Nanotube Confinement Denatures Protein Helices

BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation

Understanding the influence of the cellular environment on protein conformations is crucial for elucidating protein functions within living cells. In studies using molecular dynamics (MD) simulation, carbon nanotubes and hydrophobic cages have been widely used to emulate the cellular environment inside specific large biomolecules such as ribosome tunnels and chaperones. However, recent studies suggest that these uniform hydrophobic models may not adequately capture the environmental effects inside each biomolecule. Based on these facts, it is necessary to generate spherical and cylindrical models with varied chemical properties corresponding to the components within target biomolecules. We developed a biomolecular environment-mimicking model generator (BEMM-GEN) that generates spherical and cylindrical models with user-specified chemical properties and allows the integration of arbitrary protein conformations into the generated models. BEMM-GEN provides model and protein complex structures, along with the corresponding parameter files for MD simulation (AMBER and GROMACS), and users immediately run their MD simulation based on the generated input files. BEMM-GEN can be freely downloaded and installed via a Python package manager (pip install BEMM-gen). The source code files and a user manual for operation are provided on GitHub (https://github.com/y4suda/BEMM-GEN).

The molecular basis for the increased stability of the FUS-LC fibril at the anionic membrane- and air-water interfaces

Self-organization of biomolecules can lead to the formation of liquid droplets, hydrogels, and irreversible aggregates that bear immense significance in biology and diseases. Despite the considerable number of studies conducted on biomolecular condensation in bulk solution, there is still a lack of understanding of how different surfaces regulate the condensation process. In this context, recent studies showed that, in contrast to zwitterionic lipid membranes, anionic membranes promoted the production of liquid droplets of FUsed in Sarcoma Low Complexity domain (FUS-LC) despite exhibiting no specific protein-lipid interactions. Moreover, the air-water interface led to a solid fibril-like aggregate of FUS-LC. The molecular mechanism of condensation/aggregation of proteins in response to surfaces of various charged states or levels of hydrophobicity remains to be better elucidated. Here, we provide initial insights into this question by investigating the stability of a small β fibril state of FUS-LC in bulk solution vs. membrane- and air-water interfaces. We perform multiple independent molecular dynamics simulations with distinct starting conformations for each system to demonstrate the statistical significance of our findings. Our study demonstrates the stability of the FUS-LC fibril in the presence of anionic membranes on the μs timescale while the fibril falls apart in bulk solution. We observe that a zwitterionic membrane does not enhance the stability of the fibril and 1,2-dioleoyl-sn-glycero-3-phospho-l-serine (DOPS) has a higher propensity to stabilize the fibril than dioleoylphosphatidylglycerol (DOPG), in qualitative agreement with experiments. We further show that the fibril becomes more stable at the air-water interface. We pinpoint interfacial solvation at the membrane- and air-water interfaces as a key factor that contributes to the stabilization of the peptide assembly.

Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding

Protein conformations in cells are not solely determined by amino acid sequences; they also depend on cellular environments. For instance, the ribosome tunnel induces its specific α-helix formation during cotranslational folding. Owing to the link between these temporally α-helix and biological functions, the mechanism of α-helix formation inside the ribosome tunnel has been previously explored. Consequently, the conformational restrictions of the tunnel were considered one of the driving forces of α-helix formation. Conversely, the ribosomal tunnel environment, including its chemical properties, appears to influence the α-helix formation. However, a comprehensive analysis of the ribosome tunnel environment's impact on the α-helix formation has not been conducted yet due to challenges in experimentally controlling it. Therefore, as a new computational approach, we proposed a ribosome environment-mimicking model (REMM) based on the radius and components of the experimentally determined ribosome tunnel structures. Using REMM, we assessed the impact of the ribosome tunnel environment on α-helix formation. Herein, we employed carbon nanotubes (CNT) as a reference model alongside REMM because CNT reproduce conformational restrictions rather than the ribosome tunnel environment. Quantitatively, the ability to reproduce the α-helix of nascent peptides in the experimental structure was compared between the CNT and REMM using enhanced all-atom molecular dynamics simulations. Consequently, the REMM more accurately reproduced the α-helix of the nascent peptides than the CNT, highlighting the significance of the ribosome tunnel environment in α-helix formation. Additionally, we analyzed the properties of the peptide inside each model to reveal the mechanism of ribosome tunnel-specific α-helix formation. Consequently, we revealed that the chemical diversities of the tunnel are essential for the formation of backbone-to-backbone hydrogen bonds in the peptides. In conclusion, the ribosome tunnel environment, with the diverse chemical properties, drives its specific α-helix formation. By proposing REMM, we newly provide the technical basis for investigating the protein conformations in various cellular environments.

Folding@home: Achievements from over 20 years of citizen science herald the exascale era

Simulations of biomolecules have enormous potential to inform our understanding of biology but require extremely demanding calculations. For over 20 years, the Folding@home distributed computing project has pioneered a massively parallel approach to biomolecular simulation, harnessing the resources of citizen scientists across the globe. Here, we summarize the scientific and technical advances this perspective has enabled. As the project's name implies, the early years of Folding@home focused on driving advances in our understanding of protein folding by developing statistical methods for capturing long-timescale processes and facilitating insight into complex dynamical processes. Success laid a foundation for broadening the scope of Folding@home to address other functionally relevant conformational changes, such as receptor signaling, enzyme dynamics, and ligand binding. Continued algorithmic advances, hardware developments such as graphics processing unit (GPU)-based computing, and the growing scale of Folding@home have enabled the project to focus on new areas where massively parallel sampling can be impactful. While previous work sought to expand toward larger proteins with slower conformational changes, new work focuses on large-scale comparative studies of different protein sequences and chemical compounds to better understand biology and inform the development of small-molecule drugs. Progress on these fronts enabled the community to pivot quickly in response to the COVID-19 pandemic, expanding to become the world's first exascale computer and deploying this massive resource to provide insight into the inner workings of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and aid the development of new antivirals. This success provides a glimpse of what is to come as exascale supercomputers come online and as Folding@home continues its work.

