Charge regulation mechanism in end-tethered weak polyampholytes.

Weak polyampholytes, containing oppositely charged dissociable groups, are expected to be responsive to changes in ionic conditions. Here, we determine structural and thermodynamic properties, including the charged groups' degrees of dissociation, of end-tethered weak polyampholyte layers as a function of salt concentration, pH, and the solvent quality. For diblock weak polyampholytes grafted by their acidic blocks, we find that the acidic monomers increase their charge while the basic monomers decrease their charge with decreasing salt concentration for pH values less than the pKa value of both monomers and vice versa when the pH > pKa. This complex charge regulation occurs because the electrostatic attraction between oppositely charged blocks is stronger than the repulsion between monomers with the same charge in both good and poor solvents when the screening by salt ions is weak. This is evidenced by the retraction of the top block into the bottom layer. In the case of poor solvent conditions to the basic block (the top block), we find lateral segregation of basic monomers into micelles, forming a two-dimensional hexagonal pattern on the surface at intermediate and high pH values for monovalent salt concentrations from 0.01 to 0.1 M. When the solvent is poor to both blocks, we find lateral segregation of the grafted acidic block into lamellae with longitudinal undulations of low and high acidic monomer density. By exploiting weak block polyampholytes, our work expands the parameter space for creating responsive surfaces stable over a wide range of pH and salt concentration.

Adsorption and insertion of polyarginine peptides into membrane pores: The trade-off between electrostatics, acid-base chemistry and pore formation energy.

The mechanism that arginine-rich cell penetrating peptides (ARCPPs) use to translocate lipid membranes is not entirely understood. In the present work, we develop a molecular theory that allows to investigate the adsorption and insertion of ARCPPs on membranes bearing hydrophilic pores. This method accounts for size, shape, conformation, protonation state and charge distribution of the peptides; it also describes the state of protonation of acidic membrane lipids. We present a systematic investigation of the effect of pore size, peptide concentration and sequence length on the extent of peptide adsorption and insertion into the pores. We show that adsorption on the intact (non-porated) lipid membrane plays a key role on peptide translocation. For peptides shorter than nona-arginine, adsorption on the intact membrane increases significantly with chain length, but it saturates for longer peptides. However, this adsorption behavior only occurs at relatively low peptide concentrations; increasing peptide concentration favors adsorption of the shorter molecules. Adsorption of longer peptides increases the intact membrane negative charge as a result of further deprotonation of acidic lipids. Peptide insertion into the pores depends non-monotonically on pore radius, which reflects the short range nature of the effective membrane-peptide interactions. The size of the pore that promotes maximum adsorption depends on the peptide chain length. Peptide translocation is a thermally activated process, so we complement our thermodynamic approach with a simple kinetic model that allows to rationalize the ARCPPs translocation rate in terms of the free energy gain of adsorption, and the energy cost of creating a transmembrane pore with peptides in it. Our results indicate that strategies to improve translocation efficiency should focus on enhancing peptide adsorption.

13Check_RNA: a tool to evaluate 13C chemical shift assignments of RNA.

Motivation: Chemical shifts (CS) are an important source of structural information of macromolecules such as RNA. In addition to the scarce availability of CS for RNA, the observed values are prone to errors due to a wrong re-calibration or miss assignments. Different groups have dedicated their efforts to correct CS systematic errors on RNA. Despite this, there are not automated and freely available algorithms for evaluating the referencing of RNA 13 C CS before their deposition to the BMRB or re-reference already deposited CS with systematic errors. Results: Based on an existent method we have implemented an open source python module to correct 13 C CS (from here on 13Cexp) systematic errors of RNAs and then return the results in 3 formats including the nmrstar one. Availability and implementation: This software is available on GitHub at https://github.com/BIOS-IMASL/13Check_RNA under a MIT license. Supplementary information: Supplementary data are available at Bioinformatics online.

The Global Relationship between Chromatin Physical Topology, Fractal Structure, and Gene Expression.

