scholarly journals Geometrical correlations in the nucleosomal DNA conformation and the role of the covalent bonds rigidity

2010 ◽  
Vol 39 (4) ◽  
pp. 1220-1230 ◽  
Author(s):  
M. Ghorbani ◽  
F. Mohammad-Rafiee
Keyword(s):  
Dna Conformation ◽  
Covalent Bonds ◽  
Nucleosomal Dna

Asymmetric breathing motions of nucleosomal DNA and the role of histone tails

2017 ◽  
Vol 147 (6) ◽  
pp. 065101 ◽  
Author(s):  
Kaushik Chakraborty ◽  
Sharon M. Loverde
Keyword(s):  
Histone Tails ◽  
Nucleosomal Dna

d Orbitals in the noble-gas dihalides

1970 ◽  
Vol 48 (17) ◽  
pp. 2695-2701 ◽  
Author(s):  
R. C. Catton ◽  
K. A. R. Mitchell
Keyword(s):  
Noble Gas ◽  
Valence Bond ◽  
Ionic Character ◽  
Orbital Exponent ◽  
Covalent Bonds ◽  
Model Calculations ◽  
Pair Bonds ◽  
Electron Repulsion Integrals ◽  
D Orbitals

Model calculations are reported for ArF2, KrF2, XeF2, ArCl2, KrCl2, and XeCl2. The approach is to compare the energies of a number of valence-bond structures for each molecule. The calculations use Slater-type radial functions and simplify the electron repulsion integrals with the Mulliken approximation. Energies are optimized by varying the d orbital exponent and a parameter which governs the ionic character of the covalent bonds. For all the molecules it is found that the structures such as (X—M+X− + X−M+—X) and X−M2+X−, which maintain the octet rule and exclude the use of d orbitals, are less stable than the structure X—M—X which implies localized electron-pair bonds based on pd hybrids at the noble-gas atom M.Approximate molecular wave functions are obtained from a configuration interaction calculation, and the general conclusion is that the valence-bond structures incorporating d orbitals become more important as the atomic number of the central atom increases. A preliminary study of the role of the [Formula: see text] orbital is also presented, but it seems this orbital contributes mainly as a polarization effect.

scholarly journals Glassy dynamics of crystallite formation: The role of covalent bonds

Soft Matter ◽  
2012 ◽  
Vol 8 (4) ◽  
pp. 1215-1225 ◽  
Author(s):  
Robert S. Hoy ◽  
Corey S. O'Hern
Keyword(s):  
Glassy Dynamics ◽  
Covalent Bonds

scholarly journals The Modern Western Diet Rich in Advanced Glycation End-Products (AGEs): An Overview of Its Impact on Obesity and Early Progression of Renal Pathology

Nutrients ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 1748 ◽  
Author(s):  
Arianna Bettiga ◽  
Francesco Fiorio ◽  
Federico Di Marco ◽  
Francesco Trevisani ◽  
Annalisa Romani ◽  
...  
Keyword(s):  
Chronic Diseases ◽  
Advanced Glycation End Products ◽  
Cell Function ◽  
Advanced Glycation ◽  
Covalent Bonds ◽  
Physiological Processes ◽  
Glycation End Products ◽  
End Products ◽  
And Function

Advanced glycation end-products (AGEs) are an assorted group of molecules formed through covalent bonds between a reduced sugar and a free amino group of proteins, lipids, and nucleic acids. Glycation alters their structure and function, leading to impaired cell function. They can be originated by physiological processes, when not counterbalanced by detoxification mechanisms, or derive from exogenous sources such as food, cigarette smoke, and air pollution. Their accumulation increases inflammation and oxidative stress through the activation of various mechanisms mainly triggered by binding to their receptors (RAGE). So far, the pathogenic role of AGEs has been evidenced in inflammatory and chronic diseases such as chronic kidney disease, cardiovascular disease, and diabetic nephropathy. This review focuses on the AGE-induced kidney damage, by describing the molecular players involved and investigating its link to the excess of body weight and visceral fat, hallmarks of obesity. Research regarding interventions to reduce AGE accumulation has been of great interest and a nutraceutical approach that would help fighting chronic diseases could be a very useful tool for patients’ everyday lives.

scholarly journals The role of double covalent flavin binding in chito-oligosaccharide oxidase from Fusarium graminearum

