A competition between chiral characteristics alternatively attributable to either conformation or to absolute configuration is identified. Circular dichroism associated with photoexcitation of the outer orbital of configurational enantiomers of 1,3- and 2,3-butanediols has been examined with a focus on the large changes in electron chiral asymmetry produced by different molecular conformations. Experimental gas-phase measurements offer support for the theoretical modeling of this chiroptical effect. A surprising prediction is that a conformationally produced pseudo-enantiomerism in 1,3-butanediol generates a chiral response in the frontier electron dynamics that outweighs the influence of the permanent configurational handedness established at the asymmetrically substituted carbon. Induced conformation, and specifically induced conformational chirality, may thus be a dominating factor in chiral molecular recognition in such systems.
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http://dx.doi.org/10.1002/anie.201603771 | DOI Listing |
Chem Pharm Bull (Tokyo)
December 2024
Department of Marine Biotechnology and Resources, National Sun Yat-sen University.
In the present study, an algae-containing octocoral, Junceella fragilis, was subjected to chemical screening. The analysis resulted in the extraction of six polyacetoxybriaranes: a new compound, identified as fragilide Z (1), alongside previously identified analogs, which included 12-epi-fragilide G (2), fragilide P (3), junceellolide D (4), junceellonoid A (5), and juncin ZI (6). The structures of compounds 2-6 were investigated through single-crystal X-ray diffraction analysis, whereas that of 1 was examined through two-dimensional nuclear magnetic resonance analysis.
View Article and Find Full Text PDFJ Chem Theory Comput
December 2024
Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, and Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United States.
Polyphosphate nucleotides, such as ATP, ADP, GTP, and GDP, play a crucial role in modulating protein functions through binding and/or catalytically activating proteins (enzymes). However, accurately calculating the binding free energies for these charged and flexible ligands poses challenges due to slow conformational relaxation and the limitations of force fields. In this study, we examine the accuracy and reliability of alchemical free energy simulations with fixed-charge force fields for the binding of four nucleotides to nine proteins of various classes, including kinases, ATPases, and GTPases.
View Article and Find Full Text PDFNanoscale
December 2024
Department of Physics and Center for NanoScience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany.
Biomolecular structures are typically determined using frozen or crystalline samples. Measurement of intramolecular distances in solution can provide additional insights into conformational heterogeneity and dynamics of biological macromolecules and their complexes. The established molecular ruler techniques used for this (NMR, FRET, and EPR) are, however, limited in their dynamic range and require model assumptions to determine absolute distance or distance distributions.
View Article and Find Full Text PDFVet Radiol Ultrasound
January 2025
Department of Artificial Intelligence and Computer Science, Yeshiva University, New York, New York, USA.
The Norberg angle (NA) plays a crucial role in evaluating hip joint conformation, particularly in canines, by quantifying femoral head subluxation within the hip joint. Therefore, it is an important metric for evaluating hip joint quality and diagnosing canine hip dysplasia, the most prevalent hereditary orthopedic disorder in dogs. While contemporary tools offer automated quantification of the NA, their usage typically entails manual labeling and verification of radiographic images by professional veterinarians.
View Article and Find Full Text PDFProtein Sci
January 2025
Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
While there has been substantial progress in our ability to predict changes in protein stability due to amino acid substitutions, progress has been slower in methods to predict the absolute stability of a protein. Here, we show how a generative model for protein sequence can be leveraged to predict absolute protein stability. We benchmark our predictions across a broad set of proteins and find a mean error of 1.
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