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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...

Ligand Binding and Linkage

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...

Covalently Linked Protein Regulators

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein....

Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

Regulation of Nuclear Protein Sorting

Regulation of Nuclear Protein Sorting

Nuclear protein sorting regulates nucleus composition and gene expression, crucial for determining the fate of a eukaryotic cell. Hence, the entry and exit of molecules across the nuclear envelope is a tightly controlled process. Nuclear protein sorting can be inhibited by one of the following ways: 1) masking cargo signal sequences, 2) modifying the nuclear receptor's affinity for cargo, 3) controlling the nuclear pore size, 4) retaining the cargo during its transit to the cytosol or the...

Signal Sequences and Sorting Receptors

Signal Sequences and Sorting Receptors

Signal sequences are short amino acid sequences that guide newly synthesized proteins to their proper location within the cell. Classical signal sequences are fifteen to sixty amino acids long and present at the N-terminus of a polypeptide chain. Each signal sequence has a conserved segment of basic residues towards their N terminus, a hydrophobic core, and a C-terminus rich in polar residues. The C-terminus also contains a signal cleavage site and features a -3 -1 sequence motif. The -3-1...

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Evolutionary Aspects of Selenium Binding Protein (SBP).

Irene Dervisi¹, Chrysanthi Valassakis¹, Aikaterini Koletti²

¹Section of Botany, Department of Biology, National & Kapodistrian University of Athens, 15784, Athens, Greece.

Journal of Molecular Evolution

|April 11, 2023

Summary

Selenium-binding proteins (SBPs) are ancient, originating in bacteria. Their key motifs evolved across archaea, bacteria, animals, and plants, suggesting a role as methanethiol oxidases.

Keywords:

CxxC motif Motifs Phylogenetic profiling Phylogenetic tree SBP Selenium

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Area of Science:

Biochemistry
Evolutionary Biology
Molecular Biology

Background:

Selenium-binding proteins (SBPs) are a ubiquitous family, with SBP1 recently identified as a plant stress response regulator.
SBP1's function as a methanethiol oxidase is known, but its precise role requires further clarification.
In mammals, SBPs are implicated in anti-carcinogenesis, redox modulation, and detoxification.

Purpose of the Study:

To investigate the functional potential and evolutionary trajectory of conserved motifs within Selenium-binding proteins (SBPs).
To understand the evolutionary origins and diversification of SBP sequence motifs across different phyla.

Main Methods:

Phylogenetic profiling was employed to analyze the distribution and evolution of SBP motifs.
Construction of a phylogenetic tree to visualize evolutionary relationships and motif differentiation.

Main Results:

SBPs are absent in fungi and most non-eukaryotic organisms.
Characteristic SBP motifs, including CSSC and CC, show distinct evolutionary patterns.
The CC motif is conserved in plants and modified to CxxC in animals, while CSSC motifs are modified in Acidobacteria, Fungi, and Archaea.
SBP motifs primarily emerged in Archaea and Bacteria, with subsequent retention and modification in Animals and Plants.

Conclusions:

Selenium-binding proteins likely originated in bacteria, potentially functioning as methanethiol oxidases.
The evolution of SBP motifs reflects significant diversification events across major domains of life.
Understanding SBP evolution provides insights into their diverse biological roles, from stress response to metabolic regulation.