151
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Lee GR, Seok C. Galaxy7TM: flexible GPCR-ligand docking by structure refinement. Nucleic Acids Res 2016; 44:W502-6. [PMID: 27131365 PMCID: PMC4987912 DOI: 10.1093/nar/gkw360] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 04/21/2016] [Indexed: 01/21/2023] Open
Abstract
G-protein-coupled receptors (GPCRs) play important physiological roles related to signal transduction and form a major group of drug targets. Prediction of GPCR-ligand complex structures has therefore important implications to drug discovery. With previously available servers, it was only possible to first predict GPCR structures by homology modeling and then perform ligand docking on the model structures. However, model structures generated without explicit consideration of specific ligands of interest can be inaccurate because GPCR structures can be affected by ligand binding. The Galaxy7TM server, freely accessible at http://galaxy.seoklab.org/7TM, improves an input GPCR structure by simultaneous ligand docking and flexible structure refinement using GALAXY methods. The server shows better performance in both ligand docking and GPCR structure refinement than commonly used programs AutoDock Vina and Rosetta MPrelax, respectively.
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Affiliation(s)
- Gyu Rie Lee
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
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152
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Automated structure modeling of large protein assemblies using crosslinks as distance restraints. Nat Methods 2016; 13:515-20. [PMID: 27111507 DOI: 10.1038/nmeth.3838] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/19/2016] [Indexed: 11/08/2022]
Abstract
Crosslinking mass spectrometry is increasingly used for structural characterization of multisubunit protein complexes. Chemical crosslinking captures conformational heterogeneity, which typically results in conflicting crosslinks that cannot be satisfied in a single model, making detailed modeling a challenging task. Here we introduce an automated modeling method dedicated to large protein assemblies ('XL-MOD' software is available at http://aria.pasteur.fr/supplementary-data/x-links) that (i) uses a form of spatial restraints that realistically reflects the distribution of experimentally observed crosslinked distances; (ii) automatically deals with ambiguous and/or conflicting crosslinks and identifies alternative conformations within a Bayesian framework; and (iii) allows subunit structures to be flexible during conformational sampling. We demonstrate our method by testing it on known structures and available crosslinking data. We also crosslinked and modeled the 17-subunit yeast RNA polymerase III at atomic resolution; the resulting model agrees remarkably well with recently published cryoelectron microscopy structures and provides additional insights into the polymerase structure.
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153
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Busato M, Giorgetti A. Structural modeling of G-protein coupled receptors: An overview on automatic web-servers. Int J Biochem Cell Biol 2016; 77:264-74. [PMID: 27102413 DOI: 10.1016/j.biocel.2016.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/09/2016] [Accepted: 04/15/2016] [Indexed: 12/27/2022]
Abstract
Despite the significant efforts and discoveries during the last few years in G protein-coupled receptor (GPCR) expression and crystallization, the receptors with known structures to date are limited only to a small fraction of human GPCRs. The lack of experimental three-dimensional structures of the receptors represents a strong limitation that hampers a deep understanding of their function. Computational techniques are thus a valid alternative strategy to model three-dimensional structures. Indeed, recent advances in the field, together with extraordinary developments in crystallography, in particular due to its ability to capture GPCRs in different activation states, have led to encouraging results in the generation of accurate models. This, prompted the community of modelers to render their methods publicly available through dedicated databases and web-servers. Here, we present an extensive overview on these services, focusing on their advantages, drawbacks and their role in successful applications. Future challenges in the field of GPCR modeling, such as the predictions of long loop regions and the modeling of receptor activation states are presented as well.
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Affiliation(s)
- Mirko Busato
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy.
| | - Alejandro Giorgetti
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy; Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Computational Biomedicine, Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Germany.