Most of what we know about gene transcription comes from the view of cells as molecular machines: focusing on the role of molecular modifications to the proteins carrying out transcriptional reactions at a loci-by-loci basis. This view ignores a critical reality: biological reactions do not happen in an empty space, but in a highly complex, interrelated, and dense nanoenvironment that profoundly influences chemical interactions. We explored the relationship between the physical nanoenvironment of chromatin and gene transcription in vitro. We analytically show that changes in the fractal dimension, D, of chromatin correspond to simultaneous increases in chromatin accessibility and compaction heterogeneity. Using these predictions, we demonstrate experimentally that nanoscopic changes to chromatin D within thirty minutes correlate with concomitant enhancement and suppression of transcription. Further, we show that the increased heterogeneity of physical structure of chromatin due to increase in fractal dimension correlates with increased heterogeneity of gene networks. These findings indicate that the higher order folding of chromatin topology may act as a molecular-pathway independent code regulating global patterns of gene expression. Since physical organization of chromatin is frequently altered in oncogenesis, this work provides evidence pairing molecular function to physical structure for processes frequently altered during tumorigenesis.

Dynamics of dissipative self-assembly of particles interacting through oscillatory forces.

Dissipative self-assembly is the formation of ordered structures far from equilibrium, which continuously uptake energy and dissipate it into the environment. Due to its dynamical nature, dissipative self-assembly can lead to new phenomena and possibilities of self-organization that are unavailable to equilibrium systems. Understanding the dynamics of dissipative self-assembly is required in order to direct the assembly to structures of interest. In the present work, Brownian dynamics simulations and analytical theory were used to study the dynamics of self-assembly of a mixture of particles coated with weak acids and bases under continuous oscillations of the pH. The pH of the system modulates the charge of the particles and, therefore, the interparticle forces oscillate in time. This system produces a variety of self-assembled structures, including colloidal molecules, fibers and different types of crystalline lattices. The most important conclusions of our study are: (i) in the limit of fast oscillations, the whole dynamics (and not only those at the non-equilibrium steady state) of a system of particles interacting through time-oscillating interparticle forces can be described by an effective potential that is the time average of the time-dependent potential over one oscillation period; (ii) the oscillation period is critical to determine the order of the system. In some cases the order is favored by very fast oscillations while in others small oscillation frequencies increase the order. In the latter case, it is shown that slow oscillations remove kinetic traps and, thus, allow the system to evolve towards the most stable non-equilibrium steady state.

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.

Electrostatic unfolding and interactions of albumin driven by pH changes: a molecular dynamics study.

A better understanding of protein aggregation is bound to translate into critical advances in several areas, including the treatment of misfolded protein disorders and the development of self-assembling biomaterials for novel commercial applications. Because of its ubiquity and clinical potential, albumin is one of the best-characterized models in protein aggregation research; but its properties in different conditions are not completely understood. Here, we carried out all-atom molecular dynamics simulations of albumin to understand how electrostatics can affect the conformation of a single albumin molecule just prior to self-assembly. We then analyzed the tertiary structure and solvent accessible surface area of albumin after electrostatically triggered partial denaturation. The data obtained from these single protein simulations allowed us to investigate the effect of electrostatic interactions between two proteins. The results of these simulations suggested that hydrophobic attractions and counterion binding may be strong enough to effectively overcome the electrostatic repulsions between the highly charged monomers. This work contributes to our general understanding of protein aggregation mechanisms, the importance of explicit consideration of free ions in protein solutions, provides critical new insights about the equilibrium conformation of albumin in its partially denatured state at low pH, and may spur significant progress in our efforts to develop biocompatible protein hydrogels driven by electrostatic partial denaturation.

Born energy, acid-base equilibrium, structure and interactions of end-grafted weak polyelectrolyte layers.

