RESUMO
In nature, enzymatic pathways often involve compartmentalization effects that can modify the intrinsic activity and specificity of the different enzymes involved. Consequently, extensive research has focused on replicating and studying the compartmentalization effects on individual enzymes and on multistep enzyme "cascade" reactions. This study explores the influence of compartmentalization achieved using molecular crowding on the glucose oxidase/horseradish peroxidase (GOx/HRP) cascade reaction. The crowder tested is methoxy poly(ethylene glycol) (mPEG) that can, depending on conditions, promote GOx and HRP coassociation at the nanoscale and extend their contact time. Low-molecular-weight mPEG (0.35 kDa), but not mPEG of higher molecular weights (5 or 20 kDa), significantly enhanced the cascade reaction where up to a 20-fold increase in the rate of the cascade reaction was observed under some conditions. The combined analyses emphasize the particularity of low-molecular-weight mPEG and point toward mPEG-induced coassociation of HRP and GOx, producing nearest crowded neighbor effects of HRP on GOx, and vice versa. These altered the nanoscale environments of these enzymes, which influenced substrate affinity. Using mPEG to promote protein coassociation is simple and does not chemically modify the proteins studied. This approach could be of interest for more broadly characterizing nearest crowded neighbor effects (i.e., protein-protein interactions) for multiprotein systems (i.e., more than just two), thus making it an interesting tool for studying very complex systems, such as those found in nature.
RESUMO
Due to their programmability via specific base pairing, self-assembled DNA origami structures have proven to be useful for a wide variety of applications, including diagnostics, molecular computation, drug delivery, and therapeutics. Measuring and characterizing these structures is therefore of great interest and an important part of quality control. Here, we show the extent to which DNA nanostructures can be characterized by a solid-state nanopore; a non-destructive, label-free, single-molecule sensor capable of electrically detecting and characterizing charged biomolecules. We demonstrate that in addition to geometrical dimensions, nanopore sensing can provide information on the mechanical properties, assembly yield, and stability of DNA nanostructures. For this work, we use a model structure consisting of a 3 helix-bundle (3HB), i.e. three interconnected DNA double helices using a M13 scaffold folded twice on itself by short DNA staple strands, and translocate it through solid-state nanopores fabricated by controlled breakdown. We present detailed analysis of the passage characteristics of 3HB structures through nanopores under different experimental conditions which suggest that segments of locally higher flexibility are present along the nanostructure contour that allow for the otherwise rigid 3HB to fold inside nanopores. By characterizing partially melted 3HB structures, we find that locally flexible segments are likely due to short staple oligomers missing from the fully assembled structure. The 3HB used herein is a prototypical example to establish nanopores as a sensitive, non-destructive, and label-free alternative to conventional techniques such as gel electrophoresis with which to characterize DNA nanostructures.
Assuntos
Nanoporos , Nanoestruturas , Nanoestruturas/química , DNA/química , Nanotecnologia/métodosRESUMO
Volumetric additive manufacturing techniques are a promising pathway to ultra-rapid light-based 3D fabrication. Their widespread adoption, however, demands significant improvement in print fidelity. Currently, volumetric additive manufacturing prints suffer from systematic undercuring of fine features, making it impossible to print objects containing a wide range of feature sizes, precluding effective adoption in many applications. Here, we uncover the reason for this limitation: light dose spread in the resin due to chemical diffusion and optical blurring, which becomes significant for features ⪠0.5 mm. We develop a model that quantitatively predicts the variation of print time with feature size and demonstrate a deconvolution method to correct for this error. This enables prints previously beyond the capabilities of volumetric additive manufacturing, such as a complex gyroid structure with variable thickness and a fine-toothed gear. These results position volumetric additive manufacturing as a mature 3D printing method, all but eliminating the gap to industry-standard print fidelity.
