Protein Data Bank Database Research Articles

In silico Structural Modelling of Ribokinase from Salmonella Typhi

The knowledge of identifiable differences in the metabolism and macromolecular structure between infective agents and their host can be exploited in rational drug design. Ribokinase, an enzyme that plays an important role in the phosphorylation of several metabolites is one of such that can be exploited. This study was therefore aimed at structurally modelling ribokinase from Salmonella Typhi, the causative agent of typhoid fever, with several known multi-drug resistant strains. NCBI BLASTp was carried out against Protein Data Bank (PDB) to run a similarity search. Multiple sequence alignment between the query sequence and the templates was carried out using clustal omega and MEGA6.0 software. The amino acid sequence was submitted to modelling servers. The predicted models from the servers were evaluated with RAMPAGE and superimposed in the template using PyMOL. Model with highest Ramachandran plot score was further validated. BLASTp result showed low identity of (41%) with pyridoxal kinase from Trypanosoma brucei in PDB database. Conserved sequence motifs were confirmed. Template 4X8F was chosen based on its high identity, query cover and appearance in the modeling tools. Swiss model showed best Ramachandran plot score (94.9%). ERRAT analysis showed quality factor: 92.9078 and VERIFY3D server showed that 84.43% of the residues have an average score of 3D/ ID score >=0.2. Superimposition confirmed the alignment of the active site residues having aspartic acid as the catalytic residue. This study can serve as a means for rational drug design for the treatment of typhoid fever.

Analysis of non-structural proteins, NSPs of SARS-CoV-2 as targets for computational drug designing

BackgroundThe ORF1ab of Severe Acute Respiratory Syndrome, SARS Corona Virus, SARS-CoV-2 genome is processed into 15 non-structural proteins, NSPs by proteases and each NSP has a specific role in the life cycle and pathogenicity of the virus. This research analyzes possible drugs for these proteins as targets in computational drug designing using already available experimental drugs from the drug bank database. MethodsOut of 471 proteins and 8820 drugs download from Protein Data Bank, PDB and Drug Bank database respectively, 16 proteins similar to NSP 1–15 and 31 drugs as per the “Rule of three” were selected for docking. Out of 88 docking results using PyRx, 18 proteins/chains with three promising drugs, DB01977, DB07132 and DB07535 were analyzed using PyMOL for final results. ResultsNSPs 3, 5, 11, 14 and 15 were identified as targets for the drugs, DB01977, BD07132 and DB07535. Drugs, DB01977 and DB07535 bind in the same binding pockets of NSP 5 and NSP 15. Drug, DB07132 binds with more number of residues when compared with the other two drugs and this indicates that the strength of protein-drug association is more by this drug with the NSPs than other drugs. Binding pockets of NSPs for these three drugs are very close with many sharing residues in common suggesting of similarity of pharmacophore of these drugs with the target binding pockets. ConclusionThe binding pockets of NSPs are well matched with the pharmacophore of drugs and with polar surface of drugs less than or equal to 100 A2, drugs, DB01977, DB07132 and DB07535 bind individually and effectively with NSPs 3, 5, 11, 14 and 15 of ORF1ab of SARS-CoV-2 genome to bring changes in the activity of SARS-CoV-2 which may be useful for biological and clinical considerations.

Identification of choline-degrading bacteria from healthy human feces and used for screening of trimethylamine (TMA)-lyase inhibitors

