A numerical measure of amino acid residues similarity based on the analysis of their surroundings in natural protein sequences

Rogov, S. I.; Nekrasov, A. N.

doi:10.1093/protein/14.7.459

Cited by 21 publications

(19 citation statements)

References 15 publications

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“…Li and co-workers -with various clustering schemes-used BLOSUM62 and analyzed the consequences of the reduction of the number of amino acid kinds on sequence alignments (Li et al 2003). In the same way, Rogov and Nekrasov, exploited the influence of the neighboring residues (Rogov and Nekrasov 2001), while Smith and Smith simply analyzed aligned sequences (Smith and Smith 1990).…”

Section: Introductionmentioning

confidence: 99%

A reduced amino acid alphabet for understanding and designing protein adaptation to mutation

et al. 2007

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Protein sequence world is considerably larger than structure world. In consequence, numerous non-related sequences may adopt similar 3D folds and different kinds of amino acids may thus be found in similar 3D structures. By grouping together the 20 amino acids into a smaller number of representative residues with similar features, sequence world simplification may be achieved. This clustering hence defines a reduced amino acid alphabet (reduced AAA). Numerous works have shown that protein 3D structures are composed of a limited number of building blocks, defining a structural alphabet. We previously identified such an alphabet composed of 16 representative structural motifs (5-residues length) called Protein Blocks (PBs). This alphabet permits to translate the structure (3D) in sequence of PBs (1D). Based on these two concepts, reduced AAA and PBs, we analyzed the distributions of the different kinds of amino acids and their equivalences in the structural context. Different reduced sets were considered. Recurrent amino acid associations were found in all the local structures while other were specific of some local structures (PBs) (e.g Cysteine, Histidine, Threonine and Serine for the alpha-helix Ncap). Some similar associations are found in other reduced AAAs, e.g Ile with Val, or hydrophobic aromatic residues Trp with Phe and Tyr. We put into evidence interesting alternative associations. This highlights the dependence on the information considered (sequence or structure). This approach, equivalent to a substitution matrix, could be useful for designing protein sequence with different features (for instance adaptation to environment) while preserving mainly the 3D fold.

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Section: Introductionmentioning

confidence: 99%

A reduced amino acid alphabet for understanding and designing protein adaptation to mutation

et al. 2007

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“…В качестве значений факторов для использования в методе Тагучи были выбраны пять аминокислот из пяти групп подобия, сформированных на основе окружения аминокислотных остатков в первичных структурах 168808 белков [10]. Характерные представители каждой группы составили стартовый набор значений факторов, использованных при моделировании пептидного лиганда.…”

Section: выбор значений факторовunclassified

Application of Taguchi Method for Optimization of the Peptide Ligand Structure

Danilkovich¹

2016

Math.Biol.Bioinf.

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Аннотация. Для моделирования структуры пептидного лиганда в составе комплекса белков главного комплекса гистосовместимости и Т-клеточного рецептора (PDB ID 2Z31) был использован метод Тагучи, позволивший сократить число экспериментов, требуемых для анализа вклада различных аминокислотных остатков по каждой позиции активного участка молекулы лиганда. В соответствии с методом Тагучи исследован ряд прототипов молекул лиганда в виде пространственных моделей, которые были использованы для молекулярного докинга с оптимизацией структуры комплексов по критерию минимизации внутренней молекулярно-механической энергии. Получена аминокислотная последовательность пептида, которая демонстрирует уменьшение энергии комплекса по сравнению с природным лигандом, что демонстрирует применимость метода Тагучи для оптимизации структуры пептидов с целью разработки новых молекул лигандов.Ключевые слова: метод Тагучи, оптимизация структуры, пространственная модель, первичная структура.

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“…(iv) "Information content" profile of the protein sequence was generated using parameters of residue frequencies obtained earlier. 8,9 Characteristics of residue frequencies were analyzed earlier for three different sets of non-homologous protein data sets. 8,9 (v) To determine IDIC-sites the "information content" profile of the protein sequence, obtained at the step 2, was decomposed into Gaussian curves with a Closely located IDIC-branches of low hierarchic level are of a special interest in IS.…”

Section: Information Structure (Is) Analysismentioning

confidence: 99%

Selection of Cryptic B-Cell Epitopes Using Informational Analysis of Protein Sequenses

Svirshchevskaya

Alekseeva

Marchenko

et al. 2006

J. Bioinform. Comput. Biol.

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Sub-unit vaccines are synthetic or recombinant peptides representing T- or B-cell epitopes of major protein antigens from a particular pathogen. Epitope selection requires the synthesis of peptides that overlap the protein sequences and screening for the most effective ones. In this study a new method of immunogenic peptide selection based on the analysis of information structure of protein sequences is suggested. The analysis of known B-cell epitope location in the information structure of Aspergillus fumigatus proteins Asp f 2 and Asp f 3 has shown that epitopes are scattered along the sequences of proteins for the exception of sites with Increased Degree Information Coordination (IDIC). Based on these results peptides from different allergens such as Asp f 2, Der p 1, and Fel d 1 were selected and produced in a recombinant form in the context of yeast virus-like particles (VLPs). Immunization of mice with VLPs containing peptides form allergens has induced the production of IgG able to recognize full-length antigens. This result suggests that the analysis of information structure of proteins can be used for the selection of peptides possessing cryptic B-cell epitope activity.

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A numerical measure of amino acid residues similarity based on the analysis of their surroundings in natural protein sequences

Cited by 21 publications

References 15 publications

A reduced amino acid alphabet for understanding and designing protein adaptation to mutation

A reduced amino acid alphabet for understanding and designing protein adaptation to mutation

Application of Taguchi Method for Optimization of the Peptide Ligand Structure

Selection of Cryptic B-Cell Epitopes Using Informational Analysis of Protein Sequenses

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