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The role of initiator tRNAimet in fidelity of initiation of protein synthesis

Monajemi H, Omar NY, Daud MN, Zain SM, Abdullah WA

Nucleosides Nucleotides Nucleic Acids, 2011 Sep;30(9):726-39.
PMID: 21902474 DOI: 10.1080/15257770.2011.605780

The proper arrangement of amino acids in a protein determines its proper function, which is vital for the cellular metabolism. This indicates that the process of peptide bond formation requires high fidelity. One of the most important processes for this fidelity is kinetic proofreading. As biochemical experiments suggest that kinetic proofreading plays a major role in ensuring the fidelity of protein synthesis, it is not certain whether or not a misacylated tRNA would be corrected by kinetic proofreading during the peptide bond formation. Using 2-layered ONIOM (QM/MM) computational calculations, we studied the behavior of misacylated tRNAs and compared the results with these for cognate aminoacyl-tRNAs during the process of peptide bond formation to investigate the effect of nonnative amino acids on tRNAs. The difference between the behavior of initiator tRNA(i) (met) compared to the one for the elongator tRNAs indicates that only the initiator tRNA(i) (met) specifies the amino acid side chain.

Matched MeSH terms: Crystallography, X-Ray
Synthesis, crystal structure and luminescent properties of some Zn(II) Schiff base complexes: experimental and computational study

Eltayeb NE, Teoh SG, Adnan R, Teh JB, Fun HK

J Fluoresc, 2011 Jul;21(4):1393-400.
PMID: 21222144 DOI: 10.1007/s10895-010-0822-y

A series of Zn(II)-Schiff bases I, II and III complexes were synthesized by reaction of o-phenylenediamine with 3-methylsalicylaldehyde, 4-methylsalicylaldehyde and 5-methylsalicylaldehyde. These complexes were characterized using FT-IR, UV-Vis, Diffuse reflectance UV-Vis, elemental analysis and conductivity. Complex III was characterized by XRD single crystal, which crystallizes in the triclinic system, space group P-1, with lattice parameters a=9.5444(2) Å, b=11.9407(2) Å, c=21.1732(3) Å, V=2390.24(7) Å(3), D ( c )=1.408 Mg m(-3), Z=4, F(000)=1050, GOF=0.981, R1=0.0502, wR2=0.1205. Luminescence property of these complexes was investigated in DMF solution and in the solid state. Computational study of the electronic properties of complex III showed good agreement with the experimental data.

Matched MeSH terms: Crystallography, X-Ray
Deciphering the flexibility and dynamics of Geobacillus zalihae strain T1 lipase at high temperatures by molecular dynamics simulation

Abdul Rahman MB, Karjiban RA, Salleh AB, Jacobs D, Basri M, Thean Chor AL, et al.

Protein Pept Lett, 2009;16(11):1360-70.
PMID: 20001926

The stability of biocatalysts is an important criterion for a sustainable industrial operation economically. T1 lipase is a thermoalkalophilic enzyme derived from Geobacillus zalihae strain T1 (T1 lipase) that was isolated from palm oil mill effluent (POME) in Malaysia. We report here the results of high temperatures molecular dynamics (MD) simulations of T1 lipase in explicit solvent. We found that the N-terminal moiety of this enzyme was accompanied by a large flexibility and dynamics during temperature-induced unfolding simulations which preceded and followed by clear structural changes in two specific regions; the small domain (consisting of helices alpha3 and alpha5, strands beta1 and beta2, and connecting loops) and the main catalytic domain or core domain (consisting of helices alpha6- alpha9 and connecting loops which located above the active site) of the enzyme. The results suggest that the small domain of model enzyme is a critical region to the thermostability of this organism.

