Adsorption and protonation of peptides and proteins in pH responsive gels

To describe the non-trivial features of the equilibrium protonation and physical adsorption of peptides/proteins in pH-responsive hydrogels, we summarize our recent theoretical work on the subject. In these systems, molecular confinement in nanometer-sized environments modifies the balance between chemical state, physical interactions and molecular organization, which results in a behavior that is qualitatively different from what is expected from assuming the bulk solution protonation. To enhance adsorption, the pH-dependent deprotonation curves of all amino acids of adsorbed proteins are adequately shifted and deformed, which depends, in a complex fashion, on the specific amino acid. This possibility of modifying different acid-base equilibriums gives the adsorbed protein degrees of freedom to regulate charge and enhance electrostatic attractions under a wide range of experimental conditions. Protein adsorption modifies the microenvironment inside the hydrogel, particularly the gel pH. As a result, the state of protonation of the network is different before and after adsorption. The physicochemical considerations described in this review can be useful in the design of functional materials involving protein adsorption.Facultad de Ciencias ExactasInstituto de Investigaciones Fisicoquímicas Teóricas y Aplicada

Behavior of ligand binding assays with crowded surfaces: molecular model of antigen capture by antibody-conjugated nanoparticles

Ligand-receptor binding is of utmost importance in several biologically related disciplines. Ligand binding assays (LBA) use the high specificity and high affinity of ligands to detect, target or measure a specific receptors. One particular example of ligand binding assays are Antibody conjugated Nanoparticles (AcNPs), edge-cutting technologies that are present in several novel biomedical approaches for imaging, detection and treatment of diseases. However, the nano-confinement in AcNPs and LBA nanostructures introduces extra complexity in the analysis of ligand-receptor equilibriums. Because antibodies are large voluminous ligands, the effective affinity in AcNPs is often determined by antibody orientation and surface coverage. Moreover, antibodies have two binding sites introducing an extra ligand-receptor binding equilibrium. As consequence of all this, experimental or theoretical studies providing a guidelines for the prediction of the binding behavior in AcNPs are scarce. In this work, we present a set of theoretical calculations to shed light into the complex binding behavior of AcNPs and its implications in biomedical applications. To investigate the ligand-receptor binding on AcNPs, we have used a molecular theory that predicts the probability of different molecular conformations of the system depending on the local environment. We have considered two different pathways for designing these devices: covalently conjugated antibodies and streptavidin-biotin conjugated antibodies. We also explore the effects of surface coverage, bulk concentrations, nanoparticle size and antibody-antigen affinity. Overall, this work offers a series of theoretical predictions that can be used as a guide in the design of antibody conjugated nanoparticles for different applications.Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicada

Non-monotonic swelling of surface grafted hydrogels induced by pH and/or salt concentration

We use a molecular theory to study the thermodynamics of a weak-polyacid hydrogel film that is chemically grafted to a solid surface. We investigate the response of the material to changes in the pH and salt concentration of the buffer solution. Our results show that the pH-triggered swelling of the hydrogel film has a non-monotonic dependence on the acidity of the bath solution. At most salt concentrations, the thickness of the hydrogel film presents a maximum when the pH of the solution is increased from acidic values. The quantitative details of such swelling behavior, which is not observed when the film is physically deposited on the surface, depend on the molecular architecture of the polymer network. This swelling-deswelling transition is the consequence of the complex interplay between the chemical free energy (acid-base equilibrium), the electrostatic repulsions between charged monomers, which are both modulated by the absorption of ions, and the ability of the polymer network to regulate charge and control its volume (molecular organization). In the absence of such competition, for example, for high salt concentrations, the film swells monotonically with increasing pH. A deswelling-swelling transition is similarly predicted as a function of the salt concentration at intermediate pH values. This reentrant behavior, which is due to the coupling between charge regulation and the two opposing effects triggered by salt concentration (screening electrostatic interactions and charging/discharging the acid groups), is similar to that found in end-grafted weak polyelectrolyte layers. Understanding how to control the response of the material to different stimuli, in terms of its molecular structure and local chemical composition, can help the targeted design of applications with extended functionality. We describe the response of the material to an applied pressure and an electric potential. We present profiles that outline the local chemical composition of the hydrogel, which can be useful information when designing applications that pursue or require the absorption of biomolecules or pH-sensitive molecules within different regions of the film.Facultad de Ciencias ExactasInstituto de Investigaciones Fisicoquímicas Teóricas y Aplicada

