Flexible Fitting of Small Molecules into Electron Microscopy Maps Using Molecular Dynamics Simulations with Neural Network Potentials.

Despite significant advances in resolution, the potential for cryo-electron microscopy (EM) to be used in determining the structures of protein-drug complexes remains unrealized. Determination of accurate structures and coordination of bound ligands necessitates simultaneous fitting of the models into the density envelopes, exhaustive sampling of the ligand geometries, and, most importantly, concomitant rearrangements in the side chains to optimize the binding energy changes. In this article, we present a flexible-fitting pipeline where molecular dynamics flexible fitting (MDFF) is used to refine structures of protein-ligand complexes from 3 to 5 Å electron density data.

Immune protection is dependent on the gut microbiome in a lethal mouse gammaherpesviral infection.

Immunopathogenesis in systemic viral infections can induce a septic state with leaky capillary syndrome, disseminated coagulopathy, and high mortality with limited treatment options. Murine gammaherpesvirus-68 (MHV-68) intraperitoneal infection is a gammaherpesvirus model for producing severe vasculitis, colitis and lethal hemorrhagic pneumonia in interferon gamma receptor-deficient (IFNγR) mice. In prior work, treatment with myxomavirus-derived Serp-1 or a derivative peptide S-7 (GTTASSDTAITLIPR) induced immune protection, reduced disease severity and improved survival after MHV-68 infection.

Serp-2, a virus-derived apoptosis and inflammasome inhibitor, attenuates liver ischemia-reperfusion injury in mice.

Background: Ischemia-reperfusion injury (IRI) is an antigen-independent, innate immune response to arterial occlusion and ischemia with subsequent paradoxical exacerbation after reperfusion. IRI remains a critical problem after vessel occlusion and infarction or during harvest and surgery in transplants. After transplant, liver IRI (LIRI) contributes to increased acute and chronic rejection and graft loss.

Computational Study of the Formation of C8, C5, and C4 Guanine:Lysine Adducts via Oxidation of Guanine by Sulfate Radical Anion.

Oxidative damage to DNA can lead to DNA-protein cross-links which can interfere with DNA transcription, replication, and repair. In experimental studies modeling oxidative damage to DNA, oxidation of guanosine by sulfate radical anion in the presence of lysine produced a mixture of lysine (Lys)-substituted spiroiminodihydantoins (Sp): ∼65% 5-Lys-Sp, ∼30% 8-Lys-Sp, and ∼5% 5,8-diLys-Sp. Pathways for formation of the lysine adducts during the oxidation of guanine by sulfate radical anions have been mapped out using B3LYP density functional theory and the SMD solvation model.

Modifying the Organ Matrix Pre-engraftment: A New Transplant Paradigm?

The availability of solid organs for transplantation remains low and there is a substantial need for methods to preserve the viability of grafted tissues. Suppression of solid-organ transplant rejection has traditionally focused on highly effective T cell inhibitors that block host immune lymphocyte responses. However, persistent and destructive innate and acquired immune reactions remain difficult to treat, causing late graft loss.

Computational Study of Oxidation of Guanine by Singlet Oxygen ( Δ ) and Formation of Guanine:Lysine Cross-Links.

Oxidation of guanine in the presence of lysine can lead to guanine-lysine cross-links. The ratio of the C4, C5 and C8 crosslinks depends on the manner of oxidation. Type II photosensitizers such as Rose Bengal and methylene blue can generate singlet oxygen, which leads to a different ratio of products than oxidation by type I photosensitizers or by one electron oxidants.

Computational Study of the Radical Mediated Mechanism of the Formation of C8, C5, and C4 Guanine:Lysine Adducts in the Presence of the Benzophenone Photosensitizer.

The oxidation of guanine by triplet benzophenone in the presence of lysine has been shown to produce mono- and dilysine-substituted spiroiminodihydantion products, 8-Lys-Sp and 5,8-diLys-Sp. The potential energy surfaces for C8, C5, and C4 nucleophilic addition have been mapped out using the B3LYP/aug-cc-pVTZ//B3LYP/6-31+G(d,p) level of density functional theory with the SMD solvation model and employing methylamine as a model for the side chain of lysine. Enthalpies, barrier heights, pKa's, and reduction potentials were calculated for intermediates to find the lowest energy paths.

Theoretical Determination of One-Electron Oxidation Potentials for Nucleic Acid Bases.

The oxidation potentials for N-methyl substituted nucleic acid bases guanine, adenine, cytosine, thymine, uracil, xanthine, and 8-oxoguanine were computed using B3LYP and CBS-QB3 with the SMD solvation model. Acid-base and tautomeric equilibria present in aqueous solution were accounted for by combining standard redox potentials with calculated pKa and tautomerization energies to produce an ensemble averaged pH dependent potential. Gas phase free energies were computed using B3LYP/aug-cc-pVTZ//B3LYP/6-31+G(d,p) and CBS-QB3.

Mechanistic aspects of the formation of guanidinohydantoin from spiroiminodihydantoin under acidic conditions.

Experimentally, it was observed that the oxidized guanine lesion spiroiminodihydantoin (Sp) contained in highly purified oligodeoxynucleotides slowly converts to guanidinohydantoin (Gh). The reaction is accelerated in the presence of acid. The possible mechanisms of this transformation have been analyzed computationally.

Calculation of pKa values of nucleobases and the guanine oxidation products guanidinohydantoin and spiroiminodihydantoin using density functional theory and a polarizable continuum model.

An efficient computational method has been identified that uses B3LYP density functional theory, IEF-PCM solvation modeling with a modified UFF cavity, and Boltzmann weighting of tautomers to predict the site-specific and global pKa of DNA nucleobases and their oxidation products. The method has been used to evaluate the acidity of guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp), two highly mutagenic guanine oxidation products. The trend observed for the pKa values of Gh (9.

An exploration of mechanisms for the transformation of 8-oxoguanine to guanidinohydantoin and spiroiminodihydantoin by density functional theory.

The potential energy surface for formation of 2-amino-5-hydroxy-7,9-dihydropurine-6,8-dione (5-OH-OG), guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp) from 8-oxoguanine (8-oxoG) has been mapped out using B3LYP density functional theory, the aug-cc-pVTZ and 6-31+G(d,p) basis sets and the IEF-polarizable continuum model (PCM) solvation model. Three pathways for formation of 5-OH-OG from 8-oxoG were evaluated: (A) stepwise loss of two electrons and two protons to form the quinonoid intermediate 2-amino-7,9-dihydro-purine-6,8-dione (8-oxoG(ox)) followed by hydration; (B) stepwise loss of two electrons and one proton and net addition of hydroxide, in which the key step is nucleophilic addition to the 8-oxoG radical cation; and (C) stepwise loss of one electron and one proton and addition of hydroxyl radical to the 8-oxoG radical cation. The data suggest that all three pathways are energetically feasible mechanisms for the formation of 5-OH-OG, however, Pathway A may be kinetically favored over Pathway B.

Exploration of mechanisms for the transformation of 8-hydroxy guanine radical to FAPyG by density functional theory.

The potential energy surface for the transformation of 8-hydroxy guanine radical to formamidopyrimidine adducts via four pathways has been mapped out using B3LYP density functional theory and the IEF-polarizable continuum model (PCM) solvation model. Results of the calculations are consistent with experimental studies indicating that numerous compounds may be formed during the oxidation and subsequent reduction of guanine, some of which can react over time to form the observed 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FAPyG) adduct. All four pathways begin with the 8-hydroxyguanine radical (8-OHGrad) species.