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Recent News | molsim.org

Recent News

  • New papers in 2018
    11 January 2019

    1: Bonartsev AP, Zharkova II, Voinova VV, Kuznetsova ES, Zhuikov VA, Makhina TK,
    Myshkina VL, Potashnikova DM, Chesnokova DV, Khaydapova DD, Bonartseva GA,
    Shaitan KV. Poly(3-hydroxybutyrate)/poly(ethylene glycol) scaffolds with
    different microstructure: the effect on growth of mesenchymal stem cells. 3
    Biotech. 2018 Aug;8(8):328. doi: 10.1007/s13205-018-1350-8. Epub 2018 Jul 18.
    PubMed PMID: 30073113; PubMed Central PMCID: PMC6051946.

    2: Moldogazieva NT, Shaitan KV, Antonov MY, Mokhosoev IM, Levtsova OV, Terentiev
    AA. Human EGF-derived direct and reverse short linear motifs: conformational
    dynamics insight into the receptor-binding residues. J Biomol Struct Dyn. 2018
    Apr;36(5):1286-1305. doi: 10.1080/07391102.2017.1321502. Epub 2017 May 7. PubMed
    PMID: 28447543.

    3: Armeev GA, Gribkova AK, Pospelova I, Komarova GA, Shaytan AK. Linking
    chromatin composition and structural dynamics at the nucleosome level. Curr Opin
    Struct Biol. 2018 Dec 4;56:46-55. doi: 10.1016/j.sbi.2018.11.006. [Epub ahead of
    print] Review. PubMed PMID: 30529788.

    4: Shaytan AK, Xiao H, Armeev GA, Gaykalova DA, Komarova GA, Wu C, Studitsky VM,
    Landsman D, Panchenko AR. Structural interpretation of DNA-protein
    hydroxyl-radical footprinting experiments with high resolution using HYDROID. Nat
    Proton. 2018 Nov;13(11):2535-2556. doi: 10.1038/s41596-018-0048-z. PubMed PMID:
    30341436; PubMed Central PMCID: PMC6322412.

    5: Glyakina AV, Likhachev IV, Balabaev NK, Galzitskaya OV. Comparative mechanical
    unfolding studies of spectrin domains R15, R16 and R17. J Struct Biol. 2018
    Feb;201(2):162-170. doi: 10.1016/j.jsb.2017.12.003. Epub 2017 Dec 5. PubMed PMID:
    29221897.

    6: Kurbatov AO, Balabaev NK, Mazo MA, Kramarenko EY. Molecular dynamics
    simulations of single siloxane dendrimers: Molecular structure and intramolecular
    mobility of terminal groups. J Chem Phys. 2018 Jan 7;148(1):014902. doi:
    10.1063/1.5009988. PubMed PMID: 29306281.

    read more...
  • New papers in 2017
    15 January 2018

    1: Orekhov P, Bothe A, Steinhoff HJ, Shaitan KV, Raunser S, Fotiadis D,
    Schlesinger R, Klare JP, Engelhard M. Sensory Rhodopsin I and Sensory Rhodopsin
    II Form Trimers of Dimers in Complex with their Cognate Transducers. Photochem
    Photobiol. 2017 May;93(3):796-804. doi: 10.1111/php.12763. PubMed PMID: 28500714.

    2: Allard-Vannier E, Hervé-Aubert K, Kaaki K, Blondy T, Shebanova A, Shaitan KV,
    Ignatova AA, Saboungi ML, Feofanov AV, Chourpa I. Folic acid-capped PEGylated
    magnetic nanoparticles enter cancer cells mostly via clathrin-dependent
    endocytosis. Biochim Biophys Acta Gen Subj. 2017 Jun;1861(6):1578-1586. doi:
    10.1016/j.bbagen.2016.11.045. Epub 2016 Dec 2. PubMed PMID: 27919801.

    3: Nekrasova OV, Volyntseva AD, Kudryashova KS, Novoseletsky VN, Lyapina EA,
    Illarionova AV, Yakimov SA, Korolkova YV, Shaitan KV, Kirpichnikov MP, Feofanov
    AV. Complexes of Peptide Blockers with Kv1.6 Pore Domain: Molecular Modeling and
    Studies with KcsA-Kv1.6 Channel. J Neuroimmune Pharmacol. 2017 Jun;12(2):260-276.
    doi: 10.1007/s11481-016-9710-9. Epub 2016 Sep 17. PubMed PMID: 27640211.

    4: Ermakova NP, Bonartsev AP, Zernov AL, Konyaeva OI, Kulbachevskaya NY,
    Merkulova IB, Abramovac TV, Chaley VA, Zharkova II, Yakovlev SG, Myshkina VL,
    Mahina TK, Bonartseva GA, Shaitan KV, Bukhman VM. Preclinical Toxicity of
    Paclitaxel Biopolymer Formulation. Anticancer Agents Med Chem.
    2017;17(12):1661-1668. doi: 10.2174/1871520616666160817104529. PubMed PMID:
    27539319.

