Zobrazeno 1 - 10
of 32
pro vyhledávání: '"Alexander Nemukhin"'
Autor:
Igor Polyakov, Alexander Nemukhin
Publikováno v:
Biophysica, Vol 3, Iss 2, Pp 373-384 (2023)
We report the results of computational studies of the guanosine triphosphate (GTP) hydrolysis in the active site of the KRas-NF1 protein complex, where KRas stands for the K-isoform of the Ras (ras sarcoma) protein and NF1 (neurofbromin-1) is the act
Externí odkaz:
https://doaj.org/article/b2bfe1cffce24230bf2b46465014951a
Publikováno v:
Biophysica, Vol 3, Iss 2, Pp 252-262 (2023)
Interaction of molecular oxygen 3O2 with the flavin-dependent protein miniSOG after light illumination results in creation of singlet oxygen 1O2 and superoxide O2●−. Despite the recently resolved crystal structures of miniSOG variants, oxygen-bin
Externí odkaz:
https://doaj.org/article/d644868447b342baa0735afb88f0e38c
Publikováno v:
Molecules, Vol 28, Iss 5, p 2405 (2023)
Oxygenase activity of the flavin-dependent enzyme RutA is commonly associated with the formation of flavin-oxygen adducts in the enzyme active site. We report the results of quantum mechanics/molecular mechanics (QM/MM) modeling of possible reaction
Externí odkaz:
https://doaj.org/article/cdd13a03668841b3ab70b02b31e4f1f0
Autor:
Bella Grigorenko, Igor Polyakov, Maria Khrenova, Goran Giudetti, Shirin Faraji, Anna Krylov, Alexander Nemukhin
These files are required to reproduce the analysis of the components of the collective variable CV2=d(NE-HS)-d(HS-OWat1)+d(OWat1-HWat1)-d(HWat1-OWat2)+d(OWat2-HWat2)-d(N-HWat2) used for biased umbrella sampling calculations of the 2nd stage of the re
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2d0ea5a41b7d22922019dda40190b972
Autor:
Igor Polyakov, Alexander Nemukhin
Data required to reproduce Figures 3.1.X of the paper: jupyter notebook file used to conduct trajectory analysis pandas dataframe dumps from the analysis results parameters used in the simulation initial pdb structure and psf topology umbrella sampli
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2e4c53fa3e9cc4937559746fc2a51756
The increase of organophosphorus compounds, pesticides and flame-retardants, in wastes is an emerging ecological problem. Bacterial phosphotriesterases are capable for hydrolysis of some of them. We utilize modern molecular modeling tools to study hy
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::8aa10f34cf81085d732190e76870f25a
https://doi.org/10.26434/chemrxiv-2023-2t34g
https://doi.org/10.26434/chemrxiv-2023-2t34g
We report the results of a computational study of the mechanism of the light-induced chemical reaction of chromophore hydration in the fluorescent protein Dreiklang responsible for its switching from the fluorescent ON-state to the dark OFF-state. We
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::5d8cc214843108dae6b85438f1cc3dc1
https://doi.org/10.26434/chemrxiv-2022-g91vh
https://doi.org/10.26434/chemrxiv-2022-g91vh
Active sites of enzymes are able to activate substrates and perform chemical reactions that cannot occur in solutions. We focus here on hydrolysis reactions catalyzed by enzymes and initiated by the nucleophilic attack of the carbonyl carbon atom of
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::921dbf74121d5fd79a975f6225a7cce3
https://doi.org/10.26434/chemrxiv-2022-gxbbk
https://doi.org/10.26434/chemrxiv-2022-gxbbk
Modern quantum-based methods are employed to model interaction of the flavin-dependent enzyme RutA with the uracil and oxygen molecules. This complex presents the structure of reactants for the chain of chemical reactions of monooxygenation in the en
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::b20807a943079c929ca07eb799af17dd
https://doi.org/10.26434/chemrxiv-2022-s8m5s
https://doi.org/10.26434/chemrxiv-2022-s8m5s
We describe a model for spectral tuning in red fluorescent proteins (RFPs) based on the relation between an electronic structure descriptor, the dipole moment variation upon excitation (DMV), and the excitation energy of a protein. This approach aims
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::9db4747c2ddf4c7ca4cd201db3a6e15f
https://doi.org/10.26434/chemrxiv-2021-b1rdn
https://doi.org/10.26434/chemrxiv-2021-b1rdn