RESUMO
We examine methods for calculating the effective mobilities of molecules driven through periodic geometries in the context of particle-based simulation. The standard formulation of the mobility, based on the long-time limit of the mean drift velocity, is compared to a formulation based on the mean first-passage time of molecules crossing a single period of the system geometry. The equivalence of the two definitions is derived under weaker assumptions than similar conclusions obtained previously, requiring only that the state of the system at subsequent period crossings satisfy the Markov property. Approximate theoretical analyses of the computational costs of estimating these two mobility formulations via particle simulations suggest that the definition based on first-passage times may be substantially better suited to exploiting parallel computation hardware. This claim is investigated numerically on an example system modeling the passage of nanoparticles through the slit-well device. In this case, the traditional mobility formulation is found to perform best when the Péclet number is small, whereas the mean first-passage time formulation is found to converge much more quickly when the Péclet number is moderate or large. The results suggest that, given relatively modest access to modern GPU hardware, this alternative mobility formulation may be an order of magnitude faster than the standard technique for computing effective mobilities of biomolecules through periodic geometries.
RESUMO
Bioconjugation reactions, such as protein PEGylation, generally require excess reagents because of their inefficiency. Intriguingly, few reports have investigated the fundamental causes of this inefficiency. This study demonstrates that the excluded volume effect (EVE)âcaused by the mutual repulsion of methoxy poly(ethylene glycol) (mPEG) and proteins under typical PEGylation conditionsâcauses proteins and protein-reactive mPEG (5 kDa) to self-associate into separate "protein-rich" and "mPEG-rich" nano-domains (i.e., soluble self-assemblies). To overcome this obstacle to reaction, "unreactive" low-molecular-weight mPEG was added as a co-solvent to promote the association between the larger protein and the reactive mPEG molecules by harnessing the same EVE. The near complete PEGylation of lysozyme could be achieved with close to stoichiometric amounts of reactive mPEG, and beneficial effects were observed for other proteins. Considering the general nature of the EVE (e.g., salting-out and PEGying-out), this study provides important perspectives on enhancing bioconjugation reactions, which are relevant to many nanoscale systems.
Assuntos
Polietilenoglicóis , Proteínas , Polietilenoglicóis/metabolismo , Peso MolecularRESUMO
This study presents deep neural network solutions to a time-integrated Smoluchowski equation modeling the mean first passage time of nanoparticles traversing the slit-well microfluidic device. This physical scenario is representative of a broader class of parametrized first passage problems in which key output metrics are dictated by a complicated interplay of problem parameters and system geometry. Specifically, whereas these types of problems are commonly studied using particle simulations of stochastic differential equation models, here the corresponding partial differential equation model is solved using a method based on deep neural networks. The results illustrate that the neural network method is synergistic with the time-integrated Smoluchowski model: together, these are used to construct continuous mappings from key physical inputs (applied voltage and particle diameter) to key output metrics (mean first passage time and effective mobility). In particular, this capability is a unique advantage of the time-integrated Smoluchowski model over the corresponding stochastic differential equation models. Furthermore, the neural network method is demonstrated to easily and reliably handle geometry-modifying parameters, which is generally difficult to accomplish using other methods.
RESUMO
The UNC-49 receptor is a Cys-loop GABA receptor that is unique to the nematode phylum. The receptor differs from mammalian GABA receptors both in amino acid sequence and pharmacology which highlights its potential as a novel anthelmintic target. Sequence differences within and near the various ligand-binding loops of the nematode receptor suggest that there could be structural differences compared to mammalian receptors that result in different pharmacological and functional features. Here we investigated three residues in the UNC-49 receptor from the parasitic nematode Haemonchus contortus: K181, E183, and T230. Analysis of these residues was conducted via site-directed mutagenesis, electrophysiology, MD simulations, and mutant cycling analysis. In the UNC-49 receptor, E183 lies in close proximity to K181 where together they appear to play a role in GABA sensitivity and pharmacology, possibly interacting via an ionic bond. While the introduction of single alanine residues at each position separately had a negative impact on GABA EC50, the double alanine mutant (K181A/E183A) exhibited wildtype-level GABA EC50 and some differences in pharmacology. Overall, this study has revealed a potentially novel role for these two residues in nematode UNC-49 GABA receptors that could aid in understanding their function.
