Study on molecular modeling and the difference of PC lipase-catalyzed degradation of poly (butylene succinate) copolymers modified by linear monomers

2015 ◽  
Vol 116 ◽  
pp. 75-80 ◽  
Author(s):  
Cheng-tao Li ◽  
Min Zhang ◽  
Jia-xiang Qin ◽  
Yi Zhang ◽  
Jian-hui Qiu
RSC Advances ◽  
2016 ◽  
Vol 6 (22) ◽  
pp. 17896-17905 ◽  
Author(s):  
Jia-xiang Qin ◽  
Min Zhang ◽  
Chi Zhang ◽  
Cheng-tao Li ◽  
Yi Zhang ◽  
...  

In the present work, the difference of enzymatic degradation of PBS-based polyesters was investigated from the molecular level with molecular modeling.


2019 ◽  
Vol 15 ◽  
pp. 2982-2989 ◽  
Author(s):  
Enrique A Del Vigo ◽  
Carlos A Stortz ◽  
Carla Marino

Regioselective glycosylations allow planning simpler strategies for the synthesis of oligosaccharides, and thus reducing the need of using protecting groups. With the idea of gaining further understanding of such regioselectivity, we analyzed the relative reactivity of the OH-3 and OH-4 groups of 2,6-diprotected methyl α- and β-galactopyranoside derivatives in glycosylation reactions. The glycosyl acceptors were efficiently prepared by simple methodologies, and glycosyl donors with different reactivities were assessed. High regioselectivities were achieved in favor of the 1→3 products due to the equatorial orientation of the OH-3 group. A molecular modeling approach endorsed this general trend of favoring O-3 substitution, although it showed some failures to explain subtler factors governing the difference in regioselectivity between some of the acceptors. However, the Galp-(β1→3)-Galp linkage could be regioselectively installed by using some of the acceptors assayed herein.


2020 ◽  
Author(s):  
Ya.V. Solovev ◽  
A.A. Igolkina ◽  
P.O. Kuliaev ◽  
A.S. Sulima ◽  
V.A. Zhukov ◽  
...  

AbstractThe difference in symbiotic specificity between peas of Afghanistan and European phenotypes was interrogated using molecular modeling. Considering segregating amino acid polymorphism, we examined interactions of pea LykX-Sym10 receptor heterodimers with four forms of Nod factor (NF) that varied in natural decorations (acetylation and length of the glucosamine chain). First, we showed the stability of the LykX-Sym10 dimer during molecular dynamics (MD) in solvent and in the presence of a membrane. Then, four NFs were separately docked to one European and two Afghanistan dimers, and the results of these interactions were in line with corresponding pea symbiotic phenotypes. The European variant of the LykX-Sym10 dimer effectively interacts with both acetylated and non-acetylated forms of NF, while the Afghanistan variants successfully interact with the acetylated form only. We additionally demonstrated that the length of the NF glucosamine chain contributes to controlling the effectiveness of the symbiotic interaction. The obtained results support a recent hypothesis that the LykX gene is a suitable candidate for the unidentified Sym2 allele, the determinant of pea specificity towards Rhizobium leguminosarum bv. viciae strains producing NFs with or without an acetylation decoration. The developed modeling methodology demonstrated its power in multiple searches for genetic determinants, when experimental detection of such determinants has proven extremely difficult.


2019 ◽  
Vol 65 (2) ◽  
pp. 86-90 ◽  
Author(s):  
N.A. Zefirov ◽  
E.A. Lavrushkina ◽  
S.A. Kuznetsov ◽  
O.N. Zefirova

C4-Ester derivatives of the anticancer agent podophyllotoxin with bridged moieties can either inhibit polymerization of alpha,beta-tubulin with the formation of microtubules (analogously to the parent molecule) or cause an unusual effect of “curling and shortening” of the microtubules (MT). In order to predict the effect of bridged podophyllotoxin derivatives on the MT network using computer molecular modeling it is desirable to enhance the structural diversity of their bridged substituents. In the present work we synthesized novel podophyllotoxin ester with bicyclo[3.2.1]octane moiety annelated with indole core. The target compound was obtained by Steglich esterification of podophyllotoxin by rac-exo-(indolo[2,3-b])bicyclo[3.2.1]oct-2-ene-6-carboxylic acid as diastereomeric (6RS,8SR,9RS) mixture, which could not be separated by thin layer or preparative column chromatography on silica gel. Results of biotesting of 4-O-{(6R,8S,9R)-5,6,7,8,9,10-hexahydro-6,9-methanocyclohepto[b]indol-8-ylcarbonyl}-Lpodophyllotoxin on the carcinoma A549 cells proved its ability to cause full depolymerization of microtubules without curling effect at a concentration 10 μM. Cytotoxicity value of the compound estimated in MTT test was in a high nanomolar concentration interval (EC50=710±30 nM). Computer molecular docking of both isomers of novel compound and earlier synthesized podophyllotoxin esters with bridged moieties into the 3D model of the colchicine domain in alpha,beta-tubulin revealed the difference in positions of the bridge moieties of new compound and MT-curling ligands and allowed to hypothesize that the atypical action on MT might be caused by positioning of their bridge groups near the GTP binding site in alpha-tubulin.


