The Frequencies of Amino Acids in Secondary Structural Elements of Globular Proteins

Year 2023, Volume: 13 Issue: 2, 261 - 266, 15.06.2023

Cevdet Nacar

https://doi.org/10.33808/clinexphealthsci.1239176

Cited By: 2

Abstract

Objective: The frequencies of amino acids in proteins for different structural levels have been determined by many studies. However, due to the different content of data sets, findings from these studies are inconsistent for some amino acids. This study aims to eliminate the contradictions in the findings of the studies by determining the frequencies of the amino acids in all structural level of globular proteins.
Methods: The frequencies of the amino acids in overall protein, in secondary structural elements (helix, sheet, coil) and in subtypes of secondary structural elements (α-, π-, and 310-helices, and first, parallel and anti-parallel strands) were calculated separately using a data set including 4.882 dissimilar globular peptides. The frequencies of the amino acids were calculated as the ratio of the total number of a specific residue in related structure to the total number of all residues in the related structure.
Results: The frequencies of residues determined in this study is partially in consistent with the other studies. The differences are probably due to the data set contents of the studies. The frequencies of the amino acids in subtypes of secondary structural elements were determined for the first time in this study.
Conclusions: Variations in the frequencies of PRO residue in 310-helix structure and of ILE, LEU, and VAL residues in strands of sheet structure are valuable findings for the improvement of secondary structure prediction methods, as they can be used as secondary structural elements markers.

