Article
Biochemical Research Methods
Isak Johansson-Akhe, Bjorn Wallner
Summary: InterPepScore, a graph neural network, is introduced as an additional scoring term to enhance the Rosetta FlexPepDock refinement protocol. Trained on simulation trajectories from FlexPepDock refinement of thousands of peptide-protein complexes generated by various docking schemes, the inclusion of InterPepScore consistently improves model quality. Its addition results in an increase in the number of complexes meeting a DockQ-score of 0.49 (Medium quality) or better in an independent benchmark, from 14.8% to 26.1%.
Article
Chemistry, Multidisciplinary
Mikhail Ignatov, Akhil Jindal, Sergei Kotelnikov, Dmitri Beglov, Ganna Posternak, Xiaojing Tang, Pierre Maisonneuve, Gennady Poda, Robert A. Batey, Frank Sicheri, Adrian Whitty, Peter J. Tonge, Sandor Vajda, Dima Kozakov
Summary: The design of PROTACs involves bringing an E3 ligase close to a target protein for ubiquitination and degradation. A method for generating accurate structural models of E3 ligase-PROTAC-target protein complexes is presented, which uses computational innovations to eliminate unfavorable protein poses and cluster models. The results demonstrate the predictability of the models and their application in predicting the activity of PROTACs. The method is validated with known PROTAC structures and a blind test.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biotechnology & Applied Microbiology
Helena Engel, Felix Guischard, Fabian Krause, Janina Nandy, Paulina Kaas, Nico Hoefflin, Maja Koehn, Normann Kilb, Karsten Voigt, Steffen Wolf, Tahira Aslan, Fabian Baezner, Salome Hahne, Carolin Ruckes, Joshua Weygant, Alisa Zinina, Emir Bora Akmeric, Enoch B. Antwi, Dennis Dombrovskij, Philipp Franke, Klara L. Lesch, Niklas Vesper, Daniel Weis, Nicole Gensch, Barbara Di Ventura, Mehmet Ali Oeztuerk
Summary: The use of D-peptides, composed of dextrorotatory enantiomers, offers improved stability and efficacy in peptide therapeutics. The web server finDr allows for the computational identification and optimization of D-peptide ligands to any protein structure, providing a tool for predicting optimal binders. This approach facilitates D-peptide discovery in biotechnology and biomedicine, presenting a cost-effective and user-friendly alternative to conventional methods.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Sungwoo Choi, Seung Han Son, Min Young Kim, Insung Na, Vladimir N. Uversky, Chul Geun Kim
Summary: Proteins play a crucial role in biological processes, and abnormal protein-protein interactions (PPIs) are associated with diseases such as cancer. Studying protein-peptide interactions (PpIs) is challenging due to their dynamic and transient nature. In this study, an improved molecular docking method (3SD) was developed to predict PpI poses, addressing issues like intrinsically disordered regions (IDRs) and artificial intelligence-predicted structures. The study provides an improved solution to studying PpIs through computational docking and has the potential to contribute to PPIs-targeted drug discovery.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemical Research Methods
Aleksandra E. Badaczewska-Dawid, Sebastian Kmiecik, Michal Kolinski
Summary: The three-stage molecular docking protocol for GPCR-peptide ligands produces high resolution models for the top-scored complexes, which can be further refined and improved to sub-angstrom accuracy through high-resolution refinement and minimization.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Sameera Sastry Panchangam
Summary: The study focuses on Baby Boom (BBM), a transcription factor that plays a crucial role in embryogenesis, transformation, and development in plants. By conducting in silico analysis, the study aims to understand BBM's sequence and conservation, predict protein interactions and ligands, and determine the binding site residues. Additionally, the study also predicts peptide sequences that interact with BBM, which could be used for further research and design of peptide mimetics.
Article
Biochemistry & Molecular Biology
Reena Guntamadugu, Ranjani Ramakrishnan, Gowtham Darala, Sangeetha Kothandan
Summary: Peptides, with high specificity and biological activity, have been used to develop antiviral drugs. This study focused on investigating protein-peptide interactions against Dengue virus and identified two potential peptides with stable binding and desirable properties. Further studies are needed to confirm their efficacy.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Multidisciplinary
Shafi Mahmud, Suvro Biswas, Gobindo Kumar Paul, Mohasana Akter Mita, Shamima Afrose, Md Robiul Hasan, Mst Sharmin Sultana Shimu, Mohammad Abu Raihan Uddin, Md Salah Uddin, Shahriar Zaman, K. M. Kaderi Kibria, Md Arif Khan, Talha Bin Emran, Md Abu Saleh
Summary: This study explored the potential of antiviral peptides in inhibiting the main protease of SARS-CoV-2, showing promising results in binding energy and stability of peptide-main protease complexes. Further wet-lab experiments are needed to confirm these findings.
