scholarly journals Alpha-helical folding of SilE models upon Ag(His)(Met) motif formation

2018 ◽  
Vol 54 (74) ◽  
pp. 10419-10422 ◽  
Author(s):  
Valentin Chabert ◽  
Maggy Hologne ◽  
Olivier Sénèque ◽  
Olivier Walker ◽  
Katharina M. Fromm

The first structures and silver binding affinities of SilE key sequences provide insights in the functioning of the Sil system.

2012 ◽  
Vol 84 (4) ◽  
pp. 953-964 ◽  
Author(s):  
Jae-min Suk ◽  
Min Kyung Chae ◽  
Kyu-Sung Jeong

A number of indolocarbazole-based anion receptors were prepared and their anion-binding behaviors were characterized in solution and in the solid state. First, chain-length-dependent binding affinities of chloride ion were revealed using a series of indolocarbazoles that consisted of one to four indolocarbazole units. The binding affinities were steadily enhanced from monomer to dimer, then to trimer by Gibb’s free energy (–∆∆G) = 2.4 ± 0.1 kcal/mol, and then nearly saturated. Second, a water-soluble trimer folded to generate an internal helical cavity with six convergent NHs, wherein small halides bound in water in the order of Cl– (65 M–1) > F– (46 M–1), and Br– (19 M–1). Third, X-ray crystal structures clearly proved helical folding of a trimer in the presence of sulfate ion, in which left- and right-handed helices stacked alternatively. It was also shown that the selectivity of anion binding could be varied by the modification of the spacer groups connecting indolocarbazole units. Finally, we prepared chiral indolocabazole dimers that adopted helical structures by intramolecular hydrogen bonds and displayed complete inversion of the helical sense upon anion binding. The dimers gave characteristic optical readouts in a reversible manner according to chemical stimuli, thus functioning as chirooptical molecular switches.


2008 ◽  
Vol 80 (3) ◽  
pp. 599-608 ◽  
Author(s):  
Jae-min Suk ◽  
Min Kyung Chae ◽  
Nam-Kyun Kim ◽  
Uk-Il Kim ◽  
Kyu-Sung Jeong

Indole-based synthetic receptors which bind anions by multiple hydrogen bonds in organic solvents have been prepared. The biindole scaffold bearing two good hydrogen bond donors of indole NHs has been used as a molecular building block to construct the receptors. Incorporation of more hydrogen bond donors or acceptors increases the binding strength and selectivity toward a specific ion. Two macrocycles having different sizes of the internal cavities have been also synthesized, and their binding properties have been compared. Two macrocycles display distinct binding modes with polyatomic anions such as azide, as unequivocally proven by X-ray crystal structures. Finally, a series of oligoindoles containing four, six, and eight indoles have been prepared by Sonogashira reactions. The oligoindoles fold into helical structures upon binding with chloride. The binding affinities of the oligoindoles with chloride increase with increasing of the chain length, which provides an additional evidence for helical folding of the complexes.


Author(s):  
Bernd Tesche ◽  
Tobias Schilling

The objective of our work is to determine:a) whether both of the imaging methods (TEM, STM) yield comparable data andb) which method is better suited for a reliable structure analysis of microclusters smaller than 1.5 nm, where a deviation of the bulk structure is expected.The silver was evaporated in a bell-jar system (p 10−5 pa) and deposited onto a 6 nm thick amorphous carbon film and a freshly cleaved highly oriented pyrolytic graphite (HOPG).The average deposited Ag thickness is 0.1 nm, controlled by a quartz crystal microbalance at a deposition rate of 0.02 nm/sec. The high resolution TEM investigations (100 kV) were executed by a hollow-cone illumination (HCI). For the STM investigations a commercial STM was used. With special vibration isolation we achieved a resolution of 0.06 nm (inserted diffraction image in Fig. 1c). The carbon film shows the remarkable reduction in noise by using HCI (Fig. 1a). The HOPG substrate (Fig. 1b), cleaved in sheets thinner than 30 nm for the TEM investigations, shows the typical arrangement of a nearly perfect stacking order and varying degrees of rotational disorder (i.e. artificial single crystals). The STM image (Fig. 1c) demonstrates the high degree of order in HOPG with atomic resolution.


2020 ◽  
Vol 64 (2) ◽  
pp. 325-336 ◽  
Author(s):  
Dimitriya H. Garvanska ◽  
Jakob Nilsson

Abstract Kinetochores are instrumental for accurate chromosome segregation by binding to microtubules in order to move chromosomes and by delaying anaphase onset through the spindle assembly checkpoint (SAC). Dynamic phosphorylation of kinetochore components is key to control these activities and is tightly regulated by temporal and spatial recruitment of kinases and phosphoprotein phosphatases (PPPs). Here we focus on PP1, PP2A-B56 and PP2A-B55, three PPPs that are important regulators of mitosis. Despite the fact that these PPPs share a very similar active site, they target unique ser/thr phosphorylation sites to control kinetochore function. Specificity is in part achieved by PPPs binding to short linear motifs (SLiMs) that guide their substrate specificity. SLiMs bind to conserved pockets on PPPs and are degenerate in nature, giving rise to a range of binding affinities. These SLiMs control the assembly of numerous substrate specifying complexes and their position and binding strength allow PPPs to target specific phosphorylation sites. In addition, the activity of PPPs is regulated by mitotic kinases and inhibitors, either directly at the activity level or through affecting PPP–SLiM interactions. Here, we discuss recent progress in understanding the regulation of PPP specificity and activity and how this controls kinetochore biology.


