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Article ; Online: Crystallization of Microbial Rhodopsins.

Kovalev, Kirill / Astashkin, Roman / Gordeliy, Valentin / Cherezov, Vadim

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2501, Page(s) 125–146

Abstract: Microbial rhodopsins are light-sensitive transmembrane proteins, evolutionary adapted by various organisms like archaea, bacteria, simple eukaryote, and viruses to utilize solar energy for their survival. A complete understanding of functional mechanisms ...

Abstract	Microbial rhodopsins are light-sensitive transmembrane proteins, evolutionary adapted by various organisms like archaea, bacteria, simple eukaryote, and viruses to utilize solar energy for their survival. A complete understanding of functional mechanisms of these proteins is not possible without the knowledge of their high-resolution structures, which can be primarily obtained by X-ray crystallography. This technique, however, requires high-quality crystals, growing of which is a great challenge especially in case of membrane proteins. In this chapter, we summarize methods applied for crystallization of microbial rhodopsins with the emphasis on crystallization in lipidic mesophases, also known as in meso approach. In particular, we describe in detail the methods of crystallization using lipidic cubic phase to grow both large crystals optimized for traditional crystallographic data collection and microcrystals for serial crystallography.
MeSH term(s)	Crystallization/methods ; Crystallography, X-Ray ; Lipids/chemistry ; Membrane Proteins/chemistry ; Rhodopsins, Microbial
Chemical Substances	Lipids ; Membrane Proteins ; Rhodopsins, Microbial
Language	English
Publishing date	2022-07-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2329-9_6
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Article: Custom Design of a Humidifier Chamber for

Marin, Egor / Kovalev, Kirill / Poelman, Therese / Veenstra, Rick / Borshchevskiy, Valentin / Guskov, Albert

Crystal growth & design

2023 Volume 24, Issue 1, Page(s) 325–330

Abstract: Membrane proteins are indispensable for every living organism, yet their structural organization remains underexplored. Despite the recent advancements in single-particle cryogenic electron microscopy and cryogenic electron tomography, which have ... ...

Abstract	Membrane proteins are indispensable for every living organism, yet their structural organization remains underexplored. Despite the recent advancements in single-particle cryogenic electron microscopy and cryogenic electron tomography, which have significantly increased the structural coverage of membrane proteins across various kingdoms, certain scientific methods, such as time-resolved crystallography, still mostly rely on crystallization techniques, such as lipidic cubic phase (LCP) or
Language	English
Publishing date	2023-12-12
Publishing country	United States
Document type	Journal Article
ISSN	1528-7483
ISSN	1528-7483
DOI	10.1021/acs.cgd.3c01034
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Article ; Online: Engineering the Catalytic Properties of Two-Domain Laccase from

Kolyadenko, Ilya / Scherbakova, Anastasia / Kovalev, Kirill / Gabdulkhakov, Azat / Tishchenko, Svetlana

International journal of molecular sciences

2021 Volume 23, Issue 1

Abstract: Laccases catalyze the oxidation of substrates with the concomitant reduction of oxygen to water. Recently, we found that polar residues located in tunnels leading to Cu2 and Cu3 ions control oxygen entrance (His 165) and proton transport (Arg 240) of two- ...

Abstract	Laccases catalyze the oxidation of substrates with the concomitant reduction of oxygen to water. Recently, we found that polar residues located in tunnels leading to Cu2 and Cu3 ions control oxygen entrance (His 165) and proton transport (Arg 240) of two-domain laccase (2D) from
MeSH term(s)	Amino Acid Substitution/physiology ; Bacterial Proteins/metabolism ; Catalysis ; Copper/metabolism ; Laccase/metabolism ; Oxidation-Reduction ; Streptomyces/metabolism
Chemical Substances	Bacterial Proteins ; Copper (789U1901C5) ; Laccase (EC 1.10.3.2)
Language	English
Publishing date	2021-12-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23010065
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Article ; Online: E. coli Expression and Purification of Microbial and Viral Rhodopsins.

Balandin, Taras / Volkov, Dmytro / Alekseev, Alexey / Kovalev, Kirill / Bratanov, Dmitry / Gordeliy, Valentin

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2501, Page(s) 109–124

Abstract: Microbial rhodopsins have become an indispensable tool for neurobiology. Of thousands of identified microbial rhodopsins, a minute fraction has been studied so far and they have shown remarkable functional diversity suggesting more great promises that ... ...

