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JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 02/2018, Volume 122, Issue 4, pp. 1378 - 1386
The transient absorption spectroscopy of hydrolysis of the chromogenic substrate nitrocefin by the Ll metallo-beta-lactamase (M beta A), a bacterial enzyme... 
BACTEROIDES-FRAGILIS | PSEUDOPOTENTIALS | STENOTROPHOMONAS-MALTOPHILIA | QUANTUM | CHEMISTRY, PHYSICAL | QM/MM | MOLECULAR-DYNAMICS SIMULATIONS | CATALYTIC MECHANISM | FORCE-FIELDS | ZINC
Journal Article
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 10/2015, Volume 119, Issue 40, pp. 12838 - 12845
Molecular mechanisms of the hydrolysis of guanosine triphosphate (GTP) to guanosine diphosphate (GDP) and inorganic phosphate (Pi) by the Ras center dot GAP... 
P21(RAS) | ACTIVATING PROTEIN | CATALYZED-HYDROLYSIS | FTIR | QM/MM METHODS | CHEMISTRY, PHYSICAL | INTERMEDIATE | STATE | SIMULATION
Journal Article
Chemical Reviews, ISSN 0009-2665, 01/2017, Volume 117, Issue 2, pp. 758 - 795
Journal Article
ORGANIC & BIOMOLECULAR CHEMISTRY, ISSN 1477-0520, 10/2018, Volume 16, Issue 40, pp. 7518 - 7529
In this work, we disclose a mechanism of competing chemical reactions of protein assembly for a bacterial phytochrome using modern methods of molecular... 
MOLECULAR-DYNAMICS | MECHANISM | CHROMOPHORE | FREQUENCY SCALE FACTORS | GLUTATHIONE | CHEMISTRY, ORGANIC | GENERAL FORCE-FIELD | SIMULATIONS | DENSITY-FUNCTIONAL THEORY | PROTON-TRANSFER | INFRARED FLUORESCENT PROTEINS
Journal Article
CHEMICAL PHYSICS, ISSN 0301-0104, 06/2019, Volume 522, pp. 32 - 38
We present the results of computational studies of the shifts in absorption bands in the 4-hydroxybenzylidene-1,2-dimethylimidazolinone (HBDI), a synthetic... 
COMPLEXES | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | NONCOVALENT INTERACTIONS | SANDWICH | Absorption band shift | Organic chromophores | RED | GFP | pi-stacking | ASSEMBLIES | TRIPLE-DECKER MOTIF | CRYSTALS | Ab initio calculations | ENERGIES | ELECTRON-DENSITY PROPERTIES
Journal Article
Journal of Physical Chemistry B, ISSN 1520-6106, 04/2015, Volume 119, Issue 16, pp. 5176 - 5183
Journal Article
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 10/2019, Volume 123, Issue 42, pp. 8901 - 8909
The unique properties of the photoswitchable protein Dreiklang are attributed to a reversible hydration/dehydration reaction at the imidazolinone ring of the... 
GFP | MUTANT | CHROMOPHORE | DYNAMICS | CHEMISTRY | CHEMISTRY, PHYSICAL | SIMULATION | BOND | CYCLIZATION
Journal Article
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 07/2019, Volume 123, Issue 29, pp. 6133 - 6149
Remarkable success in engineering novel efficient biomarkers based on fluorescent and photoactive proteins provokes a question of whether computational... 
WILD-TYPE | GREEN FLUORESCENT PROTEIN | MOLECULAR-DYNAMICS | TRIPLE-DECKER MOTIF | STRUCTURAL BASIS | OPTICAL-PROPERTIES | CHEMISTRY, PHYSICAL | DENSITY-FUNCTIONAL THEORY | PROTON-TRANSFER | CHROMOPHORE MATURATION | RATIONAL DESIGN
Journal Article
Journal of the American Chemical Society, ISSN 0002-7863, 08/2017, Volume 139, Issue 30, pp. 10239 - 10249
Journal Article
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, ISSN 1463-9076, 10/2018, Volume 20, Issue 37, pp. 23827 - 23836
Amide-imide tautomerization presents a pervasive class of chemical transformations in organic chemistry of natural compounds. In this Perspective, we describe... 
