Quantifying Steric and Hydrophobic Influence of Non-Standard Amino Acids in Proteins That Undergo Post-Translational Modifications
Biochemistry and Molecular Biology
Volume 2, Issue 2, March 2017, Pages: 12-24
Received: Feb. 18, 2017; Accepted: Mar. 1, 2017; Published: Mar. 23, 2017
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Luiz F. O. Rocha, Department of Physics and Chemistry, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
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Non-standard amino acids in protein post-translational modifications aid in a wide variety of biological functions and processes, furnishing expansion from the genome to the proteome. First, from structural examinations in unmodified proteins with only standard amino acids, this work empirically obtains numeric relations that reveal how instruction transfers occur between native-state structures. Next, from these relations, the influence of non-standard amino acids inside post-translationally modified proteins is quantified by successfully predicting the contents of large and hydrophobic residues in helices and β-strands for 210 inspections performed. This suggests a twofold molecular mechanism by the fundamental biophysicochemical properties (residue volume and hydrophobicity), and concludes that the utilized non-standard amino acids have limited global influence at the residue level. Our prediction method provides a better underlying understanding of molecular interactions and mechanisms, and is particularly promising in terms of surveying further modified proteins.
Protein Physicochemical Property, Protein Synthesis, Proteome Diversification, Residue Content Prediction, Translation
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Luiz F. O. Rocha, Quantifying Steric and Hydrophobic Influence of Non-Standard Amino Acids in Proteins That Undergo Post-Translational Modifications, Biochemistry and Molecular Biology. Vol. 2, No. 2, 2017, pp. 12-24. doi: 10.11648/j.bmb.20170202.11
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