Abstract	Microbial rhodopsins have become an indispensable tool for neurobiology. Of thousands of identified microbial rhodopsins, a minute fraction has been studied so far and they have shown remarkable functional diversity suggesting more great promises that this large family holds. Effective production of recombinant microbial and viral rhodopsins is a prerequisite for the success of functional and structural studies of these proteins. Escherichia coli (E. coli) are suitable for high yield expression of many of microbial and viral rhodopsins and they facilitate rapid exploration of this large protein family.
MeSH term(s)	Escherichia coli/genetics ; Escherichia coli/metabolism ; Rhodopsin/chemistry ; Rhodopsins, Microbial/chemistry ; Rhodopsins, Microbial/genetics
Chemical Substances	Rhodopsins, Microbial ; Rhodopsin (9009-81-8)
Language	English
Publishing date	2022-07-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2329-9_5
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Article ; Online: Flotillin-associated rhodopsin (FArhodopsin), a widespread paralog of proteorhodopsin in aquatic bacteria with streamlined genomes.

Haro-Moreno, Jose M / López-Pérez, Mario / Alekseev, Alexey / Podoliak, Elizaveta / Kovalev, Kirill / Gordeliy, Valentin / Stepanauskas, Ramunas / Rodriguez-Valera, Francisco

mSystems

2023 Volume 8, Issue 3, Page(s) e0000823

Abstract: Microbial rhodopsins are found more than once in a single genome (paralogs) often have different functions. We screened a large dataset of open ocean single-amplified genomes (SAGs) for co-occurrences of multiple rhodopsin genes. Many such cases were ... ...

Abstract	Microbial rhodopsins are found more than once in a single genome (paralogs) often have different functions. We screened a large dataset of open ocean single-amplified genomes (SAGs) for co-occurrences of multiple rhodopsin genes. Many such cases were found among Pelagibacterales (SAR11), HIMB59, and the Gammaproteobacteria
MeSH term(s)	Rhodopsin/chemistry ; Rhodopsins, Microbial/genetics ; Bacteria/metabolism
Chemical Substances	proteorhodopsin ; Rhodopsin (9009-81-8) ; flotillins ; Rhodopsins, Microbial
Language	English
Publishing date	2023-05-24
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN (online)	2379-5077
DOI	10.1128/msystems.00008-23
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Article ; Online: Rhodopsin Channel Activity Can Be Evaluated by Measuring the Photocurrent Voltage Dependence in Planar Bilayer Lipid Membranes.

Rokitskaya, Tatyana I / Maliar, Nina / Kovalev, Kirill V / Volkov, Oleksandr / Gordeliy, Valentin I / Antonenko, Yuri N

Biochemistry. Biokhimiia

2021 Volume 86, Issue 4, Page(s) 409–419

Abstract: The studies of the functional properties of retinal-containing proteins often include experiments in model membrane systems, e.g., measurements of electric current through planar bilayer lipid membranes (BLMs) with proteoliposomes adsorbed on one of the ... ...

Abstract	The studies of the functional properties of retinal-containing proteins often include experiments in model membrane systems, e.g., measurements of electric current through planar bilayer lipid membranes (BLMs) with proteoliposomes adsorbed on one of the membrane surfaces. However, the possibilities of this method have not been fully explored yet. We demonstrated that the voltage dependence of stationary photocurrents for two light-sensitive proteins, bacteriorhodopsin (bR) and channelrhodopsin 2 (ChR2), in the presence of protonophore had very different characteristics. In the case of the bR (proton pump), the photocurrent through the BLM did not change direction when the polarity of the applied voltage was switched. In the case of the photosensitive channel protein ChR2, the photocurrent increased with the increase in voltage and the current polarity changed with the change in the voltage polarity. The protonophore 4,5,6,7-tetrachloro-2-trifluoromethyl benzimidazole (TTFB) was more efficient in the maximizing stationary photocurrents. In the presence of carbonyl cyanide-m-chlorophenylhydrazone (CCCP), the amplitude of the measured photocurrents for bR significantly decreased, while in the case of ChR2, the photocurrents virtually disappeared. The difference between the effects of TTFB and CCCP was apparently due to the fact that, in contrast to TTFB, CCCP transfers protons across the liposome membranes with a higher rate than through the decane-containing BLM used as a surface for the proteoliposome adsorption.
MeSH term(s)	Bacteriorhodopsins/metabolism ; Channelrhodopsins/metabolism ; Ion Transport ; Lipid Bilayers/metabolism ; Proteolipids
Chemical Substances	Channelrhodopsins ; Lipid Bilayers ; Proteolipids ; proteoliposomes ; Bacteriorhodopsins (53026-44-1)
Language	English
Publishing date	2021-04-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	1109-5
ISSN	1608-3040 ; 0006-2979 ; 0320-9717
ISSN (online)	1608-3040
ISSN	0006-2979 ; 0320-9717
DOI	10.1134/S0006297921040039
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Article ; Online: Crystal structure of human 14-3-3ζ complexed with the noncanonical phosphopeptide from proapoptotic BAD.

