scholarly journals Purification, crystallization and X-ray crystallographic studies on a putative methyltransferase, YtqB, fromBacillus subtilis

2014 ◽  
Vol 70 (4) ◽  
pp. 482-484
Author(s):  
Sun Cheol Park ◽  
Wan Seok Song ◽  
Jimin Wi ◽  
Sung-il Yoon
Keyword(s):  
Biological Function ◽  
Expression System ◽  
Regulation Of Gene Expression ◽  
Specific Substrate ◽  
Asymmetric Unit ◽  
Cellular Functions ◽  
Methyl Group ◽  
X Ray ◽  
Structural Insights

S-Adenosyl-L-methionine (SAM)-dependent methyltransferases (MTases) catalyze the transfer of a methyl group from a SAM cofactor to specific substrate molecules, including small chemicals, proteins, DNAs and RNAs, and are required for various cellular functions, such as regulation of gene expression and biosynthesis of metabolites.Bacillus subtilisYtqB is a putative SAM-dependent MTase whose biological function has not been characterized. To provide biochemical and structural insights into the role of YtqB in bacteria, the recombinant YtqB protein was overexpressed in theEscherichia coliexpression system and purified by chromatographic methods. YtqB crystals were obtained in PEG-containing conditions and diffracted to 1.68 Å resolution. The YtqB crystals belonged to space groupP212121, with two molecules in the asymmetric unit.

The Role of microRNAs in the Viral Infections

2019 ◽  
Vol 24 (39) ◽  
pp. 4659-4667 ◽  
Author(s):  
Mona Fani ◽  
Milad Zandi ◽  
Majid Rezayi ◽  
Nastaran Khodadad ◽  
Hadis Langari ◽  
...  
Keyword(s):  
Viral Infections ◽  
Rna Viruses ◽  
Regulation Of Gene Expression ◽  
Molecular Structures ◽  
Main Function ◽  
Cellular Functions ◽  
Viral Genes ◽  
Non Coding Rnas ◽  
Post Transcriptional Regulation

MicroRNAs (miRNAs) are non-coding RNAs with 19 to 24 nucleotides which are evolutionally conserved. MicroRNAs play a regulatory role in many cellular functions such as immune mechanisms, apoptosis, and tumorigenesis. The main function of miRNAs is the post-transcriptional regulation of gene expression via mRNA degradation or inhibition of translation. In fact, many of them act as an oncogene or tumor suppressor. These molecular structures participate in many physiological and pathological processes of the cell. The virus can also produce them for developing its pathogenic processes. It was initially thought that viruses without nuclear replication cycle such as Poxviridae and RNA viruses can not code miRNA, but recently, it has been proven that RNA viruses can also produce miRNA. The aim of this articles is to describe viral miRNAs biogenesis and their effects on cellular and viral genes.

The Role of miR-210 in the Biological System: A Current Overview

2019 ◽  
Vol 84 (6) ◽  
pp. 233-239
Author(s):  
Xu Hui ◽  
Hisham Al-Ward ◽  
Fahmi Shaher ◽  
Chun-Yang Liu ◽  
Ning Liu
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Low Oxygen ◽  
Cellular Functions ◽  
Regulate Gene Expression ◽  
System A ◽  
Non Coding Rnas ◽  
Post Transcriptional Regulation ◽  
A Current

<b><i>Background:</i></b> MicroRNAs (miRNAs) represent a group of non-coding RNAs measuring 19–23 nucleotides in length and are recognized as powerful molecules that regulate gene expression in eukaryotic cells. miRNAs stimulate the post-transcriptional regulation of gene expression via direct or indirect mechanisms. <b><i>Summary:</i></b> miR-210 is highly upregulated in cells under hypoxia, thereby revealing its significance to cell endurance. Induction of this mRNA expression is an important feature of the cellular low-oxygen response and the most consistent and vigorous target of HIF. <b><i>Key Message:</i></b> miR-210 is involved in many cellular functions under the effect of HIF-1α, including the cell cycle, DNA repair, immunity and inflammation, angiogenesis, metabolism, and macrophage regulation. It also plays an important regulatory role in T-cell differentiation and stimulation.

