Perspective on Integrative Simulations of Bioenergetic Domains.

Bioenergetic processes in cells, such as photosynthesis or respiration, integrate many time and length scales, which makes the simulation of energy conversion with a mere single level of theory impossible. Just like the myriad of experimental techniques required to examine each level of organization, an array of overlapping computational techniques is necessary to model energy conversion. Here, a perspective is presented on recent efforts for modeling bioenergetic phenomena with a focus on molecular dynamics simulations and its variants as a primary method. An overview of the various classical, quantum mechanical, enhanced sampling, coarse-grained, Brownian dynamics, and Monte Carlo methods is presented. Example applications discussed include multiscale simulations of membrane-wide electron transport, rate kinetics of ATP turnover from electrochemical gradients, and finally, integrative modeling of the chromatophore, a photosynthetic pseudo-organelle.

Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge.

The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein/nucleic-acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 Å) resolution. Three published maps were selected as targets: E. coli beta-galactosidase with inhibitor, SARS-CoV-2 RNA-dependent RNA polymerase with covalently bound nucleotide analog, and SARS-CoV-2 ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. We found that (1) the quality of submitted ligand models and surrounding atoms varied, as judged by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics, and contact scores, and (2) a composite rather than a single score was needed to assess macromolecule+ligand model quality. These observations lead us to recommend best practices for assessing cryo-EM structures of liganded macromolecules reported at near-atomic resolution.

Ab initio Modeling of Hydrogen Bonding of Remdesivir and Adenosine with Uridine.

Remdesivir (RDV) emerged as an effective drug against the SARS-CoV-2 virus pandemic. One of the crucial steps in the mechanism of action of RDV is its incorporation into the growing RNA strand. RDV, an adenosine analogue, forms Watson-Crick (WC) type hydrogen bonds with uridine in the complementary strand and the strength of this interaction will control efficacy of RDV. While there is a plethora of structural and energetic information available about WC H-bonds in natural base pairs, the interaction of RDV with uridine has not been studied yet at the atomic level. In this article, we aim to bridge this gap, to understand RDV and its hydrogen bonding interactions, by employing density functional theory (DFT) at the M06-2X/cc-pVDZ level. The interaction energy, QTAIM analysis, NBO and SAPT2 are performed for RDV, adenosine, and their complex with uridine to gain insights into the nature of hydrogen bonding. The computations show that RDV has similar geometry, energetic, molecular orbitals, and aromaticity as adenosine, suggesting that RDV is an effective adenosine analogue. The important geometrical parameters, such as bond distances and red-shift in the stretching vibrational modes of adenosine, RDV and uridine identify two WC-type H-bonds. The relative strength of these two H-bonds is computed using QTAIM parameters and the computed hydrogen bond energy. Finally, the SAPT2 study is performed at the minima and at non-equilibrium base pair distances to understand the dominant intermolecular physical force. This study, based on a thorough analysis of a variety of computations, suggests that both adenosine and RDV have similar structure, energetic, and hydrogen bonding behaviour.

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.

This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density.

Continuous infusion of vancomycin improved therapeutic levels in term and preterm infants.

BACKGROUND: Growing evidence suggests that continuous infusion of vancomycin (CIV) is superior to intermittent infusion of vancomycin (IIV) in neonates. This quality improvement (QI) project aimed to transition from IIV to CIV with earlier and improved attainment of therapeutic vancomycin levels. METHODS: The Model for Improvement framework with Plan Do Study Act cycles was used. Prospective data were collected during three phases: IIV, CIV-1 and CIV-2. INTERVENTIONS: A QI team developed a CIV drug monograph and a multidisciplinary education package. RESULTS: Using IIV, 36% (9/25) of first vancomycin levels were within target range. CIV achieved therapeutic levels twice as quickly as IIV (p < 0.05) with improved first vancomycin target levels (IIV 36%, 9/25; CIV-1 55%, 16/29; CIV-2 61%, 14/23) and total therapeutic levels (IIV 44%, 37/84; CIV-1 56%, 55/98; CIV-2 69%, 79/114). CONCLUSIONS: This QI project demonstrated a successful transition from IIV to CIV with reduced time to achieve target vancomycin and an increased proportion of therapeutic levels.

