Divalent Ion Parameterization Strongly Affects Conformation and Interactions of an Anionic Biomimetic Polymer

Initiation of Medial Calcification: Revisiting Calcium Ion Binding to Elastin

Pathological calcification of elastin, a key connective tissue protein in the medial layers of blood vessels, starts with the binding of calcium ions. This Mini-Review focuses on understanding how calcium ions interact with elastin to initiate calcification at a molecular level, and emphasizes water's critical role in mediating this interaction. In the past decade, great strides have been made in understanding and modeling ion-specific hydration and its effects on biomolecule interactions. However, these advances have been largely absent from our understanding of elastin calcification. Historically, charge-neutral backbone carbonyls and negatively charged carboxyl groups have been proposed as elastin's calcium binding sites. Recently, tropoelastin's only four carboxyl groups have been identified as binding sites from classical molecular dynamics (MD). While carboxyl groups have a much higher affinity for binding calcium ions than backbone carbonyls, conflicting evidence persists for both functional group's importance in elastin calcification. This can be attributed to the fact that divalent ions strongly polarize water, leading to a hydration shell that shields electrostatic forces. The hydration shell surrounding both a calcium ion and either of the proposed binding sites must be displaced to enable binding. Providing our own extended X-ray absorption fine structure (EXAFS) data and complementary simulations, we discuss the potential structures of calcium binding in elastin and review prior knowledge regarding the relative importance of the two proposed binding sites.

Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations To Accurately Model Glycosaminoglycan Electrostatic Interactions

Glycosaminoglycans (GAGs) are negatively charged polysaccharides found on cell surfaces, where they regulate transport pathways of foreign molecules toward the cell. The structural and functional diversity of GAGs is largely attributed to varied sulfation patterns along the polymer chains, which makes understanding their molecular recognition mechanisms crucial. Molecular dynamics (MD) simulations, thanks to their unmatched microscopic resolution, have the potential to be a reference tool for exploring the patterns responsible for biologically relevant interactions. However, the capability of molecular dynamics force fields used in biosimulations to accurately capture sulfation-specific interactions is not well established, partly due to the intrinsic properties of GAGs that pose challenges for most experimental techniques. In this work, we evaluate the performance of molecular dynamics force fields for sulfated GAGs by studying ion pairing of Ca2+ to sulfated moieties─N-methylsulfamate and methylsulfate─that resemble N- and O-sulfation found in GAGs, respectively. We tested available nonpolarizable (CHARMM36 and GLYCAM06) and explicitly polarizable (Drude and AMOEBA) force fields, and derived new implicitly polarizable models through charge scaling (prosECCo75 and GLYCAM-ECC75) that are consistent with our developed "charge-scaling" framework. The calcium-sulfamate/sulfate interaction free energy profiles obtained with the tested force fields were compared against reference ab initio molecular dynamics (AIMD) simulations, which serve as a robust alternative to experiments. AIMD simulations indicate that the preferential Ca2+ binding mode to sulfated GAG groups is solvent-shared pairing. Only our scaled-charge models agree satisfactorily with the AIMD data, while all other force fields exhibit poorer agreement, sometimes even qualitatively. Surprisingly, even explicitly polarizable force fields display a notable disagreement with the AIMD data, likely attributed to difficulties in their optimization and possible inherent limitations in depicting high-charge-density ion interactions accurately. Finally, the underperforming force fields lead to unrealistic aggregation of sulfated saccharides, which qualitatively disagrees with our understanding of the soft glycocalyx environment. Our results highlight the importance of accurately treating electronic polarization in MD simulations of sulfated GAGs and caution against over-reliance on currently available models without thorough validation and optimization.

Mechanisms of Biomolecular Self-Assembly Investigated Through In Situ Observations of Structures and Dynamics

Biomolecular self-assembly of hierarchical materials is a precise and adaptable bottom-up approach to synthesizing across scales with considerable energy, health, environment, sustainability, and information technology applications. To achieve desired functions in biomaterials, it is essential to directly observe assembly dynamics and structural evolutions that reflect the underlying energy landscape and the assembly mechanism. This review will summarize the current understanding of biomolecular assembly mechanisms based on in situ characterization and discuss the broader significance and achievements of newly gained insights. In addition, we will also introduce how emerging deep learning/machine learning-based approaches, multiparametric characterization, and high-throughput methods can boost the development of biomolecular self-assembly. The objective of this review is to accelerate the development of in situ characterization approaches for biomolecular self-assembly and to inspire the next generation of biomimetic materials.

