Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022;40(24):13738-13746.
doi: 10.1080/07391102.2021.1993343. Epub 2021 Oct 27.

Microproteins: a 3D protein structure prediction analysis

Kishan Thambu  1 , Victoria Glomb  1 , Rolando Hernandez Trapero  1 , Julio C Facelli  1   2
Affiliations

Microproteins: a 3D protein structure prediction analysis

Kishan Thambu et al. J Biomol Struct Dyn. 2022.

Abstract

Microproteins are a novel and expanding group of small proteins encoded by less than 100-150 codons that are translated from small open reading frames (smORFs). It has been shown that smORFs and their corresponding microproteins make up a sizable fraction of the genome and proteome, but very little information on microproteins' structural features exists in the literature. In this paper, we present the results of analyzing the predicted structures of 44 microproteins. The results show that this set of microproteins have a different amino acid composition profiles, similar structural characteristics and fewer small-molecule ligand binding sites than regular proteins.Communicated by Ramaswamy H. Sarma.

Keywords: Gene ontology; ligand binding sites; microproteins; protein structure; protein structure prediction.

PubMed Disclaimer

Conflict of interest statement

Conflict of Interest: The authors do not have any conflict of interest to declare.

Figures

Figure 1.
Figure 1.
Histogram showing the distribution of amino acids, represented by corresponding three letter symbols, found in the in microproteins considered here. Amino acids are color coded by their distinct basic property of acidic, basic, polar, and non-polar.
Figure 2.
Figure 2.
Stacked bar plot with percent frequency of secondary structural features for each of the microproteins studied here. (Each stacked bar represents corresponding averages over the five calculated models for each microprotein).
Figure 3.
Figure 3.
Frequency of secondary structure elements for the microprotein studied here. The proteins have been arranged in rack order according to the percentage of Alpha helix to compare with Figure 14 in Biro’s analysis of 81 common proteins (23), showing that there is an over representation of helical structure and almost no beta-sheets. (Values correspond averages of five calculated models for each microprotein).
Figure 4.
Figure 4.
Log of the total SASA as a function of the log of the number of residues for the 44 proteins analyzed.
Figure 5.
Figure 5.
Cluster plot of GO-term collections (y-axis: semantic space, x-axis: semantic space). See Reference for definition of semantic space.
See this image and copyright information in PMC

References

    1. Rathore A, Martinez TF, Chu Q, Saghatelian A. Small, but mighty? Searching for human microproteins and their potential for understanding health and disease. Expert Rev Proteomics. 2018;15(12):963–5. Epub 2018/11/15. doi: 10.1080/14789450.2018.1547194.. - DOI - PMC - PubMed
    1. Ma J, Ward CC, Jungreis I, Slavoff SA, Schwaid AG, Neveu J, et al. Discovery of Human sORF-Encoded Polypeptides (SEPs) in Cell Lines and Tissue. Journal of Proteome Research. 2014;13(3):1757–65. doi: 10.1021/pr401280w. - DOI - PMC - PubMed
    1. Saghatelian A, Couso JP. Discovery and characterization of smORF-encoded bioactive polypeptides. Nature Chemical Biology. 2015;11(12):909–16. doi: 10.1038/nchembio.1964. - DOI - PMC - PubMed
    1. Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. Critical assessment of methods of protein structure prediction (CASP)—Round XIII. Proteins: Structure, Function, and Bioinformatics. 2019;87(12):1011–20. doi: 10.1002/prot.25823. - DOI - PMC - PubMed
    1. Kryshtafovych A, Venclovas Č, Fidelis K, Moult J. Progress over the first decade of CASP experiments. Proteins: Structure, Function, and Bioinformatics. 2005;61(S7):225–36. doi: 10.1002/prot.20740. - DOI - PubMed

Publication types