scholarly journals Experimental and computational studies of a fungal chitinase

2015 ◽  
Author(s):  
◽  
Faez Iqbal Khan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Weight ◽  
Active Sites ◽  
Three Dimensional ◽  
Biotechnological Applications ◽  
Thermostable Enzymes ◽  
Acid Protein ◽  
Wide Range ◽  
Dynamics Simulations ◽  
Amino Acid Protein

Chitin, the second most abundant natural biopolymer, is composed of repeating units of N-acetyl-β-D-glucosamine and primarily forms the structural component of protective biological matrices such as fungal cell walls and exoskeletons of insects. Chitinases are a ubiquitous class of extracellular enzymes that have gained attention in the past few years due to their wide range of biotechnological applications, especially in the field of agriculture for bio-control of fungal phytopathogens. They play an important role in the defense of organisms against chitin-containing parasites by hydrolyzing the β-1,4-linkages in chitin and hence act as anti-fungal as well as anti-biofouling agents. Moreover, the effectiveness of conventional insecticides is increasingly compromised by the occurrence of resistance and thus, chitinases offer a potential alternative to the use of chemical fungicides. In recent years, thermostable enzymes isolated from thermophilic microorganisms have gained widespread attention in industrial, medical, environmental and biotechnological applications due to their inherent stability at high temperatures and a wide range of pH optima. Determination of the three- dimensional structure of a protein can provide important details about its biological functions and its mode of action. However, despite their significance, the precise three-dimensional structures of most of the chitinases, including those isolated from Thermomyces lanuginosus is not fully characterized so far. Hence, the main focus of the present study was to gain a better understanding of the structural features of chitinases obtained from this thermostable fungus using both experimental and computational techniques, and their relationship with their activity profiles. The genes encoding thermostable chitinase II from T. lanuginosus were isolated and cloned in both E. coli as well as the Pichia pastoris expression system. Analysis of the nucleotide sequences revealed that the chitinase II gene (1196 bp) encodes a 343 amino acid protein of molecular weight 36.65 kDa whereas the chitinase I gene (1538 bp) encodes a 400 amino acid protein of molecular weight 44.14 kDa. In silico protein modeling was helpful in predicting the 3D models of the novel chitinase II enzyme, followed by the prediction of its active sites. The presence of Glu176 was found to be essential for the activity of chitinase II. Similarly, analysis of chitinase I revealed several active sites in its structural framework. A 10 ns Molecular dynamics (MD) simulations was implemented to assess the conformational preferences of chitinases. The MD trajectories at different temperatures clearly revealed that the stability of the enzymes were maintained at higher temperatures. Additionally, a constant pH molecular dynamics simulations at a pH range 2-6 was performed to establish the optimum activity and stability profiles of chitinase I and chitinase II. For this purpose, the Molecular Dynamics simulations were carried out at fixed protonation states in an explicit water environment to evaluate the effect of the physiological pH on chitinase I and II enzymes obtained from T. lanuginosus. The results suggest a strong conformational pH dependence of chitinases. These enzymes retained their characteristic TIM Barrel fold at the respective protonated conditions, thus validated the experimental outcomes. Further, the different stability and flexibility predictions were used to assess the relation of point mutations and enzyme stabilities. Our results pave the way to engineer new and better thermostable enzymes.

scholarly journals Polymer cyclization for the emergence of hierarchical nanostructures

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chaojian Chen ◽  
Manjesh Kumar Singh ◽  
Katrin Wunderlich ◽  
Sean Harvey ◽  
Colette J. Whitfield ◽  
...  
Keyword(s):  
Self Assembly ◽  
Three Dimensional ◽  
Hierarchical Structures ◽  
Structural Similarity ◽  
Vital Role ◽  
Nanomaterial Synthesis ◽  
Wide Range ◽  
Linear Poly ◽  
Polymer Folding ◽  
Dynamics Simulations

AbstractThe creation of synthetic polymer nanoobjects with well-defined hierarchical structures is important for a wide range of applications such as nanomaterial synthesis, catalysis, and therapeutics. Inspired by the programmability and precise three-dimensional architectures of biomolecules, here we demonstrate the strategy of fabricating controlled hierarchical structures through self-assembly of folded synthetic polymers. Linear poly(2-hydroxyethyl methacrylate) of different lengths are folded into cyclic polymers and their self-assembly into hierarchical structures is elucidated by various experimental techniques and molecular dynamics simulations. Based on their structural similarity, macrocyclic brush polymers with amphiphilic block side chains are synthesized, which can self-assemble into wormlike and higher-ordered structures. Our work points out the vital role of polymer folding in macromolecular self-assembly and establishes a versatile approach for constructing biomimetic hierarchical assemblies.

