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Related Concept Videos

Point and Frameshift Mutations01:30

Point and Frameshift Mutations

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Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
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Mutation, Gene Flow, and Genetic Drift01:09

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In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
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Mismatch Repair01:20

Mismatch Repair

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Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
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Mutations01:35

Mutations

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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...
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Conservative Site-specific Recombination and Phase Variation02:53

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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
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Spontaneous and Induced Mutations01:30

Spontaneous and Induced Mutations

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Spontaneous mutations arise infrequently during DNA replication due to errors in the process. A key factor behind these errors is tautomeric shifts in nitrogenous bases, where bases transition from keto to enol forms or amino to imino forms. This shift can alter base-pairing rules, leading to mutations. Additionally, reactive oxygen species (ROS) arising from aerobic metabolism can damage DNA, resulting in depurination (loss of a purine base) or depyrimidination (loss of a pyrimidine base).
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Analyses of Mutation Displacements from Homology Models.

Mathilde Carpentier1, Jacques Chomilier2

  • 1Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, Paris, France. mathilde.carpentier@mnhn.fr.

Methods in Molecular Biology (Clifton, N.J.)
|March 24, 2023
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Summary
This summary is machine-generated.

Understanding protein structure changes from mutations is key. New methods use molecular modeling to separate mutation effects from local flexibility, improving accuracy for protein structural biology research.

Keywords:
Allosteric effectBackbone flexibilityHomology modelPoint mutationProtein structure

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Area of Science:

  • Protein structural biology
  • Biophysics
  • Computational biology

Background:

  • Assessing structural changes from single amino acid mutations is crucial in protein structural biology.
  • Existing methods struggle to differentiate between the direct effect of a substitution and the inherent flexibility of the mutated site.

Purpose of the Study:

  • To present advanced methods for distinguishing mutation-induced structural perturbations from local flexibility contributions.
  • To introduce molecular modeling as a viable approach to overcome limitations of experimental structure determination for studying mutations.

Main Methods:

  • Utilizing molecular modeling software to build protein models from templates based on sequence information.
  • Employing human lysozyme as a model system, with available wild-type and mutant structures in the Protein Data Bank (PDB).
  • Analyzing the impact of specific mutations, including those leading to amyloid fibril formation and neutral variants.

Main Results:

  • Demonstrated the reliability of side chain conformations at the mutation site using various modeling algorithms.
  • Validated the approach using human lysozyme, a well-characterized protein with known mutations.
  • Identified limitations of current molecular modeling tools in predicting long-range structural effects.

Conclusions:

  • Molecular modeling provides reliable predictions for local side chain conformations at mutation sites.
  • This approach effectively bypasses the need for numerous experimentally determined mutant structures.
  • Further development is needed to accurately model long-range structural perturbations caused by mutations.