Matched MeSH terms: Crystallography, X-Ray
The manganese(III) complex with chelating Schiff base ligand: X-ray structure, spectroscopic and computational studies

Eltayeb NE, Teoh SG, Kusrini E, Adnan R, Fun HK

Spectrochim Acta A Mol Biomol Spectrosc, 2010 Jan;75(1):453-7.
PMID: 20004137 DOI: 10.1016/j.saa.2009.11.006

A new Mn(III) complex, [MnCl(H(2)O)(L)].H(2)O.C(2)H(5)OH, where L=2,2'-[1,2-phenylenebis[nitrilomethylylidene]]bis(6-methoxyphenolate), has been synthesized and characterized by single-crystal X-ray diffraction. There is a good agreement between calculated and experimental structural data. The complex is crystallized in orthorhombic with space group Pbca. The Mn1 atom is coordinated with one Schiff base ligand, one water molecule and one chloride anion, forming a six-coordination number. The electronic and fluorescence spectra of the complex were also studied.

Matched MeSH terms: Crystallography, X-Ray
Coordination of Ce(III) and Nd(III) with pentaethylene glycol in the presence of picrate anion: spectroscopic and X-ray structural studies

Kusrini E, Saleh MI, Lecomte C

Spectrochim Acta A Mol Biomol Spectrosc, 2009 Sep 15;74(1):120-6.
PMID: 19560960 DOI: 10.1016/j.saa.2009.05.024

(1)H NMR evidence for direct coordination between the Ln(III) ion and the oxygen atoms of the pentaethylene glycol (EO5) ligand and the picrate anion (Pic) in [Ln(Pic)(2)(EO5)][Pic] {Ln=Ce and Nd} complexes are confirmed by single X-ray diffraction. No dissociation of Ln-O bonds in dimethyl sulfoxide-d solution was observed in NMR studies conducted at different temperatures ranging 25-100 degrees C. The Ln(III) ion was chelated to nine oxygen atoms from the EO5 ligand in a hexadentate manner and the two Pic anions in each bidentate and monodentate modes. Both compounds are isostructural and crystallized in monoclinic with space group P2(1)/c. Coordination environment around the Ce1 and Nd1 atoms can be described as tricapped trigonal prismatic and monocapped square antiprismatic geometries, respectively. The crystal packing of the complexes have stabilized by one dimensional (1D) chains along the [001] direction to form intermolecular O-Hcdots, three dots, centeredO and C-Hcdots, three dots, centeredO hydrogen bonding. The molar conductance of the complexes in DMSO solution indicated that both compounds are ionic. The complexes had a good thermal stability. Under the UV-excitation, these complexes exhibited the red-shift emission.

Matched MeSH terms: Crystallography, X-Ray
Fabrication of synthetic apatites by solid-state reactions

Fazan F, Shahida KB

Med J Malaysia, 2004 May;59 Suppl B:69-70.
PMID: 15468823

The paper presents a method of producing synthetic Hydroxyapatite (HA) Ca10(PO4)6(OH)2 and other apatites for biological use by solid-state reaction. The solid-state reaction involves mix-grinding dry powders of beta-tricalcium phosphate powder (TCP) and either calcium hydroxide (Ca(OH)2) or calcium carbonate (CaCO3) or combination thereof, from pure commercial chemicals or derived from natural limestone or from seashells, of total calcium/phosphorus molar ratio between 1.5 to 2.0, to particle size of less than 10 microns, and firing the resultant powder to temperature between 600 degrees C - 1250 degrees C in atmosphere or in controlled atmospheric condition. The resultant apatites formed were characterised using XRD, SEM-EDX and FTIR. The presented reaction process was found to be much simpler compared to conventional methods of producing synthetic apatites since it involves only dry mix-grinding of the reactants before firing at high temperatures based on the required levels of purity. It can also produce synthetic apatites with good reproducibility in a shorter time. Thus the presented method has a great industrial value.

Matched MeSH terms: Crystallography, X-Ray
Fulltext Crystal structure of Anoxybacillus α-amylase provides insights into maltose binding of a new glycosyl hydrolase subclass

Chai KP, Othman NF, Teh AH, Ho KL, Chan KG, Shamsir MS, et al.