Molecular Dynamics Study of Ion Impact Phenomena and Compressive Stress in Thin Films

1993 ◽  
Vol 317 ◽  
Author(s):  
N.A. Marks ◽  
P. Guan ◽  
D.R. Mckenzie ◽  
B.A. PailThorpe
Keyword(s):  
Molecular Dynamics ◽  
Three Dimensional ◽  
Carbon Films ◽  
Loss Mechanism ◽  
Ion Energy ◽  
Lennard Jones ◽  
Impact Phenomena ◽  
Ion Impact ◽  
Dynamics Simulations ◽  
The Impact

ABSTRACTMolecular dynamics simulations of nickel and carbon have been used to study the phenomena due to ion impact. The nickel and carbon interactions were described using the Lennard-Jones and Stillinger-Weber potentials respectively. The phenomena occurring after the impact of 100 e V to 1 keV ions were studied in the nickel simulations, which were both two and three-dimensional. Supersonic focussed collision sequences (or focusons) were observed, and associated with these focusons were unexpected sonic bow waves, which were a major energy loss mechanism for the focuson. A number of 2D carbon films were grown and the stress in the films as a function of incident ion energy was Measured. With increasing energy the stress changed from tensile to compressive and reached a maximum around 50 eV, in agreement with experiment.

Molecular Dynamics Simulations of High Energy Cascades in Iron

1994 ◽  
Vol 373 ◽  
Author(s):  
Roger E. Stoller
Keyword(s):  
Molecular Dynamics ◽  
Three Dimensional ◽  
High Energy ◽  
Dynamics Simulation ◽  
Method Of Molecular Dynamics ◽  
Energy Cascades ◽  
Iron Based ◽  
The Many ◽  
Property Changes ◽  
Dynamics Simulations

AbstractA series of high-energy, up to 20 keV, displacement cascades in iron have been investigated for times up to 200 ps at 100 K using the method of molecular dynamics simulation. Thesimulations were carried out using the MOLDY code and a modified version of the many-bodyinteratomic potential developed by Finnis and Sinclair. The paper focuses on those results obtained at the highest energies, 10 and 20 keV. The results indicate that the fraction of the Frenkel pairs surviving in-cascade recombination remains fairly high in iron and that the fraction of the surviving point defects that cluster is lower than in materials such as copper. In particular, vacancy clustering appears to be inhibited in iron. Some of the interstitial clusters were observed to exhibit an unexpectedly complex, three-dimensional morphology. The observations are discussed in terms of their relevance to microstructural evolution and mechanical property changes in irradiated iron-based alloys.

scholarly journals Structure and Dynamics of FosA-Mediated Fosfomycin Resistance in Klebsiella pneumoniae and Escherichia coli

2017 ◽  
Vol 61 (11) ◽  
Author(s):  
Erik H. Klontz ◽  
Adam D. Tomich ◽  
Sebastian Günther ◽  
Justin A. Lemkul ◽  
Daniel Deredge ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Dynamics ◽  
Klebsiella Pneumoniae ◽  
Crystal Structures ◽  
Active Sites ◽  
Content Type ◽  
Dimer Interface ◽  
Fosfomycin Resistance ◽  
Gram Negative Organisms ◽  
Dynamics Simulations

