Effects of Ligand Density on Hydrophobic Charge Induction Chromatography: Molecular Dynamics Simulation

All-atom modeling of methacrylate-based multi-modal chromatography resins for Langmuir constant prediction of peptides

In downstream processing, the intricate nature of the interactions between biomolecules and adsorbent materials presents a significant challenge in the prediction of their binding and elution behaviors. This complexity is further heightened in multi-modal chromatography (MMC), which employs two distinct binding mechanisms. To gain a deeper understanding of the involved interactions, simulating the adsorption of biomolecules on resin surfaces is a focal point of ongoing research. However, previous studies often simplified the adsorbent surface, modeling it as a flat or slightly curved plane without including a realistic backbone structure. Here, we introduce and validate two novel workflows aimed at predicting peptide binding behaviors in MMC, specifically targeting methacrylate-based resins. Our first achievement was the development of an all-atom model of a commercial MMC resin surface, incorporating its polymethacrylic backbone. Furthermore, we established and tested a workflow for rapid calculations of binding free energies (ΔG) with 10 linear peptides as target molecules. These ΔG calculations were effectively used to predict Langmuir constants, achieving a high coefficient of determination (R²) of 0.96. In subsequent benchmarking tests, our model outperformed established, simpler resin surface models in terms of predictive capabilities.

Exploring preferred binding domains of IgG1 mAbs to multimodal adsorbents using a combined biophysics and simulation approach

In this work, we employ a recently developed biophysical technique that uses diethylpyrocarbonate (DEPC) covalent labeling and mass spectrometry for the identification of mAb binding patches to two multimodal cation exchange resins at different pH. This approach compares the labeling results obtained in the bound and unbound states to identify residues that are sterically shielded and thus located in the mAb binding domains. The results at pH 6 for one mAb (mAb B) indicated that while the complementarity determining region (CDR) had minimal interactions with both resins, the FC domain was actively involved in binding. In contrast, DEPC/MS data with another mAb (mAb C) indicated that both the CDR and FC domains were actively involved in binding. These results corroborated chromatographic retention data with these two mAbs and their fragments and helped to explain the significantly stronger retention of both the intact mAb C and its Fab fragment. In contrast, labeling results with mAb C at pH 7, indicated that only the CDR played a significant role in resin binding, again corroborating chromatographic data. The binding domains identified from the DEPC/MS experiments were also examined using protein surface hydrophobicity maps obtained using a recently developed sparse sampling molecular dynamics (MD) approach in concert with electrostatic potential maps. These results demonstrate that the DEPC covalent labeling/mass spectrometry technique can provide important information about the domain contributions of multidomain proteins such as monoclonal antibodies when interacting with multimodal resins over a range of pH conditions.

Simulation of gas chromatographic separation based on random diffusion

色谱分离过程中的粒子扩散问题是色谱动力学研究的基础,深入理解粒子的扩散行为对优化分离操作条件、提升色谱性能和开发新型色谱柱尤为关键。现有的模拟方法多集中于局部过程的热力学研究,而整体的扩散分离过程报道并不多见。为此,该文基于微尺度受限空间内随机扩散的方法,通过动态追踪粒子的运动轨迹,实现粒子在气相色谱开管柱内的扩散全过程模拟。基于前期烷烃同系物的分离模拟研究,结合Kovats保留指数,分别建立了吸附步数与温度、吸附步数与碳数的函数关系,由此获得不同类型的同系物在不同温度条件下的分离参数系统。以醇类同系物的分离验证模拟的可靠性,结果表明保留时间的相对误差基本控制在5%以内,而峰宽相对误差在0.75%~60%之间。峰宽误差较大的原因在于:(1)参数化计算过程中未能充分迭代以及使用外推法;(2)模型中忽略了醇分子之间的氢键作用。该文提出的模拟方法虽然可以准确地预测色谱保留时间以及合理描述色谱峰的基本形貌特征,但尚有进一步发展空间,特别是增加对分子间相互作用的细节处理,例如可参考分子力学的方法建立分子间势函数和吸附步数的关系,利用分子力学计算的能量来取代参数化的吸附步数,从而实现更为精确的分离过程模拟。总体而言,该文所提出的模拟方法为优化色谱分离操作条件和开发新型色谱分离技术提供了有价值的参考。

Hydrophobic Modification of Carboxyl-Terminated Polyamidoamine Dendrimer Surface Creates a Potent Inhibitor of Amyloid-β Fibrillation