Molecular Dynamics Flexible Fitting: All You Want to Know About Resolution Exchange.

In recent years, owing to the advances in instrumentation, cryo-EM has emerged as the go-to tool for obtaining high-resolution structures of biomolecular systems. However, building three-dimensional atomic structures of biomolecules from these high-resolution maps remains a concern for the traditional map-guided structure-determination schemes. Recently, we developed a computational tool, Resolution Exchange Molecular Dynamics Flexible Fitting (ReMDFF) to address this problem by re-refining a search model against a series of maps of progressively higher resolutions, which ends with the original experimental resolution (Wang et al., J Struct Biol 204(2):319-328, 2018). In this chapter, we present a step-by-step outline for preparing, executing, and analyzing ReMDFF refinements of simple proteins and multimeric complexes. The structure determination of carbon monoxide dehydrogenase and Mg2+-channel CorA are employed as case studies. All scripts are provided via GitHub (Vant, Resolution exchange molecular dynamics flexible fitting (ReMDFF) all you want to know about flexible fitting, 2019, https://github.com/jvant/ReMDFF_Singharoy_Group.git ).

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. Enhanced sampling is employed to explore the binding pocket rearrangements. To provide a model that can accurately describe the conformational dynamics of the chemically diverse set of small-molecule drugs inside MDFF, we use QM/MM and neural-network potential (NNP)/MM models of protein-ligand complexes, where the ligand is represented using the QM or NNP model, and the protein is represented using established molecular mechanical force fields (e.g., CHARMM). This pipeline offers structures commensurate to or better than recently submitted high-resolution cryo-EM or X-ray models, even when given medium to low-resolution data as input. The use of the NNPs makes the algorithm more robust to the choice of search models, offering a radius of convergence of 6.5 Å for ligand structure determination. The quality of the predicted structures was also judged by density functional theory calculations of ligand strain energy. This strain potential energy is found to systematically decrease with better fitting to density and improved ligand coordination, indicating correct binding interactions. A computationally inexpensive protocol for computing strain energy is reported as part of the model analysis protocol that monitors both the ligand fit as well as model quality.

Solvent-Enhanced Conformational Flexibility of Cyclic Tetrapeptides.

Solvent and temperature can affect the structural properties of cyclic peptides by controlling their flexibility. Here, we investigate two cyclic peptides, featuring beta turns. Using temperature-dependent NMR and FT-IR, we observed a pronounced temperature effect on the conformation of the cyclic peptide D-1 in CHCl3 but a much smaller effect in CH3 CN. Almost no effect was observed for its diastereomer L-1 within a similar temperature range and using the same solvents. With the aid of Replica Exchange Molecular Dynamics simulations and Quantum Mechanics/Molecular Mechanics calculations, we were able to explain this behavior based on the increased flexibility of D-1 (in CHCl3 ) in terms of intramolecular hydrogen bonding. The largest temperature dependence is observed for D-1 in CHCl3 , while the temperature effect is less pronounced for L-1 in CHCl3 and for both peptides in CH3 CN. This work provides new insights into the role of the environment and temperature on the conformations of cyclic peptides.

Ferrites: magnetic materials as an alternate source of green electrical energy.

Ferrites samples Mg1-xLixFe2O4 for x = 0.0, 0.1, 0.2, 0.3, were synthesized by solid-state sintering method. Detailed investigations were made on the structural, morphological, magnetic and electrical proprieties of these samples. A detailed investigation was performed on power generation of these samples and role of Li-doping has been discussed. The X-ray Diffraction (XRD) pattern confirms the spinel phase formation in samples without any impurity. It is observed from Scanning Electron Microscopy that average grain size of samples decreases with lithium doping in MgFe2O4. The saturation magnetization of MgFe2O4 (15.4 emu/g) is found to increase with Lithium percentage and maximum 39.3 emu/g for Mg0.7Li0.3Fe2O4 sample. Ferrites play a crucial role in magnetic recording, microwave magnetic devices and many applications in medical sciences. Recently, it was observed that ferrites can be an alternate source of green energy by inventing hydroelectric cell (HEC). The processes of water adsorption and dissociation on the metal-oxide surface, plays an important role in production of electricity in ferrites. When, water is sprayed on hydroelectric cell the thermodynamic driving force is responsible for the formation of stable metal-oxygen or metal-hydroxyl bonds. The reactivity of ferrite surface towards water is based on the interaction of these ions and the d orbital of the Fe atom. Due to this interaction, water dissociated in H3O+ and OH- ions and migrates toward silver and zinc electrodes respectively. A typical hydroelectric cell of 2 inch diameter produces 17.1 mA of peak current and 949 mV voltage with a maximum output power of 15.85 mW for Li = 0.2 doped MgFe2O4 sample.

