Area of Science:

Evolutionary biology
Bioinformatics
Biochemistry

Background:

Protein sequences are unevenly distributed, forming clusters rather than a uniform spread.
Existing protein sequence space is vast and largely unexplored, shaped by evolutionary processes.

Purpose of the Study:

To analyze the distribution of protein sequence clusters and understand the connectedness of sequence space.
To explore the evolutionary implications of sequence space topology and identify potential biotechnological applications.

Main Methods:

Analysis of cluster size distribution for six protein superfamilies with diverse folds and functions.
Application of percolation theory to model the connectedness of extant protein sequence space.

Main Results:

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Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Published on: November 12, 2012

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Last Updated: Feb 16, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

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

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

Published on: July 16, 2017

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Published on: November 12, 2012

Cluster size distributions for studied superfamilies followed a power law (slopes 2.4-3.3).
This power law distribution supports the concept of a highly connected protein sequence space network.
Connectedness facilitates efficient evolution by overcoming potential evolutionary roadblocks.

Conclusions:

Protein sequence space is a highly connected network, crucial for efficient evolution.
The Fisher exponent serves as a metric for sequence space connectedness and saturation.
Bridging sequences between homologous families are identified as promising candidates for enzyme engineering in biotechnology due to potential substrate ambiguity.