Assessment of Different Parameters on the Accuracy of Computational Alanine Scanning of Protein-Protein Complexes with the Molecular Mechanics/Generalized Born Surface Area Method.

Computational alanine scanning with the molecular mechanics generalized Born surface area (MM/GBSA) method constitutes a widely used approach for identifying critical residues at protein-protein interfaces. Despite its popularity, the MM/GBSA method still has certain drawbacks due to its dependence on many factors. Here, we performed a systematical study on the impact of four different parameters, namely, the internal dielectric constant, the generalized Born model, the entropic term, and the inclusion of structural waters on the accuracy of computational alanine scanning calculations with the MM/GBSA method. Our results show that the internal dielectric constant is the most critical parameter for getting accurate predictions. The introduction of entropy and interfacial water molecules decreased the quality of the predictions, while the generalized Born model had little to no effect. Considering the significance of the internal dielectric value, we proposed a methodology based on the energetic predominance of a particular set of amino acids at the protein-protein interface for selecting an appropriate value for this variable. We hope that these results serve as a guideline for future studies of protein-protein complexes using the MM/GBSA method.

Direct and Catalytic C-Glycosylation of Arenes: Expeditious Synthesis of the Remdesivir Nucleoside.

Since early 2020, scientists have strived to find an effective solution to fight SARS-CoV-2, in particular by developing reliable vaccines that inhibit the spread of the disease and repurposing drugs for combatting its effects on the human body. The antiviral prodrug Remdesivir is still the most widely used therapeutic during the early stages of the infection. However, the current synthetic routes rely on the use of protecting groups, air-sensitive reagents, and cryogenic conditions, thus impeding a cost-efficient supply to patients. We have, therefore, focused on the development of a straightforward, direct addition of (hetero)arenes to unprotected sugars. Here we report a silylium-catalyzed and completely stereoselective C-glycosylation that initially yields the open-chain polyols, which can be selectively cyclized to provide either the kinetic α-furanose or the thermodynamically favored ß-anomer. The method significantly expedites the synthesis of Remdesivir precursor GS-441524 after a subsequent Mn-catalyzed C-H oxidation and deoxycyanation.

Comparative assessment of favipiravir and remdesivir against human coronavirus NL63 in molecular docking and cell culture models.

Human coronavirus NL63 (HCoV-NL63) mainly affects young children and immunocompromised patients, causing morbidity and mortality in a subset of patients. Since no specific treatment is available, this study aims to explore the anti-SARS-CoV-2 agents including favipiravir and remdesivir for treating HCoV-NL63 infection. We first successfully modelled the 3D structure of HCoV-NL63 RNA-dependent RNA polymerase (RdRp) based on the experimentally solved SARS-CoV-2 RdRp structure. Molecular docking indicated that favipiravir has similar binding affinities to SARS-CoV-2 and HCoV-NL63 RdRp with LibDock scores of 75 and 74, respectively. The LibDock scores of remdesivir to SARS-CoV-2 and HCoV-NL63 were 135 and 151, suggesting that remdesivir may have a higher affinity to HCoV-NL63 compared to SARS-CoV-2 RdRp. In cell culture models infected with HCoV-NL63, both favipiravir and remdesivir significantly inhibited viral replication and production of infectious viruses. Overall, remdesivir compared to favipiravir is more potent in inhibiting HCoV-NL63 in cell culture. Importantly, there is no evidence of resistance development upon long-term exposure to remdesivir. Furthermore, combining favipiravir or remdesivir with the clinically used antiviral cytokine interferon-alpha resulted in synergistic effects. These findings provided a proof-of-concept that anti-SARS-CoV-2 drugs, in particular remdesivir, have the potential to be repurposed for treating HCoV-NL63 infection.

Fluorescent Amino Acid Initiated de novo Cyclic Peptides for the Label-Free Assessment of Cell Permeability*.

