Thermodynamic extent of counterion release upon binding oligolysines to single-stranded nucleic acids

A DNA condensation code for linker histones

Linker histones play an essential role in chromatin packaging by facilitating compaction of the 11-nm fiber of nucleosomal "beads on a string." The result is a heterogeneous condensed state with local properties that range from dynamic, irregular, and liquid-like to stable and regular structures (the 30-nm fiber), which in turn impact chromatin-dependent activities at a fundamental level. The properties of the condensed state depend on the type of linker histone, particularly on the highly disordered C-terminal tail, which is the most variable region of the protein, both between species, and within the various subtypes and cell-type specific variants of a given organism. We have developed an in vitro model system comprising linker histone tail and linker DNA, which although very minimal, displays surprisingly complex behavior, and is sufficient to model the known states of linker histone-condensed chromatin: disordered "fuzzy" complexes ("open" chromatin), dense liquid-like assemblies (dynamic condensates), and higher-order structures (organized 30-nm fibers). A crucial advantage of such a simple model is that it allows the study of the various condensed states by NMR, circular dichroism, and scattering methods. Moreover, it allows capture of the thermodynamics underpinning the transitions between states through calorimetry. We have leveraged this to rationalize the distinct condensing properties of linker histone subtypes and variants across species that are encoded by the amino acid content of their C-terminal tails. Three properties emerge as key to defining the condensed state: charge density, lysine/arginine ratio, and proline-free regions, and we evaluate each separately using a strategic mutagenesis approach.

Macromolecular condensation organizes nucleolar sub-phases to set up a pH gradient

Nucleoli are multicomponent condensates defined by coexisting sub-phases. We identified distinct intrinsically disordered regions (IDRs), including acidic (D/E) tracts and K-blocks interspersed by E-rich regions, as defining features of nucleolar proteins. We show that the localization preferences of nucleolar proteins are determined by their IDRs and the types of RNA or DNA binding domains they encompass. In vitro reconstitutions and studies in cells showed how condensation, which combines binding and complex coacervation of nucleolar components, contributes to nucleolar organization. D/E tracts of nucleolar proteins contribute to lowering the pH of co-condensates formed with nucleolar RNAs in vitro. In cells, this sets up a pH gradient between nucleoli and the nucleoplasm. By contrast, juxta-nucleolar bodies, which have different macromolecular compositions, featuring protein IDRs with very different charge profiles, have pH values that are equivalent to or higher than the nucleoplasm. Our findings show that distinct compositional specificities generate distinct physicochemical properties for condensates.

Single molecule technique unveils the role of electrostatic interactions in ssDNA-gp32 molecular complex stability

The exploration of single-strand DNA-binding protein (SSB)-ssDNA interactions and their crucial roles in essential biological processes lagged behind other types of protein-nucleic acid interactions, such as protein-dsDNA and protein-RNA interactions. The ssDNA binding protein gene product 32 (gp32) of the T4 bacteriophage is a central integrating component of the replication complex that must continuously bind to and unbind from transiently exposed template strands during the DNA synthesis. To gain deeper insights into the electrostatic conditions influencing the stability of the ssDNA-gp32 molecular complex, like the salt concentration or some metal ions proven to specifically bind to gp32, we employed a method that performs rapid measurements of the DNA-protein stability using an α-Hemolysin (α-HL) protein nanopore. We indirectly probed the stability of a protein-nucleic acid complex by monitoring the dissociation process between the gp32 protein and the ssDNA molecular complex in single-molecular electrophysiology experiments, but also through fluorescence spectroscopy techniques. We have shown that the complex is more stable in 0.5 M KCl solution than in 2 M KCl solution and that the presence of Zn2+ ions further increases this stability for any salt used in the present study. This method can be applied to other nucleic acid-protein molecular complexes, as well as for an accurate determination of the drug-protein carrier stability.

Molecular Structure and Conformation of Biodegradable Water-Soluble Polymers Control Adsorption and Transport in Model Soil Mineral Systems

Water-soluble polymers (WSPs) are used in diverse applications, including agricultural formulations, that can result in the release of WSPs to soils. WSP biodegradability in soils is desirable to prevent long-term accumulation and potential associated adverse effects. In this work, we assessed adsorption of five candidate biodegradable WSPs with varying chemistry, charge, and polarity characteristics (i.e., dextran, diethylaminoethyl dextran, carboxymethyl dextran, polyethylene glycol monomethyl ether, and poly-l-lysine) and of one nonbiodegradable WSP (poly(acrylic acid)) to sand and iron oxide-coated sand particles that represent important soil minerals. Combined adsorption studies using solution-depletion measurements, direct surface adsorption techniques, and column transport experiments over varying solution pH and ionic strengths revealed electrostatics dominating interactions of charged WSPs with the sorbents as well as WSP conformations and packing densities in the adsorbed states. Hydrogen bonding controls adsorption of noncharged WSPs. Under transport in columns, WSP adsorption exhibited fast and slow kinetic adsorption regimes with time scales of minutes to hours. Slow adsorption kinetics in soil may lead to enhanced transport but also shorter lifetimes of biodegradable WSPs, assuming more rapid biodegradation when dissolved than adsorbed. This work establishes a basis for understanding the coupled adsorption and biodegradation dynamics of biodegradable WSPs in agricultural soils.

Drug Encapsulation via Peptide-Based Polyelectrolyte Complexes

Peptide-based polyelectrolyte complexes are biocompatible materials that can encapsulate molecules with different polarities due to their ability to be precisely designed. Here we use UV-Vis spectroscopy, fluorescence microscopy, and infrared spectroscopy to investigate the encapsulation of model drugs, doxorubicin (DOX) and methylene blue (MB) using a series of rationally designed polypeptides. For both drugs, we find an overall higher encapsulation efficiency with sequences that have higher charge density, highlighting the importance of ionic interactions between the small molecules and the peptides. However, comparing molecules with the same charge density, illustrated that the most hydrophobic sequence pairs had the highest encapsulation of both DOX and MB molecules. The phase behavior and stability of DOX-containing complexes did not change compared to the complexes without drugs. However, MB encapsulation caused changes in the stabilities of the complexes. The sequence pair with the highest charge density and hydrophobicity had the most dramatic increase in stability, which coincided with a phase change from liquid to solid. This study illustrates how multiple types of molecular interactions are required for efficient encapsulation of poorly soluble drugs and provides insights into the molecular design of delivery carriers.

