A Computational Strategy for the Rapid Identification and Ranking of Patient-Specific T Cell Receptors Bound to Neoantigens.

T cell receptor (TCR) recognition of a peptide-major histocompatibility complex (pMHC) is crucial for adaptive immune response. The identification of therapeutically relevant TCR-pMHC protein pairs is a bottleneck in the implementation of TCR-based immunotherapies. The ability to computationally design TCRs to target a specific pMHC requires automated integration of next-generation sequencing, protein-protein structure prediction, molecular dynamics, and TCR ranking. A pipeline to evaluate patient-specific, sequence-based TCRs to a target pMHC is presented. Using the three most frequently expressed TCRs from 16 colorectal cancer patients, the protein-protein structure of the TCRs to the target CEA peptide-MHC is predicted using Modeller and ColabFold. TCR-pMHC structures are compared using automated equilibration and successive analysis. ColabFold generated configurations require an ≈2.5× reduction in equilibration time of TCR-pMHC structures compared to Modeller. The structural differences between Modeller and ColabFold are demonstrated by root mean square deviation (≈0.20 nm) between clusters of equilibrated configurations, which impact the number of hydrogen bonds and Lennard-Jones contacts between the TCR and pMHC. TCR ranking criteria that may prioritize TCRs for evaluation of in vitro immunogenicity are identified, and this ranking is validated by comparing to state-of-the-art machine learning-based methods trained to predict the probability of TCR-pMHC binding.

Coarse-grained modeling of polystyrene-modified CNTs and their interactions with lipid bilayers.

In the present work, we describe Martini3 coarse-grained models of polystyrene and carboxyl-terminated polystyrene functionalized carbon nanotubes (CNTs) and investigate their interactions with lipid bilayers with and without cholesterol (CHOL) using molecular dynamics simulations. By changing the polystyrene chain length and grafting density at the end ring of the CNTs at two different nanotube concentrations, we observe the translocation of nanoparticles as well as changes in the lipid bilayer properties. Our results show that all developed models passively diffuse into the membranes without causing any damage to the membrane integrity, although high concentrations of CNTs induce structural and elastic changes in lipid bilayers. In the presence of CHOL, increasing CNT concentration results in decreased rates of CHOL transmembrane motions. On the other hand, CNTs are prone to lipid and polystyrene blockage, which affects their equilibrated configurations, and tilting behavior within the membranes. Hence, we demonstrate that polystyrene-functionalized CNTs are promising drug-carrier agents. However, polystyrene chain length and grafting density are important factors to consider to enhance the efficiency of drug delivery.

A dynamic biomimetic model of the membrane-bound CD4-CD3-TCR complex during pMHC disengagement.

The coordinated (dis)engagement of the membrane-bound T cell receptor (TCR)-CD3-CD4 complex from the peptide-major histocompatibility complex (pMHC) is fundamental to TCR signal transduction and T cell effector function. As such, an atomic-scale understanding would not only enhance our basic understanding of the adaptive immune response but would also accelerate the rational design of TCRs for immunotherapy. In this study, we explore the impact of the CD4 coreceptor on the TCR-pMHC (dis)engagement by constructing a molecular-level biomimetic model of the CD3-TCR-pMHC and CD4-CD3-TCR-pMHC complexes within a lipid bilayer. After allowing the system complexes to equilibrate (engage), we use steered molecular dynamics to dissociate (disengage) the pMHC. We find that 1) the CD4 confines the pMHC closer to the T cell by 1.8 nm at equilibrium; 2) CD4 confinement shifts the TCR along the MHC binding groove engaging a different set of amino acids and enhancing the TCR-pMHC bond lifetime; 3) the CD4 translocates under load increasing the interaction strength between the CD4-pMHC, CD4-TCR, and CD4-CD3; and 4) upon dissociation, the CD3-TCR complex undergoes structural oscillation and increased energetic fluctuation between the CD3-TCR and CD3-lipids. These atomic-level simulations provide mechanistic insight on how the CD4 coreceptor impacts TCR-pMHC (dis)engagement. More specifically, our results provide further support (enhanced bond lifetime) for a force-dependent kinetic proofreading model and identify an alternate set of amino acids in the TCR that dominate the TCR-pMHC interaction and could thus impact the design of TCRs for immunotherapy.

Polystyrene-modified carbon nanotubes: Promising carriers in targeted drug delivery.

