Mesoscopic coarse-grained simulations of lysozyme adsorption

Simulation Study of Polyethylene Terephthalate Hydrolase Adsorption on Self-Assembled Monolayers

Polyethylene terephthalate (PET) hydrolase, discovered in Ideonella sakaiensis (IsPETase), is a promising agent for the biodegradation of PET under mild reaction conditions, yet the thermal stability is poor. The efficient immobilization and orientation of IsPETase on different solid substrates are essential for its application. In this work, the combined parallel tempering Monte Carlo simulation with the all-atom molecular dynamics simulation approach was adopted to reveal the adsorption mechanism, orientation, and conformational changes of IsPETase adsorbed on charged self-assembled monolayers (SAMs), including COOH-SAM and NH2-SAM with different surface charge densities (SCDs). The results show that the protein adsorption orientation was determined not only by attraction interactions but also by repulsion interactions. IsPETase is adsorbed on the COOH-SAM surface with an "end-on" orientation, which favors the exposure of the catalyzed triplet to the solution. In addition, the entrance to the catalytic active center is larger on the COOH-SAM surface with a low SCD. This work reveals the controlled orientation and conformational information on IsPETase on charged surfaces at the atomistic level. This study would certainly promote our understanding of the mechanism of IsPETase adsorption and provide theoretical support for the design of substrates for IsPETase immobilization.

Effect of Oil Polarity on the Protein Adsorption at Oil-Water Interfaces

Protein adsorption at oil-water interfaces has received much attention in applications of food emulsion and biocatalysis. The protein activity is influenced by the protein orientation and conformation. The oil polarity is expected to influence the orientation and conformation of adsorbed proteins by modulating intermolecular interactions. Hence, it is possible to tune the protein emulsion stability and activity by varying the oil polarity. Martini v3.0-based coarse-grained molecular dynamics (CGMD) simulations were employed to investigate the effect of oil polarity on the orientation and conformation of hydrophobin (HFBI) and Candida antarctica lipase B (CALB) adsorbed at triolein-water, hexadecane-water, and octanol-water interfaces for the first time. The protein adsorption orientation was predicted through the hydrophobic dipole, indicating that protein adsorption exists in preferred orientations at hydrophobic oil interfaces. The conformation of the adsorbed HFBI is well conserved, whereas relatively larger conformational changes occur during the CALB adsorption as the oil hydrophobicity increases. Comparisons on the adsorption interaction energy of proteins with oils confirm the relationship between the oil polarity and the interaction strength of proteins with oils. In addition, CGMD simulations allow longer time scale simulations of the behaviors of protein adsorption at oil-water interfaces.

Prevention strategies of postoperative adhesion in soft tissues by applying biomaterials: Based on the mechanisms of occurrence and development of adhesions

Postoperative adhesion (POA) widely occurs in soft tissues and usually leads to chronic pain, dysfunction of adjacent organs and some acute complications, seriously reducing patients' quality of life and even being life-threatening. Except for adhesiolysis, there are few effective methods to release existing adhesion. However, it requires a second operation and inpatient care and usually triggers recurrent adhesion in a great incidence. Hence, preventing POA formation has been regarded as the most effective clinical strategy. Biomaterials have attracted great attention in preventing POA because they can act as both barriers and drug carriers. Nevertheless, even though much reported research has been demonstrated their efficacy on POA inhibition to a certain extent, thoroughly preventing POA formation is still challenging. Meanwhile, most biomaterials for POA prevention were designed based on limited experiences, not a solid theoretical basis, showing blindness. Hence, we aimed to provide guidance for designing anti-adhesion materials applied in different soft tissues based on the mechanisms of POA occurrence and development. We first classified the postoperative adhesions into four categories according to the different components of diverse adhesion tissues, and named them as "membranous adhesion", "vascular adhesion", "adhesive adhesion" and "scarred adhesion", respectively. Then, the process of the occurrence and development of POA were analyzed, and the main influencing factors in different stages were clarified. Further, we proposed seven strategies for POA prevention by using biomaterials according to these influencing factors. Meanwhile, the relevant practices were summarized according to the corresponding strategies and the future perspectives were analyzed.