Polysaccharide-based polyampholyte complex formation: Investigating the role of intra-chain interactions

The difference in inter-chain and intra-chain electrostatic attraction was investigated in polyelectrolyte and polyampholyte electrostatic complex formation. Three polymers with similar backbone molecular structures including chitosan (Ch) polycation, carboxymethyl cellulose (CMCe) polyanion, and carboxymethyl chitosan (CMCh) polyampholyte were used for this purpose. The turbidimetric, water content, and rheological measurements for polyampholyte self-complex showed more dependence on the ionic strength rather than the polyelectrolyte one. The degree of dissociation (α), dissociation constant (pKa), and intrinsic persistence length were calculated by applying the Katchalsky-Lifson model to potentiometric data. We studied the gyration radii as a function of Debye length and observed the polyampholyte chain contractions due to the intra-chain electrostatic attractions, which minimize the entropic gain of the inter-chain complex formation. This is in accordance with the decrease in pKa by α_c for CMCh which is the opposite of that for the Ch and CMCe samples. We also found that the polyampholyte has less intrinsic and electrostatic persistence length compared with both polyanion and polycation with similar chain structures indicating the impact of the inter-chain electrostatic interaction on the complex properties. This study deepens our insight about the behavior of CMCh and the nature of difference between CMCh and Ch/CMCe electrostatic complexes.

Microfluidic dual picoinjection based encapsulation of hemoglobin in alginate microcapsules reinforced by a poly(L-lysine)-g-poly(ethylene glycol)

Hemoglobin (Hb) encapsulation inside polysaccharide hydrogels has been considered a possible red blood cell (RBC) surrogate in transfusiology. Here we report on the microfluidic dual picoinjection assisted synthesis of Hb encapsulated alginate-poly(L-lysine)-g-poly(ethylene glycol) beads. This process is realized by the on-chip injections of blended Hb alginate solutions in emulsified aqueous calcium chloride (CaCl₂) droplets followed by a subsequent injection of an aqueous PLL-g-PEG into each emulsified aqueous droplet. The proposed fabrication approach was realized using a flow-focusing and two picoinjection sites in a single PDMS device. Aqueous CaCl₂ solution was emulsified and infused with Hb-alginate solution as the squeezed droplet passed through the first picoinjection site. The injection of PLL-g-PEG to reinforce the microgel and minimize the protein leaching was realized in the second picoinjection site located downstream from the first in the same microfluidic channel. In this process, monodisperse Hb-alginate-PLL-g-PEG particles with a diameter around the size of RBCs (9 μm) were obtained with around 80% of the 7.5 mg ml^-1 Hb included in the injected aqueous alginate retaining in the obtained microparticles. Microparticles with Hb loading (32.8 pg per bead) and retention (28.8 pg per bead) over a week of storage at 4 °C are in accordance with the average amount of Hb per RBC. The Hb-alginate-PLL-g-PEG microbeads fabricated in the size range of RBCs are significant for further exploration.

Characterization of the Interaction of Polymeric Micelles with siRNA: A Combined Experimental and Molecular Dynamics Study

The simulation of large molecular systems remains a daunting challenge, which justifies the exploration of novel methodologies to keep computers as an ideal companion tool for everyday laboratory work. Whole micelles, bigger than 20 nm in size, formed by the self-assembly of hundreds of copolymers containing more than 50 repeating units, have until now rarely been simulated, due to a lack of computational power. Therefore, a flexible amphiphilic triblock copolymer (mPEG45-α-PLL10-PLA25) containing a total of 80 repeating units, has been emulated and synthesized to embody compactified nanoconstructs of over 900 assembled copolymers, sized between 80 and 100 nm, for siRNA complexing purposes. In this study, the tailored triblock copolymers containing a controlled number of amino groups, were used as a support model to address the binding behavior of STAT3-siRNA, in the formation of micelleplexes. Since increasingly complex drug delivery systems require an ever more optimized physicochemical characterization, a converging description has been implemented by a combination of experimentation and computational simulations. The computational data were advantageous in allowing for the assumption of an optimal N/P ratio favoring both conformational rigidifications of STAT3-siRNA with low competitive phenomena at the binding sites of the micellar carriers. These calculations were consistent with the experimental data showing that an N/P ratio of 1.5 resulted in a sufficient amount of complexed STAT3-siRNA with an electrical potential at the slipping plane of the nanopharmaceuticals, close to the charge neutralization.

Cooperative kinetics of ligand binding to linear polymers

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Cooperative kinetic equation for large ligands binding to long polymers.

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Cooperativity in general affects binding and release rates.

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Appropriate counting of the available binding sites for a ligand to a linear polymer.

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Positive cooperativity increases polymer coverage by the ligand.

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Large ligand size reduces cooperativity effects.

Ligands change the chemical and mechanical properties of polymers. In particular, single strand binding protein (SSB) non-specifically bounds to single-stranded DNA (ssDNA), modifying the ssDNA stiffness and the DNA replication rate, as recently measured with single-molecule techniques. SSB is a large ligand presenting cooperativity in some of its binding modes. We aim to develop an accurate kinetic model for the cooperative binding kinetics of large ligands. Cooperativity accounts for the changes in the affinity of a ligand to the polymer due to the presence of another bound ligand. Large ligands, attaching to several binding sites, require a detailed counting of the available binding possibilities. This counting has been done by McGhee and von Hippel to obtain the equilibrium state of the ligands-polymer complex. The same procedure allows to obtain the kinetic equations for the cooperative binding of ligands to long polymers, for all ligand sizes. Here, we also derive approximate cooperative kinetic equations in the large ligand limit, at the leading and next-to-leading orders. We found cooperativity is negligible at the leading-order, and appears at the next-to-leading order. Positive cooperativity (increased affinity) can be originated by increased binding affinity or by decreased release affinity, implying different kinetics. Nevertheless, the equilibrium state is independent of the origin of cooperativity and only depends on the overall increase in affinity. Next-to-leading approximation is found to be accurate, particularly for small cooperativity. These results allow to understand and characterize relevant ligand binding processes, as the binding kinetics of SSB to ssDNA, which has been reported to affect the DNA replication rate for several SSB-polymerase pairs.

