scholarly journals Tripodal, Squaramide-Based Ion Pair Receptor for Effective Extraction of Sulfate Salt

Molecules ◽  
2021 ◽  
Vol 26 (9) ◽  
pp. 2751
Author(s):  
Damian Jagleniec ◽  
Marcin Wilczek ◽  
Jan Romański
Keyword(s):  
Ion Pairs ◽  
Binding Mode ◽  
Selective Extraction ◽  
Ion Pair ◽  
Hofmeister Series ◽  
Sulfate Salt ◽  
Lower Affinity ◽  
High Affinity ◽  
Binding Domains ◽  
Hydrated Sulfate

Combining three features—the high affinity of squaramides toward anions, cooperation in ion pair binding and preorganization of the binding domains in the tripodal platform—led to the effective receptor 2. The lack of at least one of these key elements in the structures of reference receptors 3 and 4 caused a lower affinity towards ion pairs. Receptor 2 was found to form an intramolecular network in wet chloroform, which changed into inorganic–organic associates after contact with ions and allowed salts to be extracted from an aqueous to an organic phase. The disparity in the binding mode of 2 with sulfates and with other monovalent anions led to the selective extraction of extremely hydrated sulfate anions in the presence of more lipophilic salts, thus overcoming the Hofmeister series.

scholarly journals The Effect of Substitution Pattern on Binding Ability in Regioisomeric Ion Pair Receptors Based on an Aminobenzoic Platform

Molecules ◽  
2019 ◽  
Vol 24 (16) ◽  
pp. 2990 ◽  
Author(s):  
Damian Jagleniec ◽  
Krzysztof Ziach ◽  
Kajetan Dąbrowa ◽  
Jan Romański
Keyword(s):  
1H Nmr ◽  
Ion Pairs ◽  
Ion Pair ◽  
Mutual Orientation ◽  
Substitution Pattern ◽  
X Ray ◽  
Binding Domains ◽  
Sodium Cations ◽  
Solution Studies ◽  
Intramolecular Hydrogen

A series of ditopic ion pair receptors equipped with 4-nitrophenylurea and 1-aza-18-crown-6-ether linked by ortho-(1), meta-(2), and para-(3) substituted benzoic acid were readily synthesized in three steps from commercially available materials. The binding properties of these regioisomeric receptors were determined using UV-vis and 1H NMR spectroscopy in MeCN and in the solid state by single-crystal X-ray diffraction crystallography. The solution studies revealed that, apart from carboxylates, all the anions tested formed stronger complexes in the presence of sodium cations. Receptors 2 and 3 were found to interact with ion pairs with remarkably higher affinity than ortho-substituted 1. 1H NMR titration experiments showed that both urea NH protons interacted with anions with comparable strength in the case of receptors 2 and 3, but only one of the NHs was effective in anion binding in the case of receptor 1. X-ray analysis of the crystal structure of receptor 1 and 1·NaPF6 complex showed that binding was hampered due to the formation of an intramolecular hydrogen bond. Analysis of the crystal structures of 2·NaBr and 3·NaBr complexes revealed that proper mutual orientation of binding domains was responsible for the improved binding of the sodium salts.

Combination of ribosome and phage display for fast selection of high affinity VHH antibody fragments

2019 ◽  
pp. 27-33
Author(s):  
YuE Kravchenko ◽  
SV Ivanov ◽  
DS Kravchenko ◽  
EI Frolova ◽  
SP Chumakov
Keyword(s):  
Phage Display ◽  
Selection Procedure ◽  
Free System ◽  
Phage Displays ◽  
High Affinity ◽  
Binding Domains ◽  
A Cell ◽  
Vhh Antibodies ◽  
Efficiency Of Selection ◽  
Selection Of