The major obstacle in applying peptides to intracellular targets is their low inherent cell permeability. Standard approaches to attach a fluorophore (e. g. FITC, TAMRA) can change the physicochemical properties of the parent peptide and influence their ability to penetrate and localize in cells. We report a label-free strategy for evaluating the cell permeability of cyclic peptide leads. Fluorescent tryptophan analogues 4-cyanotryptophan (4CNW) and ß-(1-azulenyl)-L-alanine (AzAla) were incorporated into in vitro translated macrocyclic peptides by initiator reprogramming. We then demonstrate these efficient blue fluorescent emitters are good tools for monitoring peptide penetration into cells.

Position-Dependent Diffusion from Biased Simulations and Markov State Model Analysis.

A variety of enhanced statistical and numerical methods are now routinely used to extract important thermodynamic and kinetic information from the vast amount of complex, high-dimensional data obtained from molecular simulations. For the characterization of kinetic properties, Markov state models, in which the long-time statistical dynamics of a system is approximated by a Markov chain on a discrete partition of configuration space, have seen widespread use in recent years. However, obtaining kinetic properties for molecular systems with high energy barriers remains challenging as often enhanced sampling techniques are required with biased simulations to observe the relevant rare events. Particularly, the calculation of diffusion coefficients remains elusive from biased molecular simulation data. Here, we propose a novel method that can calculate multidimensional position-dependent diffusion coefficients equally from either biased or unbiased simulations using the same formalism. Our method builds on Markov state model analysis and the Kramers-Moyal expansion. We demonstrate the validity of our formalism using one- and two-dimensional analytic potentials and also apply it to data from explicit solvent molecular dynamics simulations, including the water-mediated conformations of alanine dipeptide and umbrella sampling simulations of drug transport across a lipid bilayer. Importantly, the developed algorithm presents significant improvement compared to standard methods when the transport of solute across three-dimensional heterogeneous porous media is studied, for example, the prediction of membrane permeation of drug molecules.

Robosample: A rigid-body molecular simulation program based on robot mechanics.

BACKGROUND: Compared with all-atom molecular dynamics (MD), constrained MD methods allow for larger time steps, potentially reducing computational cost. For this reason, there has been continued interest in improving constrained MD algorithms to increase configuration space sampling in molecular simulations. METHODS: Here, we introduce Robosample, a software package that implements high-performance constrained dynamics algorithms, originally developed for robotics, and applies them to simulations of biomolecular systems. As in the gMolmodel package developed by Spiridon and Minh in 2017, Robosample uses Constrained Dynamics Hamiltonian Monte Carlo (CDHMC) as a Gibbs sampling move - a type of Monte Carlo move where a subset of coordinates is allowed to change. In addition to the previously described Cartesian and torsional dynamics moves, Robosample implements spherical and cylindrical joints that can be distributed along the molecule by the user. RESULTS: In alanine dipeptide simulations, the free energy surface is recovered by mixing fully flexible with torsional, cylindrical, or spherical dynamics moves. Ramachandran dynamics, where only the two key torsions are mobile, accelerate the slowest transition by an order of magnitude. We also show that simulations of a complex glycan cover significantly larger regions of the configuration space when mixed with constrained dynamics. MAJOR CONCLUSIONS: Robosample is a tool of choice for efficient conformational sampling of large biomolecules. GENERAL SIGNIFICANCE: Robosample is intended as a reliable and user-friendly simulation package for fast biomolecular sampling that does not require extensive expertise in mechanical engineering or in the statistical mechanics of reduced coordinates.

Machine Learning Approaches for Protein⁻Protein Interaction Hot Spot Prediction: Progress and Comparative Assessment.

Hot spots are the subset of interface residues that account for most of the binding free energy, and they play essential roles in the stability of protein binding. Effectively identifying which specific interface residues of protein⁻protein complexes form the hot spots is critical for understanding the principles of protein interactions, and it has broad application prospects in protein design and drug development. Experimental methods like alanine scanning mutagenesis are labor-intensive and time-consuming. At present, the experimentally measured hot spots are very limited. Hence, the use of computational approaches to predicting hot spots is becoming increasingly important. Here, we describe the basic concepts and recent advances of machine learning applications in inferring the protein⁻protein interaction hot spots, and assess the performance of widely used features, machine learning algorithms, and existing state-of-the-art approaches. We also discuss the challenges and future directions in the prediction of hot spots.