Intrinsically disordered protein regions and phase separation: sequence determinants of assembly or lack thereof

Intrinsically disordered protein regions (IDRs) - regions that do not fold into a fixed three-dimensional structure but instead exist in a heterogeneous ensemble of conformations - have recently entered mainstream cell biology in the context of liquid-liquid phase separation (LLPS). IDRs are frequently found to be enriched in phase-separated compartments. Due to this observation, the presence of an IDR in a protein is frequently assumed to be diagnostic of its ability to phase separate. In this review, we clarify the role of IDRs in biological assembly and explore the physical principles through which amino acids can confer the attractive molecular interactions that underlie phase separation. While some disordered regions will robustly drive phase separation, many others will not. We emphasize that rather than 'disorder' driving phase separation, multivalency drives phase separation. As such, whether or not a disordered region is capable of driving phase separation will depend on the physical chemistry encoded within its amino acid sequence. Consequently, an in-depth understanding of that physical chemistry is a prerequisite to make informed inferences on how and why an IDR may be involved in phase separation or, more generally, in protein-mediated intermolecular interactions.

Deciphering the Role of π-Interactions in Polyelectrolyte Complexes Using Rationally Designed Peptides

Electrostatic interactions, and specifically π-interactions play a significant role in the liquid-liquid phase separation of proteins and formation of membraneless organelles/or biological condensates. Sequence patterning of peptides allows creating protein-like structures and controlling the chemistry and interactions of the mimetic molecules. A library of oppositely charged polypeptides was designed and synthesized to investigate the role of π-interactions on phase separation and secondary structures of polyelectrolyte complexes. Phenylalanine was chosen as the π-containing residue and was used together with lysine or glutamic acid in the design of positively or negatively charged sequences. The effect of charge density and also the substitution of fluorine on the phenylalanine ring, known to disrupt π-interactions, were investigated. Characterization analysis using MALDI-TOF mass spectroscopy, H NMR, and circular dichroism (CD) confirmed the molecular structure and chiral pattern of peptide sequences. Despite an alternating sequence of chirality previously shown to promote liquid-liquid phase separation, complexes appeared as solid precipitates, suggesting strong interactions between the sequence pairs. The secondary structures of sequence pairs showed the formation of hydrogen-bonded structures with a β-sheet signal in FTIR spectroscopy. The presence of fluorine decreased hydrogen bonding due to its inhibitory effect on π-interactions. π-interactions resulted in enhanced stability of complexes against salt, and higher critical salt concentrations for complexes with more π-containing amino acids. Furthermore, UV-vis spectroscopy showed that sequences containing π-interactions and increased charge density encapsulated a small charged molecule with π-bonds with high efficiency. These findings highlight the interplay between ionic, hydrophobic, hydrogen bonding, and π-interactions in polyelectrolyte complex formation and enhance our understanding of phase separation phenomena in protein-like structures.

Interaction of Polyelectrolytes with Proteins: Quantifying the Role of Water

A theoretical model is presented for the free energy ΔGb of complex formation between a highly charged polyelectrolyte and a protein. The model introduced here comprises both the effect of released counterions and the uptake or release of water molecules during complex formation. The resulting expression for ΔGb is hence capable of describing the dependence of ΔGb on temperature as well as on the concentration of salt in the system: An increase of the salt concentration in the solution increases the activity of the ions and counterion release becomes less effective for binding. On the other hand, an increased salt concentration leads to the decrease of the activity of water in bulk. Hence, release of water molecules during complex formation will be more advantageous and lead to an increase of the magnitude of ΔGb and the binding constant. It is furthermore demonstrated that the release or uptake of water molecules is the origin of the marked enthalpy-entropy cancellation observed during complex formation of polyelectrolytes with proteins. The comparison with experimental data on complex formation between a synthetic (sulfated dendritic polyglycerol) and natural polyelectrolytes (DNA; heparin) with proteins shows full agreement with theory.

Osmotic-pressure-induced phase transition of a surfactant-DNA complex

We have studied the effect of osmotic pressure on complexes formed by DNA with the cationic surfactant cetyltrimethylammonium tosylate using small-angle x-ray scattering. Earlier studies have shown that these complexes exhibit three different phases depending on the DNA and surfactant concentrations in the solution. The hexagonal superlattice phase (H_{I,s}^{c}) is found to be corralled into the hexagonal phase (H_{I}^{c}) above a threshold osmotic pressure. We have also estimated the DNA to surfactant micelle stoichiometry of the complexes in the three phases using elemental analysis. Our results provide further support for the structures of these complexes proposed earlier based on small-angle x-ray scattering data.

Impact of Self-Association on the Architectural Properties of Bacterial Nucleoid Proteins

The chromosomal DNA of bacteria is folded into a compact body called the nucleoid, which is composed essentially of DNA (∼80%), RNA (∼10%), and a number of different proteins (∼10%). These nucleoid proteins act as regulators of gene expression and influence the organization of the nucleoid by bridging, bending, or wrapping the DNA. These so-called architectural properties of nucleoid proteins are still poorly understood. For example, the reason why certain proteins compact the DNA coil in certain environments but make the DNA more rigid instead in other environments is the subject of ongoing debates. Here, we address the question of the impact of the self-association of nucleoid proteins on their architectural properties and try to determine whether differences in self-association are sufficient to induce large changes in the organization of the DNA coil. More specifically, we developed two coarse-grained models of proteins, which interact identically with the DNA but self-associate differently by forming either clusters or filaments in the absence of the DNA. We showed through Brownian dynamics simulations that self-association of the proteins dramatically increases their ability to shape the DNA coil. Moreover, we observed that cluster-forming proteins significantly compact the DNA coil (similar to the DNA-bridging mode of H-NS proteins), whereas filament-forming proteins significantly increase the stiffness of the DNA chain instead (similar to the DNA-stiffening mode of H-NS proteins). This work consequently suggests that the knowledge of the DNA-binding properties of the proteins is in itself not sufficient to understand their architectural properties. Rather, their self-association properties must also be investigated in detail because they might actually drive the formation of different DNA-protein complexes.