On the Performance of a Ready-to-Use Electrospun Sulfonated Poly(Ether Ether Ketone) Membrane Adsorber

Motivated by the need for efficient purification methods for the recovery of valuable resources, we developed a wire-electrospun membrane adsorber without the need for post-modification. The relationship between the fiber structure, functional-group density, and performance of electrospun sulfonated poly(ether ether ketone) (sPEEK) membrane adsorbers was explored. The sulfonate groups enable selective binding of lysozyme at neutral pH through electrostatic interactions. Our results show a dynamic lysozyme adsorption capacity of 59.3 mg/g at 10% breakthrough, which is independent of the flow velocity confirming dominant convective mass transport. Membrane adsorbers with three different fiber diameters (measured by SEM) were fabricated by altering the concentration of the polymer solution. The specific surface area as measured with BET and the dynamic adsorption capacity were minimally affected by variations in fiber diameter, offering membrane adsorbers with consistent performance. To study the effect of functional-group density, membrane adsorbers from sPEEK with different sulfonation degrees (52%, 62%, and 72%) were fabricated. Despite the increased functional-group density, the dynamic adsorption capacity did not increase accordingly. However, in all presented cases, at least a monolayer coverage was obtained, demonstrating ample functional groups available within the area occupied by a lysozyme molecule. Our study showcases a ready-to-use membrane adsorber for the recovery of positively charged molecules, using lysozyme as a model protein, with potential applications in removing heavy metals, dyes, and pharmaceutical components from process streams. Furthermore, this study highlights factors, such as fiber diameter and functional-group density, for optimizing the membrane adsorber's performance.

Amphiphilic Nanointerface: Inducing the Interfacial Activation for Lipase

Graphene-based materials are widely used in the field of immobilized enzymes due to their easily tunable interfacial properties. We designed amphiphilic nanobiological interfaces between graphene oxide (GO) and lipase TL (Thermomyces lanuginosus) with tunable reduction degrees through molecular dynamics simulations and a facile chemical modulation, thus revealing the optimal interface for the interfacial activation of lipase TL and addressing the weakness of lipase TL, which exhibits weak catalytic activity due to an inconspicuous active site lid. It was demonstrated that the reduced graphene oxide (rGO) after 4 h of ascorbic acid reduction could boost the relative enzyme activity of lipase TL to reach 208%, which was 48% higher than the pristine GO and 120% higher than the rGO after 48 h of reduction. Moreover, TL-GO-4 h's tolerance against heat, organic solvent, and long-term storage environment was higher than that of free TL. The drawbacks of strong hydrophobic nanomaterials on lipase production were explored in depth with the help of molecular dynamics simulations, which explained the mechanism of enzyme activity enhancement. We demonstrated that nanomaterials with certain hydrophilicity could facilitate the lipase to undergo interfacial activation and improve its stability and protein loading rate, displaying the potential of the extensive application.

Interactions on Proteins Arising from the Self-Assembly of a Polyelectrolyte Brush

Surfaces grafted with polyelectrolyte chains for excellent performance in protein antifouling are highly desired in many applications, such as biomedical implants and devices. In general, the adsorbing/resisting behaviors of proteins can be mainly attributed to the electrostatic interactions that are associated with the charge properties of proteins and polyelectrolytes. By coarse-grained molecular dynamics simulations, we examined the self-assembled structures of polyanion and polyzwitterion brushes as well as the interactions on negatively and positively charged proteins. We found that in addition to charges, the structural polarization induced by self-assembly with a certain charge distribution shows significant influences on protein behavior. The large-scale dipole-dipole interactions between brushes and proteins can dominate the behavior of proteins on the brushes under certain circumstances. To ensure simulation accuracy, we compared two models and found a polar Martini model that explicitly treats electrostatic interactions as long-ranged ones, giving a more reasonable structural description compared with the normal Martini model that truncates electrostatic interactions.

