Roy Anupom, Karttunen Mikko
Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A5B7, Canada.
Department of Physics and Astronomy, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A3K7, Canada.
J Chem Inf Model. 2024 Feb 12;64(3):983-1003. doi: 10.1021/acs.jcim.3c01966. Epub 2024 Jan 30.
L-tryptophan (l-Trp), a vital amino acid for the survival of various organisms, is synthesized by the enzyme tryptophan synthase (TS) in organisms such as eubacteria, archaebacteria, protista, fungi, and plantae. TS, a pyridoxal 5'-phosphate (PLP)-dependent enzyme, comprises α and β subunits that typically form an αβ tetramer. The enzyme's activity is regulated by the conformational switching of its α and β subunits between the open (T state) and closed (R state) conformations. Many microorganisms rely on TS for growth and replication, making the enzyme and the l-Trp biosynthetic pathway potential drug targets. For instance, , bacteria, , , bacteria, and parasitic protozoa depend on l-Trp synthesis. Antibiotic-resistant strains have emerged, underscoring the need for novel drugs targeting the l-Trp biosynthetic pathway, especially for salmonella-related infections. A single amino acid mutation can significantly impact enzyme function, affecting stability, conformational dynamics, and active or allosteric sites. These changes influence interactions, catalytic activity, and protein-ligand/protein-protein interactions. This study focuses on the impact of mutating the βGln114 residue on the catalytic and allosteric sites of TS. Extensive molecular dynamics simulations were conducted on E(PLP), E(AEX), E(A-A), and E(C) forms of TS using the WT, βQ114A, and βQ114N versions. The results show that both the βQ114A and βQ114N mutations increase protein backbone root mean square deviation fluctuations, destabilizing all TS forms. Conformational and hydrogen bond analyses suggest the significance of βGln114 drifting away from cofactor/intermediates and forming hydrogen bonds with water molecules necessary for l-Trp biosynthesis. The βQ114A mutation creates a gap between βAla114 and cofactor/intermediates, hindering hydrogen bond formation due to short side chains and disrupting β-sites. Conversely, the βQ114N mutation positions βAsn114 closer to cofactor/intermediates, forming hydrogen bonds with O3 of cofactors/intermediates and nearby water molecules, potentially disrupting the l-Trp biosynthetic mechanism.
L-色氨酸（L-Trp）是各种生物体生存所必需的氨基酸，在真细菌、古细菌、原生生物、真菌和植物等生物体中由色氨酸合酶（TS）合成。TS是一种依赖于磷酸吡哆醛（PLP）的酶，由α和β亚基组成，通常形成αβ四聚体。该酶的活性通过其α和β亚基在开放（T态）和闭合（R态）构象之间的构象转换来调节。许多微生物依靠TS进行生长和复制，这使得该酶和L-Trp生物合成途径成为潜在的药物靶点。例如，细菌、细菌、寄生虫原生动物依赖L-Trp合成。耐抗生素菌株的出现，凸显了针对L-Trp生物合成途径的新型药物的需求，特别是对于沙门氏菌相关感染。单个氨基酸突变可显著影响酶的功能，影响稳定性、构象动力学以及活性或别构位点。这些变化会影响相互作用、催化活性以及蛋白质-配体/蛋白质-蛋白质相互作用。本研究聚焦于βGln114残基突变对TS催化和别构位点的影响。使用野生型、βQ114A和βQ114N版本对TS的E(PLP)、E(AEX)、E(A-A)和E(C)形式进行了广泛的分子动力学模拟。结果表明，βQ114A和βQ114N突变均增加了蛋白质主链均方根偏差波动，使所有TS形式不稳定。构象和氢键分析表明，βGln114远离辅因子/中间体并与L-Trp生物合成所需的水分子形成氢键具有重要意义。βQ114A突变在βAla114与辅因子/中间体之间形成间隙，由于侧链短而阻碍氢键形成并破坏β位点。相反，βQ114N突变使βAsn114更靠近辅因子/中间体，与辅因子/中间体的O3和附近水分子形成氢键，可能破坏L-Trp生物合成机制。
