Structural insights and binding of a natural ligand, succinic acid with serine and cysteine proteases

Manohar, R.; Kutumbarao, N.H.V.; Nagampalli, Raghavendra Sashi Krishna; Velmurugan, D.; Gunasekaran, Krishnasamy

doi:10.1016/j.bbrc.2017.11.033

Cited by 10 publications

(8 citation statements)

References 21 publications

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“…Thus, the van der Waals interactions with these amino acids would cause a partial occupation of the substrate binding cleft and a subsequent steric hindrance to bind it. Similar findings were obtained with succinic acid, which interacted with the His57 (catalytic residue) of Trypsin (Manohar et al, 2018).…”

Section: Molecular Dockingsupporting

confidence: 81%

LIPIDS AS COMPETITIVE INHIBITORS OF SUBTILISIN CARLSBERG IN THE ENZYMATIC HYDROLYSIS OF PROTEINS IN RED TILAPIA (Oreochromis sp.) VISCERA: INSIGHTS FROM KINETIC MODELS AND A MOLECULAR DOCKING STUDY

Sampedro

Grimaldos

Pereañez

et al. 2019

Braz. J. Chem. Eng.

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Protein hydrolysis can improve food's nutritional, techno-functional and biological properties, which can increase the possibilities of application in industry. The objective of this research article was to study the effect of lipids on the enzymatic kinetics of red tilapia viscera (RTV) hydrolysis with subtilisin Carlsberg. The RTV were hydrolyzed in an enzyme/substrate ratio of 0.153 (U/g), at 53° C, at a pH of 9.5, initial concentrations of lipids of 1, 19 and 50 g/L, and different initial substrate concentrations for each initial lipid concentration. To explain the lipid action mechanism, we evaluated a Michaelis-Menten model and another semi-physical model based on kinetic expressions and mass balances. Additionally, a molecular docking analysis was performed between subtilisin Carlsberg and the main fatty acid in RTV (palmitic acid). For both models, the results suggest a strong competitive inhibition by lipids, with an inhibition constant of 2.36 and 3.01 g/L for the first and second models, respectively. On the other hand, docking suggested that palmitic acid could form van der Waals interactions and hydrogen bonds with the residues of the active site of subtilisin Carlsberg and occupy part of the substrate binding site, thus acting as an effective competitive inhibitor.

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Section: Molecular Dockingsupporting

confidence: 81%

LIPIDS AS COMPETITIVE INHIBITORS OF SUBTILISIN CARLSBERG IN THE ENZYMATIC HYDROLYSIS OF PROTEINS IN RED TILAPIA (Oreochromis sp.) VISCERA: INSIGHTS FROM KINETIC MODELS AND A MOLECULAR DOCKING STUDY

Sampedro

Grimaldos

Pereañez

et al. 2019

Braz. J. Chem. Eng.

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“…Trypsin contains some alpha helices and beta-pleated sheets (RCSB entries 5GXP [65] and 5JYI [66]). The spectrum reported in Supplementary Information 3 agrees with this by the positive maximum at 193 nm [63].…”

Section: Circular Dichroismmentioning

confidence: 99%

Probing polydopamine adhesion to protein and polymer films: microscopic and spectroscopic evaluation

2017

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Polydopamine has been found to be a biocompatible polymer capable of supporting cell growth and attachment, and to have antibacterial and antifouling properties. Together with its ease of manufacture and application, it ought to make an ideal biomaterial and function well as a coating for implants. In this paper, atomic force microscope was used to measure the adhesive forces between polymer-, protein-or polydopamine-coated surfaces and a silicon nitride or polydopamine-functionalised probes. Surfaces were further characterised by contact angle goniometry, and solutions by circular dichroism. Polydopamine was further characterised with infrared spectroscopy and Raman spectroscopy. It was found that polydopamine functionalisation of the atomic force microscope probe significantly reduced adhesion to all tested surfaces. For example, adhesion to mica fell from 0.27 ± 0.7 to 0.05 ± 0.01 nN nm -1 . The results suggest that polydopamine coatings are suitable to be used for a variety of biomedical applications.