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154
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Krishna KH, Vadlamudi Y, Kumar MS. Viral Evolved Inhibition Mechanism of the RNA Dependent Protein Kinase PKR's Kinase Domain, a Structural Perspective. PLoS One 2016; 11:e0153680. [PMID: 27088597 PMCID: PMC4835081 DOI: 10.1371/journal.pone.0153680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/01/2016] [Indexed: 11/18/2022] Open
Abstract
The protein kinase PKR activated by viral dsRNA, phosphorylates the eIF2α, which inhibit the mechanism of translation initiation. Viral evolved proteins mimicking the eIF2α block its phosphorylation and help in the viral replication. To decipher the molecular basis for the PKR’s substrate and inhibitor interaction mechanisms, we carried the molecular dynamics studies on the catalytic domain of PKR in complex with substrate eIF2α, and inhibitors TAT and K3L. The studies conducted show the altered domain movements of N lobe, which confers open and close state to the substrate-binding cavity. In addition, PKR exhibits variations in the secondary structural transition of the activation loop residues, and inter molecular contacts with the substrate and the inhibitors. Phosphorylation of the P+1 loop at the Thr-451 increases the affinity of the binding proteins exhibiting its role in the phosphorylation events. The implications of structural mechanisms uncovered will help to understand the basis of the evolution of the host-viral and the viral replication mechanisms.
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Affiliation(s)
- K. Hari Krishna
- Centre for Bioinformatics, Pondicherry University, Kalapet, Pondicherry, India
| | | | - Muthuvel Suresh Kumar
- Centre for Bioinformatics, Pondicherry University, Kalapet, Pondicherry, India
- * E-mail:
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155
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Patel D, Mahdavi S, Kuyucak S. Computational Study of Binding of μ-Conotoxin GIIIA to Bacterial Sodium Channels NaVAb and NaVRh. Biochemistry 2016; 55:1929-38. [PMID: 26959170 DOI: 10.1021/acs.biochem.5b01324] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Structures of several voltage-gated sodium (NaV) channels from bacteria have been determined recently, but the same feat might not be achieved for the mammalian counterparts in the near future. Thus, at present, computational studies of the mammalian NaV channels have to be performed using homology models based on the bacterial crystal structures. A successful homology model for the mammalian NaV1.4 channel was recently constructed using the extensive mutation data for binding of μ-conotoxin GIIIA to NaV1.4, which was further validated through studies of binding of other μ-conotoxins and ion permeation. Understanding the similarities and differences between the bacterial and mammalian NaV channels is an important issue, and the NaV1.4-GIIIA system provides a good opportunity for such a comparison. To this end, we study the binding of GIIIA to the bacterial channels NaVAb and NaVRh. The complex structures are obtained using docking and molecular dynamics simulations, and the dissociation of GIIIA is studied through umbrella sampling simulations. The results are compared to those obtained from the NaV1.4-GIIIA system, and the differences in the binding modes arising from the changes in the selectivity filters are highlighted.
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Affiliation(s)
- Dharmeshkumar Patel
- School of Physics, University of Sydney , Sydney, New South Wales 2006, Australia
| | - Somayeh Mahdavi
- School of Physics, University of Sydney , Sydney, New South Wales 2006, Australia
| | - Serdar Kuyucak
- School of Physics, University of Sydney , Sydney, New South Wales 2006, Australia
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156
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Zhu L, Jiang H, Sheong FK, Cui X, Gao X, Wang Y, Huang X. A Flexible Domain-Domain Hinge Promotes an Induced-fit Dominant Mechanism for the Loading of Guide-DNA into Argonaute Protein in Thermus thermophilus. J Phys Chem B 2016; 120:2709-20. [PMID: 26908081 DOI: 10.1021/acs.jpcb.5b12426] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Argonaute proteins (Ago) are core components of the RNA Induced Silencing Complex (RISC) that load and utilize small guide nucleic acids to silence mRNAs or cleave foreign DNAs. Despite the essential role of Ago in gene regulation and defense against virus, the molecular mechanism of guide-strand loading into Ago remains unclear. We explore such a mechanism in the bacterium Thermus thermophilus Ago (TtAgo), via a computational approach combining molecular dynamics, bias-exchange metadynamics, and protein-DNA docking. We show that apo TtAgo adopts multiple closed states that are unable to accommodate guide-DNA. Conformations able to accommodate the guide are beyond the reach of thermal fluctuations from the closed states. These results suggest an induced-fit dominant mechanism for guide-strand loading in TtAgo, drastically different from the two-step mechanism for human Ago 2 (hAgo2) identified in our previous study. Such a difference between TtAgo and hAgo2 is found to mainly originate from the distinct rigidity of their L1-PAZ hinge. Further comparison among known Ago structures from various species indicates that the L1-PAZ hinge may be flexible in general for prokaryotic Ago's but rigid for eukaryotic Ago's.
