Amino acid content of beta strands and alpha helices depends on their flanking secondary structure elements

Khrustalev, Vladislav Victorovich; Khrustaleva, Tatyana Aleksandrovna; Poboinev, Victor Vitoldovich

doi:10.1016/j.biosystems.2018.04.002

Cited by 11 publications

(4 citation statements)

References 21 publications

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“…It might be that the Ser126Cys substitution is significant for the stability of the secondary structure elements and/or the overall 3D structure of the protein. By applying the PentaFOLD 2.0 algorithm (Khrustalev et al, 2018) to the model of the N-terminal fragment of M1 built based on PDB ID 4PUS Chain A, we found that a long stretch of hydrophobic amino acids (AGALA C CMGLIY), that appears to be due to the Ser126Cys change, destabilizes α-helix H8 (Fig. 7a).…”

Section: Resultsmentioning

confidence: 99%

“…The multiple sequence comparison by log-expectation (MUSCLE) server (https://www.ebi.ac.uk/Tools/msa/muscle/) was used for multiple amino acid sequence alignments; the PentaFOLD 2.0 algorithm (http://chemres.bsmu.by/) (Khrustalev et al, 2018) was applied to examine the stability of the α-helices of the M1 protein; the Swiss Model server (https://swissmodel.expasy.org) and Swiss protein data bank (PDB) viewer were used for 3D modeling and visualization; the Protein Interactions Calculator (http:// pic.mbu.iisc.ernet.in) was applied to identify the amino acid residues involved in protein-protein interactions; and the DSSP (http://www.cmbi.ru.nl/xssp/) method was applied to calculate relative protein surface accessibility values.…”

Section: Bioinformatics Approachesmentioning

confidence: 99%

“…However, this α-helix is not quite stable even with the presence of Ser-126 ( Fig. 7b) since completely hydrophobic pentapeptides tend to form beta sheets autonomously (Khrustalev et al, 2018). Unlike the hydroxyl group of Ser-126, the sulfhydryl group of Cys-126 is able to form additional hydrogen bonds with the main chain oxygen atom of Asn-85 and the main chain nitrogen atom of Gly-86.…”

Section: M1 Protein Bioinformatics and Structural Analysismentioning

confidence: 99%

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Filamentous versus Spherical Morphology: A Case Study of the Recombinant A/WSN/33 (H1N1) Virus

et al. 2020

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Influenza A virus is a serious human pathogen that assembles enveloped virions on the plasma membrane of the host cell. The pleiomorphic morphology of influenza A virus, represented by spherical, elongated, or filamentous particles, is important for the spread of the virus in nature. Using fixative protocols for sample preparation and negative staining electron microscopy, we found that the recombinant A/WSN/33 (H1N1) (rWSN) virus, a strain considered to be strictly spherical, may produce filamentous particles when amplified in the allantoic cavity of chicken embryos. In contrast, the laboratory WSN strain and the rWSN virus amplified in Madin–Darby canine kidney cells exhibited a spherical morphology. Next-generation sequencing (NGS) suggested a rare Ser126Cys substitution in the M1 protein of rWSN, which was confirmed by the mass spectrometric analysis. No structurally relevant substitutions were found by NGS in other proteins of rWSN. Bioinformatics algorithms predicted a neutral structural effect of the Ser126Cys mutation. The mrWSN_M1_126S virus generated after the introduction of the reverse Cys126Ser substitution exhibited a similar host-dependent partially filamentous phenotype. We hypothesize that a shortage of some as-yet-undefined cellular components involved in virion budding and membrane scission may result in the appearance of filamentous particles in the case of usually “nonfilamentous” virus strains.

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Section: Resultsmentioning

confidence: 99%

Section: Bioinformatics Approachesmentioning

confidence: 99%

Section: M1 Protein Bioinformatics and Structural Analysismentioning

confidence: 99%

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Filamentous versus Spherical Morphology: A Case Study of the Recombinant A/WSN/33 (H1N1) Virus

et al. 2020

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“…Transitions of β-strand to α-helix are known to occur in proteins [57], as for example in amyloid peptides in Alzheimer [58] and the prion protein in scrapie [59], but it is not known whether a similar β-strand/α-helix transition occurs in the CaM-BD of Grb7 during Ca 2þ /CaM binding. This is a possibility of interest to be further studied in the future.…”

Section: Discussionmentioning

confidence: 99%

Grb7-derived calmodulin-binding peptides inhibit proliferation, migration and invasiveness of tumor cells while they enhance attachment to the substrate

Alcalde

González‐Muñoz

Villalobo

2020

Heliyon

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The growth factor receptor bound protein 7 (Grb7) is a Ca 2þ -dependent calmodulin (CaM)-binding adaptor protein implicated, among other functions, in cell proliferation, migration and tumor-associated angiogenesis. The goal of this study was to determine whether a peptide based on the CaM binding site of Grb7 disrupts cellular processes, relevant for the malignancy of tumor cells, in which this adaptor protein is implicated. We designed synthetic myristoylated and non-myristoylated peptides corresponding to the CaM-binding domain of human Grb7 with the sequence 243 RKLWKRFFCFLRRS 256 and a variant peptide with the mutated sequence RKLERFFCFLRRE (W246E-ΔK247-S256E). The two non-myristoylated peptides bind dansyl-CaM with higher efficiency in the presence than in the absence of Ca 2þ and they enter into the cell, as tested with 5(6)-carboxytetramethylrhodamine (TAMRA)-labeled peptides. The myristoylated and non-myristoylated peptides inhibit the proliferation, migration and invasiveness of A431 tumor cells while they enhance their adhesion to the substrate. The myristoylated peptides have stronger inhibitory effect than the non-myristoylated counterparts, in agreement with their expected higher cell-permeant capacity. The myristoylated and non-myristoylated W246E-ΔK247-S256E mutant peptide has a lesser inhibitory effect on cell proliferation as compared to the wild-type peptide. We also demonstrated that the myristoylated peptides were more efficient than the CaM antagonist N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide (W-7) inhibiting cell migration and equally efficient inhibiting cell proliferation.

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Microenvironment of tryptophan residues in proteins of four structural classes: applications for fluorescence and circular dichroism spectroscopy

et al. 2019

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Amino acid content of beta strands and alpha helices depends on their flanking secondary structure elements

Cited by 11 publications

References 21 publications

Filamentous versus Spherical Morphology: A Case Study of the Recombinant A/WSN/33 (H1N1) Virus

Filamentous versus Spherical Morphology: A Case Study of the Recombinant A/WSN/33 (H1N1) Virus

Grb7-derived calmodulin-binding peptides inhibit proliferation, migration and invasiveness of tumor cells while they enhance attachment to the substrate

Microenvironment of tryptophan residues in proteins of four structural classes: applications for fluorescence and circular dichroism spectroscopy

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