Sci Rep, 2016 Mar 15;6:23126.
PMID: 26975884 DOI: 10.1038/srep23126

A new subfamily of glycosyl hydrolase family GH13 was recently proposed for α-amylases from Anoxybacillus species (ASKA and ADTA), Geobacillus thermoleovorans (GTA, Pizzo, and GtamyII), Bacillus aquimaris (BaqA), and 95 other putative protein homologues. To understand this new GH13 subfamily, we report crystal structures of truncated ASKA (TASKA). ASKA is a thermostable enzyme capable of producing high levels of maltose. Unlike GTA, biochemical analysis showed that Ca(2+) ion supplementation enhances the catalytic activities of ASKA and TASKA. The crystal structures reveal the presence of four Ca(2+) ion binding sites, with three of these binding sites are highly conserved among Anoxybacillus α-amylases. This work provides structural insights into this new GH13 subfamily both in the apo form and in complex with maltose. Furthermore, structural comparison of TASKA and GTA provides an overview of the conformational changes accompanying maltose binding at each subsite.

Matched MeSH terms: Crystallography, X-Ray
Cd(2+) Triggered the FRET "ON": A New Molecular Switch for the Ratiometric Detection of Cd(2+) with Live-Cell Imaging and Bound X-ray Structure

Aich K, Goswami S, Das S, Mukhopadhyay CD, Quah CK, Fun HK

Inorg Chem, 2015 Aug 3;54(15):7309-15.
PMID: 26192906 DOI: 10.1021/acs.inorgchem.5b00784

On the basis of the Förster resonance energy transfer mechanism between rhodamine and quinoline-benzothiazole conjugated dyad, a new colorimetric as well as fluorescence ratiometric probe was synthesized for the selective detection of Cd(2+). The complex formation of the probe with Cd(2+) was confirmed through Cd(2+)-bound single-crystal structure. Capability of the probe as imaging agent to detect the cellular uptake of Cd(2+) was demonstrated here using living RAW cells.

Matched MeSH terms: Crystallography, X-Ray
Fulltext Synthesis, spectral characterization and crystals structure of some arsane derivatives of gold (I) complexes: a comparative density functional theory study

Shawkataly OB, Goh CP, Tariq A, Khan IA, Fun HK, Rosli MM

PLoS One, 2015;10(3):e0119620.
PMID: 25798915 DOI: 10.1371/journal.pone.0119620

A series of complexes of the type LAuCl where L = tris(p-tolylarsane), tris(m-tolylarsane), bis(diphenylarsano)ethane, and tris(naphthyl)arsane have been synthesized. All of the new complexes, 1-4, have been fully characterized by means of ¹H NMR and ¹³C NMR spectroscopy and single crystal X-ray crystallography. The structures of complexes 1-4 have been determined from X-ray diffraction data. The linear molecules have an average bond distance between gold-arsenic and gold-chlorine of 2.3390Å and 2.2846Å, respectively. Aurophilic interaction was prominent in complex 1 and 3, whereas complex 2 and 4 do not show any such interaction. The intermolecular gold interaction bond length was affected by the electronegativity of the molecule. The computed values calculated at DFT level using B3LYP function are in good agreement with the experimental results.

Matched MeSH terms: Crystallography, X-Ray
3-Iodobenzaldehyde: XRD, FT-IR, Raman and DFT studies

Kumar CS, Parlak C, Tursun M, Fun HK, Rhyman L, Ramasami P, et al.

Spectrochim Acta A Mol Biomol Spectrosc, 2015 Jun 15;145:90-7.
PMID: 25767992 DOI: 10.1016/j.saa.2015.02.079

The structure of 3-iodobenzaldehyde (3IB) was characterized by FT-IR, Raman and single-crystal X-ray diffraction techniques. The conformational isomers, optimized geometric parameters, normal mode frequencies and corresponding vibrational assignments of 3IB were examined using density functional theory (DFT) method, with the Becke-3-Lee-Yang-Parr (B3LYP) functional and the 6-311+G(3df,p) basis set for all atoms except for iodine. The LANL2DZ effective core basis set was used for iodine. Potential energy distribution (PED) analysis of normal modes was performed to identify characteristic frequencies. 3IB crystallizes in monoclinic space group P21/c with the O-trans form. There is a good agreement between the theoretically predicted structural parameters, and vibrational frequencies and those obtained experimentally. In order to understand halogen effect, 3-halogenobenzaldehyde [XC6H4CHO; X=F, Cl and Br] was also studied theoretically. The free energy difference between the isomers is small but the rotational barrier is about 8kcal/mol. An atypical behavior of fluorine affecting conformational preference is observed.

