The solution conformations of complexes of valinomycin with magnesium and strontium were investigated by circular dichroism, nuclear magnetic resonance and infrared techniques. The results were compared with our earlier results on lithium, calcium, manganese and barium complexes. All these cations, except lithium, form 2:1 ion sandwich and 1:1 carrier-cation complexes with valinomycin. The 1:1 complex has a conformation different from that of the valinomycin-potassium complex. Lithium forms only the 1:1 complex. Strontium and barium form a large number of 1:2 complexes with open conformations rapidly interconverting in solution in addition to the above 2:1 and 1:1 complexes. These observations are rationalized taking into account the ionic radii and coordination numbers of the cations and the conformational restraints of valinomycin molecules. It is suggested that cations with co-ordination numbers of about six (magnesium and calcium) form the 2:1 and 1:1 complexes whereas those with higher co-ordination numbers (strontium and barium) form 1:2 complexes also.
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While novel deep learning and statistics-based techniques predict accurate structural models for proteins and non-coding RNA, describing their macromolecular conformations in solution is still challenging. Small-angle X-ray scattering (SAXS) in solution is an efficient technique to validate structural predictions by comparing the experimental SAXS profile with those calculated from predicted structures. There are two main challenges in comparing SAXS profiles to RNA structures: the structures often lack cations necessary for stability and charge neutralization, and a single structure inadequately represents the conformational plasticity of RNA.
View Article and Find Full Text PDFExoribonuclease-resistant RNAs (xrRNAs) are viral RNA structures that block degradation by cellular 5'-3' exoribonucleases to produce subgenomic viral RNAs during infection. Initially discovered in flaviviruses, xrRNAs have since been identified in wide range of RNA viruses, including those that infect plants. High sequence variability among viral xrRNAs raises questions about the shared molecular features that characterize this functional RNA class.
View Article and Find Full Text PDFIn duplex DNA, A-T and G-C form Watson-Crick base pairs, and Hoogsteen pairing only dominates upon protein binding or DNA damage. Using NMR, we show that an A-T Hoogsteen base pair previously observed in crystal structures of transposon DNA hairpins bound to TnpA protein forms in solution even in the absence of TnpA. This Hoogsteen base pair, located adjacent to a dinucleotide apical loop, exists in dynamic equilibrium with a minor Watson-Crick conformation (population ∼11% and lifetime ∼55 µs).
View Article and Find Full Text PDFAdv Sci (Weinh)
January 2025
Center of Super-Diamond and Advanced Films (COSDAF) and Department of Chemistry, City University of Hong Kong, Hong Kong SAR, 999077, P. R. China.
A new aggregation-induced emission (AIE) luminogen is obtained by dimerizing acridin-9(10H)-one (Ac), an aggregation-caused quenching (ACQ) effect monomer via an N─N bond and forming 9H,9'H-[10,10'-biacridine]-9,9'-dione (DiAc) with D symmetry. The quenching of DiAc in solution is ascribed to the enhanced basicity promoting hydrogen bonding and then a hydrogen abstraction (HA) reaction and/or an unallowed transition in frontier orbitals with the same symmetry facilitating intersystem crossing. It is found that emissive Ac is one product of the non-emissive DiAc solution in the HA reaction activated by UV irradiation.
View Article and Find Full Text PDFSci Rep
January 2025
Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, Poznan, 61 614, Poland.
The embellishing of the macrocycle core with sulfur substituents of varied sterical requirements changes the structural dynamics of chiral, triangular polyimines. Despite their formal high symmetry, these compounds adopt diverse conformations, in which the macrocycle core represents a non-changeable unit. DFT calculations reveal that the mutual arrangement of sulfur-containing substituents is controlled mainly by sterical interactions.
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