Noncooperative thermodynamics and kinetic models of ligand binding to polymers: Connecting McGhee-von Hippel model with the Tonks gas model

Ligand binding to polymers modifies the physical and chemical properties of the polymers, leading to physical, chemical, and biological implications. McGhee and von Hippel obtained the equilibrium coverage as a function of the ligand affinity, through the computation of the possible binding sites for the ligand. Here, we complete this theory deriving the kinetic model for the ligand-binding dynamics and the associated equilibrium chemical potential, which turns out to be of the Tonks gas model type. At low coverage, the Tonks chemical potential becomes the Fermi chemical potential and even the ideal gas chemical potential. We also discuss kinetic models associated with these chemical potentials. These results clarify the kinetic models of ligand binding, their relations with the chemical potentials, and their range of validity. Our results highlight the inaccuracy of ideal and simplified kinetic approaches for medium and high coverages.

Recent progress in the science of complex coacervation

Complex coacervation is an associative, liquid-liquid phase separation that can occur in solutions of oppositely-charged macromolecular species, such as proteins, polymers, and colloids. This process results in a coacervate phase, which is a dense mix of the oppositely-charged components, and a supernatant phase, which is primarily devoid of these same species. First observed almost a century ago, coacervates have since found relevance in a wide range of applications; they are used in personal care and food products, cutting edge biotechnology, and as a motif for materials design and self-assembly. There has recently been a renaissance in our understanding of this important class of material phenomena, bringing the science of coacervation to the forefront of polymer and colloid science, biophysics, and industrial materials design. In this review, we describe the emergence of a number of these new research directions, specifically in the context of polymer-polymer complex coacervates, which are inspired by a number of key physical and chemical insights and driven by a diverse range of experimental, theoretical, and computational approaches.

How do DNA-bound proteins leave their binding sites? The role of facilitated dissociation

Dissociation of a protein from DNA is often assumed to be described by an off rate that is independent of other molecules in solution. Recent experiments and computational analyses have challenged this view by showing that unbinding rates (residence times) of DNA-bound proteins can depend on concentrations of nearby molecules that are competing for binding. This 'facilitated dissociation' (FD) process can occur at the single-binding site level via formation of a ternary complex, and can dominate over 'spontaneous dissociation' at low (submicromolar) concentrations. In the crowded intracellular environment FD introduces new regulatory possibilities at the level of individual biomolecule interactions.

Thermodynamic study of the effect of ions on the interaction between dengue virus NS3 helicase and single stranded RNA

Dengue virus nonstructural protein 3 (NS3) fulfills multiple essential functions during the viral replication and constitutes a prominent drug target. NS3 is composed by a superfamily-2 RNA helicase domain joined to a serine protease domain. Quantitative fluorescence titrations employing a fluorescein-tagged RNA oligonucleotide were used to investigate the effect of salts on the interaction between NS3 and single stranded RNA (ssRNA). We found a strong dependence of the observed equilibrium binding constant, K_obs, with the salt concentration, decreasing at least 7-fold for a 1-fold increase on cation concentration. As a result of the effective neutralization of ~10 phosphate groups, binding of helicase domain of NS3 to ssRNA is accompanied by the release of 5 or 7 monovalent cations from an oligonucleotide or a polynucleotide, respectively and of 3 divalent cations from the same oligonucleotide. Such estimates are not affected by the type of cation, either monovalent (KCl, NaCl and RbCl) or divalent (MgCl₂ and CaCl₂), nor by the presence of the protease domain or the fluorescein label. Combined effect of mono and divalent cations was well described by a simple equilibrium binding model which allows to predict the values of K_obs at any concentration of cations.

Disordered domains in chromatin-binding proteins

Chromatin comprises proteins, DNA and RNA, and its function is to condense and package the genome in a way that allows the necessary transactions such as transcription, replication and repair to occur in a highly organised and regulated manner. The packaging of chromatin is often thought of in a hierarchical fashion starting from the most basic unit of DNA packaging, the nucleosome, to the condensation of nucleosomal 'beads on a string' by linker histones to form the 30-nm fibre and eventually large chromatin domains. However, a picture of a more heterogeneous, dynamic and liquid-like assembly is emerging, in which intrinsically disordered proteins (IDPs) and proteins containing intrinsically disordered regions (IDRs) play a central role. Disorder features at all levels of chromatin organisation, from the histone tails, which are sites of extensive post-translational modification (PTM) that change the fate of the underlying genomic information, right through to transcription hubs, and the recently elucidated roles of IDPs and IDRs in the condensation of large regions of the genome through liquid-liquid phase separation.

Role of Associative Charging in the Entropy-Energy Balance of Polyelectrolyte Complexes

Polyelectrolytes may be classified into two primary categories (strong and weak) depending on how their charge state responds to the local environment. Both of these find use in many applications, including drug delivery, gene therapy, layer-by-layer films, and fabrication of ion filtration membranes. The mechanism of polyelectrolyte complexation is, however, still not completely understood, though experimental investigations suggest that entropy gain due to release of counterions is the key driving force for strong polyelectrolyte complexation. Here we perform a comprehensive thermodynamic investigation through coarse-grained molecular simulations permitting us to calculate the free energy of complex formation. Importantly, our expanded-ensemble methods permit the explicit separation of energetic and entropic contributions to the free energy. Our investigations indicate that entropic contributions indeed dominate the free energy of complex formation for strong polyelectrolytes, but are less important than energetic contributions when weak electrostatic coupling or weak polyelectrolytes are present. Our results provide a new view of the free energy of polyelectrolyte complex formation driven by polymer association, which should also arise in systems with large charge spacings or bulky counterions, both of which act to weaken ion-polymer binding.

Highly disordered histone H1-DNA model complexes and their condensates

Disordered proteins play an essential role in a wide variety of biological processes, and are often posttranslationally modified. One such protein is histone H1; its highly disordered C-terminal tail (CH1) condenses internucleosomal linker DNA in chromatin in a way that is still poorly understood. Moreover, CH1 is phosphorylated in a cell cycle-dependent manner that correlates with changes in the chromatin condensation level. Here we present a model system that recapitulates key aspects of the in vivo process, and also allows a detailed structural and biophysical analysis of the stages before and after condensation. CH1 remains disordered in the DNA-bound state, despite its nanomolar affinity. Phase-separated droplets (coacervates) form, containing higher-order assemblies of CH1/DNA complexes. Phosphorylation at three serine residues, spaced along the length of the tail, has little effect on the local properties of the condensate. However, it dramatically alters higher-order structure in the coacervate and reduces partitioning to the coacervate phase. These observations show that disordered proteins can bind tightly to DNA without a disorder-to-order transition. Importantly, they also provide mechanistic insights into how higher-order structures can be exquisitely sensitive to perturbation by posttranslational modifications, thus broadening the repertoire of mechanisms that might regulate chromatin and other macromolecular assemblies.

