Molecular dynamics simulation of lysozyme adsorption/desorption on hydrophobic surfaces

Hydration and Antibiofouling Behavior of Zwitterionic Polycarboxybetaine-Grafted Surfaces Studied with Atomistic Simulations

Fouling-resistant coating materials have important applications in marine industry and biomedicine. Zwitterionic carboxybetaine polymers have demonstrated robust antibiofouling functionalities in experiments. In this work, we performed atomistic molecular dynamics simulations to study the molecular mechanism of hydration and antibiofouling of poly(carboxybetaine acrylamide) (polyCBAA) brush surfaces. We focused on the zwitterionic carboxybetaine, which has only a short methylene spacer between the positive quaternary ammonium and the negative carboxylate groups. Our study shows that a large amount of water is present within the polyCBAA surface, and a condensed water layer of single-molecular thickness covers the top of the polymer surface. Moreover, the clustering of the zwitterionic chains results in an amorphous structure of the polymer surface, a reduced degree of order in the interfacial water molecules, and weak protein attachment. The low protein desorption free energy demonstrates that the polyCBAA surface exhibits strong fouling resistance due to its significant interfacial hydration and the small dipole moment of the carboxybetaine group, minimizing protein-surface electrostatic interactions. Our study at the molecular level will be important to the future development of zwitterionic materials.

Sensing lead ions in water: a comprehensive review on strategies and sensor materials

It is well-known fact that elevated lead ions (Pb2+), the third most toxic among heavy metal ions in aqueous systems, pose a threat to human health and aquatic ecosystems when they exceed permissible limits. Pb2+ is commonly found in industrial waste and fertilizers, contaminating water sources and subsequently entering the human body, causing various adverse health conditions. Unlike being expelled, Pb2+ accumulates within the body, posing potential health risks. The harmful impact of presence of Pb2+ in water have prompted researchers to diligently work toward maintaining water quality. Recognizing the importance of Pb2+, this review article makes a sincere and effective effort to address the issues associated with Pb2+. This overview article gives insights into various sensing approaches to detect Pb2+ in water using different sensing materials, including 2-dimensional materials, thiols, quantum dots, and polymers. Herein, different sensing approaches such as electrochemical, optical, field effect transistor-based, micro-electromechanical system-based, and chemi resistive are thoroughly explained. Field effect transistor-based and chemiresistive work on similar principles and are compared on the basis of their fabrication processes and sensing capabilities. In conclusion, future directions for chemiresistive sensors in Pb2+ detection are proposed, emphasizing their simplicity, portability, straightforward functionality, and ease of fabrication. Notably, it sheds light on various thiol and ligand compounds and coupling strategies utilized in Pb2+ detection. This comprehensive study is expected to benefit individuals engaged in Pb2+ detection.

Simulation insights into the lipase adsorption on zeolitic imidazolate framework-8

Zeolitic imidazolate frameworks (ZIFs) have recently emerged as immobilization matrices for biomolecules, most notably enzymes. Understanding the key factors that dominate the enzyme's catalytic activity on/in ZIFs is crucial for the development of new immobilization matrices. In this work, a combination of the parallel tempering Monte Carlo simulation and all-atom molecular dynamics simulation is performed to study the orientation and conformation of the Candida rugose lipase (CRL) adsorbed on oppositely charged and neutral ZIF-8 (i.e., ZIF-8-COOH, ZIF-8-NH2, and ZIF-8-neutral) surfaces. The results show that CRL could adsorb on all ZIF-8 surfaces, with an ordered orientation obtained on charged ZIF-8 surfaces. ZIF-8-NH2 is a good candidate for CRL immobilization since it can maximize the catalytic activity of CRL. The native conformation of CRL is well preserved on all three surfaces due to the partially water-containing surface of ZIF-8. The results could provide theoretical support for the application of porous materials in enzyme immobilization.

Challenges in making ideal cryo-EM samples

Recognizing that interaction with the air-water interface (AWI) is a major challenge for cryo-EM, we first review current approaches designed to avoid it. Of these, immobilizing particles on affinity grids is arguably the most promising. In addition, we review efforts to gain more reliable control of the sample thicknesses, not the least important reason being to prevent immobilized particles from coming in contact with the AWI of the remaining buffer. It is emphasized that avoiding such a contact is as important for cryo-ET as for single-particle cryo-EM. Finally, looking to the future, it is proposed that immobilized samples might be used to perform time-resolved biochemical experiments directly on EM grids rather than just in test tubes or cuvettes.

Hydration behaviors of nonfouling zwitterionic materials

Zwitterionic materials have emerged as highly effective ultralow fouling materials for many applications, however the underlying mechanism of fouling resistance remains unclear. Using ab initio molecular dynamics simulations and surface-sensitive sum frequency generation vibrational spectroscopy, we studied the hydration behaviors of zwitterionic materials, including trimethylamine-N-oxide (TMAO) and carboxybetaines of different charge-separation distances, to understand their fouling-resistant mechanism and provide a design principle for improved performance. Our study reveals that the interplay among hydrogen bonding, net charge, and dipole moment is crucial to the fouling-resistant capabilities of zwitterionic materials. Shortening of the zwitterionic spacing strengthens hydrogen bonding with water against biomolecule attachment due to the increased electrostatic and induction interactions, charge transfer, and improved structural stability. Moreover, the shortened charge separation reduces the dipole moment of zwitterionic materials with an intrinsic near-neutral net charge, decreasing their electrostatic and dipole-dipole interactions with biofoulers, and increasing their resistance to fouling. Compared to carboxybetaine compounds, TMAO has the shortest zwitterionic spacing and exhibits the strongest hydrogen bonding, the smallest net charge, and the minimum dipole moment, making it an excellent nonfouling material.

