scholarly journals Quantitative prediction of charge regulation in oligopeptides

Author(s):  
Raju Lunkad ◽  
Anastasiia Murmiliuk ◽  
Pascal Hebbeker ◽  
Milan Boublík ◽  
Zdeněk Tošner ◽  
...  

Charge regulation in the peptide Glu5–His5 as a model weak ampholyte: simulations predict deviations from the ideal ionization of free aminoacids, in quantitative agreement with experiments.

2020 ◽  
Author(s):  
Raju Lunkad ◽  
Anastasiia Murmiliuk ◽  
Pascal Hebbeker ◽  
Milan Boublík ◽  
Zdeněk Tošner ◽  
...  

Weak ampholytes are ubiquitous in nature and commonly found in artificial pH-responsive systems. However, our limited understanding of their charge regulation and the lack of predictive capabilities hinder the bottom-up design of such systems. Here, we used a coarse-grained model of a flexible polymer with weakly ionisable monomer units to quantitatively analyse the ionisation behaviour of two oligopeptides. Our model predicts differences in the charge states between oligopeptides and monomeric amino acids, showing that conformational flexibility and electrostatic interactions between weak acid and base side chains play a key role in the charge regulation. By comparing our simulations with experimental results from potentiometric titration, capillary zone electrophoresis and NMR, we demonstrated that our model reliably predicts the charge state of various peptide sequences. Ultimately, our model is the first step towards understanding the charge regualtion in flexible disordered proteins, and towards using predictive bottom-up design of responsive ampholytes to tailor their<br>properties as a function of charge and pH.<br>


MRS Advances ◽  
2019 ◽  
Vol 5 (12-13) ◽  
pp. 679-691
Author(s):  
Rainhard Machatschek ◽  
Shivam Saretia ◽  
Andreas Lendlein

ABSTRACTNetwork formation by cross-linking is a common method to incorporate functions like elastic deformability, shape-memory capability or hydrogel formation into polymer materials for medical applications. Since these materials are often intended to degrade, their design would benefit from a quantitative prediction of the interdependence between network architecture and degradation behavior. Here, we introduce a quantitative description of the degradation behavior of polymer networks. A simplified model was developed under the assumption of having an ideal network, where all network strands are terminated by network nodes and each node is connected to the same number of strands. To describe the degradation of real networks, the model was modified by allowing for a varying connectivity of network nodes, which also included free chain-ends. The models were validated by comparison with Langmuir monolayer degradation data from 2D networks formed by cross-linking oligo(ε-caprolactone)diols with dialdehydes. We found that both the ideal network hypothesis and the real network model were in excellent agreement with the experimental data, with the ideal network hypothesis requiring longer network strands than the real network to result in the same degradation behavior. The models were further used to calculate the degradation curves of the corresponding, non cross-linked molecules. By comparison, it was found that the network formation increases the time required to reach 50% degradation of oligo(ε-caprolactone)diols by only 20%. This difference mainly arises from attaching free chain ends to network points.


2020 ◽  
Author(s):  
Raju Lunkad ◽  
Anastasiia Murmiliuk ◽  
Pascal Hebbeker ◽  
Milan Boublík ◽  
Zdeněk Tošner ◽  
...  

Weak ampholytes are ubiquitous in nature and commonly found in artificial pH-responsive systems. However, our limited understanding of their charge regulation and the lack of predictive capabilities hinder the bottom-up design of such systems. Here, we used a coarse-grained model of a flexible polymer with weakly ionisable monomer units to quantitatively analyse the ionisation behaviour of two oligopeptides. Our model predicts differences in the charge states between oligopeptides and monomeric amino acids, showing that conformational flexibility and electrostatic interactions between weak acid and base side chains play a key role in the charge regulation. By comparing our simulations with experimental results from potentiometric titration, capillary zone electrophoresis and NMR, we demonstrated that our model reliably predicts the charge state of various peptide sequences. Ultimately, our model is the first step towards understanding the charge regualtion in flexible disordered proteins, and towards using predictive bottom-up design of responsive ampholytes to tailor their<br>properties as a function of charge and pH.<br>


2020 ◽  
Author(s):  
Raju Lunkad ◽  
Anastasiia Murmiliuk ◽  
Pascal Hebbeker ◽  
Milan Boublík ◽  
Zdeněk Tošner ◽  
...  

