Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.8K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.8K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

6.2K
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...
6.2K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

2.5K
2.5K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

11.7K
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...
11.7K
Protein Families02:47

Protein Families

13.3K
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
13.3K
Conserved Binding Sites01:49

Conserved Binding Sites

4.1K
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...
4.1K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Computational validation of inhibitors for human phosphatidylinositol 4-phosphate 5-kinase-type 1 α protein implicated in cancer.

Journal of biomolecular structure & dynamics·2026
Same author

Elucidating the structural basis of Fgd1-mediated resistance to Delamanid in Mycobacterium tuberculosis.

Journal of molecular graphics & modelling·2026
Same author

Structure-based computational investigation of potential TarA inhibitors in Staphylococcus aureus.

Molecular diversity·2026
Same author

Hexagonal Boron Nitride Nanoparticles for Inhibition of Small Fragment Tau Aggregation.

The journal of physical chemistry. B·2025
Same author

Application of chemical similarity and bioisosteres to find allosteric inhibitors of type 2 lipid kinase γ.

Scientific reports·2025
Same author

Coenzyme A protects against ferroptosis via CoAlation of mitochondrial thioredoxin reductase.

The Journal of clinical investigation·2025

Related Experiment Video

Updated: Apr 26, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

14.3K

Structure and sequence based analysis of alpha-amylase evolution.

Swati Singh, Lalitha Guruprasad1

  • 1School of Chemistry, University of Hyderabad, Hyderabad, 500046, India. lgpsc@uohyd.ernet.in.

Protein and Peptide Letters
|July 19, 2014
PubMed
Summary
This summary is machine-generated.

Structural analysis of alpha-amylases reveals evolutionary insights. Enzyme structures, not just sequences, accurately reflect functional conservation and speciation, highlighting key differences in ion binding and disulfide bonds.

More Related Videos

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

16.2K
X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050
11:27

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

Published on: May 13, 2020

3.4K

Related Experiment Videos

Last Updated: Apr 26, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

14.3K
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

16.2K
X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050
11:27

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

Published on: May 13, 2020

3.4K

Area of Science:

  • Biochemistry and Molecular Biology
  • Enzymology
  • Structural Biology

Background:

  • Alpha-amylases are crucial enzymes that hydrolyze alpha-1,4-glycosidic bonds in biological macromolecules.
  • Extensive sequence data and solved 3D structures exist for alpha-amylases across diverse organisms.

Purpose of the Study:

  • To investigate the evolutionary conservation of alpha-amylases using phylogenetic analysis.
  • To compare the efficacy of sequence-based versus structure-based phylogenetic analysis in representing enzyme function.
  • To identify structural features that differentiate alpha-amylases across evolutionary lineages.

Main Methods:

  • Generation of phylogenetic trees from both sequence and 3D structure data.
  • Structure-based sequence analysis to quantify evolutionary conservation.
  • Comparative analysis of conserved regions, insertion/deletion patterns, ion-binding sites, and disulfide connectivity.

Main Results:

  • Structure-based phylogenetic trees show greater similarity to reference NCBI trees than sequence-based trees.
  • Structural analysis reveals conserved and variable regions that correlate with speciation.
  • Distinct differences were identified in Ca(2+) and Cl(-) ion binding sites and disulfide connectivity patterns across evolutionary divergence.

Conclusions:

  • Enzyme 3D structures provide a more accurate representation of functional aspects and evolutionary relationships than sequence data alone.
  • Structural variations in conserved regions, ion-binding sites, and disulfide bonds are key discriminators of alpha-amylase evolution.
  • This study offers a refined metric for evolutionary conservation based on structural data.