Molecular theory of glyphosate adsorption to pH‑responsive polymer layers

By means of a molecular-level theory we investigate glyphosate adsorption from aqueous solutions to surface-grafted poly(allylamine) layers. Our molecular model of glyphosate and the polymeric material includes description of size, shape, conformational freedom, and state of protonation of both components. The composition of the bulk solution (pH, salt concentration and glyphosate concentration) plays a critical role to determine adsorption. Adsorption is a non-monotonic function of the solution pH, which can be explained in terms of the pH-dependent protonation behavior of both adsorbate and adsorbent material. Lowering the solution salinity is an efficient way to enhance glyphosate adsorption. This is because glyphosate and salt anions compete for adsorption to the polymer layer. In this competition, glyphosate deprotonation, to increase its negative charge upon entering the polymer layer, plays an critical role to favor its adsorption under a variety of solution conditions. This deprotonation is the result of the higher pH that establishes inside the polymer. Our results show that such pH increase can be controlled, while achieving significant glyphosate adsorption, through varying the grafting density of the material. This result is important since glyphosate degradation by microbial activity is pH-dependent. These polymeric systems are excellent candidates for the development functional materials that combine glyphosate sequestration and in situ biodegradation.Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicada

Using Polymer Hydrogels for Glyphosate Sequestration from Aqueous Solutions: Molecular Theory Study of Adsorption to Polyallylamine Films

A molecular theory has been applied to study the equilibrium conditions of glyphosate and aminomethylphosphonic acid (AMPA) adsorption from aqueous solutions to hydrogel films of cross-linked polyallylamine (PAH). This theoretical framework allows for describing the size, shape, state of charge/protonation, and configurational freedom of all chemical species in the system. Adsorption of glyphosate is a nonmonotonic function of the solution pH, which results from the protonation behavior of both the adsorbate and adsorbent material. Glyphosate and chloride ions compete for adsorption to neutralize the polymer charge; lowering the solution salt concentration enhances the partition of glyphosate inside the hydrogel film. AMPA adsorption is qualitatively similar to that of glyphosate but orders of magnitude smaller under the same conditions. AMPA is less charged than glyphosate, which unbalances the competition for adsorption with salt counter ions. In mixed solutions, glyphosate presence can significantly hinder AMPA adsorption. A higher pH establishes inside the film than in the bulk solution, which has important implications for the herbicide biodegradation because microbial activity is pH-dependent. Thus, PAH hydrogel films can be considered as functional materials that combine glyphosate sequestration and in situ degradation. In devising these materials, the polymer density is an important variable of design; polymer networks with high density of titratable units can enhance adsorption; this density can also be used to modify the pH inside the material.Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicada

Localization of adhesins on the surface of a pathogenic bacterial envelope through atomic force microscopy

