Structures, dynamics, and water permeation free energy across bilayers of Lipid A and its analog studied with molecular dynamics simulation

Translocation of Endo-Functionalized Molecular Tubes across Different Lipid Bilayers: Atomistic Molecular Dynamics Simulation Study

Various artificial receptors, such as calixarenes, cyclodextrins, cucurbit[n]urils, and their acyclic compounds, pliiar[n]arenes, deep cavitands, and molecular tweezers, can permeate the lipid membranes and they are used as drug carriers to improve the drug solubility, stability, and bioavailability. Inspired by these, we have employed atomistic molecular dynamics simulation to examine the effects of endo-functionalized molecular tubes or naphthotubes (host-1a and host-1b) on seven different types of model lipid bilayers and the permeation properties of these receptors through these model lipid bilayers. Lipid types include six model lipid bilayers (POPC, POPE, DOPC, POPG, DPPE, POPE/POPG) and one realistic membrane (Yeast). We observe that these receptors are spontaneously translocated toward these model lipid bilayer head regions and do not proceed further into these lipid bilayer tail regions (reside at the interface between lipid head and lipid tail region), except for the DPPE-containing systems. In the DPPE model lipid bilayer-containing systems (1a-dppe and 1b-dppe), receptor molecules are only adsorbed on the bilayer surface and reside at the interface between lipid head and water. This finding is also supported by the biased free-energy profiles of these translocation processes. Passive transport of these receptors may be possible through these model lipid bilayers (due to low barrier height), except for DPPE bilayer-containing systems (that have a very high energy barrier at the center). The results from these simulations provide insight into the biocompatibility of host-1a or host-1b in microscopic detail. Based on this work, more research is needed to fully comprehend the role of these synthesized receptors as a prospective drug carrier.

Molecular Structure of the Surface-Immobilized Super Uranyl Binding Protein

Recently, a super uranyl binding protein (SUP) was developed, which exhibits excellent sensitivity/selectivity to bind uranyl ions. It can be immobilized onto a surface in sensing devices to detect uranyl ions. Here, sum frequency generation (SFG) vibrational spectroscopy was applied to probe the interfacial structures of surface-immobilized SUP. The collected SFG spectra were compared to the calculated orientation-dependent SUP SFG spectra using a one-excitonic Hamiltonian approach based on the SUP crystal structures to deduce the most likely surface-immobilized SUP orientation(s). Furthermore, discrete molecular dynamics (DMD) simulation was applied to refine the surface-immobilized SUP conformations and orientations. The immobilized SUP structures calculated from DMD simulations confirmed the SUP orientations obtained from SFG data analyzed based on the crystal structures and were then used for a new round of SFG orientation analysis to more accurately determine the interfacial orientations and conformations of immobilized SUP before and after uranyl ion binding, providing an in-depth understanding of molecular interactions between SUP and the surface and the effect of uranyl ion binding on the SUP interfacial structures. We believe that the developed method of combining SFG measurements, DMD simulation, and Hamiltonian data analysis approach is widely applicable to study biomolecules at solid/liquid interfaces.

Emerging Emulsifiers: Conceptual Basis for the Identification and Rational Design of Peptides with Surface Activity

Emulsifiers are gradually evolving from synthetic molecules of petrochemical origin to biomolecules mainly due to health and environmental concerns. Peptides represent a type of biomolecules whose molecular structure is composed of a sequence of amino acids that can be easily tailored to have specific properties. However, the lack of knowledge about emulsifier behavior, structure-performance relationships, and the implementation of different design routes have limited the application of these peptides. Some computational and experimental approaches have tried to close this knowledge gap, but restrictions in understanding the fundamental phenomena and the limited property data availability have made the performance prediction for emulsifier peptides an area of intensive research. This study provides the concepts necessary to understand the emulsifying behavior of peptides. Additionally, a straightforward description is given of how the molecular structure and conditions of the system directly impact the peptides' ability to stabilize emulsion droplets. Moreover, the routes to design and discover novel peptides with interfacial and emulsifying activity are also discussed, along with the strategies to address some of their major pitfalls and challenges. Finally, this contribution reviews methodologies to build and use data sets containing standard properties of emulsifying peptides by looking at successful applications in different fields.

Discontinuous Molecular Dynamics Simulations of Biomolecule Interfacial Behavior: Study of Ovispirin-1 Adsorption on a Graphene Surface

Fundamental understanding of biomolecular interfacial behavior, such as protein adsorption at the microscopic scale, is critical to broad applications in biomaterials, nanomedicine, and nanoparticle-based biosensing techniques. The goal of achieving both computational efficiency and accuracy presents a major challenge for simulation studies at both atomistic and molecular scales. In this work, we developed a unique, accurate, high-throughput simulation method which, by integrating discontinuous molecular dynamics (DMD) simulations with the Go-like protein-surface interaction model, not only solves the dynamics efficiently, but also describes precisely the protein intramolecular and intermolecular interactions at the atomistic scale and the protein-surface interactions at the coarse-grained scale. Using our simulation method and in-house developed software, we performed a systematic study of α-helical ovispirin-1 peptide adsorption on a graphene surface, and our study focused on the effect of surface hydrophobic interactions and π-π stacking on protein adsorption. Our DMD simulations were consistent with full-atom molecular dynamics simulations and showed that a single ovispirin-1 peptide lay down on the flat graphene surface with randomized secondary structure due to strong protein-surface interactions. Peptide aggregates were formed with an internal hydrophobic core driven by strong interactions of hydrophobic residues in the bulk environment. However, upon adsorption, the hydrophobic graphene surface can break the hydrophobic core by denaturing individual peptide structures, leading to disassembling the aggregate structure and further randomizing the ovispirin-1 peptide's secondary structures.