Gut microbiota-based choline metabolism produces trimethylamine (TMA), which is then further converted to the atherosclerosis-promoting metabolite trimethylamine-N-oxide (TMAO) by hepatic flavin-containing monooxygenases (FMOs) and TMAO plays an essential role in cardiovascular disease (CVD). Many Chinese herbal medicines had been used for the treatment of CVD. This study aimed to screen choline-degrading bacteria from healthy human feces and establish a platform in silico and in vitro approaches for screening TMA-lyase inhibitors from Chinese herbal medicines. Choline-degrading bacteria were screened from healthy human feces in basic salt medium using culture method. The isolated strains were identified as Klebsiella pneumoniae based on 16S rRNA and the presence of CutC gene. Structure of CutC choline lyase was obtained from the RCSB Protein Data Bank database, and the modeled structure was docked with natural compounds of Chinese herbal medicines origin using MOE. Further, we investigated the inhibitory effects of selected compounds by picric acid–toluene method using K. pneumoniae as bioassay indicator. We found that TMA level was significantly decreased when treated with β-sitosterol and resveratrol. This study initially demonstrates the inhibitory effect of β-sitosterol and resveratrol on the gut microbiota responsible for choline metabolism to TMA and sets up an inhibitor-screening platform for further experiments. It can be used as a model to evaluate herbal drug sources and their effects on the gut microbiota for cardiovascular disease.

In silico investigation on alkaloids of Rauwolfia serpentina as potential inhibitors of 3-hydroxy-3-methyl-glutaryl-CoA reductase.

Present work aimed to investigate the in silico activity of the alkaloids of roots of Rauwolfia serpentina as inhibitors of 3-hydroxy-3-methyl-glutaryl-CoA reductase (HMGCR). For this purpose, the three-dimensional (3D) structure of the protein HMGCR (PDB ID: 1HW9) was downloaded from Protein Data Bank (PDB) database, as a target enzyme. The structures of twelve alkaloids from the roots of R. serpentina were selected as ligands and docked with the selected HMGCR enzyme using Molegro Virtual Docker (MVD) software. The software ‘MVD’ computes the binding (atom) energies of selected protein (enzyme) and each ligand at minimum energetic conformation state by using the PLP (Piecewise Linear Potential) scoring mechanism. Docking results of twelve tested alkaloids showed that five alkaloids including compound 1 (ajmalicine), 2 (reserpine), 3 (indobinine), 4 (yohimbine), and 5 (indobine) have displayed the highest MolDock scores and best fit within the prominent active site residues (positioned between 684 and 692 of cis-loop) of HMGCR. According to the lowest MolDock energies obtained through non-covalent interactions of alkaloids with HMGCR, these are characterized to be the potential inhibitors of HMGCR. Therefore, the alkaloids from R. serpentina can effectively suppress the cholesterol biosynthesis pathway through inhibition of HMGCR and can serve as potential lead compounds for the development of new drugs for the treatment of hyperlipidaemia.

Molecular Binding and Simulation Studies of Staphylococcus aureus Superantigens with Flavonoid Compounds.

Superantigens of Staphylococcus aureus namely enterotoxin A, exfoliative toxin A, and Toxic shock syndrome toxin-1 cause detrimental effects on the cells of the immune system. In this work, the toxins were downloaded from the Protein DataBank database and energies were minimized using KoBaMIN server. Forty flavonoids compounds were identified by pubchem compound database through extensive literature study and their 3D structures were obtained by submitting SMILES to CORINA tool. Based on Lipinski's rule of five, the molecules were filtered that resulted in 27 compounds. Molecular docking was performed for identifying the binding and interaction sites of flavonoids with the toxins using Autodock 4. The docked complexes were then subjected to molecular dynamics simulation using Gromacs. The analysis revealed the stability of the complexes as indicated by three hydrogen bonds formed during the simulation time period of 20 ns.