To design drug-delivery agents for therapeutic and diagnostic applications, understanding the mechanisms by which covalently functionalized carbon nanotubes penetrate and interact with cell membranes is of great importance. Here, we report all-atom molecular dynamics results from polystyrene and carboxyl-terminated polystyrene-modified carbon nanotubes and show their translocation behavior across a model lipid bilayer together with their potential to deliver a molecule of the drug ibuprofen into the cell. Our results indicate that functionalized carbon nanotubes are internalized by the membrane in hundreds of nanoseconds and that drug loading increases the internalization speed further. Both loaded and unloaded tubes cross the closest leaflet of the bilayer by nonendocytic pathways, and for the times studied, the drug molecule remains trapped inside the pristine tube while remaining attached at the end of polystyrene-modified tube. On the other hand, carboxyl-terminated polystyrene functionalization allows the drug to be completely released into the lower leaflet of the bilayer without imposing damage to the membrane. This study shows that polystyrene functionalization is a promising alternative and facilitates drug delivery as a benchmark case.

SARS-CoV-2 spike binding to ACE2 is stronger and longer ranged due to glycan interaction.

Highly detailed steered molecular dynamics simulations are performed on differently glycosylated receptor binding domains of the severe acute respiratory syndrome coronavirus-2 spike protein. The binding strength and the binding range increase with glycosylation. The interaction energy rises very quickly when pulling the proteins apart and only slowly drops at larger distances. We see a catch-slip-type behavior whereby interactions during pulling break and are taken over by new interactions forming. The dominant interaction mode is hydrogen bonds, but Lennard-Jones and electrostatic interactions are relevant as well.

Impact of Surface Polarity on Lipid Assembly under Spatial Confinement.

Molecular dynamics (MD) simulations in the MARTINI model are used to study the assembly of 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) molecules under spatial confinement, such as during solvent evaporation from ultrasmall (femtoliter quantity) droplets. The impact of surface polarity on molecular assembly is discussed in detail. To the best of our knowledge, this work represents the first of its kind. Our results reveal that solvent evaporation gives rise to the formation of well-defined stacks of lipid bilayers in a smectic alignment. These smectic mesophases form on both polar and nonpolar surfaces but with a notable distinction. On polar surfaces, the director of the stack is oriented perpendicular to the support surface. By contrast, the stacks orient at an angle on the nonpolar surfaces. The packing of head groups on surfaces and lipid molecular mobility exhibits significant differences as surface polarity changes. The role of glycerol in the assembly and stability is also revealed. The insights revealed from the simulation have a significant impact on additive manufacturing, biomaterials, model membranes, and engineering protocells. For example, POPC assemblies via evaporation of ultrasmall droplets were produced and characterized. The trends compare well with the bilayer stack models. The surface polarity influences the local morphology and structures at the interfaces, which could be rationalized via the molecule-surface interactions observed from simulations.

Contributions of the international plant science community to the fight against human infectious diseases - part 1: epidemic and pandemic diseases.

Infectious diseases, also known as transmissible or communicable diseases, are caused by pathogens or parasites that spread in communities by direct contact with infected individuals or contaminated materials, through droplets and aerosols, or via vectors such as insects. Such diseases cause ˜17% of all human deaths and their management and control places an immense burden on healthcare systems worldwide. Traditional approaches for the prevention and control of infectious diseases include vaccination programmes, hygiene measures and drugs that suppress the pathogen, treat the disease symptoms or attenuate aggressive reactions of the host immune system. The provision of vaccines and biologic drugs such as antibodies is hampered by the high cost and limited scalability of traditional manufacturing platforms based on microbial and animal cells, particularly in developing countries where infectious diseases are prevalent and poorly controlled. Molecular farming, which uses plants for protein expression, is a promising strategy to address the drawbacks of current manufacturing platforms. In this review article, we consider the potential of molecular farming to address healthcare demands for the most prevalent and important epidemic and pandemic diseases, focussing on recent outbreaks of high-mortality coronavirus infections and diseases that disproportionately affect the developing world.

Contributions of the international plant science community to the fight against infectious diseases in humans-part 2: Affordable drugs in edible plants for endemic and re-emerging diseases.

