Integrated All-Atom and Coarse-Grained Simulations Uncover Structural, Dynamics and Energetic Shifts in SARS-CoV-2 JN.1 and BA.2.86 Variants.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, is an enveloped, positive-stranded RNA virus that enters human cells by using its spike protein to bind to the human angiotensin-converting enzyme 2 (ACE2) receptor. Since its emergence, the virus has mutated, producing variants with increased transmissibility, immune evasion, and infectivity. The JN.1 variant, detected in January 2024, features a single substitution mutation (L455S) in the receptor-binding domain (RBD) of its spike protein, setting it apart from its parent lineage, BA.2.86. This variant has rapidly become globally predominant due to its enhanced transmission and significant epidemiological impact. To understand the causes behind the dominance of the JN.1 variant, we conducted a comprehensive study using all-atom MD molecular dynamics (MD) and coarse-grained MD simulations. This allowed us to examine the structural, dynamic, energetics and binding properties of the wild-type (Wuhan strain), BA.2.86, and JN.1 variants. Principal component and free energy landscape analyses revealed enhanced structural stability in the JN.1 variant. Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) assessments indicated lower binding affinity for JN.1 as compared to BA.2.86. Intermolecular interaction analyses further confirmed BA.2.86's superior binding affinity over JN.1 and wild-type. Additionally, we compared and validated our findings against experimentally determined cryo-electron microscopy (cryo-EM) structures of JN.1 and BA.2.86 variants, confirming the reliability of our simulation results. Overall, this study provides crucial insights into the structural-dynamics-energetics and physicochemical features that have contributed to the global prevalence of the JN.1 variant and sheds light on its potential to generate future subvariants.

Insertion and Anchoring of HIV-1 Fusion Peptide into Complex Membrane Mimicking Human T-cell.

A fundamental understanding of how HIV-1 envelope (Env) protein facilitates fusion is still lacking. The HIV-1 fusion peptide, consisting of 15 to 22 residues, is the N-terminus of the gp41 subunit of the Env protein. Further, this peptide, a promising vaccine candidate, initiates viral entry into target cells by inserting and anchoring into human immune cells. The influence of membrane lipid reorganization and the conformational changes of the fusion peptide during the membrane insertion and anchoring processes, which can significantly affect HIV-1 cell entry, remains largely unexplored due to the limitations of experimental measurements. In this work, we investigate the insertion of the fusion peptide into an immune cell membrane mimic through multiscale molecular dynamics simulations. We mimic the native T-cell by constructing a 9-lipid asymmetric membrane, along with geometrical restraints accounting for insertion in the context of gp41. To account for the slow timescale of lipid mixing while enabling conformational changes, we implement a protocol to go back and forth between atomistic and coarse-grained simulations. Our study provides a molecular understanding of the interactions between the HIV-1 fusion peptide and the T-cell membrane, highlighting the importance of conformational flexibility of fusion peptides and local lipid reorganization in stabilizing the anchoring of gp41 into the targeted host membrane during the early events of HIV-1 cell entry. Importantly, we identify a motif within the fusion peptide critical for fusion that can be further manipulated in future immunological studies.

Drug solubilization in dog intestinal fluids with and without administration of lipid-based formulations.

The use of animal experiments can be minimized with computational models capable of reflecting the simulated environments. One such environment is intestinal fluid and the colloids formed in it. In this study we used molecular dynamics simulations to investigate solubilization patterns for three model drugs (carvedilol, felodipine and probucol) in dog intestinal fluid, a lipid-based formulation, and a mixture of both. We observed morphological transformations that lipids undergo due to the digestion process in the intestinal environment. Further, we evaluated the effect of bile salt concentration and observed the importance of interindividual variability. We applied two methods of estimating solubility enhancement based on the simulated data, of which one was in good qualitative agreement with the experimentally observed solubility enhancement. In addition to the computational simulations, we also measured solubility in i) aspirated dog intestinal fluid samples and ii) simulated canine intestinal fluid in the fasted state, and found there was no statistical difference between the two. Hence, a simplified dissolution medium suitable for in vitro studies provided physiologically relevant data for the systems explored. The computational protocol used in this study, coupled with in vitro studies using simulated intestinal fluids, can serve as a useful prescreening tool in the process of drug delivery strategies development.