2008 ◽  
Vol 413 (1) ◽  
pp. 175-183 ◽  
Author(s):  
Dominic P. H. M. Heuts ◽  
Remko T. Winter ◽  
Gerke E. Damsma ◽  
Dick B. Janssen ◽  
Marco W. Fraaije
Keyword(s):  
Redox Potential ◽  
Fusarium Graminearum ◽  
Covalent Binding ◽  
Site Directed Mutagenesis ◽  
Wild Type ◽  
Covalent Bonds ◽  
Regioselective Oxidation ◽  
Flavin Binding ◽  
High Redox Potential

ChitO (chito-oligosaccharide oxidase) from Fusarium graminearum catalyses the regioselective oxidation of N-acetylated oligosaccharides. The enzyme harbours an FAD cofactor that is covalently attached to His94 and Cys154. The functional role of this unusual bi-covalent flavin–protein linkage was studied by site-directed mutagenesis. The double mutant (H94A/C154A) was not expressed, which suggests that a covalent flavin–protein bond is needed for protein stability. The single mutants H94A and C154A were expressed as FAD-containing enzymes in which one of the covalent FAD–protein bonds was disrupted relative to the wild-type enzyme. Both mutants were poorly active, as the kcat decreased (8.3- and 3-fold respectively) and the Km increased drastically (34- and 75-fold respectively) when using GlcNac as the substrate. Pre-steady-state analysis revealed that the rate of reduction in the mutant enzymes is decreased by 3 orders of magnitude when compared with wild-type ChitO (kred=750 s−1) and thereby limits the turnover rate. Spectroelectrochemical titrations revealed that wild-type ChitO exhibits a relatively high redox potential (+131 mV) and the C154A mutant displays a lower potential (+70 mV), while the H94A mutant displays a relatively high potential of approximately +164 mV. The results show that a high redox potential is not the only prerequisite to ensure efficient catalysis and that removal of either of the covalent bonds may perturb the geometry of the Michaelis complex. Besides tuning the redox properties, the bi-covalent binding of the FAD cofactor in ChitO is essential for a catalytically competent conformation of the active site.

HMGN dynamics and chromatin function

2003 ◽  
Vol 81 (3) ◽  
pp. 113-122 ◽  
Author(s):  
Frédéric Catez ◽  
Jae-Hwan Lim ◽  
Robert Hock ◽  
Yuri V Postnikov ◽  
Michael Bustin
Keyword(s):  
Binding Sites ◽  
Protein Composition ◽  
Nuclear Proteins ◽  
Chromatin Interactions ◽  
Binding Partners ◽  
Nucleosomal Dna ◽  
Transient Interactions ◽  
And Function ◽  
Nucleosome Binding

Recent studies indicate that most nuclear proteins, including histone H1 and HMG are highly mobile and their interaction with chromatin is transient. These findings suggest that the structure of chromatin is dynamic and the protein composition at any particular chromatin site is not fixed. Here we discuss how the dynamic behavior of the nucleosome binding HMGN proteins affects the structure and function of chromatin. The high intranuclear mobility of HMGN insures adequate supply of protein throughout the nucleus and serves to target these proteins to their binding sites. Transient interactions of the proteins with nucleosomes destabilize the higher order chromatin, enhance the access to nucleosomal DNA, and impart flexibility to the chromatin fiber. While roaming the nucleus, the HMGN proteins encounter binding partners and form metastable multiprotein complexes, which modulate their chromatin interactions. Studies with HMGN proteins underscore the important role of protein dynamics in chromatin function.Key words: HMG, nuclear proteins, chromatin, HMGN.

scholarly journals Porous Covalent Organic Nanotubes and Toroids: A Carbon Nanotube Analogue

2021 ◽  
Author(s):  
Rahul Banerjee ◽  
Kalipada Koner ◽  
Shayan Karak ◽  
Sharath Kandambeth ◽  
Suvendu Karak ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Driving Force ◽  
Bet Surface Area ◽  
Computational Studies ◽  
Covalent Bonds ◽  
Organic Nanotubes ◽  
Role Of Solvent ◽  
Thermal And Chemical Stability ◽  
Made In

Abstract Despite the noteworthy progress made in the nanotubular architectures with well-defined lengths and diameter, the synthesis of a purely covalent bonded organic nanotube, so far, proved to be elusive. Our work includes a hitherto unavailable structure, "Covalent Organic Nanotubes (CONTs)," to the repertoire. Strong covalent bonds between C, N, and O imparts high thermal and chemical stability of CONTs. This novel bottom-up approach provides an edge over the carbon nanotubes (CNTs) in functionalization, synthetic conditions, and porosity. CONT-1 exhibits a BET surface area of 321 m2g-1. These flexible CONTs intertwine with each other. The computational studies establish the role of solvent as the critical driving force for this type of convolution. Upon ultrasonication, the intertwined CONT-1 coil to form the toroidal superstructure.

scholarly journals Role of biochemical factors in the pathogenesis of keratoconus.