Construction of Enzyme-Responsive Micelles Based on Theranostic Zwitterionic Conjugated Bottlebrush Copolymers with Brush-on-Brush Architecture for Cell Imaging and Anticancer Drug Delivery

Bottlebrush copolymers with different chemical structures and compositions as well as diverse architectures represent an important kind of material for various applications, such as biomedical devices. To our knowledge, zwitterionic conjugated bottlebrush copolymers integrating fluorescence imaging and tumor microenvironment-specific responsiveness for efficient intracellular drug release have been rarely reported, likely because of the lack of an efficient synthetic approach. For this purpose, in this study, we reported the successful preparation of well-defined theranostic zwitterionic bottlebrush copolymers with unique brush-on-brush architecture. Specifically, the bottlebrush copolymers were composed of a fluorescent backbone of polyfluorene derivate (PFONPN) possessing the fluorescence resonance energy transfer with doxorubicin (DOX), primary brushes of poly(2-hydroxyethyl methacrylate) (PHEMA), and secondary graft brushes of an enzyme-degradable polytyrosine (PTyr) block as well as a zwitterionic poly(oligo (ethylene glycol) monomethyl ether methacrylate-co-sulfobetaine methacrylate) (P(OEGMA-co-SBMA)) chain with super hydrophilicity and highly antifouling ability via elegant integration of Suzuki coupling, NCA ROP and ATRP techniques. Notably, the resulting bottlebrush copolymer, PFONPN9-g-(PHEMA15-g-(PTyr16-b-P(OEGMA6-co-SBMA6)2)) (P2) with a lower MW ratio of the hydrophobic side chains of PTyr and hydrophilic side chains of P(OEGMA-co-SBMA) could self-assemble into stabilized unimolecular micelles in an aqueous phase. The resulting unimolecular micelles showed a fluorescence quantum yield of 3.9% that is mainly affected by the pendant phenol groups of PTyr side chains and a drug-loading content (DLC) of approximately 15.4% and entrapment efficiency (EE) of 90.6% for DOX, higher than the other micelle analogs, because of the efficient supramolecular interactions of π–π stacking between the PTyr blocks and drug molecules, as well as the moderate hydrophilic chain length. The fluorescence of the PFONPN backbone enables fluorescence resonance energy transfer (FRET) with DOX and visualization of intracellular trafficking of the theranostic micelles. Most importantly, the drug-loaded micelles showed accelerated drug release in the presence of proteinase K because of the enzyme-triggered degradation of PTyr blocks and subsequent deshielding of P(OEGMA-co-SBMA) corona for micelle destruction. Taken together, we developed an efficient approach for the synthesis of enzyme-responsive theranostic zwitterionic conjugated bottlebrush copolymers with a brush-on-brush architecture, and the resulting theranostic micelles with high DLC and tumor microenvironment-specific responsiveness represent a novel nanoplatform for simultaneous cell image and drug delivery.

Selective Separation of Highly Similar Proteins on Ionic Liquid-Loaded Mesoporous TiO2

Separating proteins from their mixtures is an important process in a great variety of applications, but it faces difficult challenges as soon as the proteins are simultaneously of similar sizes and carry comparable net charges. To develop both efficient and sustainable strategies for the selective separation of similar proteins and to understand the underlying molecular mechanisms to enable the separation are crucial. In this work, we propose a novel strategy where the cholinium-based amino acid [Cho][Pro] ionic liquid (IL) is used as the trace additive and loaded physically on a mesoporous TiO₂ surface for separating two similar proteins (lysozyme and cytochrome c). The observed selective adsorption behavior is explained by the hydration properties of the [Cho][Pro] loaded on the TiO₂ surface and their partially dissociated ions under different pH conditions. As the pH is increased from 5.0 to 9.8, the degree of hydration of IL ions also increases, gradually weakening the interaction strength of the proteins with the substrates, more for lysozymes, leading to their effective separation. These findings were further used to guide the detection of the retention behavior of a binary mixture of proteins in high-performance liquid chromatography, where the introduction of ILs did effectively separate the two similar proteins. Our results should further stimulate the use of ILs in the separation of proteins with a high degree of mutual similarity.