Selection of antibodies using phage display involves the preliminary cloning of the repertoire of sequences encoding antigen-binding domains into phagemid, which is considered the bottleneck of the method, limiting the resulting diversity of libraries and leading to the loss of poorly represented variants before the start of the selection procedure. Selection in cell-free conditions using a ribosomal display is devoid from this drawback, however is highly sensitive to PCR artifacts and the RNase contamination. The aim of the study was to test the efficiency of a combination of both methods, including pre-selection in a cell-free system to enrich the source library, followed by cloning and final selection using phage display. This approach may eliminate the shortcomings of each method and increase the efficiency of selection. For selection, alpaca VHH antibody sequences suitable for building an immune library were used due to the lack of VL domains. Analysis of immune libraries from the genes of the VH3, VHH3 and VH4 families showed that the VHH antibodies share in the VH3 and VH4 gene groups is insignificant, and selection from the combined library is less effective than from the VHH3 family of sequences. We found that the combination of ribosomal and phage displays leads to a higher enrichment of high-affinity fragments and avoids the loss of the original diversity during cloning. The combined method allowed us to obtain a greater number of different high-affinity sequences, and all the tested VHH fragments were able to specifically recognize the target, including the total protein extracts of cell cultures.

Stereospecific 1,3-H Transfer of Indenols Proceeds via Persistent Ion-Pairs Anchored By NH···Pi Interactions

2018 ◽  
Author(s):  
David Ascough ◽  
Fernanda Duarte ◽  
Robert Paton
Keyword(s):  
Computational Analysis ◽  
Ion Pairs ◽  
Ion Pair ◽  
Hydrogen Atom Transfer ◽  
Polar Solvents ◽  
Chirality Transfer ◽  
Activation Barriers ◽  
Sense And Avoid ◽  
Phase Dynamics ◽  
Pi Interactions

The base-catalyzed rearrangement of arylindenols is a rare example of a suprafacial [1,3]-hydrogen atom transfer. The mechanism has been proposed to proceed via sequential [1,5]-sigmatropic shifts, which occur in a selective sense and avoid an achiral intermediate. A computational analysis using quantum chemistry casts serious doubt on these suggestions: these pathways have enormous activation barriers and in constrast to what is observed experimentally, they overwhelmingly favor a racemic product. Instead we propose that a suprafacial [1,3]-prototopic shift occurs in a two-step deprotonation/reprotonation sequence. This mechanism is favored by 15 kcal mol<sup>-1</sup> over that previously proposed. Most importantly, this is also consistent with stereospecificity since reprotonation occurs rapidly on the same p-face. We have used explicitly-solvated molecular dynamics studies to study the persistence and condensed-phase dynamics of the intermediate ion-pair formed in this reaction. Chirality transfer is the result of a particularly resilient contact ion-pair, held together by electrostatic attraction and a critical NH···p interaction which ensures that this species has an appreciable lifetime even in polar solvents such as DMSO and MeOH.

scholarly journals Spanning the gap: unraveling RSC dynamics in vivo

2021 ◽  
Author(s):  
Heinz Neumann ◽  
Bryan J. Wilkins
Keyword(s):  
Cell Cycle ◽  
Posttranslational Modifications ◽  
Transcriptional Activation ◽  
Binding Mode ◽  
Binding Modes ◽  
Binding Domains ◽  
Binding Interface ◽  
The Many ◽  
And Function

AbstractMultiple reports over the past 2 years have provided the first complete structural analyses for the essential yeast chromatin remodeler, RSC, providing elaborate molecular details for its engagement with the nucleosome. However, there still remain gaps in resolution, particularly within the many RSC subunits that harbor histone binding domains.Solving contacts at these interfaces is crucial because they are regulated by posttranslational modifications that control remodeler binding modes and function. Modifications are dynamic in nature often corresponding to transcriptional activation states and cell cycle stage, highlighting not only a need for enriched spatial resolution but also temporal understanding of remodeler engagement with the nucleosome. Our recent work sheds light on some of those gaps by exploring the binding interface between the RSC catalytic motor protein, Sth1, and the nucleosome, in the living nucleus. Using genetically encoded photo-activatable amino acids incorporated into histones of living yeast we are able to monitor the nucleosomal binding of RSC, emphasizing the regulatory roles of histone modifications in a spatiotemporal manner. We observe that RSC prefers to bind H2B SUMOylated nucleosomes in vivo and interacts with neighboring nucleosomes via H3K14ac. Additionally, we establish that RSC is constitutively bound to the nucleosome and is not ejected during mitotic chromatin compaction but alters its binding mode as it progresses through the cell cycle. Our data offer a renewed perspective on RSC mechanics under true physiological conditions.