In Silico Screening of Schleichera oleosa Phytocompounds as Estrogen Receptors Alpha Inhibitors for Breast Cancer

Abstrak : This study aimed to predict the potential activity, toxicity, and interaction of fifteen bioactive compounds from Schleichera oleosa as estrogen receptors alpha inhibitors via in silico analysis. Active compound was downloaded from the PubChem database, and the 3D structure of the human estrogen receptor alpha (ERα) was obtained from the Protein Data Bank database with 4-Hydroxytamoxyfen as a positive control. The interaction of bioactive compounds with macromolecule was examined via a molecular specific docking using AutoDock Vina with PyRx 9.5 software. The protein was visualized using Discovery Studio 4.1. The drug-likeness property and human intestinal absorption of those fifteen bioactive compounds were evaluated through absorption, distribution, metabolism, and excretion (ADME) analysis using the pkCSM online tool program. The interactions between proteins and ligands are largely through the formation of hydrogen and van der Waals bonds. The binding energy of lupeol acetate, lupeol, schleicheol 1, betulinic acid, betulin, beta-sitosterol, schleicherastatin 7, schleicherastatin 2, schleicherastatin 4, scopoletin, schleicherastatin 3, schleicherastatin 1, schleicherastatin 6, schleicherastatin 5 alpha and schleicherastatin receptors including -8.3, -8.3, -7.1, -7.1, -6.7, -6.6, -6.6, -6.5, -6.5, -6.3, -6.2, -6.2 -6.1, -5.9 and -5.5 kcal / mol, respectively . The in silico ADME analysis also revealed that lupeol and lupeol acetate were the best active compound that passes the test based on the Lipinski rule, ADME, and toxicity. Therefore, it can be stated that Schleichera oleosa has potential as an inhibitor of alpha estrogen receptors. The inhibitory activity of alpha estrogen receptors has led to new breakthroughs in plant-based medicinal products, particularly for breast cancer . Keyword : Schleichera oleosa, alpha estrogen receptors, phytocompound, breast cancer and in silico

Efficient Synthesis, In-Vitro Antioxidant, Anticancer and Molecular Docking Studies of Bidentate Schiff Base Complexes of Vo(Ii) and Zn(Ii) by Green Route Method

Vanadium(II) and Zn(II) chelates with Schiff base derived from the condensation of orthophenylenediamine and cinnamaldehyde. Schiff base are multilateral ligand and offer resistant series of ligand to coordinate with metals. The Schiff base and its metal complexes were synthesized and characterized by elemental analysis, metal estimation, molar conductance, magnetic moment, UV-Visible, IR, Far-IR and NMR spectral studies. The elemental analysis suggest the stoichiometry to be 1:1 (M:L).The complexes are non-electrolyte in acetonitrile solution. The molar conductance and spectral properties indicate the complexes don’t dissociate in acetonitrile solution and retain their coordination. Melting points support the thermal stability of the complex. Coordination of ligand was confirmed by constant change of FT-IR. The electronic spectral data support octahedral geometry of VO(II) and square planar geometry of Zn(II) complexes. IR spectral data suggest that the ligand coordinated to the metal ion by imino nitrogen and amine nitrogen as bidentate manner. The NMR (1H & 13C) spectrum of schiff base and its diamagnetic Zn(II) complex was carried out and confirmed by the geometry and magnetic property of them. The antibacterial activity of the schiff base and VO(II) and Zn(II) complexes was assessed against Staphylococcus aureus, Enterococcus as Gram-positive bacteria and further against Escherichia coli, Vibrio parahaemolyticus and Pseudomonas as Gram–negative bacteria and one pathogenic yeast C.albicans by agar well diffusion method. The results of anticancer activity of schiff base and VO(II) and Zn(II) complexes indicated that the metal complex have moderately active than the corresponding ligand. The cell cycle proteins, CDK4 (PDB ID: 3G33), P-53 (PDB ID: 1YCS) were downloaded from the RCSB PDB (protein data bank) database and the auto Dock (V. 4.0) in the PyRx GUI has been used to confirm the binding abilities of the selected ligand and VO(II) complex.

