IgG1 conformational behavior: elucidation of the N-glycosylation role via molecular dynamics

2021 ◽  
Author(s):  
Simona Saporiti ◽  
Chiara Parravicini ◽  
Carlo Pergola ◽  
Uliano Guerrini ◽  
Mara Rossi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Conformational Behavior

Charge Distribution and Conformations of Weak Polyelectrolyte Chains in Poor Solvents

2008 ◽  
Vol 73 (4) ◽  
pp. 439-458 ◽  
Author(s):  
Peter Košovan ◽  
Zuzana Limpouchová ◽  
Karel Procházka
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
Charge Distribution ◽  
The Other ◽  
Conformational Behavior ◽  
Local Degree ◽  
Simulation Techniques

In this work we study the effect of mobility of charges in annealed polyelectrolytes on their conformational behavior in poor solvents. A combination of molecular dynamics and Monte Carlo simulation techniques was used to take the dissociation into account. We investigated the relation between the conformation of the polyelectrolyte and the distribution of charges along the chain. The results suggest that in sufficiently poor solvents the local degree of charging differs significantly from the average. When a pearl-necklace conformation is formed, the degree of charging of the pearls is significantly lower than that of the strings. The redistribution of charges stabilizes the pearl-necklace conformation and enables the formation of asymmetric conformations with a single pearl at one chain end and a string at the other end.

scholarly journals Adsorption of Silicon-Containing Dendrimers: Effects of Chemical Composition, Structure, and Generation Number

Polymers ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 552
Author(s):  
Andrey O. Kurbatov ◽  
Nikolay K. Balabaev ◽  
Mikhail A. Mazo ◽  
Elena Yu. Kramarenko
Keyword(s):  
Molecular Dynamics ◽  
Functional Materials ◽  
Md Simulations ◽  
Conformational Behavior ◽  
Carbosilane Dendrimers ◽  
Density Profiles ◽  
The Core ◽  
Adsorbed Atoms ◽  
Composition Structure ◽  
Surface Spreading

We studied the conformational behavior of silicon-containing dendrimers during their adsorption onto a flat impenetrable surface by molecular dynamics (MD) simulations. Four homologous series of dendrimers from the 4th up to the 7th generations were modeled, namely, two types of carbosilane dendrimers differing by the functionality of the core Si atom and two types of siloxane dendrimers with different lengths of the spacers. Comparative analysis of the fractions of adsorbed atoms belonging to various structural layers within dendrimers as well as density profiles allowed us to elucidate not only some general trends but also the effects determined by dendrimer specificity. In particular, it was found that in contrast to the carbosilane dendrimers interacting with the adsorbing surface mainly by their peripheral layers, the siloxane dendrimers with the longer –O–Si(CH3)2–O spacers expose atoms from their interior to the surface spreading out on it. These findings are important for the design of functional materials on the basis of silicon-containing dendrimers.

scholarly journals Functional and Structural Analysis of Predicted Proteins Obtained from Homo sapiens’ Minisatellite 33.15-Tagged Transcript pAKT-45 Variants

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Mohd Shahbaaz ◽  
Awad Saeed Al-Samghan ◽  
Arshi Malik ◽  
Sarah Afaq ◽  
Afaf S. Alwabli ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Homo Sapiens ◽  
Md Simulations ◽  
Early Embryogenesis ◽  
Cellular Proteins ◽  
Conformational Behavior ◽  
Gene Functions ◽  
Mrna Transcripts ◽  
Water Conditions ◽  
Explicit Water

The spermatozoa are transcriptionally dormant entities which have been recognized to be an archive of mRNA, coding for a variety of functionally crucial cellular proteins. This significant repository of mRNA is predicted to be associated with early embryogenesis and postfertilization. The mRNA transcripts which are tagged with minisatellites have been involved in the regulation of the gene functions as well as their organization. However, very little information is available regarding the expression of the transcripts tagged with minisatellites in spermatozoa. Therefore, in order to understand the functions and the conformational behavior of the proteins expressed from these minisatellite-tagged transcripts, we have performed a detailed in silico analysis using the sequences of the transcripts. The protein predicted from KF274549 showed the functionalities similar to uncharacterized C4orf26 proteins, while that obtained from KF274557 predicted to be a metallophosphoesterase. Furthermore, the structural folds in the structure of these predicted proteins were analyzed by using the homology modeling and their conformational behaviors in the explicit water conditions were analyzed by using the techniques of Molecular Dynamics (MD) simulations. This detailed analysis will facilitate the understanding of these proteins in the spermatozoon region and can be used for uncovering other attributes of the metabolic network.

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