    5: Bonartsev AP, Zharkova II, Yakovlev SG, Myshkina VL, Mahina TK, Voinova VV,
    Zernov AL, Zhuikov VA, Akoulina EA, Ivanova EV, Kuznetsova ES, Shaitan KV,
    Bonartseva GA. Biosynthesis of poly(3-hydroxybutyrate) copolymers by Azotobacter
    chroococcum 7B: A precursor feeding strategy. Prep Biochem Biotechnol. 2017 Feb
    7;47(2):173-184. doi: 10.1080/10826068.2016.1188317. Epub 2016 May 23. PubMed
    PMID: 27215309.

    6: Bonartsev AP, Zernov AL, Yakovlev SG, Zharkova II, Myshkina VL, Mahina TK,
    Bonartseva GA, Andronova NV, Smirnova GB, Borisova JA, Kalishjan MS, Shaitan KV,
    Treshalina HM. New Poly(3-hydroxybutyrate) Microparticles with Paclitaxel
    Sustained Release for Intraperitoneal Administration. Anticancer Agents Med Chem.
    2017;17(3):434-441. doi: 10.2174/1871520615666160504095433. PubMed PMID:
    27141874.

    read more...
  • New papers in 2016
    14 January 2017

    1: Shaitan KV, Armeev GA, Shaytan AK. [Dynamics of Irreversible Evaporation of a
    Water-Protein Droplet and a Problem of Structural and Dynamical Experiments with
    Single Molecules]. Biofizika. 2016 Mar-Apr;61(2):213-21. Russian. PubMed PMID:
    27192821.

    2: Novoseletsky VN, Volyntseva AD, Shaitan KV, Kirpichnikov MP, Feofanov AV.
    Modeling of the Binding of Peptide Blockers to Voltage-Gated Potassium Channels:
    Approaches and Evidence. Acta Naturae. 2016 Apr-Jun;8(2):35-46. PubMed PMID:
    27437138; PubMed Central PMCID: PMC4947987.

    3: Bonartsev AP, Bonartseva GA, Myshkina VL, Voinova VV, Mahina TK, Zharkova II,
    Yakovlev SG, Zernov AL, Ivanova EV, Akoulina EA, Kuznetsova ES, Zhuikov VA,
    Alekseeva SG, Podgorskii VV, Bessonov IV, Kopitsyna MN, Morozov AS, Milanovskiy
    EY, Tyugay ZN, Bykova GS, Kirpichnikov MP, Shaitan KV. Biosynthesis of
    poly(3-hydroxybutyrateco-3-hydroxy-4-methylvalerate) by Strain Azotobacter
    chroococcum 7B. Acta Naturae. 2016 Jul-Sep;8(3):77-87. PubMed PMID: 27795846;
    PubMed Central PMCID: PMC5081702.

    read more...
  • New papers in 2015
    11 January 2016

    1: Efremov YM, Dokrunova AA, Efremenko AV, Kirpichnikov MP, Shaitan KV, Sokolova
    OS. Distinct impact of targeted actin cytoskeleton reorganization on mechanical
    properties of normal and malignant cells. Biochim Biophys Acta. 2015 Nov;1853(11
    Pt B):3117-25. doi: 10.1016/j.bbamcr.2015.05.008. Epub 2015 May 10. PubMed PMID:
    25970206.

    2: Efremov YM, Bagrov DV, Kirpichnikov MP, Shaitan KV. Application of the
    Johnson-Kendall-Roberts model in AFM-based mechanical measurements on cells and
    gel. Colloids Surf B Biointerfaces. 2015 Oct 1;134:131-9. doi:
    10.1016/j.colsurfb.2015.06.044. Epub 2015 Jun 26. PubMed PMID: 26186106.

    3: Shaitan KV, Fedik IV. [Molecular Dynamics Simulations of Self-organization of
    the Structure of Model Biomimetic Polymers]. Biofizika. 2015 May-Jun;60(3):421-7.
    Russian. PubMed PMID: 26349205.

    4: Orshanskiy IA, Popinako AV, Volokh OI, Shaitan KV, Sokolova OS. [Molecular
    Dynamics of N- and C-terminal Interactions during Autoinhibition and Activation
    of Formin mDial]. Biofizika. 2015 May-Jun;60(3):451-6. Russian. PubMed PMID:
    26349208.

    5: Andreeva NV, Bonartsev AP, Zharkova II, Makhina TK, Myshkina VL, Kharitonova
    EP, Voinova VV, Bonartseva GA, Shaitan KV, Belyavskii AV. Culturing of Mouse
    Mesenchymal Stem Cells on Poly-3-Hydroxybutyrate Scaffolds. Bull Exp Biol Med.
    2015 Aug;159(4):567-71. doi: 10.1007/s10517-015-3015-5. Epub 2015 Sep 21. PubMed
    PMID: 26388561.

    6: Shaitan KV, Orshanskiy IA. [Molecular Dynamics of Self-assembling and Rheology
    of Superhelical Structure of Protofiber of Spider Web]. Biofizika. 2015
    Jul-Aug;60(4):656-60. Russian. PubMed PMID: 26394464.