Determination of protein conformation and orientation at buried solid/liquid interfaces

Protein structures at solid/liquid interfaces mediate interfacial protein functions, which are important for many applications. It is difficult to probe interfacial protein structures at buried solid/liquid interfaces in situ at the molecular level. Here, a systematic methodology to determine protein molecular structures (orientation and conformation) at buried solid/liquid interfaces in situ was successfully developed with a combined approach using a nonlinear optical spectroscopic technique - sum frequency generation (SFG) vibrational spectroscopy, isotope labeling, spectra calculation, and computer simulation. With this approach, molecular structures of protein GB1 and its mutant (with two amino acids mutated) were investigated at the polymer/solution interface. Markedly different orientations and similar (but not identical) conformations of the wild-type protein GB1 and its mutant at the interface were detected, due to the varied molecular interfacial interactions. This systematic strategy is general and can be widely used to elucidate protein structures at buried interfaces in situ.

Physicochemical properties of soybean β-conglycinin-based films affected by linoleic acid

To explore the interaction between lipids and proteins during emulsion film formation, the linoleic acid concentration effects on the physicochemical properties of soybean β-conglycinin (7S) films were studied. The viscosity and size of oil droplets in the film-forming solution gradually increased with the increasing linoleic acid concentration. As the linoleic acid concentration increased, the number of oil droplets on the film surfaces and elongation at break of films gradually increased, whereas the tensile strength decreased. The films containing 20% linoleic acid had the highest water vapor permeability value, which was decreased by increasing or decreasing the linoleic acid concentration. According to the molecular dynamics simulation and chemical interactions, 7S could be adsorbed at the linoleic acid interface and bind stably, resulting in the decreased ionic and hydrogen bonds but the increased hydrophobic interactions and covalent bonds among proteins in the films.

Graph Clustering Analyses of Discontinuous Molecular Dynamics Simulations: Study of Lysozyme Adsorption on a Graphene Surface

Understanding the interfacial behaviors of biomolecules is crucial to applications in biomaterials and nanoparticle-based biosensing technologies. In this work, we utilized autoencoder-based graph clustering to analyze discontinuous molecular dynamics (DMD) simulations of lysozyme adsorption on a graphene surface. Our high-throughput DMD simulations integrated with a Go̅-like protein-surface interaction model makes it possible to explore protein adsorption at a large temporal scale with sufficient accuracy. The graph autoencoder extracts a low-dimensional feature vector from a contact map. The sequence of the extracted feature vectors is then clustered, and thus the evolution of the protein molecule structure in the absorption process is segmented into stages. Our study demonstrated that the residue-surface hydrophobic interactions and the π-π stacking interactions play key roles in the five-stage adsorption. Upon adsorption, the tertiary structure of lysozyme collapsed, and the secondary structure was also affected. The folding stages obtained by autoencoder-based graph clustering were consistent with detailed analyses of the protein structure. The combination of machine learning analysis and efficient DMD simulations developed in this work could be an important tool to study biomolecules' interfacial behaviors.

Molecular understanding of acetylcholinesterase adsorption on functionalized carbon nanotubes for enzymatic biosensors

The immobilization of acetylcholinesterase on different nanomaterials has been widely used in the field of amperometric organophosphorus pesticide (OP) biosensors. However, the molecular adsorption mechanism of acetylcholinesterase on a nanomaterial's surface is still unclear. In this work, multiscale simulations were utilized to study the adsorption behavior of acetylcholinesterase from Torpedo californica (TcAChE) on amino-functionalized carbon nanotube (CNT) (NH₂-CNT), carboxyl-functionalized CNT (COOH-CNT) and pristine CNT surfaces. The simulation results show that the active center and enzyme substrate tunnel of TcAChE are both close to and oriented toward the surface when adsorbed on the positively charged NH₂-CNT, which is beneficial to the direct electron transfer (DET) and accessibility of the substrate molecule. Meanwhile, the NH₂-CNT can also reduce the tunnel cost of the enzyme substrate of TcAChE, thereby further accelerating the transfer rate of the substrate from the surface or solution to the active center. However, for the cases of TcAChE adsorbed on COOH-CNT and pristine CNT, the active center and substrate tunnel are far away from the surface and face toward the solution, which is disadvantageous for the DET and transportation of enzyme substrate. These results indicate that NH₂-CNT is more suitable for the immobilization of TcAChE. This work provides a better molecular understanding of the adsorption mechanism of TcAChE on functionalized CNT, and also provides theoretical guidance for the ordered immobilization of TcAChE and the design, development and improvement of TcAChE-OPs biosensors based on functionalized carbon nanomaterials.