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Affiliation(s)
| | | | | | - Xuefeng Cui
- Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology , Thuwal 23955-6900, Saudi Arabia
| | - Xin Gao
- Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology , Thuwal 23955-6900, Saudi Arabia
| | - Yanli Wang
- Laboratory of Non-Coding RNA, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China
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157
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Serena M, Giorgetti A, Busato M, Gasparini F, Diani E, Romanelli MG, Zipeto D. Molecular characterization of HIV-1 Nef and ACOT8 interaction: insights from in silico structural predictions and in vitro functional assays. Sci Rep 2016; 6:22319. [PMID: 26927806 PMCID: PMC4772117 DOI: 10.1038/srep22319] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 02/11/2016] [Indexed: 11/29/2022] Open
Abstract
HIV-1 Nef interacts with several cellular proteins, among which the human peroxisomal thioesterase 8 (ACOT8). This interaction may be involved in the endocytosis regulation of membrane proteins and might modulate lipid composition in membrane rafts. Nef regions involved in the interaction have been experimentally characterized, whereas structural details of the ACOT8 protein are unknown. The lack of structural information hampers the comprehension of the functional consequences of the complex formation during HIV-1 infection. We modelled, through in silico predictions, the ACOT8 structure and we observed a high charge complementarity between Nef and ACOT8 surfaces, which allowed the identification of the ACOT8 putative contact points involved in the interaction. The predictions were validated by in vitro assays through the development of ACOT8 deletion mutants. Coimmunoprecipitation and immunofluorescence analyses showed that ACOT8 Arg45-Phe55 and Arg86-Pro93 regions are involved in Nef association. In addition, K91S mutation abrogated the interaction with Nef, indicating that Lys91 plays a key role in the interaction. Finally, when associated with ACOT8, Nef may be preserved from degradation. These findings improve the comprehension of the association between HIV-1 Nef and ACOT8, helping elucidating the biological effect of their interaction.
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Affiliation(s)
- Michela Serena
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134 Verona, Italy
| | - Alejandro Giorgetti
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Mirko Busato
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Francesca Gasparini
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134 Verona, Italy.,Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Erica Diani
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134 Verona, Italy
| | - Maria Grazia Romanelli
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134 Verona, Italy
| | - Donato Zipeto
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134 Verona, Italy
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158
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Zhang S, Zhou J, Hu H, Gong H, Chen L, Cheng C, Zeng J. A deep learning framework for modeling structural features of RNA-binding protein targets. Nucleic Acids Res 2016; 44:e32. [PMID: 26467480 PMCID: PMC4770198 DOI: 10.1093/nar/gkv1025] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 09/11/2015] [Accepted: 09/28/2015] [Indexed: 12/21/2022] Open
Abstract
RNA-binding proteins (RBPs) play important roles in the post-transcriptional control of RNAs. Identifying RBP binding sites and characterizing RBP binding preferences are key steps toward understanding the basic mechanisms of the post-transcriptional gene regulation. Though numerous computational methods have been developed for modeling RBP binding preferences, discovering a complete structural representation of the RBP targets by integrating their available structural features in all three dimensions is still a challenging task. In this paper, we develop a general and flexible deep learning framework for modeling structural binding preferences and predicting binding sites of RBPs, which takes (predicted) RNA tertiary structural information into account for the first time. Our framework constructs a unified representation that characterizes the structural specificities of RBP targets in all three dimensions, which can be further used to predict novel candidate binding sites and discover potential binding motifs. Through testing on the real CLIP-seq datasets, we have demonstrated that our deep learning framework can automatically extract effective hidden structural features from the encoded raw sequence and structural profiles, and predict accurate RBP binding sites. In addition, we have conducted the first study to show that integrating the additional RNA tertiary structural features can improve the model performance in predicting RBP binding sites, especially for the polypyrimidine tract-binding protein (PTB), which also provides a new evidence to support the view that RBPs may own specific tertiary structural binding preferences. In particular, the tests on the internal ribosome entry site (IRES) segments yield satisfiable results with experimental support from the literature and further demonstrate the necessity of incorporating RNA tertiary structural information into the prediction model. The source code of our approach can be found in https://github.com/thucombio/deepnet-rbp.
