Prediction of structural alphabet protein blocks using data mining

Maljković, Mirjana; Mitić, Nenad S.; Brevern, Alexandre G. de

doi:10.1016/j.biochi.2022.01.019

Cited by 4 publications

(1 citation statement)

References 37 publications

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“…Unger et al (1989) showed that six amino acid-long sections of the backbone cluster into about 100 specific conformations and that entire protein structures can be well reconstructed from these building blocks (4). The idea of creating such structural alphabets from the common conformations formed by consecutive residues has since been explored and used extensively, commonly as “Protein Blocks” of 16 prototypes defined by five consecutive amino acids (5–7). Alternative to the fragment-based approach, attempts to capture local structure have included describing rotation, twist and rise-per-residue parameters in helical structures (8), using tripeptides and a measurement of their rigidity (9), and defining a (φ, ψ) 2 motif (10–11).…”

mentioning

confidence: 99%

Defining amino acid pairs as structural units suggests mutation sensitivity to adjacent residues

Rosenberg

Yehishalom

Marx

et al. 2022

Preprint

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Proteins fold from chains of amino acids, forming secondary structures, α-helices and β-strands, that, at least for globular proteins, subsequently fold into a three-dimensional structure. A large-scale analysis of high-resolution protein structures suggests that amino acid pairs constitute another layer of ordered structure, more local than these conventionally defined secondary structures. We develop a cross-peptide-bond Ramachandran plot that captures the conformational preferences of the amino acid pairs and show that the effect of a particular mutation on the stability of a protein depends in a predictable manner on the adjacent amino acid context.One-Sentence SummaryLarge-scale protein backbone analysis reveals amino acid pair conformational preferences and predicts how sequence context affects mutant stability.

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mentioning

confidence: 99%

Defining amino acid pairs as structural units suggests mutation sensitivity to adjacent residues

Rosenberg

Yehishalom

Marx

et al. 2022

Preprint

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Designing a structure-function alphabet of helix based on reduced amino acid clusters

Yang,

Liu,

Song

et al. 2024

Archives of Biochemistry and Biophysics

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An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units

Rosenberg,

Yehishalom,

Marx

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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Protein structure, both at the global and local level, dictates function. Proteins fold from chains of amino acids, forming secondary structures, α-helices and β-strands, that, at least for globular proteins, subsequently fold into a three-dimensional structure. Here, we show that a Ramachandran-type plot focusing on the two dihedral angles separated by the peptide bond, and entirely contained within an amino acid pair, defines a local structural unit. We further demonstrate the usefulness of this cross-peptide-bond Ramachandran plot by showing that it captures β-turn conformations in coil regions, that traditional Ramachandran plot outliers fall into occupied regions of our plot, and that thermophilic proteins prefer specific amino acid pair conformations. Further, we demonstrate experimentally that the effect of a point mutation on backbone conformation and protein stability depends on the amino acid pair context, i.e., the identity of the adjacent amino acid, in a manner predictable by our method.

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Prediction of structural alphabet protein blocks using data mining

Cited by 4 publications

References 37 publications

Defining amino acid pairs as structural units suggests mutation sensitivity to adjacent residues

Defining amino acid pairs as structural units suggests mutation sensitivity to adjacent residues

Designing a structure-function alphabet of helix based on reduced amino acid clusters

An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units

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