水溶液中蛋白质构象转换的分子模拟研究
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摘要
蛋白质构象转换是涉及蛋白质异体表达、分离和制剂等过程的基础科学问题,研究溶液中蛋白质构象转换及其调控机制对于发展新型蛋白质复性、分离以及制剂技术具有重要意义。本文首先综述了分子模拟方法及其在蛋白质复性、分离和制剂等方面的研究现状与存在问题,提出以蛋白质构象转换为核心,以分子模拟为工具,研究渗透质、界面以及高分子等调控水溶液中蛋白质构象转换的微观机制,推进重组蛋白质复性、分离和制剂技术的创新和应用。
采用分子动力学方法研究尿素溶液中S肽链全原子模型蛋白质的去折叠过程。结果显示:低浓度时尿素通过与极性残基侧链的氢键作用富集于蛋白质表面形成包覆层,限制其结构伸展而稳定蛋白质;高浓度时尿素则通过与主链的氢键作用破坏蛋白质疏水核心和刚性骨架结构,导致其结构伸展变性。模拟结果与相关实验研究具有一致性。TMAO、甜菜碱、山梨醇、脯氨酸和甘油等渗透质呈现类似的作用规律,它们对于蛋白质构象的影响作用取决于其与蛋白质间形成氢键的强弱和分布。
采用分子动力学方法研究疏水孔道中46粒子β桶状粗粒化模型蛋白质构象转换及操作参数的影响规律。结果显示:强疏水性壁面吸附并分散蛋白质而抑制其聚集,但同时造成蛋白质结构伸展而变性。洗脱时蛋白质折叠和聚集过程同时启动并相互竞争。采用优化的吸附强度、吸附时间和洗脱强度以及快速梯度洗脱方式,可提高蛋白质天然构象的收率并抑制聚集。
采用动态Monte Carlo方法研究高分子抑制HP模型蛋白质聚集的作用机制。结果显示:溶液中部分变性态构象导致蛋白质聚集。具有合适疏水性和链长的高分子可通过疏水相互作用形成蛋白质-高分子复合物并进而抑制蛋白质聚集。调整高分子属性可调控溶液中蛋白质构象分布。
上述分子模拟结果展示了尿素、渗透质、疏水孔道和高分子等对蛋白质构象转换的微观作用机制,与实验研究结果具有一致性。模拟结果还显示通过人工构建微环境调控蛋白质构象转换的可行性。本文的研究成果对于蛋白质复性、分离和制剂新技术的研究及应用具有重要基础意义。
The understanding and manipulation of the conformational transition of protein in aqueous solution, which underlies protein refolding, separation and product formulation, is essential to technological development, particularly for recombinant proteins. This dissertation started with an overview of the recent advancement of molecular simulation methods as well as their application in the protein refolding, separation and aggregation. While the major objective of the present study was to explore the way to establish a favorable conformational transition via manipulating the microenviroment by osmolyte, solid surface and polymer, the ultimate goal was to provide a molecular insight for the innovation and application of protein processing techniques.
Molecular dynamics simulation of the unfolding of S-peptide as a model protein in urea solution was performed. It was shown that at a low concentration, urea molecules formed hydrogen bonds with the side chains of polar residues and thus restrained the unfolding of the S-peptide and led to an improved stability. In contrast, at a high concentration, urea molecules formed hydrogen bonds with the amino acids served as the backbone of the peptide and thus led to the unfolding of the peptide. The simulation results resembled the experimental observations reported elsewhere. The same mechanism was also valid to those osmolytes including TMAO, betaine, sorbitol, proline and glycerol, indicating that the effect of an osmolyte on the protein stability was determined by both the number and the distribution of hydrogen bonds formed with the protein.
Molecular dynamics simulation of a 46 beadsβ-barrel coarse-grained model protein in hydrophobic pore showed that the protein molecules in strong hydrophobic pore likely existed in the single but unfolded states while the aggregation was inhibited by a forced dispersion of protein molecules on the pore surface. Protein conformational transition, including both refolding and aggregating, was triggered simultaneously once the elution started in which the hydrophobic interaction with the pore surface was declined. High yield of native conformation could be obtained when performing the adsorption driven by a moderate intensity of hydrophobic interaction, followed by a fast gradient elution that favored the maximum partition of native protein.
Dynamic Monte Carlo simulation was performed to give a molecular insight into the inhibition of protein aggregation with polymer in aqueous solution. Here a lattice HP model was applied for both protein and polymer molecules. It was shown that the native protein aggregated once its native conformation became extended. The protein aggregation was intensified when the solution conditions favored the partially unfolded conformation as opposed to either the native or fully unfolded conformations. Introducing polymers of appropriate hydrophobicity and chain length into the solution was effective to inhibit protein aggregation, in which polymer molecules wrapped around proteins and formed protein-polymer complex thereby segregated the protein molecules. The conformation distribution of protein molecules can be manipulated by polymer compositions.