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Affiliation(s)
- Sai Zhang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China
| | - Jingtian Zhou
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Hailin Hu
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Haipeng Gong
- School of Life Sciences, Tsinghua University, Beijing 100084, China MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
| | - Ligong Chen
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Chao Cheng
- Department of Genetics, Institute for Quantitative Biomedical Sciences, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
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159
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Berardi A, Quilici G, Spiliotopoulos D, Corral-Rodriguez MA, Martin-Garcia F, Degano M, Tonon G, Ghitti M, Musco G. Structural basis for PHDVC5HCHNSD1-C2HRNizp1 interaction: implications for Sotos syndrome. Nucleic Acids Res 2016; 44:3448-63. [PMID: 26896805 PMCID: PMC4838375 DOI: 10.1093/nar/gkw103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 02/09/2016] [Indexed: 12/19/2022] Open
Abstract
Sotos syndrome is an overgrowth syndrome caused by mutations within the functional domains ofNSD1 gene coding for NSD1, a multidomain protein regulating chromatin structure and gene expression. In particular, PHDVC5HCHNSD1 tandem domain, composed by a classical (PHDV) and an atypical (C5HCH) plant homeo-domain (PHD) finger, is target of several pathological missense-mutations. PHDVC5HCHNSD1 is also crucial for NSD1-dependent transcriptional regulation and interacts with the C2HR domain of transcriptional repressor Nizp1 (C2HRNizp1)in vitro To get molecular insights into the mechanisms dictating the patho-physiological relevance of the PHD finger tandem domain, we solved its solution structure and provided a structural rationale for the effects of seven Sotos syndrome point-mutations. To investigate PHDVC5HCHNSD1 role as structural platform for multiple interactions, we characterized its binding to histone H3 peptides and to C2HRNizp1 by ITC and NMR. We observed only very weak electrostatic interactions with histone H3 N-terminal tails, conversely we proved specific binding to C2HRNizp1 We solved C2HRNizp1 solution structure and generated a 3D model of the complex, corroborated by site-directed mutagenesis. We suggest a mechanistic scenario where NSD1 interactions with cofactors such as Nizp1 are impaired by PHDVC5HCHNSD1 pathological mutations, thus impacting on the repression of growth-promoting genes, leading to overgrowth conditions.
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Affiliation(s)
- Andrea Berardi
- Biomolecular NMR Unit, Division of Genetics and Cell Biology, IRCCS S. Raffaele Scientific Institute, Milan 20132, Italy Università degli Studi di Milano, Italy
| | - Giacomo Quilici
- Biomolecular NMR Unit, Division of Genetics and Cell Biology, IRCCS S. Raffaele Scientific Institute, Milan 20132, Italy
| | - Dimitrios Spiliotopoulos
- Biomolecular NMR Unit, Division of Genetics and Cell Biology, IRCCS S. Raffaele Scientific Institute, Milan 20132, Italy Università Vita e Salute San Raffaele, Milano 21032, Italy
| | - Maria Angeles Corral-Rodriguez
- Biomolecular NMR Unit, Division of Genetics and Cell Biology, IRCCS S. Raffaele Scientific Institute, Milan 20132, Italy Università Vita e Salute San Raffaele, Milano 21032, Italy
| | - Fernando Martin-Garcia
- Biomolecular NMR Unit, Division of Genetics and Cell Biology, IRCCS S. Raffaele Scientific Institute, Milan 20132, Italy
| | - Massimo Degano
- Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, IRCCS S. Raffaele Scientific Institute, Milan 20132, Italy
| | - Giovanni Tonon
- Functional genomics of cancer, Division of Experimental Oncology, IRCCS S. Raffaele Scientific Institute, Milan 20132, Italy
| | - Michela Ghitti
- Biomolecular NMR Unit, Division of Genetics and Cell Biology, IRCCS S. Raffaele Scientific Institute, Milan 20132, Italy
| | - Giovanna Musco
- Biomolecular NMR Unit, Division of Genetics and Cell Biology, IRCCS S. Raffaele Scientific Institute, Milan 20132, Italy
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160
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Yadav BS, Singh S, Shaw AK, Mani A. Structure prediction and docking-based molecular insights of human YB-1 and nucleic acid interaction. J Biomol Struct Dyn 2016; 34:2561-2580. [PMID: 26609765 DOI: 10.1080/07391102.2015.1124050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Y-box-binding protein 1 (YB-1), a cold shock domain protein, is one of the most conserved nucleic acid-binding proteins. The multifunctional human YB-1 is a member of a large family of proteins with an evolutionary ancient cold shock domain. The presence of a cold shock domain is a specific feature of Y-box-binding proteins and allows attributing them to a wider group of proteins containing a cold shock domain. This protein is involved in a number of cellular processes including proliferation, differentiation and stress response. The YB-1 performs its function both in the cytoplasm and in the cell nucleus. In this study, we present the structure of full-length human YB-1 protein along with investigation of their nucleic acid-binding preferential. The study also focuses on biases for particular purine and pyrimidine bases. The overall goal of this study was to model and validate full-length YB-1 protein and to compare its nucleic acid-binding studies with previous reports.