The crystal structure of 5-O-Acetyl-1,2 : 3,4-di-O-isopropylidene-α-D-glucoseptanose, C14H22O7, by use of X-ray and neutrondiffraction data

1983 ◽  
Vol 36 (11) ◽  
pp. 2269 ◽  
Author(s):  
RA Wood ◽  
VJ James ◽  
AD Rae ◽  
JD Stevens ◽  
FH Moore
Keyword(s):  
Crystal Structure ◽  
Neutron Diffraction ◽  
Diffraction Analysis ◽  
Chair Conformation ◽  
Asymmetric Unit ◽  
Methyl Group ◽  
Neutron Diffraction Analysis ◽  
X Ray ◽  
Acetate Methyl ◽  
Independent Molecules

The crystal structure of 5-O-acetyl-1,2:3,4-di-O-isopropylidene-α-D-glucoseptanose [P212121, Z 8, a 14.329(5), b 22.075(5), c 10.012(5) �] has been determined by X-ray and neutron diffraction analyses. For the neutron diffraction analysis, the acetate group and the trans-O-isopropylidene group were deuterated. Constrained refinement was used in the neutron diffraction analysis to counter over parameterization in the block-diagonal least-squares refinement. Final unweighted R-values were 0.038 [X-ray for 3070 reflections with [Fo > 2.58σ (Fo)] and 0.061 [neutron for 1118 reflections with Fo > 4σ ([Fo)]The neutron refinement revealed a disordering of the acetate methyl group in each of the two independent molecules in the asymmetric unit. The septanose ring in each molecule adopted the same twist-chair conformation but the dioxolan rings assumed different twist and envelope conformations.

Structure Investigations of Agonists of the Natural Neurotransmitter Acetylcholine VI [1]. X-Ray Structure Analysis of Trimethyl[2-(propionyloxy)ethyl]- ammonium-iodide (O-Propionylcholine-iodide)

1986 ◽  
Vol 41 (5-6) ◽  
pp. 641-646 ◽  
Author(s):  
Alfred Gieren ◽  
Michail Kokkinidis
Keyword(s):  
Crystal Structure ◽  
Nitrogen Atom ◽  
Formula Unit ◽  
Ammonium Iodide ◽  
Asymmetric Unit ◽  
Torsion Angles ◽  
Methyl Group ◽  
X Ray ◽  
Acetylcholine Chloride ◽  
Structure Investigations

The title compound (1) crystallizes in the orthorhombic, noncentrosymmetric space group Pna21 with a = 10.241(11), b = 12.903(12), c = 9.312(9) Å and with one formula unit per asymmetric unit. The stereochemically comparable torsion angles of the cation of 1 and of acetylcholine chloride are analogous. In the crystal structure the trimethylammonio methyl group is surrounded by three anions in the first coordination sphere. The geometry of a triangle formed by one of these counterions which occupies a special face of the N+C4 tetrahedron of the (CH3)3N+-CH2-R moiety, the nitrogen atom of the ammonium group and the oxygen atom of the carbonyl group is typical for nicotinic agonists.

scholarly journals On the role of DNA biomechanics in the regulation of gene expression

2011 ◽  
Vol 8 (65) ◽  
pp. 1673-1681 ◽  
Author(s):  
J. N. Milstein ◽  
J.-C. Meiners
Keyword(s):  
Gene Expression ◽  
Genetic Regulation ◽  
Regulation Of Gene Expression ◽  
Cellular Functions ◽  
Biochemical Processes ◽  
Regulatory Processes ◽  
Linear Sequence ◽  
Cellular Environment ◽  
Cellular Dna

DNA is traditionally seen as a linear sequence of instructions for cellular functions that are expressed through biochemical processes. Cellular DNA, however, is also organized as a complex hierarchical structure with a mosaic of mechanical features, and a growing body of evidence is now emerging to imply that these mechanical features are connected to genetic function. Mechanical tension, for instance, which must be felt by DNA within the heavily constrained and continually fluctuating cellular environment, can affect a number of regulatory processes implicating a role for biomechanics in gene expression complementary to that of biochemical regulation. In this article, we review evidence for such mechanical pathways of genetic regulation.

