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Mutations

Mutations

Mutations

Mutations

Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations can be characterized in a number of different ways: whether and how they alter the amino acid sequence of the protein, whether they occur over a small or large area of DNA, and whether they occur in somatic cells or germline cells.
Chromosomal Alterations Are Large-Scale Mutations
While point mutations are changes in a single nucleotide in...

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.

Protein Denaturation

Protein Denaturation

The function of proteins depends on their native three-dimensional structure, which is dictated by the amino acid sequence of the specific protein. Folding of the polypeptide chain takes place under specific conditions that energetically favor the folded conformation. In contrast, protein denaturation occurs spontaneously under unfavorable conditions that disrupt the integrity of the folded conformation. Thus, the chemical and physical environment of a protein, such as significant changes in pH...

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 form...

Protein Folding

Protein Folding

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Related Experiment Video

Updated: Jun 10, 2026

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

Published on: October 13, 2022

Computational evaluation of protein stability change upon mutations.

Shuangye Yin¹, Feng Ding, Nikolay V Dokholyan

¹Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

Methods in Molecular Biology (Clifton, N.J.)

|August 3, 2010

Summary

Estimating protein stability changes (Delta DG) from mutations is vital. The new Eris protocols accurately predict Delta DG using flexible protein structures, improving upon fixed-backbone methods.

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Published on: July 14, 2015

Area of Science:

Biochemistry
Structural Biology
Computational Biology

Background:

Estimating protein stability changes (Delta DG) upon mutation is critical for protein design and engineering.
Accurate and rapid computational prediction of Delta DG remains a significant challenge in bioinformatics.

Purpose of the Study:

To introduce and detail the Eris protocols, a novel computational method for in silico evaluation of protein stability changes.
To demonstrate the accuracy and efficiency of the Eris protocols in predicting Delta DG.

Main Methods:

The Eris protocols utilize the tertiary structure of wild-type proteins to model mutant structures.
Employs a fast rotamer-based algorithm for efficient side-chain conformation optimization.
Incorporates protein backbone flexibility during structural modeling for improved accuracy.

Main Results:

Eris protocols effectively resolve steric clashes introduced by mutations.
Achieved more accurate Delta DG predictions compared to fixed-backbone approaches.
Demonstrated efficient in silico evaluation of protein stability changes.

Conclusions:

The Eris protocols offer an efficient and accurate computational approach for predicting protein stability changes (Delta DG).
Allowing backbone flexibility significantly enhances the accuracy of Delta DG predictions.
Eris protocols represent a valuable tool for mutagenesis experiment design and protein engineering.