Airborne Transmission of COVID-19: Aerosol Dispersion, Lung Deposition, and Virus-Receptor Interactions

Coronavirus disease 2019 (COVID-19), due to infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is now causing a global pandemic. Aerosol transmission of COVID-19, although plausible, has not been confirmed by the World Health Organization (WHO) as a general transmission route. Considering the rapid spread of SARS-CoV-2, especially nosocomial outbreaks and other superspreading events, there is an urgent need to study the possibility of airborne transmission and its impact on the lung, the primary body organ attacked by the virus. Here, we review the complete pathway of airborne transmission of SARS-CoV-2 from aerosol dispersion in air to subsequent biological uptake after inhalation. In particular, we first review the aerodynamic and colloidal mechanisms by which aerosols disperse and transmit in air and deposit onto surfaces. We then review the fundamental mechanisms that govern regional deposition of micro- and nanoparticles in the lung. Focus is given to biophysical interactions between particles and the pulmonary surfactant film, the initial alveolar-capillary barrier and first-line host defense system against inhaled particles and pathogens. Finally, we summarize the current understanding about the structural dynamics of the SARS-CoV-2 spike protein and its interactions with receptors at the atomistic and molecular scales, primarily as revealed by molecular dynamics simulations. This review provides urgent and multidisciplinary knowledge toward understanding the airborne transmission of SARS-CoV-2 and its health impact on the respiratory system.

Machine Learning Analysis of the Thermodynamic Responses of In Situ Dielectric Spectroscopy Data in Amino Acids and Inorganic Electrolytes

Dielectric spectroscopy (DS) can be a robust in situ technique for geochemical applications. In this study, we applied deep-learning techniques to DS measurement data to enable rapid science interrogation and identification of electrolyte solutions containing salts and amino acids over a wide temperature range (20 to -60 °C). For the purpose of searching for signs of life, detecting amino acids is a fundamental high priority for field and planetary instruments as amino acids are one of the building blocks for life as we know it. A convolutional neural network (CNN) with channel-wise one-dimensional filters is proposed to fulfill the task, using the DS data of amino acid and inorganic salt solutions. Experimental results show that the CNN with two convolutional layers and one fully connected layer can effectively differentiate solutions containing amino acids from those containing salts in both the liquid and solid (water ice) states. To complement the experimental measurements and CNN analysis, the diffusive behaviors of ions (K⁺, Cl^-, and OH^-) were further discussed with atomistic molecular dynamics simulations performed in this work as well as the quantum simulation published in the literature. Combining DS with machine-learning techniques and simulations will greatly facilitate more real-time decision-making of mobility systems for future exploratory endeavors in other worlds beyond Earth.

Mechanism of polyamine induced colistin resistance through electrostatic networks on bacterial outer membranes

Naturally occurring linear polyamines are known to enable bacteria to be resistant to cationic membrane active peptides. To understand this protective mechanism, molecular dynamics simulations are employed to probe their effect on a model bacterial outer membrane. Being protonated at physiological pH, the amine groups of the polyamine engage in favorable electrostatic interactions with the negatively charged phosphate groups of the membrane. Additionally, the amine groups form large number of hydrogen bonds with the phosphate groups. At high concentrations, these hydrogen bonds and the electrostatic network can non-covalently crosslink the lipid A molecules, resulting in stabilization of the outer membrane against membrane active antibiotics such as colistin and polymyxin B. Moreover, large polyamine molecules (e.g., spermidine) have a stronger stabilization effect than small polyamine molecules (e.g., ethylene diamine). The atomistic insights provide useful guidance for the design of next generation membrane active amine-rich antibiotics, especially to tackle the growing threat of multi-drug resistance of Gram negative bacteria.