Construction of a biomimetic core-shell PDA@Lac bioreactor from intracellular laccase as a nano-confined biocatalyst for decolorization

Enzymes immobilized on the surface of the carriers are difficult to maintain their conformation and high activity due to the influence of the external harsh environments. A biomimetic core-shell PDA@Lac bioreactor was constructed by depositing polydopamine (PDA) on the surface of the recombinant Escherichia coli with CotA laccase gene, and releasing intracellular laccase into the PDA shell using ultrasound to break the cell wall of the bacteria. The bioreactor provided a nano-confined environment for the laccase and accelerated the mass and electron transfer in the volume-confined space, with a 2.77-fold increase in Km compared with the free laccase. Since there was no barrier of the cell wall, the crystal violet dye can enter the bioreactor to participate in the enzymatic reaction. As a result, PDA@Lac achieved excellent decolorization performance even without ABTS as an electron mediator. Moreover, the cytoplasmic solution retained in the PDA shell promoted the enzyme's tolerance to pH, temperature and harsh environments. In addition to PDA encapsulation, carbonyl and -NH₂ groups of PDA were bound covalently with -NH₂ and -COOH on the laccase in the PDA@Lac, resulting in an extremely high laccase loading of 817.59 mg/g. Also, the relative activity of the bioreactor maintained approximately 75% after 10 cycles of reuse. In addition, the protection of the PDA shell increased the resistance of laccase to UV irradiation. This work provides a novel method of laccase immobilization for application in wastewater treatment.

Spatial confinement: A green pathway to promote the oxidation processes for organic pollutants removal from water

Organic pollutants removal from water is pressing owing to the great demand for clean water. Oxidation processes (OPs) are the commonly used method. However, the efficiency of most OPs is limited owing to the poor mass transfer process. Spatial confinement is a burgeoning way to solve this limitation by use of nanoreactor. Spatial confinement in OPs would (i) alter the transport characteristics of protons and charges; (ii) bring about molecular orientation and rearrangement; (iii) cause the dynamic redistribution of active sites in catalyst and reduce the entropic barrier that is high in unconfined space. So far, spatial confinement has been utilized for various OPs, such as Fenton, persulfate, and photocatalytic oxidation. A comprehensive summary and discussion on the fundamental mechanisms of spatial confinement mediated OPs is needed. Herein, the application, performance and mechanisms of spatial confinement mediated OPs are overviewed firstly. Subsequently, the features of spatial confinement and their effects on OPs are discussed in detail. Furthermore, environmental influences (including environmental pH, organic matter and inorganic ions) are studied with analyzing their intrinsic connection with the features of spatial confinement in OPs. Lastly, challenges and future development direction of spatial confinement mediated OPs are proposed.

Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel

The ribosome is a fundamental biomolecular complex that synthesizes proteins in cells. Nascent proteins emerge from the ribosome through a tunnel, where they may interact with the tunnel walls or small molecules such as antibiotics. These interactions can cause translational arrest with notable physiological consequences. Here, we studied the arrest caused by the regulatory peptide VemP, which is known to form α-helices inside the ribosome tunnel near the peptidyl transferase center under specific conditions. We used all-atom molecular dynamics simulations of the entire ribosome and circular dichroism spectroscopy to study the driving forces of helix formation and how VemP causes the translational arrest. To that aim, we compared VemP dynamics in the ribosome tunnel with its dynamics in solution. We show that the VemP peptide has a low helical propensity in water and that the propensity is higher in mixtures of water and trifluorethanol. We propose that helix formation within the ribosome is driven by the interactions of VemP with the tunnel and that a part of VemP acts as an anchor. This anchor might slow down VemP progression through the tunnel enabling α-helix formation, which causes the elongation arrest.

Hydration of a small protein under carbon nanotube confinement: Adsorbed substates induce selective separation of the dynamical response

The co-involvement of biological molecules and nanomaterials has increasingly come to the fore in modern-day applications. While the "bio-nano" (BN) interface presents physico-chemical characteristics that are manifestly different from those observed in isotropic bulk conditions, the underlying molecular reasons remain little understood; this is especially true of anomalies in interfacial hydration. In this paper, we leverage atomistic simulations to study differential adsorption characteristics of a small protein on the inner (concave) surface of a single-walled carbon nanotube whose diameter exceeds dimensions conducive to single-file water movement. Our findings indicate that the extent of adsorption is decided by the degree of foldedness of the protein conformational substate. Importantly, we find that partially folded substates, but not the natively folded one, induce reorganization of the protein hydration layer into an inner layer water closer to the nanotube axis and an outer layer water in the interstitial space near the nanotube walls. Further analyses reveal sharp dynamical differences between water molecules in the two layers as observed in the onset of increased heterogeneity in rotational relaxation and the enhanced deviation from Fickian behavior. The vibrational density of states reveals that the dynamical distinctions are correlated with differences in crucial bands in the power spectra. The current results set the stage for further systematic studies of various BN interfaces vis-à-vis control of hydration properties.