    7: Orekhov PS, Klose D, Mulkidjanian AY, Shaitan KV, Engelhard M, Klare JP,
    Steinhoff HJ. Signaling and Adaptation Modulate the Dynamics of the Photosensoric
    Complex of Natronomonas pharaonis. PLoS Comput Biol. 2015 Oct 23;11(10):e1004561.
    doi: 10.1371/journal.pcbi.1004561. eCollection 2015 Oct. PubMed PMID: 26496122;
    PubMed Central PMCID: PMC4651059.

    8: Shumyantseva VV, Shebanova AS, Chalenko YM, Voeikova TA, Kirpichnikov MP,
    Shaitan KV, Debabov VG. Electroanalysis of Shewanella oneidensis MR-1. Dokl
    Biochem Biophys. 2015;464:325-8. doi: 10.1134/S1607672915050154. Epub 2015 Oct
    31. PubMed PMID: 26518560.

    9: Shaitan KV. [The Relaxation Model of Ideal Folding in a Homogeneous Viscous
    Medium]. Biofizika. 2015 Sep-Oct;60(5):843-52. Russian. PubMed PMID: 26591594.

    10: Ivanov SY, Bonartsev AP, Gazhva YV, Zharkova II, Mukhametshin RF, Mahina TK,
    Myshkina VL, Bonartseva GA, Voinova VV, Andreeva NV, Akulina EA, Kharitonova ES,
    Shaitan KV, Muraev AA. [Development and preclinical studies of insulating
    membranes based on poly-3-hydroxybutyrate-co-3-hydroxyvalerate for guided bone
    regeneration]. Biomed Khim. 2015 Nov-Dec;61(6):717-23. doi:
    10.18097/PBMC20156106717. Russian. PubMed PMID: 26716743.

    11: Volokh OI, Bozdaganyan ME, Shaitan KV. [Assessment of Binding Properties of
    Actinomycin and Its Derivatives with DNA Molecule Using Molecular Dynamics
    Simulation Method]. Biofizika. 2015 Nov-Dec;60(6):1077-84. Russian. PubMed PMID:
    26841500.

    read more...
  • New papers in 2014
    31 December 2014

    Voltage-gated ion channel modulation by lipids: insights from molecular dynamics simulations.
    Kasimova MA, Tarek M, Shaytan AK, Shaitan KV, Delemotte L.
    Biochim Biophys Acta.

    Investigation of the influence of external factors on the conformational dynamics of rhodopsin-like receptors by means of molecular dynamics simulation.
    Novikov GV, Sivozhelezov VS, Kolesnikov SS, Shaitan KV.
    J Recept Signal Transduct Res.

    Comparative computational study of interaction of C60-fullerene and tris-malonyl-C60-fullerene isomers with lipid bilayer: relation to their antioxidant effect.
    Bozdaganyan ME, Orekhov PS, Shaytan AK, Shaitan KV.
    PLoS One.

    Identification of best protein crystallization methods by molecular dynamics (MD).
    Bozdaganyan M, Bragazzi NL, Pechkova E, Shaitan KV, Nicolini C.
    Crit Rev Eukaryot Gene Expr.

    Influence of the orthosteric ligands binding on the conformational dynamics of the B-2-adrenergic receptor by means of essential dynamics sampling simulation
    Novikov GV, Sivozhelezov VS, Shaitan KV.
    Mol Biol (Mosk).

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  • Lab seminar 25.02
    21 February 2013

    25 February (Monday) at 2 p.m., room 542, laboratory building B.

    Topic: " Influence of lipid composition on the functioning of voltage-gated potassium channels: insights from molecular simulations"
    M.A. Kasimova, MSU/University of Lorraine

    Some results including published elsewhere ( http://www.jbc.org/content/287/43/36158.long )
    will be presented.

    read more...
  • Peptide nanofibrils boost retroviral gene transfer and provide a rapid means for concentrating viruses
    21 February 2013

    New paper in Nature Nanotechnology resulted from a wide collaboration between the scientist of Moscow State University and german colleagues. http://dx.doi.org/10.1038/nnano.2012.248
    The work presents new peptides that form nanofibrils boosting the retroviral gene transfer and providing a rapid means for concentrating viruses
    The simulations at the Lomonosov supercomputer at MSU were used to reveal the structure and morphology of the self-assembling fibrils according the methodology developed in our previous works.

    Further links in Russian:
    http://www.msu.ru/science/articles/20130215.html
    http://www.gazeta.ru/science/2013/02/16_a_4968793.shtml

    read more...
  • New online MD simulations tutorial has been published
    27 May 2012

    A brief hands-on tutorial on 100ns MD simulation of H3-H4 tetramer and covariance analysis using Gromacs can be found via this link.

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  • Videos in LAMMPS gallery
    30 January 2012

    Our videos have appeared on LAMMPS movies web page.
    Thanks to Steve Plimpton!

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  • New Molsimmsu Youtube channel
    15 November 2011

    We have created a youtube channel http://www.youtube.com/molsimmsu

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