scholarly journals Measurement and modelling solubility of amino acids and peptides in aqueous 2-propanol solutions

Author(s):  
Hoang Tam Do ◽  
Patrick Franke ◽  
Sophia Volpert ◽  
Marcel Klinksiek ◽  
Max Thome ◽  
...  

In this work the solubility of 15 amino acids and 18 peptides in aqueous 2-propanol solutions was successfully modelled using PC-SAFT that used recently determined experimental melting properties as input data.

RSC Advances ◽  
2018 ◽  
Vol 8 (12) ◽  
pp. 6365-6372 ◽  
Author(s):  
Yeong Zen Chua ◽  
Hoang Tam Do ◽  
Christoph Schick ◽  
Dzmitry Zaitsau ◽  
Christoph Held

New experimental melting properties combined with PC-SAFT allow quantitative solubility predictions of amino acids in water.


2019 ◽  
Author(s):  
Thammakorn Saethang ◽  
Kenneth Hodge ◽  
Chin-Rang Yang ◽  
Yue Zhao ◽  
Ingorn Kimkong ◽  
...  

Abstract Summary Identification of the amino-acid motifs in proteins that are targeted for post-translational modifications (PTMs) is of great importance in understanding regulatory networks. Information about targeted motifs can be derived from mass spectrometry data that identify peptides containing specific PTMs such as phosphorylation, ubiquitylation and acetylation. Comparison of input data against a standardized ‘background’ set allows identification of over- and under-represented amino acids surrounding the modified site. Conventionally, calculation of targeted motifs assumes a random background distribution of amino acids surrounding the modified position. However, we show that probabilities of amino acids depend on (i) the type of the modification and (ii) their positions relative to the modified site. Thus, software that identifies such over- and under-represented amino acids should make appropriate adjustments for these effects. Here we present a new program, PTM-Logo, that generates representations of these amino acid preferences (‘logos’) based on position-specific amino-acid probability backgrounds calculated either from user-input data or curated databases. Availability and implementation PTM-Logo is freely available online at http://sysbio.chula.ac.th/PTMLogo/ or https://hpcwebapps.cit.nih.gov/PTMLogo/. Supplementary information Supplementary data are available at Bioinformatics online.


2021 ◽  
Author(s):  
Yeong Zen Chua ◽  
Hoang Tam Do ◽  
Aarti Kumar ◽  
Moritz Hallermann ◽  
Dzmitry Zaitsau ◽  
...  

Abstract Saccharides are still commonly isolated from biological feedstock by crystallization from aqueous solutions. Precise thermodynamic data on solubility are essential to optimize the downstream crystallization process. Solubility modeling, in turn, requires knowledge of melting properties. In the first part of this work, following our previous work on amino acids and peptides, D-α-glucose, D-β-fructose, D-sucrose, D-α-galactose, and D-α-xylose were investigated with Fast Scanning Calorimetry (FSC) in a wide scanning rate range (2000 K·s−1 to 10000 K·s−1). Using the experimental melting properties of saccharides from FSC allowed successfully modeling aqueous solubility for D-sucrose and D-α-galactose with the equation of state PC-SAFT. This provides cross-validation of the measurement methods to determine accurate experimental melting properties with FSC. Unexpectedly, the experimental FSC melting temperatures, extrapolated to zero scanning rates for thermal lag correction, were higher than results determined with DSC and available literature data. To clarify this inconsistency, FSC measurements towards low scanning rates from 10000 K·s−1 to 1 K·s−1 (D-α-glucose, D-β-fructose, D-sucrose) overlapping with the scanning rates of DSC and literature data were combined. At scanning rates below 1000 K·s−1, the melting properties followed a consistent non-linear trend, observed in both the FSC and the literature data. In order to understand the non-linear decrease of apparent melting temperatures with decreasing heating rate, the endothermic peaks were investigated in terms of isoconversional kinetics. The activation energies in the non-linear dependency region are in the range of $$300<{E}_{A}< 600 {\text{kJ}}\bullet {\text{mo}}{\text{l}}^{-1}$$ 300 < E A < 600 kJ ∙ mol - 1 . These values are higher than the enthalpy of sublimation for D-α-glucose, indicating that the non-linear behavior does not have a physical nature but attributes to chemical processes corresponding to the decomposition of molecular compounds within the crystal lattice before melting. The melting properties reported in the literature, commonly determined with conventional methods such as DSC, lead to inaccurate results due to the decomposition of these biomolecules at low heating rates. In addition, the FSC results at lower scanning rates coincide with results from DSC and literature in the overlapping scanning rate range, further validating the accuracy of FSC measurements to determine reliable melting properties of thermally labile biomolecules. The experimental FSC melting properties determined at higher scanning rates are considered as the correct equilibrium melting properties, which are not influenced by any chemical processes. The combination of FSC and PC-SAFT opens the door to model solubility of solid compounds that commonly decompose before melting.


Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4475
Author(s):  
Atsushi Yoshimori

Prediction of molecular properties plays a critical role towards rational drug design. In this study, the Molecular Topographic Map (MTM) is proposed, which is a two-dimensional (2D) map that can be used to represent a molecule. An MTM is generated from the atomic features set of a molecule using generative topographic mapping and is then used as input data for analyzing structure-property/activity relationships. In the visualization and classification of 20 amino acids, differences of the amino acids can be visually confirmed from and revealed by hierarchical clustering with a similarity matrix of their MTMs. The prediction of molecular properties was performed on the basis of convolutional neural networks using MTMs as input data. The performance of the predictive models using MTM was found to be equal to or better than that using Morgan fingerprint or MACCS keys. Furthermore, data augmentation of MTMs using mixup has improved the prediction performance. Since molecules converted to MTMs can be treated like 2D images, they can be easily used with existing neural networks for image recognition and related technologies. MTM can be effectively utilized to predict molecular properties of small molecules to aid drug discovery research.


