scholarly journals Advanced Molecular Dynamics Approaches to Model a Tertiary Complex APRIL/TACI with Long Glycosaminoglycans

Biomolecules ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1349
Author(s):  
Mateusz Marcisz ◽  
Martyna Maszota-Zieleniak ◽  
Bertrand Huard ◽  
Sergey A. Samsonov
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Protein Targets ◽  
Biologically Relevant ◽  
Hamiltonian Replica Exchange ◽  
Theoretical Approaches ◽  
B Cell Maturation ◽  
Docking Program ◽  
First Time

Glycosaminoglycans (GAGs) are linear anionic periodic polysaccharides participating in a number of biologically relevant processes in the extracellular matrix via interactions with their protein targets. Due to their periodicity, conformational flexibility, pseudo-symmetry of the sulfation pattern, and the key role of electrostatics, these molecules are challenging for both experimental and theoretical approaches. In particular, conventional molecular docking applied for GAGs longer than 10-mer experiences severe difficulties. In this work, for the first time, 24- and 48-meric GAGs were docked using all-atomic repulsive-scaling Hamiltonian replica exchange molecular dynamics (RS-REMD), a novel methodology based on replicas with van der Waals radii of interacting molecules being scaled. This approach performed well for proteins complexed with oligomeric GAGs and is independent of their length, which distinguishes it from other molecular docking approaches. We built a model of long GAGs in complex with a proliferation-inducing ligand (APRIL) prebound to its receptors, the B cell maturation antigen and the transmembrane activator and calcium modulator and cyclophilin ligand interactor (TACI). Furthermore, the prediction power of the RS-REMD for this tertiary complex was evaluated. We conclude that the TACI–GAG interaction could be potentially amplified by TACI’s binding to APRIL. RS-REMD outperformed Autodock3, the docking program previously proven the best for short GAGs.

PHOTOACOUSTIC MEASUREMENT AND MOLECULAR DYNAMICS SIMULATION FOR THERMAL CONDUCTIVITY OF Al0.3Ga0.7As

2003 ◽  
Vol 14 (01) ◽  
pp. 61-72 ◽  
Author(s):  
S. CHITRA ◽  
A. JALAL ◽  
K. RAMACHANDRAN ◽  
S. RAJAGOPAL
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Thermal Property ◽  
Dynamics Simulation ◽  
Experimental Setup ◽  
Photoacoustic Technique ◽  
Photoacoustic Measurement ◽  
First Time

The thermal conductivity of Al 0.3 Ga 0.7 As is studied using photoacoustic technique and molecular dynamics simulation. Tersoff's potential is used for the simulation, for the first time, to this alloy. Thermal conductivity, determined experimentally by photoacoustic technique using our experimental setup, agrees well with the molecular dynamics simulation and literature values. The results are compared with the host GaAs and the role of DX centers in thermal property is discussed.

scholarly journals Molecular Docking and Molecular Dynamics Studies of Role of Anti-Allergic Medicines as Inhibitors Against Covid-19

2022 ◽  
Author(s):  
Mrinal Kanti Si
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Halogen Bond ◽  
Treatment Options ◽  
Docking Studies ◽  
Dynamics Simulation ◽  
Runny Nose ◽  
Drug Molecules ◽  
Main Protease

Abstract The 2019-nCoV virus is a human-infectious coronavirus (CoV). Very few treatment options are available to healthcare professionals who are fighting this outbreak at the front. The main warning symptoms of COVID-19, the disease caused by the new coronavirus, are fever, fatigue, and a dry cough, sometimes it also causes cold-like symptoms like a runny nose which are sometimes similar to symptoms of allergies and sometimes difficult to differentiate between COVID-19 and allergies. The anti-allergic drug molecules can behave as good inhibitor against COVID-19. Molecular docking studies have been performed to examine the inhibitor properties of anti-allergic molecules against Covid-19. The searching of better inhibitors have been examined interns of various non-covalent interactions like hydrogen bond, halogen bond, vander waal’s interactions, alkyl-πand π-π interactions between small molecules (Anti-allergic medicines) with main protease of Covid-19 using molecular docking and Molecular Dynamics simulation which reveals that astemizole is best inhibitor among ten Anti-allergic drug molecules.

