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1.

001-es BibID:BIBFORM031436
035-os BibID:WOS:000298552800027
Első szerző:Bernstein, Noam
Cím:QM/MM simulation of liquid water with an adaptive quantum region / Noam Bernstein, Csilla Várnai, Iván Solt, Steven A. Winfield, Mike C. Payne, István Simon, Mónika Fuxreiter, Gábor Csányi
Dátum:2012
ISSN:1463-9076
Megjegyzések:The simulation of complex chemical systems often requires a multi-level description, in which a region of special interest is treated using a computationally expensive quantum mechanical (QM) model while its environment is described by a faster, simpler molecular mechanical (MM) model. Furthermore, studying dynamic effects in solvated systems or bio-molecules requires a variable definition of the two regions, so that atoms or molecules can be dynamically re-assigned between the QM and MM descriptions during the course of the simulation. Such reassignments pose a problem for traditional QM/MM schemes by exacerbating the errors that stem from switching the model at the boundary. Here we show that stable, long adaptive simulations can be carried out using density functional theory with the BLYP exchange-correlation functional for the QM model and a flexible TIP3P force field for the MM model without requiring adjustments of either. Using a primary benchmark system of pure water, we investigate the convergence of the liquid structure with the size of the QM region, and demonstrate that by using a sufficiently large QM region (with radius 6 angstrom) it is possible to obtain radial and angular distributions that, in the QM region, match the results of fully quantum mechanical calculations with periodic boundary conditions, and, after a smooth transition, also agree with fully MM calculations in the MM region. The key ingredient is the accurate evaluation of forces in the QM subsystem which we achieve by including an extended buffer region in the QM calculations. We also show that our buffered-force QM/MM scheme is transferable by simulating the solvated Cl(-) ion.
Tárgyszavak:Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban
egyetemen (Magyarországon) készült közlemény
Megjelenés:Physical chemistry chemical physics. - 14 : 2 (2012), p. 646-656. -
További szerzők:Várnai Csilla Solt Iván Winfield, Steven Payne, Mike C. Simon István Fuxreiter Mónika (1969-) (kutató vegyész) Csányi Gábor
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2.

001-es BibID:BIBFORM031410
035-os BibID:PMID:17442645 WOS:000246867300007
Első szerző:Chuluunbaatar, Tungalag
Cím:An EcoRI-RsrI chimeric restriction endonuclease retains parental sequence specificity / Tungalag Chuluunbaatar, Tetiana Ivanenko-Johnston, Mónika Fuxreiter, Ruslan Meleshko, Tamás Raskó, István Simon, Joseph Heitman, Antal Kiss
Dátum:2007
ISSN:1570-9639
Megjegyzések:o test their structural and functional similarity, hybrids were constructed between EcoRI and RsrI, two restriction endonucleases recognizing the same DNA sequence and sharing 50% amino acid sequence identity. One of the chimeric proteins (EERE), in which the EcoRI segment His147-Ala206 was replaced with the corresponding RsrI segment, showed EcoRI/RsrI-specific endonuclease activity. EERE purified from inclusion bodies was found to have approximately 100-fold weaker activity but higher specific DNA binding affinity, than EcoRI. Increased binding is consistent with results of molecular dynamics simulations, which indicate that the number of hydrogen bonds formed with the recognition sequence increased in the chimera as compared to EcoRI. The success of obtaining an EcoRI-RsrI hybrid endonuclease, which differs from EcoRI by 22 RsrI-specific amino acid substitutions and still preserves canonical cleavage specificity, is a sign of structural and functional similarity shared by the parental enzymes. This conclusion is also supported by computational studies, which indicate that construction of the EERE chimera did not induce substantial changes in the structure of EcoRI. Surprisingly, the chimeric endonuclease was more toxic to cells not protected by EcoRI methyltransferase, than the parental EcoRI mutant. Molecular modelling revealed structural alterations, which are likely to impede coupling between substrate recognition and cleavage and suggest a possible explanation for the toxic phenotype.
Tárgyszavak:Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban
egyetemen (Magyarországon) készült közlemény
Megjelenés:Biochimica et Biophysica Acta (BBA). Proteins and Proteomics. - 1774 : 5 (2007), p. 583-594. -
További szerzők:Ivanenko-Johnston, Tetiana Fuxreiter Mónika (1969-) (kutató vegyész) Meleshko, Ruslan Raskó Tamás Simon István Heitman, Joseph Kiss Antal (MTA, Szeged)
Internet cím:Intézményi repozitóriumban (DEA) tárolt változat
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3.