Keywords

amino acid, globular protein, secondary structure

Supporting Institution

None

Project Number

None

Thanks

None

References

• Baud F, Karlin S. Measures of residue density in protein structures. Proceedings of the National Academy of Sciences of the United States of America. 1999; 96(22): 12494-9.
• Itzkovitz S, Alon U. The genetic code is nearly optimal for allowing additional information within protein-coding sequences. Genome Res. 2007; 17(4): 405-12.
• King JL, Jukes TH. Non-Darwinian evolution. Science. 1969; 164(3881): 788-98.
• Moura A, Savageau MA, Alves R. Relative Amino Acid Composition Signatures of Organisms and Environments. Plos One. 2013; 8(10).
• Trinquier G, Sanejouand YH. Which effective property of amino acids is best preserved by the genetic code? Protein Engineering. 1998; 11(3): 153-69.
• Tripathi V, Tripathi P, Gupta D. Statistical approach for lysosomal membrane proteins (LMPs) identification. Syst Synth Biol. 2014; 8(4): 313-9.
• Vacic V, Uversky VN, Dunker AK, Lonardi S. Composition Profiler: a tool for discovery and visualization of amino acid composition differences. BMC Bioinformatics. 2007; 8: 211.
• Varfolomeev SD, Uporov IV, Fedorov EV. Bioinformatics and molecular modeling in chemical enzymology. Active sites of hydrolases. Biochemistry (Mosc). 2002; 67(10): 1099-108.
• Xia X, Xie Z. Protein structure, neighbor effect, and a new index of amino acid dissimilarities. Mol Biol Evol. 2002; 19(1): 58-67.
• Bogatyreva NS, Finkelstein AV, Galzitskaya OV. Trend of amino acid composition of proteins of different taxa. J Bioinform Comput Biol. 2006; 4(2): 597-608.
• Dyer KF. The Quiet Revolution: A New Synthesis of Biological Knowledge. Journal of Biological Education. 1971; 5: 15-24.
• Fagerlund A, Myrset AH, Kulseth MA. Construction and characterization of a 9-mer phage display pVIII-library with regulated peptide density. Appl Microbiol Biotechnol. 2008; 80(5): 925-36.
• Gaur RK. Amino acid frequency distribution among eukaryotic proteins. IIOAB Journal. 2014; 5(2): 6-11.
• Lehmann J. Genetic code degeneracy and amino acid frequency in proteomes. Grandcolas P, Maurel M-C, editors: Elsevier; 2018.
• Rao Y, Wang Z, Luo W, Sheng W, Zhang R, Chai X. Base composition is the primary factor responsible for the variation of amino acid usage in zebra finch (Taeniopygia guttata). PLoS One. 2018; 13(12): e0204796.
• Switzar L, Giera M, Niessen WM. Protein digestion: an overview of the available techniques and recent developments. J Proteome Res. 2013; 12(3): 1067-77.
• Tian L, Liu SJ, Wang S, Wang LS. Ligand-binding specificity and promiscuity of the main lignocellulolytic enzyme families as revealed by active-site architecture analysis. Sci Rep-Uk. 2016; 6.
• Tsuji J, Nydza R, Wolcott E, Mannor E, Moran B, Hesson G, et al. The frequencies of amino acids encoded by genomes that utilize standard and nonstandard genetic codes. Bios. 2010; 81(1): 22-31.
• Akashi H, Gojobori T. Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proceedings of the National Academy of Sciences of the United States of America. 2002; 99(6): 3695-700.
• Berezovsky IN, Kilosanidze GT, Tumanyan VG, Kisselev LL. Amino acid composition of protein termini are biased in different manners. Protein Engineering. 1999; 12(1): 23-30.
• Bouziane H, Chouarfia A. Sequence- and structure-based prediction of amyloidogenic regions in proteins. Soft Comput. 2020; 24(5): 3285-308.
• Brooks DJ, Fresco JR, Lesk AM, Singh M. Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code. Mol Biol Evol. 2002; 19(10): 1645-55.
• Brune D, Andrade-Navarro MA, Mier P. Proteome-wide comparison between the amino acid composition of domains and linkers. BMC Res Notes. 2018; 11(1): 117.
• Carugo O. Amino acid composition and protein dimension. Protein Sci. 2008; 17(12): 2187-91.
• dos Reis M, Yang ZH. Why Do More Divergent Sequences Produce Smaller Nonsynonymous/Synonymous Rate Ratios in Pairwise Sequence Comparisons? Genetics. 2013; 195(1): 195-204.
• Du MZ, Liu S, Zeng Z, Alemayehu LA, Wei W, Guo FB. Amino acid compositions contribute to the proteins' evolution under the influence of their abundances and genomic GC content. Sci Rep-Uk. 2018; 8.
• Flores SC, Lu LJ, Yang JL, Carriero N, Gerstein MB. Hinge Atlas: relating protein sequence to sites of structural flexibility. Bmc Bioinformatics. 2007; 8.
• Ganguli S, Datta A. Residue frequencies and conserved phylogenetic signatures in amino acid sequences of plant glutathione peroxidases, indicates habitat specific adaptation and dictates interactions with key ligands. American Journal of Bioinformatics Research. 2015; 5(1): 9-15.
• Gardini S, Cheli S, Baroni S, Di Lascio G, Mangiavacchi G, Micheletti N, et al. On Nature's Strategy for Assigning Genetic Code Multiplicity. Plos One. 2016; 11(2).
• Hormoz S. Amino acid composition of proteins reduces deleterious impact of mutations. Sci Rep. 2013; 3: 2919.
• ılardo M, Bose R, Meringer M, Rasulev B, Grefenstette N, Stephenson J, et al. Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets. Sci Rep. 2019; 9(1): 12468.
• Jackson EL, Ollikainen N, Covert AW, 3rd, Kortemme T, Wilke CO. Amino-acid site variability among natural and designed proteins. PeerJ. 2013; 1: e211.
• Karlin S, Brocchieri L, Bergman A, Mrazek J, Gentles AJ. Amino acid runs in eukaryotic proteomes and disease associations. Proceedings of the National Academy of Sciences of the United States of America. 2002; 99(1): 333-8.
• Liu J, Bu CP, Wipfler B, Liang AP. Comparative Analysis of the Mitochondrial Genomes of Callitettixini Spittlebugs (Hemiptera: Cercopidae) Confirms the Overall High Evolutionary Speed of the AT-Rich Region but Reveals the Presence of Short Conservative Elements at the Tribal Level. Plos One. 2014; 9(10).
• Mbaye MN, Hou Q, Basu S, Teheux F, Pucci F, Rooman M. A comprehensive computational study of amino acid interactions in membrane proteins. Sci Rep. 2019; 9(1): 12043.
• McNair K, Ecale Zhou CL, Souza B, Malfatti S, Edwards RA. Utilizing Amino Acid Composition and Entropy of Potential Open Reading Frames to Identify Protein-Coding Genes. Microorganisms. 2021; 9(1).
• Tekaia F, Yeramian E, Dujon B. Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: a global picture with correspondence analysis. Gene. 2002; 297(1-2): 51-60.
• Wang HC, Li K, Susko E, Roger AJ. A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny. BMC Evol Biol. 2008; 8: 331.
• Zalucki YM, Power PM, Jennings MP. Selection for efficient translation initiation biases codon usage at second amino acid position in secretory proteins. Nucleic Acids Res. 2007; 35(17): 5748-54.
• Nacar C. Propensities of Amino Acid Pairings in Secondary Structure of Globular Proteins. Protein J. 2020; 39(1): 21-32.
• Berman H, Henrick K, Nakamura H. Announcing the worldwide Protein Data Bank. Nat Struct Biol. 2003; 10(12): 980.