Ion pair binding by an l-tyrosine-based polymerizable molecular receptor

2015 ◽  
Vol 39 (8) ◽  
pp. 6216-6222 ◽  
Author(s):  
Szymon Zdanowski ◽  
Jan Romański
Keyword(s):  
Ion Pairs ◽  
Functional Polymers ◽  
Ion Pair

A polymerizable molecular receptor able to bind ion pairs and new functional polymers containing the receptor units were synthesized and characterized.

scholarly journals The STK2 gene, which encodes a putative Ser/Thr protein kinase, is required for high-affinity spermidine transport in Saccharomyces cerevisiae.

1997 ◽  
Vol 17 (6) ◽  
pp. 2994-3004 ◽  
Author(s):  
M Kaouass ◽  
M Audette ◽  
D Ramotar ◽  
S Verma ◽  
D De Montigny ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Kinase ◽  
Fusion Gene ◽  
Transport Systems ◽  
Coding Region ◽  
Kinase Gene ◽  
Lower Affinity ◽  
High Affinity ◽  
Polyamine Transport ◽  
Exogenous Spermidine

Eukaryotic polyamine transport systems have not yet been characterized at the molecular level. We have used transposon mutagenesis to identify genes controlling polyamine transport in Saccharomyces cerevisiae. A haploid yeast strain was transformed with a genomic minitransposon- and lacZ-tagged library, and positive clones were selected for growth resistance to methylglyoxal bis(guanylhydrazone) (MGBG), a toxic polyamine analog. A 747-bp DNA fragment adjacent to the lacZ fusion gene rescued from one MGBG-resistant clone mapped to chromosome X within the coding region of a putative Ser/Thr protein kinase gene of previously unknown function (YJR059w, or STK2). A 304-amino-acid stretch comprising 11 of the 12 catalytic subdomains of Stk2p is approximately 83% homologous to the putative Pot1p/Kkt8p (Stk1p) protein kinase, a recently described activator of low-affinity spermine uptake in yeast. Saturable spermidine transport in stk2::lacZ mutants had an approximately fivefold-lower affinity and twofold-lower Vmax than in the parental strain. Transformation of stk2::lacZ cells with the STK2 gene cloned into a single-copy expression vector restored spermidine transport to wild-type levels. Single mutants lacking the catalytic kinase subdomains of STK1 exhibited normal parameters for the initial rate of spermidine transport but showed a time-dependent decrease in total polyamine accumulation and a low-level resistance to toxic polyamine analogs. Spermidine transport was repressed by prior incubation with exogenous spermidine. Exogenous polyamine deprivation also derepressed residual spermidine transport in stk2::lacZ mutants, but simultaneous disruption of STK1 and STK2 virtually abolished high-affinity spermidine transport under both repressed and derepressed conditions. On the other hand, putrescine uptake was also deficient in stk2::lacZ mutants but was not repressed by exogenous spermidine. Interestingly, stk2::lacZ mutants showed increased growth resistance to Li+ and Na+, suggesting a regulatory relationship between polyamine and monovalent inorganic cation transport. These results indicate that the putative STK2 Ser/Thr kinase gene is an essential determinant of high-affinity polyamine transport in yeast whereas its close homolog STK1 mostly affects a lower-affinity, low-capacity polyamine transport activity.

Axle component separated ion-pair recognition by a neutral heteroditopic [2]rotaxane

2014 ◽  
Vol 50 (13) ◽  
pp. 1540-1542 ◽  
Author(s):  
Richard C. Knighton ◽  
Paul D. Beer
Keyword(s):  
Alkali Metal ◽  
Metal Cation ◽  
Alkali Metal Cation ◽  
Ion Pairs ◽  
Ion Pair ◽  
Sodium Cation ◽  
Halide Anion ◽  
Cooperative Recognition

A neutral heteroditopic pyridine N-oxide axle containing [2]rotaxane, synthesised via sodium cation templation, displays cooperative recognition of alkali metal cation-halide anion ion-pairs in an unprecedented axle component separated ion-pair binding fashion.

scholarly journals DapE Can Function as an Aspartyl Peptidase in the Presence of Mn2+

2003 ◽  
Vol 185 (16) ◽  
pp. 4748-4754 ◽  
Author(s):  
Daniel H. Broder ◽  
Charles G. Miller
Keyword(s):  
Divalent Cations ◽  
The Other ◽  
Expression Vectors ◽  
Peptidase Activity ◽  
Native Protein ◽  
Lower Affinity ◽  
High Affinity ◽  
High Affinity Site ◽  
Serovar Typhimurium ◽  
Dipeptidase Activity