Coarse grained MD simulation of bulk and interfacial behavior of mixture of CTAB/SDS surfactants.

CONTEXT: This study involves simulating the process of inhibiting corrosion through the formation of micelles by surfactants and their deposition on iron (Fe) surfaces. The primary focus is on examining CTAB/SDS mixtures in aqueous solutions with different concentrations. Micelle properties, including size, shape, aggregation number, cluster size, and surfactant diffusion, were calculated and validated with experimental data. The coarse-grained Fe surface was modeled and validated against experimental water contact-angle data. Subsequently, the deposition of CTAB/SDS mixtures on the Fe surface and air-water interface was studied systematically. We found that the relative ratio of CTAB/SDS in the solution directly influences surfactant deposition behavior, which might impact the corrosion inhibition efficiency. METHODS: All the MD simulations were performed using the GROMACS software with MARTINI2 force field and Martini polar water. The molecules are packed using PACKMOL software. Both NVT and NPT simulations are caried out at temperature and pressure of 303 K and 1 bar respectively, with a nonbonded interaction cut-off (rcut) of 1.1 nm. The LJ potential was shifted from 0.9 nm to rcut, while the electrostatic potential was shifted from 0.0 nm to rcut. For electrostatics, reaction-field coulomb type is used, relative dielectric constant (epsilon-r) and the reaction field dielectric constant (epsilon-rf) are equal to 2.5 and infinity respectively. The dielectric constant below rcut is epsilon-r, and beyond the cut-off is epsilon-rf. Coulomb-modifier used as potential-shift which leads to shift in the coulomb potential by a constant such that it is zero at the rcut. This makes the potential of the integral of the force . The neighbor list was updated every 10 steps, employing a neighbor list cut-off equal to rcut. Using a polar water model, we used a constant time step of 0.02 ps throughout the simulation. The used epsilon-r = 2.5, is recommended for polar water.

Ligand Lipophilicity Determines Molecular Mechanisms of Nanoparticle Adsorption to Lipid Bilayers.

The interactions of ligand-functionalized nanoparticles with the cell membrane affect cellular uptake, cytotoxicity, and related behaviors, but relating these interactions to ligand properties remains challenging. In this work, we perform coarse-grained molecular dynamics simulations to study how the adsorption of ligand-functionalized cationic gold nanoparticles (NPs) to a single-component lipid bilayer (as a model cell membrane) is influenced by ligand end group lipophilicity. A set of 2 nm diameter NPs, each coated with a monolayer of organic ligands that differ only in their end groups, was simulated to mimic NPs recently studied experimentally. Metadynamics calculations were performed to determine key features of the free energy landscape for adsorption as a function of the distance of the NP from the bilayer and the number of NP-lipid contacts. These simulations revealed that NP adsorption is thermodynamically favorable for all NPs due to the extraction of lipids from the bilayer and into the NP monolayer. To resolve ligand-dependent differences in adsorption behavior, string method calculations were performed to compute minimum free energy pathways for adsorption. These calculations revealed a surprising nonmonotonic dependence of the free energy barrier for adsorption on ligand end group lipophilicity. Large free energy barriers are predicted for the least lipophilic end groups because favorable NP-lipid contacts are initiated only through the unfavorable protrusion of lipid tail groups out of the bilayer. The smallest free energy barriers are predicted for end groups of intermediate lipophilicity which promote NP-lipid contacts by intercalating within the bilayer. Unexpectedly, large free energy barriers are also predicted for the most lipophilic end groups which remain sequestered within the ligand monolayer rather than intercalating within the bilayer. These trends are broadly in agreement with past experimental measurements and reveal how subtle variations in ligand lipophilicity dictate adsorption mechanisms and associated kinetics by influencing the interplay of lipid-ligand interactions.

Adsorption of pulmonary and exogeneous surfactants on SARS-CoV-2 spike protein.