It is time to crowd your cell culture media - Physicochemical considerations with biological consequences

In vivo, the interior and exterior of cells is populated by various macromolecules that create an extremely crowded milieu. Yet again, in vitro eukaryotic cell culture is conducted in dilute culture media that hardly imitate the native tissue density. Herein, the concept of macromolecular crowding is discussed in both intracellular and extracellular context. Particular emphasis is given on how the physicochemical properties of the crowding molecules govern and determine kinetics, equilibria and mechanism of action of biochemical and biological reactions, processes and functions. It is evidenced that we are still at the beginning of appreciating, let alone effectively implementing, the potential of macromolecular crowding in permanently differentiated and stem cell culture systems.

Water-Mediated Interactions Determine Helix Formation of Peptides in Open Nanotubes

Water-mediated interactions (WMIs) play diverse roles in molecular biology. They are particularly relevant in geometrically confined spaces such as the interior of the chaperonin, at the interface between ligands and their binding partners, and in the ribosome tunnel. Inspired in part by the geometry of the ribosome tunnel, we consider confinement effects on the stability of peptides. We describe results from replica exchange molecular dynamics simulations of a system containing a 23-alanine or 23-serine polypeptide confined to nonpolar and polar nanotubes in the gas phase and when open to a water reservoir. We quantify the effect of water in determining the preferred conformational states of these polypeptides by calculating the difference in the solvation free energy for the helix and coil states in the open nanotube in the two phases. Our simulations reveal several possibilities. We find that nanoscopic confinement preferentially stabilizes the helical state of polypeptides with hydrophobic side chains, which is explained by the entropic stabilization mechanism proposed on the basis of polymer physics. Polypeptide chains with hydrophilic side chains can adopt helical structures within nanotubes, but helix formation is sensitive to the nature of the nanotube due to WMIs. We elaborate on the potential implications of our findings to the stability of peptides in the ribosome tunnel.

Nanoconfinement-Mediated Water Treatment: From Fundamental to Application

Safe and clean water is of pivotal importance to all living species and the ecosystem on earth. However, the accelerating economy and industrialization of mankind generate water pollutants with much larger quantity and higher complexity than ever before, challenging the efficacy of traditional water treatment technologies. The flourishing researches on nanomaterials and nanotechnologies in the past decade have generated new understandings on many fundamental processes and brought revolutionary upgrades to various traditional technologies in almost all areas, including water treatment. An indispensable step toward the real application of nanomaterials in water treatment is to confine them in large processable substrate to address various inherent issues, such as spontaneous aggregation, difficult operation and potential environmental risks. Strikingly, when the size of the spatial restriction provided by the substrate is on the order of only one or several nanometers, referred to as nanoconfinement, the phase behavior of matter and the energy diagram of a chemical reaction could be utterly changed. Nevertheless, the relationship between such changes under nanoconfinement and their implications for water treatment is rarely elucidated systematically. In this Critical Review, we will briefly summarize the current state-of-the-art of the nanomaterials, as well as the nanoconfined analogues (i.e., nanocomposites) developed for water treatment. Afterward, we will put emphasis on the effects of nanoconfinement from three aspects, that is, on the structure and behavior of water molecules, on the formation (e.g., crystallization) of confined nanomaterials, and on the nanoenabled chemical reactions. For each aspect, we will build the correlation between the nanoconfinement effects and the current studies for water treatment. More importantly, we will make proposals for future studies based on the missing links between some of the nanoconfinement effects and the water treatment technologies. Through this Critical Review, we aim to raise the research attention on using nanoconfinement as a fundamental guide or even tool to advance water treatment technologies.

Theoretical study of the reduction in sensitivity of copper azide following encapsulation in carbon nanotubes

Research aimed at reducing the sensitivity of primary explosives with excellent ignition performance is of great significance for their practical application. In this work, we theoretically studied the effect of inserting the primary explosive copper azide (Cu(N₃)₂) into single-walled carbon nanotubes (SWCNTs) on the sensitivity of the explosive to changes in hydrostatic pressure. The electronic structure of Cu(N₃)₂ was found to be more sensitive to external pressure than lead azide, which is consistent with their experimental impact sensitivities. A composite of Cu(N₃)₂ molecules and SWCNTs (Cu(N₃)₂/CNTs) was prepared in which the components mainly interacted electrostatically and the Cu(N₃)₂ molecules formed semi-arc structures along the nanotube walls, rather than exhibiting their usual planar structure. The electrostatic potential and electronic structure of the composite indicate that it is more stable than crystalline Cu(N₃)₂. Notably, combining the Cu(N₃)₂ with the SWCNTs reduces the sensitivity of the Cu(N₃)₂ to external pressure, implying that carbon nanotubes can reduce the sensitivity of Cu(N₃)₂. This work should aid the development of highly efficient green primary explosives.

Compressing Θ-Chain in Slit Geometry

When compressed in a slit of width D, a Θ-chain that displays the scaling of size R₀ (diameter) with respect to the number of monomers N, R₀ ∼ aN^1/2, expands in the lateral direction as R_|| ∼ aN^ν(a/D)^2ν-1. Provided that the Θ condition is strictly maintained throughout the compression, the well-known scaling exponent of Θ-chain in two dimensions, ν = 4/7, is anticipated in a perfect confinement. However, numerics shows that upon increasing compression from R₀/D < 1 to R₀/D ≫ 1, ν gradually deviates from ν = 1/2 and plateaus at ν = 3/4, the exponent associated with the self-avoiding walk in two dimensions. Using both theoretical considerations and numerics, we argue that it is highly nontrivial to maintain the Θ condition under confinement because of two major effects. First, as the dimension is reduced from three to two dimensions, the contributions of higher order virial terms, which can be ignored in three dimensions at large N, become significant, making the perturbative expansion used in Flory-type approach inherently problematic. Second and more importantly, the geometrical confinement, which is regarded as an applied external field, alters the second virial coefficient (B₂) changes from B₂ = 0 (Θ condition) in free space to B₂ > 0 (good-solvent condition) in confinement. Our study provides practical insight into how confinement affects the conformation of a single polymer chain.