Bacterial adhesion is the first and a significant step in establishing infection. This adhesion normally occurs in presence of flow of fluids. Therefore, bacterial adhesins must be able to provide high strength interactions with their target surface in order to maintain the adhered bacteria under hydromechanical stressing conditions. In the case of B. pertussis, a Gram-negative bacterium responsible of pertussis, a highly contagious human respiratory tract infection, an important protein participating in the adhesion process is a 220 KDa adhesin named Filamentous haemagglutinin (FHA), an outer membrane and also secreted protein that contains recognition domains to adhere to ciliated respiratory epithelial cells and macrophages. In this work, we obtained information of the cell-surface localization and distribution of the B. pertussis adhesin FHA using an antibody-functionalized AFM tip. Through the analysis of specific molecular recognition events we built a map of the spatial distribution of the adhesin which revealed a non-homogenous pattern. Moreover, our experiments showed a force induced reorganization of the adhesin in the surface of the cells, which could explain a reinforced adhesive response under external forces. This single-molecule information contributes to the understanding of basic molecular mechanisms used by bacterial pathogens to cause infectious disease and to gain insight into the structural features by which adhesins can act as force sensors under mechanical shear conditions.Centro de Investigación y Desarrollo en Fermentaciones IndustrialesInstituto de Investigaciones Fisicoquímicas Teóricas y Aplicada

Unusual temperature-induced swelling of ionizable poly(N-isopropylacrylamide)-based microgels: experimental and theoretical insights into its molecular origin

In the traditional view of temperature-driven volume phase transitions in PNIPAM-based microgel solutions, a monotonic and sharp decrease in the particle size occurs upon heating the solution to above the volume phase transition temperature (VPTT). However, at sufficiently high microgel concentrations and under low salt conditions, our dynamic light scattering experiments reveal an unexpected non-monotonic evolution of the particle size when increasing the solution temperature. These findings show that poly(N-isopropylacrylamide-co-methacrylic acid) (P(NIPAM-co-MAA)) microgels swell upon heating the solution in the temperature range where NIPAM is water-soluble (i.e., below the VPPT). Further heating the microgel solution leads to microgel collapse as typically observed at temperatures above the VPTT. This novel behavior depends on the particle and salt concentration. We have observed the expected monotonic temperature-response of P(NIPAm-co-MAA) microgel solutions at low particle density and high salt concentration. To gain insights into the molecular origin of the unusual behavior of these microgel solutions, we have combined nuclear magnetic resonance studies and molecular-level theoretical calculations of the system. A delicate balance between inter-particle steric compressions and intra-microgel physical interactions and chemical equilibria determines the size of these microgels. Both steric compression, due to finite density, and hydrogen bond formation in the interior of the microgels favors a more compact particle. On the contrary, at the pH of the experiments the acid–base equilibrium constrains the polymer charge to increase, which favors particle swelling due to intra-microgel electrostatic repulsions. This interplay between physical interactions and chemical equilibria occurring at the nanometer length-scale determines the unusual thermal-induced swelling of P(NIPAM-co-MAA) microgels.Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicada

Mesoporous thin films on graphene FETs: Nanofiltered, amplified and extended field-effect sensing

The ionic screening and the response of non-specific molecules are great challenges of biosensors based on field-effect transistors (FETs). In this work, we report the construction of graphene based transistors modified with mesoporous silica thin films (MTF-GFETs) and the unique (bio)sensing properties that arise from their synergy. The developed method allows the preparation of mesoporous thin films free of fissures, with an easily tunable thickness, and prepared on graphene-surfaces, preserving their electronic properties. The MTF-GFETs show good sensing capacity to small probes that diffuse inside the mesopores and reach the graphene semiconductor channel such as H+, OH-, dopamine and H2O2. Interestingly, MTF-GFETs display a greater electrostatic gating response in terms of amplitude and sensing range compared to bare-GFETs for charged macromolecules that infiltrate the pores. For example, for polyelectrolytes and proteins of low MW, the amplitude increases almost 100% and the sensing range extends more than one order of magnitude. Moreover, these devices show a size-excluded electrostatic gating response given by the pore size. These features are even displayed at physiological ionic strength. Finally, a developed thermodynamic model evidences that the amplification and extended field-effect properties arise from the decrease of free ions inside the MTFs due to the entropy loss of confining ions in the mesopores. Our results demonstrate that the synergistic coupling of mesoporous films with FETs leads to nanofiltered, amplified and extended field-effect sensing (NAExFES).Fil: Alberti, Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas; ArgentinaFil: Piccinini, Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas; ArgentinaFil: Ramírez, Pedro Germán. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; ArgentinaFil: Longo, Gabriel Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas; ArgentinaFil: Ceolin, Marcelo Raul. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas; ArgentinaFil: Azzaroni, Omar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas; Argentin

