NMR as a routine analytical method provides important three-dimensional structure information of compounds in solution. Here we apply the recently released CRENSO computational workflow for the automated generation of conformer ensembles to the quantum mechanical calculation of C-NMR spectra of a series of flexible cycloalkanes up to C H . We evaluate the computed chemical shifts in comparison with corresponding experimental data in chloroform. It is shown that accurate and properly averaged theoretical NMR data can be obtained in about a day of computation time on a standard workstation computer. The excellent agreement between theory and experiment enables one to deduce preferred conformations of large, non-rigid macrocycles under ambient conditions from our automated procedure.
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http://dx.doi.org/10.1002/anie.202113905 | DOI Listing |
J Comput Chem
January 2025
School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, India.
The ensemble properties of a system are obtained by averaging over the properties calculated for the various configurations it can have at a finite temperature and thus cannot be captured by a single molecular structure. Such ensemble properties are often important in material discovery. In designing new materials, the goal is to predict those ensemble structures that display a tailored property.
View Article and Find Full Text PDFProteins drive biochemical transformations by transitioning through distinct conformational states. Understanding these states is essential for modulating protein function. Although X-ray crystallography has enabled revolutionary advances in protein structure prediction by machine learning, this connection was made at the level of atomic models, not the underlying data.
View Article and Find Full Text PDFCurr Issues Mol Biol
January 2025
College of Pharmacy, Chongqing Medical University, Chongqing 400016, China.
P21-activated kinase 4 (PAK4) plays a crucial role in the proliferation and metastasis of various cancers. However, developing selective PAK4 inhibitors remains challenging due to the high homology within the PAK family. Therefore, developing highly selective PAK4 inhibitors is critical to overcoming the limitations of existing inhibitors.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
Time-averaged restraints from nuclear magnetic resonance (NMR) measurements have been implemented in the UNRES coarse-grained model of polypeptide chains in order to develop a tool for data-assisted modeling of the conformational ensembles of multistate proteins, intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs), many of which are essential in cell biology. A numerically stable variant of molecular dynamics with time-averaged restraints has been introduced, in which the total energy is conserved in sections of a trajectory in microcanonical runs, the bath temperature is maintained in canonical runs, and the time-average-restraint-force components are scaled up with the length of the memory window so that the restraints affect the simulated structures. The new approach restores the conformational ensembles used to generate ensemble-averaged distances, as demonstrated with synthetic restraints.
View Article and Find Full Text PDFdescribes the ability of biological macromolecules to transmit signals spatially through the molecule from an site – a site that is distinct from binding sites of primary, endogenous ligands – to the functional or active site. This review starts with a historical overview and a description of the classical example of allostery – hemoglobin – and other well-known examples (aspartate transcarbamoylase, Lac repressor, kinases, G-protein-coupled receptors, adenosine triphosphate synthase, and chaperonin). We then discuss fringe examples of allostery, including intrinsically disordered proteins and inter-enzyme allostery, and the influence of dynamics, entropy, and conformational ensembles and landscapes on allosteric mechanisms, to capture the essence of the field.
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