Refining Collective Coordinates and Improving Free Energy Representation in Variational Enhanced Sampling.

Collective variables are used often in many enhanced sampling methods, and their choice is a crucial factor in determining sampling efficiency. However, at times, searching for good collective variables can be challenging. In a recent paper, we combined time-lagged independent component analysis with well-tempered metadynamics in order to obtain improved collective variables from metadynamics runs that use lower quality collective variables [ McCarty, J.; Parrinello, M. J. Chem. Phys. 2017 , 147 , 204109 ]. In this work, we extend these ideas to variationally enhanced sampling. This leads to an efficient scheme that is able to make use of the many advantages of the variational scheme. We apply the method to alanine-3 in water. From an alanine-3 variationally enhanced sampling trajectory in which all the six dihedral angles are biased, we extract much better collective variables able to describe in exquisite detail the protein complex free energy surface in a low dimensional representation. The success of this investigation is helped by a more accurate way of calculating the correlation functions needed in the time-lagged independent component analysis and from the introduction of a new basis set to describe the dihedral angles arrangement.

End-to-end tests using alanine dosimetry in scanned proton beams.

This paper describes end-to-end test procedures as the last fundamental step of medical commissioning before starting clinical operation of the MedAustron synchrotron-based pencil beam scanning (PBS) therapy facility with protons. One in-house homogeneous phantom and two anthropomorphic heterogeneous (head and pelvis) phantoms were used for end-to-end tests at MedAustron. The phantoms were equipped with alanine detectors, radiochromic films and ionization chambers. The correction for the 'quenching' effect of alanine pellets was implemented in the Monte Carlo platform of the evaluation version of RayStation TPS. During the end-to-end tests, the phantoms were transferred through the workflow like real patients to simulate the entire clinical workflow: immobilization, imaging, treatment planning and dose delivery. Different clinical scenarios of increasing complexity were simulated: delivery of a single beam, two oblique beams without and with range shifter. In addition to the dose comparison in the plastic phantoms the dose obtained from alanine pellet readings was compared with the dose determined with the Farmer ionization chamber in water. A consistent systematic deviation of about 2% was found between alanine dosimetry and the ionization chamber dosimetry in water and plastic materials. Acceptable agreement of planned and delivered doses was observed together with consistent and reproducible results of the end-to-end testing performed with different dosimetric techniques (alanine detectors, ionization chambers and EBT3 radiochromic films). The results confirmed the adequate implementation and integration of the new PBS technology at MedAustron. This work demonstrates that alanine pellets are suitable detectors for end-to-end tests in proton beam therapy and the developed procedures with customized anthropomorphic phantoms can be used to support implementation of PBS technology in clinical practice.

Dissipation kinetics, pre-harvest residue limits, and dietary risk assessment of the systemic fungicide metalaxyl in Swiss chard grown under greenhouse conditions.

The residual behavior of the systemic fungicide, metalaxyl, in Swiss chard cultivated at two different locations under greenhouse conditions was investigated using high-performance liquid chromatography coupled with an ultraviolet detector (HPLC-UVD). Samples were randomly collected over 14 days and extracted using acetonitrile, partitioned using solid sodium chloride, and a solid-phase extraction (SPE) NH2 cartridge was used for cleanup. The linearity over a concentration range 0.05-50 mg/L was excellent with a coefficient of determination (R2) of 0.9997. The recovery rate ranged from 77.05 to 88.92% with relative standard deviations (RSDs) ≤ 10.74, and the limits of detection (LOD) and quantification (LOQ) were 0.0033 and 0.01 mg/kg, respectively. The initial (2 h after application) deposits were 4.69 and 5.90 mg/kg for sites 1 and 2, respectively, which increased to 4.95 and 6.57 mg/kg, respectively, one day post-application, owing to the systemic properties of the fungicide. The dissipation half-life was 5.3 and 6.0 days for sites 1 and 2, respectively. The pre-harvest residue limit (PHRL) suggested that if 55.38 and 47.23 mg/kg was applied 10 days before harvest or 33.28 and 30.73 mg/kg was applied 5 days before harvest (for sites 1 and 2, respectively) then the concentration will fall below the maximum residue limit (MRL = 20.0 mg/kg) at the time of harvest. The dietary risk assessment, estimated as hazard quotient (RQ%), indicate that metalaxyl can be safely used in/on Swiss chard, with no hazardous effects expected for consumers.