Pushing the Boundaries of Interfacial Sensitivity in Graphene FET Sensors: Polyelectrolyte Multilayers Strongly Increase the Debye Screening Length

Nanomaterial-based FET sensors represent an attractive platform for ultrasensitive, real-time, and label-free detection of chemical and biological species. Nevertheless, because their response is screened by mobile ions, it remains a challenge to use them to sense in physiological ionic strength solutions. In this work, it is demonstrated, both experimentally and theoretically, that polyelectrolyte multilayers are capable of increasing the sensing range of graphene-based FETs. Potential shifts at graphene surfaces and film thickness are recorded upon the construction of PDADMAC/PSS polyelectrolyte multilayer (PEM) films. By correlation of the potential shift with the film thickness, the electrostatic screening length and the concentration of mobile ion inside the films have been deduced. Across the polymer interface the Debye length is increased more than 1 order of magnitude. The fundamentals of this strategy are described by a conceptually simple thermodynamic model, which accounts for the entropy loss of ion confinement and incorporates the effect of ions finite volume. Interestingly, the electrostatic screening inside the film strongly depends on the polymer density and the ionic strength of the solution. Of particular interest in physiological condition sensing, the PEM interfaces can extend the Debye length from 0.8 to 10 nm.Fil: Piccinini, Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas; ArgentinaFil: Alberti, Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas; ArgentinaFil: Longo, Gabriel Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas; ArgentinaFil: Berninger, Teresa. Austrian Institute of Technology; AustriaFil: Breu, Josef. University of Bayreuth; AlemaniaFil: Dostalek, Jakub. Austrian Institute of Technology; AustriaFil: Azzaroni, Omar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas; ArgentinaFil: Knoll, Wolfgang. Austrian Institute of Technology; Austri

NEOTROPICAL CARNIVORES: a data set on carnivore distribution in the Neotropics

Mammalian carnivores are considered a key group in maintaining ecological health and can indicate potential ecological integrity in landscapes where they occur. Carnivores also hold high conservation value and their habitat requirements can guide management and conservation plans. The order Carnivora has 84 species from 8 families in the Neotropical region: Canidae; Felidae; Mephitidae; Mustelidae; Otariidae; Phocidae; Procyonidae; and Ursidae. Herein, we include published and unpublished data on native terrestrial Neotropical carnivores (Canidae; Felidae; Mephitidae; Mustelidae; Procyonidae; and Ursidae). NEOTROPICAL CARNIVORES is a publicly available data set that includes 99,605 data entries from 35,511 unique georeferenced coordinates. Detection/non-detection and quantitative data were obtained from 1818 to 2018 by researchers, governmental agencies, non-governmental organizations, and private consultants. Data were collected using several methods including camera trapping, museum collections, roadkill, line transect, and opportunistic records. Literature (peer-reviewed and grey literature) from Portuguese, Spanish and English were incorporated in this compilation. Most of the data set consists of detection data entries (n = 79,343; 79.7%) but also includes non-detection data (n = 20,262; 20.3%). Of those, 43.3% also include count data (n = 43,151). The information available in NEOTROPICAL CARNIVORES will contribute to macroecological, ecological, and conservation questions in multiple spatio-temporal perspectives. As carnivores play key roles in trophic interactions, a better understanding of their distribution and habitat requirements are essential to establish conservation management plans and safeguard the future ecological health of Neotropical ecosystems. Our data paper, combined with other large-scale data sets, has great potential to clarify species distribution and related ecological processes within the Neotropics. There are no copyright restrictions and no restriction for using data from this data paper, as long as the data paper is cited as the source of the information used. We also request that users inform us of how they intend to use the data