Article
Agricultural Engineering
Lijie Wang, Chao Xue, Gary Owens, Zuliang Chen
Summary: The study found that the laccase enzymes from Comamonas testosteroni FJ17 played a significant role in delignifying rice straw, resulting in a decrease in crystallinity and lignin content. Laccase primarily acted through the cleavage of beta-o-4 and alpha-aryl ether bonds to generate small molecular products.
BIORESOURCE TECHNOLOGY
(2022)
Article
Environmental Sciences
Wei-hao Yao, Ling-yun Mo, Liu-sen Fang, Li-tang Qin
Summary: A large number of antibiotics have been extensively used in various industries in recent years, which may lead to pollution in the aquatic environment and pose a threat to human health. This study aims to investigate the toxicity mechanism of five antibiotics on luciferase. Through a combination of toxicity testing, molecular docking, molecular dynamics, and binding free energy analysis, the researchers found that the toxicity and binding energy of the antibiotics were correlated. The shape compensation and specific interactions between the antibiotics and luciferase were identified as important factors in their toxicity. This research provides insights into the toxicity mechanisms of antibiotics and contributes to the risk assessment of antibiotic contaminants in the aquatic environment.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Biochemistry & Molecular Biology
Gizem Tatar, Tugba Taskin Tok, Bulent Ozpolat, A. Y. Mehmet
Summary: Protein kinases are successful drug targets, and eEF-2K has been identified as a potential therapeutic target for certain aggressive solid cancers. This study used modeling, docking analysis, and molecular dynamics simulations to understand the binding mechanism of eEF-2K with inhibitors, providing insights for the development of new selective and potential eEF-2K inhibitors.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Syarifuddin Husain, Ruzianisra Mohamed, Khairul Bariyyah Abd Halim, Siti Syairah Mohd Mutalip
Summary: In this study, a computational approach was used to identify the protein model of BAP1 and its potential inhibitors. The study revealed the molecular mechanism by which BAP1 regulates cancer and its crystal structure. Docking and simulating experiments showed that rearrangement of specific residues and conformational switching of BAP1 occurred upon binding to ubiquitin. Screening results shortlisted two potential BAP1 inhibitors, and molecular dynamics simulations further confirmed the stability of the BAP1-FDA755 complex.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Satya Narayan Sahu, Sneha Shriparna Satpathy, Chandana Mohanty, Subrat Kumar Pattanayak
Summary: The function of a protein is closely related to its structural properties, and mutations can impact protein functionality. Boerhavia diffusa contains various bioactive compounds, with Boeravinone J showing the best binding affinity to CDKAP1.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Avinash Kumar, Vinay Kumar Singh, Arvind M. Kayastha
Summary: This study determined the three-dimensional structure of fenugreek α-amylase using homology modeling and analyzed its molecular basis and mode of action through molecular dynamics simulations and molecular docking. The study identified functional groupings and binding interactions between the enzyme and its substrate maltose. The research provides valuable insights into the atomic-level molecular underpinnings of α-amylase interaction with maltose.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biotechnology & Applied Microbiology
Xiaoli Qin, Jinfeng Zhong, Yonghua Wang
Summary: This study investigated the interactions between Mut-T1 lipase and various fatty acids through molecular docking and molecular dynamics simulation. The results showed that Mut-T1 lipase had lower binding affinity for shorter-chain caprylic acid, but the complex remained stable during simulation, with decreasing solvent accessible surface area as the chain length of the fatty acid increased.
JOURNAL OF BIOTECHNOLOGY
(2021)
Article
Biochemical Research Methods
Sakshi Singh, Geeta Rai
Summary: This study presents a computational method that successfully designs the structure of IL12R and reveals its tight binding with IL12 ligand. The simulated molecular structure of IL12:IL12R complex provides a promising target complex for future IL12-based drug design.
COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING
(2022)
Article
Biochemistry & Molecular Biology
Sunita Kumari Yadav, Deepak Panwar, Ankita Singh, Meenakshi B. Tellis, Rakesh Shamsunder Joshi, Aparna Dixit
Summary: Aeromonas hydrophila, a Gram-negative bacterium, causes diseases in fish leading to significant losses in the aquaculture industry. The variability in virulence factors and toxins among different Aeromonas strains contributes to the heterogeneity of this bacteria genus. Through phylogenetic analysis and homology modeling, the aerolysin of Ah(EUS112) is identified as a channel protein and a potential drug target. Validation of the model using bioinformatics tools confirms its high quality, and specific drugs show higher affinity for binding to aerolysin and potentially inhibiting pore formation.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Yuying Yuan, Mst Nushrat Yiasmin, Nerissa Arviana Tristanto, Yujie Chen, Yaxian Liu, Shuyi Guan, Zijie Wang, Xiao Hua
Summary: The taste mechanism of steviol glycoside (SG) was investigated through molecular docking simulations and molecular dynamics simulations. The results showed that the sweetness intensity of SG can be attributed to its durative concurrent interaction with the receptor's binding site, while the bitterness is determined by the size and structure of the molecule.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Article
Biochemistry & Molecular Biology
Vishwanath Yadav, Jebin Ahmed, Abhijeet Thakur, Poorvi Vishwakarma, Shubha Singh, Punit Kaur, Arun Goyal
Summary: Structural and conformational insights of a putative beta-1,4-xylosidase (PsGH43F) of glycoside hydrolase family 43 from Pseudopedobacter saltans were investigated. The results revealed the presence of three conserved catalytic amino acid residues and the maximum binding affinity of PsGH43F with xylobiose. These findings are important for understanding the function and mechanism of PsGH43F.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Xi Gu, Ying Wang, Hanxun Wang, Hairui Wu, Wei Li, Jian Wang, Ning Li
Summary: This study utilized computational methods to build the structure of ETAR and predict its binding patterns with antagonists, identifying potential ETAR antagonists. Through virtual screening of a Traditional Chinese Medicine database, six compounds with the best binding energies were screened out, providing new therapeutic approaches for treating PAH.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Environmental Sciences
Xiaotong Wang, Fanping Meng, Bo Zhang, Yufan Xia
Summary: Long-term exposure to low levels of antibiotics leads to the accumulation of antibiotics in the environment and organisms, inducing the formation of antibiotic resistance genes. Seawater, as an important sink for contaminants, was used to degrade tetracyclines at environmentally relevant levels using laccase from Aspergillus sp. and mediators. The enzymatic structure of laccase was affected by the high salinity and alkaline of seawater, resulting in reduced affinity to the substrate. However, the laccase-SA system was able to completely degrade tetracyclines within 2 hours, demonstrating its potential for pollutant elimination in the marine environment.
