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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...

Lipids as Anchors

Lipids as Anchors

In the plasma membrane, the lipids forming the bilayer can also act as an anchor to tether proteins to the membrane. The three main types of lipid anchors found in eukaryotes are – prenyl groups, fatty acyl groups, and glycosylphosphatidylinositol or GPI groups. Prenyl and fatty acyl groups act as anchors on the cytosolic surface of the membrane, whereas GPI anchors proteins on the extracellular side.
The carboxy-terminal of most of the prenylated proteins, such as Ras proteins, contains...

Conserved Binding Sites

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.
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Structure of Lipids

Structure of Lipids

Lipids include a diverse group of compounds that are largely nonpolar in nature. This is because they are hydrocarbons that include mostly nonpolar carbon-carbon or carbon-hydrogen bonds. Non-polar molecules are hydrophobic (“water fearing”), or insoluble in water. Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of fats. Lipids also provide insulation from the environment for plants and animals. For example, they help keep aquatic...

Structure of Lipids

Structure of Lipids

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Related Experiment Video

Updated: Oct 26, 2025

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

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Published on: April 13, 2022

Experimental lipophilicity scale for coded and noncoded amino acid residues.

Vladimir Kubyshkin¹

¹Chemistry Department, University of Manitoba, 144 Dysart road, Winnipeg, Manitoba R3T 2N2, Canada. vladimir.kubyshkin@umanitoba.ca.

Organic & Biomolecular Chemistry

|August 1, 2021

Summary

Researchers developed a universal polarity scale for amino acids, including both natural and engineered types. This scale, based on experimental lipophilicity, helps understand amino acid roles in proteins and guides genetic code engineering.

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A New Straightforward Method for Lipophilicity logP Measurement using 19F NMR Spectroscopy

A New Straightforward Method for Lipophilicity logP Measurement using 19F NMR Spectroscopy

Published on: January 30, 2019

Area of Science:

Biochemistry
Protein Science
Chemical Biology

Background:

Amino acid polarity is crucial for protein function.
Protein modifications and genetic engineering necessitate a unified polarity scale for canonical and noncanonical residues.

Purpose of the Study:

To establish an experimental polarity scale applicable to both coded and noncoded amino acids.
To provide a universal measure of amino acid lipophilicity.

Main Methods:

Amino acids were derivatized into methyl esters of N-acetylamino acids under mild conditions.
Lipophilicity was quantified by measuring partitioning between octan-1-ol and water/buffer using NMR signal intensity.

Main Results:

A polarity scale was generated for the 20 coded amino acids, showing a 5.1 log P range from hydrophobic tryptophan to hydrophilic aspartate.
Lipophilicity data were also collected for various natural and laboratory analogues of key amino acids.

Conclusions:

The developed polarity scale integrates canonical and noncanonical amino acids.
This scale will aid in understanding amino acid substitutions in proteins and advance experimental genetic code engineering.