Mechanism of Inhibition of Beta Amyloid Toxicity by Supramolecular Tweezers.

The Aß1-42 dimer is the smallest oligomer of the 42-residue Aß peptide (Aß1-42), which is involved in Alzheimer's disease. The molecular tweezer CLR01 is a synthetic molecule that selectively binds lysine and arginine residues to inhibit toxic aggregation of amyloidogenic peptides. Here, we performed replica exchange molecular dynamics simulations of Aß1-42 in explicit water to study, at the molecular level, the effect of CLR01 binding to the lysine and arginine residues in the dimer. We found that CLR01 molecules encapsulate both lysine residues of each Aß1-42 monomer while only establishing labile interactions with the arginine residues. This encapsulation leads to the noncovalent disruption of inter- and intramolecular interactions involving the monomers. Additionally, the total ß-sheet content in the Aß1-42 dimer decreases because of this binding. With CLR03, a negative control molecule that shares the charged core of CLR01 but does not form inclusion complexes, Aß1-42 dimer formation is observed, similar to the reference system without ligands. Our work allows establishing a molecular mechanism for the modulation of protein-protein interactions in Aß1-42 by CLR01. This mechanism is characterized by an aggregation pathway driven by the encapsulation of lysine residues as well as by the secondary interactions of tweezers with the peptide units and with other CLR01 molecules.

Rational Design, Binding Studies, and Crystal-Structure Evaluation of the First Ligand Targeting the Dimerization Interface of the 14-3-3ζ Adapter Protein.

14-3-3 Proteins play a central role in signalling pathways in cells: they interact as gatekeeper proteins with a huge number of binding partners. Their function as hub for intracellular communication can explain why these adapter proteins are associated with a wide range of diseases. How they control the various cellular mechanisms is still unclear, but it is assumed that the dimeric nature of the 14-3-3 proteins plays a key role in their activity. Here, we present, to the best of our knowledge, the first example of a small molecule binding to the 14-3-3ζ dimerisation interface. This compound was designed by rational in silico optimisation of a peptidic ligand identified from biochemical screening of a peptidic library, and the binding was characterised by UV/Vis spectroscopy, microscale thermophoresis, multiscale simulations, and X-ray crystallography.

The Molecular Tweezer CLR01 Stabilizes a Disordered Protein-Protein Interface.

Protein regions that are involved in protein-protein interactions (PPIs) very often display a high degree of intrinsic disorder, which is reduced during the recognition process. A prime example is binding of the rigid 14-3-3 adapter proteins to their numerous partner proteins, whose recognition motifs undergo an extensive disorder-to-order transition. In this context, it is highly desirable to control this entropy-costly process using tailored stabilizing agents. This study reveals how the molecular tweezer CLR01 tunes the 14-3-3/Cdc25CpS216 protein-protein interaction. Protein crystallography, biophysical affinity determination and biomolecular simulations unanimously deliver a remarkable finding: a supramolecular "Janus" ligand can bind simultaneously to a flexible peptidic PPI recognition motif and to a well-structured adapter protein. This binding fills a gap in the protein-protein interface, "freezes" one of the conformational states of the intrinsically disordered Cdc25C protein partner and enhances the apparent affinity of the interaction. This is the first structural and functional proof of a supramolecular ligand targeting a PPI interface and stabilizing the binding of an intrinsically disordered recognition motif to a rigid partner protein.

Inhibition of Huntingtin Exon-1 Aggregation by the Molecular Tweezer CLR01.

