The Role of General Acid Catalysis in the Mechanism of an Alkyl Transferase Ribozyme.

MTR1 is an in vitro-selected alkyl transferase ribozyme that transfers an alkyl group from -alkylguanine to N1 of the target adenine in the RNA substrate (A63). The structure of the ribozyme suggested a mechanism in which a cytosine (C10) acts as a general acid to protonate -alkylguanine N1. Here, we have analyzed the role of the C10 general acid and the A63 nucleophile by atomic mutagenesis and computation.

Assessing variations in care delivered to rural out of hospital cardiac arrest patients in the interfacility transfer setting.

Objective: There is significant variation in out-of-hospital cardiac arrest (OHCA) outcomes between different regions. We sought to evaluate outcomes of OHCA patients in the interfacility transfer (IFT) setting, between critical care transport (LifeFlight) and community Emergency Medical Services (EMS), in the state of Maine.

Methods: This was a retrospective analysis of our institution's electronic medical record and the Maine EMS database.

Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach.

Accurate predictions of how strongly small molecules bind to proteins, such as those afforded by relative binding free energy (RBFE) calculations, can greatly increase the efficiency of the hit-to-lead and lead optimization stages of the drug discovery process. The success of such calculations, however, relies heavily on their precision. Here, we show that a recently developed alchemical enhanced sampling (ACES) approach can consistently improve the precision of RBFE calculations on a large and diverse set of proteins and small molecule ligands.

Adsorption of Flavonoids in a Transcriptional Regulator TtgR: Relative Binding Free Energies and Intermolecular Interactions.

Antimicrobial resistance in bacteria often arises from their ability to actively identify and expel toxic compounds. The bacterium strain DOT-T1E utilizes its TtgABC efflux pump to confer robust resistance against antibiotics, flavonoids, and organic solvents. This resistance mechanism is intricately regulated at the transcriptional level by the TtgR protein.

Software Infrastructure for Next-Generation QM/MM-ΔMLP Force Fields.

We present software infrastructure for the design and testing of new quantum mechanical/molecular mechanical and machine-learning potential (QM/MM-ΔMLP) force fields for a wide range of applications. The software integrates Amber's molecular dynamics simulation capabilities with fast, approximate quantum models in the xtb package and machine-learning potential corrections in DeePMD-kit. The xtb package implements the recently developed density-functional tight-binding QM models with multipolar electrostatics and density-dependent dispersion (GFN2-xTB), and the interface with Amber enables their use in periodic boundary QM/MM simulations with linear-scaling QM/MM particle-mesh Ewald electrostatics.

Electronic and Nuclear Quantum Effects on Proton Transfer Reactions of Guanine-Thymine (G-T) Mispairs Using Combined Quantum Mechanical/Molecular Mechanical and Machine Learning Potentials.

Rare tautomeric forms of nucleobases can lead to Watson-Crick-like (WC-like) mispairs in DNA, but the process of proton transfer is fast and difficult to detect experimentally. NMR studies show evidence for the existence of short-time WC-like guanine-thymine (G-T) mispairs; however, the mechanism of proton transfer and the degree to which nuclear quantum effects play a role are unclear. We use a B-DNA helix exhibiting a wGT mispair as a model system to study tautomerization reactions.

Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials.

We report the development and testing of new integrated cyberinfrastructure for performing free energy simulations with generalized hybrid quantum mechanical/molecular mechanical (QM/MM) and machine learning potentials (MLPs) in Amber. The Sander molecular dynamics program has been extended to leverage fast, density-functional tight-binding models implemented in the DFTB+ and xTB packages, and an interface to the DeePMD-kit software enables the use of MLPs. The software is integrated through application program interfaces that circumvent the need to perform "system calls" and enable the incorporation of long-range Ewald electrostatics into the external software's self-consistent field procedure.

Alchemical Enhanced Sampling with Optimized Phase Space Overlap.

An alchemical enhanced sampling (ACES) method has recently been introduced to facilitate importance sampling in free energy simulations. The method achieves enhanced sampling from Hamiltonian replica exchange within a dual topology framework while utilizing new smoothstep softcore potentials. A common sampling problem encountered in lead optimization is the functionalization of aromatic rings that exhibit distinct conformational preferences when interacting with the protein.

Surface-Accelerated String Method for Locating Minimum Free Energy Paths.

We present a surface-accelerated string method (SASM) to efficiently optimize low-dimensional reaction pathways from the sampling performed with expensive quantum mechanical/molecular mechanical (QM/MM) Hamiltonians. The SASM accelerates the convergence of the path using the aggregate sampling obtained from the current and previous string iterations, whereas approaches like the string method in collective variables (SMCV) or the modified string method in collective variables (MSMCV) update the path only from the sampling obtained from the current iteration. Furthermore, the SASM decouples the number of images used to perform sampling from the number of synthetic images used to represent the path.

Modern Alchemical Free Energy Methods for Drug Discovery Explained.

This Perspective provides a contextual explanation of the current state-of-the-art alchemical free energy methods and their role in drug discovery as well as highlights select emerging technologies. The narrative attempts to answer basic questions about what goes on "under the hood" in free energy simulations and provide general guidelines for how to run simulations and analyze the results. It is the hope that this work will provide a valuable introduction to students and scientists in the field.

A variant in the 5'UTR of ERBB4 is associated with lifespan in Golden Retrievers.

Genome-wide association studies (GWAS) in long-lived human populations have led to identification of variants associated with Alzheimer's disease and cardiovascular disease, the latter being the most common cause of mortality in people worldwide. In contrast, naturally occurring cancer represents the leading cause of death in pet dogs, and specific breeds like the Golden Retriever (GR) carry up to a 65% cancer-related death rate. We hypothesized that GWAS of long-lived GRs might lead to the identification of genetic variants capable of modifying longevity within this cancer-predisposed breed.