Matched MeSH terms: Crystallography, X-Ray
Four new clerodane diterpenoids from Callicarpa pentandra

Xu J, Harrison LJ, Vittal JJ, Xu YJ, Goh SH

J Nat Prod, 2000 Aug;63(8):1062-5.
PMID: 10978198

Leaf extracts of Callicarpa pentandra provided four new clerodane-type diterpenoids (1-4), of which 1, 2, and 4 have ring-A-contracted structures. Their structures and stereochemistry were established by spectral data interpretation, and for 3 also by single-crystal X-ray diffraction.

Matched MeSH terms: Crystallography, X-Ray
Nickel and zinc complexes of testosterone N4-substituted thiosemicarbazone: Selective cytotoxicity towards human colorectal carcinoma cell line HCT 116 and their cell death mechanisms

Heng MP, Sim KS, Tan KW

J Inorg Biochem, 2020 07;208:111097.
PMID: 32438269 DOI: 10.1016/j.jinorgbio.2020.111097

Two new Schiff base ligands (TE and TF) were prepared from conjugation of testosterone with 4-(4-ethylphenyl)-3-thiosemicarbazide and 4-(4-fluorophenyl)-3-thiosemicarbazide, respectively. Their nickel (NE and NF) and zinc (ZE and ZF) complexes were reported. X-ray crystallography revealed a distorted square planar geometry was adopted by NE. The compounds demonstrated excellent selectivity towards the colorectal carcinoma cell line HCT 116 despite their weak preferences towards the prostate cancer cell lines (PC-3 and LNCaP). Against HCT 116, all these compounds were able to arrest cell cycle at G0/G1 phase and induce apoptosis via mitochondria-dependent (TE, NE, and TF) and extrinsic apoptotic pathway (ZE, NF, and ZF). Moreover, only ZE was able to act as topoisomease I poison and halt its enzymatic reactions although all compounds presented excellent affinity towards DNA.

Matched MeSH terms: Crystallography, X-Ray
Fulltext Computational, crystallographic studies, cytotoxicity and anti-tubercular activity of substituted 7-methoxy-indolizine analogues

Venugopala KN, Chandrashekharappa S, Pillay M, Abdallah HH, Mahomoodally FM, Bhandary S, et al.

PLoS One, 2019;14(6):e0217270.
PMID: 31163040 DOI: 10.1371/journal.pone.0217270

Indolizines are heteroaromatic compounds, and their synthetic analogues have reportedly showed promising pharmacological properties. In this study, a series of synthetic 7-methoxy-indolizine derivatives were synthesised, characterised and evaluated for in vitro whole-cell anti-tuberculosis (TB) screening against susceptible (H37Rv) and multi-drug-resistant (MDR) strains of Mycobacterium tuberculosis (MTB) using the resazurin microplate assay method. The cytotoxicity was evaluated using the MTT assay. In silico molecular-docking study was conducted for compounds 5a-j against enoyl-[acyl-carrier] protein reductase, a key enzyme of the type II fatty acid synthesis that has attracted much interest for the development of novel anti-TB compounds. Thereafter, molecular dynamic (MD) simulation was undertaken for the most active inhibitors. Compounds 5i and 5j with the methoxy functional group at the meta position of the benzoyl group, which was at the third position of the indolizine nucleus, demonstrated encouraging anti-TB activity against MDR strains of MTB at 16 μg/mL. In silico studies showed binding affinity within the range of 7.07-8.57 kcal/mol, with 5i showing the highest binding affinity. Hydrogen bonding, π-π- interactions, and electrostatic interactions were common with the active site. Most of these interactions occurred with the catalytic amino acids (Pro193, Tyr158, Phe149, and Lys165). MD simulation showed that 5j possessed the highest binding affinity toward the enzyme, according to the two calculation methods (MM/PBSA and MM/GBSA). The single-crystal X-ray studies of compounds 5c and 5d revealed that the molecular arrangements in these two structures were mostly guided by C-H···O hydrogen-bonded dimeric motifs and C-H···N hydrogen bonds, while various secondary interactions (such as π···π and C-H···F) also contributed to crystal formation. Compounds 5a, 5c, 5i, and 5j exhibited no toxicity up to 500 μg/mL. In conclusion, 5i and 5j are promising anti-TB compounds that have shown high affinity based on docking and MD simulation results.

