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Molecular dynamics simulations of nucleosomes are coming of age

WIREs Computational Molecular Science
2024-07 | Journal article
DOI: 10.1002/wcms.1728
Contributors: Anastasiia S. Fedulova; Grigoriy A. Armeev; Tatiana A. Romanova; Lovepreet Singh‐Palchevskaia; Nikita A. Kosarim; Nikita A. Motorin; Galina A. Komarova; Alexey K. Shaytan
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Crossref

DIVERSITY OF H2A HISTONES AND THEIR IMPLICATIONS FOR NUCLEOSOME STRUCTURAL PROPERTIES

Vestnik Moskovskogo universiteta. Seria 16. Biologia
2024-03-08 | Journal article
DOI: 10.55959/MSU0137-0952-16-78-4-4
Contributors: L. SINGH-PALCHEVSKAIA; A.K. SHAYTAN
Source: check_circle
Crossref

Diversity of H2A Histones and Their Effect on Nucleosome Structural Properties

Moscow University Biological Sciences Bulletin
2023-12 | Journal article
DOI: 10.3103/S0096392523600734
Contributors: L. Singhpalchevsk; A. K. Shaytan
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Crossref

NucleosomeDB - a database of 3D nucleosome structures and their complexes with comparative analysis toolkit

2023-04-18 | Preprint
DOI: 10.1101/2023.04.17.537230
Contributors: Grigoriy A. Armeev; Anna K. Gribkova; Alexey K. Shaytan
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Crossref

Electron microscopy analysis of ATP-independent nucleosome unfolding by FACT

Communications Biology
2022-01-10 | Journal article
DOI: 10.1038/s42003-021-02948-8
Contributors: Anastasiia L. Sivkina; Maria G. Karlova; Maria E. Valieva; Laura L. McCullough; Timothy Formosa; Alexey K. Shaytan; Alexey V. Feofanov; Mikhail P. Kirpichnikov; Olga S. Sokolova; Vasily M. Studitsky
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Crossref

DNA mapping in the capsid of giant bacteriophage phiEL (Caudovirales: Myoviridae: Elvirus) by analytical electron microscopy

Problems of Virology
2021-12-09 | Journal article
DOI: 10.36233/0507-4088-80
Contributors: T. S. Trifonova; A. V. Moiseenko; M. V. Bourkaltseva; O. V. Shaburova; A. K. Shaytan; V. N. Krylov; O. S. Sokolova
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Crossref

ATP-Independent Nucleosome Unfolding by FACT: Electron Microscopy Analysis

2021-08-20 | Preprint
DOI: 10.21203/rs.3.rs-726173/v1
Contributors: Vasily Studitsky; Anastasiia Sivkina; Maria Karlova; Maria Valieva; Laura McCullough; Tim Formosa; Alexey Shaytan; Alexey Feofanov; Mikhail Kirpichnikov; Olga Sokolova
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Crossref

Design of Nucleic Acid Biosensors Based on CRISPR/Cas Systems and Reporter Split Proteins

Moscow University Biological Sciences Bulletin
2021-04 | Journal article
DOI: 10.3103/S0096392521020036
Contributors: R. V. Novikov; A. K. Gribkova; J. G. Kacher; P. A. Zaytsev; G. A. Armeev; G. S. Gluhov; A. K. Shaytan
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Crossref

Histone dynamics mediate DNA unwrapping and sliding in nucleosomes

Nature Communications
2021-04-22 | Journal article
DOI: 10.1038/s41467-021-22636-9
Contributors: Grigoriy A. Armeev; Anastasiia S. Kniazeva; Galina A. Komarova; Mikhail P. Kirpichnikov; Alexey K. Shaytan
Source: check_circle
Crossref

Histone dynamics mediate DNA unwrapping and sliding in nucleosomes: insights from multi-microsecond molecular dynamics simulations

2021-01-21 | Preprint
DOI: 10.1101/2021.01.20.426793
Contributors: Grigoriy A. Armeev; Anastasia S. Kniazeva; Galina A. Komarova; Mikhail P. Kirpichnikov; Alexey K. Shaytan
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Crossref

MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones

Epigenetics & Chromatin
2017 | Journal article
DOI: 10.1186/s13072-016-0109-x
WOSUID:

WOS:000391513800001
Contributors: El Kennani, Sara; Adrait, Annie; Shaytan, Alexey K.; Khochbin, Saadi; Bruley, Christophe; Panchenko, Anna R.; Landsman, David; Pflieger, Delphine; Govin, Jerome
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions

Journal of Molecular Biology
2016 | Journal article
DOI: 10.1016/j.jmb.2015.12.004
WOSUID:

WOS:000370676700018
Contributors: Shaytan, Alexey K.; Armeev, Grigoriy A.; Goncearenco, Alexander; Zhurkin, Victor B.; Landsman, David; Panchenko, Anna R.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Dynamics of Irreversible Evaporation of a Water-Protein Droplet and a Problem of Structural and Dynamical Experiments with Single Molecules

Biofizika
2016 | Journal article
WOSUID:

BCI:BCI201600447575
Contributors: Shaitan, K. V.; Armeev, G. A.; Shaytan, A. K.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Genomic profiling of multiple sequentially acquired tumor metastatic sites from an "exceptional responder" lung adenocarcinoma patient reveals extensive genomic heterogeneity and novel somatic variants driving treatment response.

Cold Spring Harbor molecular case studies
2016 | Journal article
WOSUID:

MEDLINE:27900369
Contributors: Biswas, Romi; Gao, Shaojian; Cultraro, Constance M; Maity, Tapan K; Venugopalan, Abhilash; Abdullaev, Zied; Shaytan, Alexey K; Carter, Corey A; Thomas, Anish; Rajan, Arun et al.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

HistoneDB 2.0: a histone database with variants-an integrated resource to explore histones and their variants

Database-the Journal of Biological Databases and Curation
2016 | Journal article
DOI: 10.1093/database/baw014
WOSUID:

WOS:000374089900001
Contributors: Draizen, Eli J.; Shaytan, Alexey K.; Marino-Ramirez, Leonardo; Talbert, Paul B.; Landsman, David; Panchenko, Anna R.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Large-scale ATP-independent nucleosome unfolding by a histone chaperone

Nature Structural & Molecular Biology
2016 | Journal article
DOI: 10.1038/nsmb.3321
WOSUID:

WOS:000389559300013
Contributors: Valieva, Maria E.; Armeev, Grigoriy A.; Kudryashova, Kseniya S.; Gerasimova, Nadezhda S.; Shaytan, Alexey K.; Kulaeva, Olga I.; McCullough, Laura L.; Formosa, Tim; Georgiev, Pavel G.; Kirpichnikov, Mikhail P. et al.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Nucleosomal Barrier to Transcription: Structural Determinants and Changes in Chromatin Structure.

Biochemistry & molecular biology journal
2016 | Journal article
WOSUID:

MEDLINE:27754494
Contributors: Studitsky, Vasily M; Nizovtseva, Ekaterina V; Shaytan, Alexey K; Luse, Donal S
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Nucleosome Dynamics at Microsecond Timescale: DNA-Protein Interactions, Water-Mediated Interactions and Nucleosome Formation

Biophysical Journal
2016 | Journal article
DOI: 10.1016/j.bpj.2015.11.2189
WOSUID:

WOS:000375142200472
Contributors: Shaytan, Alexey K.; Armeev, Grigory A.; Goncearenco, Alexander; Zhurkin, Victor B.; Landsman, David; Panchenko, Anna R.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Structure and Functions of Linker Histones

Biochemistry-Moscow
2016 | Journal article
DOI: 10.1134/s0006297916030032
WOSUID:

WOS:000373346300003
Contributors: Lyubitelev, A. V.; Nikitin, D. V.; Shaytan, A. K.; Studitsky, V. M.; Kirpichnikov, M. P.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles.

