A QM/MM MD study of the pH-dependent ring-opening catalysis and lid motif flexibility in glucosamine 6-phosphate deaminase
文献信息
Yuan Zhao, Nanhao Chen, Ruibo Wu, Zexing Cao
The glucosamine 6-phosphate deaminase (NagB), which catalyzes the conversion of D-glucosamine 6-phosphate (GlcN6P) into D-fructose 6-phosphate (F6P) and ammonia, determines the final metabolic fate of N-acetylglucosamine (GlcNAc). Here using state-of-the-art ab initio QM/MM MD simulations, we have explored the plausible mechanisms for the enzymatic ring-opening of GlcN6P in the basic environment. Two different proton-shuttle mechanisms have been proposed. Calculations show that the protonated state of the amino group in the substrate dominates the concerted and stepwise catalytic pathways and a catalytic triad plays an important role in mediating the proton transfer and the resulting ring-opening process. The free energy barrier for the rate-determining step in the low-energy stepwise reaction is 17.9 kcal mol−1. In acidic solution, the lid motif prefers a closed state while it always stays in the open state in basic solution upon substrate binding, which is basically dominated by the protonated state of the residue His145.
期刊推荐

Chemical Reviews

Chemistry of Heterocyclic Compounds

Doklady Chemistry

Chemical & Pharmaceutical Bulletin

Australian Journal of Chemistry

Journal of the American Chemical Society

Accounts of Chemical Research

Journal of the Chinese Chemical Society

Anti-Corrosion Methods and Materials

Canadian Metallurgical Quarterly
相关文献
Influence of Er3+ concentration and Ln3+ on the Judd–Ofelt parameters in LnOCl (Ln = Y, La, Gd) phosphors
Chunfeng Yu, Baojiu Chen, Xizhen Zhang, Xiangping Li, Jinsu Zhang, Sai Xu, Hongquan Yu, Jiashi Sun, Yongze Cao, Haiping Xia
DOI: 10.1039/C9CP06755H
Molecular design of anti-spindle-like molecules by use of siloxanyl terminals for a thermotropic bicontinuous cubic phase
Akane Kawafuchi, Shoichi Kutsumizu, Yuki Kawase, Issei Tokiwa, Taro Udagawa, Yohei Miwa
DOI: 10.1039/C9CP06831G
Solar-driven plasmonic heterostructure Ti/TiO2−x with gradient doping for sustainable plasmon-enhanced catalysis
Chaoqun Cheng, Muhammad Nadeem Akram, Ola Nilsen, Nini Pryds, Kaiying Wang
DOI: 10.1039/D0CP00672F
Clarifying the impacts of surface hydroxyls on CO oxidation on CeO2(100) surfaces: a DFT+U study
Hui Zhou, Dong Wang, Xue-Qing Gong
DOI: 10.1039/D0CP00204F
Dynamic nuclear polarization and ESR hole burning in As doped silicon
J. Järvinen, D. Zvezdov, J. Ahokas, S. Sheludiakov, L. Lehtonen, S. Vasiliev, L. Vlasenko, Y. Ishikawa, Y. Fujii
DOI: 10.1039/C9CP06859G