Atomistic Simulations of Biofouling and Molecular Transfer of a Cross-linked Aromatic Polyamide Membrane for Desalination

Reverse osmosis through a polyamide (PA) membrane is an important technique for water desalination and purification. In this study, molecular dynamics simulations were performed to study the biofouling mechanism (i.e., protein adsorption) and nonequilibrium steady-state water transfer of a cross-linked PA membrane. Our results demonstrated that the PA membrane surface's roughness is a key factor of surface's biofouling, as the lysozyme protein adsorbed on the surface's cavity site displays extremely low surface diffusivity, blocking water passage, and decreasing water flux. The adsorbed protein undergoes secondary structural changes, particularly in the pressure-driven flowing conditions, leading to strong protein-surface interactions. Our simulations were able to present water permeation close to the experimental conditions with a pressure difference as low as 5 MPa, while all the electrolytes, which are tightly surrounded by hydration water, were effectively rejected at the membrane surfaces. The analysis of the self-intermediate scattering function demonstrates that the dynamics of water molecules coordinated with hydrogen bonds is faster inside the pores than during the translation across the pores. The pressure difference applied shows a negligible effect on the water structure and content inside the membrane but facilitates the transportation of hydrogen-bonded water molecules through the membrane's sub-nanopores with a reduced coordination number. The linear relationship between the water flux and the pressure difference demonstrates the applicability of continuum hydrodynamic principles and thus the stability of the membrane structure.

Molecular Dynamics Simulation of Small Molecules Interacting with Biological Membranes

Cell membranes protect and compartmentalise cells and their organelles. The semi-permeable nature of these membranes controls the exchange of solutes across their structure. Characterising the interaction of small molecules with biological membranes is critical to understanding of physiological processes, drug action and permeation, and many biotechnological applications. This review provides an overview of how molecular simulations are used to study the interaction of small molecules with biological membranes, with a particular focus on the interactions of water, organic compounds, drugs and short peptides with models of plasma cell membrane and stratum corneum lipid bilayers. This review will not delve on other types of membranes which might have different composition and arrangement, such as thylakoid or mitochondrial membranes. The application of unbiased molecular dynamics simulations and enhanced sampling methods such as umbrella sampling, metadynamics and replica exchange are described using key examples. This review demonstrates how state-of-the-art molecular simulations have been used successfully to describe the mechanism of binding and permeation of small molecules with biological membranes, as well as associated changes to the structure and dynamics of these membranes. The review concludes with an outlook on future directions in this field.

Atomic-Level Simulation Study of n-Hexane Pyrolysis on Silicon Carbide Surfaces

Ethylene production plays a key role in the petrochemical industry. The severe operation conditions of ethylene thermal cracking, such as high-temperature and coke-formation, pose challenges for the development of new corrosion-resistant and coking-resistant materials for ethylene reactor radiant coils tubes (RCTs). We investigated the performance of ceramic materials such as silicon carbide (SiC) in severe pyrolysis conditions by using reactive force field molecular dynamics (ReaxFF MD) simulation method. Our results indicate that β-SiC surface remains fully stable at 1500 K, whereas increased temperature results in melted interface. At 2500 K, fully grown cross-linked-graphene-like polycyclic aromatic hydrocarbon coking structure on SiC surfaces was observed. Such coking was particularly severe in the carbon-side of the surface slab. The coking structures were mainly derived from surface atoms at the initial 3.0 ns, as a result of the loss of interfacial hydroxyl layer and further hydrothermal corrosion. The SiC substrate surface enhances the ethylene cracking rate and also leads to different intermediate-state compounds. Our fundamental research will have significant and broad impact on both petrochemical industry and academic research in materials science, petrochemistry, and combustion chemistry.

Aromatic Polyamide Reverse-Osmosis Membrane: An Atomistic Molecular Dynamics Simulation

Polyamide (PA) membrane-based reverse-osmosis (RO) serves as one of the most important techniques for water desalination and purification. Fundamental understanding of PA RO membranes at the atomistic level is critical to enhance their separation capabilities, leading to significant societal and commercial benefits. In this paper, a fully atomistic molecular dynamics simulation was performed to investigate PA membrane. Our simulated cross-linked membrane exhibits structural properties similar to those reported in experiments. Our results also reveal the presence of small local two-layer slip structures in PA membrane with 70% cross-linking, primarily due to short-range anisotropic interactions among aromatic benzene rings. Inside the inhomogeneous polymeric structure of the membrane, water molecules show heterogeneous diffusivities and converge adjacent to polar groups. Increased diffusion of water molecules is observed through the less cross-linked pathways. The existence of the fast pathways for water permeation has no effect on membrane's salt rejections.

Self-Assembled Monolayers of an Azobenzene Derivative on Silica and Their Interactions with Lysozyme

The capability of the photoresponsive isomerization of azobenzene derivatives in self-assembled monolayer (SAM) surfaces to control protein adsorption behavior has very promising applications in antifouling materials and biotechnology. In this study, we performed an atomistic molecular dynamics (MD) simulation in combination with free-energy calculations to study the morphology of azobenzene-terminated SAMs (Azo-SAMs) grafted on a silica substrate and their interactions with lysozyme. Results show that the Azo-SAM surface morphology and the terminal benzene rings' packing are highly correlated with the surface density and the isomer state. Higher surface coverage and the trans-isomer state lead to a more ordered polycrystalline backbone as well as more ordered local packing of benzene rings. On the Azo-SAM surface, water retains a high interfacial diffusivity, whereas the adsorbed lysozyme is found to have extremely low mobility but a relative stable secondary structure. The moderate desorption free energy (∼60 kT) from the trans-Azo-SAM surface was estimated by using both the nonequilibrium-theorem-based Jarzynski's equality and equilibrium umbrella sampling.