Functionally Significant Amino Acid Motifs of Heat Shock Proteins: Structural and Bioinformatics Analyses of Hsp60/Hsp10 in Five Classes of Chordata

Tikhomirova, Tatyana S.; Galzitskaya, Oxana V.

doi:10.1134/s0026893318050138

Cited by 3 publications

(19 citation statements)

References 61 publications

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“…Average PID values were calculated for 19220 Hsp60 sequences in 19 phyla (Table 1), where they ranged from 28±4% (Viruses) to 84±6% (Chordata). The maximum average PID value was determined for the Hsp60 sequences belonging to Chordata, which was expected in accordance with our previous work 14 . The minimum average PID value corresponds to Viruses, which can be explained by their high mutation rate.…”

Section: Pid Estimationsupporting

confidence: 85%

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In-depth analysis of amino acid and nucleotide sequences of Hsp60: how conserved is this protein?

Tikhomirova

Matyunin

Лобанов

et al. 2021

Preprint

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Chaperonin Hsp60, as a protein found in all organisms, is of great interest in medicine, since it is present in many tissues and can be used both as a drug and as an object of targeted therapy. Hence, Hsp60 deserves a fundamental comparative analysis to assess its evolutionary characteristics. It was found that the percent identity of Hsp60 amino acid sequences both within and between phyla was not high enough to identify Hsp60s as highly conserved proteins. In turn, their amino acid composition remained relatively constant. At the same time, the analysis of the nucleotide sequences showed that GC content in the Hsp60 genes was comparable to or greater than the genomic values, which may indicate a high resistance to mutations due to tight control of the nucleotide composition by DNA repair systems. Natural selection plays a dominant role in the evolution of Hsp60 genes. The degree of mutational pressure affecting the Hsp60 genes is quite low, and its direction does not depend on taxonomy. Interestingly, for the Hsp60 genes from Chordata, Arthropoda, and Proteobacteria the exact direction of mutational pressure could not be determined. However, upon further division into classes, it was found that the direction of the mutational pressure for Hsp60 genes from Fish differs from that for other chordates. The direction of the mutational pressure affects the synonymous codon usage bias. The number of high and low represented codons increases with increasing GC content, which can improve codon usage.

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Section: Pid Estimationsupporting

confidence: 85%

“…At present, in-depth analysis of Hsp60 sequences in silico is quite rare, although it is a very interesting object for research. Since Hsp60 is ubiquitous, it can be used in evolutionary analysis of organisms belonging to different taxonomic groups [12][13][14][15] . Using bioinformatics, epitopes in Hsp60 can be predicted 16,17 .…”

Section: Introductionmentioning

confidence: 99%

In-depth analysis of amino acid and nucleotide sequences of Hsp60: how conserved is this protein?

Tikhomirova

Matyunin

Лобанов

et al. 2021

Preprint

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“…In addition, amino acid residues at position from 330 to 360 can also be considered disordered. This region is located between the apical and intermediate domain of Hsp60 14 . The presence of disordered amino acid residues here can contribute to conformational changes during the ATP hydrolysis.…”

Section: Resultsmentioning

confidence: 96%

“…The ENC values and the GC 3 content of the Hsp60 genes in cluster #2 differ more than in cluster #1. This feature can be explained by the fact that Hsp60 from Fish is evolutionarily far from Hsp60 from other Chordata classes 14 …”

Section: Resultsmentioning

confidence: 99%

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In‐depth analysis of amino acid and nucleotide sequences of Hsp60: How conserved is this protein?

