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Scoring Conformational Metastability of Macrocyclic Peptides with Binding Pose Metadynamics.
J Chem Inf Model
January 2025
Department of Modeling and Informatics, Merck & Co., Inc., Rahway, New Jersey 07065, United States.
Potency optimization of macrocyclic peptides can include both modifying intermolecular interactions and modifying the conformational stability of the bioactive conformation. However, the number of possible modifications is vast. To identify modifications that enhance the stability of the binding conformations in a cost-effective manner, there is a need for a high-throughput in-silico method that scores the conformational stability of these modified molecules.
View Article and Find Full Text PDFA novel ADP-directed chaperone function facilitates the ATP-driven motor activity of SARS-CoV helicase.
Nucleic Acids Res
January 2025
Single-Molecule and Cell Mechanobiology Laboratory, Daejeon, 34141, South Korea.
Helicase is a nucleic acid motor that catalyses the unwinding of double-stranded (ds) RNA and DNA via ATP hydrolysis. Helicases can act either as a nucleic acid motor that unwinds its ds substrates or as a chaperone that alters the stability of its substrates, but the two activities have not yet been reported to act simultaneously. Here, we used single-molecule techniques to unravel the synergistic coordination of helicase and chaperone activities, and found that the severe acute respiratory syndrome coronavirus helicase (nsp13) is capable of two modes of action: (i) binding of nsp13 in tandem with the fork junction of the substrate mechanically unwinds the substrate by an ATP-driven synchronous power stroke; and (ii) free nsp13, which is not bound to the substrate but complexed with ADP in solution, destabilizes the substrate through collisions between transient binding and unbinding events with unprecedented melting capability.
View Article and Find Full Text PDFAccessing Different Protein Conformer Ensembles with Tunable Capillary Vibrating Sharp-Edge Spray Ionization.
J Phys Chem B
January 2025
Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States.
Capillary vibrating sharp-edge spray ionization (cVSSI) has been used to control the droplet charging of nebulized microdroplets and monitor effects on protein ion conformation makeup as determined by mass spectrometry (MS). Here it is observed that the application of voltage results in noticeable differences to the charge state distributions (CSDs) of ubiquitin ions. The data can be described most generally in three distinct voltage regions: Under low-voltage conditions (<+200 V, LV regime), low charge states (2+ to 4+ ions) dominate the mass spectra.
View Article and Find Full Text PDFSequential and Time-Controlled Sol-Gel Transitions by Mechanical Switching of Molecular Tweezers.
J Am Chem Soc
January 2025
Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, IPCM, 4 place Jussieu, Paris 75005, France.
Controlling the motion of molecular machines to influence higher-order structures is well-established in biological systems but remains a significant challenge for synthetic analogs. Herein, we aim to harness the mechanical switching of switchable molecular tweezers to modulate their self-assembly and produce stimuli-responsive organogels. We report a series of terpy(Pt-salphen) molecular tweezers functionalized with alkyl chains that act as low-molecular-weight gelators (LMWGs) in their open conformation.
View Article and Find Full Text PDFProbing London Dispersion in Proton-Bound Onium Ions: Are Alkyl-Alkyl Steric Interactions Reliably Modeled?
J Am Chem Soc
January 2025
Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich 8093, Switzerland.
We report spectroscopic and spectrometric experiments that probe the London dispersion interaction between -butyl substituents in three series of covalently linked, protonated -pyridines in the gas phase. Molecular ions in the three test series, along with several reference molecules for control, were electrosprayed from solution into the gas phase and then probed by infrared multiphoton dissociation spectroscopy and trapped ion mobility spectrometry. The observed N-H stretching frequencies provided an experimental readout diagnostic of the ground-state geometry of each ion, which could be furthermore compared to a second, independent structural readout via the collision cross section.
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