pH‐Dependent Protonation of Surface Carboxylate Groups in PsbO Enables Local Buffering and Triggers Structural Changes

Gerland, Lisa Maria; Stöppler, Daniel; Hopf, L.; Donovan, Eavan; Wallmann, Arndt; Erdmann, Natalja; Diehl, Anne; Bommer, Martin; Buzar, Krzysztof; Ibrahim, Mohamed; Schmieder, Peter; Dobbek, Holger; Zouni, Athina; Bondar, Ana‐Nicoleta; Dau, Holger; Oschkinat, Hartmut

doi:10.1002/cbic.201900739

Cited by 18 publications

(7 citation statements)

References 43 publications

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“…Given the large number of carboxylate groups and net negative charge carried by protein S sequences, we sought to find out whether protein S has patches of carboxylate and histidine groups, as such patches are of potential interest for proton binding ( Bondar and Lemieux, 2019 , Checover et al, 2001 , Gerland et al, 2020 , Guerra and Bondar, 2015 , Kemmler et al, 2019 , Lorch et al, 2015 , Shutova et al, 2007 ). We found that the sequence of SARS-CoV-2 protein S has multiple positions where Asp, Glu or His groups are adjacent or separated by 1–2 amino acid residues; of the 17 His groups of the protein, 7 are within the C-terminal ~220 residue fragment ( Fig.…”

Section: Resultsmentioning

confidence: 99%

A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2

Karathanou

Lazaratos

Bertalan

et al. 2020

Journal of Structural Biology

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Section: Resultsmentioning

confidence: 99%

A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2

Karathanou

Lazaratos

Bertalan

et al. 2020

Journal of Structural Biology

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“…This is an additional indication for a slight expansion of dPSIIcc in buffer solution. Since the latter expansion concerns largely the membrane-extrinsic parts of PS II, it may also be caused by a larger conformational flexibility in this region of dPSIIcc. ,− …”

Section: Resultsmentioning

confidence: 99%

Solution Structure of the Detergent–Photosystem II Core Complex Investigated by Small-Angle Scattering Techniques

et al. 2020

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Albeit achieving the X-ray diffraction structure of dimeric photosystem II core complexes (dPSIIcc) at the atomic resolution, the nature of the detergent belt surrounding dPSIIcc remains ambiguous. Therefore, the solution structure of the whole detergent−protein complex of dPSIIcc of Thermosynechococcus elongatus (T. elongatus) solubilized in n-dodecyl-ß-D-maltoside (ßDM) was investigated by a combination of small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) with contrast variation. First, the structure of dPSIIcc was studied separately in SANS experiments using a contrast of 5% D 2 O. Guinier analysis reveals that the dPSIIcc solution is virtually free of aggregation in the studied concentration range of 2−10 mg/mL dPSIIcc, and characterized by a radius of gyration of 62 Å. A structure reconstitution shows that dPSIIcc in buffer solution widely retains the crystal structure reported by Xray free electron laser studies at room temperature with a slight expansion of the entire protein. Additional SANS experiments on dPSIIcc samples in a buffer solution containing 75% D 2 O provide information about the size and shape of the whole detergent− dPSIIcc. The maximum position of P(r) function increases to 68 Å, i.e., it is about 6 Å larger than that of dPSIIcc only, thus indicating the presence of an additional structure. Thus, it can be concluded that dPSIIcc is surrounded by a monomolecular belt of detergent molecules under appropriate solubilization conditions. The homogeneity of the ßDM−dPSIIcc solutions was also verified using dynamic light scattering. Complementary SAXS experiments indicate the presence of unbound detergent micelles by a separate peak consistent with a spherical shape possessing a radius of about 40 Å. The latter structure also contributes to the SANS data but rather broadens the SANS curve artificially. Without the simultaneous inspection of SANS and SAXS data, this effect may lead to an apparent underestimation of the size of the PS II−detergent complex. The formation of larger unbound detergent aggregates in solution prior to crystallization may have a significant effect on the crystal formation or quality of the ßDM−dPSIIcc.

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“…Oryza sativa normally grows emerged in water ( Yan et al., 2023 ), whereas Zea mays grows under more dry conditions on land. Differences in the charge distributions of Zm Chi19A and Os Chi19A may be adaptations to specific ecological niches, lifestyles, or host-pathogen interactions ( Vanhoye et al., 2004 ; Garcia-Moreno, 2009 ; Gerland et al., 2020 ; Kim et al., 2020 ; Panja et al., 2020 ; Di Savino et al., 2021 ; Doan et al., 2022 ; Vallina Estrada et al., 2023 ).…”

Section: Discussionmentioning

confidence: 99%

Plant root associated chitinases: structures and functions

Shobade,

Zabotina,

Nilsen-Hamilton

2024

Front. Plant Sci.

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Chitinases degrade chitin, a linear homopolymer of β-1,4-linked N-acetyl-D-glucosamine (GlcNAc) residues found in the cell walls of fungi and the exoskeletons of arthropods. They are secreted by the roots into the rhizosphere, a complex and dynamic environment where intense nutrient exchange occurs between plants and microbes. Here we modeled, expressed, purified, and characterized Zea mays and Oryza sativa root chitinases, and the chitinase of a symbiotic bacterium, Chitinophaga oryzae 1303 for their activities with chitin, di-, tri-, and tetra-saccharides and Aspergillus niger, with the goal of determining their role(s) in the rhizosphere and better understanding the molecular mechanisms underlying plant-microbe interactions. We show that Zea mays basic endochitinase (ZmChi19A) and Oryza sativa chitinase (OsChi19A) are from the GH19 chitinase family. The Chitinophaga oryzae 1303 chitinase (CspCh18A) belongs to the GH18 family. The three enzymes have similar apparent KM values of (20-40 µM) for the substrate 4-MU-GlcNAc3. They vary in their pH and temperature optima with OsChi19A activity optimal between pH 5–7 and 30–40°C while ZmChi19A and CspCh18A activities were optimal at pH 7-9 and 50–60°C. Modeling and site-directed mutation of ZmChi19A identified the catalytic cleft and the active residues E147 and E169 strategically positioned at ~8.6Å from each other in the folded protein. Cleavage of 4-MU-GlcNAc3 was unaffected by the absence of the CBD but diminished in the absence of the flexible C-terminal domain. However, unlike for the soluble substrate, the CBD and the newly identified flexible C-terminal domain were vital for inhibiting Aspergillus niger growth. The results are consistent with the involvement of the plant chitinases in defense against pathogens like fungi that have chitin exoskeletons. In summary, we have characterized the functional features and structural domains necessary for the activity of two plant root chitinases that are believed to be involved in plant defense and a bacterial chitinase that, along with the plant chitinases, may participate in nutrient recycling in the rhizosphere.

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pH‐Dependent Protonation of Surface Carboxylate Groups in PsbO Enables Local Buffering and Triggers Structural Changes

Cited by 18 publications

References 43 publications

A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2

A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2

Solution Structure of the Detergent–Photosystem II Core Complex Investigated by Small-Angle Scattering Techniques

Plant root associated chitinases: structures and functions

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