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Using a viral 2A peptide-based strategy to reconstruct the bovine P450scc steroidogenic system in S. cerevisiae

Efimova, Vera S. ; Isaeva, Ludmila V. ; Orekhov, Philipp S. ; [et al.]

Elsevier BV ; 2021

In: Journal of Biotechnology Vol. 325 ( 2021-01), p. 186-195

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In: Journal of Biotechnology, Elsevier BV, Vol. 325 ( 2021-01), p. 186-195

Type of Medium: Online Resource

ISSN: 0168-1656

URL: Article

DOI: 10.1016/j.jbiotec.2020.10.028

Language: English

Publisher: Elsevier BV

Publication Date: 2021

detail.hit.zdb_id: 2016476-2

SSG: 12

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Mechanisms of Formation, Structure, and Dynamics of Lipoprotein Discs Stabilized by Amphiphilic Copolymers: A Comprehensive Review

Orekhov, Philipp S. ; Bozdaganyan, Marine E. ; Voskoboynikova, Natalia ; [et al.]

MDPI AG ; 2022

In: Nanomaterials Vol. 12, No. 3 ( 2022-01-23), p. 361-

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In: Nanomaterials, MDPI AG, Vol. 12, No. 3 ( 2022-01-23), p. 361-

Abstract: Amphiphilic copolymers consisting of alternating hydrophilic and hydrophobic units account for a major recent methodical breakthrough in the investigations of membrane proteins. Styrene–maleic acid (SMA), diisobutylene–maleic acid (DIBMA), and related copolymers have been shown to extract membrane proteins directly from lipid membranes without the need for classical detergents. Within the particular experimental setup, they form disc-shaped nanoparticles with a narrow size distribution, which serve as a suitable platform for diverse kinds of spectroscopy and other biophysical techniques that require relatively small, homogeneous, water-soluble particles of separate membrane proteins in their native lipid environment. In recent years, copolymer-encased nanolipoparticles have been proven as suitable protein carriers for various structural biology applications, including cryo-electron microscopy (cryo-EM), small-angle scattering, and conventional and single-molecule X-ray diffraction experiments. Here, we review the current understanding of how such nanolipoparticles are formed and organized at the molecular level with an emphasis on their chemical diversity and factors affecting their size and solubilization efficiency.

Type of Medium: Online Resource

ISSN: 2079-4991

URL: Article

DOI: 10.3390/nano12030361

Language: English

Publisher: MDPI AG

Publication Date: 2022

detail.hit.zdb_id: 2662255-5

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Computational Analysis of Mutations in the Receptor-Binding Domain of SARS-CoV-2 Spike and Their Effects on Antibody Binding

Bozdaganyan, Marine E. ; Shaitan, Konstantin V. ; Kirpichnikov, Mikhail P. ; [et al.]

MDPI AG ; 2022

In: Viruses Vol. 14, No. 2 ( 2022-01-30), p. 295-

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In: Viruses, MDPI AG, Vol. 14, No. 2 ( 2022-01-30), p. 295-

Abstract: Currently, SARS-CoV-2 causing coronavirus disease 2019 (COVID-19) is responsible for one of the most deleterious pandemics of our time. The interaction between the ACE2 receptors at the surface of human cells and the viral Spike (S) protein triggers the infection, making the receptor-binding domain (RBD) of the SARS-CoV-2 S-protein a focal target for the neutralizing antibodies (Abs). Despite the recent progress in the development and deployment of vaccines, the emergence of novel variants of SARS-CoV-2 insensitive to Abs produced in response to the vaccine administration and/or monoclonal ones represent a potential danger. Here, we analyzed the diversity of neutralizing Ab epitopes and assessed the possible effects of single and multiple mutations in the RBD of SARS-CoV-2 S-protein on its binding affinity to various antibodies and the human ACE2 receptor using bioinformatics approaches. The RBD-Ab complexes with experimentally resolved structures were grouped into four clusters with distinct features at sequence and structure level. The performed computational analysis indicates that while single amino acid replacements in RBD may only cause partial impairment of the Abs binding, moreover, limited to specific epitopes, the variants of SARS-CoV-2 with multiple mutations, including some which were already detected in the population, may potentially result in a much broader antigenic escape. Further analysis of the existing RBD variants pointed to the trade-off between ACE2 binding and antigenic escape as a key limiting factor for the emergence of novel SAR-CoV-2 strains, as the naturally occurring mutations in RBD tend to reduce its binding affinity to Abs but not to ACE2. The results provide guidelines for further experimental studies aiming to identify high-risk RBD mutations that allow for an antigenic escape.

