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Dynamic properties of dipeptidyl peptidase III from Bacteroides thetaiotaomicron and the structural basis for its substrate specificity – a computational study
Molecular BioSystems Pub Date : 2017-09-12 00:00:00 , DOI: 10.1039/c7mb00310b
M. Tomin 1, 2, 3 , S. Tomić 1, 2, 3
Affiliation  

Dipeptidyl peptidase III (DPP III) from the human gut symbiont Bacteroides thetaiotaomicron (Bt) is the first identified prokaryotic DPP III orthologue. It has low sequence similarity to the thoroughly studied human DPP III, and differently from eukaryotic orthologues it has a cysteine (Cys450) residue in the zinc-binding motif HEXXGH (HECLGH). The recently determined crystal structure of BtDPP III showed that its 3D structure, similar to the structure of the human DPP III, consists of two domains with a wide cleft in between. Although such a striking similarity of the 3D structures of orthologues with low sequence similarity is not surprising, it is no guarantee for similarity of their dynamic properties and the catalytic performance. Here, we report the results of the molecular modelling study of BtDPP III, wild type and its C450S mutant, as well as their complexes with characteristic DPP III substrates Arg–Arg–2-naphthylamide (RRNA) and Lys–Ala–2-naphtylamide (KANA). During several hundred nanoseconds of all-atom MD simulations of the wild type protein, the long range conformational changes, which can be described as protein ‘closing’, have been traced. We have determined a similar conformational change for the human orthologue as well. However, the amplitude of the change is lower for BtDPP III than for the human DPP III. The MD simulations have been performed using ff03, ff12SB and ff14SB force fields wherein the results of the last two better fit to the experimental results. The hydrogen bond analysis indicates reasons for higher substrate specificity of BtDPP III towards RRNA than KANA as well as for the decrease of the RRNA hydrolysis rate induced by the Cys450 to Ser mutation. The obtained results are in line with the experimental data.

中文翻译:

拟杆菌(Theactotaides thetaiotaomicron)二肽基肽酶III的动态性质及其底物特异性的结构基础-计算研究

来自人肠道共生细菌拟杆菌拟杆菌Bt)的二肽基肽酶III(DPP III)是最早鉴定的原核DPP III直系同源物。它与经过深入研究的人DPP III具有较低的序列相似性,并且与真核直向同源物不同,它在锌结合基序HEXXGH(HECLGH)中具有半胱氨酸(Cys450)残基。最近确定的Bt晶体结构DPP III表明,其3D结构与人DPP III的结构相似,由两个域组成,两个域之间有宽裂隙。尽管具有低序列相似性的直向同源物的3D结构如此惊人的相似性不足为奇,但不能保证它们的动态特性和催化性能具有相似性。在这里,我们报告Bt分子模型研究的结果DPP III,野生型及其C450S突变体,以及与DPP III特有底物Arg–Arg–2-萘酰胺(RRNA)和Lys–Ala–2-萘酰胺(KANA)的复合物。在野生型蛋白质的全原子MD模拟的几百纳秒内,可以追踪到远距离构象变化,这可以描述为蛋白质“关闭”。我们还确定了人类直系同源物的类似构象变化。但是,Bt DPP III的变化幅度要比人类DPP III的变化幅度低。使用ff03,ff12SB和ff14SB力场进行了MD仿真,其中最后两个的结果更好地适合了实验结果。氢键分析表明Bt底物特异性较高的原因DPP III比KANA更适合RRNA,并且可降低Cys450到Ser突变诱导的RRNA水解速率。所得结果与实验数据吻合。
更新日期:2017-10-25
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