Multiscale Simulation of Protein Corona Formation on Silver Nanoparticles: Study of Ovispirin-1 Peptide Adsorption

The exposure of nanoparticles (NPs) to biofluids leads to the rapid coverage of proteins, named protein corona, which alters the NPs' chemicophysical and biological properties. Fundamental studies of the protein corona are thus critical to the increasing applications of NPs in nanotechnology and nanomedicines. The present work utilizes multiscale simulations of a model biological system, small ovispirin-1 peptides, and bare silver nanoparticles (AgNPs) to examine the NPs' size and surface hydrophilicity effects on formation dynamics and the structure of the peptide corona. Our simulations revealed the different adsorption dynamics of ovispirin-1 peptides on the NPs, including the direct adsorption of a single peptide and peptide aggregates and multistep adsorption, as well as an intermediate cycle of desorption and readsorption. Notably, the whole process of peptide adsorption on hydrophilic AgNP surfaces can be generalized as three stages: diffusion to the surface, initial landing via hydrophilic residues, and the final attachment. The decrease in AgNP's size leads to faster adsorption with more heterogeneous peptide interfacial dynamics, a denser and inhomogeneous peptide packing structure, and a wider distribution of adsorption orientations. Subsequent atomistic molecular dynamics simulations demonstrated that on the hydrophilic AgNP surfaces, adsorbed peptides display moderate changes in their secondary structure, resulting in further changes of corona composition, i.e., amino acid residue distribution on the surface.

Strong Surface Hydration and Salt Resistant Mechanism of a New Nonfouling Zwitterionic Polymer Based on Protein Stabilizer TMAO

Zwitterionic polymers exhibit excellent nonfouling performance due to their strong surface hydrations. However, salt molecules may severely reduce the surface hydrations of typical zwitterionic polymers, making the application of these polymers in real biological and marine environments challenging. Recently, a new zwitterionic polymer brush based on the protein stabilizer trimethylamine N-oxide (TMAO) was developed as an outstanding nonfouling material. Using surface-sensitive sum frequency generation (SFG) vibrational spectroscopy, we investigated the surface hydration of TMAO polymer brushes (pTMAO) and the effects of salts and proteins on such surface hydration. It was discovered that exposure to highly concentrated salt solutions such as seawater only moderately reduced surface hydration. This superior resistance to salt effects compared to other zwitterionic polymers is due to the shorter distance between the positively and negatively charged groups, thus a smaller dipole in pTMAO and strong hydration around TMAO zwitterion. This results in strong bonding interactions between the O- in pTMAO and water, and weaker interaction between O- and metal cations due to the strong repulsion from the N+ and hydration water. Computer simulations at quantum and atomistic scales were performed to support SFG analyses. In addition to the salt effect, it was discovered that exposure to proteins in seawater exerted minimal influence on the pTMAO surface hydration, indicating complete exclusion of protein attachment. The excellent nonfouling performance of pTMAO originates from its extremely strong surface hydration that exhibits effective resistance to disruptions induced by salts and proteins.

Adsorption of lysozyme on gold surfaces in the presence of an external electric potential

Adsorbed protein films consist of essential building blocks of many biotechnological and biomedical devices. The electrostatic potential may significantly modulate the protein behaviour on surfaces, affecting their structure and biological activity. In this study, lysozyme was used to investigate the effects of applied electric potentials on adsorption and the protein structure. The pH and the surface charge determine the amount and secondary structure of adsorbed lysozyme on a gold surface. In-situ measurements using polarization modulation infrared reflection absorption spectroscopy indicated that the concentration of both the adsorbed anions and the lysozyme led to conformational changes in the protein film, which was demonstrated by a greater amount of aggregated β-sheets in films fabricated at net positive charges of the Au electrode (E_ads > E_pzc). The changes in secondary structure involved two parallel processes. One comprised changes in the hydration/hydrogen-bond network at helices, leading to diverse helical structures: α-, 3₁₀- and/or π-helices. In the second process β-turns, β-sheets, and random coils displayed an ability to form aggregated β-sheet structures. The study illuminates the understanding of electrical potential-dependent changes involved in the protein misfolding process.

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.

Brownian Dynamics Simulations of Proteins in the Presence of Surfaces: Long-Range Electrostatics and Mean-Field Hydrodynamics

Simulations of macromolecular diffusion and adsorption in confined environments can offer valuable mechanistic insights into numerous biophysical processes. In order to model solutes at atomic detail on relevant time scales, Brownian dynamics simulations can be carried out with the approximation of rigid body solutes moving through a continuum solvent. This allows the precomputation of interaction potential grids for the solutes, thereby allowing the computationally efficient calculation of forces. However, hydrodynamic and long-range electrostatic interactions cannot be fully treated with grid-based approaches alone. Here, we develop a treatment of both hydrodynamic and electrostatic interactions to include the presence of surfaces by modeling grid-based and long-range interactions. We describe its application to simulate the self-association and many-molecule adsorption of the well-characterized protein hen egg-white lysozyme to mica-like and silica-like surfaces. We find that the computational model can recover a number of experimental observables of the adsorption process and provide insights into their determinants. The computational model is implemented in the Simulation of Diffusional Association (SDA) software package.

