PROTEIN SCIENCE
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2024
·Vol. 33
·期 9
·e5097
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IF 4.5
Ran Xu,Qican Pan,Guoliang Zhu,Yilin Ye,Minghui Xin,Zechen Wang,Sheng Wang,Weifeng Li,Yanjie Wei,Jingjing Guo,Liangzhen Zheng
Disulfide bonds, covalently formed by sulfur atoms in cysteine residues, play a crucial role in protein folding and structure stability. Considering their significance, artificial disulfide bonds are often introduced to enhance protein thermostability. Although an increasing number of tools can assist with this task, significant amounts of time and resources are often wasted owing to inadequate consideration. To enhance the accuracy and efficiency of designing disulfide bonds for protein thermostability improvement, we initially collected disulfide bond and protein thermostability data from extensive literature sources. Thereafter, we extracted various sequence- and structure-based features and constructed machine-learning models to predict whether disulfide bonds can improve protein thermostability. Among all models, the neighborhood context model based on the Adaboost-DT algorithm performed the best, yielding “area under the receiver operating characteristic curve” and accuracy scores of 0.773 and 0.714, respectively. Furthermore, we also found AlphaFold2 to exhibit high superiority in predicting disulfide bonds, and to some extent, the coevolutionary relationship between residue pairs potentially guided artificial disulfide bond design. Moreover, several mutants of imine reductase 89 (IR89) with artificially designed thermostable disulfide bonds were experimentally proven to be considerably efficient for substrate catalysis. The SS-bond data have been integrated into an online server, namely, ThermoLink, available at guolab.mpu.edu.mo/thermoLink .
研究领域:
生物信息学
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蛋白质工程
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计算生物学
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产品关联
DOI
PubMed
高影响因子
Membranes
·
2022
·Vol. 12
·期 2
·107
·
IF 4.562
Shukun Wei,Yaqing Yang,Yuan Yuan,Lingyu Du,Hongjuan Xue,Bo OuYang
The gaseous plant hormone ethylene influences many physiological processes in plant growth and development. Plant ethylene responses are mediated by a family of ethylene receptors, in which the N-terminal transmembrane domains are responsible for ethylene binding and membrane localization. Until now, little structural information was available on the molecular mechanism of ethylene responses by the transmembrane binding domain of ethylene receptors. Here, we screened different constructs, fusion tags, detergents, and purification methods of the transmembrane sensor domain of ethylene receptors. However, due to their highly hydrophobic transmembrane domain (TMD), only a KSI-fused LeETR21–131from tomato yielded a good-quality nuclear magnetic resonance (NMR) spectrum in the organic solvent. Interestingly, a dimer model of LeETR21–131built by the AlphaFold2 algorithm showed greatly converged structures. The interaction analysis of ethylene and LeETR21–131using molecular docking and molecular dynamics (MD) simulations demonstrated the potential binding sites of ethylene in LeETR21–131. Our exploration provides valuable knowledge for further understanding of the ethylene-perception process in ethylene receptors.Keywords:LeETR2;AlphaFold2;membrane protein expression;solution NMR;organic solvent;molecular docking;molecular dynamics simulation
研究领域:
植物生物学
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结构生物学
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生物化学
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产品关联
DOI
PubMed
高影响因子
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
·
2024
·
IF 2.7
Chunying Du,Hua Yin,Aowei Xie,Junhong Yu,Yifan Wang,Fengli Yao,Siyu Zhang,Yidan Zhang,Lu Liu,Peng Wang,Jianjun Dong,Ximing Xu
Hyperuricemia is mainly caused by insufficient renal urate excretion. Urate transporter 1 (URAT1), an organic anion transporter, is the main protein responsible for urate reabsorption. In this study, we utilized artificial intelligence-based AlphaFold2 program to construct URAT1 structural model. After molecular docking and conformational evaluation, four e-pharmacophoric models were constructed based on the complex structures of probenecid-URAT1, benzbromarone-URAT1, lesinurad-URAT1, and verinurad-URAT1. Combining pharmacophore modeling, molecular docking, MM/GBSA calculation and ADME prediction, 25 flavonoids were selected from the natural products database containing 10,968 molecules. Then, a model of HEK-293T cells overexpressing URAT1 was constructed, and the inhibitory activity to URAT1 of 25 flavonoids was evaluated by measuring their effect on cellular uptake of 6-carboxyfluorescein (6-CFL). Fisetin, baicalein, and acacetin showed the best activity with IC50 values of 12.77, 26.71, and 57.30 µM, respectively. Finally, the structure-activity relationship of these three flavonoids was analyzed by molecular docking and molecular dynamics simulations. The results showed that the carbonyl group on C-4 and hydroxyl group on C-7, C-4', and C-5’ in flavonoids were conducive for URAT1 inhibitory effects. This study facilitates the application of flavonoids in the development of URAT1 inhibitors.Communicated by Ramaswamy H. Sarma
研究领域:
药理学
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生物信息学
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分子生物学
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药物发现
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DOI
PubMed
高影响因子
BIOTECHNOLOGY AND BIOENGINEERING
·
2024
·
IF 3.5
Feng Cheng,Ke-Xiang Sun,Xiao-Xiao Gong,Wei Peng,Hua-Yue Zhang,Xi-Hang Liang,Ya-Ping Xue,Yu-Guo Zheng
D-amino acid oxidase (DAAO)-catalyzed selective oxidative deamination is a very promising process for synthesizing l -amino acids including l -phosphinothricin ( l -PPT, a high-efficiency and broad-spectrum herbicide). However, the wild-type DAAO's low activity toward unnatural substrates like d -phosphinothricin ( d -PPT) hampers its application. Herein, a DAAO from Caenorhabditis elegans ( Ce DAAO) was screened and engineered to improve the catalytic potential on d -PPT. First, we designed a novel growth selection system, taking into account the intricate relationship between the growth of Escherichia coli ( E. coli ) and the catalytic mechanism of DAAO. The developed system was used for high-throughput screening of gene libraries, resulting in the discovery of a variant (M6) with significantly increased catalytic activity against d -PPT. The variant displays different catalytic properties on substrates with varying hydrophobicity and hydrophilicity. Analysis using Alphafold2 modeling and molecular dynamic simulations showed that the reason for the enhanced activity was the substrate-binding pocket with enlarged size and suitable charge distribution. Further QM/MM calculations revealed that the crucial factor for enhancing activity lies in reducing the initial energy barrier of the reductive half reaction. Finally, a comprehensive binding-model index to predict the enhanced activity of DAAO toward d -PPT, and an enzymatic deracemization approach was developed, enabling the efficient synthesis of l -PPT with remarkable efficiency.
研究领域:
生物技术
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酶学
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蛋白质工程
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计算生物学
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化学生物学
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产品关联
DOI
PubMed
高影响因子
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