Article
Biochemistry & Molecular Biology
Faizul Azam, Masood Alam Khan, Arif Khan, Shifa Ahmad, Syeda Fauzia Farheen Zofair, Hina Younus
Summary: In this study, ellagic acid (EA) was found to inhibit the activity of Cryptococcus neoformans laccase and the proliferation of the yeast cells. The molecular basis of the interaction between laccase and EA was unveiled, providing insights for the development of laccase inhibitors as potential anti-cryptococcal agents.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Arman Abdalla Ali, Shakhawan Ahmad Mhamad, Aso Hameed Hasan, Iqrar Ahmad, Siti Awanis Abdullah, Shajarahtunnur Jamil, Harun Patel, Sankaranarayanan Murugesan, Joazaizulfazli Jamalis
Summary: Acetylcholinesterase inhibitors (AChEIs) have been investigated for the treatment of Alzheimer's disease. This study focused on synthesizing chalcone derivatives with anti-cholinesterase potential. The compounds exhibited potent inhibitory activity against AChE, with compound 11i showing the most potent activity compared to the positive compound, Galantamine. Docking studies and molecular dynamics simulation confirmed the significant binding affinity and stability of compound 11i in the acetylcholinesterase enzyme.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Sameeksha Tiwari, Manika Awasthi, Swati Singh, Veda P. Pandey, Upendra N. Dwivedi
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2018)
Article
Biochemistry & Molecular Biology
Manika Awasthi, Swati Singh, Veda P. Pandey, Upendra N. Dwivedi
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2018)
Article
Chemistry, Physical
Manika Awasthi, Arun K. Upadhyay, Swati Singh, Veda P. Pandey, Upendra N. Dwivedi
MOLECULAR SIMULATION
(2018)
Review
Biochemistry & Molecular Biology
Swati Singh, Manika Awasthi, Veda P. Pandey, Upendra N. Dwivedi
CURRENT PROTEIN & PEPTIDE SCIENCE
(2018)
Article
Biochemistry & Molecular Biology
Chhedi Lal Gupta, Mohd Babu Khan, Dinakara Rao Ampasala, Salman Akhtar, Upendra Nath Dwivedi, Preeti Bajpai
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2019)
Article
Biochemistry & Molecular Biology
Om Prakash, Upendra Nath Dwivedi
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2020)
Article
Biochemistry & Molecular Biology
Akanksha Sharma, M. Hayatul Islam, Nida Fatima, Tarun K. Upadhyay, M. Kalim A. Khan, Upendra N. Dwivedi, Rolee Sharma
MOLECULAR BIOLOGY REPORTS
(2019)
Article
Multidisciplinary Sciences
Shubhra Rastogi, Saumya Shah, Ritesh Kumar, Divya Vashisth, Md Qussen Akhtar, Ajay Kumar, Upendra Nath Dwivedi, Ajit Kumar Shasany
Review
Biochemistry & Molecular Biology
Kusum Yadav, Anurag Yadav, Priyanka Vashistha, Veda P. Pandey, Upendra N. Dwivedi
CURRENT PROTEIN & PEPTIDE SCIENCE
(2019)
Review
Plant Sciences
Tanya Biswas, Upendra N. Dwivedi
Review
Biochemistry & Molecular Biology
Swati Singh, Veda P. Pandey, Kusum Yadav, Anurag Yadav, U. N. Dwivedi
CURRENT PROTEIN & PEPTIDE SCIENCE
(2020)
Article
Pharmacology & Pharmacy
Ankita Sharma, Sumit Kr Anand, Neha Singh, Upendra Nath Dwivedi, Poonam Kakkar
EUROPEAN JOURNAL OF PHARMACOLOGY
(2020)
Article
Agricultural Engineering
Tanya Biswas, Orusa Parveen, Veda P. Pandey, Archana Mathur, Upendra N. Dwivedi
INDUSTRIAL CROPS AND PRODUCTS
(2020)
Article
Biochemistry & Molecular Biology
Ankita Sharma, Sumit Kr Anand, Neha Singh, Akshay Dwarkanath, Upendra Nath Dwivedi, Poonam Kakkar
Summary: Berbamine alleviates non-alcoholic fatty liver disease by regulating the SIRT1/LKB1/AMPK pathway and modulating the expression of PPARs to improve lipid metabolism disorders. It also induces autophagy to alleviate fatty liver conditions.
Review
Biotechnology & Applied Microbiology
Sameeksha Tiwari, Upendra N. Dwivedi
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2019)