Spontaneous desorption of protein from self-assembled monolayer (SAM)-coated gold nanoparticles induced by high temperature

The nonspecific binding of proteins with nanomaterials (NMs) is a dynamic reversible process including both protein adsorption and desorption parts, which is crucial for controlled release of protein drug loaded by nanocarriers. The nonspecific binding of proteins is susceptible to high temperature, whereas its underlying mechanism still remains elusive. Here, the binding behavior of human serum albumin (HSA) with an amino-terminated self-assembled monolayer (SAM)-coated gold (111) surface was investigated by using molecular dynamics (MD) simulations. HSA binds to the SAM surface through salt bridges at 300 K. As the temperature increases to 350 K, HSA maintains its native structure, while the salt bridges largely diminish owing to the considerable lateral diffusion of HSA on the SAM. Moreover, the interfacial water located between HSA and the SAM gets increased and prevents the reformation of the salt bridges of HSA with the SAM, which reduces the binding affinity of HSA. And HSA eventually desorbs from the SAM. The depiction of thermally induced spontaneous protein desorption enriches our understanding of reversible binding behavior of protein with NMs, and may provide new insights into the controlled release of protein drugs delivered by using nanocarriers under the regulation of high temperature.

Adsorption of lysozyme into a charged confining pore

Several applications arise from the confinement of proteins on surfaces because their stability and biological activity are enhanced. It is also known that the way in which a protein adsorbs on the surface is important for its biological function since its active sites should not be obstructed. In this study, the adsorption properties of hen egg-white lysozyme, HEWL, into a negatively charged silica pore is examined by employing a coarse-grained model and constant-pH Monte Carlo simulations. The role of electrostatic interactions is taken into account via including the Debye-Hückel potentials into the Cα structure-based model. We evaluate the effects of pH, salt concentration, and pore radius on the protein preferential orientation and spatial distribution of its residues regarding the pore surface. By mapping the residues that stay closer to the pore surface, we find that the increase of pH leads to orientational changes of the adsorbed protein when the solution pH gets closer to the HEWL isoelectric point. Under these conditions, the pK_a shift of these important residues caused by the adsorption into the charged confining surface results in a HEWL charge distribution that stabilizes the adsorption in the observed protein orientation. We compare our observations to the results of the pK_a shift for HEWL available in the literature and to some experimental data.

Adsorption of Mussel Protein on Polymer Antifouling Membranes: A Molecular Dynamics Study

Biofouling is one of the most difficult problems in the field of marine engineering. In this work, molecular dynamics simulation was used to study the adsorption process of mussel protein on the surface of two antifouling films-hydrophilic film and hydrophobic film-trying to reveal the mechanism of protein adsorption and the antifouling mechanism of materials at the molecular level. The simulated conclusion is helpful to design and find new antifouling coatings for the experiments in the future.

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.

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 time scales of cluster-forming systems

A microscopic model of adsorption in cluster forming systems with competing interaction is considered. The adsorption process is described by the master equation and modelled by a kinetic Monte Carlo method. The evolution of the particle concentration and interaction energy during the adsorption of particles on a plane triangular lattice is investigated. The simulation results show a diverse behavior of the system time evolution depending on the temperature and chemical potential and finally on the formation of clusters in the system. The characteristic relaxation times of adsorption vary in several orders of magnitude depending on the thermodynamic parameters of the final equilibrium state of the adsorbate. A very fast adsorption of particles is observed for highly ordered adsorbate equilibrium states.

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.

Constant-pH Brownian Dynamics Simulations of a Protein near a Charged Surface

We have developed a rigid-body Brownian dynamics algorithm that allows for simulations of a globular protein suspended in an ionic solution confined by a charged planar boundary, with an explicit treatment of pH-dependent protein protonation equilibria and their couplings to the electrostatic potential of the plane. Electrostatic interactions are described within a framework of the continuum Poisson-Boltzmann model, whereas protein-plane hydrodynamic interactions are evaluated based on analytical expressions for the position- and orientation-dependent near-wall friction tensor of a spheroid. The algorithm was applied to simulate near-surface diffusion of lysozyme in solutions having pH in the range 4-10 and ionic strengths of 10 and 150 mM. As a reference, we performed Brownian dynamics simulations in which the protein is assigned a fixed, most probable protonation state, appropriate for given solution conditions and unaffected by the presence of the charged plane, and Brownian dynamics simulations in which the protein probes possible protonation states with the pH-dependent probability, but these variations are not coupled to the electric field generated by the boundary. We show that electrostatic interactions with the negatively charged plane substantially modify probabilities of different protonation states of lysozyme and shift protonation equilibria of both acidic and basic amino acid side chains toward higher pH values. Consequently, equilibrium energy distributions, equilibrium position-orientation distributions, and functions that characterize rotational dynamics, which for a protein with multiple ionization sites, such as lysozyme, in the presence of a charged obstacle are pH-dependent, are significantly affected by the approach taken to incorporate the solution pH into simulations.

