HP35 Protein in the Mesopore of MIL-101(Cr) MOF: A Model to Study Cotranslocational Unfolding.

The immobilization of enzymes in metal-organic framework (MOF) cages is important in biotechnology. In this context, the mechanism of translocation of proteins through the cavities of the MOF and the roles played by confinement and MOF chemistry in giving rise to stable protein intermediates that are otherwise transiently populated in the physiological environment are important questions to be addressed. These unexplored aspects are examined with villin headpiece (HP35) as a model protein confined within a mesopore of MIL-101(Cr) using molecular dynamics simulations. At equilibrium, the protein is located farther from the center of the cavity and closer to the MOF surface. Molecular interactions with the MOF partially unfold helix-1 at its N-terminus. Umbrella sampling simulations inform the range of conformations that HP35 undertakes during translocation from one cavity to another and associated changes in free energy. Relative to its equilibrium state within the cavity, the free energy barrier for the unfolded protein at the cage window is estimated to be 16 kcal/mol. This study of MOF-based protein conformation can also be a general approach to observing intermediates in folding-unfolding pathways.

Red Circularly Polarized Luminescence from Dimeric H-Aggregates of Acridine Orange by Chiral Induction.

Understanding the mechanism of chirality transfer from a chiral surface to an achiral molecule is essential for designing molecular systems with tunable chiroptical properties. These aspects are explored herein using l- and d-isomers of alkyl valine amphiphiles, which self-assemble in water as nanofibers possessing a negative surface charge. An achiral chromophore, acridine orange, upon electrostatic binding on these surfaces displays mirror-imaged bisignated circular dichroism and red-emitting circularly polarized luminescence signals with a high dissymmetry factor. Experimental and computational investigations establish that the chiroptical properties emerge from surface-bound asymmetric H-type dimers of acridine orange, further supported by fluorescence lifetime imaging studies. Specifically, atomistic molecular dynamics simulations show that the experimentally observed chiral signatures have their origin in van der Waals interactions between acridine orange dimers and the amphiphile head groups as well as in the extent of solvent exposure of the chromophore.

Liquid-Vapor Interface of Aqueous Ethylene Glycol Solutions: A Molecular Dynamics Study.

While the organic constituent in an aqueous binary solution enriches its liquid-vapor (l-v) interface, the extent of enrichment can depend nonlinearly on its mole fraction. A microscopic quantification and rationalization of this behavior are crucial to understand the dependence of properties such as surface tension and evaporation rate of the solution on its composition. Extensive all-atom molecular dynamics simulations of aqueous ethylene glycol (EG) solutions show that the composition of the solution at the l-v interface deviates the most from that in the bulk solution at an EG mole fraction of 0.3. The population of EG molecules with their central C-C dihedral in the gauche conformation was found to be higher at the l-v interface than that in the bulk solution to facilitate the orientation of its hydrophobic methyl groups toward the vapor phase. Free energy calculations reveal that in dilute EG solutions, an EG molecule is most stable at the l-v interface. The behavior of vapor pressure in aqueous EG solutions is ideal and follows Raoult's law, while in contrast, the aqueous solution of dimethyl sulfoxide does not. A rationale for the same is provided through the orientational distribution of interfacial water molecules in the respective solutions.

Noncovalent interaction guided selectivity of haloaromatic isomers in a flexible porous coordination polymer.

Porous, supramolecular structures exhibit preferential encapsulation of guest molecules, primarily by means of differences in the order of (noncovalent) interactions. The encapsulation preferences can be for geometry (dimension and shape) and the chemical nature of the guest. While geometry-based sorting is relatively straightforward using advanced porous materials, designing a "chemical nature" specific host is not. To introduce "chemical specificity", the host must retain an accessible and complementary recognition site. In the case of a supramolecular, porous coordination polymer (PCP) [Zn(o-phen)(ndc)] (o-phen: 1,10-phenanthroline, ndc: 2,6-naphthalenedicarboxylate) host, equipped with an adaptable recognition pocket, we have discovered that the preferential encapsulation of a haloaromatic isomer is not only for dimension and shape, but also for the "chemical nature" of the guest. This selectivity, i.e., preference for the dimension, shape and chemical nature, is not guided by any complementary recognition site, which is commonly required for "chemical specificity". Insights from crystal structures and computational studies unveil that the differences in the different types of noncovalent host-guest interaction strengths, acting in a concerted fashion, yield the unique selectivity.

