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001-es BibID:	BIBFORM113505
035-os BibID:	(cikkazonosító)795 (wos)000995540500001 (scopus)85160380650
Első szerző:	Balogh Gábor (gyógyszerész)
Cím:	The Interaction of Factor Xa and IXa with Non-Activated Antithrombin in Michaelis Complex : Insights from Enhanced-Sampling Molecular Dynamics Simulations / Balogh Gábor, Bereczky Zsuzsanna
Dátum:	2023
ISSN:	2218-273X
Megjegyzések:	The interaction between coagulation factors Xa and IXa and the activated state of their inhibitor, antithrombin (AT),have been investigated using X-ray diffraction studies. However, only mutagenesis data are available for non-activated AT. Our aim was to propose a model based on docking and advanced-sampling molecular dynamics simulations that can reveal the conformational behavior of the systems when AT is not binding a pentasaccharide. We built the initial structure for non-activated AT-FXa and AT-FIXa complexes using HADDOCK 2.4. The conformational behavior was studied using Gaussian accelerated molecular dynamics simulations. In addition to the docked complexes, two systems based on the X-ray structures were also simulated, with and without the ligand. The simulations revealed large variability in conformation for both factors. In the docking-based complex of AT-FIXa, conformations with stable Arg150?AT interactions can exist for longer time periods but the system also has a higher tendency for reaching states with very limited interaction with the "exosite" of AT. By comparing simulations with or without the pentasaccharide, we were able to gain insights into the effects of conformational activation on the Michaelis complexes. RMSF analysis and correlation calculations for the alpha-carbon atoms revealed important details of the allosteric mechanisms. Our simulations provide atomistic models for better understanding the conformational activation mechanism of AT against its target factors.
Tárgyszavak:	Orvostudományok Klinikai orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk
Megjelenés:	Biomolecules. - 13 : 5 (2023), p. 1-21. -
További szerzők:	Bereczky Zsuzsanna (1974-) (orvosi laboratóriumi diagnosztika szakorvos)
Pályázati támogatás:	OTKA-139293 OTKA OTKA-106294 OTKA OTKA-116228 OTKA
Internet cím:	Szerző által megadott URL DOI Intézményi repozitóriumban (DEA) tárolt változat
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001-es BibID:	BIBFORM122753
035-os BibID:	(WoS)001254476800001 (Scopus)85197183804
Első szerző:	Balogh Gábor
Cím:	Molecular Mechanisms of the Impaired Heparin Pentasaccharide Interactions in 10 Antithrombin Heparin Binding Site Mutants Revealed by Enhanced Sampling Molecular Dynamics / Gábor Balogh, Zsuzsanna Bereczky
Dátum:	2024
ISSN:	2218-273X
Megjegyzések:	Antithrombin (AT) is a critical regulator of the coagulation cascade by inhibiting multiple coagulation factors including thrombin and FXa. Binding of heparinoids to this serpin enhances the inhibition considerably. Mutations located in the heparin binding site of AT result in thrombophilia in affected individuals. Our aim was to study 10 antithrombin mutations known to affect their heparin binding in a heparin pentasaccharide bound state using two molecular dynamics (MD) based methods providing enhanced sampling, GaMD and LiGaMD2. The latter provides an additional boost to the ligand and the most important binding site residues. From our GaMD simulations we were able to identify four variants (three affecting amino acid Arg47 and one affecting Lys114) that have a particularly large effect on binding. The additional acceleration provided by LiGaMD2 allowed us to study the consequences of several other mutants including those affecting Arg13 and Arg129. We were able to identify several conformational types by cluster analysis. Analysis of the simulation trajectories revealed the causes of the impaired pentasaccharide binding including pentasaccharide subunit conformational changes and altered allosteric pathways in the AT protein. Our results provide insights into the effects of AT mutations interfering with heparin binding at an atomic level and can facilitate the design or interpretation of in vitro experiments.
Tárgyszavak:	Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk antithrombin mutations molecular dynamics enhanced sampling simulation methods
Megjelenés:	Biomolecules. - 14 : 6 (2024), p. 1-22. -
További szerzők:	Bereczky Zsuzsanna (1974-) (orvosi laboratóriumi diagnosztika szakorvos)
Pályázati támogatás:	OTKA K-139293 OTKA OTKA-106294 OTKA OTKA-116228 OTKA
Internet cím:	Szerző által megadott URL DOI Intézményi repozitóriumban (DEA) tárolt változat
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001-es BibID:	BIBFORM093898
035-os BibID:	(cikkazonosító)544 (WoS)000642809000001 (Scopus)85103814901
Első szerző:	Gindele Réka (molekuláris biológus)
Cím:	Investigation of the Differences in Antithrombin to Heparin Binding among Antithrombin Budapest 3, Basel, and Padua Mutations by Biochemical and In Silico Methods / Gindele Réka, Pénzes-Daku Krisztina, Balogh Gábor, Kállai Judit, Bogáti Réka, Bécsi Bálint, Erdődi Ferenc, Katona Éva, Bereczky Zsuzsanna
Dátum:	2021
ISSN:	2218-273X
Megjegyzések:	Antithrombin (AT) is a serine protease inhibitor, its activity is highly accelerated by heparin. Mutations at the heparin-binding region lead to functional defect, type II heparin-binding site (IIHBS) AT deficiency. The aim of this study was to investigate and compare the molecular background of AT Budapest 3 (p.Leu131Phe, ATBp3), AT Basel (p.Pro73Leu), and AT Padua (p.Arg79His) mutations. Advanced in silico methods and heparin-binding studies of recombinant AT proteins using surface plasmon resonance method were used. Crossed immunoelectrophoresis and Differential Scanning Fluorimetry (NanoDSF) were performed in plasma samples. Heparin affinity of AT Padua was the lowest (KD = 1.08 x 10(-6) M) and had the most severe consequences affecting the allosteric pathways of activation, moreover significant destabilizing effects on AT were also observed. KD values for AT Basel, ATBp3 and wild-type AT were 7.64 x 10(-7) M, 2.15 x 10(-8) M and 6.4 x 10(-10) M, respectively. Heparin-binding of AT Basel was slower, however once the complex was formed the mutation had only minor effect on the secondary and tertiary structures. Allosteric activation of ATBp3 was altered, moreover decreased thermostability in ATBp3 homozygous plasma and increased fluctuations in multiple regions of ATBp3 were observed by in silico methods suggesting the presence of a quantitative component in the pathogenicity of this mutation due to molecular instability.
Tárgyszavak:	Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk
Megjelenés:	Biomolecules. - 11 : 4 (2021), p. 1-18. -
További szerzők:	Pénzes-Daku Krisztina (1978-) (biológus) Balogh Gábor (1991-) (gyógyszerész) Kállai Judit (1983-) (molekuláris biológus) Kissné Bogáti Réka (1988-) (tudományos segédmunkatárs) Bécsi Bálint (1981-) (vegyészmérnök) Erdődi Ferenc (1953-) (biokémikus) Katona Éva (1961-) (klinikai biokémikus) Bereczky Zsuzsanna (1974-) (orvosi laboratóriumi diagnosztika szakorvos)
Pályázati támogatás:	GINOP-2.3.2-15-2016-00039 GINOP GINOP-2.3.2-15-2016-00044 GINOP GINOP-2.3.3-15-2016-00020 GINOP
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