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.

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 .

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.

The effects of tether placement on antibody stability on surfaces

Despite their potential benefits, antibody microarrays have fallen short of performing reliably and have not found widespread use outside of the research setting. Experimental techniques have been unable to determine what is occurring on the surface of an atomic level, so molecular simulation has emerged as the primary method of investigating protein/surface interactions. Simulations of small proteins have indicated that the stability of the protein is a function of the residue on the protein where a tether is placed. The purpose of this research is to see whether these findings also apply to antibodies, with their greater size and complexity. To determine this, 24 tethering locations were selected on the antibody Protein Data Bank (PDB) ID: 1IGT. Replica exchange simulations were run on two different surfaces, one hydrophobic and one hydrophilic, to determine the degree to which these tethering sites stabilize or destabilize the antibody. Results showed that antibodies tethered to hydrophobic surfaces were in general less stable than antibodies tethered to hydrophilic surfaces. Moreover, the stability of the antibody was a function of the tether location on hydrophobic surfaces but not hydrophilic surfaces.

Understanding the curvature effect of silica nanoparticles on lysozyme adsorption orientation and conformation: a mesoscopic coarse-grained simulation study

In nanobiotechnology applications, curvature of nanoparticles has a significant effect on protein activities. In this work, lysozyme adsorption on different-sized silica nanoparticles (SNPs) was simulated at the microsecond timescale by using mesoscopic coarse-grained molecular dynamics simulations. It is found that, with the increase of nanoparticle size, which indicates a decrease of surface curvature, adsorbed lysozyme shows a narrower orientation distribution and a greater conformation change, as the electrostatic attraction dominates lysozyme adsorption, and this trend is more pronounced on larger SNPs. Interestingly, the effect induced by different SNP surface curvatures is not related to the direct contact area between lysozyme and SNPs, but to the interfacial hydration layer above the silica surface, since a smaller curvature can lead to a stronger interfacial hydration and make the distribution of interfacial water molecules more ordered. Besides, at higher ionic strength, lysozyme conformation is less affected by strongly negatively charged SNPs, especially for larger nanoparticles. This work might shed some light on how to prepare protein coronas with higher bioactivities in nanobiotechnology.

Spontaneous protein desorption from self-assembled monolayer (SAM)-coated gold nanoparticles

Interfacial water molecules and lateral diffusion of protein reduce the adsorption affinity of protein and promote protein desorption.

Hamiltonian replica exchange simulations of glucose oxidase adsorption on charged surfaces

Hamiltonian replica exchange Monte Carlo simulations efficiently identify the lowest-energy orientations of proteins on charged surfaces at variable ionic strengths.

Hydrogen bonding induced protein adsorption on polymer brushes: a Monte Carlo study

The protein adsorption behaviors on polymer brushes in the presence of hydrogen bonding between proteins and polymer brushes.

Immobilization of lysozyme proteins on a hierarchical zeolitic imidazolate framework (ZIF-8)

A hierarchical zeolitic imidazolate framework-8 containing micropores and mesopores showed superior adsorption activity than micro-ZIF-8 towards enzyme proteins.

Modeling the Hydrophobicity of Nanoparticles and Their Interaction with Lipids and Proteins

We present a method of modeling nanoparticle (NP) hydrophobicity using coarse-grained molecular dynamics (CG MD) simulations, and apply this to the interaction of lipids with nanoparticles. To model at a coarse-grained level the wettability or hydrophobicity of a given material, we choose the MARTINI coarse-grained force field, and determine through simulation the contact angles of MARTINI water droplets residing on flat regular surfaces composed of various MARTINI bead types (C1, C2, etc.). Each surface is composed of a single bead type in each of three crystallographic symmetries (FCC, BCC, and HCP). While this method lumps together several atoms (for example, one cerium and two oxygens of CeO₂) into a single CG bead, we can still capture the overall hydrophobicity of the actual material by choosing the MARTINI bead type that gives the best fit of the contact angle to that of the actual material, as determined by either experimental or all-atom simulations. For different MARTINI bead types, the macroscopic contact angle is obtained by extrapolating the microscopic contact angles of droplets of eight different sizes (containing N_w = 3224-22978 water molecules) to infinite droplet size. For each droplet, the contact angle was computed from a best fit of a circular curve to the droplet interface extrapolated to the first layer of the surface. We then examine how small nanoparticles of differing wettability interact with MARTINI dipalmitoylphosphotidylcholine (DPPC) lipids and SP-C peptides (a component of lung surfactant). The DPPC shows a transition from tails coating the nanoparticle to a hemimicelle coating the water-wet NP, as the contact angle of a water droplet on the surface is lowered below ∼60°. The results are relevant to developing a taxonomy describing the potential nanotoxicity of nanoparticle interactions with components in the lung.

