2023/12/12 by Tatjana Škrbić, Škrbić, Tatjana, Achille Giacometti +7 · 1 citation
Biochemistry, Genetics and Molecular Biology · Materials Science · #Protein Structure and Dynamics #Enzyme Structure and Function #Genomics and Phylogenetic Studies
paper · pdf · doi:10.48550/arxiv.2312.07304
We present a geometrical analysis of the protrusion statistics of side chains in more than 4,000 high-resolution protein structures. We employ a coarse-grained representation of the protein backbone viewed as a linear chain of Cα 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.