Author(s):  
Didier Debaise

Process and Reality ends with a warning: ‘[t]he chief danger to philosophy is narrowness in the selection of evidence’ (PR, 337). Although this danger of narrowness might emerge from the ‘idiosyncrasies and timidities of particular authors, of particular social groups, of particular schools of thought, of particular epochs in the history of civilization’ (PR, 337), we should not be mistaken: it occurs within philosophy, in its activity, its method. And the fact that this issue arises at the end of Process and Reality reveals the ambition that has accompanied its composition: Whitehead has resisted this danger through the form and ambition of his speculative construction. The temptation of a narrowness in selection attempts to expel speculative philosophy at the same time as it haunts each part of its system.


Author(s):  
Tomotaka WADA ◽  
Yuki NAKANISHI ◽  
Ryohta YAMAGUCHI ◽  
Kazushi FUJIMOTO ◽  
Hiromi OKADA

2020 ◽  
Author(s):  
Maximilian Kuhn ◽  
Stuart Firth-Clark ◽  
Paolo Tosco ◽  
Antonia S. J. S. Mey ◽  
Mark Mackey ◽  
...  

Free energy calculations have seen increased usage in structure-based drug design. Despite the rising interest, automation of the complex calculations and subsequent analysis of their results are still hampered by the restricted choice of available tools. In this work, an application for automated setup and processing of free energy calculations is presented. Several sanity checks for assessing the reliability of the calculations were implemented, constituting a distinct advantage over existing open-source tools. The underlying workflow is built on top of the software Sire, SOMD, BioSimSpace and OpenMM and uses the AMBER14SB and GAFF2.1 force fields. It was validated on two datasets originally composed by Schrödinger, consisting of 14 protein structures and 220 ligands. Predicted binding affinities were in good agreement with experimental values. For the larger dataset the average correlation coefficient Rp was 0.70 ± 0.05 and average Kendall’s τ was 0.53 ± 0.05 which is broadly comparable to or better than previously reported results using other methods. <br>


2020 ◽  
Author(s):  
Zhaoxi Sun

Host-guest binding remains a major challenge in modern computational modelling. The newest 7<sup>th</sup> statistical assessment of the modeling of proteins and ligands (SAMPL) challenge contains a new series of host-guest systems. The TrimerTrip host binds to 16 structurally diverse guests. Previously, we have successfully employed the spherical coordinates as the collective variables coupled with the enhanced sampling technique metadynamics to enhance the sampling of the binding/unbinding event, search for possible binding poses and predict the binding affinities in all three host-guest binding cases of the 6<sup>th</sup> SAMPL challenge. In this work, we employed the same protocol to investigate the TrimerTrip host in the SAMPL7 challenge. As no binding pose is provided by the SAMPL7 host, our simulations initiate from randomly selected configurations and are proceeded long enough to obtain converged free energy estimates and search for possible binding poses. The predicted binding affinities are in good agreement with the experimental reference, and the obtained binding poses serve as a nice starting point for end-point or alchemical free energy calculations.


2019 ◽  
Author(s):  
Elena Prigorchenko ◽  
Sandra Kaabel ◽  
Triin Narva ◽  
Anastassia Baškir ◽  
Maria Fomitšenko ◽  
...  

Amplification of a thermodynamically unfavoured macrocyclic product through the directed shift of the equilibrium between dynamic covalent chemistry library members is difficult to achieve. We show for the first time that during condensation of formaldehyde and <i>cis</i>-<i>N,N'</i>-cyclohexa-1,2-diylurea formation of <i>inverted-cis</i>-cyclohexanohemicucurbit[6]uril (<i>i-cis</i>-cycHC[6]) can be induced at the expense of thermodynamically favoured <i>cis</i>-cyclohexanohemicucurbit[6]uril (<i>cis</i>-cycHC[6]). The formation of <i>i-cis-</i>cycHC[6] is enhanced in low concentration of the templating chloride anion and suppressed in excess of this template. We found that reaction selectivity is governed by the solution-based template-aided dynamic combinatorial chemistry and continuous removal of the formed cycHC[6] macrocycles from the equilibrating solution by precipitation. Notably, the <i>i-cis</i>-cycHC[6] was isolated with 33% yield. Different binding affinities of three diastereomeric <i>i-cis</i>-, <i>cis</i>-cycHC[6] and their chiral isomer (<i>R,R</i>)-cycHC[6] for trifluoroacetic acid demonstrate the influence of macrocycle geometry on complex formation.


2013 ◽  
Vol 14 (4) ◽  
pp. 393-398

The occurrence of trihalomethanes (THMs) was studied in the drinking water samples from urban water supply network of Karachi city that served more than 18 million people. Drinking water samples were collected from 58 locations in summer (May-August) and winter (November-February) seasons. The major constituent of THMs detected was chloroform in winter (92.34%) and summer (93.07%), while the other THMs determined at lower concentrations. Summer and winter concentrations of total THMs at places exceed the levels regulated by UEPA (80 μg l-1) and WHO (100 μg l-1). GIS linked temporal variability in two seasons showed significantly higher median concentration (2.5%-23.06%) of THMs compared to winter.


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