Hydrolysis-controlled protein adsorption and antifouling behaviors of mixed charged self-assembled monolayer: A molecular simulation study

Understanding the mechanism of the antimicrobial and antifouling properties of mixed charged materials is of great significance. The interactions between human gamma fibrinogen (γFg) and mixed carboxylic methyl ether-terminated (COOCH3-) and trimethylamino-terminated (N(CH3)3(+)-) SAMs and the influence of hydrolysis were studied by molecular simulations. After hydrolysis, the mixed SAMs exhibit behaviors from antimicrobial to antifouling, since the COOCH3-thiols were translated into carboxylic acid (COO(-)-) terminated thiols, which carried a net charge of -1 e. Simulation results showed that the main differences between COOCH3-/N(CH3)3(+)-SAM and COO(-)-/N(CH3)3(+)-SAM are the charged property and the hydration layer above the surface. γFg could stably adsorb on the positively-charged COOCH3-/N(CH3)3(+)-SAM. The adsorption behavior is mainly induced by the strong electrostatic attraction. There is a single hydration layer bound to the surface, which is related to the N(CH3)3(+) groups. The van der Waals repulsion between γFg and the single hydration layer are not strong enough to compensate the strong electrostatic attraction. After hydrolysis, the positively-charged SAM was transferred to a neutral mixed charged surface, the electrostatic attraction between γFg and the surface disappears. Meanwhile, the SAM surface is covered by double hydration layers, which is induced by the N(CH3)3(+) and COO(-) groups; water molecules around COO(-) groups are obviously denser than that around N(CH3)3(+) groups. With the combined contribution from double hydration layers and the vanishment of electrostatic attraction, γFg is forced to desorb from the surface. After hydrolysis, the internal structure of mixed SAM appears more ordered due to the electrostatic interactions between charged groups on the top of SAMs.

STATEMENT OF SIGNIFICANCE

The antimicrobial and antifouling materials are of great importance in many biological applications. The strong hydration property of surfaces and the interactions between proteins and surfaces play a key role in resisting protein adsorption. The mixed SAMs, constructed from a 1:1 combination of COOCH3- and N(CH3)3(+)-terminated thiols, can induce protein adsorption mainly through the electrostatic interaction. When the COOCH3-terminated thiols were hydrolyzed to negatively charged COO(-)-terminated thiols, the mixed-charged SAMs switched from antimicrobial to antifouling. Due to the strong hydration property of the mixed charged SAMs, the adsorbed γFg moved away from the surface. Understanding the interactions between protein and mixed-charged SAMs in the atomistic level is important for the practical design and development of new antimicrobial and antifouling materials.

Protein-Mineral Interactions: Molecular Dynamics Simulations Capture Importance of Variations in Mineral Surface Composition and Structure

Molecular dynamics simulations, conventional and metadynamics, were performed to determine the interaction of model protein Gb1 over kaolinite (001), Na(+)-montmorillonite (001), Ca(2+)-montmorillonite (001), goethite (100), and Na(+)-birnessite (001) mineral surfaces. Gb1, a small (56 residue) protein with a well-characterized solution-state nuclear magnetic resonance (NMR) structure and having α-helix, 4-fold β-sheet, and hydrophobic core features, is used as a model protein to study protein soil mineral interactions and gain insights on structural changes and potential degradation of protein. From our simulations, we observe little change to the hydrated Gb1 structure over the kaolinite, montmorillonite, and goethite surfaces relative to its solvated structure without these mineral surfaces present. Over the Na(+)-birnessite basal surface, however, the Gb1 structure is highly disturbed as a result of interaction with this birnessite surface. Unraveling of the Gb1 β-sheet at specific turns and a partial unraveling of the α-helix is observed over birnessite, which suggests specific vulnerable residue sites for oxidation or hydrolysis possibly leading to fragmentation.