Structural insights into methyl- or methoxy-substituted 1-(α-aminobenzyl)-2-naphthol structures: the role of C—H...π interactions

2019 ◽  
Vol 75 (2) ◽  
pp. 189-195 ◽  
Author(s):  
Maria Annunziata M. Capozzi ◽  
Giancarlo Terraneo ◽  
Cosimo Cardellicchio
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Methoxy Group ◽  
Crystal Packing ◽  
Molecular Surface ◽  
Methyl Group ◽  
Π Interactions ◽  
Substituted 1 ◽  
Structural Insights

Aminobenzylnaphthols are a class of compounds containing a large aromatic molecular surface which makes them suitable candidates to study the role of C—H...π interactions. We have investigated the effect of methyl or methoxy substituents on the assembling of aromatic units by preparing and determining the crystal structures of (S,S)-1-{(4-methylphenyl)[(1-phenylethyl)amino]methyl}naphthalen-2-ol, C26H25NO, and (S,S)-1-{(4-methoxyphenyl)[(1-phenylethyl)amino]methyl}naphthalen-2-ol, C26H25NO2. The methyl group influenced the overall crystal packing even if the H atoms of the methyl group did not participate directly either in hydrogen bonding or C—H...π interactions. The introduction of the methoxy moiety caused the formation of new hydrogen bonds, in which the O atom of the methoxy group was directly involved. Moreover, the methoxy group promoted the formation of an interesting C—H...π interaction which altered the orientation of an aromatic unit.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of Xaa-Pro dipeptidase fromXanthomonas campestris

2014 ◽  
Vol 70 (9) ◽  
pp. 1268-1271 ◽  
Author(s):  
Ashwani Kumar ◽  
Venkata Narayana Are ◽  
Biplab Ghosh ◽  
Utsavi Agrawal ◽  
Sahayog N. Jamdar ◽  
...  
Keyword(s):  
Asymmetric Unit ◽  
Carboxy Terminus ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Conserved Residues ◽  
X Ray ◽  
Cell Parameters ◽  
Sequence Identity ◽  
Aminopeptidase P

Xaa-Pro dipeptidase (XPD; prolidase; EC 3.4.13.9) specifically hydrolyzes dipeptides with a prolyl residue at the carboxy-terminus.Xanthomonasspp. possess two different isoforms of XPD (48 and 43 kDa) which share ∼24% sequence identity. The XPD of 43 kDa in size (XPD43) fromXanthomonasspp. is unusual as it lacks the strictly conserved tyrosine residue (equivalent to Tyr387 inEscherichia coliaminopeptidase P) that is suggested to be important in the proton-shuttle transfer required for catalysis in the M24B (MEROPS) family. Here, the crystallization and preliminary X-ray analysis of XPD43 fromX. campestris(GenBank accession No. NP_637763) are reported. Recombinant XPD43 was crystallized using the microbatch-under-oil technique. Diffraction data were collected on the recently commissioned protein crystallography beamline (PX-BL21) at the Indian synchrotron (Indus-2, 2.5 GeV) to 1.83 Å resolution with 100% completeness. The crystal belonged to space groupP212121, with unit-cell parametersa= 84.32,b= 105.51,c= 111.35 Å. Two monomers are expected to be present in the asymmetric unit of the crystal, corresponding to a solvent content of 58%. Structural analysis of XPD43 will provide new insights into the role of the conserved residues in catalysis in the M24B family.

scholarly journals Purification, crystallization and preliminary X-ray analysis of the periplasmic haem-binding protein HutB fromVibrio cholerae

2015 ◽  
Vol 71 (4) ◽  
pp. 401-404 ◽  
Author(s):  
Shubhangi Agarwal ◽  
Maitree Biswas ◽  
Jhimli Dasgupta
Keyword(s):  
Pathogenic Bacteria ◽  
Molecular Level ◽  
Binding Protein ◽  
Molecular Replacement ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Structural Insights