Uji Efek Inhibitorik Komponen Bioaktif Bawang Putih (Allium sativum) terhadap Lanosterol 14α-demethylase pada Candida albicans melalui Studi In Silico

Candida albicans is a unicellular fungi which causes candidiasis in human and livestock animals especially chicken. Candidiasis could reduce productivity significantly by early culling and causing a great deficit in the farm. Allium sativum or garlic is widely known as herbal which has an inhibitory effect in fungi’s growth. This research’s aim is to prove the effectivity of bioactive compound in Allium sativum to lanosterol 14α-demethylase which plays a role in ergosterol synthesis as a basic structure in fungi’s cell membrane. The ligand sheet retrieved from PubChem database and for the receptor in Protein Data Bank database. Molecular docking conducted by using Autodock Vina and then ligand-receptor complex is visualized with PyMOL and Ligplot+. From compounds that we have been analyzed, Gallic Acid has the most negative binding energy than other compounds have and it has the same amino acid residue with control. In conclusion of that, Gallic Acid in Allium sativum has potential as anti-candidiasis drug.

In Silico Study of the Effect of Thymoquinone on Three Pre-apoptotic Factors of Bad, Bak, and Bim

Background: Apoptosis is one of the most vital mechanisms in the removal of old and damaged cells, especially cancer cells. Many polyphenolic and antioxidant compounds can inhibit the growth and proliferation of cancer cells by inducing apoptosis. This study intended to evaluate the effect of the thymoquinone (TQ) on the three pre-apoptotic factors Bad, Bak, and Bim in the simulation environment. Methods: The Protein Data Bank (PDB) files of three pre-apoptotic proteins Bad, Bak, and Bim were obtained from PDB database and the molecular structure of TQ from PubChem database. The optimization, simulation, molecular docking, and molecular dynamics (MD) computation were performed using AutoDock, VMD, and GROMACS packages on each one of the proteins in free mode and ligand binding mode. Results: The number and type of hydrogen and hydrophobic bonds at the binding site of TQ and pre-apoptotic factors Bad, Bak, and Bim were detected at the lowest level of energy. The lowest binding energy level of TQ had the highest tendency to bind to the BAD molecule. After the binding of TQ to proteins, the radius of gyration (Rg) of Bim increased while the Rg of Bad and Bak decreased. However, the secondary structures (Turn, Coil, Helix, and Bend) were greatly affected in the binding of TQ to Bad, Bak, and Bim. Conclusion: The variations of binding energy indicated that TQ can affect the three pre-apoptotic factors Bad, Bak, and Bim. This bond seems to increase their activity by variation in the secondary structure of the Bim specific residues.

Structural basis for the function and inhibition of dihydroorotate dehydrogenase from Schistosomamansoni.

Schistosomiasis is a serious public health problem, prevalent in tropical and subtropical areas, especially in poor communities without access to safe drinking water and adequate sanitation. Transmission has been reported in 78 countries, and its control depends on a single drug, praziquantel, which has been used over the past 30years. Our work is focused on exploiting target-based drug discovery strategies to develop new therapeutics to treat schistosomiasis. In particular, we are interested in evaluating the enzyme dihydroorotate dehydrogenase (DHODH) as a drug target. DHODH is a flavoenzyme that catalyzes the stereospecific oxidation of (S)-dihydroorotate (DHO) to orotate during the fourth and only redox step of the denovo pyrimidine nucleotide biosynthetic pathway. Previously, we identified atovaquone, used in the treatment of malaria, and its analogues, as potent and selective inhibitors against Schistosomamansoni DHODH (SmDHODH). In the present article, we report the first crystal structure of SmDHODH in complex with the atovaquone analogue inhibitor 2-((4-fluorophenyl)amino)-3-hydroxynaphthalene-1,4-dione (QLA). We discuss three major findings: (a) the open conformation of the active site loop and the unveiling of a novel transient druggable pocket for class 2 DHODHs; (b) the presence of a protuberant domain, only present in Schistosoma spp DHODHs, that was found to control and modulate the dynamics of the inhibitor binding site; (c) a detailed description of an unexpected binding mode for the atovaquone analogue to SmDHODH. Our findings contribute to the understanding of the catalytic mechanism performed by class 2 DHODHs and provide the molecular basis for structure-guided design of SmDHODH inhibitors. DATABASE: The structural data are available in Protein Data Bank (PDB) database under the accession code number 6UY4.