Identification of an Additional Metal-Binding Site in Human Dipeptidyl Peptidase III

Dipeptidyl peptidase III (DPP III, EC 3.4.14.4) is a monozinc metalloexopeptidase that hydrolyzes dipeptides from the N-terminus of peptides consisting of three or more amino acids. Recently, DPP III has attracted great interest from scientists, and numerous studies have been conducted showing that it is involved in the regulation of various physiological processes. Since it is the only metalloenzyme among the dipeptidyl peptidases, we considered it important to study the process of binding and exchange of physiologically relevant metal dications in DPP III. Using fluorimetry, we measured the Kd values for the binding of Zn2+, Cu2+, and Co2+ to the catalytic site, and using isothermal titration calorimetry (ITC), we measured the Kd values for the binding of these metals to an additional binding site. The structure of the catalytic metal's binding site is known from previous studies, and in this work, the affinities for this site were calculated for Zn2+, Cu2+, Co2+, and Mn2+ using the QM approach. The structures of the additional binding sites for the Zn2+ and Cu2+ were also identified, and MD simulations showed that two Cu2+ ions bound to the catalytic and inhibitory sites exchanged less frequently than the Zn2+ ions bound to these sites.

Development of a Systematic and Extensible Force Field for Peptoids (STEPs)

Peptoids (N-substituted glycines) are a class of biomimetic polymers that have attracted significant attention due to their accessible synthesis and enzymatic and thermal stability relative to their naturally occurring counterparts (polypeptides). While these polymers provide the promise of more robust functional materials via hierarchical approaches, they present a new challenge for computational structure prediction for material design. The reliability of calculations hinges on the accuracy of interactions represented in the force field used to model peptoids. For proteins, structure prediction based on sequence and de novo design has made dramatic progress in recent years; however, these models are not readily transferable for peptoids. Current efforts to develop and implement peptoid-specific force fields are spread out, leading to replicated efforts and a fragmented collection of parameterized sidechains. Here, we developed a peptoid-specific force field containing 70 different side chains, using GAFF2 as starting point. The new model is validated based on the generation of Ramachandran-like plots from DFT optimization compared against force field reproduced potential energy and free energy surfaces as well as the reproduction of equilibrium cis/trans values for some residues experimentally known to form helical structures. Equilibrium cis/trans distributions (Kct) are estimated for all parameterized residues to identify which residues have an intrinsic propensity for cis or trans states in the monomeric state.

Local Molecular Field Theory for Coulomb Interactions in Aqueous Solutions

Coulomb interactions play a crucial role in a wide array of processes in aqueous solutions but present conceptual and computational challenges to both theory and simulations. We review recent developments in an approach addressing these challenges─local molecular field (LMF) theory. LMF theory exploits an exact and physically suggestive separation of intermolecular Coulomb interactions into strong short-range and uniformly slowly varying long-range components. This allows us to accurately determine the averaged effects of the long-range components on the short-range structure using effective single particle fields and analytical corrections, greatly reducing the need for complex lattice summation techniques used in most standard approaches. The simplest use of these ideas in aqueous solutions leads to the short solvent (SS) model, where both solvent-solvent and solute-solvent Coulomb interactions have only short-range components. Here we use the SS model to give a simple description of pairing of nucleobases and biologically relevant ions in water.

Role of Hydration in Magnesium versus Calcium Ion Pairing with Carboxylate: Solution and the Aqueous Interface

The binding of group II metal cations such as Ca²⁺ and Mg²⁺ has been largely categorized as electrostatic or ionic using carboxylate symmetric and asymmetric stretching frequency assignments that have been historically used with little regard for the solvation environment of aqueous solutions. However, given the importance of these cations and their binding mechanisms related to biological function and in revealing surface enrichment factors for ocean to marine aerosol transfer, it is imperative that a deeper understanding be sought to include hydration effects. Here, infrared reflection-absorption and Raman spectra for surface and solution phase carboxylate binding information, respectively, are compared against bare (unbound) carboxylate and bidentate Zn²⁺:carboxylate spectral signatures. Spectral non-coincidence effect analysis, temperature studies, and spectral and potential of mean force calculations result in a concise interpretation of binding motifs that include the role of mediating water molecules, that is, contact and solvent-shared ion pairs. Calcium directly binds to the carboxylate group in contact ion pairs where magnesium rarely does. Moreover, we reveal the dominance of the solvent-shared ion pair of magnesium with carboxylate at the air-water interface and in solution.