Biomolecules ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 579 ◽  
Author(s):  
Weronika Wanat ◽  
Michał Talma ◽  
Błażej Dziuk ◽  
Jean-Luc Pirat ◽  
Paweł Kafarski

A library of phosphonic acid analogs of phenylalanine substituted with fluorine, chlorine and trifluoromethyl moieties on the aromatic ring was synthesized and evaluated for inhibitory activity against human (hAPN) and porcine (pAPN) aminopeptidases. Fluorogenic screening indicated that these analogs are micromolar or submicromolar inhibitors, both enzymes being more active against hAPN. In order to better understand the mode of the action of the most active compounds, molecular modeling was used. It confirmed that aminophosphonic portion of the enzyme is bound nearly identically in the case of all the studied compounds, whereas the difference in activity results from the placement of aromatic side chain of an inhibitor. Interestingly, both enantiomers of the individual compounds are usually bound quite similarly.


2021 ◽  
Vol 12 ◽  
Author(s):  
Yaroslav V. Solovev ◽  
Anna A. Igolkina ◽  
Pavel O. Kuliaev ◽  
Anton S. Sulima ◽  
Vladimir A. Zhukov ◽  
...  

The difference in symbiotic specificity between peas of Afghanistan and European phenotypes was investigated using molecular modeling. Considering segregating amino acid polymorphism, we examined interactions of pea LykX-Sym10 receptor heterodimers with four forms of Nodulation factor (NF) that varied in natural decorations (acetylation and length of the glucosamine chain). First, we showed the stability of the LykX-Sym10 dimer during molecular dynamics (MD) in solvent and in the presence of a membrane. Then, four NFs were separately docked to one European and two Afghanistan dimers, and the results of these interactions were in line with corresponding pea symbiotic phenotypes. The European variant of the LykX-Sym10 dimer effectively interacts with both acetylated and non-acetylated forms of NF, while the Afghanistan variants successfully interact with the acetylated form only. We additionally demonstrated that the length of the NF glucosamine chain contributes to controlling the effectiveness of the symbiotic interaction. The obtained results support a recent hypothesis that the LykX gene is a suitable candidate for the unidentified Sym2 allele, the determinant of pea specificity toward Rhizobium leguminosarum bv. viciae strains producing NFs with or without an acetylation decoration. The developed modeling methodology demonstrated its power in multiple searches for genetic determinants, when experimental detection of such determinants has proven extremely difficult.


1962 ◽  
Vol 14 ◽  
pp. 149-155 ◽  
Author(s):  
E. L. Ruskol

The difference between average densities of the Moon and Earth was interpreted in the preceding report by Professor H. Urey as indicating a difference in their chemical composition. Therefore, Urey assumes the Moon's formation to have taken place far away from the Earth, under conditions differing substantially from the conditions of Earth's formation. In such a case, the Earth should have captured the Moon. As is admitted by Professor Urey himself, such a capture is a very improbable event. In addition, an assumption that the “lunar” dimensions were representative of protoplanetary bodies in the entire solar system encounters great difficulties.


1997 ◽  
Vol 161 ◽  
pp. 491-504 ◽  
Author(s):  
Frances Westall

AbstractThe oldest cell-like structures on Earth are preserved in silicified lagoonal, shallow sea or hydrothermal sediments, such as some Archean formations in Western Australia and South Africa. Previous studies concentrated on the search for organic fossils in Archean rocks. Observations of silicified bacteria (as silica minerals) are scarce for both the Precambrian and the Phanerozoic, but reports of mineral bacteria finds, in general, are increasing. The problems associated with the identification of authentic fossil bacteria and, if possible, closer identification of bacteria type can, in part, be overcome by experimental fossilisation studies. These have shown that not all bacteria fossilise in the same way and, indeed, some seem to be very resistent to fossilisation. This paper deals with a transmission electron microscope investigation of the silicification of four species of bacteria commonly found in the environment. The Gram positiveBacillus laterosporusand its spore produced a robust, durable crust upon silicification, whereas the Gram negativePseudomonas fluorescens, Ps. vesicularis, andPs. acidovoranspresented delicately preserved walls. The greater amount of peptidoglycan, containing abundant metal cation binding sites, in the cell wall of the Gram positive bacterium, probably accounts for the difference in the mode of fossilisation. The Gram positive bacteria are, therefore, probably most likely to be preserved in the terrestrial and extraterrestrial rock record.


1994 ◽  
Vol 144 ◽  
pp. 421-426
Author(s):  
N. F. Tyagun

AbstractThe interrelationship of half-widths and intensities for the red, green and yellow lines is considered. This is a direct relationship for the green and yellow line and an inverse one for the red line. The difference in the relationships of half-widths and intensities for different lines appears to be due to substantially dissimilar structuring and to a set of line-of-sight motions in ”hot“ and ”cold“ corona regions.When diagnosing the coronal plasma, one cannot neglect the filling factor - each line has such a factor of its own.


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