Positional Isomerism and Conformational Flexibility Directed Structural Variations in the Molecular Complexes of Dihydroxybenzoic Acids

2015 ◽  
Vol 15 (8) ◽  
pp. 3832-3841 ◽  
Author(s):  
Sunil Varughese ◽  
Anna A. Hoser ◽  
Katarzyna N. Jarzembska ◽  
V. R. Pedireddi ◽  
Krzysztof Woźniak
Keyword(s):  
Molecular Complexes ◽  
Conformational Flexibility ◽  
Structural Variations ◽  
Positional Isomerism

scholarly journals Molecular complexes of cyclohexanehexacarboxylic acid with aza-donors

2014 ◽  
Vol 70 (a1) ◽  
pp. C536-C536
Author(s):  
Sharmita Biswas ◽  
V. Pedireddi
Keyword(s):  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Molecular Complexes ◽  
Structural Diversity ◽  
Solvent Mixture ◽  
Water Molecules ◽  
Crystal Lattices ◽  
Supramolecular Architectures ◽  
Molecular Adduct ◽  
Positional Isomerism

Hydrogen bond mediated molecular complexes of cyclohexane-1,2,3,4,5,6-hexacarboxylic acid (1) with aza-donors distinguished by positional isomerism like 4,4'-bipyridine (a), 2,2'-bipyridine (b), trans-1,2-bis(4-pyridyl)ethylene (c), trans-1,2-bis(2-pyridyl)ethylene (d), 4,7-phenanthroline (e) and 1,10-phenanthroline (f) have been prepared either from a solvent mixture of methanol-water or from DMSO by solvent evaporation method. All the complexes crystallized as hydrates with different molecular ratios of 1, aza-donor and water. Detailed structural analyses of these molecular complexes have been investigated by single crystal X-ray diffraction. Structural diversity was found in the landscape of these molecular complexes depending upon the flexibility and positional isomerism of organic spacers (aza-donors) as well. Both intra and inter molecular hydrogen bonds played an important role in the formation of supramolecular architectures. Intramolecular O-H...O hydrogen bonds are present in the acid molecule due to the favourable orientation of -COOH groups in the chair form of the cyclohexane ring. In basic recognition pattern of each complex, it has been noted that acid molecules interact with aza-donors as well as water molecules through O-H...N and O-H...O hydrogen bonds, respectively. Different topological patterns like sheets, tapes, ribbons and host-guest networks have been observed in three dimensional arrangements. Inclusion of water molecules in each molecular adduct indicates the importance of water molecules to stabilise the molecular ensembles of 1 and the corresponding aza-donors. Presence of water molecules in the crystal lattices was also supported by thermogravimetric analysis (TGA).

scholarly journals ID:2034 Structural and Functional Polymorphism in Hepatitis B Virus Oncogene, HBx

2017 ◽  
Vol 4 (S) ◽  
pp. 65
Author(s):  
Nusrat Jabeen ◽  
Mushtaq Hussain
Keyword(s):  
Structural Characteristics ◽  
Molecular Complexes ◽  
Helical Conformation ◽  
Structural Variations ◽  
Oncogenic Potential ◽  
Docking Analysis ◽  
Consensus Sequences ◽  
Hbv Genotypes ◽  
B Virus ◽  
Multiple Binding

Background: HBV is now firmly associated with the incidence of Hepatocellular Carcinoma. This oncogenic potential of HBV is primarily due to an oncogene referred to as HBx. The present study deals with the sequential and structural variations found in the HBx protein encoded by the genomes of different HBV genotypes.   Methods: In total 5991 sequences of HBx belonging to different genotypes of HBV were aligned to procure consensus sequences of each genotype. The sequence was than used to construct molecular structure of HBx employing iterative threading alignment. The models were optimized and refined for the structural and thermodynamic parameters. The selected models were used to develop structures of HBx of each genotype which were in turn compared for their structural attributes, dimer formation and molecular interactions with p53.   Results: The sequence alignment reveals considerable conservation in the HBx sequences of different genotypes. The strongly conserved C-terminal region is a component of p53 interaction region of HBx. The most diverged region was found to be dimerization region spanning 25 to 50 aa. Structurally, HBx molecule has found to be nearly disordered except the C-terminal p53 binding region that adopts helical conformation. This in turn may explain in part the promiscuous nature of HBx in terms of binding with multiple binding partners. These observations have been further verified by GlobPlot analysis. The disordered region potentially rendered variations in the intra and inter molecular complexes of HBx as observed by molecular docking analysis.   Conclusion: The data highlights the variations in the structural characteristics of HBx that underscores the variations in the pathological and oncogenic consequences of HBV infections rendered by different HBV genotypes.

scholarly journals Understanding the Role of Geometric and Electronic Structure in Bioinspired Catalyst Design: the Case of Formate Dehydrogenase