Data in brief
2016 | Journal article
DOI: 10.1016/j.dib.2016.04.073
WOSUID:

MEDLINE:27222871
Contributors: Shaytan, Alexey K; Armeev, Grigoriy A; Goncearenco, Alexander; Zhurkin, Victor B; Landsman, David; Panchenko, Anna R
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Моделирование структуры ДНК-белковых комплексов с использованием экспериментальных данных по резонансному переносу энергии и перекисному окислению

2016 | Journal article
SOURCE-WORK-ID:

1026171711951-42
Contributors: Армеев, Григорий Алексеевич; Горковец, Татьяна Константиновна; Ефимова, Дарья Андреевна; Шайтан, Константин Вольдемарович; Шайтан, Алексей Константинович; Armeev, G.A.; Gorkovets, T.K.; Efimova, D.A.; Shaitan, K.V.; Shaytan, A.K.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Релаксация структуры нуклеосомы при отворачивании ДНК: исследование методом молекулярной динамики

2016 | Journal article
SOURCE-WORK-ID:

1026171711952-41
Contributors: Армеев, Григорий Алексеевич; Шайтан, Константин Вольдемарович; Шайтан, Алексей Константинович; Armeev, G.A.; Shaitan, K.V.; Shaytan, A.K.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Combined influence of linker DNA and histone tails on nucleosome dynamics as revealed by microsecond molecular dynamics simulations

Journal of Biomolecular Structure & Dynamics
2015 | Journal article
DOI: 10.1080/07391102.2015.1032631
WOSUID:

WOS:000356688600007
Contributors: Shaytan, Alexey K.; Armeev, Grigoriy A.; Goncearenco, Alexander; Zhurkin, Victor B.; Landsman, David; Panchenko, Anna R.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Direct prediction of residual dipolar couplings of small molecules in a stretched gel by stochastic molecular dynamics simulations

Magnetic Resonance in Chemistry
2015 | Journal article
DOI: 10.1002/mrc.4181
WOSUID:

WOS:000350304600006
Contributors: Frank, Andreas O.; Freudenberger, J. Christoph; Shaytan, Alexey K.; Kessler, Horst; Luy, Burkhard
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Nucleosome adaptability conferred by sequence and structural variations in histone H2A-H2B dimers

Current Opinion in Structural Biology
2015 | Journal article
DOI: 10.1016/j.sbi.2015.02.004
WOSUID:

WOS:000359032300009
Contributors: Shaytan, Alexey K.; Landsman, David; Panchenko, Anna R.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Polymorphism of Histone Tail Interactions in Nucleosome

Biophysical Journal
2015 | Journal article
DOI: 10.1016/j.bpj.2014.11.431
WOSUID:

WOS:000359471700369
Contributors: Shaytan, Alexey K.; Armeev, Grigory A.; Zhurkin, Victor B.; Landsman, David; Panchenko, Anna R.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Structural analysis of nucleosomal barrier to transcription

Proceedings of the National Academy of Sciences of the United States of America
2015 | Journal article
DOI: 10.1073/pnas.1508371112
WOSUID:

WOS:000363458100006
Contributors: Gaykalova, Daria A.; Kulaeva, Olga I.; Volokh, Olesya; Shaytan, Alexey K.; Hsieh, Fu-Kai; Kirpichnikov, Mikhail P.; Sokolova, Olga S.; Studitsky, Vasily M.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites

Biophysical Journal
2015 | Journal article
DOI: 10.1016/j.bpj.2015.06.056
WOSUID:

WOS:000361565400024
Contributors: Goncearenco, Alexander; Shaytan, Alexey K.; Shoemaker, Benjamin A.; Panchenko, Anna R.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Исследование ионного окружения и электрических характеристик нуклеосом методом молекулярной динамики

2015 | Journal article
SOURCE-WORK-ID:

1026171711956-43
Contributors: Армеев, Григорий Алексеевич; Шайтан, Константин Вольдемарович; Шайтан, Алексей Константинович; Armeev, G.A.; Shaitan, K.V.; Shaytan, A.K.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Конформационная подвижность нуклеосомы: исследование методом молекулярной динамики

2015 | Journal article
SOURCE-WORK-ID:

1026171711956-48
Contributors: Армеев, Григорий Алексеевич; Шайтан, Константин Вольдемарович; Шайтан, Алексей Константинович; Armeev, G.A.; Shaitan, K.V.; Shaytan, A.K.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Analysis of the mechanism of nucleosome survival during transcription