Matched MeSH terms: Crystallography, X-Ray
The inophyllums, novel inhibitors of HIV-1 reverse transcriptase isolated from the Malaysian tree, Calophyllum inophyllum Linn

Patil AD, Freyer AJ, Eggleston DS, Haltiwanger RC, Bean MF, Taylor PB, et al.

J Med Chem, 1993 Dec 24;36(26):4131-8.
PMID: 7506311

As part of a search for novel inhibitors of HIV-1 reverse transcriptase, the acetone extract of the giant African snail, Achatina fulica, was shown to be active. Fractionation of the extract yielded inophyllums A, B, C, and E and calophyllolide (1a, 2a, 3a, 3b, and 6), previously isolated from Calophyllum inophyllum Linn., a known source of nutrition for A. fulica. From a methanol/methylene chloride extract of C. inophyllum, the same natural products in considerably greater yield were isolated in addition to a novel enantiomer of soulattrolide (4), inophyllum P (2b), and two other novel compounds, inophyllums G-1 (7) and G-2 (8). The absolute stereochemistry of inophyllum A (1a) was determined to be 10(R), 11(S), 12(S) from a single-crystal X-ray analysis of its 4-bromobenzoate derivative, and the relative stereochemistries of the other inophyllums isolated from C. inophyllum were established by a comparison of their 1H NMR NOE values and coupling constants to those of inophyllum A (1a). Inophyllums B and P (2a and 2b) inhibited HIV reverse transcriptase with IC50 values of 38 and 130 nM, respectively, and both were active against HIV-1 in cell culture (IC50 of 1.4 and 1.6 microM). Closely related inophyllums A, C, D, and E, including calophyllic acids, were significantly less active or totally inactive, indicating certain structural requirements in the chromanol ring. Altogether, 11 compounds of the inophyllum class were isolated from C. inophyllum and are described together with the SAR of these novel anti-HIV compounds.

Matched MeSH terms: Crystallography, X-Ray
Fulltext Microwave synthesis, crystal structure, antioxidant, and antimicrobial study of new 6-heptyl-5,6-dihydrobenzo[4,5]imidazo[1,2-c]quinazoline compound

Hasan HA, Abdulmalek E, Rahman MBA, Shaari KB, Yamin BM, Chan KW

Chem Cent J, 2018 Dec 20;12(1):145.
PMID: 30570683 DOI: 10.1186/s13065-018-0509-z

BACKGROUND: Although the development of antibiotic and antioxidant manufacturing, the problem of bacterial resistance and food and/or cosmetics oxidation still needs more efforts to design new derivatives which can help to minimize these troubles. Benzimidazo[1,2-c]quinazolines are nitrogen-rich heterocyclic compounds that possess many pharmaceutical properties such as antimicrobial, anticonvulsant, immunoenhancer, and anticancer.
RESULTS: A comparative study between two methods, (microwave-assisted and conventional heating approaches), was performed to synthesise a new quinazoline derivative from 2-(2-aminophenyl)-1H-benzimidazole and octanal to produce 6-heptyl-5,6-dihydrobenzo[4,5]imidazo[1,2-c]quinazoline (OCT). The compound was characterised using FTIR, 1H and 13C NMR, DIMS, as well as X-ray crystallography. The most significant peak in the 13C NMR spectrum is C-7 at 65.5 ppm which confirms the cyclisation process. Crystal structure analysis revealed that the molecule grows in the monoclinic crystal system P21/n space group and stabilised by an intermolecular hydrogen bond between the N1-H1A…N3 atoms. The crystal packing analysis showed that the molecule adopts zig-zag one dimensional chains. Fluorescence study of OCT revealed that it produces blue light when expose to UV-light and its' quantum yield equal to 26%. Antioxidant activity, which included DPPH· and ABTS·+ assays was also performed and statistical analysis was achieved via a paired T-test using Minitab 16 software with P

Matched MeSH terms: Crystallography, X-Ray
Unravelling protein -organic solvent interaction of organic solvent tolerant elastase from Pseudomonas aeruginosa strain K crystal structure

Said ZSAM, Arifi FAM, Salleh AB, Rahman RNZRA, Leow ATC, Latip W, et al.