RSC Advances ◽  
2020 ◽  
Vol 10 (72) ◽  
pp. 44205-44215 ◽  
Author(s):  
Hoang Tam Do ◽  
Yeong Zen Chua ◽  
Aarti Kumar ◽  
Daniel Pabsch ◽  
Moritz Hallermann ◽  
...  

We report the melting properties of amino acids for the first time and highlight the usefulness of such data to predict material properties such as aqueous solubility of amino acids.


1997 ◽  
Vol 161 ◽  
pp. 505-510
Author(s):  
Alexandra J. MacDermott ◽  
Laurence D. Barron ◽  
Andrè Brack ◽  
Thomas Buhse ◽  
John R. Cronin ◽  
...  

AbstractThe most characteristic hallmark of life is its homochirality: all biomolecules are usually of one hand, e.g. on Earth life uses only L-amino acids for protein synthesis and not their D mirror images. We therefore suggest that a search for extra-terrestrial life can be approached as a Search for Extra- Terrestrial Homochirality (SETH). The natural choice for a SETH instrument is optical rotation, and we describe a novel miniaturized space polarimeter, called the SETH Cigar, which could be used to detect optical rotation as the homochiral signature of life on other planets. Moving parts are avoided by replacing the normal rotating polarizer by multiple fixed polarizers at different angles as in the eye of the bee. We believe that homochirality may be found in the subsurface layers on Mars as a relic of extinct life, and on other solar system bodies as a sign of advanced pre-biotic chemistry. We discuss the chiral GC-MS planned for the Roland lander of the Rosetta mission to a comet and conclude with theories of the physical origin of homochirality.


1997 ◽  
Vol 161 ◽  
pp. 179-187
Author(s):  
Clifford N. Matthews ◽  
Rose A. Pesce-Rodriguez ◽  
Shirley A. Liebman

AbstractHydrogen cyanide polymers – heterogeneous solids ranging in color from yellow to orange to brown to black – may be among the organic macromolecules most readily formed within the Solar System. The non-volatile black crust of comet Halley, for example, as well as the extensive orangebrown streaks in the atmosphere of Jupiter, might consist largely of such polymers synthesized from HCN formed by photolysis of methane and ammonia, the color observed depending on the concentration of HCN involved. Laboratory studies of these ubiquitous compounds point to the presence of polyamidine structures synthesized directly from hydrogen cyanide. These would be converted by water to polypeptides which can be further hydrolyzed to α-amino acids. Black polymers and multimers with conjugated ladder structures derived from HCN could also be formed and might well be the source of the many nitrogen heterocycles, adenine included, observed after pyrolysis. The dark brown color arising from the impacts of comet P/Shoemaker-Levy 9 on Jupiter might therefore be mainly caused by the presence of HCN polymers, whether originally present, deposited by the impactor or synthesized directly from HCN. Spectroscopic detection of these predicted macromolecules and their hydrolytic and pyrolytic by-products would strengthen significantly the hypothesis that cyanide polymerization is a preferred pathway for prebiotic and extraterrestrial chemistry.


Author(s):  
R.A. Ploc ◽  
G.H. Keech

An unambiguous analysis of transmission electron diffraction effects requires two samplings of the reciprocal lattice (RL). However, extracting definitive information from the patterns is difficult even for a general orthorhombic case. The usual procedure has been to deduce the approximate variables controlling the formation of the patterns from qualitative observations. Our present purpose is to illustrate two applications of a computer programme written for the analysis of transmission, selected area diffraction (SAD) patterns; the studies of RL spot shapes and epitaxy.When a specimen contains fine structure the RL spots become complex shapes with extensions in one or more directions. If the number and directions of these extensions can be estimated from an SAD pattern the exact spot shape can be determined by a series of refinements of the computer input data.


Author(s):  
E.M. Kuhn ◽  
K.D. Marenus ◽  
M. Beer

Fibers composed of different types of collagen cannot be differentiated by conventional electron microscopic stains. We are developing staining procedures aimed at identifying collagen fibers of different types.Pt(Gly-L-Met)Cl binds specifically to sulfur-containing amino acids. Different collagens have methionine (met) residues at somewhat different positions. A good correspondence has been reported between known met positions and Pt(GLM) bands in rat Type I SLS (collagen aggregates in which molecules lie adjacent to each other in exact register). We have confirmed this relationship in Type III collagen SLS (Fig. 1).


Author(s):  
R. W. Yaklich ◽  
E. L. Vigil ◽  
W. P. Wergin

The legume seed coat is the site of sucrose unloading and the metabolism of imported ureides and synthesis of amino acids for the developing embryo. The cell types directly responsible for these functions in the seed coat are not known. We recently described a convex layer of tissue on the inside surface of the soybean (Glycine max L. Merr.) seed coat that was termed “antipit” because it was in direct opposition to the concave pit on the abaxial surface of the cotyledon. Cone cells of the antipit contained numerous hypertrophied Golgi apparatus and laminated rough endoplasmic reticulum common to actively secreting cells. The initial report by Dzikowski (1936) described the morphology of the pit and antipit in G. max and found these structures in only 68 of the 169 seed accessions examined.


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