COVID-19 is transmitted by airborne particles containing virions of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Coronavirus virions represent nanoparticles enveloped by a lipid bilayer decorated by a "crown" of Spike protein protrusions. Virus transmission into the cells is induced by binding of Spike proteins with ACE2 receptors of alveolar epithelial cells. Active clinical search is ongoing for exogenous surfactants and biologically active chemicals capable of hindering virion-receptor binding. Here, we explore by using coarse-grained molecular dynamics simulations the physico-chemical mechanisms of adsorption of selected pulmonary surfactants, zwitterionic dipalmitoyl phosphatidyl choline and cholesterol, and exogeneous anionic surfactant, sodium dodecyl sulfate, on the S1-domain of the Spike protein. We show that surfactants form micellar aggregates that selectively adhere to the specific regions of the S1-domain that are responsible for binding with ACE2 receptors. We find distinctly higher cholesterol adsorption and stronger cholesterol-S1 interactions in comparison with other surfactants, that is consistent with the experimental observations of the effects of cholesterol on COVID-19 infection. Distribution of adsorbed surfactant along the protein residue chain is highly specific and inhomogeneous with preferential adsorption around specific amino acid sequences. We observe preferential adsorption of surfactants on cationic arginine and lysine residues in the receptor-binding domain (RBD) that play an important role in ACE2 binding and are present in higher amounts in Delta and Omicron variants, which may lead to blocking direct Spike-ACE2 interactions. Our findings of strong selective adhesion of surfactant aggregates to Spike proteins have important implications for informing clinical search for therapeutic surfactants for curing and preventing COVID-19 caused by SARS-CoV-2 and its variants.

Combining Molecular Dynamics Simulations and Biophysical Characterization to Investigate Protein-Specific Excipient Effects on Reteplase during Freeze Drying.

We performed molecular dynamics simulations of Reteplase in the presence of different excipients to study the stabilizing mechanisms and to identify the role of excipients during freeze drying. To simulate the freeze-drying process, we divided the process into five distinct steps: (i) protein-excipient formulations at room temperature, (ii) the ice-growth process, (iii)-(iv) the partially solvated and fully dried formulations, and (v) the reconstitution. Furthermore, coarse-grained (CG) simulations were employed to explore the protein-aggregation process in the presence of arginine. By using a coarse-grained representation, we could observe the collective behavior and interactions between protein molecules during the aggregation process. The CG simulations revealed that the presence of arginine prevented intermolecular interactions of the catalytic domain of Reteplase, thus reducing the aggregation propensity. This suggests that arginine played a stabilizing role by interacting with protein-specific regions. From the freeze-drying simulations, we could identify several protein-specific events: (i) collapse of the domain structure, (ii) recovery of the drying-induced damages during reconstitution, and (iii) stabilization of the local aggregation-prone region via direct interactions with excipients. Complementary to the simulations, we employed nanoDSF, size-exclusion chromatography, and CD spectroscopy to investigate the effect of the freeze-drying process on the protein structure and stability.

Physicochemical Properties and Route of Systemic Delivery Control the In Vivo Dynamics and Breakdown of Radiolabeled Gold Nanostars.

The in vivo dynamics of nanoparticles requires a mechanistic understanding of multiple factors. Here, for the first time, the surprising breakdown of functionalized gold nanostars (F-AuNSs) conjugated with antibodies and 64 Cu radiolabels in vivo and in artificial lysosomal fluid ex vivo, is shown. The short-term biodistribution of F-AuNSs is driven by the route of systemic delivery (intravenous vs intraperitoneal) and long-term fate is controlled by the tissue type in vivo. In vitro studies including endocytosis pathways, intracellular trafficking, and opsonization, are combined with in vivo studies integrating a milieu of spectroscopy and microcopy techniques that show F-AuNSs dynamics is driven by their physicochemical properties and route of delivery. F-AuNSs break down into sub-20 nm broken nanoparticles as early as 7 days postinjection. Martini coarse-grained simulations are performed to support the in vivo findings. Simulations suggest that shape, size, and charge of the broken nanoparticles, and composition of the lipid membrane depicting various tissues govern the interaction of the nanoparticles with the membrane, and the rate of translocation across the membrane to ultimately enable tissue clearance. The fundamental study addresses critical gaps in the knowledge regarding the fate of nanoparticles in vivo that remain a bottleneck in their clinical translation.