The co-existence of cold activity and thermal stability in an Antarctic GH42 β-galactosidase relies on its hexameric quaternary arrangement.

To survive in cold environments, psychrophilic organisms produce enzymes endowed with high specific activity at low temperature. The structure of these enzymes is usually flexible and mostly thermolabile. In this work, we investigate the structural basis of cold adaptation of a GH42 β-galactosidase from the psychrophilic Marinomonas ef1. This enzyme couples cold activity with astonishing robustness for a psychrophilic protein, for it retains 23% of its highest activity at 5°C and it is stable for several days at 37°C and even 50°C. Phylogenetic analyses indicate a close relationship with thermophilic β-galactosidases, suggesting that the present-day enzyme evolved from a thermostable scaffold modeled by environmental selective pressure. The crystallographic structure reveals the overall similarity with GH42 enzymes, along with a hexameric arrangement (dimer of trimers) not found in psychrophilic, mesophilic, and thermophilic homologues. In the quaternary structure, protomers form a large central cavity, whose accessibility to the substrate is promoted by the dynamic behavior of surface loops, even at low temperature. A peculiar cooperative behavior of the enzyme is likely related to the increase of the internal cavity permeability triggered by heating. Overall, our results highlight a novel strategy of enzyme cold adaptation, based on the oligomerization state of the enzyme, which effectively challenges the paradigm of cold activity coupled with intrinsic thermolability. DATABASE: Structural data are available in the Protein Data Bank database under the accession number 6Y2K.

Structural plasticity of a designer protein sheds light on β-propeller protein evolution.

β-propeller proteins are common in nature, where they are observed to adopt 4- to 10-fold internal rotational pseudo-symmetry. This size diversity can be explained by the evolutionary process of gene duplication and fusion. In this study, we investigated a distorted β-propeller protein, an apparent intermediate between two symmetries. From this template, we created a perfectly symmetric 9-bladed β-propeller named Cake, using computational design and ancestral sequence reconstruction. The designed repeat sequence was found to be capable of generating both 8-fold and 9-fold propellers which are highly stable. Cake variants with 2-10 identical copies of the repeat sequence were characterised by X-ray crystallography and in solution. They were found to be highly stable, and to self-assemble into 8- or 9-fold symmetrical propellers. These findings show that the β-propeller fold allows sufficient structural plasticity to permit a given blade to assemble different forms, a transition from even to odd changes in blade number, and provide a potential explanation for the wide diversity of repeat numbers observed in natural propeller proteins. DATABASE: Structural data are available in Protein Data Bank database under the accession numbers 6TJB, 6TJC, 6TJD, 6TJE, 6TJF, 6TJG, 6TJH and 6TJI.

Network Proteins of Angiotensin-converting Enzyme 2 But Not Angiotensin-converting Enzyme 2 itself are Host Cell Receptors for SARS-Coronavirus-2 Attachment