The fight against infectious diseases often focuses on epidemics and pandemics, which demand urgent resources and command attention from the health authorities and media. However, the vast majority of deaths caused by infectious diseases occur in endemic zones, particularly in developing countries, placing a disproportionate burden on underfunded health systems and often requiring international interventions. The provision of vaccines and other biologics is hampered not only by the high cost and limited scalability of traditional manufacturing platforms based on microbial and animal cells, but also by challenges caused by distribution and storage, particularly in regions without a complete cold chain. In this review article, we consider the potential of molecular farming to address the challenges of endemic and re-emerging diseases, focusing on edible plants for the development of oral drugs. Key recent developments in this field include successful clinical trials based on orally delivered dried leaves of Artemisia annua against malarial parasite strains resistant to artemisinin combination therapy, the ability to produce clinical-grade protein drugs in leaves to treat infectious diseases and the long-term storage of protein drugs in dried leaves at ambient temperatures. Recent FDA approval of the first orally delivered protein drug encapsulated in plant cells to treat peanut allergy has opened the door for the development of affordable oral drugs that can be manufactured and distributed in remote areas without cold storage infrastructure and that eliminate the need for expensive purification steps and sterile delivery by injection.

Harnessed Dopant Block Copolymers Assist Decorating Membrane Pores: A Dissipative Particle Dynamics Study.

Self-assembly of asymmetric block copolymers (BCPs) around active pore edges has emerged as an important strategy to produce smart membranes with tunable pathways for solute transport. However, thus far, it is still challenging to manipulate pore shape and functionality for directional transformation under external stimuli. Here, a versatile strategy by mesoscale simulations to design stimuli-responsive pores with various edge decorations in hybrid membranes is reported. Dopant BCPs are used as decorators to stabilize pore edges and extend their function in reconfiguring pores in response to repeated membrane stretching/shrinking caused by external stimuli. The decoration morphologies are predictable since the assemblies of dopant BCPs around pore edges are closely related to their self-assemblies in solution. The coassembly between different BCPs in the hybrid membrane for the control of pore morphology is featured, and the parameter settings, including block incompatibility and molecular architecture for the construction of a specific pore, are determined. Results show that harnessed dopant BCPs in the hybrid membrane can enhance pore formation and induce directional pore shape and functionality transformation. Diversified pore decorations exhibit potential that can be further explored in selective solute transport and the design of stimuli-responsive smart nanodevices.

Computational modelling of atomic layer etching of chlorinated germanium surfaces by argon.

The atomic layer etching of chlorinated germanium surfaces under argon bombardment was simulated using molecular dynamics with a newly fitted Tersoff potential. The chlorination energy determines the threshold energy for etching and the number of etched atoms in the bombardment phase. Etch rate is determined by bombardment energy.

Molecular Dynamics Modeling of Methylene Blue-DOPC Lipid Bilayer Interactions.

We present a coarse-grained MARTINI model for methylene blue (MB) and investigate the interactions of MB with dioleylphosphatidylcholine (DOPC) lipid bilayers by molecular dynamics simulations. Our results show that the charge state of MB and the oxidation degree of the DOPC bilayer play critical roles on membrane properties. Oxidation of the DOPC bilayer significantly increases permeability of water and MB molecules, irrespective of the charge state of MB. The most significant changes in membrane properties are obtained for peroxidized lipid bilayers in the presence of cationic MB, with ∼11% increase in the membrane area per lipid head group and ∼7 and 44% reduction in membrane thickness and lateral diffusivity, respectively.

Atomistic modeling of La3+ doping segregation effect on nanocrystalline yttria-stabilized zirconia.

The effect of La3+ doping on the structure and ionic conductivity change in nanocrystalline yttria-stabilized zirconia (YSZ) was studied using a combination of Monte Carlo and molecular dynamics simulations. The simulation revealed the segregation of La3+ at eight tilt grain boundary (GB) structures and predicted an average grain boundary (GB) energy decrease of 0.25 J m-2, which is close to the experimental values reported in the literature. Cation stabilization was found to be the main reason for the GB energy decrease, and energy fluctuations near the grain boundary are smoothed out with La3+ segregation. Both dynamic and energetic analysis on the Σ13(510)/[001] GB structure revealed La3+ doping hinders O2- diffusion in the GB region, where the diffusion coefficient monotonically decreases with increasing La3+ doping concentration. The effect was attributed to the increase in the site-dependent migration barriers for O2- hopping caused by segregated La3+, which also leads to anisotropic diffusion at the GB.

Molecular modeling of lipid probes and their influence on the membrane.

In this review a number of Molecular Dynamics simulation studies are discussed which focus on the understanding of the behavior of lipid probes in biomembranes. Experiments often use specialized probe moieties or molecules to report on the behavior of a membrane and try to gain information on the membrane as a whole from the probe lipids as these probes are the only things an experiment sees. Probes can be used to make NMR, EPR and fluorescence accessible to the membrane and use fluorescent or spin-active moieties for this purpose. Clearly membranes with and without probes are not identical which makes it worthwhile to elucidate the differences between them with detailed atomistic simulations. In almost all cases these differences are confined to the local neighborhood of the probe molecules which are sparsely used and generally present as single molecules. In general, the behavior of the bulk membrane lipids can be qualitatively understood from the probes but in most cases their properties cannot be directly quantitatively deduced from the probe behavior. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

Tunable Permeability of Cross-Linked Microcapsules from pH-Responsive Amphiphilic Diblock Copolymers: A Dissipative Particle Dynamics Study.