This work addresses the effect of the Born self-energy contribution in the modeling of the structural and thermodynamical properties of weak polyelectrolytes confined to planar and curved surfaces. The theoretical framework is based on a theory that explicitly includes the conformations, size, shape, and charge distribution of all molecular species and considers the acid-base equilibrium of the weak polyelectrolyte. Namely, the degree of charge in the polymers is not imposed but it is a local varying property that results from the minimization of the total free energy. Inclusion of the dielectric properties of the polyelectrolyte is important as the environment of a polymer layer is very different from that in the adjacent aqueous solution. The main effect of the Born energy contribution on the molecular organization of an end-grafted weak polyacid layer is uncharging the weak acid (or basic) groups and consequently decreasing the concentration of mobile ions within the layer. The magnitude of the effect increases with polymer density and, in the case of the average degree of charge, it is qualitatively equivalent to a small shift in the equilibrium constant for the acid-base equilibrium of the weak polyelectrolyte monomers. The degree of charge is established by the competition between electrostatic interactions, the polymer conformational entropy, the excluded volume interactions, the translational entropy of the counterions and the acid-base chemical equilibrium. Consideration of the Born energy introduces an additional energetic penalty to the presence of charged groups in the polyelectrolyte layer, whose effect is mitigated by down-regulating the amount of charge, i.e., by shifting the local-acid base equilibrium towards its uncharged state. Shifting of the local acid-base equilibrium and its effect on the properties of the polyelectrolyte layer, without considering the Born energy, have been theoretically predicted previously. Account of the Born energy leads to systematic, but in general small, corrections to earlier theoretical predictions describing the behavior of weak polyelectrolyte layers. However, polyelectrolyte uncharging results in a decrease in the concentration of counterions and inclusion of the Born Energy can result in a substantial decrease of the counterion concentration. The effect of considering the Born energy contribution is explored for end-grafted weak polyelectrolyte layers by calculating experimental observables which are known to depend on the presence of charges within the polyelectrolyte layer: inclusion of the Born energy contribution leads to a decrease in the capacitance of polyelectrolyte-modified electrodes, a decrease of conductivity of polyelectrolyte-modified nanopores and an increase in the repulsion exerted by a planar polyelectrolyte layer confined by an opposing wall.

Adsorption of acid and polymer coated nanoparticles: a statistical thermodynamics approach.

A molecular theoretical description is developed to describe the adsorption of nanoparticles (NPs) that are coated with polymers and functionalized with (surface) acid groups. Results are presented for the adsorption onto both negatively and positively charged surfaces as a function of pH and salt concentration, polymer coating, and NP size. An important finding is that nanoparticles that are coated with weak charge regulating acid molecules such as citric acid develop an asymmetric charge distribution close to a charged surface, due to their finite size. Depending on the sign of the surface charge of the adsorbing surface, a nanoparticle close to the surface either gains more charge or loses charge compared to its "bulk" degree of charge. This in turn influences the amount of NPs that adsorb. The effect of adsorption of negatively charged NPs onto a positively charged surface shows a nonmonotonical variation with pH. The described charging mechanism reveals that details such as size of the NP and acid distribution on the NP need to be considered to provide an accurate understanding of the adsorption process.

How to Optimize Binding of Coated Nanoparticles: Coupling of Physical Interactions, Molecular Organization and Chemical State.

One of the key challenges in the development of nano carriers for drug delivery and imaging is the design of a system that selectively binds to target cells. A common strategy is to coat the delivery device with specific ligands that bind strongly to overexpressed receptors. However such devices are usually unable to discriminate between receptors found on benign and malignant cells. We demonstrate, theoretically, how one can achieve enhanced binding to target cells by using multiple physical and chemical interactions. We study the effective interactions between a polymer decorated nano micelle or nanoparticle with three types of model lipid membranes that differ in the composition of their outer leaflet. They are: i) lipid membranes with overexpressed receptors, ii) membranes with a given fraction of negatively charged lipids and iii) membranes with both overexpressed receptors and negatively charged lipids. The coating contains a mixtures of two short polymers, one neutral for protection and the other a polybase with a functional end-group to optimize specific binding with the overexpressed receptors and electrostatic interactions with charged lipid head-groups. The strength of the binding for the combined system is much larger than the sum of the independent electrostatic or specific interactions binding. We find a range of distances where the addition of two effective repulsive interactions become an attraction in the combined case. The changes in the strength and shape of the effective interaction are due to the coupling that exists between molecular organization, physical interactions and chemical state, e.g., protonation. The predictions provide guidelines for the design of carrier devices for targeted drug and nanoparticle delivery and give insight in the competing and highly non-additive nature of the different effective interactions in nanoscale systems in constrained environments that are ubiquitous in synthetic and biological systems.

Structure of supercooled water in clusters and bulk and its relation to the two-state picture of water: results from the TIP4P-ice model.

The structure of water clusters (H(2)O)(n) (n = 40-200) and bulk water were examined by molecular dynamics simulations using the TIP4P-ice water model. The analysis of the low-temperature structures in terms of the local structure index (LSI) showed a bimodal distribution. This finding supports the two-state picture derived from the analysis of the inherent dynamics of bulk SPC/E water. The water molecules at the outer interface of the coldest clusters are more structured than those in the inner core. The geometrical constraint of the interface forces the surface molecules to lose one neighbor and adopt a local angular distribution of hydrogen bonds resembling that found in the basal plane of ice Ih.

