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001-es BibID:	BIBFORM031396
035-os BibID:	PMID:15971204 WOS:000230778100016
Első szerző:	Fuxreiter Mónika (kutató vegyész)
Cím:	Flexibility of prolyl oligopeptidase : molecular dynamics and molecular framework analysis of the potential substrate pathways / Monika Fuxreiter, Csaba Magyar, Tünde Juhász, Zoltán Szeltner, László Polgár, István Simon
Dátum:	2005
Megjegyzések:	The flexibility of prolyl oligopeptidase has been investigated using molecular dynamics (MD) and molecular framework approaches to delineate the route of the substrate to the active site. The selectivity of the enzyme is mediated by a seven-bladed beta-propeller that in the crystal structure does not indicate the possible passage for the substrate to the catalytic center. Its open topology however, could allow the blades to move apart and let the substrate into the large central cavity. Flexibility analysis of prolyl oligopeptidase structure using the FIRST (Floppy Inclusion and Rigid Substructure Topology) approach and the atomic fluctuations derived from MD simulations demonstrated the rigidity of the propeller domain, which does not permit the substrate to approach the active site through this domain. Instead, a smaller tunnel at the inter-domain region comprising the highly flexible N-terminal segment of the peptidase domain and a facing hydrophilic loop from the propeller (residues 192-205) was identified by cross-correlation analysis and essential dynamics as the only potential pathway for the substrate. The functional importance of the flexible loop has been also verified by kinetic analysis of the enzyme with a split loop. Catalytic effect of engineered disulfide bridges was rationalized by characterizing the concerted motions of the two domains.
Tárgyszavak:	Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban egyetemen (Magyarországon) készült közlemény
Megjelenés:	Proteins. - 60 : 3 (2005), p. 504-512. -
További szerzők:	Magyar Csaba Juhász Tünde Szeltner Zoltán Polgár László Simon István
Internet cím:	Intézményi repozitóriumban (DEA) tárolt változat DOI
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001-es BibID:	BIBFORM031405
035-os BibID:	WOS:000239103800017 PMID:16761278
Első szerző:	Solt Iván
Cím:	Phosphorylation-induced transient intrinsic structure in the kinase-inducible domain of CREB facilitates its recognition by the KIX domain of CBP / Iván Solt, Csaba Magyar, István Simon, Peter Tompa, Monika Fuxreiter
Dátum:	2006
ISSN:	0887-3585
Megjegyzések:	Phosphorylation at Ser-133 of the kinase inducible domain of CREB (KID) triggers its binding to the KIX domain of CBP via a concomitant coil-to-helix transition. The exact role of this key event is still puzzling: it does not switch between disordered and ordered states, nor its direct interactions fully account for selectivity. Hence, we reasoned that phosphorylation may shift the conformational preferences of KID towards a binding-competent state. To this end we investigated the intrinsic structural properties of the unbound KID in phosphorylated and unphosphorylated forms by simulated annealing and molecular dynamics simulations. Although helical populations show subtle differences, phosphorylation reduces the flexibility of the turn segment connecting the two helices in the complexed structure and induces a transient structural element that corresponds to its bound conformation. It is stabilized by the pSer-133-Arg-131 interaction, which is absent from the unphosphorylated KID. Diminishing this coupling decreases the 3.1 kcal/mol contribution of pSer-133 to the binding free energy (Delta G(bind)) of the phosphorylated KID to KIX by 1.1 kcal/mol, as computed in reference to Ser-133. In a binding competent form of the S133E KID mutant, the contribution of Glu-133 to Delta G(bind) is by 1.5 kcal/mol smaller than that of pSer, suggesting that altered structural properties due to pSer -> Glu replacement impair the binding affinity. Thus, we propose that phoshorylation contributes to selectivity not merely by the direct interactions of the phosphate group with KIX, but also by promoting the formation of a transient structural element in the highly conserved turn segment.
Tárgyszavak:	Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban egyetemen (Magyarországon) készült közlemény
Megjelenés:	Proteins. - 64 : 3 (2006), p. 749-757. -
További szerzők:	Magyar Csaba Simon István Tompa Péter Fuxreiter Mónika (1969-) (kutató vegyész)
Internet cím:	Intézményi repozitóriumban (DEA) tárolt változat DOI
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001-es BibID:	BIBFORM031397
035-os BibID:	WOS:000220320000010 PMID:15032510
Első szerző:	Tüdős Éva
Cím:	Noncovalent cross-links in context with other structural and functional elements of proteins / Éva Tüdős, András Fiser, Ágnes Simon, Zsuzsanna Dosztányi, Mónika Fuxreiter, Csaba Magyar, István Simon
Dátum:	2004
ISSN:	0095-2338
Megjegyzések:	Proteins are heteropolymers with evolutionary selected native sequences of residues. These native sequences code for unique and stable 3D structures indispensable for biochemical activity and for proteolysis resistance, the latter which guarantees an appropriate lifetime for the protein in the protease rich cellular environment. Cross-links between residues close in space but far in the primary structure are required to maintain the folded structure of proteins. Some of these cross-links are covalent, most frequently disulfide bonds, but the majority of the cross-links are sets of cooperative noncovalent long-range interactions. In this paper we focus on special clusters of noncovalent long-range interactions: the Stabilization Centers (SCs). The relation between the SCs and secondary structural elements as well as the relation between SCs and functionally important regions of proteins are presented to show a detailed picture of these clusters, which are believed to be primarily responsible for major aspects of protein stability.
Tárgyszavak:	Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban egyetemen (Magyarországon) készült közlemény
Megjelenés:	Journal of chemical information and computer sciences. - 44 : 2 (2004), p. 347-351. -
További szerzők:	Fiser András Simon Ágnes Dosztányi Zsuzsanna Fuxreiter Mónika (1969-) (kutató vegyész) Magyar Csaba Simon István
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