Effect of the geometry of confining media on the stability and folding rate of α -helix proteins

Protein folding in confined media has attracted wide attention over the past 15 years due to its importance to both in vivo and in vitro applications. It is generally believed that protein stability increases by decreasing the size of the confining medium, if the medium's walls are repulsive, and that the maximum folding temperature in confinement is in a pore whose size D ₀ is only slightly larger than the smallest dimension of a protein's folded state. Until recently, the stability of proteins in pores with a size very close to that of the folded state has not received the attention it deserves. In a previous paper [L. Javidpour and M. Sahimi, J. Chem. Phys. 135, 125101 (2011)], we showed that, contrary to the current theoretical predictions, the maximum folding temperature occurs in larger pores for smaller α-helices. Moreover, in very tight pores, the free energy surface becomes rough, giving rise to a new barrier for protein folding close to the unfolded state. In contrast to unbounded domains, in small nanopores proteins with an α-helical native state that contain the β structures are entropically stabilized implying that folding rates decrease notably and that the free energy surface becomes rougher. In view of the potential significance of such results to interpretation of many sets of experimental data that could not be explained by the current theories, particularly the reported anomalously low rates of folding and the importance of entropic effects on proteins' misfolded states in highly confined environments, we address the following question in the present paper: To what extent the geometry of a confined medium affects the stability and folding rates of proteins? Using millisecond-long molecular dynamics simulations, we study the problem in three types of confining media, namely, cylindrical and slit pores and spherical cavities. Most importantly, we find that the prediction of the previous theories that the dependence of the maximum folding temperature T _f on the size D of a confined medium occurs in larger media for larger proteins is correct only in spherical geometry, whereas the opposite is true in the two other geometries that we study. Also studied is the effect of the strength of the interaction between the confined media's walls and the proteins. If the walls are only weakly or moderately attractive, a complex behavior emerges that depends on the size of the confining medium.

Confinement effects and mechanistic aspects for montmorillonite nanopores

Owing to the ubiquity, critical importance and special properties, confined microenvironments have recently triggered overwhelming interest. In this work, all-atom molecular dynamics simulations have been conducted to address the confinement effects and ion-specific effects for electrolyte solutions within montmorillonite nanopores, where the pore widths vary with a wide range. The adsorption number, structure, dynamics and stability of inner- and outer-sphere metal ions are affected by the change of pore widths (confinement effects), while the extents are significantly dependent on the type of adsorbed species. The type of adsorbed species is, however, not altered by the magnitude of confinement effects, and confinement effects are similar for different electrolyte concentrations. Ion-specific effects are pronounced for all magnitudes of confinement effects (from non- to strong confined conditions), and Hofmeister sequences of outer-sphere species are closely associated with the magnitude of confinement effects while those of inner-sphere species remain consistent. In addition, mechanistic aspects of confinement have been posed using the electrical double layer theories, and the results can be generalized to other confined systems that are ubiquitous in biology, chemistry, geology and nanotechnology.

Adsorption mechanism of an antimicrobial peptide on carbonaceous surfaces: A molecular dynamics study

Peptides are versatile molecules with applications spanning from biotechnology to nanomedicine. They exhibit a good capability to unbundle carbon nanotubes (CNT) by improving their solubility in water. Furthermore, they are a powerful drug delivery system since they can easily be uptaken by living cells, and their high surface-to-volume ratio facilitates the adsorption of molecules of different natures. Therefore, understanding the interaction mechanism between peptides and CNT is important for designing novel therapeutical agents. In this paper, the mechanisms of the adsorption of antimicrobial peptide Cecropin A-Magainin 2 (CA-MA) on a graphene nanosheet (GNS) and on an ultra-short single-walled CNT are characterized using molecular dynamics simulations. The results show that the peptide coats both GNS and CNT surfaces through preferential contacts with aromatic side chains. The peptide packs compactly on the carbon surfaces where the polar and functionalizable Lys side chains protrude into the bulk solvent. It is shown that the adsorption is strongly correlated to the loss of the peptide helical structure. In the case of the CNT, the outer surface is significantly more accessible for adsorption. Nevertheless when the outer surface is already covered by other peptides, a spontaneous diffusion, via the amidated C-terminus into the interior of the CNT, was observed within 150 ns of simulation time. We found that this spontaneous insertion into the CNT interior can be controlled by the polarity of the entrance rim. For the positively charged CA-MA peptide studied, hydrogenated and fluorinated rims, respectively, hinder and promote the insertion.

Nanoconfinement in Slit Pores Enhances Water Self-Dissociation

We investigate the self-dissociation of water that is nanoconfined between the sheets of a realistic layered mineral, FeS mackinawite, as well as between Lennard-Jones walls via ab initio simulations. By comparing it with the same reaction in bulk water under various thermodynamic conditions, we show that such strong two-dimensional confinement between hard surfaces greatly enhances the self-dissociation process of water-thus increasing its ionic product K_{w} due to nanoconfinement. In addition to providing free energies, we analyze in detail the underlying dielectric properties in terms of dipole moment distributions, and thus the polarity of the liquid, as well as local polarization fluctuations as quantified by dielectric tensor profiles perpendicular to the lamella.

Chemistry in nanoconfined water

Nanoconfined liquids have extremely different properties from the bulk, which profoundly affects chemical reactions taking place in nanosolvation.