Assuntos
Nematoides , Receptores de GABA , Animais , Receptores de GABA/genética , Receptores de GABA/química , Receptores de GABA/metabolismo , Sítios de Ligação , Nematoides/metabolismo , Ácido gama-Aminobutírico/metabolismo , Alanina , MamíferosRESUMO
3D printing has enabled materials, geometries and functional properties to be combined in unique ways otherwise unattainable via traditional manufacturing techniques, yet its adoption as a mainstream manufacturing platform for functional objects is hindered by the physical challenges in printing multiple materials. Vat polymerization offers a polymer chemistry-based approach to generating smart objects, in which phase separation is used to control the spatial positioning of materials and thus at once, achieve desirable morphological and functional properties of final 3D printed objects. This study demonstrates how the spatial distribution of different material phases can be modulated by controlling the kinetics of gelation, cross-linking density and material diffusivity through the judicious selection of photoresin components. A continuum of morphologies, ranging from functional coatings, gradients and composites are generated, enabling the fabrication of 3D piezoresistive sensors, 5G antennas and antimicrobial objects and thus illustrating a promising way forward in the integration of dissimilar materials in 3D printing of smart or functional parts.
RESUMO
Amylose is a linear polymer chain of α-d-glucose units connected through α(1 â 4) glycosidic bonds. Experimental studies show that in non-polar solvents, single amylose chains form helical structures containing precise H-bond patterns. However, both experimental and computational studies indicate that these perfectly H-bonded helices are not stable in pure water. Nevertheless, amylose chains are observed to form helix-like structures in molecular dynamics (MD) simulations that exhibit imperfect H-bond patterns. In this paper, we study the structure of amylose chains in water using MD simulations to identify and characterize these "imperfect" helical structures. To this end we devise geometry-based criteria to define imperfect helical structures in amylose chains. Using this approach, the propensity of amylose chains to form these structures is quantified as a function of chain length and solvent temperature. This analysis also uncovers both short and long time helix-breaking mechanisms such as band-flips and kinks in the chain. This geometric approach to defining imperfect helices thus allows us to give new insight into the secondary structure of single amylose chains in spite of imperfect H-bond patterns.
RESUMO
Pseudomonas aeruginosa, like many bacilliforms, are not limited only to swimming motility but rather possess many motility strategies. In particular, twitching-mode motility employs hair-like pili to transverse moist surfaces with a jittery irregular crawl. Twitching motility plays a critical role in redistributing cells on surfaces prior to and during colony formation. We combine molecular dynamics and rule-based simulations to study twitching-mode motility of model bacilliforms and show that there is a critical surface coverage fraction at which collective effects arise. Our simulations demonstrate dynamic clustering of twitcher-type bacteria with polydomains of local alignment that exhibit spontaneous correlated motions, similar to rafts in many bacterial communities.
Assuntos
Fímbrias Bacterianas/fisiologia , Movimento , Pseudomonas aeruginosa/fisiologia , Algoritmos , Proteínas de Bactérias/fisiologia , Biofilmes , Proteínas de Fímbrias/fisiologia , Simulação de Dinâmica Molecular , Distribuição NormalRESUMO
We examine the electrophoresis of spherical particles in microfluidic devices made of alternating wells and narrow channels, including a system previously used to separate DNA molecules. Our computer simulations predict that such systems can be used to separate spherical particles of different sizes that share the same free-solution mobility. Interestingly, the electrophoretic velocity shows an inversion as the field intensity is increased: while small particles have higher velocities at low field, the situation is reversed at high fields with the larger particles then moving faster. The resulting nonlinearity suggests that asymmetric pulsed electric fields could be used to build separation ratchets: particles then have a net size-dependent velocity in the presence of a zero-mean external field. Exploiting the inversion mentioned above, we show how to design pulsed field sequences that make particles move against the mean field (an example of negative mobility). Finally, we demonstrate that it is possible to use pulsed fields to make particles of different sizes move in opposite directions, even though their charge have the same sign.