Amyloid β-peptide (Aβ) fibrillogenesis is a major hallmark of Alzheimer's disease (AD); inhibition of Aβ fibrillation is thus considered as a promising strategy for AD prevention and treatment. Our group has previously proposed the hydrophobic binding-electrostatic repulsion (HyBER) hypothesis, which provides guidance for the design of new amyloid inhibitors. Inspired by the HyBER hypothesis, we have herein proposed to synthesize hydrophobic-modified generation 5 carboxyl-terminated polyamidoamine dendrimer, denoted as PAMP, to create a potent inhibitor with a negatively charged hydrophobic surface. Results indicate that the PAMP with a proper degree of phenyl substitution (30-42%) alters the conformation of Aβ₄₂ through both hydrophobic binding and electrostatic repulsive forces on its surface. With these well-balanced interactions, the inhibitor can even completely inhibit the formation of β-sheet structure of the peptide, accompanied by changes at the level of the fibrillary architecture. Moreover, the results also indicate that changes of Aβ₄₂ aggregation pathway influenced by the PAMP occur at the very early stage, so the PAMP can significantly avoid the formation of toxic intermediates of Aβ₄₂ aggregation.

Charged Surface Regulates the Molecular Interactions of Electrostatically Repulsive Peptides by Inducing Oriented Alignment

Regulation of molecular orientation of charged dipeptides and involved interactions by electrostatic repulsion from like-charged surfaces were studied using all-atom molecular dynamics simulations. It was found that a charged surface can induce oriented alignment of like-charged peptides, and the oriented alignment leads to enhanced electrostatic repulsion between the peptide molecules. The findings are consistent with previous experimental results about the inhibition of charged protein aggregation using like-charged ion-exchange resin. Furthermore, the simulations provided molecular insights into this process, and demonstrated the distinct regulation effect of like-charged surfaces on the molecular interactions between peptides that possess an electric dipole structure. Both the charged surface and the electric dipole structure of peptides were confirmed to be crucial for the regulation. The research is expected to facilitate the rational design of surfaces or devices to regulate the behavior of amphoteric molecules such as proteins for both in vivo and in vitro applications, which would contribute to the regulation of protein-protein interactions and its application in life science and biotechnology.

Ionic strength-dependent changes in tentacular ion exchangers with variable ligand density. I. Structural properties

The ligand density critically affects the performance of ion-exchange resins in such measures as the adsorption capacity and transport characteristics. However, for tentacular and other polymer-modified exchangers, the mechanistic basis of the effect of ligand density on performance is not yet fully understood. In this study we map the ionic strength-dependent structural changes in tentacular cation exchangers with variable ligand densities as the basis for subsequent investigation of effects on functional properties. Inverse size-exclusion chromatography (ISEC), scanning electron microscopy (SEM) and small-angle x-ray scattering (SAXS) were used to assess the effect of ionic strength on the pore size and intraparticle architecture of resin variants with different ligand densities. Comparison of ISEC and cryo-SEM results shows a considerable reduction in average pore size with increasing ligand density; these methods also confirm an increase of average pore size at higher ionic strengths. SAXS analysis of ionic strength-dependent conformational changes in the grafted polyelectrolyte layer shows a characteristic ionomer peak at values of the scattering vector q (0.1-0.2Å(-1)) that depend on the ligand density and the ionic strength of the solution. This peak attribution reflects nanoscale changes in the structure of the grafted polyelectrolyte chains that can in turn be responsible for observed pore-size changes in the resins. Finally, salt breakthrough experiments confirm a stronger Donnan exclusion effect on pore accessibility for small ions in the high ligand density variant.

Molecular simulation study of feruloyl esterase adsorption on charged surfaces: effects of surface charge density and ionic strength

The surrounding conditions, such as surface charge density and ionic strength, play an important role in enzyme adsorption. The adsorption of a nonmodular type-A feruloyl esterase from Aspergillus niger (AnFaeA) on charged surfaces was investigated by parallel tempering Monte Carlo (PTMC) and all-atom molecular dynamics (AAMD) simulations at different surface charge densities (±0.05 and ±0.16 C·m(-2)) and ionic strengths (0.007 and 0.154 M). The adsorption energy, orientation, and conformational changes were analyzed. Simulation results show that whether AnFaeA can adsorb onto a charged surface is mainly controlled by electrostatic interactions between AnFaeA and the charged surface. The electrostatic interactions between AnFaeA and charged surfaces are weakened when the ionic strength increases. The positively charged surface at low surface charge density and high ionic strength conditions can maximize the utilization of the immobilized AnFaeA. The counterion layer plays a key role in the adsorption of AnFaeA on the negatively charged COOH-SAM. The native conformation of AnFaeA is well preserved under all of these conditions. The results of this work can be used for the controlled immobilization of AnFaeA.