Evolutionary radiation of lanthipeptides in marine cyanobacteria.

Lanthipeptides are ribosomally derived peptide secondary metabolites that undergo extensive posttranslational modification. Prochlorosins are a group of lanthipeptides produced by certain strains of the ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus Unlike other lanthipeptide-producing bacteria, picocyanobacteria use an unprecedented mechanism of substrate promiscuity for the production of numerous and diverse lanthipeptides using a single lanthionine synthetase. Through a cross-scale analysis of prochlorosin biosynthesis genes-from genomes to oceanic populations-we show that marine picocyanobacteria have the collective capacity to encode thousands of different cyclic peptides, few of which would display similar ring topologies. To understand how this extensive structural diversity arises, we used deep sequencing of wild populations to reveal genetic variation patterns in prochlorosin genes. We present evidence that structural variability among prochlorosins is the result of a diversifying selection process that favors large, rather than small, sequence changes in the precursor peptide genes. This mode of molecular evolution disregards any conservation of the ancestral structure and enables the emergence of extensively different cyclic peptides through short mutational paths based on indels. Contrary to its fast-evolving peptide substrates, the prochlorosin lanthionine synthetase evolves under a strong purifying selection, indicating that the diversification of prochlorosins is not constrained by commensurate changes in the biosynthetic enzyme. This evolutionary interplay between the prochlorosin peptide substrates and the lanthionine synthetase suggests that structure diversification, rather than structure refinement, is the driving force behind the creation of new prochlorosin structures and represents an intriguing mechanism by which natural product diversity arises.

Alzheimer's Protective Cross-Interaction between Wild-Type and A2T Variants Alters Aß42 Dimer Structure.

Whole genome sequencing has recently revealed the protective effect of a single A2T mutation in heterozygous carriers against Alzheimer's disease (AD) and age-related cognitive decline. The impact of the protective cross-interaction between the wild-type (WT) and A2T variants on the dimer structure is therefore of high interest, as the Aß dimers are the smallest known neurotoxic species. Toward this goal, extensive atomistic replica exchange molecular dynamics simulations of the solvated WT homo- and A2T hetero- Aß1-42 dimers have been performed, resulting into a total of 51 µs of sampling for each system. Weakening of a set of transient, intrachain contacts formed between the central and C-terminal hydrophobic residues is observed in the heterodimeric system. The majority of the heterodimers with reduced interaction between central and C-terminal regions lack any significant secondary structure and display a weak interchain interface. Interestingly, the A2T N-terminus, particularly residue F4, is frequently engaged in tertiary and quaternary interactions with central and C-terminal hydrophobic residues in those distinct structures, leading to hydrophobic burial. This atypical involvement of the N-terminus within A2T heterodimer revealed in our simulations implies possible interference on Aß42 aggregation and toxic oligomer formation, which is consistent with experiments. In conclusion, the present study provides detailed structural insights onto A2T Aß42 heterodimer, which might provide molecular insights onto the AD protective effect of the A2T mutation in the heterozygous state.

In vivo assessment of intracellular redox state in rat liver using hyperpolarized [1-13 C]Alanine.