Assuntos
Eletroforese/métodos , Técnicas Analíticas Microfluídicas/métodos , Modelos Químicos , Simulação por Computador , Tamanho da PartículaRESUMO
Monoclonal antibodies (mAb) are a major focus of the pharmaceutical industry, and polyclonal immunoglobulin G (IgG) therapy is used to treat a wide variety of health conditions. As some individuals require mAb/IgG therapy their entire life, there is currently a great desire to formulate antibodies for bolus injection rather than infusion. However, to achieve the required doses, very concentrated antibody solutions may be required. Unfortunately, mAb/IgG self-assembly at high concentration can produce an unacceptably high viscosity for injection. To address this challenge, this study expands the concept of "dynamic covalent chemistry" to "dynamic bioconjugation" in order to reduce viscosity by interfering with antibody-antibody interactions. Ultra-sub-stoichiometric amounts of dynamic PEGylation agents (down to the nanomolar) significantly reduced the viscosity of concentrated antibody solutions by interfering with oligomerization.
Assuntos
Anticorpos Monoclonais/imunologia , Imunoconjugados/imunologia , Imunoglobulina G/imunologia , Viscosidade , Anticorpos Monoclonais/química , Anticorpos Monoclonais/uso terapêutico , Humanos , Imunoconjugados/química , Imunoconjugados/uso terapêutico , Imunoglobulina G/química , Imunoglobulina G/uso terapêuticoRESUMO
The average number of methoxy poly(ethylene glycol) (mPEG) chains grafted to a protein - also known as the degree of PEGylation - is a fundamental parameter for characterizing a bioconjugate. The degree of PEGylation is typically determined by chromatographic or electrophoretic methods, which are subject to certain biases. This contribution describes an analytical approach alongside technical precautions for quantitatively determining the degree of PEGylation of protein bioconjugates by 1H NMR spectroscopy. An accompanying dataset, corresponding to the raw 1H NMR spectra of thirteen bioconjugates with different degrees of PEGylation and different mPEG molecular weights, is provided for the reader to become familiar with the analysis. The exemplary bioconjugate system used in this Data article is the enzyme glutamate dehydrogenase (GDH) modified with multiple copies of mPEG (0.5-20 kDa). These bioconjugates correspond to those discussed in-depth in the article "Mechanisms of activity loss for a multi-PEGylated protein by experiment and simulation" by Zaghmi et al., 2019 The described approach to calculate degree of PEGylation is quantitative, applicable to other proteins, and can be adapted to other types of polymers.
RESUMO
This study demonstrates that pH-responsive polymers have a very high buffering capacity in their immediate vicinity, a phenomenon termed "nanobuffering". This can be exploited to dissociate local nanoscale pH from bulk solution pH. Herein, a series of pH-responsive polymers were conjugated to Protein-A to rationally manipulate the latter's binding affinity toward antibodies via nanobuffering ( i. e., this interaction is pH dependent), independently of bulk solution pH. Moreover, the nanobuffering effect could be terminated using low concentrations of strong ion-pairing salts, to achieve quantitative release of the antibodies from the bioconjugate. These complementary discoveries are showcased in the context of the development of a homogeneous affinity precipitation agent ( i. e., a scavenger) for the purification of polyclonal immunoglobulin G and two monoclonal antibodies from cell culture supernatant. Indeed, while bulk solution pH was used to induce precipitation of the scavenger, maintaining local nanoscale pH via nanobuffering maximized binding interaction with the antibodies. A 2:1 binding stoichiometry was observed, which was similar to that observed for native protein. The scavenger could be recycled multiple times, and the purification protocol circumvented lengthy/tedious physical purification processes typically associated with mAb manufacturing. Overall, this study provides perspectives on the local nanoscale pH near pH-responsive polymers and establishes lines of thought for predictably manipulating or even terminating nanobuffering, to control the activity of proteins.
