Quantifying Steric and Hydrophobic Influence of Non-Standard Amino Acids in Proteins That Undergo Post-Translational Modifications

Luiz F. O. Rocha

doi:doi:10.11648/j.bmb.20170202.11

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Quantifying Steric and Hydrophobic Influence of Non-Standard Amino Acids in Proteins That Undergo Post-Translational Modifications

Luiz F. O. Rocha

Published in Biochemistry and Molecular Biology (Volume 2, Issue 2)

Received: 18 February 2017 Accepted: 1 March 2017 Published: 23 March 2017

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Abstract

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.

Published in	Biochemistry and Molecular Biology (Volume 2, Issue 2)
DOI	10.11648/j.bmb.20170202.11
Page(s)	12-24
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2024. Published by Science Publishing Group

Keywords

Protein Physicochemical Property, Protein Synthesis, Proteome Diversification, Residue Content Prediction, Translation

References

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Luiz F. O. Rocha. (2017). Quantifying Steric and Hydrophobic Influence of Non-Standard Amino Acids in Proteins That Undergo Post-Translational Modifications. Biochemistry and Molecular Biology, 2(2), 12-24. https://doi.org/10.11648/j.bmb.20170202.11

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ACS Style

Luiz F. O. Rocha. Quantifying Steric and Hydrophobic Influence of Non-Standard Amino Acids in Proteins That Undergo Post-Translational Modifications. Biochem. Mol. Biol. 2017, 2(2), 12-24. doi: 10.11648/j.bmb.20170202.11

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AMA Style

Luiz F. O. Rocha. Quantifying Steric and Hydrophobic Influence of Non-Standard Amino Acids in Proteins That Undergo Post-Translational Modifications. Biochem Mol Biol. 2017;2(2):12-24. doi: 10.11648/j.bmb.20170202.11

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@article{10.11648/j.bmb.20170202.11,
  author = {Luiz F. O. Rocha},
  title = {Quantifying Steric and Hydrophobic Influence of Non-Standard Amino Acids in Proteins That Undergo Post-Translational Modifications},
  journal = {Biochemistry and Molecular Biology},
  volume = {2},
  number = {2},
  pages = {12-24},
  doi = {10.11648/j.bmb.20170202.11},
  url = {https://doi.org/10.11648/j.bmb.20170202.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.bmb.20170202.11},
  abstract = {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.},
 year = {2017}
}

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TY  - JOUR
T1  - Quantifying Steric and Hydrophobic Influence of Non-Standard Amino Acids in Proteins That Undergo Post-Translational Modifications
AU  - Luiz F. O. Rocha
Y1  - 2017/03/23
PY  - 2017
N1  - https://doi.org/10.11648/j.bmb.20170202.11
DO  - 10.11648/j.bmb.20170202.11
T2  - Biochemistry and Molecular Biology
JF  - Biochemistry and Molecular Biology
JO  - Biochemistry and Molecular Biology
SP  - 12
EP  - 24
PB  - Science Publishing Group
SN  - 2575-5048
UR  - https://doi.org/10.11648/j.bmb.20170202.11
AB  - 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.
VL  - 2
IS  - 2
ER  -

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Luiz F. O. Rocha

Department of Physics and Chemistry, Faculty of Pharmaceutical Sciences of Ribeir?o Preto, University of S?o Paulo, Ribeir?o Preto, S?o Paulo, Brazil

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Luiz F. O. Rocha. (2017). Quantifying Steric and Hydrophobic Influence of Non-Standard Amino Acids in Proteins That Undergo Post-Translational Modifications. Biochemistry and Molecular Biology, 2(2), 12-24. https://doi.org/10.11648/j.bmb.20170202.11

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ACS Style

Luiz F. O. Rocha. Quantifying Steric and Hydrophobic Influence of Non-Standard Amino Acids in Proteins That Undergo Post-Translational Modifications. Biochem. Mol. Biol. 2017, 2(2), 12-24. doi: 10.11648/j.bmb.20170202.11

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AMA Style

Luiz F. O. Rocha. Quantifying Steric and Hydrophobic Influence of Non-Standard Amino Acids in Proteins That Undergo Post-Translational Modifications. Biochem Mol Biol. 2017;2(2):12-24. doi: 10.11648/j.bmb.20170202.11

Copy | Download

@article{10.11648/j.bmb.20170202.11,
  author = {Luiz F. O. Rocha},
  title = {Quantifying Steric and Hydrophobic Influence of Non-Standard Amino Acids in Proteins That Undergo Post-Translational Modifications},
  journal = {Biochemistry and Molecular Biology},
  volume = {2},
  number = {2},
  pages = {12-24},
  doi = {10.11648/j.bmb.20170202.11},
  url = {https://doi.org/10.11648/j.bmb.20170202.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.bmb.20170202.11},
  abstract = {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.},
 year = {2017}
}

Copy | Download

TY  - JOUR
T1  - Quantifying Steric and Hydrophobic Influence of Non-Standard Amino Acids in Proteins That Undergo Post-Translational Modifications
AU  - Luiz F. O. Rocha
Y1  - 2017/03/23
PY  - 2017
N1  - https://doi.org/10.11648/j.bmb.20170202.11
DO  - 10.11648/j.bmb.20170202.11
T2  - Biochemistry and Molecular Biology
JF  - Biochemistry and Molecular Biology
JO  - Biochemistry and Molecular Biology
SP  - 12
EP  - 24
PB  - Science Publishing Group
SN  - 2575-5048
UR  - https://doi.org/10.11648/j.bmb.20170202.11
AB  - 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.
VL  - 2
IS  - 2
ER  -

Copy | Download