A Y-Shaped Three-Arm Structure for Probing Bivalent Interactions between Protein Receptor-Ligand Using AFM and SPR

The goal of this research was to develop linkage chemistry for the study of bivalent interactions between a receptor and its ligand using atomic force microscopy (AFM) and surface plasmon resonance (SPR). We conceived a three-arm structure composed of flexible chains connected to a large rigid core with orthogonal functional groups at their ends for formation and attachment (or immobilization) of bivalent ligands. To demonstrate the principle, we chose the well-known biotin-streptavidin interaction as a model system. On the basis of a crystal structure of the biotin-streptavidin complex, we designed and synthesized a bisbiotin ligand to have a Y shape with two biotin motifs on its arms for binding and a functional group on its stem for immobilization or attachment, referred to as y-bisbiotin. First, we found that the y-bisbiotin ligand stabilized the streptavidin more than its monobiotin counterpart did in solution, which indicates that the bivalent interaction was synergistic. The y-bisbiotin was attached to AFM tips through a click reaction for the force measurement experiments, which showed that unbinding the bisbiotin from streptavidin needed twice the force of unbinding a monobiotin. For the SPR study, we added a ω-thiolated alkyl chain to y-bisbiotin for its incorporation into a monolayer. The SPR data indicated that the streptavidin dissociated from a mixed monolayer bearing y-bisbiotin much slower than from the one bearing monobiotin. This work demonstrates unique chemistry for the study of bivalent interactions using AFM and SPR.

Role of Salt Valency in the Switch of H-NS Proteins between DNA-Bridging and DNA-Stiffening Modes

This work investigates the interactions of H-NS proteins and bacterial genomic DNA through computer simulations performed with a coarse-grained model. The model was developed specifically to study the switch of H-NS proteins from the DNA-stiffening to the DNA-bridging mode, which has been observed repeatedly upon addition of multivalent cations to the buffer but is still not understood. Unraveling the corresponding mechanism is all the more crucial, as the regulation properties of H-NS proteins, as well as other nucleoid proteins, are linked to their DNA-binding properties. The simulations reported here support a mechanism, according to which the primary role of multivalent cations consists in decreasing the strength of H-NS/DNA interactions compared to H-NS/H-NS interactions, with the latter ones becoming energetically favored with respect to the former ones above a certain threshold of the effective valency of the cations of the buffer. Below the threshold, H-NS dimers form filaments, which stretch along the DNA molecule but are quite inefficient in bridging genomically distant DNA sites (DNA-stiffening mode). In contrast, just above the threshold, H-NS dimers form three-dimensional clusters, which are able to connect DNA sites that are distant from the genomic point of view (DNA-bridging mode). The model provides clear rationales for the experimental observations that the switch between the two modes is a threshold effect and that the ability of H-NS dimers to form higher order oligomers is crucial for their bridging capabilities.

Effects of electrostatic interactions on ligand dissociation kinetics

We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics simulations are suggested by single-molecule studies of protein-DNA interactions. We consider univalent salt concentrations spanning roughly a 1000-fold range, together with various concentrations of excess ligands in solution. To reveal the ionic effects on unbinding kinetics of spontaneous and facilitated dissociation mechanisms, we treat electrostatic interactions both at a Debye-Hückel (DH) (or implicit ions, i.e., use of an electrostatic potential with a prescribed decay length) level and by the more precise approach of considering all ionic species explicitly in the simulations. We find that the DH approach systematically overestimates unbinding rates, relative to the calculations where all ion pairs are present explicitly in solution, although many aspects of the two types of calculation are qualitatively similar. For facilitated dissociation (FD) (acceleration of unbinding by free ligands in solution) explicit-ion simulations lead to unbinding at lower free-ligand concentrations. Our simulations predict a variety of FD regimes as a function of free-ligand and ion concentrations; a particularly interesting regime is at intermediate concentrations of ligands where nonelectrostatic binding strength controls FD. We conclude that explicit-ion electrostatic modeling is an essential component to quantitatively tackle problems in molecular ligand dissociation, including nucleic-acid-binding proteins.

Oligonucleotide-Peptide Complexes: Phase Control by Hybridization

When oppositely charged polymers are mixed, counterion release drives phase separation; understanding this process is a key unsolved problem in polymer science and biophysical chemistry, particularly for nucleic acids, polyanions whose biological functions are intimately related to their high charge density. In the cell, complexation by basic proteins condenses DNA into chromatin, and membraneless organelles formed by liquid-liquid phase separation of RNA and proteins perform vital functions and have been linked to disease. Electrostatic interactions are also the primary method used for assembly of nanoparticles to deliver therapeutic nucleic acids into cells. This work describes complexation experiments with oligonucleotides and cationic peptides spanning a wide range of polymer lengths, concentrations, and structures, including RNA and methylphosphonate backbones. We find that the phase of the complexes is controlled by the hybridization state of the nucleic acid, with double-stranded nucleic acids forming solid precipitates while single-stranded oligonucleotides form liquid coacervates, apparently due to their lower charge density. Adding salt "melts" precipitates into coacervates, and oligonucleotides in coacervates remain competent for sequence-specific hybridization and phase change, suggesting the possibility of environmentally responsive complexes and nanoparticles for therapeutic or sensing applications.

Counterion-Release Entropy Governs the Inhibition of Serum Proteins by Polyelectrolyte Drugs

Dendritic polyelectrolytes constitute high potential drugs and carrier systems for biomedical purposes. Still, their biomolecular interaction modes, in particular those determining the binding affinity to proteins, have not been rationalized. We study the interaction of the drug candidate dendritic polyglycerol sulfate (dPGS) with serum proteins using isothermal titration calorimetry (ITC) interpreted and complemented with molecular computer simulations. Lysozyme is first studied as a well-defined model protein to verify theoretical concepts, which are then applied to the important cell adhesion protein family of selectins. We demonstrate that the driving force of the strong complexation, leading to a distinct protein corona, originates mainly from the release of only a few condensed counterions from the dPGS upon binding. The binding constant shows a surprisingly weak dependence on dPGS size (and bare charge) which can be understood by colloidal charge-renormalization effects and by the fact that the magnitude of the dominating counterion-release mechanism almost exclusively depends on the interfacial charge structure of the protein-specific binding patch. Our findings explain the high selectivity of P- and L-selectins over E-selectin for dPGS to act as a highly anti-inflammatory drug. The entire analysis demonstrates that the interaction of proteins with charged polymeric drugs can be predicted by simulations with unprecedented accuracy. Thus, our results open new perspectives for the rational design of charged polymeric drugs and carrier systems.

