Molecular Dynamics Investigation into pH Dependent Metal Binding of the Intrinsically Disordered Worm Jaw Protein, Nvjp-1.

Sclerotization of the Nereis virens jaw is mediated by metal binding to the histidine-rich jaw protein, Nvjp-1. Previous studies showed that the mechanical properties of Nvjp-1 hydrogels could be modulated with zinc binding as well as the associated anion. Here, we show that the mechanical properties of Nvjp-1 hydrogels can be modulated by pH and that zinc binding to Nvjp-1 is stable at both acidic and alkaline pH conditions. To probe the mechanism of Zn2+ binding to Nvjp-1 at different pH conditions, we utilized all atom molecular dynamics simulations employing a polarizable force field. At low pH conditions, polar residues predominantly interacted with Zn2+, with at most two residues interacting with a given zinc ion. Surprisingly, little to no Zn2+ binding was observed with the abundant Nvjp-1 acidic residues, which form salt-bridges with the protonated histidines to effectively block their binding to Zn2+ ions. As the pH was shifted to alkaline conditions, Zn2+ binding residues reconfigured to form additional coordination bonds with histidine, resulting in a reduction in the radius of gyration that correlated with hydrogel sclerotization. Furthermore, acetate ions were shown to facilitate the capture of zinc ions through association with protonated histidines at low pH, freeing acidic residues to interact with Zn2+ ions and increasing the number of Zn2+ ions that diffuse into the Nvjp-1 interior. Thus, these studies provide valuable molecular insights into how amino acid residues in Nvjp-1 manage metal salt binding and coordination in hydrogels as a function of the pH and ionic environments.

AlphaFold2 models indicate that protein sequence determines both structure and dynamics.

AlphaFold 2 (AF2) has placed Molecular Biology in a new era where we can visualize, analyze and interpret the structures and functions of all proteins solely from their primary sequences. We performed AF2 structure predictions for various protein systems, including globular proteins, a multi-domain protein, an intrinsically disordered protein (IDP), a randomized protein, two larger proteins (> 1000 AA), a heterodimer and a homodimer protein complex. Our results show that along with the three dimensional (3D) structures, AF2 also decodes protein sequences into residue flexibilities via both the predicted local distance difference test (pLDDT) scores of the models, and the predicted aligned error (PAE) maps. We show that PAE maps from AF2 are correlated with the distance variation (DV) matrices from molecular dynamics (MD) simulations, which reveals that the PAE maps can predict the dynamical nature of protein residues. Here, we introduce the AF2-scores, which are simply derived from pLDDT scores and are in the range of [0, 1]. We found that for most protein models, including large proteins and protein complexes, the AF2-scores are highly correlated with the root mean square fluctuations (RMSF) calculated from MD simulations. However, for an IDP and a randomized protein, the AF2-scores do not correlate with the RMSF from MD, especially for the IDP. Our results indicate that the protein structures predicted by AF2 also convey information of the residue flexibility, i.e., protein dynamics.

Rational Control of Self-Recognition of Macroionic γ-Cyclodextrin by Host-Guest Interaction with Super-Chaotropic Borate Cluster Ions.

We report a feasible method to control self-recognition during the self-assembly of a hydrophilic macroion, phosphate-functionalized γ-cyclodextrin (γ-CD-P), though host-guest interactions. We confirmed that γ-CD-P can form a host-guest complex with a super-chaotropic anion, namely the B12 F122- borate cluster, by using NMR spectroscopy and isothermal titration calorimetry. The loaded γ-CD-P, which has a higher charge density, can be distinguished from the uncomplexed γ-CD-P, leading to self-sorting behavior during the self-assembly process, confirmed by the formation of two types of individual supramolecular structures (Rh of ca. 57 nm and 18 nm, determined by light scattering) instead of hybrid structures in mixed dilute solution. This self-recognition behavior is accounted for by the difference in intermolecular electrostatic interactions arising from the loading.

Hydrogen bond directed surface dynamics at tactic poly(methyl methacrylate)/water interface.

