Novel pathogenic variants in a female with normal neurodevelopment.

Electron transport chain (ETC) disorders are a group of rare, multisystem diseases caused by impaired oxidative phosphorylation and energy production. Deficiencies in complex III (CIII), also known as ubiquinol-cytochrome reductase, are particularly rare in humans. Ubiquinol-cytochrome reductase core protein 2 () encodes a subunit of CIII that plays a crucial role in dimerization.

Electron transport chain inhibition increases cellular dependence on purine transport and salvage.

Cancer cells reprogram their metabolism to support cell growth and proliferation in harsh environments. While many studies have documented the importance of mitochondrial oxidative phosphorylation (OXPHOS) in tumor growth, some cancer cells experience conditions of reduced OXPHOS in vivo and induce alternative metabolic pathways to compensate. To assess how human cells respond to mitochondrial dysfunction, we performed metabolomics in fibroblasts and plasma from patients with inborn errors of mitochondrial metabolism, and in cancer cells subjected to inhibition of the electron transport chain (ETC).

Assessment of proton-coupled conformational dynamics of SARS and MERS coronavirus papain-like proteases: Implication for designing broad-spectrum antiviral inhibitors.

Broad-spectrum antiviral drugs are urgently needed to stop the Coronavirus Disease 2019 pandemic and prevent future ones. The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is related to the SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), which have caused the previous outbreaks. The papain-like protease (PLpro) is an attractive drug target due to its essential roles in the viral life cycle.

Predicting Reactive Cysteines with Implicit-Solvent-Based Continuous Constant pH Molecular Dynamics in Amber.

Cysteines existing in the deprotonated thiolate form or having a tendency to become deprotonated are important players in enzymatic and cellular redox functions and frequently exploited in covalent drug design; however, most computational studies assume cysteines as protonated. Thus, developing an efficient tool that can make accurate and reliable predictions of cysteine protonation states is timely needed. We recently implemented a generalized Born (GB) based continuous constant pH molecular dynamics (CpHMD) method in Amber for protein p calculations on CPUs and GPUs.

GPU-Accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: p Predictions with Single-pH Simulations.

We present a GPU implementation of the continuous constant pH molecular dynamics (CpHMD) based on the most recent generalized Born implicit-solvent model in the engine of the Amber molecular dynamics package. To test the accuracy of the tool for rapid p predictions, a series of 2 ns single-pH simulations were performed for over 120 titratable residues in 10 benchmark proteins that were previously used to test the various continuous CpHMD methods. The calculated p's showed a root-mean-square deviation of 0.

How Ligand Protonation State Controls Water in Protein-Ligand Binding.

The role of water in protein-ligand binding has been an intensely studied topic in recent years; however, how ligand protonation state change perturbs water has not been considered. Here we show that water dynamics and interactions can be controlled by the protonation state of ligand using continuous constant pH molecular dynamics simulations of two closely related model systems, β-secretase 1 and 2 (BACE1 and BACE2), in complex with a small-molecule inhibitor. Simulations revealed that, upon binding, the inhibitor pyrimidine ring remains deprotonated in BACE1 but becomes protonated in BACE2.

Generalized Born Based Continuous Constant pH Molecular Dynamics in Amber: Implementation, Benchmarking and Analysis.

Solution pH plays an important role in structure and dynamics of biomolecular systems; however, pH effects cannot be accurately accounted for in conventional molecular dynamics simulations based on fixed protonation states. Continuous constant pH molecular dynamics (CpHMD) based on the λ-dynamics framework calculates protonation states on the fly during dynamical simulation at a specified pH condition. Here we report the CPU-based implementation of the CpHMD method based on the GBNeck2 generalized Born (GB) implicit-solvent model in the pmemd engine of the Amber molecular dynamics package.

Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies.