ARABIAN JOURNAL OF CHEMISTRY
(2021)
Article
Chemistry, Physical
Christopher D. Fage, Simone Kosol, Matthew Jenner, Carl Oster, Angelo Gallo, Milda Kaniusaite, Roman Steinbach, Michael Staniforth, Vasilios G. Stavros, Mohamed A. Marahiel, Max J. Cryle, Jozef R. Lewandowski
Summary: Nonribosomal peptides are a type of natural products constructed by nonribosomal peptide synthetases (NRPSs), and the communication between donor epimerization (E) and acceptor condensation (C) domains found at the termini of NRPS subunits is mediated by COM domains. Biophysical studies using X-ray crystallography, circular dichroism spectroscopy, NMR spectroscopy, and molecular dynamics simulations show that the donor COM region is intrinsically disordered and folds into a helical motif upon binding to an acceptor, suggesting a dynamic interaction interface. Further experiments demonstrate the importance of donor COM region in binding the acceptor C domain, pointing towards potential noncognate domain crosstalk.
Article
Biochemistry & Molecular Biology
Mateusz Zalewski, Sebastian Kmiecik, Michal Kolinski
Summary: This study proposes an MD-based scoring approach to identify high-accuracy protein-peptide models from CG docking simulations. The accuracy of the scoring can be significantly affected by the quality of the reconstructed protein receptor structures.
Article
Food Science & Technology
Haopeng Dai, Min He, Guilin Hu, Zhongrong Li, Abdulbaset Al-Romaima, Zhouwei Wu, Xiaocui Liu, Minghua Qiu
Summary: The study aimed to investigate the ACE inhibitory effect of bioactive peptides from green coffee beans. Through in vitro and in silico methods, it was found that two peptides have the potential to be used as antihypertensive agents.
Article
Astronomy & Astrophysics
Pan-Pan Shi, Zhen-Hua Zhang, Feng-Kun Guo, Zhi Yang
Summary: In this study, the properties and production of the ground-state D+D- hadronic atom A(D+D-), called dionium, are investigated. The mass, binding energy, and decay width of the dionium are predicted using nonrelativistic effective field theory. The estimated cross-sections for the prompt and direct production of the dionium provide valuable information on charmed meson interaction and understanding charmoniumlike states.
Article
Food Science & Technology
Haixi You, Tianliang Wu, Wei Wang, Yiju Li, Xuebo Liu, Long Ding
Summary: This study found that quinoa protein-derived peptides, particularly QPH1 with molecular weight less than 1 kDa, exhibited strong DPP-IV inhibitory activity. Peptides IPI, IPV, VAYPL, and IPIN showed the highest inhibitory activities and were identified as competitive inhibitors of DPP-IV.
FOOD RESEARCH INTERNATIONAL
(2022)
Article
Food Science & Technology
Fan Ying, Shiqi Lin, Jingyu Li, Xuewu Zhang, Gu Chen
Summary: MAOs, essential deamination enzymes for neurotransmitters and amines, are potential targets for treating mental and neurodegenerative disorders. By utilizing ultrafiltration purification and in silico prediction, inhibitory peptides targeting MAOs were identified from soybean protein hydrolysate, demonstrating potential as functional nutraceuticals for treating neurodegenerative and mental disorders, with PLYSN showing strong inhibition activity against MAO-B.
Article
Biochemistry & Molecular Biology
Charles Christoffer, Daisuke Kihara
Summary: Proteins play key roles in cellular processes through physical interactions with other proteins and nucleic acids. Understanding the mechanisms of these processes requires considering the 3D structures of protein complexes. Protein docking has been used to computationally generate structure models, but flexibility consideration has been limited. New methods are needed to model ordered proteins undergoing large-scale conformational changes for elucidating their molecular-level functions.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