The complexity of induced ordering for tactic poly(methyl methacrylate) (PMMA) thin films in contact with water is examined through all-atom molecular dynamics with validated potentials. We observe that for the water molecules that are hydrogen bonded to the PMMA surface, the isotactic and atactic PMMA show a 33% longer relaxation time compared to syndiotactic PMMA. Almost 94% of hydrogen bonds are with the carbonyl groups of PMMA, irrespective of temperature and tacticity. The stability in re-orientation and nature of hydrogen bond participation for the carbonyl groups as well as about 20% higher interaction energies of carbonyl group hydrogen bonded with water for atactic form indicates existence of cooperative effects. Quantifying the dynamics of hydrogen bond at the tactic interface is important in understanding the role tacticity plays in controlling adhesion and biocompatibility, a design choice that has been gaining ground in the soft material science community.

Effect of Surface Energy on Freezing Temperature of Water.

Previous studies have found that superhydrophobic surfaces are effective in delaying freezing of water droplets. However, the freezing process of water droplets on superhydrophobic surfaces depends on factors such as droplet size, surface area, roughness, and cooling rate. The role of surface energy, independent of any other parameters, in delaying freezing of water is not understood. Here, we have used infrared-visible sum frequency generation spectroscopy (SFG) to study the freezing of water next to solid substrates with water contact angles varying from 5° to 110°. We find that the freezing temperature of water decreases with increasing surface hydrophobicity only when the sample volume is small (∼10 µL). For a larger volume of water (∼300 µL), the freezing temperature is independent of surface energy. For water next to the surfaces with contact angle ≥54°, we observe a strong SFG peak associated with highly coordinated water. This research sheds new light on understanding the key factors in designing new anti-icing coatings.

Effect of Polymer/Solid and Polymer/Vapor Instantaneous Interfaces on the Interfacial Structure and Dynamics of Polymer Melt Systems.

Polymers are used in a wide range of applications that involve chemical and physical processes taking place at surfaces or interfaces which influence the interaction between the polymer material and the substance that comes into contact with it. Polymer surfaces are usually modified either chemically or physically for specific applications such as facilitating wetting, reducing friction, and enhancing adhesion. The variety and complexity of surface and interfacial processes requires a molecular-level understanding of the structural and dynamical properties of the surface/interface layer to help in the design of materials with desired functional properties. Using molecular dynamics (MD) simulations, we investigate the structure and dynamics at the surface of polymer films. We find that the density profiles of the films as a function of distance relative to an instantaneous surface have a structure indicative of a layering at the polymer/vapor interface similar to the typical layered structure observed at the polymer/substrate interface. However, the interfacial molecules at the polymer/vapor interface have a higher mobility compared to that in the bulk while the mobility of the molecules is lower at the polymer/substrate interface. Time correlation of the instantaneous polymer/vapor interface shows that surface fluctuations are strongly temperature dependent and are directly related to the mobility of polymer chains near the interface.

Interfacial properties of oxidized polystyrene and its interaction with water.

All-atom molecular dynamics simulations have been carried out to study the wetting of atactic polystyrene (aPS) thin films by water droplets. The effect of oxidation of the aPS surface on the contact angle has been studied as a function of oxygen concentration. Oxidation of aPS has been achieved by randomly replacing with oxygen the ortho and/or meta hydrogens on the aromatic rings within 1 nm of the aPS surface until the desired concentration of oxygen is reached. The simulated contact angle is found to decrease monotonically with increasing degree of oxidation, consistent with recent experimental results. The number of hydrogen bonds between water molecules and polystyrene at the interface is found to monotonically increase with oxygen concentration. By use of a modified Good-Girafalco-Fowkes-Young equation, the contribution of nondispersion interactions, γsl(P), to the interfacial energy at the aPS/water interface has been determined as a function of the degree of oxidation. The values of γsl(P) extracted appear to follow a quadratic dependence on oxygen concentration of the aPS surface. The roughness of the polystyrene surface appears to be independent of oxygen concentration when the polystyrene is exposed to vacuum, and it appears to increase slightly when it is in contact with water. The orientational ordering of the phenyl rings at the polystyrene surface exhibits no dependence on oxygen concentration for polystyrene in vacuum. However, the ordering appears to decrease slightly with increasing oxygen concentration when the polystyrene is in contact with water.