Multiscale session (1/2) : with Michel Ceotto telling us about Semiclassically Approximated Quantum Molecular Dynamics using Force Fields; G. Andrés Cisneros @CisnerosRes Interfacing QM/GEM via LICHEM, Tinker-HP and Psi4 #tinkermeeting24#compchem
Thank you @CisnerosRes for all your support. Thanks to @FulbrightPrgrm. Both the papers on unnatural base-pair (3rd BP) are now online @PCCP. Please have a look. A symphony of genetic harmony with 3rd base pair 🙂.
Our collaborative research with @NiyatiA30 and @ronsmaldone on iodine adsorption in amide functionalized COFs has now been published in @ChemicalScience. Special thanks to @CisnerosRes. Please check it out https://t.co/C3Cj4kbi14
Hey siri
Play “I like it like that” by Cardi B
2024 started good,
My paper is out and ready to serve you guys, go check it out @ChemicalScience
Special thanks to @Tanay8690 and @CisnerosRes and of course to our very own PI @ronsmaldone
Check out the latest from the @smaldonelab and @CisnerosRes on #COFs, published in @ChemicalScience. In this collaborative project we show that COFamides are excellent adsorbates for aqueous iodine, making them promising materials for water purification! https://t.co/mipwOJCAkh
@reynier_s through Coulomb interactions and residues in the finger region specially TYR671 (steric gate) interacts with the exposed UBs through vdW force. Interestingly the similar residues show altered interactions on conformation change. Thanks
@reynier_s Three conformers exhibit nWCF structures and one is found to be non-paired. Further we investigated intermolecular interactions between UBP and Taq-residues by EDA. It is observed that for three conformers the similar residues (mostly R573, R587, R746) stabilizes the UBP
@reynier_s But in binary complex of Taq polymerase I (Taq) with UBP-incorporated DNA, flexibility of the UBP has been arrested by the Taq, obtained from both AMOEBA (Tot:100 ns for each conf) and AMBER (Tot:750 ns for each conf). Four distinct conformers are modeled from PDBs (4C8L, 4C8O).
@reynier_s Total simulation time (AMBER: 15 ms, AMOEBA: 375 ns). Results: Flexible nature of UBP, conformation change (Watson-Crick-Franklin: WCF to non-WCF: nWCF), random population distribution of the conformers. In terminal position flexibility further increases.
@reynier_s We considered Unnatural Base Pair (UBP)-incorporated DNA (in the middle and in the terminal position) in aqueous solution and run the MD simulation with both polarizable AMOEBA force fields along with AMBER with different starting conformers.