光谱学与光谱分析, 2020, 40 (8): 2518, 网络出版: 2020-12-03  

分子对接模拟法与多光谱法研究盐酸金霉素与胃蛋白酶的相互作用

Study on the Interaction Between Chlortetracycline Hydrochloride and Pepsin by Multispectral and Molecular Docking
作者单位
1 内蒙古科技大学化学与化工学院, 内蒙古 包头 014010
2 中国石油大学(华东)化学工程学院, 山东 青岛 266580
3 清华大学生命科学学院, 北京 100084
摘要
通过荧光光谱法、 紫外-可见吸收光谱法、 三维荧光光谱法、 圆二色谱法(CD)、 同步荧光光谱法和分子对接模拟法等方法研究了CTC(金霉素)和PEP(胃蛋白霉)之间相互作用的机制。 通过在不同温度下进行荧光强度测定, 确定了CTC与PEP相互作用及相关的猝灭机制。 通过实验结果计算出CTC与PEP的结合常数KA(298, 303和308 K) 为4.345×107, 2.836×107和1.734×107 L·mol-1 以及结合位点数n为1.618, 1.587和1.555。 n值接近于1, 这意味着在PEP与CTC之间只有一个结合位点。 基于热力学分析, 计算得298 K的热力学参数: ΔH(-70.13 kJ·mol-1), ΔG(-43.57 kJ·mol-1)和ΔS(-89.00 J·(mol·K)-1)。 由ΔH<0和ΔS<0可知范德华力和氢键是CTC和PEP之间的主要作用力, 由ΔG<0可知该反应自发进行。 根据Frster’s偶极-偶极非辐射能量转移理论, 计算得结合距离r=3.240 nm, 证明CTC与PEP之间存在非辐射能量转移。 分子对接模拟表明, CTC与PEP的结合位置在PEP的活性中心凹槽内, CTC与PEP的氨基酸残基VAL30, SER35, TYR189, THR74, THR77, GLY78和LEU112之间存在范德华力; CTC和GLU13, GLY217, ASP32, ASP215和GLY76等残基之间存在氢键作用力; CTC还与PEP的氨基酸残基TYR75存在疏水作用力。 各种作用力使CTC和PEP形成稳定的复合物。 通过紫外-可见吸收光谱、 同步荧光光谱和三维荧光光谱等技术分析, 可知CTC使PEP中的色氨酸(Trp)氨基酸残基周围环境极性增强, 疏水性减弱, 亲水性增强, 导致PEP二级结构发生改变。 圆二色谱图则表明CTC改变了PEP的部分二级结构, PEP中的α-螺旋结构的含量从11.6%增加到21.0%, β-折叠结构的含量从47.3%降至28.2%, β-转角(β-Turn)结构的含量从19.6%增加到24.2%, 无规则结构(Random coil)的含量从27.6%增加到34.2%, 表明CTC对PEP发生了相互作用, 改变了PEP周围的微环境, 导致PEP的二级结构发生变化。 本研究结果有助于了解CTC与PEP的结合机理, 为CTC的合理使用提供了重要依据。
Abstract
The mechanism of interaction between CTC and PEP was investigated by using fluorescence spectra, UV-Vis absorption spectra, circular dichroism (CD), 3D fluorescence spectra, synchronous fluorescence spectra and molecular docking methods.The quenching mechanism associated with the CTC-PEP interaction was determined by performing fluorescence measurements at different temperatures. The binding constants (KA) at three temperatures (298, 303, and 308 K) were 4.345×107, 2.836×107 and 1.734×107 L·mol-1 respectively, and the number of binding sites (n) was 1.618, 1.587, and 1.555, respectively. The n value was close to unity, which meant that there was only one independent class of binding site on pepsin for CTC. Based on the thermodynamic analysis, thermodynamic parameters at 298 K were calculated as follows: ΔH (-70.13 kJ·mol-1), ΔG (-43.57 kJ·mol-1), and ΔS (-89.00 J·(mol·K)-1). It was known from ΔH<0 and ΔS<0 that Van der Waals’ forces and hydrogen bonds were the main forces between CTC and PEP, the reaction was spontaneous from ΔG<0. According to Frster’s dipole-dipole non-radiative energy transfer theory, the specific binding distance of CTC-PEP system was 3.240 nm, it proved that there was non-radiative energy transfer between CTC and PEP. Molecular docking further suggested that CTC molecule bound within the active pocket of PEP. There were the van der Waals forces between CTC and residues VAL30, SER35, TYR189, THR74, THR77, GLY78 and LEU112 of PEP, and hydrogen bonds between CTC and GLU13, GLY217, ASP32, ASP215 and GLY76. There also was a hydrophobic interaction between CTC and the amino acid residue TYR75 of PEP. Various forces make CTC and PEP form a stable complex.The effects of CTC on the conformation of PEP were analyzed by UV absorption spectroscopy, synchronous fluorescence spectroscopyand 3D fluorescence spectroscopy. It is demonstrated in detail that CTC can increase microenvironment polarity and decrease the hydrophobicity of tryptophan (Trp) residues in PEP. Circular dichroism spectra indicated the secondary structure of PEP was partially changed by CTC with the percentage of α-helix increasing from 11.6% to 21.0% andthe percentage of β-sheet decreasing from 47.3% to 28.2%.The content of β-Turnstructure increased from 19.6% to 24.2%, and the content of Random coil increased from 27.6% to 34.2%, indicating that CTC interacted with PEP, and CTC changed the microenvironment around PEP, and also changed the secondary structure of PEP. The results of this study are helpful to understand the binding mechanism of CTC and PEP, and provide an important basis for the rational use of CTC.

王晓霞, 于洋洋, 马力通, 聂智华, 王正德, 崔金龙, 赛华征, 赵文渊. 分子对接模拟法与多光谱法研究盐酸金霉素与胃蛋白酶的相互作用[J]. 光谱学与光谱分析, 2020, 40(8): 2518. WANG Xiao-xia, YU Yang-yang, MA Li-tong, NIE Zhi-hua, WANG Zheng-de, CUI Jin-long, SAI Hua-zheng, ZHAO Wen-yuan. Study on the Interaction Between Chlortetracycline Hydrochloride and Pepsin by Multispectral and Molecular Docking[J]. Spectroscopy and Spectral Analysis, 2020, 40(8): 2518.

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