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Affiliation(s)
- Birendra Singh Yadav
- a Department of Biotechnology , Motilal Nehru National Institute of Technology , Allahabad 211004 , India
| | - Swati Singh
- b Center of Bioinformatics , Nehru Science Center, Institute of Interdisciplinary Studies, University of Allahabad , Allahabad 211002 , India
| | - Amit Kumar Shaw
- c Department of Biotechnology , National Institute of Technology , Durgapur 713209 , India
| | - Ashutosh Mani
- a Department of Biotechnology , Motilal Nehru National Institute of Technology , Allahabad 211004 , India
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161
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Lorenz S, Bhattacharyya M, Feiler C, Rape M, Kuriyan J. Crystal Structure of a Ube2S-Ubiquitin Conjugate. PLoS One 2016; 11:e0147550. [PMID: 26828794 PMCID: PMC4734694 DOI: 10.1371/journal.pone.0147550] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 01/04/2016] [Indexed: 12/18/2022] Open
Abstract
Protein ubiquitination occurs through the sequential formation and reorganization of specific protein-protein interfaces. Ubiquitin-conjugating (E2) enzymes, such as Ube2S, catalyze the formation of an isopeptide linkage between the C-terminus of a "donor" ubiquitin and a primary amino group of an "acceptor" ubiquitin molecule. This reaction involves an intermediate, in which the C-terminus of the donor ubiquitin is thioester-bound to the active site cysteine of the E2 and a functionally important interface is formed between the two proteins. A docked model of a Ube2S-donor ubiquitin complex was generated previously, based on chemical shift mapping by NMR, and predicted contacts were validated in functional studies. We now present the crystal structure of a covalent Ube2S-ubiquitin complex. The structure contains an interface between Ube2S and ubiquitin in trans that resembles the earlier model in general terms, but differs in detail. The crystallographic interface is more hydrophobic than the earlier model and is stable in molecular dynamics (MD) simulations. Remarkably, the docked Ube2S-donor complex converges readily to the configuration seen in the crystal structure in 3 out of 8 MD trajectories. Since the crystallographic interface is fully consistent with mutational effects, this indicates that the structure provides an energetically favorable representation of the functionally critical Ube2S-donor interface.
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Affiliation(s)
- Sonja Lorenz
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Moitrayee Bhattacharyya
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Christian Feiler
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Michael Rape
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - John Kuriyan
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
- Department of Chemistry, University of California, Berkeley, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail:
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162
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de Vries SJ, Chauvot de Beauchêne I, Schindler CEM, Zacharias M. Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling. Biophys J 2016; 110:785-97. [PMID: 26846888 DOI: 10.1016/j.bpj.2015.12.038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 11/18/2015] [Accepted: 12/14/2015] [Indexed: 12/29/2022] Open
Abstract
Protein-protein interactions carry out a large variety of essential cellular processes. Cryo-electron microscopy (cryo-EM) is a powerful technique for the modeling of protein-protein interactions at a wide range of resolutions, and recent developments have caused a revolution in the field. At low resolution, cryo-EM maps can drive integrative modeling of the interaction, assembling existing structures into the map. Other experimental techniques can provide information on the interface or on the contacts between the monomers in the complex. This inevitably raises the question regarding which type of data is best suited to drive integrative modeling approaches. Systematic comparison of the prediction accuracy and specificity of the different integrative modeling paradigms is unavailable to date. Here, we compare EM-driven, interface-driven, and contact-driven integrative modeling paradigms. Models were generated for the protein docking benchmark using the ATTRACT docking engine and evaluated using the CAPRI two-star criterion. At 20 Å resolution, EM-driven modeling achieved a success rate of 100%, outperforming the other paradigms even with perfect interface and contact information. Therefore, even very low resolution cryo-EM data is superior in predicting heterodimeric and heterotrimeric protein assemblies. Our study demonstrates that a force field is not necessary, cryo-EM data alone is sufficient to accurately guide the monomers into place. The resulting rigid models successfully identify regions of conformational change, opening up perspectives for targeted flexible remodeling.
