Amino-Acid Characteristics in Protein Native State Structures

The molecular machines of life, proteins, are made up of twenty kinds of amino acids, each with distinctive side chains. We present a geometrical analysis of the protrusion statistics of side chains in more than 4000 high-resolution protein structures. We employ a coarse-grained representation of th...

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Bibliographic Details
Published in:Biomolecules (Basel, Switzerland) Switzerland), 2024-07, Vol.14 (7), p.805
Main Authors: Škrbić, Tatjana, Giacometti, Achille, Hoang, Trinh X, Maritan, Amos, Banavar, Jayanth R
Format: Article
Language:English
Subjects:
Amino acids
amino-acid classes
Datasets
Geometry
local Frenet frame
Peptides
pre-sculpted landscape
Proteins
side-chain protrusion
Statistical analysis
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Summary:The molecular machines of life, proteins, are made up of twenty kinds of amino acids, each with distinctive side chains. We present a geometrical analysis of the protrusion statistics of side chains in more than 4000 high-resolution protein structures. We employ a coarse-grained representation of the protein backbone viewed as a linear chain of C atoms and consider just the heavy atoms of the side chains. We study the large variety of behaviors of the amino acids based on both rudimentary structural chemistry as well as geometry. Our geometrical analysis uses a backbone Frenet coordinate system for the common study of all amino acids. Our analysis underscores the richness of the repertoire of amino acids that is available to nature to design protein sequences that fit within the putative native state folds.
ISSN:2218-273X
2218-273X
DOI:10.3390/biom14070805