Type of Medium: Online Resource

ISSN: 1999-4915

URL: Article

DOI: 10.3390/v14020295

Language: English

Publisher: MDPI AG

Publication Date: 2022

detail.hit.zdb_id: 2516098-9

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Ambiguities in and completeness of SAS data analysis of membrane proteins: the case of the sensory rhodopsin II–transducer complex

Ryzhykau, Yury L. ; Vlasov, Alexey V. ; Orekhov, Philipp S. ; [et al.]

International Union of Crystallography (IUCr) ; 2021

In: Acta Crystallographica Section D Structural Biology Vol. 77, No. 11 ( 2021-11-01), p. 1386-1400

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In: Acta Crystallographica Section D Structural Biology, International Union of Crystallography (IUCr), Vol. 77, No. 11 ( 2021-11-01), p. 1386-1400

Abstract: Membrane proteins (MPs) play vital roles in the function of cells and are also major drug targets. Structural information on proteins is vital for understanding their mechanism of function and is critical for the development of drugs. However, obtaining high-resolution structures of membrane proteins, in particular, under native conditions is still a great challenge. In such cases, the low-resolution methods small-angle X-ray and neutron scattering (SAXS and SANS) might provide valuable structural information. However, in some cases small-angle scattering (SAS) provides ambiguous ab initio structural information if complementary measurements are not performed and/or a priori information on the protein is not taken into account. Understanding the nature of the limitations may help to overcome these problems. One of the main problems of SAS data analysis of solubilized membrane proteins is the contribution of the detergent belt surrounding the MP. Here, a comprehensive analysis of how the detergent belt contributes to the SAS data of a membrane-protein complex of sensory rhodopsin II with its cognate transducer from Natronomonas pharaonis ( Np SRII– Np HtrII) was performed. The influence of the polydispersity of Np SRII– Np HtrII oligomerization is the second problem that is addressed here. It is shown that inhomogeneity in the scattering length density of the detergent belt surrounding a membrane part of the complex and oligomerization polydispersity significantly impacts on SAXS and SANS profiles, and therefore on 3D ab initio structures. It is described how both problems can be taken into account to improve the quality of SAS data treatment. Since SAS data for MPs are usually obtained from solubilized proteins, and their detergent belt and, to a certain extent, oligomerization polydispersity are sufficiently common phenomena, the approaches proposed in this work might be used in SAS studies of different MPs.

Type of Medium: Online Resource

ISSN: 2059-7983

URL: Article

DOI: 10.1107/S2059798321009542

Language: Unknown

Publisher: International Union of Crystallography (IUCr)

Publication Date: 2021

detail.hit.zdb_id: 2968623-4

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Lipid dynamics in nanoparticles formed by maleic acid-containing copolymers: EPR spectroscopy and molecular dynamics simulations

Colbasevici, Alexandr ; Voskoboynikova, Natalia ; Orekhov, Philipp S. ; [et al.]

Elsevier BV ; 2020

In: Biochimica et Biophysica Acta (BBA) - Biomembranes Vol. 1862, No. 5 ( 2020-05), p. 183207-

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In: Biochimica et Biophysica Acta (BBA) - Biomembranes, Elsevier BV, Vol. 1862, No. 5 ( 2020-05), p. 183207-

Type of Medium: Online Resource

ISSN: 0005-2736

URL: Article

DOI: 10.1016/j.bbamem.2020.183207

RVK:

WA 15000

Language: English

Publisher: Elsevier BV

Publication Date: 2020

detail.hit.zdb_id: 2209384-9

SSG: 12

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Molecular Mechanism of Uptake of Cationic Photoantimicrobial Phthalocyanine across Bacterial Membranes Revealed by Molecular Dynamics Simulations

Orekhov, Philipp S. ; Kholina, Ekaterina G. ; Bozdaganyan, Marine E. ; [et al.]

