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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

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...

Intrinsically Disordered Proteins

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...

Globular and Fibrous Proteins

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...

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Updated: Oct 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

Atom-specific persistent homology and its application to protein flexibility analysis.

David Bramer¹, Guo-Wei Wei²

¹Department of Mathematics, Michigan State University, MI 48824, USA.

Computational and Mathematical Biophysics

|July 19, 2021

Summary

This study introduces atom-specific persistent homology, a novel method to analyze local atomic properties in molecules. This topological approach enhances biomolecular flexibility and B-factor prediction using machine learning.

Keywords:

Atom-specific topology Convolutional neural network Element-specific persistent homology Gradient boosting tree Protein flexibility

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Last Updated: Oct 28, 2025

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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Time-Resolved Fluorescence Anisotropy from Single Molecules for Characterizing Local Flexibility in Biomolecules

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Published on: April 25, 2025

Area of Science:

Computational Biology
Topological Data Analysis
Structural Bioinformatics

Background:

Persistent homology is successful in analyzing biomolecular data by examining atomic connectivity at various scales.
However, its application to local atomic properties like flexibility and B-factor prediction is limited.

Purpose of the Study:

To introduce atom-specific persistent homology for local atomic-level molecular representation.
To apply this method for analyzing and predicting localized properties in macromolecules.

Main Methods:

Developed atom-specific persistent homology using conjugated sets of atoms and simplicial complexes.
Utilized Bottleneck and Wasserstein metrics to measure differences in topological invariants.
Integrated atom-specific topological features with machine learning algorithms (gradient boosting trees, CNN).

Main Results:

The proposed method provides localized atomic-level topological representations.
Successfully applied to protein thermal fluctuation analysis and B-factor prediction.
Demonstrated effectiveness in analyzing and predicting localized information in macromolecules.

Conclusions:

Atom-specific persistent homology offers a powerful new topological tool for biomolecular analysis.
This method enables the prediction of localized atomic properties previously difficult to assess.
The approach integrates global topological tools with local property analysis effectively.