APPA BLUF DOMAIN | REACTION-MECHANISM | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | GUANOSINE TRIPHOSPHATE HYDROLYSIS | INDUCED STRUCTURAL-CHANGES | GTPASE-ACTIVATING PROTEIN | DENSITY-FUNCTIONAL THEORY | RAS-GAP | GAP-CATALYZED-HYDROLYSIS | VIBRATIONS TELL US | AQUEOUS-SOLUTION
Journal Article
Physical Chemistry Chemical Physics, ISSN 1463-9076, 2018, Volume 20, Issue 37, pp. 23827 - 23836
Amide-imide tautomerization presents a pervasive class of chemical transformations in organic chemistry of natural compounds. In this Perspective, we describe... 
Journal Article
Chemical Physics Letters, ISSN 0009-2614, 10/2018, Volume 710, pp. 59 - 63
We characterize structures and electronic excitation of domains from a bacteriophytochrome-based infrared fluorescent protein carrying a covalently bound... 
Electronic excitation | QM/MM | Biliverdin | Bacteriophytochromes | XMCQDPT2 | Molecular modeling | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | CPH1 | FAMILY | CHROMOPHORES | DYNAMICS | SIMULATIONS | ABSORPTION | DENSITY-FUNCTIONAL THEORY | SPECTRA | PHYTOCHROME | INSIGHTS | Density functionals | Fluorescence | Models | Analysis | Protein binding
Journal Article
Chemical Physics Letters, ISSN 0009-2614, 05/2017, Volume 676, pp. 25 - 31
Photoactivation of the bacterial photoreceptor BLUF is achieved by a unique tautomerization and rotation of the conserved Gln residue. To identify interactions... 
FLAVIN | DOMAIN | ELECTRON-TRANSFER | HYDROGEN-BOND | LIGHT PHOTORECEPTOR | ADENYLYL-CYCLASE | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | SPECTROSCOPIC CHARACTERIZATION | DYNAMICS | CHEMISTRY, PHYSICAL | INDUCED STRUCTURAL-CHANGES | APPA | Hydrogen | Glutamine
Journal Article
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 11/2017, Volume 121, Issue 47, pp. 10602 - 10609
We characterize computationally a red fluorescent protein (RFP) with the chromophore (Chro) sandwiched between two aromatic tyrosine rings in a triple-decker... 
ORIGIN | STATES | EXCITATION | CHROMOPHORE | MECHANISM | NWCHEM | CHEMISTRY, PHYSICAL | RATIONAL DESIGN
Journal Article
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 04/2016, Volume 120, Issue 16, pp. 3873 - 3879
Complexes of small GTPases with GTPase-activating proteins have been intensively studied with the main focus on the complex of H-Ras with p120GAP (Ras-GAP).... 
MOLECULAR-DYNAMICS | ACTIVATION | MUTATION | CHEMISTRY, PHYSICAL | RAS-GAP | SIMULATION | GAP-CATALYZED-HYDROLYSIS | GTP HYDROLYSIS
Journal Article
Organic and Biomolecular Chemistry, ISSN 1477-0520, 2018, Volume 16, Issue 40, pp. 7518 - 7529
In this work, we disclose a mechanism of competing chemical reactions of protein assembly for a bacterial phytochrome using modern methods of molecular... 
Journal Article
ORGANIC & BIOMOLECULAR CHEMISTRY, ISSN 1477-0520, 05/2019, Volume 17, Issue 19, pp. 4879 - 4891
The mechanism of the deceptively simple reaction of guanosine triphosphate (GTP) hydrolysis catalyzed by the cellular protein Ras in complex with the... 
PHOSPHORYL TRANSFER | ACTIVATION | PROTEIN | SUBSTRATE-ASSISTED CATALYSIS | DYNAMICS | CHEMISTRY, ORGANIC | GTP-HYDROLYSIS | MUTATIONS | PHOSPHATE MONOESTER HYDROLYSIS | SMALL GTPASES | FREE-ENERGY
Journal Article
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