Background: Coronaviruses causing severe acute respiratory syndrome (SARS-CoV) are known to enter the host cells by attaching to the membrane bound angiotensin-converting enzyme 2 (ACE2). Using molecular docking the efficiency of interaction between SARS-CoV-2 surface proteins and ACE2 network proteins was assessed. Materials and Methods: The ACE2 protein network was identified using the STRING database. The reported SARS-CoV-2 target proteins were searched in the protein data bank and uniport database. The proteinprotein interactions were assessed by molecular docking using the Chimera software. The PubChem database was searched for known inhibitors of host cell receptors interacting with SARS-CoV-2 surface proteins. Molecular docking was performed to evaluate the binding efficacy of these compounds against the SARS-CoV-2 targets using Auto Dock Vina and the docked protein-ligand complex were visualised using the Chimera and PyMOL software. Results: A low binding affinity was observed between SARS-CoV-2 spike proteins (protein S, M and 6YLA) and ACE2. Coronaviruses are also reported to bind to dipeptidyl peptidase 4 (DPP4), which is a network protein of ACE2. Network analysis showed five membrane proteins associated with ACE2. The ACE2 network proteins were assessed for their binding affinity with all known SARS-CoV-2 surface proteins. The SARS-CoV-2 surface proteins showed preferential binding to network proteins such as DPP4 and Meprin A alpha but not ACE2. The binding efficacy (affinity (-5.86 to -7.10 Kcal/mol), Ki (6.32 – 22.04μM) and IC50 (12.63 – 113.71μM) values) of DPP4 inhibitors (saxagliptin and sitagliptin) against SARS-CoV-2 surface proteins, was observed to be at a therapeutically feasible concentration to prevent SARS-CoV-2 attachment and entry into host cells. Conclusion: SARS-CoV-2 surface proteins has better interactions with DPP4 and Meprin A alpha host cells receptors rather than ACE2. DPP4 inhibitors (saxagliptin and sitagliptin) by binding with SARS-CoV-2 surface proteins may be helpful in preventing the virus entry into the host cells.

ANTI-PARKINSON POTENTIAL OF PERSEA AMERICANA SEED EXTRACTS THROUGH IN-SILICO DOCKING STUDY

Objective: The aim of this study is to investigate the potential of Persea americana extracts for their Anti-Parkinson application through an in-silico docking study.
 Methods: PubChem and protein data bank databases were used to retrieve 3D structures. AutoDock4 was used to perform protein-ligand docking analysis. PyMOL was used to visualize the docking results.
 Results: Among the 30 ligand, the highest affinity was demonstrated by Hesperidin with a free binding energy of −6.8 kcal/mol and formation of five hydrogen bonds. The second highest significance was demonstrated by Biphenyl 4-(4-diethylaminobenzylidenamino) with a free binding energy of −5.9 kcal/mol with the formation of 2 hydrogen bonds. Among the three sets of phytochemicals from different solvent extracts, water extract demonstrated the highest potential as Anti-Parkinson active.
 Conclusion: P. americana extracts were analyzed for their Anti-Parkinson potential, and among the three extracts, the aqueous extract was predicted to have significant Anti-Parkinson potential, based on in silico docking analysis, due to the presence of active phytochemicals such as Hesperidin and others.

SMAtool reveals sequences and structural principles of protein-RNA interaction

Protein binding events on RNA are highly related to RNA secondary structure, which affects post-transcriptional regulation and translation. However, it remains challenging to describe the association between RNA secondary structure and protein binding events. Here, we present Structure Motif Analysis tool (SMAtool), a pipeline that integrates RNA secondary structure and protein binding site information to profile the binding structure preference of each protein. As an example of applying SMAtool, we extracted the RNA-structure and binding site information respectively from the DMS-seq and eCLIP-seq data of the K562 cell-line, and used SMAtool to analyze the structure motif of each RNA binding protein (RBP). This new approach provided results consistent with X-ray crystallography data from the protein data bank (PDB) database, demonstrating that it can help researchers investigate the structure preference of RBP, and understand the role of RNA secondary structure in gene expression. Availability and implementation: https://github.com/QuKunLab/SMAtool.