ABSTRACT Fosfomycin exhibits broad-spectrum antibacterial activity and is being reevaluated for the treatment of extensively drug-resistant pathogens. Its activity in Gram-negative organisms, however, can be compromised by expression of FosA, a metal-dependent transferase that catalyzes the conjugation of glutathione to fosfomycin, rendering the antibiotic inactive. In this study, we solved the crystal structures of two of the most clinically relevant FosA enzymes: plasmid-encoded FosA3 from Escherichia coli and chromosomally encoded FosA from Klebsiella pneumoniae (FosAKP). The structure, molecular dynamics, catalytic activity, and fosfomycin resistance of FosA3 and FosAKP were also compared to those of FosA from Pseudomonas aeruginosa (FosAPA), for which prior crystal structures exist. E. coli TOP10 transformants expressing FosA3 and FosAKP conferred significantly greater fosfomycin resistance (MIC, >1,024 μg/ml) than those expressing FosAPA (MIC, 16 μg/ml), which could be explained in part by the higher catalytic efficiencies of the FosA3 and FosAKP enzymes. Interestingly, these differences in enzyme activity could not be attributed to structural differences at their active sites. Instead, molecular dynamics simulations and hydrogen-deuterium exchange experiments with FosAKP revealed dynamic interconnectivity between its active sites and a loop structure that extends from the active site of each monomer and traverses the dimer interface. This dimer interface loop is longer and more extended in FosAKP and FosA3 than in FosAPA, and kinetic analyses of FosAKP and FosAPA loop-swapped chimeric enzymes highlighted its importance in FosA activity. Collectively, these data yield novel insights into fosfomycin resistance that could be leveraged to develop new strategies to inhibit FosA and potentiate fosfomycin activity.

scholarly journals Proton Pumping and Non-Pumping Terminal Respiratory Oxidases: Active Sites Intermediates of These Molecular Machines and Their Derivatives

2021 ◽  
Vol 22 (19) ◽  
pp. 10852
Author(s):  
Sergey A. Siletsky ◽  
Vitaliy B. Borisov
Keyword(s):  
Active Sites ◽  
Three Dimensional ◽  
Molecular Machines ◽  
Proton Pumping ◽  
Stress Reactions ◽  
Low Oxygen ◽  
Functional Studies ◽  
Wide Range ◽  
Regulatory Cascades ◽  
Respiratory Oxidases

Terminal respiratory oxidases are highly efficient molecular machines. These most important bioenergetic membrane enzymes transform the energy of chemical bonds released during the transfer of electrons along the respiratory chains of eukaryotes and prokaryotes from cytochromes or quinols to molecular oxygen into a transmembrane proton gradient. They participate in regulatory cascades and physiological anti-stress reactions in multicellular organisms. They also allow microorganisms to adapt to low-oxygen conditions, survive in chemically aggressive environments and acquire antibiotic resistance. To date, three-dimensional structures with atomic resolution of members of all major groups of terminal respiratory oxidases, heme-copper oxidases, and bd-type cytochromes, have been obtained. These groups of enzymes have different origins and a wide range of functional significance in cells. At the same time, all of them are united by a catalytic reaction of four-electron reduction in oxygen into water which proceeds without the formation and release of potentially dangerous ROS from active sites. The review analyzes recent structural and functional studies of oxygen reduction intermediates in the active sites of terminal respiratory oxidases, the features of catalytic cycles, and the properties of the active sites of these enzymes.

Molecular Dynamics Study of Anatase TiO2 Nanoparticles in Water and Vacuum Environments

2012 ◽  
Author(s):  
George Okeke ◽  
Robert B. Hammond ◽  
S. Joseph Antony
Keyword(s):  
Molecular Dynamics ◽  
Surface Tension ◽  
Surface Energy ◽  
Tio2 Nanoparticles ◽  
Anatase Tio2 ◽  
Particle Sizes ◽  
Metallic Oxides ◽  
Wide Range ◽  
Enhanced Properties ◽  
Dynamics Simulations

Nanoparticles are nanometer sized metallic oxides which possess enhanced properties that are desirable to a wide range of industries. In this study, we investigate structural and surface properties of anatase TiO2 nanoparticles in vacuum and water environments using molecular dynamics simulations. The particle sizes ranged from 2 to 6 nm and simulations were performed at 300 K. Surface energy of the particles in vacuum was seen to be higher than that of the particles in water by about 100% for the smaller particles (i.e. 2 and 3nm) and about 60% for the larger particles (i.e. 4 to 6 nm). Surface energy of the particles in both environments, is seen to increase to a maximum (optimum value) as the particle size increases after which no further significant increase is observed. In vacuum, studies carried out at temperatures ranging from 300–2500 K showed a high dependence of surface energy on temperature. The estimated surface tension of water is seen to agree quite well with that of experiments.

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