Nanoconfined liquids have extremely different properties from the bulk, which profoundly affects chemical reactions taking place in nanosolvation. Here, we present extensive ab initio simulations of a vast set of chemical reactions within a water lamella that is nanoconfined by mineral surfaces, which might be relevant to prebiotic peptide formation in aqueous environments. Our results disclose a rich interplay of distinct effects, from steric factors typical of reactions occurring in small spaces to a charge-stabilization effect in nanoconfined water at extreme conditions similar to that observed in bulk water when changing from extreme to ambient conditions. These effects are found to modify significantly not only the energetics but also the mechanisms of reactions happening in nanoconfined water in comparison to the corresponding bulk regime.

Thermodynamics of Helix-Coil Transitions of Polyalanine in Open Carbon Nanotubes

Understanding structure formation in polypeptide chains and synthetic polymers encapsulated in pores is important in biology and nanotechnology. We present replica exchange molecular dynamics studies of the phase diagram for α-helix formation of capped polyalanine in nanotubes (NT) open to a water reservoir as a function of the NT diameter and hydrophobicity. A helix forms only in a narrow range of diameters, which surprisingly is comparable to the width of the ribosome tunnel. Increasing the hydrophobicity enhances helicity in the NT. Helix formation in polyalanine is driven by a small negative enthalpy and a positive entropy change at ≈300 K, in contrast to the large negative entropy change that destabilizes the helix and favors the coiled state in bulk water. There is an anticorrelation between water density inside the nanotube and structure formation. Confinement-induced helix formation depends on amino acid sequence. There is complete absence of helix in polyglutamine and polyserine confined to a open carbon nanotube.

Conserve Water: A Method for the Analysis of Solvent in Molecular Dynamics

Molecular dynamics with explicit solvent is favored for its ability to more correctly simulate aqueous biological processes and has become routine thanks to increasingly powerful computational resources. However, analysis techniques including Markov state models (MSMs) ignore solvent atoms and focus solely on solute coordinates despite solvent being implicated in myriad biological phenomena. We present a unified framework called "solvent-shells featurization" for including solvent degrees of freedom in analysis and show that this method produces better models. We apply this method to simulations of dewetting in the two-domain protein BphC to generate a predictive MSM and identify functional water molecules. Furthermore, the proposed methodology could be easily extended for building MSMs of any systems with indistinguishable components.

Tuning Structural Changes in Glucose Oxidase for Enzyme Fuel Cell Applications

Stabilization and electrical contacting of redox enzymes with electrodes are fundamental requirements for bioelectronics devices, including biosensors and enzyme fuel cells (EFCs). In this study, we show increased glucose oxidase (GOx) stability by immobilization with Nafion. The immobilization process affected GOx conformation but was not detrimental to its activity, which was maintained for more than 120 days. The GOx/Nafion system was interfaced to a carbon cloth electrode and assembled in a prototypal EFC fed with glucose. Polarization and power density curves demonstrated that GOx/Nafion system was able to generate power, exploiting a Nafion-assisted electron transfer process to the electrode. Our findings are consistent with the onset of pH-dependent conformational equilibrium for the enzyme secondary structure and its active site. Significantly, the protective effect exerted by Nafion on the enzyme structure may be tuned by varying parameters such as the pH to fabricate durable EFCs with good electrocatalytic performance.

Separation of chiral nanotubes with an opposite handedness by chiral oligopeptide adsorption: A molecular dynamics study

The separation of enantiomeric chiral nanotubes that can form non-covalent complexes with an unlike stability upon adsorption of chiral molecules is a process of potential interest in different fields and applications. Using fully atomistic molecular dynamics simulations, we report in this paper a theoretical study of the adsorption and denaturation of an oligopeptide formed by 16 chiral amino acids having a helical structure in the native state on both the inner and the outer surface of the chiral (10, 20) and (20, 10) single-walled carbon nanotubes having an opposite handedness, and of the armchair (16, 16) nanotube with a similar diameter for comparison. In the final adsorbed state, the oligopeptide loses in all cases its native helical conformation, assuming elongated geometries that maximize its contact with the surface through all the 16 amino acids. We find that the complexes formed by the two chiral nanotubes and the chosen oligopeptide have a strongly unlike stability both when adsorption takes place on the outer convex surface of the nanotube, and when it occurs on the inner concave surface. Thus, our molecular simulations indicate that separation of chiral, enantiomeric carbon nanotubes for instance by chromatographic methods can indeed be carried out using oligopeptides of a sufficient length.

Under the lens: carbon nanotube and protein interaction at the nanoscale

The combination of the very different chemical natures of carbon nanotubes (CNTs) and proteins gives rise to systems with unprecedented performance, thanks to a rich pool of very diverse chemical, electronic, catalytic and biological properties. Here we review recent advances in the field, including innovative and imaginative aspects from a nanoscale point of view. The tubular nature of CNTs allows for internal protein encapsulation, and also for their external coating by protein cages, affording bottom-up ordering of molecules in hierarchical structures. To achieve such complex systems it is imperative to master the intermolecular forces between CNTs and proteins, including geometry effects (e.g. CNT diameter and curvature) and how they translate into changes in the local environment (e.g. water entropy). The type of interaction between proteins and CNTs has important consequences for the preservation of their structure and, in turn, function. This key aspect cannot be neglected during the design of their conjugation, be it covalent, non-covalent, or based on a combination of both methods. The review concludes with a brief discussion of the very many applications intended for CNT-protein systems that go across various fields of science, from industrial biocatalysis to nanomedicine, from innovative materials to biotechnological tools in molecular biology research.