In silico Molecular docking of Luteolin from Momordica charantia for dementia in Alzheimer's disease

Objective: In the present study, luteolin was isolated from Momordica charantia and characterized by IR and NMR spectroscopy, undergone in silico docking to study its anti-Alzheimer's role. In silico molecular docking is a computational system employed to predict the interaction vitality between two particles and the best introduction of ligand that shapes a complex with general least vitality. Methods: In this Protein Ligand Docking, we have used HEX 8.0.0 as a Docking Software. The receptors (PDB ID: 4PQE, 1P0I, 5O3L, 1J1C, 3NYJ, 2FJZ) were retrieved from the RCSB Protein Data Bank (PDB) Database while the ligand structure was retrieved as mol format from ChEBI database and it was converted as.pdb format using Chimera 1.12 and docking was done according to the specified parameters. Results: The molecular docking process for the luteolin was performed with the receptors and the E-value was determined. Further, the result of the binding site of ligand with the target proteins was interpreted by using Chimera 1.12 software. Conclusion: Luteolin was proved to have good affinity for target protein and it is having multitarget activity that is responsible for AD.

An in Silico Approach Reveals the Potential Function of Cyanidin-3-o-glucoside of Red Rice in Inhibiting the Advanced Glycation End Products (AGES)-Receptor (RAGE) Signaling Pathway.

Introduction:Advanced glycation end products (AGEs) contribute to the pathogenesis of chronic inflammation, diabetes, micro and macrovascular complications, and neurodegenerative diseases through the binding with RAGE. Natural compounds can act as an alternative in disease therapy related to the AGEs-RAGE interactions. Cyanidin-3-O-glucoside is one of the potential anthocyanins found in red rice. Cyanidin-3-O-glucoside in red rice may interfere with the AGEs-RAGE signaling so that the potential mechanism of their interaction needs to be elucidated.Aim:This study aimed to investigate the potency of cyanidin-3-O-glucoside in red rice as an inhibitor of AGE-RAGE signaling pathway through in silico analysis.Methods:Our study used the 3D structures of AGEs and Cyanidin-3-O-glucoside compounds from PubChem and Receptor for AGEs (RAGE) from the RCSB Protein Data Bank (PDB) database. The molecular interactions of those compounds and RAGE were established using Hex 8.0 software, then visualized using Discovery Studio 2016 software.Results:Argypirimidine, pentosidine, pyrralline, and imidazole bound to the ligand-binding domain of RAGE with the binding energy of -247 kcal/mol, -350.4 kcal/mol, -591.1 kcal/mol, and -100.4 kcal/mol, respectively. The presence of cyanidin-3-O-glucoside in the imidazole-RAGE-cyanidin-3-O-glucoside complex could inhibit the interaction of imidazole-RAGE with a binding energy of -299 kcal/mol, which was lower than of imidazole-RAGE complex. The establishment of AGEs-Cyanidin-3-O-glucoside-RAGE complex showed that cyanidin-3-O-glucoside, which bound first to Argypirimidine and Pyrralline, could bound to RAGE at the same residue as those two AGEs did with the binding energy of -411.8 kcal/mol and -1305 kcal/mol, respectively. Based on the binding site location and energy, cyanidin-3-O-glucoside might have a biological function as an inhibitor of AGEs-RAGE interactions, which was more likely through the establishment of AGEs-cyanidin-3-O-glucoside-RAGE.Conclusion:This study suggests that cyanidin-3-O-glucoside in red rice can be a potential AGEs-RAGE inhibitor, leading to the regulation of the pro-inflammatory and oxidative damage in the cellular pathway.

Cyclization mechanism catalyzed by an ATP-grasp enzyme essential for d-cycloserine biosynthesis.

In the biosynthetic pathway of an antitubercular antibiotic d-cycloserine (d-CS), O-ureido-d-serine (d-OUS) is converted to d-CS. We have previously demonstrated that DcsG, classified into the ATP-grasp superfamily enzyme, catalyzes the ring formation to generate d-CS, which is accompanied by the cleavage of a bond in the urea moiety of d-OUS to remove a carbamoyl group. Although the general ATP-grasp enzymes catalyze an ATP-dependent ligation reaction between two substrates, DcsG catalyzes specifically the generation of an intramolecular covalent bond. In the present study, cyanate was found in the reaction mixture, suggesting that carbamoyl group is eliminated as an isocyanic acid during the reaction. By the crystallographic and mutational investigations of DcsG, we anticipate the residues necessary for the binding of d-OUS. An acylphosphate intermediate must be bound at the narrow pocket of DcsG in a folded conformation, inducing the bond cleavage and the new bond formation to generate cyanate and d-CS, respectively. DATABASE: Structural data are available in Protein Data Bank database under the accession number 6JIL.

