Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Amino acids

Amino acids

Amino acids are the monomers that comprise proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, or the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group. There are 20 common amino acids present in proteins, each with a different R group. Variation in the amino acid sequence is responsible for...

Amino Acid Catabolism

Amino Acid Catabolism

Microorganisms rely on proteins as an essential carbon and energy source, particularly in environments with limited polysaccharides or lipids. However, proteins are too large to cross the plasma membrane unaided, necessitating enzymatic degradation. Microbes secrete extracellular proteases and peptidases that hydrolyze proteins into peptides, which can then be transported across the membrane. Once inside the cell, intracellular proteases degrade these peptides into free amino acids, which...

Amino Acid Biosynthetic Pathways

Amino Acid Biosynthetic Pathways

Amino acid biosynthesis is essential for cell growth, protein synthesis, and metabolic regulation. Cells generate essential and non-essential amino acids from metabolic intermediates to sustain vital biological functions. These intermediates originate from key metabolic pathways: glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway. Important precursors include α-ketoglutarate, pyruvate, oxaloacetate, phosphoenolpyruvate, and erythrose-4-phosphate, which...

Phase II Reactions: Sulfation and Conjugation with α-Amino Acids

Phase II Reactions: Sulfation and Conjugation with α-Amino Acids

Sulfation and α-amino acid conjugation are two critical biotransformation reactions in drug metabolism. Sulfation, a phase II biotransformation reaction, involves adding a polar sulfate group to a drug, enhancing its water solubility and promoting excretion. This process can either co-occur with or occur independently of glucuronidation. Nonmicrosomal sulfotransferase enzymes catalyze the process. The reaction involves 3'-phosphoadenosine-5'-phosphosulfate or PAPS coenzyme...

Nucleophilic Acyl Substitution of Carboxylic Acid Derivatives

Nucleophilic Acyl Substitution of Carboxylic Acid Derivatives

Nucleophilic acyl substitution is an important class of substitution reactions involving a nucleophile and an acyl compound, such as carboxylic acids and their derivatives. In these reactions, the leaving group attached to the acyl group is substituted by a nucleophile. The general mechanism proceeds via two steps.

Polyprotic Acids

Polyprotic Acids

Acids are classified by the number of protons per molecule that they can give up in a reaction. Acids such as HCl, HNO3, and HCN that contain one ionizable hydrogen atom in each molecule are called monoprotic acids. Their reactions with water are:

You might also read

Related Articles

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

Sort by

Same author

OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability.

Nature methods·2026

Same author

Small subunit isoform diversity underlies structural heterogeneity in native plant Rubisco.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

A FLOE-related protein regulates the two-dimensional to three-dimensional growth transition in the moss Physcomitrium patens.

Development (Cambridge, England)·2025

Same author

Metabolic engineering of stomatal precursor cells enhances photosynthetic water-use efficiency and vegetative growth under water-deficit conditions in Arabidopsis thaliana.

Plant biotechnology journal·2025

Same author

Increased chloroplast area in the rice bundle sheath through cell-specific perturbation of brassinosteroid signaling.

Plant physiology·2025

Same author

The metabolite transporters of C4 photosynthesis.

The Plant cell·2025

Search research articles

Related Experiment Video

Updated: Feb 12, 2026

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Published on: June 24, 2019

RECUR: identifying recurrent amino acid substitutions from multiple sequence alignments.

Elizabeth H J Robbins¹, Yi Liu¹, Steven Kelly¹

¹Department of Biology, University of Oxford, Oxford OX1 3RB, UK.

Molecular Biology and Evolution

|February 11, 2026

Summary

RECUR identifies recurrent amino acid substitutions in biological sequences, crucial for understanding evolution and disease. This method accurately detects widespread recurrent evolution in SARS-CoV-2 spike proteins, particularly at the hACE2 interface.

Keywords:

SARS-CoV-2 surface glycoprotein adaptation convergent evolution multiple sequence alignment parallel evolution phylogeny recurrent evolution

More Related Videos

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Published on: April 13, 2022

Related Experiment Videos

Last Updated: Feb 12, 2026

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Published on: June 24, 2019

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Published on: April 13, 2022

Area of Science:

Evolutionary biology
Genomics
Structural biology

Background:

Recurrent evolutionary changes in biological sequences are vital for understanding phenotypes, antibiotic resistance, and disease.
Identifying these recurrent substitutions aids in pinpointing causative genetic alterations.

Purpose of the Study:

To introduce RECUR, a novel computational method for detecting recurrent amino acid substitutions in large multiple sequence alignments.
To assess the accuracy and robustness of RECUR using simulated and real-world biological data.

Main Methods:

Development of RECUR, a fast, user-friendly, and scalable algorithm for identifying recurrent amino acid substitutions.
Validation of RECUR's accuracy (100%) on simulated data and its robustness against tree inference errors.
Application of RECUR to analyze surface glycoprotein (S) protein sequences from SARS-CoV-2.

Main Results:

RECUR achieved 100% accuracy in detecting recurrent substitutions in simulated evolutionary histories.
Widespread recurrent evolution was identified in SARS-CoV-2 S proteins, enriched in the S1 subunit and hACE2 binding interface.
Recurrent substitutions were depleted at the S protein trimeric interface, with variable stability effects at the hACE2 interface.

Conclusions:

RECUR is a highly accurate and robust tool for identifying recurrent evolutionary events in biological sequences.
Recurrent evolution in the SARS-CoV-2 S protein, especially at the hACE2 interface, suggests a balance between receptor binding and immune evasion.
The findings highlight the utility of RECUR in studying viral evolution and adaptation.