Stability and liquid-liquid phase separation in mixed saturated lipid bilayers.

The phase stability of a fluid lipid bilayer composed of a mixture of DC(18)PC, (DSPC), and a shorter DCn(s) PC, with n(s) from 8 to 17, has been studied using a self-consistent field theory that explicitly includes molecular details and configurational properties of the lipid molecules. Phase separation between two liquid phases was found when there was a sufficient mismatch between the hydrophobic thicknesses of the two bilayers composed entirely of one component or the other. This occurs when n(s) 12, we observe that the effect of the shorter lipid is to increase the susceptibility of the system to fluctuations in the concentration. This is of interest, given that a common motif for the anchoring of proteins to the plasma membrane is via a myristoyl chain, that is, one with 14 carbons.

Ligand-receptor interactions between surfaces: the role of binary polymer spacers.

The interactions between a receptor-modified planar surface and a surface grafted with a bimodal polymer layer, where one of the polymer species is ligand functionalized, are studied using a molecular theory. The effects of changing the binding energy of the ligand-receptor pair, the polymer surface coverage, the composition, and molecular weight of both the unfunctionalized and ligand functionalized polymers on the interactions between the surfaces are investigated. Our findings show that bridging exists between the surfaces including when the molecular weight of the ligand-bearing polymer is smaller than that of the unfunctionalized polymer, even though the ligand is initially buried within the polymer layer. The distance at which the surfaces bind depends only on the molecular weight of the ligand-modified polymer, while the strength of the interaction at a given surface separation can be tuned by changing the molecular weight of the polymers, the total polymer surface coverage, and the fraction of ligated polymers. The composition of the bimodal layer alters the structure of the polymer layer, thereby influencing the strength of the steric repulsions between the surfaces. Our theoretical results show good agreement with experimental data. The present theoretical study can be used as guidelines for the design of surfaces with tailored abilities for tunning the binding strength and surface-ligand separation distances for polymer-grafted surfaces bearing specific targeting ligands.

The role of hydrogen bonding in tethered polymer layers.

A molecular theory to study the properties of end-tethered polymer layers, in which the polymers have the ability to form hydrogen bonds with water, is presented. The approach combines the ideas of the single-chain mean-field theory to treat tethered layers with the approach of Dormidontova (Macromolecules, 2002, 35, 987.) to include hydrogen bonds. The generalization includes the consideration of position-dependent polymer-water and water-water hydrogen bonds. The theory is applied to model poly(ethylene oxide) (PEO), and the predictions are compared with equivalent polymer layers that do not form hydrogen bonds. It is found that increasing the temperature lowers the solubility of the PEO and results in a collapse of the layer at high enough temperatures. The properties of the layer and their temperature dependence are shown to be the result of the coupling between the conformational entropy of the chains, the ability of the polymer to form hydrogen bonds, and the intermolecular interactions. The structural and thermodynamic properties of the PEO layers, such as the lateral pressure-area isotherms and polymer chemical potentials, are studied as a function of temperature and type of tethering surface. The possibility of phase separation of the PEO layer at high enough temperature is predicted due to the reduced solubility induced by breaking of polymer-water hydrogen bonds. A discussion of the advantages and limitations of the theory, together with how to apply the approach to different hydrogen-bonding polymers, is presented.

Stability and phase separation in mixed monopolar lipid/bolalipid layers.