Enzymes immobilized in mesoporous silica: a physical-chemical perspective

Mesoporous materials as support for immobilized enzymes have been explored extensively during the last two decades, primarily not only for biocatalysis applications, but also for biosensing, biofuels and enzyme-controlled drug delivery. The activity of the immobilized enzymes inside the pores is often different compared to that of the free enzymes, and an important challenge is to understand how the immobilization affects the enzymes in order to design immobilization conditions that lead to optimal enzyme activity. This review summarizes methods that can be used to understand how material properties can be linked to changes in enzyme activity. Real-time monitoring of the immobilization process and techniques that demonstrate that the enzymes are located inside the pores is discussed by contrasting them to the common practice of indirectly measuring the depletion of the protein concentration or enzyme activity in the surrounding bulk phase. We propose that pore filling (pore volume fraction occupied by proteins) is the best standard for comparing the amount of immobilized enzymes at the molecular level, and present equations to calculate pore filling from the more commonly reported immobilized mass. Methods to detect changes in enzyme structure upon immobilization and to study the microenvironment inside the pores are discussed in detail. Combining the knowledge generated from these methodologies should aid in rationally designing biocatalyst based on enzymes immobilized in mesoporous materials.

Surface topography effects in protein adsorption on nanostructured carbon allotropes

We report a molecular dynamics (MD) simulation study of protein adsorption on the surface of nanosized carbon allotropes, namely single-walled carbon nanotubes (SWNT) considering both the convex outer surface and the concave inner surface, together with a graphene sheet for comparison. These systems are chosen to investigate the effect of the surface curvature on protein adsorption at the same surface chemistry, given by sp(2) carbon atoms in all cases. The simulations show that proteins do favorably interact with these hydrophobic surfaces, as previously found on graphite which has the same chemical nature. However, the main finding of the present study is that the adsorption strength does depend on the surface topography: in particular, it is slightly weaker on the outer convex surfaces of SWNT and is conversely enhanced on the inner concave SWNT surface, being therefore intermediate for flat graphene. We additionally find that oligopeptides may enter the cavity of common SWNT, provided their size is small enough and the tube diameter is large enough for both entropic and energetic reasons. Therefore, we suggest that proteins can effectively be used to solubilize in water single-walled (and by analogy also multiwalled) carbon nanotubes through adsorption on the outer surface, as indeed experimentally found, and to functionalize them after insertion of oligopeptides within the cavity of nanotubes of appropriate size.

Effects of confinement on the structure and dynamics of an intrinsically disordered peptide: a molecular-dynamics study

In vivo, proteins and peptides are exposed to radically different environments than those in bulk. Because of the abundance of other cellular components, proteins perform their function in crowded and confined spaces. Confinement has been shown to alter the structure, dynamics, and folding of proteins that possess a native fold. Little is known, however, of the effects of confinement on biologically important intrinsically disordered proteins or peptides (IDP). Here, we use extensive molecular dynamics simulations to investigate the effects of confinement in an IDP, the Aβ21-30, a central folding nucleus of the full length amyloid β-protein. In this study, we report results derived from 107 μs of molecular dynamics simulations that subjected the Aβ21-30 to two types of confinement: hydrophilic and hydrophobic pores. Results show that turn structures are enhanced as a function of decreasing pore size (increasing confinement) over other structures, including coils, β-hairpins, and bridges. However, the percentage occurrence of the dominant hydrogen bond between amino acids Asp23 and Ser26 shown to stabilize the turn in bulk simulations does not increase as a function of confinement signifying a disconnect between structure and internal hydrogen bonding. Differences in structure and dynamics of the decapeptide due to hydrophilic and hydrophobic confinement are more apparent at the extreme confinement conditions, where a reduction of the available phase space in hydrophilic confinement is explained in terms of interactions between the decapeptide and a layer of water at the interface between the decapeptide and the surface of the pore, and a smaller size of the decapeptide in the hydrophobic pores is rationalized in terms of peptide-surface interactions.

Myoglobin unfolding in crowding and confinement

Crowding and confinement have often been used synonymously with regard to their effect on the structure and dynamics of proteins. In this work, we have investigated the unfolding of the protein myoglobin (Mb) entrapped in the confinement of the water pool of AOT reverse micelles and in the presence of some commonly used macromolecular crowding agents (Ficoll 70, Dextran 70, and Dextran 40). Our results reveal that confinement effects can be quite destabilizing in nature for Mb with the extent of distortion depending on a host of factors apart from the size of the confining cage. Effects of the crowding agents on myoglobin also show a deviation from the general notion that synthetic macromolecular crowding agents are always stabilizing in nature. Ficoll 70 was observed to be particularly destabilizing in its influence on Mb unfolding. Moreover, tryptophan lifetime studies point to the fact that the Trp-heme distance in Mb might not always be a reliable probe of the secondary structural dissolution of the protein.

Adsorption mechanism and collapse propensities of the full-length, monomeric Aβ(1-42) on the surface of a single-walled carbon nanotube: a molecular dynamics simulation study

Though nanomaterials such as carbon nanotubes have gained recent attention in biology and medicine, there are few studies at the single-molecule level that explore their interactions with disease-causing proteins. Using atomistic molecular-dynamics simulations, we have investigated the interactions of the monomeric Aβ(1-42) peptide with a single-walled carbon nanotube of small diameter. Starting with peptide-nanotube complexes that delineate the interactions of different segments of the peptide, we find rapid convergence in the peptide's adsorption behavior on the nanotube surface, manifested in its arrested movement, the convergence of peptide-nanotube contact areas and approach distances, and in increased peptide wrapping around the nanotube. In systems where the N-terminal domain is initially distal from nanotube, the adsorption phenomena are initiated by interactions arising from the central hydrophobic core, and precipitated by those arising from the N-terminal residues. Our simulations and free energy calculations together demonstrate that the presence of the nanotube increases the energetic favorability of the open state. We note that the observation of peptide localization could be leveraged for site-specific drug delivery, while the decreased propensity of collapse appears promising for altering kinetics of the peptide's self-assembly.