2021 ◽  
Author(s):  
Mingjie Liu ◽  
Azadeh Nazemi ◽  
Michael Taylor ◽  
Aditya Nandy ◽  
Chenru Duan ◽  
...  
Keyword(s):  
High Throughput Screening ◽  
Density Functional ◽  
Large Scale ◽  
Formate Dehydrogenase ◽  
Molecular Complexes ◽  
Catalyst Design ◽  
Local Geometry ◽  
Structural Variations ◽  
Screening Study ◽  
The Individual

The design of bioinspired synthetic inorganic molecular complexes is challenging, due to a lack of understanding of enzyme action and the degree to which that action can be translated into mimics. Exemplary of this challenge is the reversible conversion of formate into CO2 by formate dehydrogenase (FDH) enzymes with Mo/W centers in large molybdopterin cofactors. Despite numerous efforts to synthesize Mo/W-containing molecular complexes, none have been demonstrated to reproduce the full reactivity of FDH. Here, we carry out a large-scale, high-throughput screening study on all mononuclear Mo/W complexes currently deposited in Cambridge Structural Database (CSD). Using density functional theory, we systematically investigate the individual effects of metal identity, ligand identity, oxidation state, and coordination number on structural, electronic and catalytic properties. We compare our results on molecular complexes with quantum mechanics/molecular mechanics simulations on a representative FDH enzyme to further elucidate the influence of the enzyme environment. These comparisons reveal that the enzyme environment primarily influences the metal-local geometry, and these metal-local structural variations can improve catalysis. Through a series of computational mutations on molecular complexes, we extend beyond the CSD structures to further identify the limits of varied chalcogen and metal identity. This broad set and comparison reveal relatively little variation of electronic properties of the metal center due to the presence of the enzyme environment or changes in metal-distant ligand chemistry. Instead, these properties are found to be much more sensitive to the identity of the metal and the nature of the bound terminal chalcogen.

Crystalloid Inclusions in Hepatocyte Mitochondria and Their Similarity to Cytoplasmic Crystalloids

1974 ◽  
Vol 32 ◽  
pp. 198-199
Author(s):  
Odell T. Minick ◽  
Hidejiro Yokoo
Keyword(s):  
Liver Disease ◽  
Alcoholic Liver Disease ◽  
Special Interest ◽  
Structural Variations ◽  
Mitochondrial Alterations ◽  
The Matrix ◽  
Crystalloid Inclusions ◽  
Liver Biopsies

Mitochondrial alterations were studied in 25 liver biopsies from patients with alcoholic liver disease. Of special interest were the morphologic resemblance of certain fine structural variations in mitochondria and crystalloid inclusions. Four types of alterations within mitochondria were found that seemed to relate to cytoplasmic crystalloids.Type 1 alteration consisted of localized groups of cristae, usually oriented in the long direction of the organelle (Fig. 1A). In this plane they appeared serrated at the periphery with blind endings in the matrix. Other sections revealed a system of equally-spaced diagonal lines lengthwise in the mitochondrion with cristae protruding from both ends (Fig. 1B). Profiles of this inclusion were not unlike tangential cuts of a crystalloid structure frequently seen in enlarged mitochondria described below.

Probing massive cold cores discovered by ISO in quiescent galactic molecular complexes

2002 ◽  
Vol 4 ◽  
pp. 133-133
Author(s):  
D. Teyssier ◽  
P. Hennebelle ◽  
M. Pérault
Keyword(s):  
Molecular Complexes

Direct Read and Quantify Damage Nucleotide from an Oligonucleotide Using a Single Molecule Interface

2019 ◽  
Author(s):  
Jiajun Wang ◽  
Meng-Yin Li ◽  
Jie Yang ◽  
Ya-Qian Wang ◽  
Xue-Yuan Wu ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Single Molecule ◽  
Genetic Diseases ◽  
High Sensitivity ◽  
Dna Lesions ◽  
Lesion Detection ◽  
The Novel ◽  
Structural Variations ◽  
Dna Lesion ◽  
Base Lesion

DNA lesion such as metholcytosine(<sup>m</sup>C), 8-OXO-guanine(<sup>O</sup>G), inosine(I) <i>etc</i> could cause the genetic diseases. Identification of the varieties of lesion bases are usually beyond the capability of conventional DNA sequencing which is mainly designed to discriminate four bases only. Therefore, lesion detection remain challenge due to the massive varieties and less distinguishable readouts for minor structural variations. Moreover, standard amplification and labelling hardly works in DNA lesions detection. Herein, we designed a single molecule interface from the mutant K238Q Aerolysin, whose confined sensing region shows the high compatible to capture and then directly convert each base lesion into distinguishable current readouts. Compared with previous single molecule sensing interface, the resolution of the K238Q Aerolysin nanopore is enhanced by 2-order. The novel K238Q could direct discriminate at least 3 types (<sup>m</sup>C, <sup>O</sup>G, I) lesions without lableing and quantify modification sites under mixed hetero-composition condition of oligonucleotide. Such nanopore could be further applied to diagnose genetic diseases at high sensitivity.

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