Search Results - "Efremov, Roman G."

Dynamic “Molecular Portraits” of Biomembranes Drawn by Their Lateral Nanoscale Inhomogeneities by Efremov, Roman G.

“…To date, it has been reliably shown that the lipid bilayer/water interface can be thoroughly characterized by a sophisticated so-called “dynamic molecular…”
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Structural mechanism of heat-induced opening of a temperature-sensitive TRP channel by Nadezhdin, Kirill D., Neuberger, Arthur, Trofimov, Yuri A., Krylov, Nikolay A., Sinica, Viktor, Kupko, Nikita, Vlachova, Viktorie, Zakharian, Eleonora, Efremov, Roman G., Sobolevsky, Alexander I.

“…Numerous physiological functions rely on distinguishing temperature through temperature-sensitive transient receptor potential channels (thermo-TRPs). Although…”
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Inconspicuous Yet Indispensable: The Coronavirus Spike Transmembrane Domain by Aliper, Elena T, Efremov, Roman G

“…Membrane-spanning portions of proteins’ polypeptide chains are commonly known as their transmembrane domains (TMDs). The structural organisation and dynamic…”
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Structural mechanism of human oncochannel TRPV6 inhibition by the natural phytoestrogen genistein by Neuberger, Arthur, Trofimov, Yury A., Yelshanskaya, Maria V., Nadezhdin, Kirill D., Krylov, Nikolay A., Efremov, Roman G., Sobolevsky, Alexander I.

“…Calcium-selective oncochannel TRPV6 is the major driver of cell proliferation in human cancers. While significant effort has been invested in the development…”
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libxtc: an efficient library for reading XTC-compressed MD trajectory data by Krylov, Nikolay A, Efremov, Roman G

“…The purpose of this work is to optimize the processing of molecular dynamics (MD) trajectory data obtained for large biomolecular systems. Two popular software…”
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Protein compactness and interaction valency define the architecture of a biomolecular condensate across scales by Polyansky, Anton A, Gallego, Laura D, Efremov, Roman G, Köhler, Alwin, Zagrovic, Bojan

“…Non-membrane-bound biomolecular condensates have been proposed to represent an important mode of subcellular organization in diverse biological settings…”
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Elastic fibers and elastin receptor complex: Neuraminidase-1 takes the center stage by Bennasroune, Amar, Romier-Crouzet, Béatrice, Blaise, Sébastien, Laffargue, Muriel, Efremov, Roman G., Martiny, Laurent, Maurice, Pascal, Duca, Laurent

“…Extracellular matrix (ECM) has for a long time being considered as a simple architectural support for cells. It is now clear that ECM presents a fundamental…”
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Molecular pathway and structural mechanism of human oncochannel TRPV6 inhibition by the phytocannabinoid tetrahydrocannabivarin by Neuberger, Arthur, Trofimov, Yury A., Yelshanskaya, Maria V., Khau, Jeffrey, Nadezhdin, Kirill D., Khosrof, Lena S., Krylov, Nikolay A., Efremov, Roman G., Sobolevsky, Alexander I.

“…The calcium-selective oncochannel TRPV6 is an important driver of cell proliferation in human cancers. Despite increasing interest of pharmacological research…”
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On a mechanistic impact of transmembrane tetramerization in the pathological activation of RTKs by Polyansky, Anton A., Efremov, Roman G.

“…Constitutive activation of receptor tyrosine kinases (RTKs) via different mutations has a strong impact on the development of severe human disorders, including…”
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Structural Analysis and Activity Correlation of Amphiphilic Cyclic Antimicrobial Peptides Derived from the [W 4 R 4 ] Scaffold by El-Mowafi, Shaima A, Konshina, Anastasia G, Mohammed, Eman H M, Krylov, Nikolay A, Efremov, Roman G, Parang, Keykavous

“…In our ongoing quest to design effective antimicrobial peptides (AMPs), this study aimed to elucidate the mechanisms governing cyclic amphiphilic AMPs and…”
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PREDDIMER: a web server for prediction of transmembrane helical dimers by Polyansky, Anton A, Chugunov, Anton O, Volynsky, Pavel E, Krylov, Nikolay A, Nolde, Dmitry E, Efremov, Roman G