Lysozyme Adsorption on Different Functionalized MXenes: A Multiscale Simulation Study

Recently, MXenes, due to their abundant advantages, have been widely applied in energy storage, separation, catalysis, biosensing, et al. In this study, parallel tempering Monte Carlo and molecular dynamics methods were performed to investigate lysozyme adsorption on different functionalized Ti₃C₂T_x (-O, -OH, and -F). The simulation results show that lysozyme can adsorb effectively on Ti₃C₂T_x surfaces, and the order of interaction strength is Ti₃C₂O₂ > Ti₃C₂F₂ > Ti₃C₂(OH)₂. Electrostatics together with van der Waals interactions control protein adsorption. The orientation distributions of lysozyme adsorbed on the Ti₃C₂O₂ and Ti₃C₂F₂ surfaces are more concentrated than that on the Ti₃C₂(OH)₂ surface. During adsorption, the conformation of lysozyme remains stable, suggesting the good biocompatibility of Ti₃C₂T_x. Besides, the distribution of the interfacial water layer on the Ti₃C₂T_x surface has a certain impact on protein adsorption. This study provides theoretical insights for understanding the biocompatibility of 2D Ti₃C₂T_x materials and may help us evaluate the engineering of their surfaces for future biorelated applications.

Adsorption rate constants of therapeutic proteins and surfactants for material surfaces

Adsorption of therapeutic proteins to material surfaces can be a pivotal issue in drug development, especially for low concentration products. Surfactants are used to limit adsorption losses. For each formulation component, surface adsorption is the result of a combination of its diffusion and surface adsorption rates. The latter are difficult to measure accurately because a depletion layer forms rapidly in the bulk solution above a bare surface, slowing down adsorption. Adapting flow conditions and local surface chemistry, we are able to minimize depletion limitations and measure apparent adsorption rate constants of three monoclonal antibodies, other proteins and surfactants with a hydrophobic surface. We show that surface adsorption rates scale with the molecular mass of the molecule, with polysorbates therefore showing thousand times slower rates than antibodies. Moreover, we observed that the desorption dynamic of polysorbates from a given hydrophobic surface depends on surface coverage, whereas this is not the case for Poloxamer 188. These novel contributions to surface adsorption dynamics enable a new perspective on the evaluation of drug surface compatibility and can, together with diffusion rates, be used to predict the protective potential of surfactants in given conditions.

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.

Artificial Photosynthesis: Is Computation Ready for the Challenge Ahead?

A tremendous effort is currently devoted to the generation of novel hybrid materials with enhanced electronic properties for the creation of artificial photosynthetic systems. This compelling and challenging problem is well-defined from an experimental point of view, as the design of such materials relies on combining organic materials or metals with biological systems like light harvesting and redox-active proteins. Such hybrid systems can be used, e.g., as bio-sensors, bio-fuel cells, biohybrid photoelectrochemical cells, and nanostructured photoelectronic devices. Despite these efforts, the main bottleneck is the formation of efficient interfaces between the biological and the organic/metal counterparts for efficient electron transfer (ET). It is within this aspect that computation can make the difference and improve the current understanding of the mechanisms underneath the interface formation and the charge transfer efficiency. Yet, the systems considered (i.e., light harvesting protein, self-assembly monolayer and surface assembly) are more and more complex, reaching (and often passing) the limit of current computation power. In this review, recent developments in computational methods for studying complex interfaces for artificial photosynthesis will be provided and selected cases discussed, to assess the inherent ability of computation to leave a mark in this field of research.

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.

Coarse-grained simulation of the translational and rotational diffusion of globular proteins by dissipative particle dynamics

With simplified interactions and degrees of freedom, coarse-grained (CG) simulations have been successfully applied to study the translational and rotational diffusion of proteins in solution. However, in order to reach larger lengths and longer timescales, many CG simulations employ an oversimplified model for proteins or an implicit-solvent model in which the hydrodynamic interactions are ignored, and thus, the real kinetics are more or less unfaithful. In this work, we develop a CG model based on the dissipative particle dynamics (DPD) that can be universally applied to different types of proteins. The proteins are modeled as a group of rigid DPD beads without conformational changes. The fluids (including solvent and ions) are also modeled as DPD beads. The electrostatic interactions between charged species are explicitly considered by including charge distributions on DPD particles. Moreover, a surface friction between the protein and fluid beads is applied to control the slip boundary condition. With this model, we investigate the self-diffusion of a single globular protein in bulk solution. The translational and rotational diffusion coefficients of the protein can be tuned by the surface frictional constant to fit the predictions of the Stokes-Einstein (SE) relation. We find that both translational and rotational diffusion coefficients that meet with the prediction of the SE relation based on experimental results of the hydrodynamic radius are reached at almost the same frictional constant for different types of proteins. Such scaling behavior indicates that the model can be applied to simulate the translational and rotational diffusion together for various types of proteins.

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.

Temperature dependent aggregation mechanism and pathway of lysozyme: By all atom and coarse grained molecular dynamics simulation

Aggregation of protein causes various diseases including Alzheimer's disease, Parkinson's disease, and type II diabetes. It was found that aggregation of protein depends on many factors like temperature, pH, salt type, salt concentration, ionic strength, protein concentration, co solutes. Here we have tried to capture the aggregation mechanism and pathway of hen egg white lysozyme using molecular dynamics simulations at two different temperatures; 300 K and 340 K. Along with the all atom simulations to get the atomistic details of aggregation mechanism, we have used coarse grained simulation with MARTINI force field to monitor the aggregation for longer duration. Our results suggest that due to the aggregation, changes in the conformation of lysozyme are more at 340 K than at 300 K. The change in the conformation of the lysozyme at 300 K is mainly due to aggregation where at 340 K change in conformation of lysozyme is due to both aggregation and temperature. Also, a more compact aggregated system is formed at 340 K.