Nucleic Acids Research
2014 | Journal article
DOI: 10.1093/nar/gkt1120
WOSUID:

WOS:000331138800023
Contributors: Chang, Han-Wen; Kulaeva, Olga I.; Shaytan, Alexey K.; Kibanov, Mikhail; Kuznedelov, Konstantin; Severinov, Konstantin V.; Kirpichnikov, Mikhail P.; Clark, David J.; Studitsky, Vasily M.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Comparative Computational Study of Interaction of C-60-Fullerene and Tris-Malonyl-C-60-Fullerene Isomers with Lipid Bilayer: Relation to Their Antioxidant Effect

Plos One
2014 | Journal article
DOI: 10.1371/journal.pone.0102487
WOSUID:

WOS:000339618600086
Contributors: Bozdaganyan, Marine E.; Orekhov, Philipp S.; Shaytan, Alexey K.; Shaitan, Konstantin V.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Comparison of available computational studies of the interaction of C60 with lipid bilayer.

Figshare
2014 | Other
DOI: 10.1371/journal.pone.0102487.t001
WOSUID:

DRCI:DATA2015149007156873
Contributors: Bozdaganyan, Marine E; Orekhov, Philipp S; Shaytan, Alexey K; Shaitan, Konstantin V
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Genome packaging in EL and Lin68, two giant phiKZ-like bacteriophages of P-aeruginosa

Virology
2014 | Journal article
DOI: 10.1016/j.virol.2014.09.002
WOSUID:

WOS:000344434400050
Contributors: Sokolova, O. S.; Shaburova, O. V.; Pechnikova, E. V.; Shaytan, A. K.; Krylov, S. V.; Kiselev, N. A.; Krylov, V. N.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Investigation of Ion Permeation through the Cx26 Hemichannel

Biophysical Journal
2014 | Journal article
DOI: 10.1016/j.bpj.2013.11.3093
WOSUID:

WOS:000337000403156
Contributors: Kasimova, Marina; Shaytan, Alexey; Shaitan, Konstantin; Tarek, Mounir
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Molecular Insights into Electroporation and Electrotransfer through Model Cell Membranes

Biophysical Journal
2014 | Journal article
DOI: 10.1016/j.bpj.2013.11.1701
WOSUID:

WOS:000337000401603
Contributors: Kasimova, Marina; Delemotte, Lucie; Polak, Andraz; Miklavcic, Damijan; Casciola, Maura; Apollonio, Francesca; Breton, Marie; Mir, Luis; Shaytan, Alexey; Shaitan, Konstantin et al.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Physicochemical mechanisms of protein regulation by phosphorylation

Frontiers in Genetics
2014 | Journal article
DOI: 10.3389/fgene.2014.00270
WOSUID:

BCI:BCI201500140040
Contributors: Nishi, Hafumi; Shaytan, Alexey; Panchenko, Anna R.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Properties of the DPPC membrane in simulations with different amount of fullerenes.

Figshare
2014 | Other
DOI: 10.1371/journal.pone.0102487.t002
WOSUID:

DRCI:DATA2015149007156877
Contributors: Bozdaganyan, Marine E; Orekhov, Philipp S; Shaytan, Alexey K; Shaitan, Konstantin V
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Voltage-gated ion channel modulation by lipids: Insights from molecular dynamics simulations

Biochimica Et Biophysica Acta-Biomembranes
2014 | Journal article
DOI: 10.1016/j.bbamem.2014.01.024
WOSUID:

WOS:000334008100015
Contributors: Kasimova, Marina A.; Tarek, Mounir; Shaytan, Alexey K.; Shaitan, Konstantin V.; Delemotte, Lucie
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Water mediated interactions in nucleosomes

Abstracts of Papers of the American Chemical Society
2014 | Journal article
WOSUID:

WOS:000349165104411
Contributors: Shaytan, Alexey; Panchenko, Anna
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Peptide nanofibrils boost retroviral gene transfer and provide a rapid means for concentrating viruses

Nature Nanotechnology
2013 | Journal article
DOI: 10.1038/NNANO.2012.248
WOSUID:

WOS:000315178800022
Contributors: Yolamanova, Maral; Meier, Christoph; Shaytan, Alexey K.; Vas, Virag; Bertoncini, Carlos W.; Arnold, Franziska; Zirafi, Onofrio; Usmani, Shariq M.; Mueller, Janis A.; Sauter, Daniel et al.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Structural Analysis of the Key Intermediate Formed during Transcription through a Nucleosome.