Antibody-ligand interactions for hydrophobic charge-induction chromatography: a surface plasmon resonance study

This article describes the use of surface plasmon resonance (SPR) spectroscopy to study antibody-ligand interactions for hydrophobic charge-induction chromatography (HCIC) and its versatility in investigating the surface and solution factors affecting the interactions. Two density model surfaces presenting the HCIC ligand (mercapto-ethyl-pyridine, MEP) were prepared on Au using a self-assembly technique. The surface chemistry and structure, ionization, and protein binding of such model surfaces were characterized by X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure (NEXAFS), contact-angle titration, and SPR, respectively. The influences of the surface and solution factors, e.g., ligand density, salt concentration, and solution pH, on protein adsorption were determined by SPR. Our results showed that ligand density affects both equilibrium and dynamic aspects of the interactions. Specifically, a dense ligand leads to an increase in binding strength, rapid adsorption, slow desorption, and low specificity. In addition, both hydrophobic interactions and hydrogen bonding contribute significantly to the protein adsorption at neutral pH, while the electrostatic repulsion is overwhelmed under acidic conditions. The hydrophobic interaction at a high concentration of lyotropic salt would cause drastic conformational changes in the adsorbed protein. Combined with the self-assembly technique, SPR proves to be a powerful tool for studying the interactions between an antibody and a chromatographic ligand.

Molecular modeling of the affinity chromatography of monoclonal antibodies

Molecular modeling is a methodology that offers the possibility of studying complex systems such as protein-ligand complexes from an atomistic point of view, making available information that can be difficultly obtained from experimental studies. Here, a protocol for the construction of molecular models of the interaction between antibodies and ligands that can be used for an affinity chromatography process is presented. The outlined methodology focuses mostly on the description of a procedure that may be adopted to determine the structure and free energy of interaction between the antibody and the affinity ligand. A procedure to extend the proposed methodology to include the effect of the environment (buffer solution, spacer, support matrix) is also briefly outlined.

Insight into the inhibition effect of acidulated serum albumin on amyloid β-protein fibrillogenesis and cytotoxicity

Alzheimer's disease (AD) is the most prevalent form of dementia, and aggregation of amyloid β-proteins (Aβ) into soluble oligomers and fibrils has been implicated in the pathogenesis of AD. Herein we developed acidulated serum albumin for the inhibition of Aβ42 fibrillogenesis. Bovine serum albumin (BSA) was modified with diglycolic anhydride, leading to the coupling of 14.5 more negative charges (carboxyl groups) on average on each protein surface. The acidulated BSA (A-BSA) was characterized and confirmed to keep the tertiary structure and stability of BSA. Extensive biophysical and biological analyses showed that A-BSA significantly inhibited Aβ42 fibrillogenesis and mitigated amyloid cytotoxicity. As compared to the Aβ42-treated group (cell viability, 50%), the cell viability increased to 88% by the addition of equimolar A-BSA. The inhibitory effect was remarkably higher than that of BSA at the same concentration. On the basis of the experimental findings, a mechanistic model was proposed. The model considers that Aβ42 is bound to the A-BSA surface by hydrophobic interactions, but the widely distributed negative charges on the A-BSA surface give rise to electrostatic repulsions to the bound Aβ42 that is also negatively charged. The two well-balanced opposite forces make Aβ42 adopt extended conformations instead of the β-sheet structure that is necessary for the on-pathway fibrillogenesis, even when the protein is released off the surface. Thus, A-BSA greatly slows down the fibrillation and changes the fibrillogenesis pathway, leading to the formation of less toxic aggregates. The findings and the mechanistic model offer new insights into the development of more potent inhibitors of Aβ fibrillogenesis and cytotoxicity.

Tris(hydroxymethyl)aminomethane-functionalized agarose particles: parameters affecting the binding of bovine serum albumin

A new protein adsorbent is introduced based on the coupling of the common buffer ion, tris(hydroxymethyl)aminomethane, to the agarose gel Sepharose HP from GE Healthcare Bio-Sciences AB, Uppsala, Sweden. The article describes the synthesis of the new adsorbent and the use of BSA as a model in a binding study. By optimization of the coupling procedure, a maximum ligand density of 63.5 μmol/mL gel could be obtained. Adsorption equilibria were investigated in the pH range 5.0-8.0 and at salt concentrations of 0-0.4 mol/L. Binding of BSA under different conditions indicated that both electrostatic interaction and hydrogen bonding were involved in the adsorption process where the former played a major role.