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Binding properties of SUMO-interacting motifs (SIMs) in yeast. J Mol Model 2015; 21:50. [PMID: 25690366 DOI: 10.1007/s00894-015-2597-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/26/2015] [Indexed: 11/27/2022]
Abstract
Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact non-covalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome.
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Erni B. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS): an interface between energy and signal transduction. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2012. [DOI: 10.1007/s13738-012-0185-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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A molecular model for the differential activation of STAT3 and STAT6 by the herpesviral oncoprotein tip. PLoS One 2012; 7:e34306. [PMID: 22509288 PMCID: PMC3320567 DOI: 10.1371/journal.pone.0034306] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 02/27/2012] [Indexed: 01/27/2023] Open
Abstract
Constitutive STAT signaling provides growth promoting signals in many forms of malignancy. We performed molecular modeling and molecular dynamics studies of the interaction between the regulatory Src homology 2 (SH2) domains of STAT3 and 6 with phosphorylated peptides of the herpesviral oncoprotein Tip, which facilitates Src kinase mediated STAT-activation and T cell proliferation. The studies give insight into the ligand binding specificity of the STAT SH2 domains and provide the first model for the differential activation of STAT3 or STAT6 by two distinct regions of the viral Tip protein. The biological relevance of the modeled interactions was then confirmed by activation studies using corresponding recombinant oncoproteins, and finally by respective recombinant viruses. The functional data give experimental validation of the molecular dynamics study, and provide evidence for the involvement of STAT6 in the herpesvirus induced T cell proliferation.
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Jardin C, Sticht H. Identification of the Structural Features that Mediate Binding Specificity in the Recognition of STAT Proteins by Dual-Specificity Phosphatases. J Biomol Struct Dyn 2012; 29:777-92. [DOI: 10.1080/07391102.2012.10507413] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Re S, Sugita Y. [Modeling the transition state of enzyme-catalyzed phosphoryl transfer reaction using QM/MM method]. YAKUGAKU ZASSHI 2011; 131:1171-82. [PMID: 21804320 DOI: 10.1248/yakushi.131.1171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Reversible phosphorylation of proteins is a post-translational modification that regulates diverse biological processes. The molecular mechanism underlying phosphoryl transfer catalyzed by enzymes, in particular the nature of transition state (TS), remains a subject of active debate. Structural evidence supports an associative TS, whereas physical organic studies point to a dissociative character. In this article, we briefly introduce our recent effort using the hybrid quantum mechanics/molecular mechanics (QM/MM) simulations to resolve the controversy. We perform QM/MM simulations for the reversible phosphorylation of phosphoserine phosphatase (PSP), which belongs to one of the largest phosphotransferase families characterized to data. Both phosphorylation and dephosphorylation reactions are investigated based on the two-dimensional energy surfaces along phosphoryl and proton transfer coordinates. The resultant structures of the active site at TS in both reactions have compact geometries but a less electron density of the phosphoryl group. This suggests that the TS of PSP has a geometrically associative yet electronically dissociative character and strongly depends on proton transfer being coupled with phosphoryl transfer. Structure and literature database searches on phosphotransferases suggest that such a hybrid TS is consistent with many structures and physical organic studies and likely holds for most enzymes catalyzing phosphoryl transfer.
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Affiliation(s)
- Suyong Re
- RIKEN Advanced Science Institute, Saitama, Japan
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Re S, Imai T, Jung J, Ten-No S, Sugita Y. Geometrically associative yet electronically dissociative character in the transition state of enzymatic reversible phosphorylation. J Comput Chem 2010; 32:260-70. [DOI: 10.1002/jcc.21615] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Ferreira DEC, Florentino BPD, Rocha WR, Nome F. Quantum Mechanical/Effective Fragment Potential (QM/EFP) Study of Phosphate Monoester Aminolysis in Aqueous Solution. J Phys Chem B 2009; 113:14831-6. [DOI: 10.1021/jp907014r] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Dalva E. C. Ferreira
- LQC-MM: Laboratório de Química Computacional e Modelagem Molecular, Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Campus Universitário, Pampulha, Belo Horizonte, MG 31270-901, Brazil, and LACFI: Laboratório de Catálise e Fenômenos Interfaciais Departamento de Química, Universidade Federal de Santa Catarina, Campus Trindade, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Bruno P. D. Florentino
- LQC-MM: Laboratório de Química Computacional e Modelagem Molecular, Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Campus Universitário, Pampulha, Belo Horizonte, MG 31270-901, Brazil, and LACFI: Laboratório de Catálise e Fenômenos Interfaciais Departamento de Química, Universidade Federal de Santa Catarina, Campus Trindade, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Willian R. Rocha
- LQC-MM: Laboratório de Química Computacional e Modelagem Molecular, Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Campus Universitário, Pampulha, Belo Horizonte, MG 31270-901, Brazil, and LACFI: Laboratório de Catálise e Fenômenos Interfaciais Departamento de Química, Universidade Federal de Santa Catarina, Campus Trindade, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Faruk Nome
- LQC-MM: Laboratório de Química Computacional e Modelagem Molecular, Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Campus Universitário, Pampulha, Belo Horizonte, MG 31270-901, Brazil, and LACFI: Laboratório de Catálise e Fenômenos Interfaciais Departamento de Química, Universidade Federal de Santa Catarina, Campus Trindade, Florianópolis, Santa Catarina 88040-900, Brazil
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Re S, Jung J, Ten-no S, Sugita Y. A two-dimensional energy surface of the phosphoryl transfer reaction catalyzed by phosphoserine phosphatase. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.08.068] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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