Implicit-Solvent Coarse-Grained Simulations of Linear-Dendritic Block Copolymer Micelles.

The design of nanoassemblies can be conveniently achieved by tuning the strength of the hydrophobic interactions of block copolymers in selective solvents. These block copolymer micelles form supramolecular aggregates, which have attracted great attention in the area of drug delivery and imaging in biomedicine due to their easy-to-tune properties and straightforward large-scale production. In the present work, we have investigated the micellization process of linear-dendritic block copolymers in order to elucidate the effect of branching on the micellar properties. We focus on block copolymers formed by linear hydrophobic blocks attached to either dendritic neutral or charged hydrophilic blocks. We have implemented a simple protocol for determining the equilibrium micellar size, which permits the study of linear-dendritic block copolymers in a wide range of block morphologies in an efficient and parallelizable manner. We have explored the impact of different topological and charge properties of the hydrophilic blocks on the equilibrium micellar properties and compared them to predictions from self-consistent field theory and scaling theory. We have found that, at higher degrees of branching in the corona and for short polymer chains, excluded volume interactions strongly influence the micellar aggregation as well as their effective charge.

Single core and multicore aggregates from a polymer mixture: A dissipative particle dynamics study.

HYPOTHESIS: Multicore block copolymer aggregates correspond to self-assembly such that the polymer system spontaneously phase separates to multiple, droplet-like cores differing in the composition from the polymer surroundings. Such multiple core aggregates are highly useful capsules for different applications, e.g., drug transport, catalysis, controlled solvation, and chemical reactions platforms. We postulate that polymer system composition provides a direct means for designing polymer systems that self-assemble to such morphologies and controlling the assembly response. SIMULATIONS: Using dissipative particle dynamics (DPD) simulations, we examine the self-assembly of a mixture of highly and weakly solvophobic homopolymers and an amphiphilic block copolymer in the presence of solvent. We map the multicore vs single core (core-shell particles) assembly response and aggregate structure in terms of block copolymer concentration, polymer component ratios, and chain length of the weakly solvophobic homopolymer. FINDINGS: For fixed components and polymer chemistries, the amount of block copolymer is the key to controlling single core vs multicore aggregation. We find a polymer system dependent critical copolymer concentration for the multicore aggregation and that a minimum level of incompatibility between the solvent and the weakly solvophobic component is required for multicore assembly. We discuss the implications for polymer system design for multicore assemblies. In summary, the study presents guidelines to produce multicore aggregates and to tune the assembly from multicore aggregation to single core core-shell particles.

Rational design of an anti-cancer peptide inhibiting CD147 / Cyp A interaction.

The CD147 / Cyp A interaction is a critical pathway in cancer types and an essential factor in entering the COVID-19 virus into the host cell. Melittin acts as an inhibitory peptide in cancer types by blocking the CD147/ Cyp A interaction. The clinical application of Melittin is limited due to weak penetration into cancer cells. TAT is an arginine-rich peptide with high penetration ability into cells widely used in drug delivery systems. This study aimed to design a hybrid peptide derived from Melittin and TAT to inhibit CD147 /Cyp A interaction. An amino acid region with high anti-cancer activity in Melittin was selected based on the physicochemical properties. Based on the results, a truncated Melittin peptide with 15 amino acids by the GGGS linker was fused to a TAT peptide (nine amino acids) to increase the penetration rate into the cell. A new hybrid peptide analog(TM) was selected by replacing the glycine with serine based on random point mutation. Docking results indicated that the TM peptide acts as an inhibitory peptide with high binding energy when interacting with CD147 and the CypA proteins. RMSD and RMSF results confirmed the high stability of the TM peptide in interaction with CD147. Also, the coarse-grained simulation showed the penetration potential of TM peptide into the DOPS-DOPC model membrane. Our findings indicated that the designed multifunctional peptide could be an attractive therapeutic candidate to halter tumor types and COVID-19 infection.

