Maiangwa Jonathan, Mohamad Ali Mohd Shukuri, Salleh Abu Bakar, Rahman Raja Noor Zaliha Raja Abd, Normi Yahaya M, Mohd Shariff Fairolniza, Leow Thean Chor
Department of Cell and Molecular Biology/Enzyme Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Serlangor, Malaysia.
Department of Biochemistry/Enzyme Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.
PeerJ. 2017 May 18;5:e3341. doi: 10.7717/peerj.3341. eCollection 2017.
The dynamics and conformational landscape of proteins in organic solvents are events of potential interest in nonaqueous process catalysis. Conformational changes, folding transitions, and stability often correspond to structural rearrangements that alter contacts between solvent molecules and amino acid residues. However, in nonaqueous enzymology, organic solvents limit stability and further application of proteins. In the present study, molecular dynamics (MD) of a thermostable T1 lipase was performed in different chain length polar organic solvents (methanol, ethanol, propanol, butanol, and pentanol) and water mixture systems to a concentration of 50%. On the basis of the MD results, the structural deviations of the backbone atoms elucidated the dynamic effects of water/organic solvent mixtures on the equilibrium state of the protein simulations in decreasing solvent polarity. The results show that the solvent mixture gives rise to deviations in enzyme structure from the native one simulated in water. The drop in the flexibility in HO, MtOH, EtOH and PrOH simulation mixtures shows that greater motions of residues were influenced in BtOH and PtOH simulation mixtures. Comparing the root mean square fluctuations value with the accessible solvent area (SASA) for every residue showed an almost correspondingly high SASA value of residues to high flexibility and low SASA value to low flexibility. The study further revealed that the organic solvents influenced the formation of more hydrogen bonds in MtOH, EtOH and PrOH and thus, it is assumed that increased intraprotein hydrogen bonding is ultimately correlated to the stability of the protein. However, the solvent accessibility analysis showed that in all solvent systems, hydrophobic residues were exposed and polar residues tended to be buried away from the solvent. Distance variation of the tetrahedral intermediate packing of the active pocket was not conserved in organic solvent systems, which could lead to weaknesses in the catalytic H-bond network and most likely a drop in catalytic activity. The conformational variation of the lid domain caused by the solvent molecules influenced its gradual opening. Formation of additional hydrogen bonds and hydrophobic interactions indicates that the contribution of the cooperative network of interactions could retain the stability of the protein in some solvent systems. Time-correlated atomic motions were used to characterize the correlations between the motions of the atoms from atomic coordinates. The resulting cross-correlation map revealed that the organic solvent mixtures performed functional, concerted, correlated motions in regions of residues of the lid domain to other residues. These observations suggest that varying lengths of polar organic solvents play a significant role in introducing dynamic conformational diversity in proteins in a decreasing order of polarity.
蛋白质在有机溶剂中的动力学和构象态势是在非水过程催化中可能令人感兴趣的事件。构象变化、折叠转变和稳定性通常对应于改变溶剂分子与氨基酸残基之间接触的结构重排。然而，在非水酶学中，有机溶剂限制了蛋白质的稳定性和进一步应用。在本研究中，在不同链长的极性有机溶剂（甲醇、乙醇、丙醇、丁醇和戊醇）与水的混合体系中进行了热稳定T1脂肪酶的分子动力学（MD）模拟，溶剂浓度为50%。基于MD结果，主链原子的结构偏差阐明了水/有机溶剂混合物对蛋白质模拟平衡态的动态影响，且溶剂极性递减。结果表明，溶剂混合物导致酶结构与在水中模拟的天然结构产生偏差。在HO、MtOH、EtOH和PrOH模拟混合物中柔性的降低表明，在BtOH和PtOH模拟混合物中残基的更大运动受到影响。将每个残基的均方根波动值与可及溶剂面积（SASA）进行比较，结果显示，残基的SASA值与高柔性几乎相应地呈高度相关，而与低柔性呈低SASA值相关。该研究进一步表明，有机溶剂影响了MtOH、EtOH和PrOH中更多氢键的形成，因此，可以推测蛋白质内氢键的增加最终与蛋白质的稳定性相关。然而，溶剂可及性分析表明，在所有溶剂体系中，疏水残基暴露在外，极性残基倾向于被埋在远离溶剂的位置。活性口袋的四面体中间体堆积的距离变化在有机溶剂体系中并不保守，这可能导致催化氢键网络减弱，很可能导致催化活性下降。溶剂分子引起的盖子结构域的构象变化影响了其逐渐打开。额外氢键和疏水相互作用的形成表明，相互作用协同网络的贡献可以在某些溶剂体系中保持蛋白质的稳定性。利用时间相关原子运动来表征原子坐标中原子运动之间的相关性。所得的交叉相关图显示，有机溶剂混合物在盖子结构域残基区域与其他残基之间进行功能性、协同性、相关性运动。这些观察结果表明，不同链长的极性有机溶剂在以递减的极性顺序引入蛋白质动态构象多样性方面发挥着重要作用。