Trends in cell & molecular biology
2013 | Journal article
WOSUID:

MEDLINE:25364155
Contributors: Chang, H-W; Shaytan, A K; Hsieh, F-K; Kulaeva, O I; Kirpichnikov, M P; Studitsky, V M
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Calculation of Spectral Shifts of the Mutants of Bacteriorhodopsin by QM/MM Methods

Biofizika
2012 | Journal article
WOSUID:

BCI:BCI201200429601
Contributors: Orekhov, Ph. S.; Shaytan, A. K.; Shaitan, K. V.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Self-Assembling Nanofibers from Thiophene - Peptide Diblock Oligomers: A Combined Experimental and Computer Simulations Study

Acs Nano
2011 | Journal article
DOI: 10.1021/nn2011943
WOSUID:

WOS:000295187400017
Contributors: Shaytan, Alexey K.; Schillinger, Eva-Kathrin; Khalatur, Pavel G.; Mena-Osteritz, Elena; Hentschel, Jens; Boerner, Hans G.; Baeuerle, Peter; Khokhlov, Alexei R.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Self-organizing bioinspired oligothiophene-oligopeptide hybrids

Beilstein Journal of Nanotechnology
2011 | Journal article
DOI: 10.3762/bjnano.2.57
WOSUID:

WOS:000300022000001
Contributors: Shaytan, Alexey K.; Schillinger, Eva-Kathrin; Mena-Osteritz, Elena; Schmid, Sylvia; Khalatur, Pavel G.; Baeuerle, Peter; Khokhlov, Alexei R.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Free Energy Profiles of Amino Acid Side Chain Analogs Near Water-Vapor Interface Obtained Via MD Simulations

Journal of Computational Chemistry
2010 | Journal article
DOI: 10.1002/jcc.21267
WOSUID:

WOS:000273186800019
Contributors: Shaytan, Alexey K.; Ivanov, Victor A.; Shaitan, Konstantin V.; Khokhlov, Alexei R.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Large-scale atomistic simulation of a nanosized fibril formed by thiophene-peptide "molecular chimeras"

Soft Matter
2010 | Journal article
DOI: 10.1039/b918562c
WOSUID:

WOS:000275947800013
Contributors: Shaytan, Alexey K.; Khokhlov, Alexei R.; Khalatur, Pavel G.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

[Molecular dynamics of zervamicin II and its analogues in water and methanol].

Biofizika
2009 | Journal article
WOSUID:

MEDLINE:19795781
Contributors: Levtsova, O V; Antonov, M Iu; Shaitan, A K; Orshanskii, I A; Nikolaev, I N; Shaitan, K V
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Solvent Accessible Surface Area of Amino Acid Residues in Globular Proteins: Correlation of Apparent Transfer Free Energies with Experimental Hydrophobicity Scales

Biomacromolecules
2009 | Journal article
DOI: 10.1021/bm8015169
WOSUID:

WOS:000265914200027
Contributors: Shaytan, Alexey K.; Shaitan, Konstantin V.; Khokhlov, Alexei R.
Source: Self-asserted source
Alexey Shaytan via ResearcherID

Peptide dynamics at water-membrane interface

Proceedings of the Fifth International Conference on Bioinformatics of Genome Regulation and Structure, Vol 1
2006 | Journal article
WOSUID:

WOS:000243856400073
Contributors: Shaytan, A. K.; Khokhlov, A. R.; Ivanov, V. A.; Kolchanov, N; Hofestadt, R
Source: Self-asserted source
Alexey Shaytan via ResearcherID
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Peer review (7 reviews for 6 publications/grants)

Review activity for Biophysical journal. (1)
Review activity for Biophysical reviews. (1)
Review activity for Communications biology. (1)
Review activity for Epigenetics & chromatin. (1)
Review activity for Journal of Molecular Biology. (2)
Review activity for Nature communications (1)
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