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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...

Conserved Binding Sites

Conserved Binding Sites

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...

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...

Ligand Binding Sites

Ligand Binding Sites

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...

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Related Experiment Video

Updated: Dec 28, 2025

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

Incorporating Nearest-Neighbor Site Dependence into Protein Evolution Models.

Gary Larson¹, Jeffrey L Thorne^2,3, Scott Schmidler^1,4

¹Department of Statistical Science, Duke University, Durham, North Carolina.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology

|February 14, 2020

Summary

This study introduces a site-dependent model (SDM) for protein structure evolution, improving phylogenetic tree reconstruction and reducing bias in evolutionary distance estimates. The new model accounts for correlated evolution among amino acid sites, unlike previous site-independent models.

Keywords:

diffusion process dynamic programming evolution phylogeny protein structure

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

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Published on: July 14, 2015

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Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

Computational biology
Molecular evolution
Bioinformatics

Background:

Protein evolutionary models are crucial for sequence alignment, homology, and phylogeny inference.
Existing models often assume independent evolution between sites, which is unrealistic.
Previous site-independent models for protein structural evolution improved alignments and phylogenetic inferences.

Purpose of the Study:

To extend protein structural evolution models to account for correlated evolution among neighboring amino acid positions.
To develop a spatiotemporal model for protein structure evolution.
To reduce bias in evolutionary distance estimation and improve phylogenetic tree reconstruction.

Main Methods:

Developed a site-dependent model (SDM) for protein structure evolution.
The SDM uses a multivariate diffusion process convolved with a spatial birth-death process.
Compared the SDM with site-independent models (SIM) for computational cost and analytical complexity.

Main Results:

The site-dependent model (SDM) significantly reduces bias in estimated evolutionary distances.
The SDM further improves phylogenetic tree reconstruction accuracy.
Demonstrated bias in standard site-independent sequence evolution models using a site-dependent sequence evolution model.

Conclusions:

Site-dependent models offer significant improvements over site-independent models for protein evolution.
The developed spatiotemporal model provides a more realistic approach to understanding protein evolution.
The SDM offers enhanced accuracy in phylogenetic analysis with minimal computational overhead.