001-es BibID:BIBFORM046026
035-os BibID:PMID:21294844 WOS:000289151700006
Első szerző:Di Paolo, Maria Luisa
Cím:Active site residue involvement in monoamine or diamine oxidation catalysed by pea seedling amine oxidase / Maria Luisa Di Paolo, Michele Lunelli, Monika Fuxreiter, Adelio Rigo, Istvan Simon, Marina Scarpa
Dátum:2011
ISSN:1742-464X
Megjegyzések:The structures of copper amine oxidases from various sources show good similarity, suggesting similar catalytic mechanisms for all members of this enzyme family. However, the optimal substrates for each member differ, depending on the source of the enzyme and its location. The structural factors underlying substrate selectivity still remain to be discovered. With this in view, we examined the kinetic behaviour of pea seedling amine oxidase with cadaverine and hexylamine, the first bearing two, and the second only one, positively charged amino group. The dependence of K(m) and catalytic constant (k(c)) values on pH, ionic strength and temperature indicates that binding of the monoamine is driven by hydrophobic interactions. Instead, binding of the diamine is strongly facilitated by electrostatic factors, controlled by polar side-chains and two titratable residues present in the active site. The position of the docked substrate is also essential for the participation of titratable amino acid residues in the following catalytic steps. A new mechanistic model explaining the substrate-dependent kinetics of the reaction is discussed. újratöltve - BIBFORM031431
Tárgyszavak:Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban
Megjelenés:Febs Journal. - 278 : 8 (2011), p. 1232-1243. -
További szerzők:Lunelli, Michele Fuxreiter Mónika (1969-) (kutató vegyész) Rigo, Adelio Simon István Scarpa, Marina
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4.

001-es BibID:BIBFORM031432
035-os BibID:WOS:000294313000003 PMID:21620710
Első szerző:Fuxreiter Mónika (kutató vegyész)
Cím:Dynamic protein-DNA recognition : beyond what can be seen / Monika Fuxreiter, Istvan Simon, Sarah Bondos
Dátum:2011
ISSN:0968-0004
Megjegyzések:Traditionally, specific DNA recognition is thought to rely on static contacts with the bases or phosphates. Recent results, however, indicate that residues far outside the binding context can crucially influence selectivity or binding affinity via transient, dynamic interactions with the DNA binding interface. These regions usually do not adopt a well-defined structure, even when bound to DNA, and thus form a fuzzy complex. Here, we propose the existence of a dynamic DNA readout mechanism, wherein distant segments modulate conformational preferences, flexibility or spacing of the DNA binding motifs or serve as competitive partners. Despite their low sequence similarity, these intrinsically disordered regions are often conserved at the structural level, and exploited for regulation of the transcription machinery via protein protein interactions, post-translational modifications or alternative splicing.
Tárgyszavak:Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban
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Megjelenés:Trends in biochemical sciences. - 36 : 8 (2011), p. 415-423. -
További szerzők:Simon István Bondos, Sarah
Internet cím:elektronikus változat
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5.

001-es BibID:BIBFORM031428
Első szerző:Fuxreiter Mónika (kutató vegyész)
Cím:Computational approaches to restriction endonucleases / M. Fuxreiter, R. Osman, I. Simon
Dátum:2004
Tárgyszavak:Természettudományok Biológiai tudományok előadáskivonat
Megjelenés:The Role of Chemistry in the Evolution of Molecular Medicine : Proceedings of the symposium held at the University of Szeged to celebrate the 110th birthday of Professor Albert Szent-Györgyi 2003.06.27-2003.06.29 Magyarország, Szeged / eds. Imre Csizmadia, Botond Penke, Gábor Toth. - p. 469-480. -
További szerzők:Osman, Roman Simon István
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6.

