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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

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 form...
Covalently Linked Protein Regulators02:04

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.
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Genetic Variation01:25

Genetic Variation

Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles, which...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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 form...
Conserved Binding Sites01:49

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 analyses the...

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Related Experiment Video

Updated: May 14, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

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

Published on: July 14, 2015

Protein engineering and stabilization from sequence statistics: variation and covariation analysis.

Venuka Durani1, Thomas J Magliery

  • 1Department of Chemistry, The Ohio State University, Columbus, Ohio, USA.

Methods in Enzymology
|February 21, 2013
PubMed
Summary
This summary is machine-generated.

This study presents a flexible methodology for analyzing multiple sequence alignments (MSAs) to predict stabilizing protein mutations. The protocol uses relative entropy and mutual information metrics for protein engineering applications.

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Last Updated: May 14, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

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Published on: July 14, 2015

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Published on: February 3, 2023

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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

Published on: July 16, 2017

Area of Science:

  • Protein engineering
  • Bioinformatics
  • Computational biology

Background:

  • Consensus and correlation in multiple sequence alignments (MSAs) are valuable for protein understanding and engineering.
  • Existing methods for acquiring MSA databases and calculating parameters vary widely.
  • A standardized yet flexible methodology is needed for robust MSA analysis.

Purpose of the Study:

  • To describe a chosen methodology for acquiring and statistically analyzing MSAs.
  • To provide a step-by-step protocol for calculating relative entropy and mutual information.
  • To demonstrate the prediction of stabilizing protein mutations using these metrics.

Main Methods:

  • Acquisition and statistical analysis of multiple sequence alignment (MSA) databases.
  • Calculation of relative entropy and mutual information metrics using Microsoft Excel.
  • Application of consensus and correlation values for mutation prediction.

Main Results:

  • A flexible, step-by-step protocol for MSA analysis was developed.
  • The protocol enables prediction of mutations likely to stabilize proteins.
  • Sample analysis on the BPTI-Kunitz protein family identified potential stabilizing mutations.

Conclusions:

  • The described methodology offers a practical approach to MSA analysis for protein stabilization.
  • Relative entropy and mutual information are effective metrics for predicting stabilizing mutations.
  • The protocol is accessible, requiring only basic tools like Microsoft Excel.