The phase stability of a fluid lipid layer that is a mixture of conventional monopolar lipids and C20 bipolar bolalipids was studied using a mean field theory that explicitly includes molecular details and configurational properties of the lipid molecules. The effect of changing the fraction of bolalipids, as well as the length of the hydrocarbon chain of the monopolar lipids, was probed. A phase separation between two liquid lipid phases was found when a mismatch exists in the optimal hydrophobic thicknesses of the pure bolalipid and monopolar lipid layers. The lipid mixture phase separates into a thin bolalipid-rich layer and a thicker monopolar-rich layer. The thin membrane phase is mainly composed of transmembrane bolalipid molecules whose polar heads are positioned at opposite membrane-water interfaces. In the monopolar lipid-rich phase, bolalipids are the minor component and most of them assume a looping configuration where both headgroups are present at the same membrane-water interface. For mixed layers that form a single lipid phase across all bolalipid concentrations, the hairpin-transmembrane ratio strongly depends on the hydrocarbon chain length of the monopolar lipid and the bolalipid concentration. The C-D bond order parameters of the different species have been calculated. Our findings suggest that the concentration-dependent phase transition should be experimentally observable by measuring of the order parameters through quadrupolar splitting experiments. The driving force for the phase separation in the monopolar lipid/bolalipid mixture is the packing mismatch between hydrophobic regions of the monopolar lipid hydrocarbon chains and the membrane-spanning bolalipid chains. The results from the molecular theory may be useful in the design of stable lipid layers for integral membrane protein sensing.

Phase behavior and charge regulation of weak polyelectrolyte grafted layers.

The stability of weak polyelectrolytes end grafted to a planar surface has been studied with a molecular theory. The effective quality of the solvent is found to depend on the interplay between polymer grafting density, acid-base equilibrium, and salt concentration. Our results reveal that increasing salt concentration results in a thermodynamically more stable layer. This reverse salt effect is due to the competition between the solvent quality and the dual role of the ionic strength in screening the electrostatic interactions (reducing stability with increasing salt concentration), and regulating the charge on the polymer (increasing charge with increasing salt concentration). Grafted weak polyelectrolyte layers are found to be thermodynamically unstable at intermediate surface coverages. Additionally, it is established that the increased solubility of the layer at low surface coverage is due to the relatively large charge of the grafted polymers. The range of stability of the film with regard to polymer surface coverage, temperature, bulk pH and salt concentration is demonstrated.

A microscopic model calculation of the phase diagram of ternary mixtures of cholesterol and saturated and unsaturated phospholipids.

The authors solved a microscopic model that describes mixtures of a saturated phospholipid, an unsaturated phospholipid, and cholesterol. The method employed was the self-consistent field approximation. The model was capable of producing several classes of phase diagram, but only one of them showed a liquid-liquid coexistence region. The phospholipids in the cholesterol-rich liquid are more ordered than those in the cholesterol-poor liquid. Within this model, coexistence of two liquids in the ternary system is intimately tied to such coexistence in the binary cholesterol-saturated phospholipid system.

Stability and phase separation in mixed self-assembled monolayers.

Recent single molecule experiments rely on the self-assembly of binary mixtures of molecules with very different properties in a stable monolayer, in order to probe the characteristics of the interspersed molecule of interest in a controlled environment. However, not all efforts at coassembly have been successful. To study systematically the behavior of such systems, we derive the free energy of multicomponent systems of rods with configurational degrees of freedom, localized on a surface, starting from a generalized van der Waals description. The molecular parameters are determined by geometrical factors of the molecules and by their pairwise van der Waals interactions computed using molecular mechanics. Applying the model to two experimental situations, we are able to use the stability analysis of the respective mixtures to explain why coassembly was successful in one set of experiments (carotene and alkanethiol) and not in another (benzenethiols and alkanethiol). We outline general guidelines for suitable choices of molecules to achieve coassembly.

Phase diagram of a ternary mixture of cholesterol and saturated and unsaturated lipids calculated from a microscopic model.

We employ a molecular model to study a ternary mixture of saturated lipid, with tails of 16 carbons, a monounsaturated lipid with tails of 18 carbons, and cholesterol. The model, solved within mean-field theory, produces several forms of phase diagrams depending upon the relative strengths of interactions, but only one that shows the coexistence of two liquid phases observed in experiment. The lipids in the phase rich in cholesterol are more ordered than those in the other. The binary cholesterol, saturated lipid system also exhibits liquid, liquid coexistence.

Controlled release of proteins from polymer-modified surfaces.

The ability to control the rate of adsorption and desorption of proteins from surfaces is studied by using a molecular theory. We show how changing the chemical structure and charge of short linear and branched grafted polymers to an electrode surface can be used to promote fast adsorption of charged proteins on a time scale of seconds and control the desorption in a time scale ranging from milliseconds to hours. The optimal controlled release is found from the interplay of electrostatic attractions at short distances from the surface and the proper electrostatic and steric repulsive barrier at distances from the surfaces larger than the proteins' size. The implications of our results to the design of controlled-release devices is discussed.