Above simulation results agreed well with experimental results while provided molecular insight of the interaction between the protein undergoing conformational transition with chemical species such as urea, osmolyte, hydrophobic pore and polymer. The feasibility of manipulating protein conformational transition through adjusting solution environment was demonstrated. The results presented above are of fundamental importance to the innovation and application of protein refolding, separation and formulation techniques.
采用分子动力学方法研究尿素溶液中S肽链全原子模型蛋白质的去折叠过程。结果显示:低浓度时尿素通过与极性残基侧链的氢键作用富集于蛋白质表面形成包覆层,限制其结构伸展而稳定蛋白质;高浓度时尿素则通过与主链的氢键作用破坏蛋白质疏水核心和刚性骨架结构,导致其结构伸展变性。模拟结果与相关实验研究具有一致性。TMAO、甜菜碱、山梨醇、脯氨酸和甘油等渗透质呈现类似的作用规律,它们对于蛋白质构象的影响作用取决于其与蛋白质间形成氢键的强弱和分布。
采用分子动力学方法研究疏水孔道中46粒子β桶状粗粒化模型蛋白质构象转换及操作参数的影响规律。结果显示:强疏水性壁面吸附并分散蛋白质而抑制其聚集,但同时造成蛋白质结构伸展而变性。洗脱时蛋白质折叠和聚集过程同时启动并相互竞争。采用优化的吸附强度、吸附时间和洗脱强度以及快速梯度洗脱方式,可提高蛋白质天然构象的收率并抑制聚集。
采用动态Monte Carlo方法研究高分子抑制HP模型蛋白质聚集的作用机制。结果显示:溶液中部分变性态构象导致蛋白质聚集。具有合适疏水性和链长的高分子可通过疏水相互作用形成蛋白质-高分子复合物并进而抑制蛋白质聚集。调整高分子属性可调控溶液中蛋白质构象分布。
上述分子模拟结果展示了尿素、渗透质、疏水孔道和高分子等对蛋白质构象转换的微观作用机制,与实验研究结果具有一致性。模拟结果还显示通过人工构建微环境调控蛋白质构象转换的可行性。本文的研究成果对于蛋白质复性、分离和制剂新技术的研究及应用具有重要基础意义。
The understanding and manipulation of the conformational transition of protein in aqueous solution, which underlies protein refolding, separation and product formulation, is essential to technological development, particularly for recombinant proteins. This dissertation started with an overview of the recent advancement of molecular simulation methods as well as their application in the protein refolding, separation and aggregation. While the major objective of the present study was to explore the way to establish a favorable conformational transition via manipulating the microenviroment by osmolyte, solid surface and polymer, the ultimate goal was to provide a molecular insight for the innovation and application of protein processing techniques.
Molecular dynamics simulation of the unfolding of S-peptide as a model protein in urea solution was performed. It was shown that at a low concentration, urea molecules formed hydrogen bonds with the side chains of polar residues and thus restrained the unfolding of the S-peptide and led to an improved stability. In contrast, at a high concentration, urea molecules formed hydrogen bonds with the amino acids served as the backbone of the peptide and thus led to the unfolding of the peptide. The simulation results resembled the experimental observations reported elsewhere. The same mechanism was also valid to those osmolytes including TMAO, betaine, sorbitol, proline and glycerol, indicating that the effect of an osmolyte on the protein stability was determined by both the number and the distribution of hydrogen bonds formed with the protein.
Molecular dynamics simulation of a 46 beadsβ-barrel coarse-grained model protein in hydrophobic pore showed that the protein molecules in strong hydrophobic pore likely existed in the single but unfolded states while the aggregation was inhibited by a forced dispersion of protein molecules on the pore surface. Protein conformational transition, including both refolding and aggregating, was triggered simultaneously once the elution started in which the hydrophobic interaction with the pore surface was declined. High yield of native conformation could be obtained when performing the adsorption driven by a moderate intensity of hydrophobic interaction, followed by a fast gradient elution that favored the maximum partition of native protein.
Dynamic Monte Carlo simulation was performed to give a molecular insight into the inhibition of protein aggregation with polymer in aqueous solution. Here a lattice HP model was applied for both protein and polymer molecules. It was shown that the native protein aggregated once its native conformation became extended. The protein aggregation was intensified when the solution conditions favored the partially unfolded conformation as opposed to either the native or fully unfolded conformations. Introducing polymers of appropriate hydrophobicity and chain length into the solution was effective to inhibit protein aggregation, in which polymer molecules wrapped around proteins and formed protein-polymer complex thereby segregated the protein molecules. The conformation distribution of protein molecules can be manipulated by polymer compositions.
Above simulation results agreed well with experimental results while provided molecular insight of the interaction between the protein undergoing conformational transition with chemical species such as urea, osmolyte, hydrophobic pore and polymer. The feasibility of manipulating protein conformational transition through adjusting solution environment was demonstrated. The results presented above are of fundamental importance to the innovation and application of protein refolding, separation and formulation techniques.
引文
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