Protein Corona on Gold Nanoparticles Studied with Coarse-Grained Simulations

Understanding protein corona formation in an aqueous environment at the molecular and atomistic levels is critical to applications such as biomolecule-detection and drug delivery. In this work, we employed mesoscopic coarse-grained simulations to study ovispirin-1 and lysozyme protein coronas on bare gold nanoparticles. Our study showed that protein corona formation is governed by protein-surface and protein-protein interactions, as well as the surface hydrophobic effect. The corona structure was found to be dependent on protein types and the size of nanoparticles. Ovispirin proteins form homogeneous single-layered adsorption in comparison with the lysozyme's inhomogeneous multilayered aggregates on gold NP surfaces. The decrease in nanoparticle size leads to more angular degrees of freedom for protein adsorption orientation. Subsequent atomistic molecular dynamics simulations further demonstrate the loss of secondary structure of ovispirin upon adsorption and the heterogeneity of its local structure.

Lysozyme Adsorption on Porous Organic Cages: A Molecular Simulation Study

Recently, porous organic cages (POCs) have emerged as a novel porous material with many merits and are widely utilized in many application fields. In this work, for the first time, molecular dynamics simulations were performed to investigate the mechanism of lysozyme adsorption onto the CC3 crystal, a kind of widely studied POC material. The simulation results show that lysozyme adsorbs onto the surface of CC3 with "top end-on," "back-on," or "side-on" orientations. It is found that the van der Waals interaction is the primary contribution to the binding; the conformation of the lysozyme is well preserved during the adsorption process. This provides some evidence for its biocompatibility and feasibility in biorelated applications. Arginine plays an important role in mediating the adsorption through nonpolar aliphatic chains. More importantly, the distribution and structure of the water layer on the POC surface has a significant impact on adsorption. This study provides insights into the development of POC materials with defined morphologies for the adsorption of biomolecules and may help the rational design of biorelated systems.

Electrostatic Effect of Functional Surfaces on the Activity of Adsorbed Enzymes: Simulations and Experiments

The efficient immobilization of haloalkane dehalogenase (DhaA) on carriers with retaining of its catalytic activity is essential for its application in environmental remediation. In this work, adsorption orientation and conformation of DhaA on different functional surfaces were investigated by computer simulations; meanwhile, the mechanism of varying the catalytic activity was also probed. The corresponding experiments were then carried out to verify the simulation results. (The simulations of DhaA on SAMs provided parallel insights into DhaA adsorption in carriers. Then, the theory-guided experiments were carried out to screen the best surface functional groups for DhaA immobilization.) The electrostatic interaction was considered as the main impact factor for the regulation of enzyme orientation, conformation, and enzyme bioactivity during DhaA adsorption. The synergy of overall conformation, enzyme substrate tunnel structural parameters, and distance between catalytic active sites and surfaces codetermined the catalytic activity of DhaA. Specifically, it was found that the positively charged surface with suitable surface charge density was helpful for the adsorption of DhaA and retaining its conformation and catalytic activity and was favorable for higher enzymatic catalysis efficiency in haloalkane decomposition and environmental remediation. The neutral, negatively charged surfaces and positively charged surfaces with high surface charge density always caused relatively larger DhaA conformation change and decreased catalytic activity. This study develops a strategy using a combination of simulation and experiment, which can be essential for guiding the rational design of the functionalization of carriers for enzyme adsorption, and provides a practical tool to rationally screen functional groups for the optimization of adsorbed enzyme functions on carriers. More importantly, the strategy is general and can be applied to control behaviors of different enzymes on functional carrier materials.

Correlation between Tribological Properties and the Quantified Structural Changes of Lysozyme on Poly (2-hydroxyethyl methacrylate) Contact Lens

The ocular discomfort is the leading cause of contact lens wear discontinuation. Although the tear proteins as a lubricant might improve contact lens adaptation, some in vitro studies suggested that the amount of adsorbed proteins could not simply explain the lubricating performance of adsorbed proteins. The purpose of this study was to quantify the structural changes and corresponding ocular lubricating properties of adsorbed protein on a conventional contact lens material, poly (2-hydroxyethyl methacrylate) (pHEMA). The adsorption behaviors of lysozyme on pHEMA were determined by the combined effects of protein–surface and protein–protein interactions. Lysozyme, the most abundant protein in tear, was first adsorbed onto the pHEMA surface under widely varying protein solution concentrations to saturate the surface, with the areal density of the adsorbed protein presenting different protein–protein effects within the layer. These values were correlated with the measured secondary structures, and corresponding friction coefficient of the adsorbed and protein covered lens surface, respectively. The decreased friction coefficient value was an indicator of the lubricated surfaces with improved adaptation. Our results indicate that the protein–protein effects help stabilize the structure of adsorbed lysozyme on pHEMA with the raised friction coefficient measured critical for the innovation of contact lens material designs with improved adaptation.

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.