PURPOSE: The intracellular lactate to pyruvate concentration ratio is a commonly used tissue assay biomarker of redox, being proportional to free cytosolic [NADH]/[NAD+ ]. In this study, we assessed the use of hyperpolarized [1-13 C]alanine and the subsequent detection of the intracellular products of [1-13 C]pyruvate and [1-13 C]lactate as a useful substrate for assessing redox levels in the liver in vivo. METHODS: Animal experiments were conducted to measure in vivo metabolism at baseline and after ethanol infusion. A solution of 80-mM hyperpolarized [1-13 C]alanine was injected intravenously at baseline (n = 8) and 45 min after ethanol infusion (n = 4), immediately followed by the dynamic acquisition of 13 C MRS spectra. RESULTS: In vivo rat liver spectra showed peaks from [1-13 C] alanine and the products of [1-13 C]lactate, [1-13 C]pyruvate, and 13 C-bicarbonate. A significantly increased 13 C-lactate/13 C-pyruvate ratio was observed after ethanol infusion (8.46 ± 0.58 at baseline versus 13.58 ± 0.69 after ethanol infusion; P < 0.001) consistent with the increased NADH produced by liver metabolism of ethanol to acetaldehyde and then acetate. A decrease in 13 C-bicarbonate production was also noted, potentially reflecting ethanol-induced mitochondrial redox changes. CONCLUSION: A method to measure in vivo tissue redox using hyperpolarized [1-13 C]alanine is presented, with the validity of the proposed 13 C-pyruvate/13 C-lactate metric tested using an ethanol challenge to alter liver redox state. Magn Reson Med 77:1741-1748, 2017. © 2017 International Society for Magnetic Resonance in Medicine.

Dynamic quantum crystallography: lattice-dynamical models refined against diffraction data. II. Applications to L-alanine, naphthalene and xylitol.

In the first paper of this series [Hoser & Madsen (2016). Acta Cryst. A72, 206-214], a new approach was introduced which enables the refinement of frequencies of normal modes obtained from ab initio periodic computations against single-crystal diffraction data. In this contribution, the performance of this approach is tested by refinement against data in the temperature range from 23 to 205 K on the molecular crystals of L-alanine, naphthalene and xylitol. The models, which are lattice-dynamical models derived at the Γ point of the Brillouin zone, are able to describe the atomic vibrations of L-alanine and naphthalene to a level where the residual densities are similar to those obtained from the independent atom model. For the more flexible molecule xylitol, larger deviations are found. Hydrogen ADPs (anisotropic displacement parameters) derived from the models are in similar or better agreement with neutron diffraction results than ADPs obtained by other procedures. The heat capacity calculated after normal mode refinement for naphthalene is in reasonable agreement with the heat capacity obtained from calorimetric measurements (to less than 1 cal mol-1 K-1 below 300 K), with deviations at higher temperatures indicating anharmonicity. Standard uncertainties and correlation of the refined parameters have been derived based on a Monte Carlo procedure. The uncertainties are quite small and probably underestimated.

Time-Dependent Markov State Models for Single Molecule Force Spectroscopy.

This Letter demonstrates that using time-dependent Markov state models (TD-MSMs) one can obtain molecular-scale insights into force-extension curves for a variety of stretching experiments. A master-MSM constructed at a reference extension forms the basis for generating the required TD-MSM, i.e., the TD-MSM that is appropriate for the stretching experiment can be constructed from a single master-MSM. In addition, the availability of state-specific force models enable calculation of force-extension behavior in a variety of ensembles. Changes in the network topology upon stretching are related through a thermodynamic quantity termed the mechanical disposition. Proof-of-principle is provided using a stretched alanine decapeptide under a time-varying pulling force.

Kinetic Analysis of Protein Stability Reveals Age-Dependent Degradation.

Do young and old protein molecules have the same probability to be degraded? We addressed this question using metabolic pulse-chase labeling and quantitative mass spectrometry to obtain degradation profiles for thousands of proteins. We find that >10% of proteins are degraded non-exponentially. Specifically, proteins are less stable in the first few hours of their life and stabilize with age. Degradation profiles are conserved and similar in two cell types. Many non-exponentially degraded (NED) proteins are subunits of complexes that are produced in super-stoichiometric amounts relative to their exponentially degraded (ED) counterparts. Within complexes, NED proteins have larger interaction interfaces and assemble earlier than ED subunits. Amplifying genes encoding NED proteins increases their initial degradation. Consistently, decay profiles can predict protein level attenuation in aneuploid cells. Together, our data show that non-exponential degradation is common, conserved, and has important consequences for complex formation and regulation of protein abundance.