Lipase A from Bacillus subtilis: Substrate Binding, Conformational Dynamics, and Signatures of a Lid.

Protein-ligand binding studies are crucial for understanding the molecular basis of biological processes and for further advancing industrial biocatalysis and drug discovery. Using computational modeling and molecular dynamics simulations, we investigated the binding of a butyrate ester substrate to the lipase A (LipA) enzyme of Bacillus subtilis. Besides obtaining a close agreement of the binding free energy with the experimental value, the study reveals a remarkable reorganization of the catalytic triad upon substrate binding, leading to increased essential hydrogen bond populations. The investigation shows the distortion of the oxyanion hole in both the substrate-bound and unbound states of LipA and highlights the strengthening of the same in the tetrahedral intermediate complex. Principal component analysis of the unbound ensemble reveals the dominant motion in LipA to be the movement of Loop-1 (Tyr129-Arg142) between two states that cover and uncover the active site, mirroring that of a lid prevalent in several lipases. This lid-like motion of Loop-1 is also supported by its tendency to spontaneously open up at an oil-water interface. Overall, this study provides valuable insights into the impact of substrate binding on the structure, flexibility, and conformational dynamics of the LipA enzyme.

Understanding the Anomalous Diffusion of Water in Aqueous Electrolytes Using Machine Learned Potentials.

The diffusivity of water in aqueous cesium iodide solutions is larger than that in neat liquid water and vice versa for sodium chloride solutions. Such peculiar ion-specific behavior, called anomalous diffusion, is not reproduced in typical force field based molecular dynamics (MD) simulations due to inadequate treatment of ion-water interactions. Herein, this hurdle is tackled by using machine learned atomic potentials (MLPs) trained on data from density functional theory calculations. MLP based atomistic MD simulations of aqueous salt solutions reproduce experimentally determined thermodynamic, structural, dynamical, and transport properties, including their varied trends in water diffusivities across salt concentration. This enables an examination of their intermolecular structure to unravel the microscopic underpinnings of the differences in their transport properties. While both ions in CsI solutions contribute to the faster diffusion of water molecules, the competition between the heavy retardation by Na ions and the slight acceleration by Cl ions in NaCl solutions reduces their water diffusivity.

Supramolecular Polymerization of a Pyrene-Substituted Diamide and Its Ensemble of Kinetically Trapped Configurations.

The prevalence of kinetically accessible states in supramolecular polymerization pathways has been exploited to control the growth of the polymer and thereby to obtain niche morphologies. Yet, these pathways themselves are not easily amenable for experimental delineation but could potentially be understood through molecular dynamics (MD) simulations. Herein, we report an extensive investigation of the self-assembly of pyrene-substituted diamide (PDA) monomers in solution, conducted using atomistic MD simulations and advanced sampling methods. We characterize such kinetic and thermodynamic states as well as the transition pathways and free energy barriers between them. PDA forms a dimeric segment with the N- to C-termini vectors of the diamide moieties arranged either in parallel or anti-parallel fashion. This characteristic, combined with the molecule's torsional flexibility and pyrene-solvent interactions, presents an ensemble of molecular configurations contributing to the kinetic state in the polymerization pathway. While this ensemble primarily comprises short oligomers containing a mix of anti-parallel and parallel dimeric segments, the thermodynamic state of the assembly is a right-handed polymer featuring parallel ones only. Our work thus offers an approach by which the landscape of any specific supramolecular polymerization can be deconstructed.