Simulated revelation of the adsorption behaviours of acetylcholinesterase on charged self-assembled monolayers

An acetylcholinesterase (AChE)-based electrochemical biosensor, as a promising alternative to detect organophosphates (OPs) and carbamate pesticides, has gained considerable attention in recent years, due to the advantages of simplicity, rapidity, reliability and low cost. The bio-activity of AChE immobilized on the surface and the direct electron transfer (DET) rate between an enzyme and an electrode directly determined the analytical performances of the AChE-based biosensor, and experimental studies have shown that the charged surfaces have a strong impact on the detectability of the AChE-based biosensor. Therefore, it is very important to reveal the behaviour of AChE in bulk solution and on charged surfaces at the molecular level. In this work, the adsorption orientation and conformation of AChE from Torpedo californica (TcAChE) on oppositely charged self-assembled monolayers (SAMs), COOH-SAM and NH₂-SAM with different surface charge densities, were investigated by parallel tempering Monte Carlo (PTMC) and all-atom molecular dynamics simulations (AAMD). Simulation results show that TcAChE could spontaneously and stably adsorb on two oppositely charged surfaces by the synergy of an electric dipole and charged residue patch, and opposite orientations were observed. The active-site gorge of TcAChE is oriented toward the surface with the "end-on" orientation and the active sites are close to the surface when it is adsorbed on the positively charged surface and the tunnel cost for the substrate is lower than that on the negatively charged surface and in bulk solution, while for TcAChE adsorbed on the negatively charged surface, the active site of TcAChE is far away from the surface and the active-site gorge is oriented toward the solution with a "back-on" orientation. It suggests that the positively charged surface could provide a better microenvironment for the efficient bio-catalytic reaction and quick DET between TcAChE and the electrode surface. Moreover, the RMSD, RMSF, dipole moment, gyration radius, eccentricity and superimposed structures show that only a slight conformational change occurred on the relatively flexible structure of TcAChE during simulations, and the native conformation is well preserved after adsorption. This work helps us better comprehend the adsorption mechanism of TcAChE on charged surfaces and might provide some guidelines for the development of new TcAChE-based amperometric biosensors for the detection of organophosphorus pesticides.

Influence of Structured Water Layers on Protein Adsorption Process: A Case Study of Cytochrome c and Carbon Nanotube Interactions and Its Implications

Cytochrome c, an essential protein of the electron transport chain, is known to be capable of amplifying the toxicity of carbon nanomaterials via free-radical generation. To understand their interaction, as well as the more general protein-nanoparticle interaction at molecular levels, we investigate the adsorptions between cytochrome c and carbon nanotubes (CNTs) in dynamic and thermodynamic ways using molecular dynamics simulations. The results reveal a well-defined three-phase process separated by two transition points: the diffusion phase where the protein diffuses in the water box, the lockdown phase I where the protein inserts into the surface-bound water layers and rearranges its conformation to fit to the surface of the CNT, and the lockdown phase II where cytochrome c repels the water molecules standing in its way to the surface of CNT and reaches stable adsorption states. The structured water layers affect the movement of atoms by electrostatic forces. In lockdown phase I, the conformation adjustment of the protein dominates the adsorption process. The most thermally favorable adsorption conformation is determined. It shows that except for the deformation of short β sheets and some portions of α helixes, most of the secondary structures of cytochrome c remain unchanged, implying that most of the functions of cytochrome c are preserved. During these processes, the energy contributions of the hydrophilic residues of cytochrome c are much larger than those of hydrophobic residues. Interestingly, the structured water layers at the CNT surface allow more hydrophilic residues such as Lys to get into close contact with the CNT, which plays a significant role during the anchoring process of adsorption. Our results demonstrate that the heme group is in close contact with the CNT in some of the adsorbed states, which hence provides a way for electron transfer from cytochrome c to the CNT surface.

Refined Empirical Force Field to Model Protein-Self-Assembled Monolayer Interactions Based on AMBER14 and GAFF

Understanding protein interaction with material surfaces is important for the development of nanotechnological devices. The structures and dynamics of proteins can be studied via molecular dynamics (MD) if the protein-surface interactions can be accurately modeled. To answer this question, we computed the adsorption free energies of peptides (representing eleven different amino acids) on a hydrophobic self-assembled monolayer (CH₃-SAM) and compared them to the benchmark experimental data set. Our result revealed that existing biomolecular force fields, GAFF and AMBER ff14sb, cannot reproduce the experimental peptide adsorption free energies by Wei and Latour (Langmuir, 2009, 25, 5637-5646). To obtain the improved force fields, we systematically tuned the Lennard-Jones parameters of selected amino acid sidechains and the functional group of SAM with repeated metadynamics and umbrella sampling simulations. The final parameter set has yielded a significant improvement in the free energy values with R = 0.83 and MSE = 0.65 kcal/mol. We applied the refined force field to predict the initial adsorption orientation of lysozyme on CH₃-SAM. Two major orientations-face-down and face-up-were predicted. Our analysis on the protein structure, solvent accessible surface area, and binding of native ligand NAG₃ suggested that lysozyme in the face-up orientation can remain active after initial adsorption. However, because of its weaker affinity (ΔΔG = 7.86 kcal/mol) for the ligand, the bioactivity of the protein is expected to reduce. Our work facilitates the use of MD for the study of protein-SAM systems. The refined force field compatible with GROMACS is available at https://cbbio.cis.um.edu.mo/software/SAMFF .