Phosphorus-based metal-free Z-scheme 2D van der Waals heterostructures for visible-light photocatalytic water splitting: a first-principles study
Junyu Lang
DOI: 10.1039/D0CP00637H
Structural and electronic properties of NaTaO3 cubic nanowires
Guilherme Ribeiro Portugal, Jeverson Teodoro Arantes
DOI: 10.1039/C9CP06769H
Molecular insights on NaCl crystal formation approaching PVDF membranes functionalized with graphene
Maria Luisa Perrotta, Francesca Macedonio, Lidietta Giorno, Wanqin Jin, Annarosa Gugliuzza, Elena Tocci
DOI: 10.1039/D0CP00928H
Binary aromatic self-assembled monolayers: electrostatic properties and charge tunneling rates across the molecular framework
Andika Asyuda, Xianglong Wan, Michael Zharnikov
DOI: 10.1039/D0CP01740J
Impact of t-butyl substitution in a rubrene emitter for solid state NIR-to-visible photon upconversion
Edvinas Radiunas, Manvydas Dapkevičius, Steponas Raišys, Saulius Juršėnas, Augustina Jozeliūnaitė, Tomas Javorskis, Ugnė Šinkevičiūtė, Edvinas Orentas, Karolis Kazlauskas
DOI: 10.1039/D0CP00144A
您可能还喜欢
3 - (二氟甲基)-1 -氟苯(CAS号:26029-52-7)适用哪些法规指南?
3 - (二氟甲基)-1 -氟苯需遵循联合国全球化学品统一分类和标签制度(GHS),包括急性毒性、皮肤腐蚀/刺激、严重眼损伤/眼刺激等分类。同时,该化合物还需符...
3,5-二甲基苯胺(CAS号:108-69-0)通常如何合成?
3,5-二甲基苯胺通常通过乙苯的氨解反应合成。反应中使用硫酸作为催化剂,反应温度为120-130°C。乙苯在硫酸存在下与氨反应,生成3,5-二甲基苯胺和苯胺副产...
3-甲基异噻唑-5-胺(CAS号:24340-76-9)安全吗?
3-甲基异噻唑-5-胺在适当使用和储存条件下是相对安全的,但在操作时应注意防护措施。应避免吸入粉尘,避免与皮肤和眼睛直接接触。在操作过程中,应穿戴适当的防护装备...
3-(1,3-Thiazol-2-yl)-1H-indole(CAS号:135531-86-1)通常如何合成?
3-(1,3-噻唑-2-基)-1H-吲哚通常通过多步合成方法制备。首先,由噻唑-2-基溴化物和吲哚进行偶联反应,得到中间体。然后,通过还原反应将中间体转化为所需...
4-溴-2-氟苯甲基氯(CAS号:85510-82-3)的主要用途是什么?
4-溴-2-氟苯甲基氯主要用于有机合成中间体,特别是在医药、农药和染料等领域。作为一种具有特定结构的化合物,它在合成复杂有机分子时扮演重要角色。
处理Fmoc-β-(3-噻吩基)-D-Ala-OH(CAS号:220497-90-5)时应注意哪些实验室安全事项?
处理Fmoc-β-(3-噻吩基)-D-Ala-OH时,应佩戴防护手套、护目镜和实验服。操作应在通风橱内进行。如发生泄露,应立即用大量水冲洗,并通知实验室管理人员...
氮化硅(CAS号:12033-89-5)通常如何合成?
氮化硅通常通过氮化硅的直接反应合成,即在高温下将四氯化硅与氨气反应。具体步骤是将四氯化硅和氨气混合并加热至1300-1700℃,在该条件下,四氯化硅与氨气反应生...
Cetirizine EP Impurity B DiHCl(CAS号:1000690-91-4)通常如何合成?
Cetirizine EP Impurity B DiHCl通常通过一锅法合成,首先将4-氯苯基-苯甲基氯甲酸酯与1-哌嗪乙酸反应,生成相应的酸,然后与盐酸反应...
如何储存1-哌啶-4-基丁-1-酮(CAS号:3509-15-7)?
1-哌啶-4-基丁-1-酮应储存在阴凉、干燥的地方,避免阳光直射。存储容器应密封,并确保通风良好。建议储存温度不超过25℃,湿度保持在相对较低的水平。
如何处理含有VORUCICLIB(CAS号:1000023-04-0)的废料?
含有VORUCICLIB的废料应进行专业的收集和处理,包括使用适当的容器进行隔离,避免与其他化学品接触。处理方法通常包括化学中和、沉淀反应或吸附过程,随后进行焚...
来源期刊
Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.



![tert-Butyl N-[(2-chloropyridin-4-yl)methyl]carbamate structure tert-Butyl N-[(2-chloropyridin-4-yl)methyl]carbamate structure](https://cnstatic.chemtradehub.com/structs/916/916210-27-0-9f95.webp)
![4-Chloro-3-(trifluoromethyl)-1H-pyrrolo[2,3-b]pyridine structure 4-Chloro-3-(trifluoromethyl)-1H-pyrrolo[2,3-b]pyridine structure](https://cnstatic.chemtradehub.com/structs/869/869335-75-1-a9d0.webp)