001-es BibID:BIBFORM031418
035-os BibID:WOS:000260955900008
Első szerző:Fuxreiter Mónika (kutató vegyész)
Cím:Malleable machines take shape in eukaryotic transcriptional regulation / Monika Fuxreiter, Peter Tompa, István Simon, Vladimir N. Uversky, Jeffrey C. Hansen, Francisco J. Asturias
Dátum:2008
ISSN:1552-4450
Megjegyzések:Transcriptional control requires the spatially and temporally coordinated action of many macromolecular complexes. Chromosomal proteins, transcription factors, co-activators and components of the general transcription machinery, including RNA polymerases, often use structurally or stoichiometrically ill-defined regions for interactions that convey regulatory information in processes ranging from chromatin remodeling to mRNA processing. Determining the functional significance of intrinsically disordered protein regions and developing conceptual models of their action will help to illuminate their key role in transcription regulation. Complexes comprising disordered regions often display short recognition elements embedded in flexible and sequentially variable environments that can lead to structural and functional malleability. This provides versatility to recognize multiple targets having different structures, facilitate conformational rearrangements and physically communicate with many partners in response to environmental changes. All these features expand the capacities of ordered complexes and give rise to efficient regulatory mechanisms.
Tárgyszavak:Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban
külföldön készült közlemény
Megjelenés:Nature Chemical Biology. - 4 : 12 (2008), p. 728-737. -
További szerzők:Tompa Péter Simon István Uversky, Vladimir N. Hansen, Jeffrey C. Asturias, Francisco J.
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7.

001-es BibID:BIBFORM031409
035-os BibID:WOS:000246293000005
Első szerző:Fuxreiter Mónika (kutató vegyész)
Cím:Local structural disorder imparts plasticity on linear motifs / Monika Fuxreiter, Peter Tompa, István Simon
Dátum:2007
ISSN:1367-4803
Megjegyzések:Motivation: The dynamic nature of protein interaction networks requires fast and transient molecular switches. The underlying recognition motifs (linear motifs, LMs) are usually short and evolutionarily variable segments, which in several cases, such as phosphorylation sites or SH3-binding regions, fall into locally disordered regions. We probed the generality of this phenomenon by predicting the intrinsic disorder of all LM-containing proteins enlisted in the Eukaryotic Linear Motif (ELM) database. Results: We demonstrated that LMs in average are embedded in locally unstructured regions, while their amino acid composition and charge/hydropathy properties exhibit a mixture characteristic of folded and disordered proteins. Overall, LMs are constructed by grafting a few specificity-determining residues favoring structural order on a highly flexible carrier region. These results establish a connection between LMs and molecular recognition elements of intrinsically unstructured proteins (IUPs), which realize a non-conventional mode of partner binding mostly in regulatory functions.
Tárgyszavak:Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban
egyetemen (Magyarországon) készült közlemény
Megjelenés:Bioinformatics. - 23 : 8 (2007), p. 950-956. -
További szerzők:Tompa Péter Simon István
Internet cím:Intézményi repozitóriumban (DEA) tárolt változat
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8.

001-es BibID:BIBFORM031404
035-os BibID:WOS:000230822200016
Első szerző:Fuxreiter Mónika (kutató vegyész)
Cím:Interfacial Water as a "Hydration Fingerprint" in the Noncognate Complex of BamHI / Monika Fuxreiter, Mihaly Mezei, István Simon, Roman Osman
Dátum:2005
ISSN:0006-3495
Megjegyzések:The molecular code of specific DNA recognition by proteins as a paradigm in molecular biology remains an unsolved puzzle primarily because of the subtle interplay between direct protein-DNA interaction and the indirect contribution from water and ions. Transformation of the nonspecific, low affinity complex to a specific, high affinity complex is accompanied by the release of interfacial water molecules. To provide insight into the conversion from the loose to the tight form, we characterized the structure and energetics of water at the protein-DNA interface of the BamHI complex with a noncognate sequence and in the specific complex. The fully hydrated models were produced with Grand Canonical Monte Carlo simulations. Proximity analysis shows that water distributions exhibit sequence dependent variations in both complexes and, in particular, in the noncognate complex they discriminate between the correct and the star site. Variations in water distributions control the number of water molecules released from a given sequence upon transformation from the loose to the tight complex as well as the local entropy contribution to the binding free energy. We propose that interfacial waters can serve as a "hydration fingerprint'' of a given DNA sequence.
Tárgyszavak:Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban
egyetemen (Magyarországon) készült közlemény
Megjelenés:Biophysical Journal. - 89 : 2 (2005), p. 903-911. -
További szerzők:Mezei Mihály Simon István Osman, Roman
Internet cím:Intézményi repozitóriumban (DEA) tárolt változat
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9.