ReaxFF MD Simulations of Peptide-Grafted Gold Nanoparticles

Functionalized gold nanoparticles have critical applications in biodetection with surface-enhanced Raman spectrum and drug delivery. In this study, reactive force field molecular dynamics simulations were performed to study gold nanoparticles, which are modified with different short-chain peptides consisting of amino acid residues of cysteine and glycine in different grafting densities in the aqueous environment. Our study showed slight facet-dependent peptide adsorption on a gold nanoparticle with the 3 nm core diameter. Peptide chains prefer to adsorb on the Au(111) facet compared to those on other facets of Au(100) and Au(110). In addition to the stable thiol interaction with gold nanoparticle surfaces, polarizable oxygen and nitrogen atoms show strong interactions with the gold surface and polarize the gold nanoparticle surfaces with an overall positive charge. Charges of gold atoms vary according to their contacts with peptide atoms and lattice positions. However, at the outmost peptide layer, the whole functionalized Au nanoparticles exhibit overall negative electrostatic potential due to the grafted peptides. Moreover, simulations show that thiol groups can be deprotonated and subsequently protons can be transferred to water molecules and carboxyl groups.

How graphene affects the misfolding of human prion protein: A combined experimental and molecular dynamics simulation study

As the broad application of graphene in the biomedical field, it is urgent and important to evaluate how the graphene affects the structure and function of the proteins in our body, especially the amyloid-related proteins. Prion protein, as a typical amyloid protein, it misfolding and aggregation will lead to serious prion diseases. To explore if graphene promotes or inhibits the formation of amyloid, here, we combined the experimental and molecular dynamics (MD) simulation methods to study the influence of graphene on the globular domain of prion protein (PrP_117-231). The results from fluorescence quenching and circular dichroism spectrum showed that the addition of graphene changed the secondary structure of prion protein largely, mainly reflecting in the reduced α-helix structure and the increased coil structure, indicating graphene may strengthen the misfolding inclination of prion. To further uncover the mechanism of conformational change of prion under the induction of graphene, the all-atoms MD simulations in explicit solvent were performed. Our simulations suggest that prion protein can be quickly and tightly adsorbed onto graphene together with the weak conformational rearrangement and may reorient when approaching the surface. The Van der Waals' force drive the adsorption process. In the induction of graphene, H1 and S2-H2 loop regions of prion become unstable and prion begins to misfold partially. Our work shows that graphene can induce the misfolding of prion protein and may cause the potential risk to biosystems.

Assessing the Accuracy of Different Solvation Models To Describe Protein Adsorption

In protein adsorption, the surrounding solvent has an important role in mediating protein-surface interactions. Therefore, it is of paramount importance that the solvent methods employed to model these kinds of processes are able to correctly capture the complex mechanisms occurring in the protein-water-surface interface. Here, we test the suitability of the two most popular implicit solvent methods based on the Generalized Born formalism to describe the adsorption process of the immunoglobulin G (IgG) on a hydrophobic graphene surface. Our results show that in both cases, IgG experiences an extreme and early (in less than 40 ns) unfolding as a result of the adsorption to the surface in contrast with previous experimental findings. A detailed energy decomposition analysis of explicit and implicit solvent simulations reveals that this discrepancy arises from the ill-characterization of two energy components in implicit solvent methods. These findings help to elucidate how implicit solvent models may be improved to accurately characterize the protein adsorption process.

Electrostatically Driven Protein Adsorption: Charge Patches versus Charge Regulation

The mechanisms of electrostatically driven adsorption of proteins on charged surfaces are studied with a new theoretical framework. The acid-base behavior, charge distribution, and electrostatic contributions to the thermodynamic properties of the proteins are modeled in the presence of a charged surface. The method is validated against experimental titration curves and apparent p K_as. The theory predicts that electrostatic interactions favor the adsorption of proteins at their isoelectric points on charged surfaces despite the fact that the protein has no net charge in solution. Two known mechanisms explain adsorption under these conditions: (i) charge regulation (the charge of the protein changes due to the presence of the surface) and (ii) charge patches (the protein orients to place charged amino acids near opposite surface charges). This work shows that both mechanisms contribute to adsorption at low ionic strengths, whereas only the charge-patch mechanism operates at high ionic strength. Interestingly, the contribution of charge regulation is insensitive to protein orientation under all conditions, which validates the use of constant-charge simulations to determine the most stable orientation of adsorbed proteins. The present study also shows that the charged surface can induce large shifts in the apparent p K_as of individual amino acids in adsorbed proteins. Our conclusions are valid for all proteins studied in this work (lysozyme, α-amylase, ribonuclease A, and β-lactoglobulin), as well as for proteins that are not isoelectric but have instead a net charge in solution of the same sign as the surface charge, i.e. the problem of protein adsorption on the "wrong side" of the isoelectric point.

Protein G selects two binding sites for carbon nanotube with dissimilar behavior; a molecular dynamics study

BACKGROUND

Study of nanostructure-protein interaction for development of various types of nano-devices is very essential. Among carbon nanostructures, carbon nanotube (CNT) provides a suitable platform for functionalization by proteins. Previous studies have confirmed that the CNT induces changes in the protein structure.