Effect of Dendrigraft Generation on the Interaction between Anionic Polyelectrolytes and Dendrigraft Poly(l-Lysine)

In this present work, three generations of dendrigraft poly(l-Lysine) (DGL) were studied regarding their ability to interact with linear poly (acrylamide-co-2-acrylamido-2-methyl-1-propanesulfonate) (PAMAMPS) of different chemical charge densities (30% and 100%). Frontal analysis continuous capillary electrophoresis (FACCE) was successfully applied to determine binding constants and binding stoichiometries. The effect of DGL generation on the interaction was evaluated for the first three generations (G2, G3, and G4) at different ionic strengths, and the effect of ligand topology (linear PLL vs. dendrigraft DGL) on binding parameters was evaluated. An increase of the biding site constants accompanied with a decrease of the DGL-PAMAMPS (n:1) stoichiometry was observed for increasing DGL generation. The logarithm of the global binding constants decreased linearly with the logarithm of the ionic strength. This double logarithmic representation allowed determining the extent of counter-ions released from the association of DGL molecules onto one PAMAMPS chain that was compared to the total entropic reservoir constituted by the total number of condensed counter-ions before the association.

Tuning DNA Condensation with Zwitterionic Polyamidoamine (zPAMAM) Dendrimers

Cationic dendrimers are promising vectors for non-viral gene due to their well-defined size and chemistry. We have synthesized a series of succinylated fourth generation (G4) PAMAM dendrimers to control the DNA packaging in dendriplexes, allowing us to probe the role of charge on DNA packaging. The self-assembly of DNA induced by these zwitterionic PAMAM (zPAMAM) was investigated using small-angle x-ray scattering (SAXS). We demonstrate that changing the degree of modification in zPAMAM-DNA significantly alters the packing density of the resulting dendriplexes. Salt sensitivities and pH dependence on the inter-DNA spacing were also examined. The swelling and stability to salt is reduced with increasing degree of PAMAM modification. Lowering the pH leads to significantly tighter hexagonal DNA packaging. In combination, these results show zPAMAM is an effective means to modulate nucleic acid packaging in a deterministic manner.

Comparative analyses of the thermodynamic RNA binding signatures of different types of RNA recognition motifs

RNA recognition motifs (RRMs) are structurally versatile domains important in regulation of alternative splicing. Structural mechanisms of sequence-specific recognition of single-stranded RNAs (ssRNAs) by RRMs are well understood. The thermodynamic strategies are however unclear. Therefore, we utilized microcalorimetry and semi-empirical analyses to comparatively analyze the cognate ssRNA binding thermodynamics of four different RRM domains, each with a different RNA binding mode. The different binding modes are: canonical binding to the β-sheet surface; canonical binding with involvement of N- and C-termini; binding to conserved loops; and binding to an α-helix. Our results identify enthalpy as the sole and general force driving association at physiological temperatures. Also, networks of weak interactions are a general feature regulating stability of the different RRM–ssRNA complexes. In agreement, non-polyelectrolyte effects contributed between ∼75 and 90% of the overall free energy of binding in the considered complexes. The various RNA binding modes also displayed enormous heat capacity differences, that upon dissection revealed large differential changes in hydration, conformations and dynamics upon binding RNA. Altogether, different modes employed by RRMs to bind cognate ssRNAs utilize various thermodynamics strategies during the association process.

Force spectroscopy unravels the role of ionic strength on DNA-cisplatin interaction: Modulating the binding parameters

In the present work we have gone a step forward in the understanding of the DNA-cisplatin interaction, investigating the role of the ionic strength on the complexes formation. To achieve this task, we use optical tweezers to perform force spectroscopy on the DNA-cisplatin complexes, determining their mechanical parameters as a function of the drug concentration in the sample for three different buffers. From such measurements, we determine the binding parameters and study their behavior as a function of the ionic strength. The equilibrium binding constant decreases with the counterion concentration ([Na]) and can be used to estimate the effective net charge of cisplatin in solution. The cooperativity degree of the binding reaction, on the other hand, increases with the ionic strength, as a result of the different conformational changes induced by the drug on the double-helix when binding under different buffer conditions. Such results can be used to modulate the drug binding to DNA, by appropriately setting the ionic strength of the surrounding buffer. The conclusions drawn provide significant new insights on the complex cooperative interactions between the DNA molecule and the class of platinum-based compounds, much used in chemotherapies.

Determination of Ion Atmosphere Effects on the Nucleic Acid Electrostatic Potential and Ligand Association Using AH+·C Wobble Formation in Double-Stranded DNA

The high charge density of nucleic acids and resulting ion atmosphere profoundly influence the conformational landscape of RNA and DNA and their association with small molecules and proteins. Electrostatic theories have been applied to quantitatively model the electrostatic potential surrounding nucleic acids and the effects of the surrounding ion atmosphere, but experimental measures of the potential and tests of these models have often been complicated by conformational changes and multisite binding equilibria, among other factors. We sought a simple system to further test the basic predictions from electrostatics theory and to measure the energetic consequences of the nucleic acid electrostatic field. We turned to a DNA system developed by Bevilacqua and co-workers that involves a proton as a ligand whose binding is accompanied by formation of an internal AH⁺·C wobble pair [Siegfried, N. A., et al. Biochemistry, 2010, 49, 3225]. Consistent with predictions from polyelectrolyte models, we observed logarithmic dependences of proton affinity versus salt concentration of −0.96 ± 0.03 and −0.52 ± 0.01 with monovalent and divalent cations, respectively, and these results help clarify prior results that appeared to conflict with these fundamental models. Strikingly, quantitation of the ion atmosphere content indicates that divalent cations are preferentially lost over monovalent cations upon A·C protonation, providing experimental indication of the preferential localization of more highly charged cations to the inner shell of the ion atmosphere. The internal AH⁺·C wobble system further allowed us to parse energetic contributions and extract estimates for the electrostatic potential at the position of protonation. The results give a potential near the DNA surface at 20 mM Mg²⁺ that is much less substantial than at 20 mM K⁺ (−120 mV vs −210 mV). These values and difference are similar to predictions from theory, and the potential is substantially reduced at higher salt, also as predicted; however, even at 1 M K⁺ the potential remains substantial, counter to common assumptions. The A·C protonation module allows extraction of new properties of the ion atmosphere and provides an electrostatic meter that will allow local electrostatic potential and energetics to be measured within nucleic acids and their complexes with proteins.