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Affiliation(s)
- Sjoerd J de Vries
- Physik-Department T38, Technische Universität München, Garching, Germany.
| | | | - Christina E M Schindler
- Physik-Department T38, Technische Universität München, Garching, Germany; Center for Integrated Protein Science Munich (CIPSM) at the Physics Department, Technische Universität München, Garching, Germany
| | - Martin Zacharias
- Physik-Department T38, Technische Universität München, Garching, Germany; Center for Integrated Protein Science Munich (CIPSM) at the Physics Department, Technische Universität München, Garching, Germany
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163
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Structural characterization of ANGPTL8 (betatrophin) with its interacting partner lipoprotein lipase. Comput Biol Chem 2016; 61:210-20. [PMID: 26908254 DOI: 10.1016/j.compbiolchem.2016.01.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 01/07/2016] [Accepted: 01/21/2016] [Indexed: 12/20/2022]
Abstract
Angiopoietin-like protein 8 (ANGPTL8) (also known as betatrophin) is a newly identified secretory protein with a potential role in autophagy, lipid metabolism and pancreatic beta-cell proliferation. Its structural characterization is required to enhance our current understanding of its mechanism of action which could help in identifying its receptor and/or other binding partners. Based on the physiological significance and necessity of exploring structural features of ANGPTL8, the present study is conducted with a specific aim to model the structure of ANGPTL8 and study its possible interactions with Lipoprotein Lipase (LPL). To the best of our knowledge, this is the first attempt to predict 3-dimensional (3D) structure of ANGPTL8. Three different approaches were used for modeling of ANGPTL8 including homology modeling, de-novo structure prediction and their amalgam which is then proceeded by structure verification using ERRATT, PROSA, Qmean and Ramachandran plot scores. The selected models of ANGPTL8 were further evaluated for protein-protein interaction (PPI) analysis with LPL using CPORT and HADDOCK server. Our results have shown that the crystal structure of iSH2 domain of Phosphatidylinositol 3-kinase (PI3K) p85β subunit (PDB entry: 3mtt) is a good candidate for homology modeling of ANGPTL8. Analysis of inter-molecular interactions between the structure of ANGPTL8 and LPL revealed existence of several non-covalent interactions. The residues of LPL involved in these interactions belong from its lid region, thrombospondin (TSP) region and heparin binding site which is suggestive of a possible role of ANGPTL8 in regulating the proteolysis, motility and localization of LPL. Besides, the conserved residues of SE1 region of ANGPTL8 formed interactions with the residues around the hinge region of LPL. Overall, our results support a model of inhibition of LPL by ANGPTL8 through the steric block of its catalytic site which will be further explored using wet lab studies in future.
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164
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Tomlinson JH, Thompson GS, Kalverda AP, Zhuravleva A, O'Neill AJ. A target-protection mechanism of antibiotic resistance at atomic resolution: insights into FusB-type fusidic acid resistance. Sci Rep 2016; 6:19524. [PMID: 26781961 PMCID: PMC4725979 DOI: 10.1038/srep19524] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/09/2015] [Indexed: 11/09/2022] Open
Abstract
Antibiotic resistance in clinically important bacteria can be mediated by proteins that physically associate with the drug target and act to protect it from the inhibitory effects of an antibiotic. We present here the first detailed structural characterization of such a target protection mechanism mediated through a protein-protein interaction, revealing the architecture of the complex formed between the FusB fusidic acid resistance protein and the drug target (EF-G) it acts to protect. Binding of FusB to EF-G induces conformational and dynamic changes in the latter, shedding light on the molecular mechanism of fusidic acid resistance.