Interactions of molecular ions with model phospholipid membranes

2011 ◽  
Vol 76 (6) ◽  
pp. 695-711 ◽  
Author(s):  
Michal Petrov ◽  
Lukasz Cwiklik ◽  
Pavel Jungwirth
Keyword(s):  
Molecular Dynamics ◽  
Molecular Ions ◽  
The Other ◽  
Dynamics Simulation ◽  
Phospholipid Membrane ◽  
Biophysical Properties ◽  
Ion Specificity ◽  
Biologically Relevant ◽  
Lipid Diffusion ◽  
First Time

The affinities of a series of biologically relevant ions for a hydrated phospholipid membrane were investigated using molecular dynamics simulation. Interactions of molecular ions, such as guanidinium, tetramethylammonium, and thiocyanate with the bilayer were computationally characterized for the first time. Simulations reveal strong ion specificity. On one hand, ions like guanidinium and thiocyanate adsorb relatively strongly to the headgroup region of the membrane. On the other hand, potassium or chloride interact very weakly with the phospholipids and merely act as neutralizing counterions. Calculations also show that these ions affect differently biophysical properties of the membrane, such as lipid diffusion, headgroup hydration and tilt angle.

scholarly journals Nitric oxide rapidly scavenges tyrosine and tryptophan radicals

1995 ◽  
Vol 310 (3) ◽  
pp. 745-749 ◽  
Author(s):  
J P Eiserich ◽  
J Butler ◽  
A van der Vliet ◽  
C E Cross ◽  
B Halliwell
Keyword(s):  
Nitric Oxide ◽  
Biologically Relevant ◽  
Tyrosine Residues ◽  
Transfer Processes ◽  
Diffusion Controlled ◽  
Electron Transfer Processes ◽  
Protein Radicals ◽  
First Time

By utilizing a pulse-radiolytic technique, we demonstrate for the first time that the rate constant for the reaction of nitric oxide (.NO) with biologically relevant tyrosine and tryptophan radicals (Tyr. and Trp. respectively) in amino acids, peptides and proteins is of the order of (1-2) x 10(9) M-1.s-1. We also show that .NO effectively interferes with electron-transfer processes between tryptophan and tyrosine residues in proteins subjected to pulse radiolysis. The near diffusion-controlled rates of these reactions, coupled with the increasingly recognized role of protein radicals in enzyme catalysis and oxidative damage, suggest that Tyr. and Trp. are likely and important targets for .NO generated in vivo.

Psychological Resilience Provides No Independent Protection From Suicidal Risk

Crisis ◽  
2016 ◽  
Vol 37 (2) ◽  
pp. 130-139 ◽  
Author(s):  
Danica W. Y. Liu ◽  
A. Kate Fairweather-Schmidt ◽  
Richard Burns ◽  
Rachel M. Roberts ◽  
Kaarin J. Anstey
Keyword(s):  
Risk Factors ◽  
Well Being ◽  
Current Status ◽  
Psychological Resilience ◽  
Cross Sectional ◽  
Life Project ◽  
Resilience Factors ◽  
First Time

Abstract. Background: Little is known about the role of resilience in the likelihood of suicidal ideation (SI) over time. Aims: We examined the association between resilience and SI in a young-adult cohort over 4 years. Our objectives were to determine whether resilience was associated with SI at follow-up or, conversely, whether SI was associated with lowered resilience at follow-up. Method: Participants were selected from the Personality and Total Health (PATH) Through Life Project from Canberra and Queanbeyan, Australia, aged 28–32 years at the first time point and 32–36 at the second. Multinomial, linear, and binary regression analyses explored the association between resilience and SI over two time points. Models were adjusted for suicidality risk factors. Results: While unadjusted analyses identified associations between resilience and SI, these effects were fully explained by the inclusion of other suicidality risk factors. Conclusion: Despite strong cross-sectional associations, resilience and SI appear to be unrelated in a longitudinal context, once risk/resilience factors are controlled for. As independent indicators of psychological well-being, suicidality and resilience are essential if current status is to be captured. However, the addition of other factors (e.g., support, mastery) makes this association tenuous. Consequently, resilience per se may not be protective of SI.

New Insights into the Nature of the Band Gap of CuGeO3 Nanoparticles: Synthesis, Electronic Structure, and Optical and Photocatalytic Properties

2019 ◽  
Author(s):  
Victor Y. Suzuki ◽  
Luís Henrique Cardozo Amorin ◽  
Natália H. de Paula ◽  
Anderson R. Albuquerque ◽  
Julio Ricardo Sambrano ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Band Gap ◽  
Material Design ◽  
Photocatalytic Properties ◽  
Critical Parameters ◽  
Synthetic Approach ◽  
Microwave Assisted ◽  
Theoretical Approaches ◽  
Nanoparticles Synthesis ◽  
First Time

<p>We report, for the first time, new insights into the nature of the band gap of <a>CuGeO<sub>3</sub> </a>(CGO) nanocrystals synthesized from a microwave-assisted hydrothermal method in the presence of citrate. To the best of our knowledge, this synthetic approach has the shortest reaction time and it works at the lowest temperatures reported in the literature for the preparation of these materials. The influence of the surfactant on the structural, electronic, optical, and photocatalytic properties of CGO nanocrystals is discussed by a combination of experimental and theoretical approaches, and that results elucidates the nature of the band gap of synthetized CGO nanocrystals. We believe that this particular strategy is one of the most critical parameters for the development of innovative applications and that result could shed some light on the emerging material design with entirely new properties.</p> <p><b> </b></p>

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