AmberTools.

AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.

DeePMD-kit v2: A software package for deep potential models.

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features, such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, DP-range correction, DP long range, graphics processing unit support for customized operators, model compression, non-von Neumann molecular dynamics, and improved usability, including documentation, compiled binary packages, graphical user interfaces, and application programming interfaces.

Rapid Kinetics of Pistol Ribozyme: Insights into Limits to RNA Catalysis.

Pistol ribozyme (Psr) is a distinct class of small endonucleolytic ribozymes, which are important experimental systems for defining fundamental principles of RNA catalysis and designing valuable tools in biotechnology. High-resolution structures of Psr, extensive structure-function studies, and computation support a mechanism involving one or more catalytic guanosine nucleobases acting as a general base and divalent metal ion-bound water acting as an acid to catalyze RNA 2'--transphosphorylation. Yet, for a wide range of pH and metal ion concentrations, the rate of Psr catalysis is too fast to measure manually and the reaction steps that limit catalysis are not well understood.

Establishment and characterization of two novel patient-derived lines from canine high-grade glioma.

High-grade glioma is an aggressive cancer that occurs naturally in pet dogs. Canine high-grade glioma (cHGG) is treated with radiation, chemotherapy or surgery, but has no curative treatment. Within the past eight years, there have been advances in our imaging and histopathology standards as well as genetic charactereization of cHGG.

Multicenter Evaluation of Frequency and Impact of Activity Infiltration in PET Imaging, Including Microscale Modeling of Skin-Absorbed Dose.

There has been significant recent interest in understanding both the frequency of nuclear medicine injection infiltration and the potential for negative impact, including skin injury. However, no large-scale study has yet correlated visualized injection site activity with actual activity measurement of an infiltrate. Additionally, current skin dosimetry approaches lack sufficient detail to account for critical factors that impact the dose to the radiosensitive epidermis.

Nailfold Capillaroscopy: A Promising, Noninvasive Approach to Predict Retinopathy of Prematurity.

Objective: To test the hypothesis that nailfold capillaroscopy can noninvasively detect dysregulated retinal angiogenesis and predict retinopathy of prematurity (ROP) in infants born premature before its development.

Methods: In a cohort of 32 infants born <33 weeks of gestation, 1386 nailfold capillary network images of the 3 middle fingers of each hand were taken during the first month of life. From these, 25 infants had paired data taken 2 weeks apart during the first month of life.

Estimation of frequency factors for the calculation of kinetic isotope effects from classical and path integral free energy simulations.

We use the modified Bigeleisen-Mayer equation to compute kinetic isotope effect values for non-enzymatic phosphoryl transfer reactions from classical and path integral molecular dynamics umbrella sampling. The modified form of the Bigeleisen-Mayer equation consists of a ratio of imaginary mode vibrational frequencies and a contribution arising from the isotopic substitution's effect on the activation free energy, which can be computed from path integral simulation. In the present study, we describe a practical method for estimating the frequency ratio correction directly from umbrella sampling in a manner that does not require normal mode analysis of many geometry optimized structures.

Biomass carbon mining to develop nature-inspired materials for a circular economy.

A transition from a linear to a circular economy is the only alternative to reduce current pressures in natural resources. Our society must redefine our material sources, rethink our supply chains, improve our waste management, and redesign materials and products. Valorizing extensively available biomass wastes, as new carbon mines, and developing biobased materials that mimic nature's efficiency and wasteless procedures are the most promising avenues to achieve technical solutions for the global challenges ahead.

Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology.

A methyltransferase ribozyme (MTR1) was selected in vitro to catalyze alkyl transfer from exogenous O6-methylguanine (O6mG) to a target adenine N1, and recently, high-resolution crystal structures have become available. We use a combination of classical molecular dynamics, ab initio quantum mechanical/molecular mechanical (QM/MM) and alchemical free energy (AFE) simulations to elucidate the atomic-level solution mechanism of MTR1. Simulations identify an active reactant state involving protonation of C10 that hydrogen bonds with O6mG:N1.

Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: Conformers, tautomers, and protonation states.

Modern semiempirical electronic structure methods have considerable promise in drug discovery as universal "force fields" that can reliably model biological and drug-like molecules, including alternative tautomers and protonation states. Herein, we compare the performance of several neglect of diatomic differential overlap-based semiempirical (MNDO/d, AM1, PM6, PM6-D3H4X, PM7, and ODM2), density-functional tight-binding based (DFTB3, DFTB/ChIMES, GFN1-xTB, and GFN2-xTB) models with pure machine learning potentials (ANI-1x and ANI-2x) and hybrid quantum mechanical/machine learning potentials (AIQM1 and QDπ) for a wide range of data computed at a consistent ωB97X/6-31G* level of theory (as in the ANI-1x database). This data includes conformational energies, intermolecular interactions, tautomers, and protonation states.

Altered Mechanisms for Acid-Catalyzed RNA Cleavage and Isomerization Reactions Models.

RNA strand cleavage by 2'-O-transphosphorylation is catalyzed not only by numerous nucleolytic RNA enzymes (ribozymes) but also by hydroxide or hydronium ions. In experiments, both cleavage of the 5'-linked nucleoside and isomerization between 3',5'- and 2',5'-phosphodiesters occur under acidic conditions, while only the cleavage reaction is observed under basic conditions. An path-integral approach for simulating kinetic isotope effects is used to reveal the reaction mechanisms for RNA cleavage and isomerization reactions under acidic conditions.