Differential interactions of resting, activated, and desensitized states of the α7 nicotinic acetylcholine receptor with lipidic modulators.

The α7 nicotinic acetylcholine receptor is a pentameric ligand-gated ion channel that modulates neuronal excitability, largely by allowing Ca2+ permeation. Agonist binding promotes transition from a resting state to an activated state, and then rapidly to a desensitized state. Recently, cryogenic electron microscopy (cryo-EM) structures of the human α7 receptor in nanodiscs were reported in multiple conformations. These were selectively stabilized by inhibitory, activating, or potentiating compounds. However, the functional annotation of these structures and their differential interactions with unresolved lipids and ligands remain incomplete. Here, we characterized their ion permeation, membrane interactions, and ligand binding using computational electrophysiology, free-energy calculations, and coarse-grained molecular dynamics. In contrast to nonconductive structures in apparent resting and desensitized states, the structure determined in the presence of the potentiator PNU-120596 was consistent with an activated state permeable to Ca2+. Transition to this state was associated with compression and rearrangement of the membrane, particularly in the vicinity of the peripheral MX helix. An intersubunit transmembrane site was implicated in selective binding of either PNU-120596 in the activated state or cholesterol in the desensitized state. This substantiates functional assignment of all three lipid-embedded α7-receptor structures with ion-permeation simulations. It also proposes testable models of their state-dependent interactions with lipophilic ligands, including a mechanism for allosteric modulation at the transmembrane subunit interface.

Plasticity of Membrane Binding by the Central Region of α-Synuclein.

Membrane binding by α-synuclein (αS), an intrinsically disordered protein whose aggregation is associated with Parkinson's disease, is a key step in determining its biological properties under both physiological and pathological conditions. Upon membrane interaction, αS retains a partial level of structural disorder despite acquiring α-helical content. In the membrane-bound state, the equilibrium between the helical-bound and disordered-detached states of the central region of αS (residues 65-97) has been involved in a double-anchor mechanism that promotes the clustering of synaptic vesicles. Herein, we investigated the underlying molecular bases of this equilibrium using enhanced coarse-grained molecular dynamics simulations. The results enabled clarifying the conformational dependencies of the membrane affinity by this protein region that, in addition to playing a role in physiological membrane binding, has key relevance for the aggregation of αS and the mechanisms of the toxicity of the resulting assemblies.

Combining Coarse-Grained Simulations and Single Molecule Analysis Reveals a Three-State Folding Model of the Guanidine-II Riboswitch.

Riboswitch RNAs regulate gene expression by conformational changes induced by environmental conditions and specific ligand binding. The guanidine-II riboswitch is proposed to bind the small molecule guanidinium and to subsequently form a kissing loop interaction between the P1 and P2 hairpins. While an interaction was shown for isolated hairpins in crystallization and electron paramagnetic resonance experiments, an intrastrand kissing loop formation has not been demonstrated. Here, we report the first evidence of this interaction in cis in a ligand and Mg2+ dependent manner. Using single-molecule FRET spectroscopy and detailed structural information from coarse-grained simulations, we observe and characterize three interconvertible states representing an open and kissing loop conformation as well as a novel Mg2+ dependent state for the guanidine-II riboswitch from E. coli. The results further substantiate the proposed switching mechanism and provide detailed insight into the regulation mechanism for the guanidine-II riboswitch class. Combining single molecule experiments and coarse-grained simulations therefore provides a promising perspective in resolving the conformational changes induced by environmental conditions and to yield molecular insights into RNA regulation.

Hybrid Nanocrystals of Small Molecules and Chemically Disordered Polymers.