001-es BibID:BIBFORM031403
035-os BibID:PMID:15111064 WOS:000221305200013
Első szerző:Fuxreiter Mónika (kutató vegyész)
Cím:Preformed structural elements feature in partner recognition by intrinsically unstructured proteins / Monika Fuxreiter, István Simon, Peter Friedrich, Peter Tompa
Dátum:2004
Megjegyzések:Intrinsically unstructured proteins (IUPs) are devoid of extensive structural order but often display signs of local and limited residual structure. To explain their effective functioning, we reasoned that such residual structure can be crucial in their interactions with their structured partner(s) in a way that preformed structural elements presage their final conformational state. To check this assumption, a database of 24 IUPs with known 3D structures in the bound state has been assembled and the distribution of secondary structure elements and backbone torsion angles have been analysed. The high proportion of residues in coil conformation and with phi, psi angles in the disallowed regions of the Ramachandran map compared to the reference set of globular proteins shows that IUPs are not fully ordered even in their bound form. To probe the effect of partner proteins on IUP folding, inherent conformational preferences of IUP sequences have been assessed by secondary structure predictions using the GOR, ALB and PROF algorithms. The accuracy of predicting secondary structure elements of IUPs is similar to that of their partner proteins and is significantly higher than the corresponding values for random sequences. We propose that strong conformational preferences mark regions in IUPs (mostly helices), which correspond to their final structural state, while regions with weak conformational preferences represent flexible linkers between them. In our interpretation, preformed elements could serve as initial contact points, the binding of which facilitates the reeling of the flexible regions onto the template. This finding implies that IUPs draw a functional advantage from preformed structural elements, as they enable their facile, kinetically and energetically less demanding, interaction with their physiological partner.
Tárgyszavak:Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban
egyetemen (Magyarországon) készült közlemény
Megjelenés:Journal of molecular biology. - 338 : 5 (2004), p. 1015-1026. -
További szerzők:Simon István Friedrich Péter Tompa Péter
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10.

001-es BibID:BIBFORM031402
035-os BibID:WOS:000188928800053
Első szerző:Fuxreiter Mónika (kutató vegyész)
Cím:Computational approaches to restriction endonucleases / M. Fuxreiter, R. Osman, I. Simon
Dátum:2003
ISSN:0166-1280
Megjegyzések:Type II restriction endonucleases catalyze phosphodiester bond hydrolysis in bacteria to protect the host cell from invading phage DNA. Due to their exquisite sequence selectivity type II restriction endonucleases serve as excellent model systems for studying protein-nucleic acid interactions. Crystal structures of the PD-(D/E)XK superfamily revealed a common alpha/beta core motif and similar active site. In contrast, these enzymes show little sequence similarity and use different strategies to interact with their substrate DNA. Computational approaches have been applied to unify the mechanism of restriction endonucleases and rationalize their diversity. The first step of type II restriction endonuclease catalysis has been studied on Bam HI by semi-microscopic version of the Protein Dipoles Langevin Dipoles method. The substrate-assisted catalysis and the general base mechanism have been concluded as less likely than the metal-catalyzed reaction. A general model for catalysis has been proposed based on the group contributions to the reduction of the activation free energy. Factors contributing to structural stability of PD-(D/E)XK type II restriction endonucleases have been analyzed to elucidate evolutionary relationship between these enzymes. Residues playing role in catalysis and recognition were highly correlated with those participating in stabilization centers. Thus the main functional motifs were concluded to be evolutionary more conserved than other parts of the structure. This observation is consistent with the proposal that these enzymes have developed from a common ancestor with divergent evolution.
Tárgyszavak:Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban
külföldön készült közlemény
Megjelenés:Journal of molecular structure. - 666-667 (2003), p. 469-479. -
További szerzők:Osman, Roman Simon István
Internet cím:Intézményi repozitóriumban (DEA) tárolt változat
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11.