Sluchanko, Nikolai N / Tugaeva, Kristina V / Gushchin, Ivan / Remeeva, Alina / Kovalev, Kirill / Cooley, Richard B

Biochemical and biophysical research communications

2021 Volume 583, Page(s) 100–105

Abstract: Several signaling pathways control phosphorylation of the proapoptotic protein BAD and its phosphorylation-dependent association with 14-3-3 proteins in the cytoplasm. The stability of the 14-3-3/BAD complex determines the cell fate: unphosphorylated BAD ...

Abstract	Several signaling pathways control phosphorylation of the proapoptotic protein BAD and its phosphorylation-dependent association with 14-3-3 proteins in the cytoplasm. The stability of the 14-3-3/BAD complex determines the cell fate: unphosphorylated BAD escapes from 14-3-3, migrates to the mitochondria and initiates apoptosis. While the 14-3-3/BAD interaction represents a promising drug target, it lacks structural characterization. Among several phosphosites identified in vivo, Ser75 and Ser99 of human BAD match the consensus sequence RXXpSXP recognized by 14-3-3 and, therefore, represent canonical 14-3-3-binding sites. Yet, BAD contains other serines phosphorylatable in vivo, whose role is less understood. Here, we report a 2.36 Å crystal structure of 14-3-3ζ complexed with a BAD fragment which includes residues Ser74 and Ser75, both being substrates for protein kinases. While the BAD peptide is anchored to 14-3-3 by phosphoserine as expected, the BAD peptide was unexpectedly phosphorylated at Ser74 instead of Ser75, revealing noncanonical binding within the amphipathic groove and leading to a one-step positional shift and reorganization of the interface. This observation exemplifies plasticity of the amphipathic 14-3-3 groove in accommodating various peptides and suggests the redundancy of Ser74 and Ser75 phosphosites with respect to binding of BAD to 14-3-3.
Language	English
Publishing date	2021-10-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2021.10.053
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Article: Crystal structure of human 14-3-3ζ complexed with the noncanonical phosphopeptide from proapoptotic BAD

Sluchanko, Nikolai N. / Tugaeva, Kristina V. / Gushchin, Ivan / Remeeva, Alina / Kovalev, Kirill / Cooley, Richard B.

Biochemical and biophysical research communications. 2021 Dec. 17, v. 583

2021

Abstract	Several signaling pathways control phosphorylation of the proapoptotic protein BAD and its phosphorylation-dependent association with 14-3-3 proteins in the cytoplasm. The stability of the 14-3-3/BAD complex determines the cell fate: unphosphorylated BAD escapes from 14-3-3, migrates to the mitochondria and initiates apoptosis. While the 14-3-3/BAD interaction represents a promising drug target, it lacks structural characterization. Among several phosphosites identified in vivo, Ser75 and Ser99 of human BAD match the consensus sequence RXXpSXP recognized by 14-3-3 and, therefore, represent canonical 14-3-3-binding sites. Yet, BAD contains other serines phosphorylatable in vivo, whose role is less understood. Here, we report a 2.36 Å crystal structure of 14-3-3ζ complexed with a BAD fragment which includes residues Ser74 and Ser75, both being substrates for protein kinases. While the BAD peptide is anchored to 14-3-3 by phosphoserine as expected, the BAD peptide was unexpectedly phosphorylated at Ser74 instead of Ser75, revealing noncanonical binding within the amphipathic groove and leading to a one-step positional shift and reorganization of the interface. This observation exemplifies plasticity of the amphipathic 14-3-3 groove in accommodating various peptides and suggests the redundancy of Ser74 and Ser75 phosphosites with respect to binding of BAD to 14-3-3.
Keywords	apoptosis ; consensus sequence ; crystal structure ; drugs ; humans ; mitochondria ; phosphopeptides ; phosphorylation ; plasticity ; protein kinases ; research ; surfactants
Language	English
Dates of publication	2021-1217
Size	p. 100-105.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	205723-2
ISSN	0006-291X ; 0006-291X
ISSN (online)	0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2021.10.053
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Article ; Online: Insights into the mechanisms of light-oxygen-voltage domain color tuning from a set of high-resolution X-ray structures.