Weak ampholytes are ubiquitous in nature and commonly found in artificial pH-responsive systems. However, our limited understanding of their charge regulation and the lack of predictive capabilities hinder the bottom-up design of such systems. Here, we used a coarse-grained model of a flexible polymer with weakly ionisable monomer units to quantitatively analyse the ionisation behaviour of two oligopeptides. Our model predicts differences in the charge states between oligopeptides and monomeric amino acids, showing that conformational flexibility and electrostatic interactions between weak acid and base side chains play a key role in the charge regulation. By comparing our simulations with experimental results from potentiometric titration, capillary zone electrophoresis and NMR, we demonstrated that our model reliably predicts the charge state of various peptide sequences. Ultimately, our model is the first step towards understanding the charge regualtion in flexible disordered proteins, and towards using predictive bottom-up design of responsive ampholytes to tailor their<br>properties as a function of charge and pH.<br>


1994 ◽  
Vol 51 (3) ◽  
pp. 381-398
Author(s):  
Wenlong Dai ◽  
Paul R. Woodward

A Riemann solver is used, and a set of numerical simulations are performed, to study the structures of reconnection layers in the approximation of the one- dimensional ideal MHD equations. Since the Riemann solver may solve general Riemarin problems, the model used in this paper is more general than those in previous investigations on this problem. Under the conditions used in the previous investigations, the structures we obtained are the same. Our numerical simulations show quantitative agreement with those obtained through the Riemann solver.


1996 ◽  
Vol 118 (3) ◽  
pp. 582-588 ◽  
Author(s):  
Hiroharu Kato ◽  
Akihisa Konno ◽  
Masatsugu Maeda ◽  
Hajime Yamaguchi

A scenario for quantitative prediction of cavitation erosion was proposed. The key value is the impact force/pressure spectrum on a solid surface caused by cavitation bubble collapse. As the first step of prediction, the authors constructed the scenario from an estimation of the cavity generation rate to the prediction of impact force spectrum, including the estimations of collapsing cavity number and impact pressure. The prediction was compared with measurements of impact force spectra on a partially cavitating hydrofoil. A good quantitative agreement was obtained between the prediction and the experiment. However, the present method predicted a larger effect of main flow velocity than that observed. The present scenario is promising as a method of predicting erosion without using a model test.


Author(s):  
M.S. Shahrabadi ◽  
T. Yamamoto

The technique of labeling of macromolecules with ferritin conjugated antibody has been successfully used for extracellular antigen by means of staining the specimen with conjugate prior to fixation and embedding. However, the ideal method to determine the location of intracellular antigen would be to do the antigen-antibody reaction in thin sections. This technique contains inherent problems such as the destruction of antigenic determinants during fixation or embedding and the non-specific attachment of conjugate to the embedding media. Certain embedding media such as polyampholytes (2) or cross-linked bovine serum albumin (3) have been introduced to overcome some of these problems.


Author(s):  
R. A. Crowther

The reconstruction of a three-dimensional image of a specimen from a set of electron micrographs reduces, under certain assumptions about the imaging process in the microscope, to the mathematical problem of reconstructing a density distribution from a set of its plane projections.In the absence of noise we can formulate a purely geometrical criterion, which, for a general object, fixes the resolution attainable from a given finite number of views in terms of the size of the object. For simplicity we take the ideal case of projections collected by a series of m equally spaced tilts about a single axis.


Author(s):  
R. Beeuwkes ◽  
A. Saubermann ◽  
P. Echlin ◽  
S. Churchill

Fifteen years ago, Hall described clearly the advantages of the thin section approach to biological x-ray microanalysis, and described clearly the ratio method for quantitive analysis in such preparations. In this now classic paper, he also made it clear that the ideal method of sample preparation would involve only freezing and sectioning at low temperature. Subsequently, Hall and his coworkers, as well as others, have applied themselves to the task of direct x-ray microanalysis of frozen sections. To achieve this goal, different methodological approachs have been developed as different groups sought solutions to a common group of technical problems. This report describes some of these problems and indicates the specific approaches and procedures developed by our group in order to overcome them. We acknowledge that the techniques evolved by our group are quite different from earlier approaches to cryomicrotomy and sample handling, hence the title of our paper. However, such departures from tradition have been based upon our attempt to apply basic physical principles to the processes involved. We feel we have demonstrated that such a break with tradition has valuable consequences.


Author(s):  
G. Van Tendeloo ◽  
J. Van Landuyt ◽  
S. Amelinckx

Polytypism has been studied for a number of years and a wide variety of stacking sequences has been detected and analysed. SiC is the prototype material in this respect; see e.g. Electron microscopy under high resolution conditions when combined with x-ray measurements is a very powerful technique to elucidate the correct stacking sequence or to study polytype transformations and deviations from the ideal stacking sequence.


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