Using dissipative particle dynamics simulation, we probe the tunable permeability of cross-linked microcapsules made from pH-sensitive diblock copolymers poly(ethylene oxide)-b-poly(N,N-diethylamino-2-ethyl methacrylate) (PEO-b-PDEAEMA). We first examine the self-assembly of non-cross-linked microcapsules and their pH-responsive collapse and then explore the effects of cross-linking and block interaction on the swelling or deswelling of cross-linked microcapsules. Our results reveal a preferential loading of hydrophobic dicyclopentadiene (DCPD) molecules in PEO-b-PDEAEMA copolymers. Upon reduction of pH, non-cross-linked microcapsules fully decompose into small wormlike clusters as a result of large self-repulsions of protonated copolymers. With increasing degree of cross-linking, the morphology of the microcapsule becomes more stable to pH change. The highly cross-linked microcapsule shell undergoes significant local polymer rearrangement in acidic solution, which eliminates the amphiphilicility and therefore enlarges the permeability of the shell. The responsive cross-linked shell experiences a disperse-to-buckle configurational transition upon reduction of pH, which is effective for the steady or pulsatile regulation of shell permeability. The swelling rate of the cross-linked shell is dependent on both electrostatic and nonelectrostatic interactions between the pH-sensitive groups as well as the other groups. Our study highlights the combination of cross-linking structure and block interactions in stabilizing microcapsules and tuning their selective permeability.

Controllable multicompartment morphologies from cooperative self-assembly of copolymer-copolymer blends.

Multicompartment nanostructures, such as microcapsules with clearly separated shell and core, are not easily accessible by conventional block copolymer self-assembly. We assess a versatile computational strategy through cooperative assembly of diblock copolymer blends to generate spherical and cylindrical compartmentalized micelles with intricate structures and morphologies. The co-assembly strategy combines the advantages of polymer blending and incompatibility-induced phase separation. Following this strategy, various nanoassemblies of pure AB, binary AB/AC and ternary AB/AC/AD systems such as compartmentalized micelles with sponge-like, Janus, capsule-like and onion-like morphologies can be obtained. The formation and structural adjustment of microcapsule micelles, in which the shell or core can be occupied by either pure or mixed diblock copolymers, were explored. The mechanism involving the separation of shell and core copolymers is attributed to the stretching force differences of copolymers which drive the arrangement of different copolymers in a pathway to minimize the total interfacial energy. Moreover, by adjusting block interactions, an efficient approach is exhibited for regulating the shell or core composition and morphology in microcapsule micelles, such as the transition from the "pure shell/mixed core" morphology to the "mixed shell/pure core" morphology in the AB/AC/AD micelle. This mesoscale simulation study identifies the key factors governing co-assembly of diblock copolymer blends and provides bottom-up insights towards the design and optimization of new multicompartment micelles.

Mechanism of the fcc-to-hcp phase transformation in solid Ar.

We present an atomistic description of the fcc-to-hcp transformation mechanism in solid argon (Ar) obtained from transition path sampling molecular dynamics simulation. The phase transition pathways collected during the sampling for an 8000-particle system reveal three transition types according to the lattice deformation and relaxation details. In all three transition types, we see a critical accumulation of defects and uniform growth of a less ordered transition state, followed by a homogeneous growth of an ordered phase. Stacking disorder is discussed to describe the transition process and the cooperative motions of atoms in {111} planes. We investigate nucleation with a larger system: in a system of 18 000 particles, the collective movements of atoms required for this transition are facilitated by the formation and growth of stacking faults. However, the enthalpy barrier is still far beyond the thermal fluctuation. The high barrier explains previous experimental observations of the inaccessibility of the bulk transition at low pressure and its sluggishness even at extremely high pressure. The transition mechanism in bulk Ar is different from Ar nanoclusters as the orthorhombic intermediate structure proposed for the latter is not observed in any of our simulations.

Reactive Molecular Dynamics Simulations of the Silanization of Silica Substrates by Methoxysilanes and Hydroxysilanes.