American Chemical Society (ACS) ; 2018

In: The Journal of Physical Chemistry B Vol. 122, No. 14 ( 2018-04-12), p. 3711-3722

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In: The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol. 122, No. 14 ( 2018-04-12), p. 3711-3722

Type of Medium: Online Resource

ISSN: 1520-6106 , 1520-5207

URL: Article

DOI: 10.1021/acs.jpcb.7b11707

DOI: 10.1021/acs.jpcb.7b11707.s001

DOI: 10.1021/acs.jpcb.7b11707.s002

DOI: 10.1021/acs.jpcb.7b11707.s003

RVK:

VA5430.B

Language: English

Publisher: American Chemical Society (ACS)

Publication Date: 2018

detail.hit.zdb_id: 1357799-2

detail.hit.zdb_id: 2006039-7

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CPE-DB: An Open Database of Chemical Penetration Enhancers

Vasyuchenko, Ekaterina P. ; Orekhov, Philipp S. ; Armeev, Grigoriy A. ; [et al.]

MDPI AG ; 2021

In: Pharmaceutics Vol. 13, No. 1 ( 2021-01-07), p. 66-

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In: Pharmaceutics, MDPI AG, Vol. 13, No. 1 ( 2021-01-07), p. 66-

Abstract: The cutaneous delivery route currently accounts for almost 10% of all administered drugs and it is becoming more common. Chemical penetration enhancers (CPEs) increase the transport of drugs across skin layers by different mechanisms that depend on the chemical nature of the penetration enhancers. In our work, we created a chemical penetration enhancer database (CPE-DB) that is, to the best of our knowledge, the first CPE database. We collected information about known enhancers and their derivatives in a single database, and classified and characterized their molecular diversity in terms of scaffold content, key chemical moieties, molecular descriptors, etc. CPE-DB can be used for virtual screening and similarity search to identify new potent and safe enhancers, building quantitative structure–activity relationship (QSAR) and quantitative structure–property relationship (QSPR) models, and other machine-learning (ML) applications for the prediction of biological activity.

Type of Medium: Online Resource

ISSN: 1999-4923

URL: Article

DOI: 10.3390/pharmaceutics13010066

Language: English

Publisher: MDPI AG

Publication Date: 2021

detail.hit.zdb_id: 2527217-2

SSG: 15,3

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Signaling and Adaptation Modulate the Dynamics of the Photosensoric Complex of Natronomonas pharaonis

Orekhov, Philipp S. ; Klose, Daniel ; Mulkidjanian, Armen Y. ; [et al.]

Public Library of Science (PLoS) ; 2015

In: PLOS Computational Biology Vol. 11, No. 10 ( 2015-10-23), p. e1004561-

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In: PLOS Computational Biology, Public Library of Science (PLoS), Vol. 11, No. 10 ( 2015-10-23), p. e1004561-