The mechanism of haem transport across the inner membrane of pathogenic bacteria is currently insufficiently understood at the molecular level and no information is available for this process inVibrio cholerae. To obtain structural insights into the periplasmic haem-binding protein HutB fromV. cholerae(VcHutB), which is involved in haem transport through the HutBCD haem-transport system, at the atomic level, VcHutB was cloned, overexpressed and crystallized using 1.6 Mammonium sulfate as a precipitant at pH 7.0. X-ray diffraction data were collected to 2.4 Å resolution on the RRCAT PX-BL-21 beamline at the Indus-2 synchrotron, Indore, India. The crystals belonged to space groupP43212, with unit-cell parametersa=b= 62.88,c= 135.8 Å. Matthews coefficient calculations indicated the presence of one monomer in the asymmetric unit, with an approximate solvent content of 45.02%. Molecular-replacement calculations withPhaserconfirmed the presence of a monomer in the asymmetric unit.

scholarly journals Regulation of gene expression by the APP family in the adult cerebral cortex

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Hye Ji Cha ◽  
Jie Shen ◽  
Jongkyun Kang
Keyword(s):  
Gene Expression ◽  
Cerebral Cortex ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Mrna Levels ◽  
Rna Seq ◽  
Cellular Functions ◽  
Organization Learning ◽  
Transcriptional Changes

AbstractAmyloid precursor protein (APP) is associated with both familial and sporadic forms of Alzheimer’s disease. APP has two homologs, amyloid precursor-like protein 1 and 2 (APLP1 and APLP2), and they have functional redundancy. APP intracellular c-terminal domain (AICD), produced by sequential α- or β- and γ-secretase cleavages, is thought to control gene expression, similarly as the ICD of Notch. To investigate the role of APP family in transcriptional regulation, we examined gene expression changes in the cerebral cortex of APP/APLP1/APLP2 conditional triple knockout (cTKO) mice, in which APP family members are selectively inactivated in excitatory neurons of the postnatal forebrain. Of the 12 previously reported AICD target genes, only Nep and Npas4 mRNA levels were significantly reduced in the cerebral cortex of cTKO mice, compared to littermate controls. We further examined global transcriptional changes by RNA-seq and identified 189 and 274 differentially expressed genes in the neocortex and hippocampus, respectively, of cTKO mice relative to controls. Gene Ontology analysis indicated that these genes are involved in a variety of cellular functions, including extracellular organization, learning and memory, and ion channels. Thus, inactivation of APP family alters transcriptional profiles of the cerebral cortex and affects wide-ranging molecular pathways.

scholarly journals Synthesis, structural elucidation, characterization and theoretical DFT study of 1-(o-tolyl)biguanidium chloride

2020 ◽  
Vol 76 (6) ◽  
pp. 572-578
Author(s):  
Kamel Kaabi ◽  
Kacem Klai ◽  
Emmanuel Wenger ◽  
Christian Jelsch ◽  
Frédéric Lefebvre ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Hydrophobic Interactions ◽  
Hirshfeld Surface ◽  
Electrostatic Energy ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Absorption Bands ◽  
Methyl Group ◽  
X Ray

The structure of the new salt 1-(o-tolyl)biguanidium chloride, C9H14N5 +·Cl−, has been determined by single-crystal X-ray diffraction. The salt crystallizes in the monoclinic space group C2/c. In this structure, the chloride and biguanidium hydrophilic ions are mostly connected to each other via N—H...N and N—H...Cl hydrogen bonds to form layers parallel to the ab plane around y = 1 \over 3 and y = 2 \over 3. The 2-methylbenzyl groups form layers between these layers around y = 0 and y = 1 \over 2, with the methyl group forming C—H...π interactions with the aromatic ring. Intermolecular interactions on the Hirshfeld surface were investigated in terms of contact enrichment and electrostatic energy, and confirm the role of strong hydrogen bonds along with hydrophobic interactions. A correlation between electrostatic energy and contact enrichment is found only for the strongly attractive (N—H...Cl−) and repulsive contacts. Electrostatic energies between ions reveal that the interacting biguanidium cation pairs are repulsive and that the crystal is maintained by attractive cation...Cl− dimers. The vibrational absorption bands were identified by IR spectroscopy.

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