Assuntos
Anticorpos Monoclonais/química , Sequestradores de Radicais Livres/química , Nanopartículas/química , Polímeros/química , Anticorpos Monoclonais/isolamento & purificação , Calorimetria , Células Cultivadas , Humanos , Concentração de Íons de Hidrogênio , Peso MolecularRESUMO
Elucidating the kinetics of DNA passage through a solid-state nanopore is a fertile field of research, and mechanisms for controlling capture, passage, and trapping of biopolymers are likely to find numerous technological applications. Here we present a nanofiltered nanopore device, which forms an entropic cage for DNA following first passage through the nanopore, trapping the translocated DNA and permitting recapture for subsequent reanalysis and investigation of kinetics of passage under confinement. We characterize the trapping properties of this nanodevice by driving individual DNA polymers into the nanoscale gap separating the nanofilter and the pore, forming an entropic cage similar to a "two pores in series" device, leaving polymers to diffuse in the cage for various time lengths, and attempting to recapture the same molecule. We show that the cage results in effectively permanent trapping when the radius of gyration of the target polymer is significantly larger than the radii of the pores in the nanofilter. We also compare translocation dynamics as a function of translocation direction in order to study the effects of confinement on DNA just prior to translocation, providing further insight into the nanopore translocation process. This nanofiltered nanopore device realizes simple fabrication of a femtoliter nanoreactor in which to study fundamental biophysics and biomolecular reactions on the single-molecule level. The device provides an electrically-permeable single-molecule trap with a higher entropic barrier to escape than previous attempts to fabricate similar structures.
RESUMO
In this work, we investigated whether a series of nanopores connected by channels can be used to separate polymer mixtures by molecular size. We conducted multiscale coarse-grained simulations of semiflexible polymers driven through such a device. Polymers were modelled as chains of beads near the nanopores and as single particles in the bulk of the channels. Since polymers rarely escape back into the bulk of the channels after coming sufficiently close to the nanopores, the more computationally expensive simulations near the pores were decoupled from those in the bulk. The distribution of polymer positions after many translocations was deduced mathematically from simulations across a single nanopore-channel pair, under the reasonable assumption of identical and independent dynamics in each channel and each nanopore. Our results reveal rich polymer dynamics in the nanopore-channel device and suggest that it can indeed produce polymer separation. As expected, the mean time to translocate across a single nanopore increases with the chain length. Conversely, the mean time to cross the channels from one nanopore to the next decreases with the chain length, as smaller chains explore more of the channel volume between translocations. As such, the time between translocations is a function of the length and width of the channels. Depending on the channel dimensions, polymers are sorted by increasing length, decreasing length, or non-monotonically by length such that polymers of an intermediate size emerge first.
RESUMO
The UNC-49 receptor is a unique nematode γ-aminobutyric acid (GABA)-gated chloride channel that may prove to be a novel target for the development of nematocides. Here we have characterized various charged amino acid residues in and near the agonist binding site of the UNC-49 receptor from the parasitic nematode Haemonchus contorts. Utilizing the Caenorhabditis elegans GluCl crystal structure as a template, a model was generated and various charged residues [D83 (loop D), E131 (loop A), H137 (pre-loop E), R159 (Loop E), E185 (Loop B) and R241 (Loop C)] were investigated based on their location and conservation. These residues may contribute to structure, function, and molecular interactions with agonists. It was found that all residues chosen were important for receptor function to varying degrees. Results of the mutational analysis and molecular simulations suggest that R159 may be interacting with D83 by an ionic interaction that may be crucial for general GABA receptor function. We have used the results from this study as well as knowledge of residues involved in GABA receptor binding to identify sequence patterns that may assist in understanding the function of lesser known GABA receptor subunits from parasitic nematodes.