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“…In a recent study, succinic acid was identified to inhibit both trypsin and papain proteases by binding to histidine residue and in altering the local pH of the active site region. [ 2 ] As it is generally believed that anti‐inflammatory compounds can be protease inhibitors, the vice versa effect was suspected and so, inhibitory activity was studied for succinic acid against PLA 2 . From the digestion zone noticed in Figure 2 it is evident that succinic acid inhibits PLA 2 activity and this inhibiting nature of succinic acid can be attributed to interaction with histidine residue at the active site of PLA 2 .…”

Section: Resultsmentioning

confidence: 99%

“…Phospholipase A 2 (PLA 2 ) is a class of enzyme which performs specific hydrolysis of ester bond at C2 position of 1,2-diacyl-3-snglycerophospholipids. [1][2][3] The specificity of the site of hydrolysis differentiates the phospholipase, where, phospholipase A 1 performs its hydrolysis at sn-1 site and phospholipase A 2 acts on sn-2 site. There has been a great interest for the past 25 years in the functional role of PLA 2 .…”

Section: Introductionmentioning

confidence: 99%

Understanding the binding mechanism of succinic acid against phospholipase A₂ from bee venom

Nidamarthi

Choudhury

Velmurugan

2021

J Biochem & Molecular Tox

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Phospholipase A2 (PLA2) is responsible for the release of fatty acids from glycerophospholipids. PLA2 is commonly found in mammalian tissues. It is also found in venom from different animals ranging from insects, arachnid, and snakes. The release of arachidonic acid in large amount results in inflammation and pain. Identification of compounds that can inhibit the activity of PLA2 is of large scientific and medicinal interest as these compounds can act as antidotes toward snake bites and bee stings. Among the different compounds that have been tested for inhibition of PLA2, a secondary metabolite succinic acid is identified to inhibit PLA2 activity. The inhibition was analyzed using an in vitro PLA2 inhibition assay and isothermal titration calorimetry (ITC) studies. The molecular mechanism of the mode of inhibition was studied using molecular docking and simulation studies.

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Structural insights and binding of a natural ligand, succinic acid with serine and cysteine proteases

Cited by 10 publications

References 21 publications

LIPIDS AS COMPETITIVE INHIBITORS OF SUBTILISIN CARLSBERG IN THE ENZYMATIC HYDROLYSIS OF PROTEINS IN RED TILAPIA (Oreochromis sp.) VISCERA: INSIGHTS FROM KINETIC MODELS AND A MOLECULAR DOCKING STUDY

LIPIDS AS COMPETITIVE INHIBITORS OF SUBTILISIN CARLSBERG IN THE ENZYMATIC HYDROLYSIS OF PROTEINS IN RED TILAPIA (Oreochromis sp.) VISCERA: INSIGHTS FROM KINETIC MODELS AND A MOLECULAR DOCKING STUDY

Probing polydopamine adhesion to protein and polymer films: microscopic and spectroscopic evaluation

Understanding the binding mechanism of succinic acid against phospholipase A₂ from bee venom

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Structural insights and binding of a natural ligand, succinic acid with serine and cysteine proteases

Cited by 10 publications

References 21 publications

LIPIDS AS COMPETITIVE INHIBITORS OF SUBTILISIN CARLSBERG IN THE ENZYMATIC HYDROLYSIS OF PROTEINS IN RED TILAPIA (Oreochromis sp.) VISCERA: INSIGHTS FROM KINETIC MODELS AND A MOLECULAR DOCKING STUDY

LIPIDS AS COMPETITIVE INHIBITORS OF SUBTILISIN CARLSBERG IN THE ENZYMATIC HYDROLYSIS OF PROTEINS IN RED TILAPIA (Oreochromis sp.) VISCERA: INSIGHTS FROM KINETIC MODELS AND A MOLECULAR DOCKING STUDY

Probing polydopamine adhesion to protein and polymer films: microscopic and spectroscopic evaluation

Understanding the binding mechanism of succinic acid against phospholipase A2 from bee venom

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Understanding the binding mechanism of succinic acid against phospholipase A₂ from bee venom