Mechanics, thermodynamics, and kinetics of ligand binding to biopolymers

Ligands binding to polymers regulate polymer functions by changing their physical and chemical properties. This ligand regulation plays a key role in many biological processes. We propose here a model to explain the mechanical, thermodynamic, and kinetic properties of the process of binding of small ligands to long biopolymers. These properties can now be measured at the single molecule level using force spectroscopy techniques. Our model performs an effective decomposition of the ligand-polymer system on its covered and uncovered regions, showing that the elastic properties of the ligand-polymer depend explicitly on the ligand coverage of the polymer (i.e., the fraction of the polymer covered by the ligand). The equilibrium coverage that minimizes the free energy of the ligand-polymer system is computed as a function of the applied force. We show how ligands tune the mechanical properties of a polymer, in particular its length and stiffness, in a force dependent manner. In addition, it is shown how ligand binding can be regulated applying mechanical tension on the polymer. Moreover, the binding kinetics study shows that, in the case where the ligand binds and organizes the polymer in different modes, the binding process can present transient shortening or lengthening of the polymer, caused by changes in the relative coverage by the different ligand modes. Our model will be useful to understand ligand-binding regulation of biological processes, such as the metabolism of nucleic acid. In particular, this model allows estimating the coverage fraction and the ligand mode characteristics from the force extension curves of a ligand-polymer system.

Facilitated dissociation of transcription factors from single DNA binding sites

The binding of transcription factors (TFs) to DNA controls most aspects of cellular function, making the understanding of their binding kinetics imperative. The standard description of bimolecular interactions posits that TF off rates are independent of TF concentration in solution. However, recent observations have revealed that proteins in solution can accelerate the dissociation of DNA-bound proteins. To study the molecular basis of facilitated dissociation (FD), we have used single-molecule imaging to measure dissociation kinetics of Fis, a key Escherichia coli TF and major bacterial nucleoid protein, from single dsDNA binding sites. We observe a strong FD effect characterized by an exchange rate [Formula: see text], establishing that FD of Fis occurs at the single-binding site level, and we find that the off rate saturates at large Fis concentrations in solution. Although spontaneous (i.e., competitor-free) dissociation shows a strong salt dependence, we find that FD depends only weakly on salt. These results are quantitatively explained by a model in which partially dissociated bound proteins are susceptible to invasion by competitor proteins in solution. We also report FD of NHP6A, a yeast TF with structure that differs significantly from Fis. We further perform molecular dynamics simulations, which indicate that FD can occur for molecules that interact far more weakly than those that we have studied. Taken together, our results indicate that FD is a general mechanism assisting in the local removal of TFs from their binding sites and does not necessarily require cooperativity, clustering, or binding site overlap.

The Effect of Molar Mass and Charge Density on the Formation of Complexes between Oppositely Charged Polyelectrolytes

The interactions between model polyanions and polycations have been studied using frontal continuous capillary electrophoresis (FACCE) which allows the determination of binding stoichiometry and binding constant of the formed polyelectrolyte complex (PEC). In this work, the effect of the poly(l-lysine) (PLL) molar mass on the interaction with statistical copolymers of acrylamide and 2-acrylamido-2-methyl-1-propanesulfonate (PAMAMPS) has been systematically investigated for different PAMAMPS chemical charge densities (15% and 100%) and different ionic strengths. The study of the ionic strength dependence of the binding constant allowed the determination of the total number of released counter-ions during the formation of the PEC, which can be compared to the total number of counter-ions initially condensed on the individual polyelectrolyte partners before the association. Interestingly, this fraction of released counter-ions, which was strongly dependent on the PLL molar mass, was almost independent of the PAMAMPS charge density. These findings are useful to predict the binding constant according to the molar mass and charge density of the polyelectrolyte partners.

Potential of mean force and transient states in polyelectrolyte pair complexation

The pair association between two polyelectrolytes (PEs) of the same size but opposite charge is systematically studied in terms of the potential of mean force (PMF) along their center-of-mass reaction coordinate via coarse-grained, implicit-solvent, explicit-salt computer simulations. The focus is set on the onset and the intermediate transient stages of complexation. At conditions above the counterion-condensation threshold, the PE association process exhibits a distinct sliding-rod-like behavior where the polymer chains approach each other by first stretching out at a critical distance close to their contour length, then "shaking hand" and sliding along each other in a parallel fashion, before eventually folding into a neutral complex. The essential part of the PMF for highly charged PEs can be very well described by a simple theory based on sliding charged "Debye-Hückel" rods with renormalized charges in addition to an explicit entropy contribution owing to the release of condensed counterions. Interestingly, at the onset of complex formation, the mean force between the PE chains is found to be discontinuous, reflecting a bimodal structural behavior that arises from the coexistence of interconnected-rod and isolated-coil states. These two microstates of the PE complex are balanced by subtle counterion release effects and separated by a free-energy barrier due to unfavorable stretching entropy.

Thermodynamics of complex coacervation

Isothermal titration calorimetry has routinely been used to understand the thermodynamic characteristics of complexation and coacervation. Most commonly, built-in models that assume independent binding sites have been employed in these studies. However, the non-covalent nature of interactions and steric effects accompanying macromolecules require (i) usage of new models such as overlapping binding sites and Satake-Yang's two-state binding models and (ii) reformed interpretations of the data as two-stage structuring. Fitting data with these models, forces driving the interaction of polyelectrolytes with oppositely charged polyelectrolytes, surfactants, and proteins have been identified as electrostatics and/or counterion release with possible contributions from hydrogen bonding and hydrophobic interactions. Additionally, for surfactant-polyelectrolyte coacervation, ITC signals indicated separate regions for formation of polymer-induced micelles and free micelles. Regardless of the type of the coacervation system, thermodynamics of coacervation is affected by the following parameters: pH and ionic strength of the medium, charge density, molecular weight of the polyelectrolyte, concentration, and mixing order of macroions. Lastly, we present a brief comparison between ITC on one hand and surface plasmon resonance or capillary electrophoresis on the other regarding their application in coacervation.