ABSTRACT Extracts of a multiply peptidase-deficient (pepNABDPQTE iadA iaaA) Salmonella enterica serovar Typhimurium strain contain an aspartyl dipeptidase activity that is dependent on Mn2+. Purification of this activity followed by N-terminal sequencing of the protein suggested that the Mn2+-dependent peptidase is DapE (N-succinyl-l,l-diaminopimelate desuccinylase). A dapE chromosomal disruption was constructed and transduced into a multiply peptidase-deficient (MPD) strain. Crude extracts of this strain showed no aspartyl peptidase activity, and the strain failed to utilize Asp-Leu as a leucine source. The dapE gene was cloned into expression vectors in order to overproduce either the native protein (DapE) or a hexahistidine fusion protein (DapE-His6). Extracts of a strain carrying the plasmid overexpresssing native DapE in the MPD dapE background showed a 3,200-fold elevation of Mn2+-dependent aspartyl peptidase activity relative to the MPD dapE+ strain. In addition, purified DapE-His6 exhibited Mn2+-dependent peptidase activity toward aspartyl dipeptides. Growth of the MPD strain carrying a single genomic copy of dapE on Asp-Leu as a Leu source was slow but detectable. Overproduction of DapE in the MPD dapE strain allowed growth on Asp-Leu at a much faster rate. DapE was found to be specific for N-terminal aspartyl dipeptides: no N-terminal Glu, Met, or Leu peptides were hydrolyzed, nor were any peptides containing more than two amino acids. DapE is known to bind two divalent cations: one with high affinity and the other with lower affinity. Our data indicate that the form of DapE active as a peptidase contains Zn2+ in the high-affinity site and Mn2+ in the low-affinity site.

scholarly journals Structure of the XPA DNA binding domain and RPA high-affinity DNA binding domains on a model NER substrate

2019 ◽  
Vol 75 (a1) ◽  
pp. a203-a203
Author(s):  
Walter J. Chazin ◽  
Agnieszka M. Topolska-Woś ◽  
Norie Sugitani ◽  
John J. Cordoba ◽  
Hyun Suk Kim ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Dna Binding Domains ◽  
High Affinity ◽  
Binding Domains

Isotope effects and activation parameters for the proton transfer reaction from 1-(4-nitrophenyl)-1-nitroethane to free anions and ion pairs of cesium n-propoxide in n-propanol solvent

1986 ◽  
Vol 64 (6) ◽  
pp. 1021-1025 ◽  
Author(s):  
Arnold Jarczewski ◽  
Grzegorz Schroeder ◽  
Przemyslaw Pruszynski ◽  
Kenneth T. Leffek
Keyword(s):  
Proton Transfer ◽  
Rate Constants ◽  
Isotope Effects ◽  
Ion Pairs ◽  
Activation Parameters ◽  
Solvation Shell ◽  
Ion Pair ◽  
Initial State ◽  
Free Ion ◽  
Deuteron Transfer

Rate constants for the proton and deuteron transfer from 1-(4-nitrophenyl)-1-nitroethane to cesium n-propoxide in n-propanol have been measured under pseudo-first-order conditions with an excess of base for four temperatures between 5 and 35 °C. Using literature values of the fraction of cesium n-propoxide ion pairs that are dissociated into free ions, separate second-order rate constants for the proton and deuteron transfer to the ion pair and to the free ion have been calculated. The cesium n-propoxide ion pair is about 2.8 times more reactive than the free n-propoxide ion. The primary kinetic isotope effects for the two reactions are the same (kH/kD = 6.1–6.3 at 25 °C) within experimental error. The enthalpy of activation is smaller for the ion-pair reaction and the entropy of activation more negative than for the free-ion reaction. For proton transfer, ΔH±ion pair = 8.3 ± 0.2 kcal mol−1, ΔH±ion = 9.6 ± 1.0 kcal mol−1, ΔS±ion pair = −12.3 ± 0.6 cal mol−1 deg−1, ΔS±ion = −10.1 ± 3.4 cal mol−1 deg−1. The greater reactivity of the ion pair relative to the free ion is interpreted in terms of the weaker solvation shell of the ion pair in the initial state.

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