Huntington's disease is a neurodegenerative disorder associated with the expansion of the polyglutamine tract in the exon-1 domain of the huntingtin protein (htte1). Above a threshold of 37 glutamine residues, htte1 starts to aggregate in a nucleation-dependent manner. A 17-residue N-terminal fragment of htte1 (N17) has been suggested to play a crucial role in modulating the aggregation propensity and toxicity of htte1. Here we identify N17 as a potential target for novel therapeutic intervention using the molecular tweezer CLR01. A combination of biochemical experiments and computer simulations shows that binding of CLR01 induces structural rearrangements within the htte1 monomer and inhibits htte1 aggregation, underpinning the key role of N17 in modulating htte1 toxicity.

Multivariate analysis of the volumetric capnograph for PaCO2 estimation.

PURPOSE: End-tidal CO2 (eTCO2) can be used to estimate the arterial CO2 (PaCO2) under steady-state conditions, but that relationship deteriorates during hemodynamic or respiratory instability. We developed a multivariate method to improve our ability to estimate the PaCO2, by using additional information contained in the volumetric capnograph (Vcap) waveform. We tested this approach using data from a porcine model of chest trauma/hemorrhage. METHODS: This experiment consisted of 3 stages: pre-injury, injury/resuscitation, and post-injury. In stage I, anesthetized pigs (n=26) underwent ventilator maneuvers (tidal volume and respiratory rate) to induce hypo-or hyper-ventilation. In stage II, pigs underwent either (A) unilateral pulmonary contusion, hemorrhage, and resuscitation (n=13); or (B) bilateral pulmonary contusion (n=13) followed by 30 min of monitoring. In stage III, the ventilator maneuvers were repeated. The following Vcap features were measured: eTCO2, phase 2 slope (p2m), phase 3 slope (p3m), and inter-breath interval. The data were fit to 2 models: (1) multivariate linear regression and (2) a machine-learning model (M5P). RESULTS: 1750 10-breath sets were analyzed. Univariate models employing eTCO2 alone were adequate during stages I and III. During stage II, mean error for the linear model was -8.44 mmHg (R(2)=0.14, P<0.001) and for M5P it was -5.98 mmHg (R(2)=0.13, P<0.01). By adding Vcap features, all models exhibited improvement. In stage II, the mean error of the linear model improved to -4.64 mmHg (R(2)=0.11, P<0.01), and that of the M5P model improved to -1.62 mmHg (R(2)=0.25, P<0.01). CONCLUSIONS: By incorporating Vcap waveform features, multivariate methods modestly improved PaCO2 estimation, especially during periods of hemodynamic and respiratory instability. Further work would be needed to produce a clinically useful CO2 monitoring system under these challenging conditions.

Molecular tweezers inhibit islet amyloid polypeptide assembly and toxicity by a new mechanism.

In type-2 diabetes (T2D), islet amyloid polypeptide (IAPP) self-associates into toxic assemblies causing islet ß-cell death. Therefore, preventing IAPP toxicity is a promising therapeutic strategy for T2D. The molecular tweezer CLR01 is a supramolecular tool for selective complexation of K residues in (poly)peptides. Surprisingly, it inhibits IAPP aggregation at substoichiometric concentrations even though IAPP has only one K residue at position 1, whereas efficient inhibition of IAPP toxicity requires excess CLR01. The basis for this peculiar behavior is not clear. Here, a combination of biochemical, biophysical, spectroscopic, and computational methods reveals a detailed mechanistic picture of the unique dual inhibition mechanism for CLR01. At low concentrations, CLR01 binds to K1, presumably nucleating nonamyloidogenic, yet toxic, structures, whereas excess CLR01 binds also to R11, leading to nontoxic structures. Encouragingly, the CLR01 concentrations needed for inhibition of IAPP toxicity are safe in vivo, supporting its development toward disease-modifying therapy for T2D.

Acanthameba meningitis with successful outcome.

We report a rare cause of sub acute meningitis in a 15-yr-old immunocompetent female child with successful outcome. The etiological agent was Acanthamoeba. The child was successfully treat with combination of Ketoconazole. Rifampicin, cotrimoxa zole and for a period of 9 month.

Unusual presentations of Salmonella Typhi infections in children.

We report on three children with Salmonella typhi presenting with fever and urticaria, thrombocytopenic purpura and meningitis. We suggest that clinicians should consider S. typhi infection as a diagnosis even when the presenting features are more typical of other illnesses.