Structurally Induced Chirality of an Achiral Chromophore on Self-Assembled Nanofibers: A Twist Makes It Chiral.

The surface domains of self-assembled amphiphiles are well-organized and can perform many physical, chemical, and biological functions. Here, we present the significance of chiral surface domains of these self-assemblies in transferring chirality to achiral chromophores. These aspects are probed using l- and d-isomers of alkyl alanine amphiphiles which self-assemble in water as nanofibers, possessing a negative surface charge. When bound on these nanofibers, positively charged cyanine dyes (CY524 and CY600), each having two quinoline rings bridged by conjugated double bonds, show contrasting chiroptical features. Interestingly, CY600 displays a bisignated circular dichroic (CD) signal with mirror-image symmetry, while CY524 is CD silent. Molecular dynamics simulations reveal that the model cylindrical micelles (CM) derived from the two isomers exhibit surface chirality and the chromophores are buried as monomers in mirror-imaged pockets on their surfaces. The monomeric nature of template-bound chromophores and their binding reversibility are established by concentration- and temperature-dependent spectroscopies and calorimetry. On the CM, CY524 displays two equally populated conformers with opposite sense, whereas CY600 is present as two pairs of twisted conformers in each of which one is in excess, due to differences in weak dye-amphiphile hydrogen bonding interactions. Infrared and NMR spectroscopies support these findings. Reduction of electronic conjugation caused by the twist establishes the two quinoline rings as independent entities. On-resonance coupling between the transition dipoles of these units generates bisignated CD signals with mirror-image symmetry. The results presented herein provide insight on the little-known structurally induced chirality of achiral chromophores through transfer of chiral surface information.

Endobronchial lesion in an adolescent with hemoptysis biopsy or not to biopsy?

An 11-year-old girl was brought with complaints of recurrent massive hemoptysis. A computerized tomography (CT) of the chest showed ground glass opacities on the right lower lobe, and a CT angiography showed hypertrophied right pulmonary artery. Flexible bronchoscopy revealed a sessile friable lesion in the right lower lobe, raising suspicion of either a tumor or a vascular malformation. An endobronchial ultrasound (EBUS) revealed a cystic lesion in the submucous plane, with vascularity noted on Doppler mode. This confirmed the diagnosis of bronchial Dieulafoy disease. A bronchial angiography revealed a vascular malformation overlying the lesion with a bronchopulmonary shunt, which was ligated. This case demonstrates the importance of EBUS in endobronchial lesions, to avoid biopsy of a vascular malformation.

Revisiting the Burden Borne by Fumarase: Enzymatic Hydration of an Olefin.

Fumarate hydratase (FH) is a remarkable catalyst that decreases the free energy of the catalyzed reaction by 30 kcal mol-1, much larger than most exceptional enzymes with extraordinary catalytic rates. Two classes of FH are observed in nature: class-I and class-II, which have different folds, yet catalyze the same reversible hydration/dehydration reaction of the dicarboxylic acids fumarate/malate, with equal efficiencies. Using class-I FH from the hyperthermophilic archaeon Methanocaldococcus jannaschii (Mj) as a model along with comparative analysis with the only other available class-I FH structure from Leishmania major (Lm), we provide insights into the molecular mechanism of catalysis in this class of enzymes. The structure of MjFH apo-protein has been determined, revealing that large intersubunit rearrangements occur across apo- and holo-protein forms, with a largely preorganized active site for substrate binding. Site-directed mutagenesis of active site residues, kinetic analysis, and computational studies, including density functional theory (DFT) and natural population analysis, together show that residues interacting with the carboxylate group of the substrate play a pivotal role in catalysis. Our study establishes that an electrostatic network at the active site of class-I FH polarizes the substrate fumarate through interactions with its carboxylate groups, thereby permitting an easier addition of a water molecule across the olefinic bond. We propose a mechanism of catalysis in FH that occurs through transition-state stabilization involving the distortion of the electronic structure of the substrate olefinic bond mediated by the charge polarization of the bound substrate at the enzyme active site.