Balancing Accuracy and Cost of Confinement Simulations by Interpolation and Extrapolation of Confinement Energies.

Improvements to the confinement method for the calculation of conformational free energy differences are presented. By taking advantage of phase space overlap between simulations at different frequencies, significant gains in accuracy and speed are reached. The optimal frequency spacing for the simulations is obtained from extrapolations of the confinement energy, and relaxation time analysis is used to determine time steps, simulation lengths, and friction coefficients. At postprocessing, interpolation of confinement energies is used to significantly reduce discretization errors in the calculation of conformational free energies. The efficiency of this protocol is illustrated by applications to alanine n-peptides and lactoferricin. For the alanine-n-peptide, errors were reduced between 2- and 10-fold and sampling times between 8- and 67-fold, while for lactoferricin the long sampling times at low frequencies were reduced 10-100-fold.

Perturbation correction for alanine dosimeters in different phantom materials in high-energy photon beams.

In modern radiotherapy the verification of complex treatments plans is often performed in inhomogeneous or even anthropomorphic phantoms. For dose verification small detectors are necessary and therefore alanine detectors are most suitable. Though the response of alanine for a wide range of clinical photon energies in water is well know, the knowledge about the influence of the surrounding phantom material on the response of alanine is sparse. Therefore we investigated the influence of twenty different surrounding/phantom materials for alanine dosimeters in clinical photon fields via Monte Carlo simulations. The relative electron density of the used materials was in the range [Formula: see text] up to 1.69, covering almost all materials appearing in inhomogeneous or anthropomorphic phantoms used in radiotherapy. The investigations were performed for three different clinical photon spectra ranging from 6 to 25 MV-X and Co-60 and as a result a perturbation correction [Formula: see text] depending on the environmental material was established. The Monte Carlo simulation show, that there is only a small dependence of [Formula: see text] on the phantom material and the photon energy, which is below ±0.6%. The results confirm the good suitability of alanine detectors for in-vivo dosimetry.

Low-Cost Peptide Microarrays for Mapping Continuous Antibody Epitopes.

With the increasing need for understanding antibody specificity in antibody and vaccine research, pepscan assays provide a rapid method for mapping and profiling antibody responses to continuous epitopes. We have developed a relatively low-cost method to generate peptide microarray slides for studying antibody binding. Using a setup of an IntavisAG MultiPep RS peptide synthesizer, a Digilab MicroGrid II 600 microarray printer robot, and an InnoScan 1100 AL scanner, the method allows the interrogation of up to 1536 overlapping, alanine-scanning, and mutant peptides derived from the target antigens. Each peptide is tagged with a polyethylene glycol aminooxy terminus to improve peptide solubility, orientation, and conjugation efficiency to the slide surface.

Reducing the cost of evaluating the committor by a fitting procedure.

Correct identification of reaction coordinates in complex systems is essential for understanding the mechanisms of their reaction dynamics. Existing methods for identifying reaction coordinates typically require knowledge of the committor--the probability of a given configuration to reach the product basin. The high computational cost of evaluating committors has limited applications of methods for identifying reaction coordinates. We proposed a fitting procedure that can reduce the cost of evaluating committors by an order of magnitude or more. The method only requires evaluating the committors of a few configurations in a transition path by the standard and costly shooting procedure. The committors of the other configurations are then estimated with great accuracy by a sigmoid function derived from fitting the few numerically evaluated committors. The method has been systematically tested on a model system of a Brownian particle moving in a one-dimensional double-well potential, and a small biomolecular system--the isomerization of alanine dipeptide in vacuum and in explicit water.