2023
Structure of the Pre-reaction Complex of FucT
ZEMANÍK, Július a Petr KULHÁNEKZákladní údaje
Originální název
Structure of the Pre-reaction Complex of FucT
Autoři
ZEMANÍK, Július a Petr KULHÁNEK
Vydání
XIX Discussions in Structural Molecular Biology and 6th User Meeting of CIISB (Czech Infrastructure for Integrative Structural Biology), 2023
Další údaje
Typ výsledku
Konferenční abstrakt
Utajení
není předmětem státního či obchodního tajemství
ISSN
Změněno: 6. 3. 2024 14:47, RNDr. Petr Kulhánek, Ph.D.
V originále
Helicobacter pylori is a severe human pathogen associated with several gastrointestinal disorders, including gastric inflammation, ulcers, and cancer. However, its primary treatment using antibiotics has become increasingly more challenging because of the emergence of antibiotic resistance. As a result, there is a growing need for novel antibacterial agents [1]. In order to design such new compounds, it is necessary to thoroughly understand the fundamental biochemical processes that could serve as therapeutic targets. The purpose of this study is to elucidate the enzyme structure of H. pylori glycosyltransferase FucT. FucT is an essential enzyme in the biosynthesis of type II blood group antigens that are thought to mask the bacteria from the host’s immune system. It consists of an N-terminal domain with the glycosyltransferase activity and a C-terminus that is responsible for dimerisation and, presumably, acceptor binding. Unfortunately, current experimental structures are monomeric and lack much of the carboxyl terminus which was removed as it hindered crystallisation efforts for X-ray studies. As a result, the crystal structures retained only 20 % of the original enzyme activity. The experimental structure of the fully active dimer complex remains unknown [2]. To resolve this limitation, we have decided to utilise a computational approach using Alphafold2. Alphafold2 is an ab initio structure prediction program capable of predicting several possible protein structures based on its primary sequence. While the program provides an internal ranking of these structures, it remains unclear if the arrangement of the polypeptide chains is optimal even in the best-ranking prediction. Using Alphafold2, we have obtained the protein dimer predictions for 3 sequences of FucT differing in their C-terminus length. We have performed molecular mechanics simulations on every structure prediction for each of the three sequences to select the most optimal structure for each one. Next, we studied the effect of the C-terminal length on the dimer complex stability. The best of these structures will be used in the future for state-of-the-art hybrid QM/MM simulations. The aim is to determine the transition state geometry of the reaction which could become the starting point for the rational drug design of transition state mimetics for new H. pylori treatment options. 1. J. C. Yang, World J Gastroenterol., 20, (2014), 5283. 2. H. Y. Sun, J. Biol. Chem., 282, (2007), 9973–9982.
Česky
Helicobacter pylori is a severe human pathogen associated with several gastrointestinal disorders, including gastric inflammation, ulcers, and cancer. However, its primary treatment using antibiotics has become increasingly more challenging because of the emergence of antibiotic resistance. As a result, there is a growing need for novel antibacterial agents [1]. In order to design such new compounds, it is necessary to thoroughly understand the fundamental biochemical processes that could serve as therapeutic targets. The purpose of this study is to elucidate the enzyme structure of H. pylori glycosyltransferase FucT. FucT is an essential enzyme in the biosynthesis of type II blood group antigens that are thought to mask the bacteria from the host’s immune system. It consists of an N-terminal domain with the glycosyltransferase activity and a C-terminus that is responsible for dimerisation and, presumably, acceptor binding. Unfortunately, current experimental structures are monomeric and lack much of the carboxyl terminus which was removed as it hindered crystallisation efforts for X-ray studies. As a result, the crystal structures retained only 20 % of the original enzyme activity. The experimental structure of the fully active dimer complex remains unknown [2]. To resolve this limitation, we have decided to utilise a computational approach using Alphafold2. Alphafold2 is an ab initio structure prediction program capable of predicting several possible protein structures based on its primary sequence. While the program provides an internal ranking of these structures, it remains unclear if the arrangement of the polypeptide chains is optimal even in the best-ranking prediction. Using Alphafold2, we have obtained the protein dimer predictions for 3 sequences of FucT differing in their C-terminus length. We have performed molecular mechanics simulations on every structure prediction for each of the three sequences to select the most optimal structure for each one. Next, we studied the effect of the C-terminal length on the dimer complex stability. The best of these structures will be used in the future for state-of-the-art hybrid QM/MM simulations. The aim is to determine the transition state geometry of the reaction which could become the starting point for the rational drug design of transition state mimetics for new H. pylori treatment options. 1. J. C. Yang, World J Gastroenterol., 20, (2014), 5283. 2. H. Y. Sun, J. Biol. Chem., 282, (2007), 9973–9982.
Anglicky
Helicobacter pylori is a severe human pathogen associated with several gastrointestinal disorders, including gastric inflammation, ulcers, and cancer. However, its primary treatment using antibiotics has become increasingly more challenging because of the emergence of antibiotic resistance. As a result, there is a growing need for novel antibacterial agents [1]. In order to design such new compounds, it is necessary to thoroughly understand the fundamental biochemical processes that could serve as therapeutic targets. The purpose of this study is to elucidate the enzyme structure of H. pylori glycosyltransferase FucT. FucT is an essential enzyme in the biosynthesis of type II blood group antigens that are thought to mask the bacteria from the host’s immune system. It consists of an N-terminal domain with the glycosyltransferase activity and a C-terminus that is responsible for dimerisation and, presumably, acceptor binding. Unfortunately, current experimental structures are monomeric and lack much of the carboxyl terminus which was removed as it hindered crystallisation efforts for X-ray studies. As a result, the crystal structures retained only 20 % of the original enzyme activity. The experimental structure of the fully active dimer complex remains unknown [2]. To resolve this limitation, we have decided to utilise a computational approach using Alphafold2. Alphafold2 is an ab initio structure prediction program capable of predicting several possible protein structures based on its primary sequence. While the program provides an internal ranking of these structures, it remains unclear if the arrangement of the polypeptide chains is optimal even in the best-ranking prediction. Using Alphafold2, we have obtained the protein dimer predictions for 3 sequences of FucT differing in their C-terminus length. We have performed molecular mechanics simulations on every structure prediction for each of the three sequences to select the most optimal structure for each one. Next, we studied the effect of the C-terminal length on the dimer complex stability. The best of these structures will be used in the future for state-of-the-art hybrid QM/MM simulations. The aim is to determine the transition state geometry of the reaction which could become the starting point for the rational drug design of transition state mimetics for new H. pylori treatment options. 1. J. C. Yang, World J Gastroenterol., 20, (2014), 5283. 2. H. Y. Sun, J. Biol. Chem., 282, (2007), 9973–9982.
Návaznosti
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