Organic crystals formed by small molecules can be highly functional but are often brittle or insoluble structures with limited possibilities for use or processing from a liquid phase. A possible solution is the nanoscale integration of polymers into organic crystals without sacrificing long-range order and therefore function. This enables the organic crystals to benefit from the advantageous mechanical and chemical properties of the polymeric component. We report here on a strategy in which small molecules cocrystallize with side chains of chemically disordered polymers to create hybrid nanostructures containing a highly ordered lattice. Synchrotron X-ray scattering, absorption spectroscopy, and coarse-grained molecular dynamics simulations reveal that the polymer backbones form an "exo-crystalline" layer of disordered chains that wrap around the nanostructures, becoming a handle for interesting properties. The morphology of this "hybrid bonding polymer" nanostructure is dictated by the competition between the polymers' entropy and the enthalpy of the lattice allowing for control over the aspect ratio of the nanocrystal by changing the degree of polymer integration. We observed that nanostructures with an exo-crystalline layer of polymer exhibit enhanced fracture strength, self-healing capacity, and dispersion in water, which benefits their use as light-harvesting assemblies in photocatalysis. Guided by computation, future work could further explore these hybrid nanostructures as components for functional materials.

Investigation of the pH-dependent aggregation mechanisms of GCSF using low resolution protein characterization techniques and advanced molecular dynamics simulations.

Granulocyte-colony stimulating factor (GCSF) is a widely used therapeutic protein to treat neutropenia. GCSF has an increased propensity to aggregate if the pH is increased above 5.0. Although GCSF is very well experimentally characterized, the exact pH-dependent aggregation mechanism of GCSF is still under debate. This study aimed to model the complex pH-dependent aggregation behavior of GCSF using state-of-the-art simulation techniques. The conformational stability of GCSF was investigated by performing metadynamics simulations, while the protein-protein interactions were investigated using coarse-grained (CG) simulations of multiple GCSF monomers. The CG simulations were directly compared with small-angle X-ray (SAXS) data. The metadynamics simulations demonstrated that the orientations of Trp residues in GCSF are dependent on pH. The conformational change of Trp residues is due to the loss of Trp-His interactions at the physiological pH, which in turn may increase protein flexibility. The helical structure of GCSF was not affected by the pH conditions of the simulations. Our CG simulations indicate that at pH 4.0, the colloidal stability may be more important than the conformational stability of GCSF. The electrostatic potential surface and CG simulations suggested that the basic residues are mainly responsible for colloidal stability as deprotonation of these residues causes a reduction of the highly positively charged electrostatic barrier close to the aggregation-prone long loop regions.

Structural dynamics of Smoothened (SMO) in the ciliary membrane and its interaction with membrane lipids.

The Smoothened receptor (SMO, a 7 pass transmembrane domain, Class F GPCR family protein) plays a crucial role in the Hedgehog (HH) signaling pathway, which is involved in embryonic development and is implicated in various types of cancer throughout the animal kingdom. In the absence of HH signaling, SMO is inhibited by Patched 1 (PTC1; a 12 pass transmembrane domain protein), which is localized in the primary cilia. HH binding leads to the dislocation of PTC1 from the cilia, thus making way for SMO to localize in the primary cilia, as an essential prerequisite for its activation. We have carried out MARTINI coarse-grained molecular dynamics simulations of SMO in POPC and in ciliary membrane models, respectively, to study the interactions of SMO with cholesterol and other lipid molecules in the ciliary membrane, and to gain molecular-level insights into the role of the primary cilia in shaping the functional dynamics of SMO. We are able to identify the interaction of membrane cholesterols with definite sites and domains within SMO and relate them with known cholesterol-binding sequence and structure motifs. We show that cholesterol interactions with the transmembrane domain TMD, unlike those with the cysteine-rich domain (CRD) and the intracellular domain (ICD), are through residues belonging to known cholesterol-binding motifs. Notably, a few persistent interactions of cholesterol with lower TM cholesterol-binding domains are governed by the presence of multiple cholesterol-binding motifs. These analyses have also helped to identify and define a strict cholesterol consensus motif (CCM), which may well steer cholesterol into the hitherto identified binding sites within the TMD of SMO. We have also reported the interaction of phosphatidylinositol 4-phosphate with the intracellular region of transmembrane (TM) helices (TM1, TM3, TM4, and TM5), intracellular loop1, helix8, and Arg/Lys clusters of the ICD. Structural analysis of SMO domains shows significant changes in the CRD and ICD, during the course of the simulation. Further detailed analysis of the dynamics of the TMD reveals the movements of TM5, TM6, and TM7, linked with the helix8, which are possibly involved in shaping the conformational disposition of the ICD. The movement of these TM helices could possibly be a consequence of interactions involving the extracellular domain and extracellular loops. In addition, our analysis also shows that phosphatidylinositol-4-phosphate (PI4P), along with some ICD cholesterols, are implicated in anchoring SMO in the membrane.