Int J Biol Macromol, 2019 Apr 15;127:575-584.
PMID: 30658145 DOI: 10.1016/j.ijbiomac.2019.01.056

The utilization of organic solvents as reaction media for enzymatic reactions provides numerous industrially attractive advantages. However, an adaptation of enzyme towards organic solvent is unpredictable and not fully understood because of limited information on the organic solvent tolerant enzymes. To understand how the enzyme can adapt to the organic solvent environment, structural and computational approaches were employed. A recombinant elastase from Pseudomonas aeruginosa strain K was an organic solvent tolerant zinc metalloprotease was successfully crystallized and diffracted up to 1.39 Å. Crystal structure of elastase from strain K showed the typical, canonical alpha-beta hydrolase fold consisting of 10-helices (118 residues), 10- β-strands (38 residues) and 142 residues were formed other secondary structure such as loop and coil to whole structure. The elastase from Pseusomonas aeruginosa strain K possess His-140, His-144 and Glu-164 served as a ligand for zinc ion. The conserved catalytic triad was composed of Glu-141, Tyr-155 and His-223. Three-dimensional structure features such as calcium-binding and presence of disulphide-bridge contribute to the stabilizing the elastase structure. Molecular dynamic (MD) simulation of elastase revealed that, amino acid residues located at the surface area and disulphide bridge in Cys-30 to Cys-58 were responsible for enzyme stability in organic solvents.

Matched MeSH terms: Crystallography, X-Ray
Fulltext Microwave-Assisted Synthesis of Mono- and Disubstituted 4-Hydroxyacetophenone Derivatives via Mannich Reaction: Synthesis, XRD and HS-Analysis

Aljohani G, Said MA, Lentz D, Basar N, Albar A, Alraqa SY, et al.

Molecules, 2019 Feb 07;24(3).
PMID: 30736403 DOI: 10.3390/molecules24030590

An efficient microwave-assisted one-step synthetic route toward Mannich bases is developed from 4-hydroxyacetophenone and different secondary amines in quantitative yields, via a regioselective substitution reaction. The reaction takes a short time and is non-catalyzed and reproducible on a gram scale. The environmentally benign methodology provides a novel alternative, to the conventional methodologies, for the synthesis of mono- and disubstituted Mannich bases of 4-hydroxyacetophenone. All compounds were well-characterized by FT-IR, ¹H NMR, 13C NMR, and mass spectrometry. The structures of 1-{4-hydroxy-3-[(morpholin-4-yl)methyl]phenyl}ethan-1-one (2a) and 1-{4-hydroxy-3-[(pyrrolidin-1-yl)methyl]phenyl}ethan-1-one (3a) were determined by single crystal X-ray crystallography. Compound 2a and 3a crystallize in monoclinic, P2₁/n, and orthorhombic, Pbca, respectively. The most characteristic features of the molecular structure of 2a is that the morpholine fragment adopts a chair conformation with strong intramolecular hydrogen bonding. Compound 3a exhibits intermolecular hydrogen bonding, too. Furthermore, the computed Hirshfeld surface analysis confirms H-bonds and π⁻π stack interactions obtained by XRD packing analyses.

Matched MeSH terms: Crystallography, X-Ray
Multiple crystallization as a potential strategy for efficient recovery of succinic acid following fermentation with immobilized cells

Luthfi AAI, Tan JP, Isa NFAM, Bukhari NA, Shah SSM, Mahmod SS, et al.

