Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia.
Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, Pierottijeva 6, 10000 Zagreb, Croatia.
Int J Mol Sci. 2023 Aug 13;24(16):12747. doi: 10.3390/ijms241612747.
Dipeptidyl peptidase III (DPP III, EC 3.4.14.4) is a monozinc metalloexopeptidase that hydrolyzes dipeptides from the N-terminus of peptides consisting of three or more amino acids. Recently, DPP III has attracted great interest from scientists, and numerous studies have been conducted showing that it is involved in the regulation of various physiological processes. Since it is the only metalloenzyme among the dipeptidyl peptidases, we considered it important to study the process of binding and exchange of physiologically relevant metal dications in DPP III. Using fluorimetry, we measured the values for the binding of Zn, Cu, and Co to the catalytic site, and using isothermal titration calorimetry (ITC), we measured the values for the binding of these metals to an additional binding site. The structure of the catalytic metal's binding site is known from previous studies, and in this work, the affinities for this site were calculated for Zn, Cu, Co, and Mn using the QM approach. The structures of the additional binding sites for the Zn and Cu were also identified, and MD simulations showed that two Cu ions bound to the catalytic and inhibitory sites exchanged less frequently than the Zn ions bound to these sites.
二肽基肽酶 III（DPP III，EC 3.4.14.4）是一种单锌金属外肽酶，可从由三个或更多氨基酸组成的肽的 N 末端水解二肽。最近，DPP III 引起了科学家们的极大兴趣，并且进行了大量研究表明它参与了各种生理过程的调节。由于它是二肽基肽酶中唯一的金属酶，因此我们认为研究 DPP III 中与生理相关的二价金属离子的结合和交换过程很重要。我们使用荧光法测量了 Zn、Cu 和 Co 与催化位点结合的 值，并用等温热滴定法（ITC）测量了这些金属与额外结合位点结合的 值。先前的研究已知催化金属结合位点的结构，在这项工作中，我们使用 QM 方法计算了 Zn、Cu、Co 和 Mn 对该位点的亲和力。还确定了 Zn 和 Cu 的额外结合位点的结构，MD 模拟表明，与结合到这些位点的 Zn 离子相比，结合到催化和抑制位点的两个 Cu 离子交换不那么频繁。