Type of Medium: Online Resource

ISSN: 1553-7358

URL: Article

DOI: 10.1371/journal.pcbi.1004561

DOI: 10.1371/journal.pcbi.1004561.g001

DOI: 10.1371/journal.pcbi.1004561.g002

DOI: 10.1371/journal.pcbi.1004561.g003

DOI: 10.1371/journal.pcbi.1004561.g004

DOI: 10.1371/journal.pcbi.1004561.g005

DOI: 10.1371/journal.pcbi.1004561.g006

DOI: 10.1371/journal.pcbi.1004561.g007

DOI: 10.1371/journal.pcbi.1004561.t001

DOI: 10.1371/journal.pcbi.1004561.s001

DOI: 10.1371/journal.pcbi.1004561.s002

DOI: 10.1371/journal.pcbi.1004561.s003

DOI: 10.1371/journal.pcbi.1004561.s004

DOI: 10.1371/journal.pcbi.1004561.s005

DOI: 10.1371/journal.pcbi.1004561.s006

DOI: 10.1371/journal.pcbi.1004561.s007

DOI: 10.1371/journal.pcbi.1004561.s008

DOI: 10.1371/journal.pcbi.1004561.s009

DOI: 10.1371/journal.pcbi.1004561.s010

DOI: 10.1371/journal.pcbi.1004561.s011

DOI: 10.1371/journal.pcbi.1004561.s012

DOI: 10.1371/journal.pcbi.1004561.s013

DOI: 10.1371/journal.pcbi.1004561.s014

DOI: 10.1371/journal.pcbi.1004561.s015

DOI: 10.1371/journal.pcbi.1004561.s016

DOI: 10.1371/journal.pcbi.1004561.s017

DOI: 10.1371/journal.pcbi.1004561.s018

DOI: 10.1371/journal.pcbi.1004561.s019

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2015

detail.hit.zdb_id: 2193340-6

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Mechanical properties of tubulin intra- and inter-dimer interfaces and their implications for microtubule dynamic instability

Fedorov, Vladimir A. ; Orekhov, Philipp S. ; Kholina, Ekaterina G. ; [et al.]

Public Library of Science (PLoS) ; 2019

In: PLOS Computational Biology Vol. 15, No. 8 ( 2019-8-30), p. e1007327-

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In: PLOS Computational Biology, Public Library of Science (PLoS), Vol. 15, No. 8 ( 2019-8-30), p. e1007327-

Type of Medium: Online Resource

ISSN: 1553-7358

URL: Article

DOI: 10.1371/journal.pcbi.1007327

DOI: 10.1371/journal.pcbi.1007327.g001

DOI: 10.1371/journal.pcbi.1007327.g002

DOI: 10.1371/journal.pcbi.1007327.g003

DOI: 10.1371/journal.pcbi.1007327.g004

DOI: 10.1371/journal.pcbi.1007327.g005

DOI: 10.1371/journal.pcbi.1007327.g006

DOI: 10.1371/journal.pcbi.1007327.g007

DOI: 10.1371/journal.pcbi.1007327.t001

DOI: 10.1371/journal.pcbi.1007327.t002

DOI: 10.1371/journal.pcbi.1007327.t003

DOI: 10.1371/journal.pcbi.1007327.t004

DOI: 10.1371/journal.pcbi.1007327.s001

DOI: 10.1371/journal.pcbi.1007327.s002

DOI: 10.1371/journal.pcbi.1007327.s003

DOI: 10.1371/journal.pcbi.1007327.s004

DOI: 10.1371/journal.pcbi.1007327.s005

DOI: 10.1371/journal.pcbi.1007327.s006

DOI: 10.1371/journal.pcbi.1007327.s007

DOI: 10.1371/journal.pcbi.1007327.s008

DOI: 10.1371/journal.pcbi.1007327.s009

DOI: 10.1371/journal.pcbi.1007327.s010

DOI: 10.1371/journal.pcbi.1007327.s011

DOI: 10.1371/journal.pcbi.1007327.s012

DOI: 10.1371/journal.pcbi.1007327.s013

DOI: 10.1371/journal.pcbi.1007327.s014

DOI: 10.1371/journal.pcbi.1007327.s015

DOI: 10.1371/journal.pcbi.1007327.s016

DOI: 10.1371/journal.pcbi.1007327.s017

DOI: 10.1371/journal.pcbi.1007327.s018

DOI: 10.1371/journal.pcbi.1007327.s019

DOI: 10.1371/journal.pcbi.1007327.s020

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2019

detail.hit.zdb_id: 2193340-6

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Replicative and radiation-induced aging: a comparison of gene expression profiles

Aliper, Alexander M. ; Bozdaganyan, Marine E. ; Orekhov, Philipp S. ; [et al.]

Impact Journals, LLC ; 2019

In: Aging Vol. 11, No. 8 ( 2019-04-19), p. 2378-2387

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In: Aging, Impact Journals, LLC, Vol. 11, No. 8 ( 2019-04-19), p. 2378-2387

Type of Medium: Online Resource

ISSN: 1945-4589

URL: Issue

URL: Article

DOI: 10.18632/aging.v11i8

DOI: 10.18632/aging.101921

Language: English

Publisher: Impact Journals, LLC

Publication Date: 2019

detail.hit.zdb_id: 2535337-8

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