Remeeva, Alina / Nazarenko, Vera V / Kovalev, Kirill / Goncharov, Ivan M / Yudenko, Anna / Astashkin, Roman / Gordeliy, Valentin / Gushchin, Ivan

Proteins

2021

Abstract: Light-oxygen-voltage (LOV) domains are widespread photosensory modules that can be used in fluorescence microscopy, optogenetics and controlled production of reactive oxygen species. All of the currently known LOV domains have absorption maxima in the ... ...

Abstract	Light-oxygen-voltage (LOV) domains are widespread photosensory modules that can be used in fluorescence microscopy, optogenetics and controlled production of reactive oxygen species. All of the currently known LOV domains have absorption maxima in the range of ~440 to ~450 nm, and it is not clear whether they can be shifted significantly using mutations. Here, we have generated a panel of LOV domain variants by mutating the key chromophore-proximal glutamine aminoacid of a thermostable flavin based fluorescent protein CagFbFP (Gln148) to asparagine, aspartate, glutamate, histidine, lysine and arginine. Absorption spectra of all of the mutants are blue-shifted, with the maximal shift of 8 nm observed for the Q148H variant. While CagFbFP and its Q148N/D/E variants are not sensitive to pH, Q148H/K/R reveal a moderate red shift induced byacidic pH. To gain further insight, we determined high resolution crystal structures of all of the mutants studied at the resolutions from 1.07 Å for Q148D to 1.63 Å for Q148R. Whereas in some of the variants, the aminoacid 148 remains in the vicinity of the flavin, in Q148K, Q148R and partially Q148D, the C-terminus of the protein unlatches and the side chain of the residue 148 is reoriented away from the chromophore. Our results explain the absence of color shifts from replacing Gln148 with charged aminoacids and pave the way for rational design of color-shifted flavin based fluorescent proteins.
Language	English
Publishing date	2021-03-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	806683-8
ISSN	1097-0134 ; 0887-3585
ISSN (online)	1097-0134
ISSN	0887-3585
DOI	10.1002/prot.26078
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Zs.A 2291: Show issues

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Article: Insertion and activation of functional Bacteriorhodopsin in a floating bilayer

Mukhina, Tetiana / Gerelli, Yuri / Hemmerle, Arnaud / Koutsioubas, Alexandros / Kovalev, Kirill / Teulon, Jean-Marie / Pellequer, Jean-Luc / Daillant, Jean / Charitat, Thierry / Fragneto, Giovanna

Journal of colloid and interface science. 2021 Sept., v. 597

2021

Abstract: The proton pump transmembrane protein bacteriorhodopsin was successfully incorporated into planar floating lipid bilayers in gel and fluid phases, by applying a detergent-mediated incorporation method. The method was optimized on single supported ... ...

Abstract	The proton pump transmembrane protein bacteriorhodopsin was successfully incorporated into planar floating lipid bilayers in gel and fluid phases, by applying a detergent-mediated incorporation method. The method was optimized on single supported bilayers by using quartz crystal microbalance, atomic force and fluorescence microscopy techniques. Neutron and X-ray reflectometry were used on both single and floating bilayers with the aim of determining the structure and composition of this membrane-protein system before and after protein reconstitution at sub-nanometer resolution. Lipid bilayer integrity and protein activity were preserved upon the reconstitution process. Reversible structural modifications of the membrane, induced by the bacteriorhodopsin functional activity triggered by visible light, were observed and characterized at the nanoscale.
Keywords	X-ray reflectivity ; fluorescence microscopy ; gels ; light ; lipid bilayers ; neutrons ; proton pump ; quartz crystal microbalance ; transmembrane proteins
Language	English
Dates of publication	2021-09
Size	p. 370-382.
Publishing place	Elsevier Inc.
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	241597-5
ISSN	1095-7103 ; 0021-9797
ISSN (online)	1095-7103
ISSN	0021-9797
DOI	10.1016/j.jcis.2021.03.155
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