We perform reactive molecular dynamics simulations of monolayer formation by silanes on hydroxylated silica substrates. Solutions composed of alkylmethoxysilanes or alkylhydroxysilanes in hexane are placed in contact with a hydroxylated silica surface and simulated using a reactive force field (ReaxFF). In particular, we have modeled the deposition of butyl-, octyl-, and dodecyltrimethoxysilane to observe the dependence of alkylsilyl chain length on monolayer formation. We additionally modeled silanization using dodecyltrihydroxysilane, which allows for the comparison of two grafting mechanisms of alkoxysilanes: (1) direct condensation of alkoxysilane with surface-bound silanols and (2) a two-step hydrolysis-condensation mechanism. To emulate an infinite reservoir of reactive solution far away from the substrate, we have developed a method in which new precursor molecules are periodically added to a region of the simulation box located away from the surface. It is determined that the contact angle of alkyl tails bound to the surface is dependent on their grafting density. During the early stages of grafting alkoxy- and hydroxysilanes to the substrate, a preference is shown for silanes to condense with silanols further from the substrate surface and also close to neighboring surface-bound silanols. The kinetics of silica silanization by hydroxysilanes was observed to be much faster than for methoxysilanes. However, the as-deposited hydroxysilane monolayers show similar morphological characteristics to those formed by methoxysilanes.

Understanding the Interaction of Pluronics L61 and L64 with a DOPC Lipid Bilayer: An Atomistic Molecular Dynamics Study.

We investigate the interactions of Pluronics L61 and L64 with a dioleylphosphatidylcholine (DOPC) lipid bilayer by atomistic molecular dynamics simulations using the all-atom OPLS force field. Our results show that the initial configuration of the polymer with respect to the bilayer determines its final conformation within the bilayer. When the polymer is initially placed at the lipid/water interface, we observe partial insertion of the polymer in a U-shaped conformation. On the other hand, when the polymer is centered at the bilayer, it stabilizes to a transmembrane state, which facilitates water transport across the bilayer. We show that membrane thickness decreases while its fluidity increases in the presence of Pluronics. When the polymer concentration inside the bilayer is high, pore formation is initiated with L64. Our results show good agreement with existing experimental data and reveal that the hydrophilic/lipophilic balance of the polymer plays a critical role in the interaction mechanisms as well as in the dynamics of Pluronics with and within the bilayer.

Response to Extreme Temperatures of Mesoporous Silica MCM-41: Porous Structure Transformation Simulation and Modification of Gas Adsorption Properties.

Molecular dynamics (MD) and Monte Carlo (MC) simulations were applied together for the first time to reveal the porous structure transformation mechanisms of mesoporous silica MCM-41 subjected to temperatures up to 2885 K. Silica was experimentally characterized to inform the models and enable prediction of changes in gas adsorption/separation properties. MD simulations suggest that the pore closure process is activated by a collective diffusion of matrix atoms into the porous region, accompanied by bond reformation at the surface. Degradation is kinetically limited, such that complete pore closure is postponed at high heating rates. We experimentally observe decreased gas adsorption with increasing temperature in mesoporous silica heated at fixed rates, due to pore closure and structural degradation consistent with simulation predictions. Applying the Kissinger equation, we find a strong correlation between the simulated pore collapse temperatures and the experimental values which implies an activation energy of 416 ± 17 kJ/mol for pore closure. MC simulations give the adsorption and selectivity for thermally treated MCM-41, for N2, Ar, Kr, and Xe at room temperature within the 1-10 000 kPa pressure range. Relative to pristine MCM-41, we observe that increased surface roughness due to decreasing pore size amplifies the difference of the absolute adsorption amount differently for different adsorbate molecules. In particular, we find that adsorption of strongly interacting molecules can be enhanced in the low-pressure region while adsorption of weakly interacting molecules is inhibited. This then results in higher selectivity in binary mixture adsorption in mesoporous silica.

A quantum chemistry study of curvature effects on boron nitride nanotubes/nanosheets for gas adsorption.

Quantum chemistry calculations were performed to investigate the effect of the surface curvature of a Boron Nitride (BN) nanotube/nanosheet on gas adsorption. Curved boron nitride layers with different curvatures interacting with a number of different gases including noble gases, oxygen, and water on both their convex and concave sides of the surface were studied using density functional theory (DFT) with a high level dispersion corrected functional. Potential energy surfaces of the gas molecules interacting with the selected BN surfaces were investigated. In addition, the charge distribution and electrostatic potential contour of the selected BN surfaces are discussed. The results reveal how the curvature of the BN surfaces affects gas adsorption. In particular, small curvatures lead to a slight difference in the physisorption energy, while large curvatures present distinct potential energy surfaces, especially for the short-range repulsion.