Signal and binding. II. Converting physico-chemical responses to macromolecule-ligand interactions into thermodynamic binding isotherms

Physico-chemical titration techniques are the most commonly used methods in characterizing molecular interactions. These methods are mainly based on spectroscopic, calorimetric, hydrodynamic, etc., measurements. However, truly quantitative physico-chemical methods are absolutely based on the determination of the relationship between the measured signal and the total average degree of binding in order to obtain meaningful interaction parameters. The relationship between the observed physico-chemical signal of whatever nature and the degree of binding must be determined and not assumed, based on some ad hoc intuitive relationship/model, leading to determination of the true binding isotherm. The quantitative methods reviewed and discussed here allow an experimenter to rigorously determine the degree of binding and the free ligand concentration, i.e., they lead to the construction of the thermodynamic binding isotherm in a model-independent fashion from physico-chemical titration curves.

Modelling and predicting the interactions between oppositely and variously charged polyelectrolytes by frontal analysis continuous capillary electrophoresis

In this work, a systematic study of the interactions between poly(l-lysine) and variously charged statistical copolymers of acrylamide and 2-acrylamido-2-methyl-1-propanesulfonate (PAMAMPS) has been carried out by frontal analysis continuous capillary electrophoresis (FACCE). FACCE was successfully implemented to obtain the interaction parameters (binding constant and stoichiometry) at different ionic strengths and for different PAMAMPS charge densities varying between 15% and 100%. The range of investigated ionic strengths was carefully adjusted according to the PAMAMPS charge density to obtain measurable binding constants by FACCE (i.e. formation binding constant typically comprised between 10⁴ and 10⁶ M^-1). The number of released counter-ions during the polyelectrolyte complex formation was systematically quantified via the ionic strength dependence of the binding constant and was compared to the total condensed counter-ion reservoir according to Manning theory on counter-ion condensation. A descriptive and predictive model relating the physico-chemical properties of the two partners, the binding constant and the ionic strength is proposed in the framework of multiple independent interaction sites of equal energy.

Facilitated Dissociation of a Nucleoid Protein from the Bacterial Chromosome

Off-rates of proteins from the DNA double helix are widely considered to be dependent only on the interactions inside the initially bound protein-DNA complex and not on the concentration of nearby molecules. However, a number of recent single-DNA experiments have shown off-rates that depend on solution protein concentration, or "facilitated dissociation." Here, we demonstrate that this effect occurs for the major Escherichia coli nucleoid protein Fis on isolated bacterial chromosomes. We isolated E. coli nucleoids and showed that dissociation of green fluorescent protein (GFP)-Fis is controlled by solution Fis concentration and exhibits an "exchange" rate constant (kexch) of ≈10(4) M(-1) s(-1), comparable to the rate observed in single-DNA experiments. We also show that this effect is strongly salt dependent. Our results establish that facilitated dissociation can be observed in vitro on chromosomes assembled in vivo

IMPORTANCE

Bacteria are important model systems for the study of gene regulation and chromosome dynamics, both of which fundamentally depend on the kinetics of binding and unbinding of proteins to DNA. In experiments on isolated E. coli chromosomes, this study showed that the prolific transcription factor and chromosome packaging protein Fis displays a strong dependence of its off-rate from the bacterial chromosome on Fis concentration, similar to that observed in in vitro experiments. Therefore, the free cellular DNA-binding protein concentration can strongly affect lifetimes of proteins bound to the chromosome and must be taken into account in quantitative considerations of gene regulation. These results have particularly profound implications for transcription factors where DNA binding lifetimes can be a critical determinant of regulatory function.

High DNA-Binding Affinity and Gene-Transfection Efficacy of Bioreducible Cationic Nanomicelles with a Fluorinated Core

During the last two decades, cationic polymers have become one of the most promising synthetic vectors for gene transfection. However, the weak interactions formed between DNA and cationic polymers result in low transfection efficacy. Furthermore, the polyplexes formed between cationic polymers and DNA generally exhibit poor stability and toxicity because of the large excess of cationic polymer typically required for complete DNA condensation. Herein, we report the preparation of a novel class of bioreducible cationic nanomicelles by the use of disulfide bonds to connect the cationic shell to the fluorocarbon core. These bioreducible nanomicelles form strong interactions with DNA and completely condense DNA at an N/P ratio of 1. The resulting nanomicelle/DNA polyplexes exhibited high biocompatibility and performed very effectively as a gene-delivery system.

DNA-Segment-Facilitated Dissociation of Fis and NHP6A from DNA Detected via Single-Molecule Mechanical Response

The rate of dissociation of a DNA-protein complex is often considered to be a property of that complex, without dependence on other nearby molecules in solution. We study the kinetics of dissociation of the abundant Escherichia coli nucleoid protein Fis from DNA, using a single-molecule mechanics assay. The rate of Fis dissociation from DNA is strongly dependent on the solution concentration of DNA. The off-rate (k(off)) of Fis from DNA shows an initially linear dependence on solution DNA concentration, characterized by an exchange rate of k(ex)≈9×10(-4) (ng/μl)(-1) s(-1) for 100 mM univalent salt buffer, with a very small off-rate at zero DNA concentration. The off-rate saturates at approximately k(off,max)≈8×10(-3) s(-1) for DNA concentrations above ≈20 ng/μl. This exchange reaction depends mainly on DNA concentration with little dependence on the length of the DNA molecules in solution or on binding affinity, but this does increase with increasing salt concentration. We also show data for the yeast HMGB protein NHP6A showing a similar DNA-concentration-dependent dissociation effect, with faster rates suggesting generally weaker DNA binding by NHP6A relative to Fis. Our results are well described by a model with an intermediate partially dissociated state where the protein is susceptible to being captured by a second DNA segment, in the manner of "direct transfer" reactions studied for other DNA-binding proteins. This type of dissociation pathway may be important to protein-DNA binding kinetics in vivo where DNA concentrations are large.

Biophysics of protein-DNA interactions and chromosome organization

The function of DNA in cells depends on its interactions with protein molecules, which recognize and act on base sequence patterns along the double helix. These notes aim to introduce basic polymer physics of DNA molecules, biophysics of protein-DNA interactions and their study in single-DNA experiments, and some aspects of large-scale chromosome structure. Mechanisms for control of chromosome topology will also be discussed.