Water organization between oppositely charged surfaces: Implications for protein sliding along DNA

Dynamics in the Intact fd Bacteriophage Revealed by Pseudo 3D REDOR-Based Magic Angle Spinning NMR

The development of robust NMR methodologies to probe dynamics on the atomic scale is vital to elucidate the close relations between structure, motion, and function in biological systems. Here, we present an automated protocol to measure, using magic-angle spinning NMR, the effective 13C-15N dipolar coupling constants between multiple spin pairs simultaneously with high accuracy. We use the experimental dipolar coupling constants to quantify the order parameters of multiple C-N bonds in the thousands of identical copies of the coat protein in intact fd-Y21M filamentous bacteriophage virus and describe its overall dynamics on the submillisecond time scale. The method is based on combining three pseudo three-dimensional NMR experiments, where a rotational echo double resonance (REDOR) dephasing block, designed to measure internuclear distances, is combined with three complementary 13C-13C mixing schemes: dipolar-assisted rotational resonance, through-bond transfer-based double quantum/single quantum correlation, and radio frequency driven recoupling. These mixing schemes result in highly resolved carbon spectra with correlations that are created by different transfer mechanisms. We show that the helical part of the coat protein undergoes a uniform small (∼30°) amplitude motion, while the N-terminus is highly flexible. In addition, our results suggest that the reduced mobility of lysine sidechains at the C-terminus are a signature of binding to the single stranded DNA.

Surface tension of aqueous electrolyte solutions. A thermomechanical approach

We determine the surface tension of aqueous electrolyte solutions in contact with non-polar dielectric media using a thermomechanical approach, which involves deriving the stress tensor from the thermodynamic potential of an inhomogeneous fluid. To obtain the surface tension, we calculate both the normal and tangential pressures using the components of the stress tensor, recently derived by us [Y. A. Budkov and P. E. Brandyshev, J. Chem. Phys. 159, 174103 (2023)] within the framework of Wang's variational field theory. Using this approach, we derive an analytical expression for the surface tension in the linear approximation. At low ionic concentrations, this expression represents the classical Onsager-Samaras limiting law. By utilizing only one fitting parameter, which is related to the affinity of anions to the dielectric boundary, we successfully approximated experimental data on the surface tension of several aqueous electrolyte solutions. This approximation applies to both the solution-air and solution-dodecane interfaces, covering a wide range of electrolyte concentrations.

In-plane structure of the electric double layer in the primitive model using classical density functional theory

The electric double layer (EDL) has a pivotal role in screening charges on surfaces as in supercapacitor electrodes or colloidal and polymer solutions. Its structure is determined by correlations between the finite-sized ionic charge carriers of the underlying electrolyte, and, this way, these correlations affect the properties of the EDL and of applications utilizing EDLs. We study the structure of EDLs within classical density functional theory (DFT) in order to uncover whether a structural transition in the first layer of the EDL that is driven by changes in the surface potential depends on specific particle interactions or has a general footing. This transition has been found in full-atom simulations. Thus far, investigating the in-plane structure of the EDL for the primitive model (PM) using DFT has proved a challenge. We show here that the use of an appropriate functional predicts the in-plane structure of EDLs in excellent agreement with molecular dynamics simulations. This provides the playground to investigate how the structure factor within a layer parallel to a charged surface changes as a function of both the applied surface potential and its separation from the surface. We discuss pitfalls in properly defining an in-plane structure factor and fully map out the structure of the EDL within the PM for a wide range of electrostatic electrode potentials. However, we do not find any signature of a structural crossover and conclude that the previously reported effect is not fundamental but rather occurs due to the specific force field of ions used in the simulations.

Nonspecific Binding-Fundamental Concepts and Consequences for Biosensing Applications

Nature achieves differentiation of specific and nonspecific binding in molecular interactions through precise control of biomolecules in space and time. Artificial systems such as biosensors that rely on distinguishing specific molecular binding events in a sea of nonspecific interactions have struggled to overcome this issue. Despite the numerous technological advancements in biosensor technologies, nonspecific binding has remained a critical bottleneck due to the lack of a fundamental understanding of the phenomenon. To date, the identity, cause, and influence of nonspecific binding remain topics of debate within the scientific community. In this review, we discuss the evolution of the concept of nonspecific binding over the past five decades based upon the thermodynamic, intermolecular, and structural perspectives to provide classification frameworks for biomolecular interactions. Further, we introduce various theoretical models that predict the expected behavior of biosensors in physiologically relevant environments to calculate the theoretical detection limit and to optimize sensor performance. We conclude by discussing existing practical approaches to tackle the nonspecific binding challenge in vitro for biosensing platforms and how we can both address and harness nonspecific interactions for in vivo systems.

Electric Double Layer and Orientational Ordering of Water Dipoles in Narrow Channels within a Modified Langevin Poisson-Boltzmann Model

The electric double layer (EDL) is an important phenomenon that arises in systems where a charged surface comes into contact with an electrolyte solution. In this work we describe the generalization of classic Poisson-Boltzmann (PB) theory for point-like ions by taking into account orientational ordering of water molecules. The modified Langevin Poisson-Boltzmann (LPB) model of EDL is derived by minimizing the corresponding Helmholtz free energy functional, which includes also orientational entropy contribution of water dipoles. The formation of EDL is important in many artificial and biological systems bound by a cylindrical geometry. We therefore numerically solve the modified LPB equation in cylindrical coordinates, determining the spatial dependencies of electric potential, relative permittivity and average orientations of water dipoles within charged tubes of different radii. Results show that for tubes of a large radius, macroscopic (net) volume charge density of coions and counterions is zero at the geometrical axis. This is attributed to effective electrolyte charge screening in the vicinity of the inner charged surface of the tube. For tubes of small radii, the screening region extends into the whole inner space of the tube, leading to non-zero net volume charge density and non-zero orientational ordering of water dipoles near the axis.

Diffusion of ring-shaped proteins along DNA: case study of sliding clamps

Several DNA-binding proteins, such as topoisomerases, helicases and sliding clamps, have a toroidal (i.e. ring) shape that topologically traps DNA, with this quality being essential to their function. Many DNA-binding proteins that function, for example, as transcription factors or enzymes were shown to be able to diffuse linearly (i.e. slide) along DNA during the search for their target binding sites. The protein's sliding properties and ability to search DNA, which often also involves hopping and dissociation, are expected to be different when it encircles the DNA. In this study, we explored the linear diffusion of four ring-shaped proteins of very similar structure: three sliding clamps (PCNA, β-clamp, and the gp45) and the 9-1-1 protein, with a particular focus on PCNA. Coarse-grained molecular dynamics simulations were performed to decipher the sliding mechanism adopted by these ring-shaped proteins and to determine how the molecular properties of the inner and outer ring govern its search speed. We designed in silico variants to dissect the contributions of ring geometry and electrostatics to the sliding speed of ring-shaped proteins along DNA. We found that the toroidal proteins diffuse when they are tilted relative to the DNA axis and able to rotate during translocation, but that coupling between rotation and translocation is quite weak. Their diffusion speed is affected by the shape of the inner ring and, to a lesser extent, by its electrostatic properties. However, breaking the symmetry of the electrostatic potential can result in deviation of the DNA from the center of the ring and cause slower linear diffusion. The findings are discussed in light of earlier computational and experimental studies on the sliding of clamps.

On the coupling between the dynamics of protein and water

The solvation entropy of flexible protein regions is higher than that of rigid regions and contributes differently to the overall thermodynamic stability.