The need for accurate yet efficient representation of the aqueous environment in biomolecular modeling has led to the development of a variety of generalized Born (GB) implicit solvent models. While many studies have focused on the accuracy of available GB models in predicting solvation free energies, a systematic assessment of the quality of these models in binding free energy calculations, crucial for rational drug design, has not been undertaken. Here, we evaluate the accuracies of eight common GB flavors (GB-HCT, GB-OBC, GB-neck2, GBNSR6, GBSW, GBMV1, GBMV2, and GBMV3), available in major molecular dynamics packages, in predicting the electrostatic binding free energies ( ΔΔ G) for a diverse set of 60 biomolecular complexes belonging to four main classes: protein-protein, protein-drug, RNA-peptide, and small complexes.

Proton-Coupled Conformational Allostery Modulates the Inhibitor Selectivity for β-Secretase.

Many important pharmaceutical targets, such as aspartyl proteases and kinases, exhibit pH-dependent dynamics, functions and inhibition. Accurate prediction of their binding free energies is challenging because current computational techniques neglect the effects of pH. Here we combine free energy perturbation calculations with continuous constant pH molecular dynamics to explore the selectivity of a small-molecule inhibitor for β-secretase (BACE1), an important drug target for Alzheimer's disease.

Numerical Difficulties Computing Electrostatic Potentials Near Interfaces with the Poisson-Boltzmann Equation.

Many researchers compute surface maps of the electrostatic potential (φ) with the Poisson-Boltzmann (PB) equation to relate the structural information obtained from X-ray and NMR experiments to biomolecular functions. Here we demonstrate that the usual method of obtaining these surface maps of φ, by interpolating from neighboring grid points on the solution grid generated by a PB solver, generates large errors because of the large discontinuity in the dielectric constant (and thus in the normal derivative of φ) at the surface. The Cartesian Poisson-Boltzmann solver contains several features that reduce the numerical noise in surface maps of φ: First, CPB introduces additional mesh points at the Cartesian grid/surface intersections where the PB equation is solved.

Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points.

Many biomolecules undergo conformational changes associated with allostery or ligand binding. Observing these changes in computer simulations is difficult if their timescales are long. These calculations can be accelerated by observing the transition on an auxiliary free energy surface with a simpler Hamiltonian and connecting this free energy surface to the target free energy surface with free energy calculations.

Correction: Molecular and ionic diffusion in aqueous - deep eutectic solvent mixtures: probing inter-molecular interactions using PFG NMR.

Correction for 'Molecular and ionic diffusion in aqueous - deep eutectic solvent mixtures: probing inter-molecular interactions using PFG NMR' by Carmine D'Agostino et al., Phys. Chem.

Glucose-dependent anaplerosis in cancer cells is required for cellular redox balance in the absence of glutamine.

Cancer cells have altered metabolism compared to normal cells, including dependence on glutamine (GLN) for survival, known as GLN addiction. However, some cancer cell lines do not require GLN for survival and the basis for this discrepancy is not well understood. GLN is a precursor for antioxidants such as glutathione (GSH) and NADPH, and GLN deprivation is therefore predicted to deplete antioxidants and increase reactive oxygen species (ROS).

Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility.

Oligoglycine is a backbone mimic for all proteins and is prevalent in the sequences of intrinsically disordered proteins. We have computed the absolute chemical potential of glycine oligomers at infinite dilution by simulation with the CHARMM36 and Amber ff12SB force fields. We performed a thermodynamic decomposition of the solvation free energy (ΔG(sol)) of Gly2-5 into enthalpic (ΔH(sol)) and entropic (ΔS(sol)) components as well as their van der Waals and electrostatic contributions.

Reconciling the understanding of 'hydrophobicity' with physics-based models of proteins.

The idea that a 'hydrophobic energy' drives protein folding, aggregation, and binding by favoring the sequestration of bulky residues from water into the protein interior is widespread. The solvation free energies (ΔGsolv) of small nonpolar solutes increase with surface area (A), and the free energies of creating macroscopic cavities in water increase linearly with A. These observations seem to imply that there is a hydrophobic component (ΔGhyd) of ΔGsolv that increases linearly with A, and this assumption is widely used in implicit solvent models.