METHODS

Molecular dynamics (MD) simulation study was employed to illustrate the changes occurring in the protein G (PGB) in the presence of a CNT. In order to predict the PGB surface patches for the CNT, Autodock tools were utilized.

RESULTS

Docking results indicate the presence of two different surface patches with diverse amino acids: the dominant polar residues in the first (PGB-CNT1) and the aromatic residues in the second (PGB-CNT2) surface patch. Displacement of amino acids in the PGB-CNT2 complex occurred during the simulation and it caused an increase in its stability at the end of simulation. The amino acids' displacements diminished the PGB α-helix structure by breakage of hydrogen bonds and generated more transient structures. Principal component analysis determined that the interaction of the CNT with the second surface patch of the PGB raised the extent and modes of the PGB motions. In contrast, insignificant structural changes induced in the PGB while the CNT bonded through the first surface patch.

CONCLUSION

Even though neither of the PGB-CNT complexes could prevent structural changes in the PGB, development of the PGB-CNT1 complex induce slight structural changes in its fragment of crystallizable receptor (FCR). Dissimilar structural changes induced in the PGB-CNT complexes are possibly related to various characteristics of the PGB binding sites.

Super-Temporal-Resolved Microscopy Reveals Multistep Desorption Kinetics of α-Lactalbumin from Nylon

Insight into the mechanisms driving protein-polymer interactions is constantly improving due to advances in experimental and computational methods. In this study, we used super-temporal-resolved microscopy (STReM) to study the interfacial kinetics of a globular protein, α-lactalbumin (α-LA), adsorbing at the water-nylon 6,6 interface. The improved temporal resolution of STReM revealed that residence time distributions involve an additional step in the desorption process. Increasing the ionic strength in the bulk solution accelerated the desorption rate of α-LA, attributed to adsorption-induced conformational changes. Ensemble circular dichroism measurements were used to support a consecutive reaction mechanism. Without the improved temporal resolution of STReM, the desorption intermediate was not resolvable, highlighting both STReM's potential to uncover new kinetic mechanisms and the continuing need to push for better time and space resolution.

Energy Landscape of Negatively Charged BSA Adsorbed on a Negatively Charged Silica Surface

We study the energy landscape of the negatively charged protein bovine serum albumin adsorbed on a negatively charged silica surface at pH 7. We use fully atomistic molecular dynamics (MD) and steered MD (SMD) to probe the energy of adsorption and the pathway for the surface diffusion of the protein and its associated activation energy. We find an adsorption energy ∼1.2 eV, which implies that adsorption is irreversible even on experimental time scales of hours. In contrast, the activation energy for surface diffusion is ∼0.4 eV so that it is observable on the MD simulation time scale of 100 ns. This analysis paves the way for a more detailed understanding of how a protein layer forms on biomaterial surfaces, even when the protein and surface share the same electrical polarity.

Adsorption of Bovine Serum Albumin on Poly(vinylidene fluoride) Surfaces in the Presence of Ions: A Molecular Dynamics Simulation

Adsorption of bovine serum albumin (BSA) on poly(vinylidene fluoride) (PVDF) surfaces in an aqueous environment was investigated in the presence and absence of excess ions using molecular dynamics simulations. The adsorption process involved diffusion of protein to the surface and dehydration of surface-protein interactions, followed by adsorption and denaturation. Although adsorption of BSA on PVDF surface was observed in the absence of excess ions, denaturation of BSA was not observed during the simulation (1 μs). Basic and acidic amino acids of BSA were found to be directly interacting with PVDF surface. Simulation in a 0.1 M NaCl solution showed delayed adsorption of BSA on PVDF surfaces in the presence of excess ions, with BSA not observed in close proximity to PVDF surface within 700 ns. Adsorption of Cl^- on PVDF surface increased its negative charge, which repelled negatively charged BSA, thereby delaying the adsorption process. These results will be helpful for understanding membrane fouling phenomena in polymeric membranes, and fundamental advancements in these areas will lead to a new generation of membrane materials with improved antifouling properties and reduced energy demands.

A green route for the cross-coupling of azide anions with aryl halides under both base and ligand-free conditions: exceptional performance of a Cu2O–CuO–Cu–C nanocomposite

Ligand-free and base-free conditions were used for the preparation of aryl azides using the cross-coupling of sodium azide and aryl halides catalysed by Cu₂O–CuO–Cu–C.

Analysis of killing of growing cells and dormant and germinated spores of Bacillus species by black silicon nanopillars

Black silicon (bSi) wafers with a high density of high-aspect ratio nanopillars have recently been suggested to have mechanical bactericidal activity. However, it remains unclear whether bSi with the nanopillars can kill only growing bacterial cells or also dormant spores that are harder to kill. We have reexamined the cidal activity of bSi on growing cells, dormant and germinated spores of B. subtilis, and dormant spores of several other Bacillus species by incubation on bSi wafers with and without nanopillars. We found that the bSi wafers with nanopillars were indeed very effective in rupturing and killing the growing bacterial cells, while wafers without nanopillars had no bactericidal effect. However, bSi wafers with or without nanopillars gave no killing or rupture of dormant spores of B. subtilis, Bacillus cereus or Bacillus megaterium, although germinated B. subtilis spores were rapidly killed. This work lays a foundation for novel bactericidal applications of bSi by elucidating the limits of mechanical bactericidal approaches.