Bioprocess Biosyst Eng, 2020 Jul;43(7):1153-1169.
PMID: 32095989 DOI: 10.1007/s00449-020-02311-x

This study aimed to enhance the crystallizability of bio-based succinic acid for its efficient recovery while maintaining the end product at the highest purity. Immobilization of Actinobacillus succinogenes was initially evaluated based on three different carriers: volcanic glass, clay pebbles, and silica particles. The adsorption capacity of metabolites with a low concentration (10 g/L) and a high concentration (40 g/L) was investigated. It was demonstrated that clay pebbles adsorbed the least succinic acid (

Matched MeSH terms: Crystallography, X-Ray
Crystal structure of a compact α-amylase from Geobacillus thermoleovorans

Mok SC, Teh AH, Saito JA, Najimudin N, Alam M

Enzyme Microb Technol, 2013 Jun 10;53(1):46-54.
PMID: 23683704 DOI: 10.1016/j.enzmictec.2013.03.009

A truncated form of an α-amylase, GTA, from thermophilic Geobacillus thermoleovorans CCB_US3_UF5 was biochemically and structurally characterized. The recombinant GTA, which lacked both the N- and C-terminal transmembrane regions, functioned optimally at 70°C and pH 6.0. While enzyme activity was not enhanced by the addition of CaCl2, GTA's thermostability was significantly improved in the presence of CaCl2. The structure, in complex with an acarbose-derived pseudo-hexasaccharide, consists of the typical three domains and binds one Ca(2+) ion. This Ca(2+) ion was strongly bound and not chelated by EDTA. A predicted second Ca(2+)-binding site, however, was disordered. With limited subsites, two novel substrate-binding residues, Y147 and Y182, may help increase substrate affinity. No distinct starch-binding domain is present, although two regions rich in aromatic residues have been observed. GTA, with a smaller domain B and several shorter loops compared to other α-amylases, has one of the most compact α-amylase folds that may contribute greatly to its tight Ca(2+) binding and thermostability.

Matched MeSH terms: Crystallography, X-Ray
Assembly of ligands interaction models for glutathione-S-transferases from Plasmodium falciparum, human and mouse using enzyme kinetics and molecular docking

Al-Qattan MN, Mordi MN, Mansor SM

Comput Biol Chem, 2016 10;64:237-249.
PMID: 27475235 DOI: 10.1016/j.compbiolchem.2016.07.007

BACKGROUND: Glutathione-s-transferases (GSTs) are enzymes that principally catalyze the conjugation of electrophilic compounds to the endogenous nucleophilic glutathione substrate, besides, they have other non-catalytic functions. The Plasmodium falciparum genome encodes a single isoform of GST (PfGST) which is involved in buffering the toxic heme, thus considered a potential anti-malarial target. In mammals several classes of GSTs are available, each of various isoforms. The human (human GST Pi-1 or hGSTP1) and mouse (murine GST Mu-1 or mGSTM1) GST isoforms control cellular apoptosis by interaction with signaling proteins, thus considered as potential anti-cancer targets. In the course of GSTs inhibitors development, the models of ligands interactions with GSTs are used to guide rational molecular modification. In the absence of X-ray crystallographic data, enzyme kinetics and molecular docking experiments can aid in addressing ligands binding modes to the enzymes.
METHODS: Kinetic studies were used to investigate the interactions between the three GSTs and each of glutathione, 1-chloro-2,4-dinitrobenzene, cibacron blue, ethacrynic acid, S-hexyl glutathione, hemin and protoporphyrin IX. Since hemin displacement is intended for PfGST inhibitors, the interactions between hemin and other ligands at PfGST binding sites were studied kinetically. Computationally determined binding modes and energies were interlinked with the kinetic results to resolve enzymes-ligands interaction models at atomic level.
RESULTS: The results showed that hemin and cibacron blue have different binding modes in the three GSTs. Hemin has two binding sites (A and B) with two binding modes at site-A depending on presence of GSH. None of the ligands were able to compete hemin binding to PfGST except ethacrynic acid. Besides bind differently in GSTs, the isolated anthraquinone moiety of cibacron blue is not maintaining sufficient interactions with GSTs to be used as a lead. Similarly, the ethacrynic acid uses water bridges to mediate interactions with GSTs and at least the conjugated form of EA is the true hemin inhibitor, thus EA may not be a suitable lead.
CONCLUSIONS: Glutathione analogues with bulky substitution at thiol of cysteine moiety or at γ-amino group of γ-glutamine moiety may be the most suitable to provide GST inhibitors with hemin competition.

Matched MeSH terms: Crystallography, X-Ray

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