2014 ◽  
Vol 61 (1) ◽  
Author(s):  
Katarzyna A Wojcik ◽  
Janusz Blasiak ◽  
Jerzy Szaflik ◽  
Jacek P Szaflik
Keyword(s):  
Lysyl Oxidase ◽  
Interleukin 1 ◽  
Covalent Bonds ◽  
Altered Expression ◽  
Expression Of Genes ◽  
Nitrative Stress ◽  
Structural Abnormalities ◽  
Increased Activity ◽  
Increased Susceptibility

Keratoconus (KC) is a corneal disease associated with structural abnormalities in the corneal epithelium, Bowman's layer and stroma and altered concentration of tear components. KC corneas show a different pattern of collagen lamellae than their normal counterparts. Also, a reduction of several collagen types in KC epithelium and stroma was observed. Altered expression and/or activity of lysyl oxidase, a critical enzyme of the biogenesis of connective tissue detected in KC corneas, may weaken covalent bonds between collagen and elastin fibrils, what may lead to biomechanical deterioration of the cornea. Increased activity of matrix metalloproteinases observed in KC may induce the degradation of the extracellular matrix causing damage to the cornea. Oxidative and nitrative stress play an important role in KC pathogenesis and KC corneas are characterized by the disturbed lipid peroxidation and nitric oxide pathways. Malfunctioning of these pathways may lead to accumulation of their toxic by-products inducing several detrimental effects, along with apoptosis of the corneal cells, which may result from the loss of β-actin or increased levels of cytokines, including interleukin-1 and -6. Change in the expression of genes associated with wound healing, including the nerve growth factor and the visual system homeobox 1, may contribute to increased susceptibility of KC corneas to injury. Consequently, biochemical changes may play an important role in KC pathophysiology and, therefore, can be considered in prevention, diagnosis, prognosis and in the therapy of this disease as well.

scholarly journals Growth of the Stress-Bearing and Shape-Maintaining Murein Sacculus of Escherichia coli

1998 ◽  
Vol 62 (1) ◽  
pp. 181-203 ◽  
Author(s):  
Joachim-Volker Höltje
Keyword(s):  
Mechanical Stability ◽  
Growth Strategy ◽  
Gram Negative Bacteria ◽  
Covalent Bonds ◽  
Protein Protein Interaction ◽  
New Material ◽  
Specific Shape ◽  
Murein Sacculus ◽  
Intracellular Pressure

SUMMARY To withstand the high intracellular pressure, the cell wall of most bacteria is stabilized by a unique cross-linked biopolymer called murein or peptidoglycan. It is made of glycan strands [poly-(GlcNAc-MurNAc)], which are linked by short peptides to form a covalently closed net. Completely surrounding the cell, the murein represents a kind of bacterial exoskeleton known as the murein sacculus. Not only does the sacculus endow bacteria with mechanical stability, but in addition it maintains the specific shape of the cell. Enlargement and division of the murein sacculus is a prerequisite for growth of the bacterium. Two groups of enzymes, hydrolases and synthases, have to cooperate to allow the insertion of new subunits into the murein net. The action of these enzymes must be well coordinated to guarantee growth of the stress-bearing sacculus without risking bacteriolysis. Protein-protein interaction studies suggest that this is accomplished by the formation of a multienzyme complex, a murein-synthesizing machinery combining murein hydrolases and synthases. Enlargement of both the multilayered murein of gram-positive and the thin, single-layered murein of gram-negative bacteria seems to follow an inside-to-outside growth strategy. New material is hooked in a relaxed state underneath the stress-bearing sacculus before it becomes inserted upon cleavage of covalent bonds in the layer(s) under tension. A model is presented that postulates that maintenance of bacterial shape is achieved by the enzyme complex copying the preexisting murein sacculus that plays the role of a template.

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