Molecular basis for GTP recognition by light-activated guanylate cyclase RhGC.

Cyclic guanosine 3′,5′‐monophosphate (cGMP) is an intracellular signalling molecule involved in many sensory and developmental processes. Synthesis of cGMP from GTP is catalysed by guanylate cyclase (GC) in a reaction analogous to cAMP formation by adenylate cyclase (AC). Although detailed structural information is available on the catalytic region of nucleotidyl cyclases (NCs) in various states, these atomic models do not provide a sufficient explanation for the substrate selectivity between GC and AC family members. Detailed structural information on the GC domain in its active conformation is largely missing, and no crystal structure of a GTP‐bound wild‐type GC domain has been published to date. Here, we describe the crystal structure of the catalytic domain of rhodopsin–GC (RhGC) from Catenaria anguillulae in complex with GTP at 1.7 Å resolution. Our study reveals the organization of a eukaryotic GC domain in its active conformation. We observe that the binding mode of the substrate GTP is similar to that of AC–ATP interaction, although surprisingly not all of the interactions predicted to be responsible for base recognition are present. The structure provides insights into potential mechanisms of substrate discrimination and activity regulation that may be common to all class III purine NCs.DatabaseStructural data are available in Protein Data Bank database under the accession number 6SIR.Enzymes EC4.6.1.2.

Structural and biochemical characterization of a family 7 highly thermostable endoglucanase from the fungus Rasamsonia emersonii.

Thermostable cellulases from glycoside hydrolase family 7 (GH7) are the main components of enzymatic mixtures for industrial saccharification of lignocellulose. Activity improvement of these enzymes via rational design is a promising strategy to alleviate the industrial costs, but it requires detailed structural knowledge. While substantial biochemical and structural data are available for GH7 cellobiohydrolases, endoglucanases are more elusive and only few structures have been solved so far. Here, we report a new crystal structure and biochemical characterization of a thermostable endoglucanase from the thermophilic ascomycete Rasamsoniaemersonii, ReCel7B. The enzyme was compared with the homologous endoglucanase from the mesophilic model ascomycete Trichodermareesei (TrCel7B), which unlike ReCel7B possesses an additional carbohydrate-binding module (CBM). With a temperature optimum of 80°C, ReCel7B displayed a number of differences in activity and ability to synergize with cellobiohydrolases compared to TrCel7B. We improved both binding and kinetics in a chimeric variant of ReCel7B and a CBM, while we observe the opposite effect when the CBM was removed in TrCel7B. The crystal structure of ReCel7B was determined at 2.48Å resolution, with Rwork and Rfree factors of 0.182 and 0.206, respectively. Structural analyses revealed that ReCel7B has increased rigidity in a number of peripheral loops compared to TrCel7B and fewer aromatics in the substrate-binding cleft. An increased number of glycosylations were identified in ReCel7B, and we propose a stabilizing mechanism for one of the glycans. Global structure-function interpretations of ReCel7B highlight the differences in temperature stability, turnover, binding, and cellulose accessibility in GH7 endoglucanases. DATABASE: Structural data are available in RCSB Protein Data Bank database under the accession number 6SU8. ENZYMES: ReCel7B, endoglucanase (EC3.2.1.4) from Rasamsoniaemersonii; ReCel7A, cellobiohydrolase (EC3.2.1.176) from Rasamsoniaemersonii; TrCel7B, endoglucanase (EC3.2.1.4) from Trichodermareesei; TrCel7A, cellobiohydrolase (EC3.2.1.176) from Trichodermareesei.