“…Here we present PREDDIMER, a web tool for prediction of dimer structure of transmembrane (TM) helices. PREDDIMER allows (i) reconstruction of a number of dimer…”
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Confined Dynamics of Water in Transmembrane Pore of TRPV1 Ion Channel by Trofimov, Yury A, Krylov, Nikolay A, Efremov, Roman G

“…Solvation effects play a key role in chemical and biological processes. The microscopic properties of water near molecular surfaces are radically different…”
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A Uniquely Stable Trimeric Model of SARS-CoV-2 Spike Transmembrane Domain by Aliper, Elena T., Krylov, Nikolay A., Nolde, Dmitry E., Polyansky, Anton A., Efremov, Roman G.

“…Understanding fusion mechanisms employed by SARS-CoV-2 spike protein entails realistic transmembrane domain (TMD) models, while no reliable approaches towards…”
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The Mechanism of Selective Recognition of Lipid Substrate by hDHHC20 Enzyme by Panina, Irina S, Krylov, Nikolay A, Chugunov, Anton O, Efremov, Roman G, Kordyukova, Larisa V

“…S-acylation is a post-translational linkage of long chain fatty acids to cysteines, playing a key role in normal physiology and disease. In human cells, the…”
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Nontrivial Behavior of Water in the Vicinity and Inside Lipid Bilayers As Probed by Molecular Dynamics Simulations by Krylov, Nikolay A, Pentkovsky, Vladimir M, Efremov, Roman G

“…The atomic-scale diffusion of water in the presence of several lipid bilayers mimicking biomembranes is characterized via unconstrained molecular dynamics (MD)…”
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Specific Binding of the α-Component of the Lantibiotic Lichenicidin to the Peptidoglycan Precursor Lipid II Predetermines Its Antimicrobial Activity by Panina, Irina S, Balandin, Sergey V, Tsarev, Andrey V, Chugunov, Anton O, Tagaev, Andrey A, Finkina, Ekaterina I, Antoshina, Daria V, Sheremeteva, Elvira V, Paramonov, Alexander S, Rickmeyer, Jasmin, Bierbaum, Gabriele, Efremov, Roman G, Shenkarev, Zakhar O, Ovchinnikova, Tatiana V

“…To date, a number of lantibiotics have been shown to use lipid II-a highly conserved peptidoglycan precursor in the cytoplasmic membrane of bacteria-as their…”
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The Conformation of the Epidermal Growth Factor Receptor Transmembrane Domain Dimer Dynamically Adapts to the Local Membrane Environment by Bocharov, Eduard V, Bragin, Pavel E, Pavlov, Konstantin V, Bocharova, Olga V, Mineev, Konstantin S, Polyansky, Anton A, Volynsky, Pavel E, Efremov, Roman G, Arseniev, Alexander S

“…The epidermal growth factor receptor (EGFR) family is an important class of receptor tyrosine kinases, mediating a variety of cellular responses in normal…”
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Fighting Celiac Disease: Improvement of pH Stability of Cathepsin L In Vitro by Computational Design by Chugunov, Anton O, Dvoryakova, Elena A, Dyuzheva, Maria A, Simonyan, Tatyana R, Tereshchenkova, Valeria F, Filippova, Irina Yu, Efremov, Roman G, Elpidina, Elena N

“…Roughly 1% of the global population is susceptible to celiac disease (CD)-inheritable autoimmune inflammation of the small intestine caused by intolerance to…”
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Structure and dynamics of cardiotoxins by Konshina, Anastasia G, Dubovskii, Peter V, Efremov, Roman G

“…Cytotoxins (or cardiotoxins; CTs) are toxins from cobra venom characterized by the three-finger (TF) fold. CTs are on average 60-residue-long peptides,…”
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Variability in the Spatial Structure of the Central Loop in Cobra Cytotoxins Revealed by X-ray Analysis and Molecular Modeling by Dubovskii, Peter V, Dubova, Kira M, Bourenkov, Gleb, Starkov, Vladislav G, Konshina, Anastasia G, Efremov, Roman G, Utkin, Yuri N, Samygina, Valeriya R

“…Cobra cytotoxins (CTs) belong to the three-fingered protein family and possess membrane activity. Here, we studied cytotoxin 13 from cobra venom (CT13Nn). For…”
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