001-es BibID:BIBFORM031401
035-os BibID:WOS:000176646100018 PMID:12112699
Első szerző:Fuxreiter Mónika (kutató vegyész)
Cím:Role of stabilization centers in 4 helix bundle proteins / M. Fuxreiter, I. Simon
Dátum:2002
ISSN:0887-3585
Megjegyzések:Stabilization centers (SCs) were shown to play an important role in preventing decay of three-dimensional protein structures. These residue clusters, stabilized by cooperative long-range interactions, were proposed to serve as anchoring points for arranging secondary structure elements. In all-alpha proteins, SC elements appear less frequently than in all-beta, alpha/beta, and alpha+beta proteins suggesting that tertiary structure formation of all-alpha proteins is governed by different principles than in other protein classes. Here we analyzed the relation between the formation of stabilization centers and the interaxial angles (Omega) of a-helices in 4 helix bundle proteins. In the distance range, where dipoles have dominant effect on the helix pair arrangement, those helix pairs, where residues from both helices participate in SC elements, appear as parallel more frequently than those helices where no SC elements are present. For SC containing helix pairs, the energetic difference between the parallel and antiparallel states decreases considerably from 1.1 kcal/mol to 0.4 kcal/mol. Although the observed effect is weak for more distant helices, a competition between the SC element formation and the optimal dipole-dipole interaction of alpha-helices is proposed as a mechanism for tertiary structure formation in 4 helix bundle proteins. The SC-forming potential of different arrangements as well as the pitfalls of the SC definition are also discussed.
Tárgyszavak:Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban
egyetemen (Magyarországon) készült közlemény
Megjelenés:Proteins. - 48 : 2 (2002), p. 320-326. -
További szerzők:Simon István
Internet cím:Intézményi repozitóriumban (DEA) tárolt változat
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12.

001-es BibID:BIBFORM031399
035-os BibID:WOS:000177036500012 PMID:12142452
Első szerző:Fuxreiter Mónika (kutató vegyész)
Cím:Protein stability indicates divergent evolution of PD-(D/E)XK type II restriction endonucleases / Monika Fuxreiter, Istvan Simon
Dátum:2002
ISSN:0961-8368
Megjegyzések:Type II restriction endonucleases recognize 4-8 base-pair-long DNA sequences and catalyze their cleavage with remarkable specificity. Crystal structures of the PD-(DE)XK superfamily revealed a common alpha/beta core motif and similar active site. In contrast, these enzymes show little sequence similarity and use different strategies to interact with their substrate DNA. The intriguing question is whether this enzyme family could have evolved from a common origin. In our present work, protein structure stability elements were analyzed and compared in three parts of PD-(DE)XK type II restriction endonucleases: (1) core motif, (2) active-site residues, and (3) residues playing role in DNA recognition. High correlation was found between the active-site residues and those stabilization factors that contribute to preventing structural decay. DNA recognition sites were also observed to participate in stabilization centers. It indicates that recognition motifs and active sites in PD-(DE)XK type II restriction endonucleases should have been evolutionary more conserved than other parts of the structure. Based on this observation it is proposed that PD-(DE)XK type II restriction endonucleases have developed from a common ancestor with divergent evolution.
Tárgyszavak:Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban
egyetemen (Magyarországon) készült közlemény
Megjelenés:Protein Science. - 11 : 8 (2002), p. 1978-1983. -
További szerzők:Simon István
Internet cím:Intézményi repozitóriumban (DEA) tárolt változat
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