Confinement-induced states in the folding landscape of the Trp-cage miniprotein

Although protein folding is typically studied in dilute solution, folding in a cell will be affected by interactions with other biomolecules and excluded volume effects. Here, we examine the effect of hydrophobic confinement on folding of the Trp-cage miniprotein. We used replica exchange molecular dynamics simulations to probe the differences between folding in the bulk, on a hydrophobic surface, and confined between two hydrophobic walls. In addition to promotion of helix formation due to reduced conformational entropy of the unfolded state upon confinement, adsorption of Trp-cage to a hydrophobic surface stabilizes intermediate structures not present in the bulk. These new intermediate structures may alter the folding mechanism and kinetics and show the importance of including environmental effects when studying protein folding.

Confinement in nanopores can destabilize α-helix folding proteins and stabilize the β structures

Protein folding in confined media has attracted wide attention over the past decade due to its importance in both in vivo and in vitro applications. Currently, it is generally believed that protein stability increases by decreasing the size of the confining medium, if its interaction with the confining walls is repulsive, and that the maximum folding temperature in confinement occurs for a pore size only slightly larger than the smallest dimension of the folded state of a protein. Protein stability in pore sizes, very close to the size of the folded state, has not however received the attention that it deserves. Using detailed, 0.3-ms-long molecular dynamics simulations, we show that proteins with an α-helix native state can have an optimal folding temperature in pore sizes that do not affect the folded-state structure. In contradiction to the current theoretical explanations, we find that the maximum folding temperature occurs in larger pores for smaller α-helices. In highly confined pores the free energy surface becomes rough, and a new barrier for protein folding may appear close to the unfolded state. In addition, in small nanopores the protein states that contain the β structures are entropically stabilized, in contrast to the bulk. As a consequence, folding rates decrease notably and the free energy surface becomes rougher. The results shed light on many recent experimental observations that cannot be explained by the current theories, and demonstrate the importance of entropic effects on proteins' misfolded states in highly confined environments. They also support the concept of passive effect of chaperonin GroEL on protein folding by preventing it from aggregation in crowded environment of biological cells, and provide deeper clues to the α → β conformational transition, believed to contribute to Alzheimer's and Parkinson's diseases. The strategy of protein and enzyme stabilization in confined media may also have to be revisited in the case of tight confinement. For in silico studies of protein folding in confined media, use of non-Go potentials may be more appropriate.

A bulk water-dependent desolvation energy model for analyzing the effects of secondary solutes on biological equilibria

A new phenomenological model for interpreting the effects of solutes on biological equilibria is presented. The model attributes changes in equilibria to differences in the desolvation energy of the reacting species that, in turn, reflect changes in the free energy of the bulk water upon addition of secondary solutes. The desolvation approach differs notably from that of other solute models by treating the free energy of bulk water as a variable and by not ascribing the observed shifts in reaction equilibria to accumulation or depletion of solutes next to the surfaces of the reacting species. On the contrary, the partitioning of solutes is viewed as a manifestation of the different subpopulations of water that arise in response to the surface boundary conditions. A thermodynamic framework consistent with the proposed model is used to derive a relationship for a specific reaction, an aqueous solubility equilibrium, in two or more solutions. The resulting equation reconciles some potential issues with the transfer free energy model of Tanford. Application of the desolvation energy model to the analysis of a two-state protein folding equilibrium is discussed and contrasted to the application of two other solute models developed by Timasheff and by Parsegian. Future tabulation of solvation energies and bulk water energies may allow biophysical chemists to confirm the mechanism by which secondary solutes influence binding and conformational equilibria and may provide a common ground on which experimentalists and theoreticians can compare and evaluate their results.

Non-bulk-like solvent behavior in the ribosome exit tunnel

As nascent proteins are synthesized by the ribosome, they depart via an exit tunnel running through the center of the large subunit. The exit tunnel likely plays an important part in various aspects of translation. Although water plays a key role in many bio-molecular processes, the nature of water confined to the exit tunnel has remained unknown. Furthermore, solvent in biological cavities has traditionally been characterized as either a continuous dielectric fluid, or a discrete tightly bound molecule. Using atomistic molecular dynamics simulations, we predict that the thermodynamic and kinetic properties of water confined within the ribosome exit tunnel are quite different from this simple two-state model. We find that the tunnel creates a complex microenvironment for the solvent resulting in perturbed rotational dynamics and heterogenous dielectric behavior. This gives rise to a very rugged solvation landscape and significantly retarded solvent diffusion. We discuss how this non-bulk-like solvent is likely to affect important biophysical processes such as sequence dependent stalling, co-translational folding, and antibiotic binding. We conclude with a discussion of the general applicability of these results to other biological cavities.

Macromolecular crowding induces polypeptide compaction and decreases folding cooperativity

A cell's interior is comprised of macromolecules that can occupy up to 40% of its available volume. Such crowded environments can influence the stability of proteins and their rates of reaction. Using discrete molecular dynamics simulations, we investigate how both the size and number of neighboring crowding reagents affect the thermodynamic and folding properties of structurally diverse proteins. We find that crowding induces higher compaction of proteins. We also find that folding becomes less cooperative with the introduction of crowders into the system. The crowders may induce alternative non-native protein conformations, thus creating barriers for protein folding in highly crowded media.

