Solvent accessibility, residue charge and residue volume, the three ingredients of a robust amino acid substitution matrix

Goodarzi, Hani; Katanforoush, Ali; Torabi, Noorossadat; Najafabadi, Hamed S.

doi:10.1016/j.jtbi.2006.12.014

Cited by 8 publications

(7 citation statements)

References 49 publications

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“…However, the polarity of charge and the effects of changing this polarity were not taken into account. As a consequence, changes in amino acid charge from positive to negative or vice versa were usually assigned only low penalties, other than changes in amino acid hydropathy and size (Berleant et al, 2009;Goodarzi et al, 2007;Miyata et al, 1979;Nemzer, 2017).…”

Section: Resultsmentioning

confidence: 99%

Global importance of RNA secondary structures in protein-coding sequences

Fricke

Gerst²,

Ibrahim

et al. 2018

Bioinformatics

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We show that the nucleotide distribution within codons is biased in all taxa of life on a global scale. Thereby, RNA secondary structures that require base-pairing between the position 1 of a codon with the position 1 of an opposing codon (here named RNA secondary structure class c1) are under-represented. We conclude that this bias may result from the co-evolution of codon sequence and mRNA secondary structure, suggesting that RNA secondary structures are generally important in protein coding regions of mRNAs. The above result also implies that codon position 2 has a smaller influence on the amino acid choice than codon position 1.

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Section: Resultsmentioning

confidence: 99%

Global importance of RNA secondary structures in protein-coding sequences

Fricke

Gerst²,

Ibrahim

et al. 2018

Bioinformatics

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“…The essence of the mutational robustness in the codon-to-residue mapping is that these more harmless mutations are more likely to result from a single point mutation or from a more probable mistranslation. In the same way, mutations that are more likely to be harmful are less likely to occur from a single point mutation, instead requiring two or three point mutations in the same codon, a much rarer occurrence [13,14,18].…”

Section: The Codon Table Buffers Mutations and Mistranslationsmentioning

confidence: 99%

The Genetic Code—More Than Just a Table

Berleant

White²,

Pierce

et al. 2009

Cell Biochem Biophys

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The standard codon table is a primary tool for basic understanding of molecular biology. In the minds of many, the table's orderly arrangement of bases and amino acids is synonymous with the true genetic code, i.e., the biological coding principle itself. However, developments in the field reveal a much more complex and interesting picture. In this article, we review the traditional codon table and its limitations in light of the true complexity of the genetic code. We suggest the codon table be brought up to date and, as a step, we present a novel superposition of the BLOSUM62 matrix and an allowed point mutation matrix. This superposition depicts an important aspect of the true genetic code-its ability to tolerate mutations and mistranslations.

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“…Among such properties, the volume and hydrophobicity have been considered as two primary components [24][25]. The residue volumes (steric contributions) and hydrophobicities (hydrophobic effect and interactions) are dominant throughout the selection and maintenance of threedimensional folded configurations under varied physiological conditions and environmental contexts [26][27].…”

Section: Amino Acid Types Primary and Secondary Structures And Predmentioning

confidence: 99%

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

Rocha¹

2017

BMB

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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 posttranslationally 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.

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Solvent accessibility, residue charge and residue volume, the three ingredients of a robust amino acid substitution matrix

Cited by 8 publications

References 49 publications

Global importance of RNA secondary structures in protein-coding sequences

Global importance of RNA secondary structures in protein-coding sequences

The Genetic Code—More Than Just a Table

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

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