Examining the assumptions underlying continuum-solvent models.

Continuum-solvent models (CSMs) have successfully predicted many quantities, including the solvation-free energies (ΔG) of small molecules, but they have not consistently succeeded at reproducing experimental binding free energies (ΔΔG), especially for protein-protein complexes. Several CSMs break ΔG into the free energy (ΔGvdw) of inserting an uncharged molecule into solution and the free energy (ΔGel) gained from charging. Some further divide ΔGvdw into the free energy (ΔGrep) of inserting a nearly hard cavity into solution and the free energy (ΔGatt) gained from turning on dispersive interactions between the solute and solvent.

Problems of robustness in Poisson-Boltzmann binding free energies.

Although models based on the Poisson–Boltzmann (PB) equation have been fairly successful at predicting some experimental quantities, such as solvation free energies (ΔG), these models have not been consistently successful at predicting binding free energies (ΔΔG). Here we found that ranking a set of protein–protein complexes by the electrostatic component (ΔΔGel) of ΔΔG was more difficult than ranking the same molecules by the electrostatic component (ΔGel) of ΔG. This finding was unexpected because ΔΔGel can be calculated by combining estimates of ΔGel for the complex and its components with estimates of the ΔΔGel in vacuum.

Protein collapse driven against solvation free energy without H-bonds.

Proteins collapse and fold because intramolecular interactions and solvent entropy, which favor collapse, outweigh solute-solvent interactions that favor expansion. Since the protein backbone actively participates in protein folding and some intrinsically disordered proteins are glycine rich, oligoglycines are good models to study the protein backbone as it collapses, both during conformational changes in disordered proteins and during folding. The solvation free energies of short glycine oligomers become increasingly favorable as chain length increases.

Molecular and ionic diffusion in aqueous - deep eutectic solvent mixtures: probing inter-molecular interactions using PFG NMR.

Pulsed field gradient (PFG) NMR has been used to probe self-diffusion of molecular and ionic species in aqueous mixtures of choline chloride (ChCl) based deep eutectic solvents (DESs), in order to elucidate the effect of water on motion and inter-molecular interactions between the different species in the mixtures, namely the Ch(+) cation and hydrogen bond donor (HBD). The results reveal an interesting and complex behaviour of such mixtures at a molecular level. In general, it is observed that the hydroxyl protons ((1)H) of Ch(+) and the hydrogen bond donor have diffusion coefficients significantly different from those measured for their parent molecules when water is added.

Multibody correlations in the hydrophobic solvation of glycine peptides.

Protein collapse during folding is often assumed to be driven by a hydrophobic solvation energy (ΔGvdw) that scales linearly with solvent-accessible surface area (A). In a previous study, we argued that ΔGvdw, as well as its attractive (ΔGatt) and repulsive (ΔGrep) components, was not simply a linear function of A. We found that the surface tensions, γrep, γatt, and γvdw, gotten from ΔGrep, ΔGatt, and ΔGvdw against A for four configurations of deca-alanine differed from those obtained for a set of alkanes.

Features of CPB: a Poisson-Boltzmann solver that uses an adaptive Cartesian grid.

The capabilities of an adaptive Cartesian grid (ACG)-based Poisson-Boltzmann (PB) solver (CPB) are demonstrated. CPB solves various PB equations with an ACG, built from a hierarchical octree decomposition of the computational domain. This procedure decreases the number of points required, thereby reducing computational demands.

Effects of geometry and chemistry on hydrophobic solvation.

Inserting an uncharged van der Waals (vdw) cavity into water disrupts the distribution of water and creates attractive dispersion interactions between the solvent and solute. This free-energy change is the hydrophobic solvation energy (ΔG(vdw)). Frequently, it is assumed to be linear in the solvent-accessible surface area, with a positive surface tension (γ) that is independent of the properties of the molecule.