Characterization of the Interfacial Orientation and Molecular Conformation in a Glass-Forming Organic Semiconductor.

The ability to control structure in molecular glasses has enabled them to play a key role in modern technology; in particular, they are ubiquitous in organic light-emitting diodes. While the interplay between bulk structure and optoelectronic properties has been extensively investigated, few studies have examined molecular orientation near buried interfaces despite its critical role in emergent functionality. Direct, quantitative measurements of buried molecular orientation are inherently challenging, and many methods are insensitive to orientation in amorphous soft matter or lack the necessary spatial resolution. To overcome these challenges, we use polarized resonant soft X-ray reflectivity (p-RSoXR) to measure nanometer-resolved, molecular orientation depth profiles of vapor-deposited thin films of an organic semiconductor Tris(4-carbazoyl-9-ylphenyl)amine (TCTA). Our depth profiling approach characterizes the vertical distribution of molecular orientation and reveals that molecules near the inorganic substrate and free surface have a different, nearly isotropic orientation compared to those of the anisotropic bulk. Comparison of p-RSoXR results with near-edge X-ray absorption fine structure spectroscopy and optical spectroscopies reveals that TCTA molecules away from the interfaces are predominantly planar, which may contribute to their attractive charge transport qualities. Buried interfaces are further investigated in a TCTA bilayer (each layer deposited under separate conditions resulting in different orientations) in which we find a narrow interface between orientationally distinct layers extending across ≈1 nm. Coupling this result with molecular dynamics simulations provides additional insight into the formation of interfacial structure. This study characterizes the local molecular orientation at various types of buried interfaces in vapor-deposited glasses and provides a foundation for future studies to develop critical structure-function relationships.

Molecular Simulations of Intrinsically Disordered Proteins and Their Binding Mechanisms.

Intrinsically disordered proteins (IDPs) lack well-defined secondary or tertiary structures in solution but are found to be involved in a wide range of critical cellular processes that highlight their functional importance. IDPs usually undergo folding upon binding to their targets. Such binding coupled to folding behavior has widened our perspective on the protein structure-dynamics-function paradigm in molecular biology. However, characterizing the folding upon binding mechanism of IDPs experimentally remains quite challenging. Molecular simulations emerge as a potentially powerful tool that offers information complementary to experiments. Here we present a general computational framework for the molecular simulations of IDP folding upon binding processes that combines all-atom molecular dynamics (MD) and coarse-grained simulations. The classical all-atom molecular dynamics approach using GPU acceleration allows the researcher to explore the properties of the IDP conformational ensemble, whereas coarse-grained structure-based models implemented with parameters carefully calibrated to available experimental measurements can be used to simulate the entire folding upon binding process. We also discuss a set of tools for the analysis of MD trajectories and describe the details of the computational protocol to follow so that it can be adapted by the user to study any IDP in isolation and in complex with partners.

Channels with Helical Modulation Display Stereospecific Sensitivity for Chiral Superstructures.

By means of coarse-grained molecular dynamics simulations, we explore chiral sensitivity of confining spaces modelled as helical channels to chiral superstructures represented by polymer knots. The simulations show that helical channels exhibit stereosensitivity to chiral knots localized on linear chains by effect of external pulling force and also to knots embedded on circular chains. The magnitude of the stereoselective effect is stronger for torus knots, the effect is weaker in the case of twist knots, and amphichiral knots do exhibit no chiral effects. The magnitude of the effect can be tuned by the so-far investigated radius of the helix, the pitch of the helix and the strength of the pulling force. The model is aimed to simulate and address a range of practical situations that may occur in experimental settings such as designing of nanotechnological devices for the detection of topological state of molecules, preparation of new gels with tailor made stereoselective properties, or diffusion of knotted DNA in biological conditions.