Evaluating molecular mechanical potentials for helical peptides and proteins

Multiple variants of the AMBER all-atom force field were quantitatively evaluated with respect to their ability to accurately characterize helix-coil equilibria in explicit solvent simulations. Using a global distributed computing network, absolute conformational convergence was achieved for large ensembles of the capped A₂₁ and F_s helical peptides. Further assessment of these AMBER variants was conducted via simulations of a flexible 164-residue five-helix-bundle protein, apolipophorin-III, on the 100 ns timescale. Of the contemporary potentials that had not been assessed previously, the AMBER-99SB force field showed significant helix-destabilizing tendencies, with beta bridge formation occurring in helical peptides, and unfolding of apolipophorin-III occurring on the tens of nanoseconds timescale. The AMBER-03 force field, while showing adequate helical propensities for both peptides and stabilizing apolipophorin-III, (i) predicts an unexpected decrease in helicity with ALA→ARG⁺ substitution, (ii) lacks experimentally observed 3₁₀ helical content, and (iii) deviates strongly from average apolipophorin-III NMR structural properties. As is observed for AMBER-99SB, AMBER-03 significantly overweighs the contribution of extended and polyproline backbone configurations to the conformational equilibrium. In contrast, the AMBER-99φ force field, which was previously shown to best reproduce experimental measurements of the helix-coil transition in model helical peptides, adequately stabilizes apolipophorin-III and yields both an average gyration radius and polar solvent exposed surface area that are in excellent agreement with the NMR ensemble.

Charge, hydrophobicity, and confined water: putting past simulations into a simple theoretical framework

Water permeates all life, and mediates forces that are essential to the process of macromolecular self-assembly. Predicting these forces in a given biological context is challenging, since water organizes itself differently next to charged and hydrophobic surfaces, both of which are typically at play on the nanoscale in vivo. In this work, we present a simple statistical mechanical model for the forces water mediates between different confining surfaces, and demonstrate that the model qualitatively unifies a wide range of phenomena known in the simulation literature, including several cases of protein folding under confinement.

Models of macromolecular crowding effects and the need for quantitative comparisons with experiment

In recent years significant effort has been devoted to exploring the potential effects of macromolecular crowding on protein folding and association phenomena. Theoretical calculations and molecular simulations have, in particular, been exploited to describe aspects of protein behavior in crowded and confined conditions and many aspects of the simulated behavior have reflected, at least at a qualitative level, the behavior observed in experiments. One major and immediate challenge for the theorists is to now produce models capable of making quantitatively accurate predictions of in vitro behavior. A second challenge is to derive models that explain results obtained from experiments performed in vivo, the results of which appear to call into question the assumed dominance of excluded-volume effects in vivo.

Bioencapsulation of apomyoglobin in nanoporous organosilica sol-gel glasses: influence of the siloxane network on the conformation and stability of a model protein

Nanoporous sol-gel glasses were used as host materials for the encapsulation of apomyoglobin, a model protein employed to probe in a rational manner the important factors that influence the protein conformation and stability in silica-based materials. The transparent glasses were prepared from tetramethoxysilane (TMOS) and modified with a series of mono-, di- and tri-substituted alkoxysilanes, R(n)Si(OCH(3))(4-n) (R = methyl-, n = 1; 2; 3) of different molar content (5, 10, 15%) to obtain the decrease of the siloxane linkage (-Si-O-Si-). The conformation and thermal stability of apomyoglobin characterized by circular dichroism spectroscopy (CD) was related to the structure of the silica host matrix characterized by (29)Si MAS NMR and N(2) adsorption. We observed that the protein transits from an unfolded state in unmodified glass (TMOS) to a native-like helical state in the organically modified glasses, but also that the secondary structure of the protein was enhanced by the decrease of the siloxane network with the methyl modification (n = 0 < n = 1 < n = 2 < n = 3; 0 < 5 < 10 < 15 mol %). In 15% trimethyl-modified glass, the protein even reached a maximum molar helicity (-24,000 deg. cm(2) mol(-1)) comparable to the stable folded heme-bound holoprotein in solution. The protein conformation and stability induced by the change of its microlocal environment (surface hydration, crowding effects, microstructure of the host matrix) were discussed owing to this trend dependency. These results can have an important impact for the design of new efficient biomaterials (sensors or implanted devices) in which properly folded protein is necessary.

Induced beta-barrel formation of the Alzheimer's Abeta25-35 oligomers on carbon nanotube surfaces: implication for amyloid fibril inhibition

Recent experimental studies show that carbon nanotubes impact the aggregation process of proteins associated with neurodegenerative diseases. However, the details of molecular interactions between proteins and carbon nanotubes are still not well understood. In this study, we investigate the initial adsorption features and dynamics of the Alzheimer's amyloid-beta peptide spanning residues 25-35 (Abeta25-35) on a single-walled carbon nanotube (SWNT) surface using fully atomic molecular dynamics simulations (MD) in explicit solvent. The initial configurations of the Abeta25-35 peptides consist of two preformed bilayer beta-sheets, each with four or five beta-strands in parallel or mixed antiparallel-parallel orientations. Our simulations show, for what we believe is the first time, that two disjointed Abeta25-35 beta-sheets with mixed antiparallel-parallel strands can assemble into beta-barrels wrapping the SWNT. In contrast, both simulations of Abeta25-35 without SWNT, and simulations of SWNT-Abeta25-35 with purely parallel beta-strands, lead to disordered aggregates. We find that Abeta25-35 beta-barrel formation involves at least two steps: i), curving of the Abeta25-35 beta-sheets as a result of strong hydrophobic interactions with carbon nanotube concomitantly with dehydration of the SWNT-peptide interface; and ii), intersheet backbone hydrogen bond formation with fluctuating intrasheet hydrogen bonds. Detailed analysis of the conversion shows that beta-barrel formation on SWNT surface results from the interplay of dehydration and peptide-SWNT/peptide-peptide interactions. Implications of our results on amyloid fibril inhibition are discussed.