et al. 2022

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Chaperonin Hsp60, as a protein found in all organisms, is of great interest in medicine, since it is present in many tissues and can be used both as a drug and as an object of targeted therapy. Hence, Hsp60 deserves a fundamental comparative analysis to assess its evolutionary characteristics. It was found that the percent identity of Hsp60 amino acid sequences both within and between phyla was not high enough to identify Hsp60s as highly conserved proteins. However, their ATP binding sites are largely conserved. The amino acid composition of Hsp60s remained relatively constant. At the same time, the analysis of the nucleotide sequences showed that GC content in the Hsp60 genes was comparable to or greater than the genomic values, which may indicate a high resistance to mutations due to tight control of the nucleotide composition by DNA repair systems. Natural selection plays a dominant role in the evolution of Hsp60 genes. The degree of mutational pressure affecting the Hsp60 genes is quite low, and its direction does not depend on taxonomy. Interestingly, for the Hsp60 genes from Chordata, Arthropoda, and Proteobacteria the exact direction of mutational pressure could not be determined. However, upon further division into classes, it was found that the direction of the mutational pressure for Hsp60 genes from Fish differs from that for other chordates. The direction of the mutational pressure affects the synonymous codon usage bias. The number of high and low represented codons increases with increasing GC content, which can improve codon usage. Special server has been created for bioinformatics analysis of Hsp60: http://oka.protres.ru:4202/.

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Inhibition of Aβ_1–42 Fibrillation by Chaperonins: Human Hsp60 Is a Stronger Inhibitor than Its Bacterial Homologue GroEL

Vilasi

Carrotta

Ricci

et al. 2019

ACS Chem. Neurosci.

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Alzheimer’s disease is a chronic neurodegenerative disease characterized by the accumulation of pathological aggregates of amyloid beta peptide. Many efforts have been focused on understanding peptide aggregation pathways and on identification of molecules able to inhibit aggregation in order to find an effective therapy. As a result, interest in neuroprotective proteins, such as molecular chaperones, has increased as their normal function is to assist in protein folding or to facilitate the disaggregation and/or clearance of abnormal aggregate proteins. Using biophysical techniques, we evaluated the effects of two chaperones, human Hsp60 and bacterial GroEL, on the fibrillogenesis of Aβ1–42. Both chaperonins interfere with Aβ1–42 aggregation, but the effect of Hsp60 is more significant and correlates with its more pronounced flexibility and stronger interaction with ANS, an indicator of hydrophobic regions. Dose-dependent ThT fluorescence kinetics and SAXS experiments reveal that Hsp60 does not change the nature of the molecular processes stochastically leading to the formation of seeds, but strongly delays them by recognition of hydrophobic sites of some peptide species crucial for triggering amyloid formation. Hsp60 reduces the initial chaotic heterogeneity of Aβ1–42 sample at high concentration regimes. The understanding of chaperone action in counteracting pathological aggregation could be a starting point for potential new therapeutic strategies against neurodegenerative diseases.

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Functionally Significant Amino Acid Motifs of Heat Shock Proteins: Structural and Bioinformatics Analyses of Hsp60/Hsp10 in Five Classes of Chordata

Cited by 3 publications

References 61 publications

In-depth analysis of amino acid and nucleotide sequences of Hsp60: how conserved is this protein?

In-depth analysis of amino acid and nucleotide sequences of Hsp60: how conserved is this protein?

In‐depth analysis of amino acid and nucleotide sequences of Hsp60: How conserved is this protein?

Inhibition of Aβ_1–42 Fibrillation by Chaperonins: Human Hsp60 Is a Stronger Inhibitor than Its Bacterial Homologue GroEL

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Functionally Significant Amino Acid Motifs of Heat Shock Proteins: Structural and Bioinformatics Analyses of Hsp60/Hsp10 in Five Classes of Chordata

Cited by 3 publications

References 61 publications

In-depth analysis of amino acid and nucleotide sequences of Hsp60: how conserved is this protein?

In-depth analysis of amino acid and nucleotide sequences of Hsp60: how conserved is this protein?

In‐depth analysis of amino acid and nucleotide sequences of Hsp60: How conserved is this protein?

Inhibition of Aβ1–42 Fibrillation by Chaperonins: Human Hsp60 Is a Stronger Inhibitor than Its Bacterial Homologue GroEL

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Inhibition of Aβ_1–42 Fibrillation by Chaperonins: Human Hsp60 Is a Stronger Inhibitor than Its Bacterial Homologue GroEL