Molecular dynamics simulation and experimental validation of the effect of pH on protein desorption in hydrophobic charge induction chromatography

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。

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.

A change in structural integrity of c-Kit mutant D816V causes constitutive signaling

Several signaling pathways, ligands, and genes that regulate proliferative and self-renewal properties of the Hematopoietic Stem Cells (HSCs) have been studied meticulously. One of the signaling pathways that play a crucial role in the process of hematopoiesis is the Stem Cell Factor (SCF) mediated c-Kit pathway. The c-Kit is a Receptor Tyrosine Kinase (RTK), which is expressed in the cells including HSCs. It undergoes dimerization upon binding with its cognate ligand SCF. As a result, phosphorylation of the Juxtamembrane (JM) domain of c-Kit takes place at Tyr568 and Tyr570 residues. These phosphorylated residues become the docking sites for protein tyrosine phosphatases (PTPs) namely SHP-1 and SHP-2, which in turn cause dephosphorylation and negative regulation of the downstream signaling responsible for the cell proliferation. Interestingly, it has been reported that the mutation of c-Kit at D816V makes it independent of SCF stimulation and SHP-1/SHP-2 inhibition, thereby, causing its constitutive activation. The present study was commenced to elucidate the structural behavior of this mutation in the JM and A-loop region of c-Kit using Molecular Dynamics (MD) simulations of the wild-type and mutant c-Kit in unphosphorylated and phosphorylated states. The energy difference computed between the wild type and mutant (D816V) c-Kit, and protein-protein docking and complex analysis revealed the impact of this single residue mutation on the integrity dynamics of c-Kit that makes it independent of SHP-1/SHP-2 negative regulation.

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.