Structural properties of polymer-brush-grafted gold nanoparticles at the oil-water interface: insights from coarse-grained simulations

In this work, the structural properties of amphiphilic polymer-brush-grafted gold nanoparticles (AuNPs) at the oil-water interface were investigated by coarse-grained simulations. The effects of grafting architecture (diblock, mixed and Janus brush-grafted AuNPs) and hydrophilicity of polymer brushes are discussed. Simulation results indicate that functionalized AuNPs present abundant morphologies including typical core-shell, Janus-type, jellyfish-like, etc., in a water or oil-water solvent environment. It is found that hydrophobic/weak hydrophilic polymer-brush-grafted AuNPs have better phase transfer performance, especially for AuNPs modified with hydrophobic chains as outer blocks and weak hydrophilic chains as inner blocks. This kind of AuNP can cross the interface region and move into the oil phase completely. For hydrophobic/strong hydrophilic polymer-brush-grafted AuNPs, they are trapped in the interface region instead of moving into any phase. The mechanism of phase transfer is ascribed to the flexibility and mobility of outer blocks. Besides, we study the desorption energy by PMF analysis. The results demonstrate that Janus brush-grafted AuNPs show the highest interfacial stability and activity, which can be further strengthened by increasing the hydrophilicity of grafted polymer brushes. This work will promote the industrial applications of polymer-brush-grafted NPs such as phase transfer catalysis and Pickering emulsion catalysis.

Molecular simulations of cytochrome c adsorption on positively charged surfaces: the influence of anion type and concentration

The influence of anion type and concentration on the adsorption of cytochrome c onto the positively charged NH₂-SAM surface.

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.

Molecular simulation study of feruloyl esterase adsorption on charged surfaces: effects of surface charge density and ionic strength

The surrounding conditions, such as surface charge density and ionic strength, play an important role in enzyme adsorption. The adsorption of a nonmodular type-A feruloyl esterase from Aspergillus niger (AnFaeA) on charged surfaces was investigated by parallel tempering Monte Carlo (PTMC) and all-atom molecular dynamics (AAMD) simulations at different surface charge densities (±0.05 and ±0.16 C·m(-2)) and ionic strengths (0.007 and 0.154 M). The adsorption energy, orientation, and conformational changes were analyzed. Simulation results show that whether AnFaeA can adsorb onto a charged surface is mainly controlled by electrostatic interactions between AnFaeA and the charged surface. The electrostatic interactions between AnFaeA and charged surfaces are weakened when the ionic strength increases. The positively charged surface at low surface charge density and high ionic strength conditions can maximize the utilization of the immobilized AnFaeA. The counterion layer plays a key role in the adsorption of AnFaeA on the negatively charged COOH-SAM. The native conformation of AnFaeA is well preserved under all of these conditions. The results of this work can be used for the controlled immobilization of AnFaeA.

Molecular understanding and design of zwitterionic materials

Zwitterionic materials have moieties possessing cationic and anionic groups. This molecular structure leads to unique properties that can be the solutions of various application problems. A typical example is that zwitterionic carboxybetaine (CB) and sulfobetaine (SB) materials resist nonspecific protein adsorption in complex media. Considering the vast number of cationic and anionic groups in the current chemical inventory, there are many possible structural variations of zwitterionic materials. The diversified structures provide the possibility to achieve many desired properties and urge a better understanding of zwitterionic materials to provide design principles. Molecular simulations and modeling are a versatile tool to understand the structure-property relationships of materials at the molecular level. This progress report summarizes recent simulation and modeling studies addressing two fundamental questions regarding zwitterionic materials and their applications as biomaterials. First, what are the differences between zwitterionic and nonionic materials? Second, what are the differences among zwitterionic materials? This report also demonstrates a molecular design of new protein-resistant zwitterionic moieties beyond conventional CB and SB based on design principles developed from these simulation studies.

Lipase adsorption on different nanomaterials: a multi-scale simulation study

Adsorption orientations of lipase on different nanomaterials with different surface chemistry.