Crystal structure of highly glycosylated human leukocyte elastase in complex with an S2′ site binding inhibitor

Hochscherf, Jennifer; Pietsch, Markus; Tieu, William; Kuan, K.; Abell, Andrew D.; Gütschow, Michael; Niefind, Karsten

doi:10.1107/s2053230x1800537x

Cited by 5 publications

(5 citation statements)

References 54 publications

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“…The functional research of HCPs is also affected by glycosylation modification, the protein antibody is difficult to obtain, and the protein glycosylation modification is difficult to investigate. Recently, more powerful mass spectrometry technique may provide effective research tools for identifying HCP glycosylation modification sites, and more advanced cryo-electron microscopy technology ( Hochscherf et al., 2018 ) has made it possible to explore the crystal structure of HCPs, especially the structure of glycosylation, which open a new insight for the future research of HCPs.…”

Section: Discussionmentioning

confidence: 99%

Identification of Hydroxyproline-Containing Proteins and Hydroxylation of Proline Residues in Rice

et al. 2020

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The hydroxyproline-containing proteins (HCPs) among secretory and vacuolar proteins play important roles in growth and development of higher plants. Many hydroxyprolinerich glycoproteins (HRGPs), including Arabinogalactan proteins (AGPs), extensins (EXTs), and proline-rich proteins (PRPs), are identified as HCPs by bioinformatics approaches. The experimental evidence for validation of novel proline hydroxylation sites is vital for understanding their functional roles. In this study, the 62 HCPs containing 114 hydroxyproline (O, Hyp) residues were identified, and it was found that hydroxylation of proline residues in the HCPs could either constitute attachment sites for glycans or have other biological function in rice. The glycomodules of AO, OA, OG, VO, LO, and OE were abundant in the 62 HCPs. Further analysis showed that the 22 of 62 HCPs contained both signal peptides and transmembrane domains, and the 19 HCPs only contained transmembrane domains, while 21 HCPs contained neither. This study indicated the feasibility of mass spectrometry-based proteomics combined with bioinformatics approaches for the large-scale characterization of Hyp sites from complex protein digest mixtures. Furthermore, the expression of AGPs in rice was detected by using b-GlcY reagent and JIM13 antibody. The results displayed that the AGPs were widely distributed in different tissues and organs of rice, especially expressed highly in lateral root, pollen and embryo. In conclusion, our study revealed that the HCPs and Hyp residues in rice were ubiquitous and that these Hyps could be candidates for linking to glycans, which laid the foundation for further studying the functions of HCPs and hydroxylation of proline residues in rice.

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Section: Discussionmentioning

confidence: 99%

Identification of Hydroxyproline-Containing Proteins and Hydroxylation of Proline Residues in Rice

et al. 2020

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“…Based on the aforementioned, human granzyme B in complex with 2-acetamido-2-deoxy-beta-D-glucopyranose [ 219 ] was downloaded from PDB (Code: 1IAU), while the crystal structure of highly glycosylated human leukocyte elastase in complex with a thiazolidinedione inhibitor (5-[[4-[[(2~{S})-4-methyl-1-oxidanylidene-1-[(2-propylphenyl)amino]pentan-2-yl]carbamoyl]phenyl]methyl]-2-oxidanylidene-1,3-thiazol-1-ium-4-olate) [ 220 ] was also downloaded from PDB (Code: 6F5M). Both enzymes were cleaned for missing amino acids or gaps in their sequences.…”

Section: Computational Studiesmentioning

confidence: 99%

Herbal Arsenal against Skin Ailments: A Review Supported by In Silico Molecular Docking Studies

et al. 2022

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Maintaining healthy skin is important for a healthy body. At present, skin diseases are numerous, representing a major health problem affecting all ages from neonates to the elderly worldwide. Many people may develop diseases that affect the skin, including cancer, herpes, and cellulitis. Long-term conventional treatment creates complicated disorders in vital organs of the body. It also imposes socioeconomic burdens on patients. Natural treatment is cheap and claimed to be safe. The use of plants is as old as mankind. Many medicinal plants and their parts are frequently used to treat these diseases, and they are also suitable raw materials for the production of new synthetic agents. A review of some plant families, viz., Fabaceae, Asteraceae, Lamiaceae, etc., used in the treatment of skin diseases is provided with their most common compounds and in silico studies that summarize the recent data that have been collected in this area.

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“…The molecular docking simulations are carried out using the AutoDock 4.0 software (Morris et al, 2009). The three-dimensional crystal structures of HLE were obtained from the Protein Data Bank (PDB IDs: 6F5M) (Hochscherf et al, 2018). The preparation of protein for docking simulations is carried out in the Discovery Studio 4.0 (BIOVIA Discovery Studio 2016).…”

Section: Theoretical Frameworkmentioning

confidence: 99%

Antioxidative and Inhibition Potency of Cynodontin

Đorović¹,

Antonijević²,

Marković³

2020

JSSCM

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The antioxidant activity of cynodontin was studied in the absence and the presence of free radical species. This in silico study was performed in water and benzene, with the aim to simulate polar and non-polar environment. To determine the most probable mechanism of antioxidant action, density functional theory (DFT) was employed. The change in reaction enthalpy of cynodontin with three different free radicals (hydroxyl, hydroperoxyl, and methyl peroxyl radical) were examined and presented. SET-PT (Single Electron Transfer – Proton Transfer) mechanism is not an operative mechanism of antioxidant action. The obtained results imply that the possible mechanism of antioxidant action in water is SPLET (Sequential Proton Loss Electron Transfer), while in benzene HAT (Hydrogen atom transfer) and SPLET are competitive mechanisms. The molecular docking study was performed in order to estimate the inhibition potency of the investigated compound toward human leukocyte elastase (HLE). The obtained results indicate that numerous interactions determine the inhibition activity towards the investigated protein.

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Crystal structure of highly glycosylated human leukocyte elastase in complex with an S2′ site binding inhibitor

Cited by 5 publications

References 54 publications

Identification of Hydroxyproline-Containing Proteins and Hydroxylation of Proline Residues in Rice

Identification of Hydroxyproline-Containing Proteins and Hydroxylation of Proline Residues in Rice

Herbal Arsenal against Skin Ailments: A Review Supported by In Silico Molecular Docking Studies

Antioxidative and Inhibition Potency of Cynodontin

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