Tomić A, Berynskyy M, Wade R C, Tomić S
Department of Physical Chemistry, Rudjer Boskovic Institute, Bijenička cesta 54, 10000, Zagreb, Croatia.
Mol Biosyst. 2015 Nov;11(11):3068-80. doi: 10.1039/c5mb00465a.
The experimentally determined structures of human dipeptidyl peptidase III (DPP III) for the wild-type protein and for the complex of its E451A mutant with the peptide substrate, tynorphin, differ significantly in their overall shape. The two domains of the enzyme are separated by a wide cleft in the structure of the ligand-free enzyme, while in the ligand-bound mutant they are very close to each other, and the protein structure is extremely compact. Here, we applied a range of molecular dynamics simulation techniques to investigate the DPP III conformational landscape and the influence of ligand binding on the protein structure and dynamics. We used conventional, accelerated and steered methods to simulate DPP III and its complexes with tynorphin and with the preferred, synthetic, substrate Arg-Arg-2-naphthylamide. We found that DPP III can adopt a number of different forms in solution. The compact forms are more stable, but the open and partially closed states, spanning a wide range of conformations, can more effectively recognize the substrate which preferentially binds to the five-stranded β-core of the lower DPP III domain. The simulations indicated the existence of a dynamic equilibrium between open and semi-closed states and revealed two ways that the protein can close, leading to two distinct compact structures. The way in which the protein closes depends on the presence of the ligand.
实验测定的野生型人二肽基肽酶III（DPP III）及其E451A突变体与肽底物酪啡肽形成的复合物的结构，在整体形状上有显著差异。在无配体酶的结构中，酶的两个结构域被一个宽裂缝隔开，而在配体结合的突变体中，它们彼此非常接近，蛋白质结构极其紧凑。在此，我们应用了一系列分子动力学模拟技术来研究DPP III的构象景观以及配体结合对蛋白质结构和动力学的影响。我们使用常规、加速和引导方法来模拟DPP III及其与酪啡肽以及优选的合成底物精氨酸-精氨酸-2-萘酰胺形成的复合物。我们发现DPP III在溶液中可以呈现多种不同形式。紧凑形式更稳定，但开放和部分封闭状态跨越广泛的构象范围，能够更有效地识别优先结合到较低DPP III结构域的五链β-核心的底物。模拟表明开放态和半封闭态之间存在动态平衡，并揭示了蛋白质可以关闭的两种方式，从而导致两种不同的紧凑结构。蛋白质关闭的方式取决于配体的存在。