Assuntos
Haemonchus/genética , Mutação , Receptores de GABA/química , Receptores de GABA/genética , Animais , Antinematódeos/farmacologia , Sítios de Ligação , Caenorhabditis elegans/química , Caenorhabditis elegans/genética , Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans , Cristalização , Agonistas de Receptores de GABA-A/isolamento & purificação , Agonistas de Receptores de GABA-A/metabolismo , Agonistas de Receptores de GABA-A/farmacologia , Haemonchus/química , Haemonchus/efeitos dos fármacos , Proteínas de Helminto/genética , Proteínas de Helminto/metabolismo , Ativação do Canal Iônico , Simulação de Dinâmica Molecular , Ligação Proteica , Receptores de GABA/efeitos dos fármacos , Receptores de GABA-A , Xenopus laevisRESUMO
Nematodes exhibit a vast array of cys-loop ligand-gated ion channels with unique pharmacologic characteristics. However, many of the structural components that govern the binding of various ligands are unknown. The nematode cys-loop GABA receptor uncoordinated 49 (UNC-49) is an important receptor found at neuromuscular junctions that plays an important role in the sinusoidal movement of worms. The unique pharmacologic features of this receptor suggest that there are structural differences in the agonist binding site when compared with mammalian receptors. In this study, we examined each amino acid in one of the main agonist binding loops (loop E) via the substituted cysteine accessibility method (SCAM) and analyzed the interaction of various residues by molecular dynamic simulations. We found that of the 18 loop E mutants analyzed, H142C, R147C, and S157C had significant changes in GABA EC50 and were accessible to modification by a methanethiosulfonate reagent (MTSET) resulting in a change in I GABA In addition, the residue H142, which is unique to nematode UNC-49 GABA receptors, appears to play a negative role in GABA sensitivity as its mutation to cysteine increased sensitivity to GABA and caused the UNC-49 receptor partial agonist 5-aminovaleric acid (DAVA) to behave as a full agonist. Overall, this study has revealed potential differences in the agonist binding pocket between nematode UNC-49 and mammalian GABA receptors that could be exploited in the design of novel anthelmintics.
Assuntos
Cisteína/metabolismo , Nematoides/metabolismo , Receptores de GABA/metabolismo , Sequência de Aminoácidos , Animais , Anti-Helmínticos/metabolismo , Anti-Helmínticos/farmacologia , Sítios de Ligação , Desenho de Fármacos , Mutagênese Sítio-Dirigida , Nematoides/efeitos dos fármacos , Receptores de GABA/química , Receptores de GABA/efeitos dos fármacos , Homologia de Sequência de AminoácidosRESUMO
Langevin dynamics simulations of polymer translocation are performed where the polymer is stretched via two opposing forces applied on the first and last monomer before and during translocation. In this setup, polymer translocation is achieved by imposing a bias between the two pulling forces such that there is net displacement towards the trans side. Under the influence of stretching forces, the elongated polymer ensemble contains less variations in conformations compared to an unstretched ensemble. Simulations demonstrate that this reduced spread in initial conformations yields a reduced variation in translocation times relative to the mean translocation time. This effect is explored for different ratios of the amplitude of thermal fluctuations to driving forces to control for the relative influence of the thermal path sampled by the polymer. Since the variance in translocation times is due to contributions coming from sampling both thermal noise and initial conformations, our simulations offer independent control over the two main sources of noise and allow us to shed light on how they both contribute to translocation dynamics. Simulation parameter space corresponding to experimentally relevant conditions is highlighted and shown to correspond to a significant decrease in the spread of translocation times, thus indicating that stretching DNA prior to translocation could assist nanopore-based sequencing and sizing applications.
RESUMO
Red blood cells suspended in quiescent plasma tend to aggregate into multicellular assemblages, including linearly stacked columnar rouleaux, which can reversibly form more complex clusters or branching networks. While these aggregates play an essential role in establishing hemorheological and pathological properties, the biophysics behind their self-assembly into dynamic mesoscopic structures remains under-explored. We employ coarse-grained molecular simulations to model low-hematocrit erythrocytes subject to short-range implicit depletion forces, and demonstrate not only that depletion interactions are sufficient to account for a sudden dispersion-aggregate transition, but also that the volume fraction of depletant macromolecules controls small aggregate morphology. We observe a sudden transition from a dispersion to a linear column rouleau, followed by a slow emergence of disorderly amorphous clusters of many short rouleaux at larger volume fractions. This work demonstrates how discocyte topology and short-range, non-specific, physical interactions are sufficient to self-assemble erythrocytes into various aggregate structures, with markedly different morphologies and biomedical consequences.