Building intuition for binding free energy calculations: Bound state definition, restraints, and symmetry

The theory behind computation of absolute binding free energies using explicit-solvent molecular simulations is well-established, yet somewhat complex, with counter-intuitive aspects. This leads to frequent frustration, common misconceptions, and sometimes erroneous numerical treatment. To improve this, we present the main practically relevant segments of the theory with constant reference to physical intuition. We pinpoint the role of the implicit or explicit definition of the bound state (or the binding site) to make a robust link between an experimental measurement and a computational result. We clarify the role of symmetry and discuss cases where symmetry number corrections have been misinterpreted. In particular, we argue that symmetry corrections as classically presented are a source of confusion and could be advantageously replaced by restraint free energy contributions. We establish that contrary to a common intuition, partial or missing sampling of some modes of symmetric bound states does not affect the calculated decoupling free energies. Finally, we review these questions and pitfalls in the context of a few common practical situations: binding to a symmetric receptor (equivalent binding sites), binding of a symmetric ligand (equivalent poses), and formation of a symmetric complex, in the case of homodimerization.

Short solvent model for ion correlations and hydrophobic association

Coulomb interactions play a major role in determining the thermodynamics, structure, and dynamics of condensed-phase systems, but often present significant challenges. Computer simulations usually use periodic boundary conditions to minimize corrections from finite cell boundaries but the long range of the Coulomb interactions generates significant contributions from distant periodic images of the simulation cell, usually calculated by Ewald sum techniques. This can add significant overhead to computer simulations and hampers the development of intuitive local pictures and simple analytic theory. In this paper, we present a general framework based on local molecular field theory to accurately determine the contributions from long-ranged Coulomb interactions to the potential of mean force between ionic or apolar hydrophobic solutes in dilute aqueous solutions described by standard classical point charge water models. The simplest approximation leads to a short solvent (SS) model, with truncated solvent-solvent and solute-solvent Coulomb interactions and long-ranged but screened Coulomb interactions only between charged solutes. The SS model accurately describes the interplay between strong short-ranged solute core interactions, local hydrogen-bond configurations, and long-ranged dielectric screening of distant charges, competing effects that are difficult to capture in standard implicit solvent models.

Binding of divalent cations to acetate: molecular simulations guided by Raman spectroscopy

We combine Raman-MCR vibrational spectroscopy experiments with ab initio and classical MD simulations to gain molecular insights into carboxylate–cation binding.

Binding of Divalent Cations to Insulin: Capillary Electrophoresis and Molecular Simulations

In the present study, we characterize the binding of divalent cations to insulin in aqueous salt solutions by means of capillary electrophoresis and molecular dynamics simulations. The results show a strong pH dependence. At low pH, at which all the carboxylate groups are protonated and the protein has an overall positive charge, all the cations exhibit only weak and rather unspecific interactions with insulin. In contrast, at close to neutral pH, when all the carboxylate groups are deprotonated and negatively charged, the charge-neutralizing effect of magnesium, calcium, and zinc, in particular, on the electrophoretic mobility of insulin is significant. This is also reflected in the results of molecular dynamics simulations showing accumulation of cations at the protein surface, which becomes smaller in magnitude upon effective inclusion of electronic polarization via charge rescaling.

Developing force fields when experimental data is sparse: AMBER/GAFF-compatible parameters for inorganic and alkyl oxoanions

We present a set of Lennard-Jones parameters for classical, all-atom models of acetate and various alkylated and non-alkylated forms of sulfate, sulfonate and phosphate ions, optimized to reproduce their interactions with water and with the physiologically relevant sodium, ammonium and methylammonium cations. The parameters are internally consistent and are fully compatible with the Generalized Amber Force Field (GAFF), the AMBER force field for proteins, the accompanying TIP3P water model and the sodium model of Joung and Cheatham. The parameters were developed primarily relying on experimental information - hydration free energies and solution activity derivatives at 0.5 m concentration - with ab initio, gas phase calculations being used for the cases where experimental information is missing. The ab initio parameterization scheme presented here is distinct from other approaches because it explicitly connects gas phase binding energies to intermolecular interactions in solution. We demonstrate that the original GAFF/AMBER parameters often overestimate anion-cation interactions, leading to an excessive number of contact ion pairs in solutions of carboxylate ions, and to aggregation in solutions of divalent ions. GAFF/AMBER parameters lead to excessive numbers of salt bridges in proteins and of contact ion pairs between sodium and acidic protein groups, issues that are resolved by using the optimized parameters presented here.

Selective complexation of divalent cations by a cyclic α,β-peptoid hexamer: a spectroscopic and computational study

The first report on metal binding ability of a cyclic α,β-peptoid hexamer towards a selection of metal cations is presented.