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Affiliation(s)
- Jennifer H Tomlinson
- School of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, UK, LS2 9JT.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK, LS2 9JT
| | - Gary S Thompson
- School of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, UK, LS2 9JT.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK, LS2 9JT
| | - Arnout P Kalverda
- School of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, UK, LS2 9JT.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK, LS2 9JT
| | - Anastasia Zhuravleva
- School of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, UK, LS2 9JT.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK, LS2 9JT
| | - Alex J O'Neill
- School of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, UK, LS2 9JT.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK, LS2 9JT
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165
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Park Y, Jowitt TA, Day AJ, Prestegard JH. Nuclear Magnetic Resonance Insight into the Multiple Glycosaminoglycan Binding Modes of the Link Module from Human TSG-6. Biochemistry 2016; 55:262-76. [PMID: 26685054 PMCID: PMC5073374 DOI: 10.1021/acs.biochem.5b01148] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Tumor necrosis factor-stimulated gene-6 (TSG-6) is a hyaluronan (HA)-binding protein that is essential for stabilizing and remodeling the extracellular matrix (ECM) during ovulation and inflammatory disease processes such as arthritis. The Link module, one of the domains of TSG-6, is responsible for binding hyaluronan and other glycosaminoglycans found in the ECM. In this study, we used a well-defined chondroitin sulfate (CS) hexasaccharide (ΔC444S) to determine the structure of the Link module, in solution, in its chondroitin sulfate-bound state. A variety of nuclear magnetic resonance techniques were employed, including chemical shift perturbation, residual dipolar couplings (RDCs), nuclear Overhauser effects, spin relaxation measurements, and paramagnetic relaxation enhancements from a spin-labeled analogue of ΔC444S. The binding site for ΔC444S on the Link module overlapped with that of HA. Surprisingly, ΔC444S binding induced dimerization of the Link module (as confirmed by analytical ultracentrifugation), and a second weak binding site that partially overlapped with a previously identified heparin site was detected. A dimer model was generated using chemical shift perturbations and RDCs as restraints in the docking program HADDOCK. We postulate that the molecular cross-linking enhanced by the multiple binding modes of the Link module might be critical for remodeling the ECM during inflammation/ovulation and might contribute to other functions of TSG-6.
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Affiliation(s)
- Younghee Park
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602, USA
| | - Thomas A. Jowitt
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Anthony J. Day
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - James H. Prestegard
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602, USA
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166
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Computational Design of TrkB Peptide Inhibitors and Their Biological Effects on Ovarian Cancer Cell Lines. Int J Pept Res Ther 2016. [DOI: 10.1007/s10989-015-9510-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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167
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Das A, Bhattacharya S. Different Types of Molecular Docking Based on Variations of Interacting Molecules. METHODS AND ALGORITHMS FOR MOLECULAR DOCKING-BASED DRUG DESIGN AND DISCOVERY 2016. [DOI: 10.4018/978-1-5225-0115-2.ch006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Molecular docking plays an important role in drug discovery research by facilitating target identification, target validation, virtual screening for lead identification and lead optimization. Depending upon the nature of the disease of interest, targets can be either protein or DNA while drugs are mostly organic small molecules. Different types of molecular docking techniques like protein-protein or protein-DNA or protein-small molecule or DNA-small molecule are employed for achieving the above mentioned objectives. This chapter provides a clear idea of the position of molecular docking in drug discovery with detailed discussion on different types of molecular docking based on the varieties of interacting partners. Subsequently the authors provide a detailed list of tools that can be used for docking in drug discovery and discus some examples of molecular docking in drug discovery before concluding with a remark on future areas of improvement in molecular docking related to drug discovery.
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168
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Torabi R, Bagherzadeh K, Ghourchian H, Amanlou M. An investigation on the interaction modes of a single-strand DNA aptamer and RBP4 protein: a molecular dynamic simulations approach. Org Biomol Chem 2016; 14:8141-53. [DOI: 10.1039/c6ob01094f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Monitoring and evaluating structural and functional alternations in RBP4 induced by its specific aptamer binding to design new aptamers for diagnostic and therapeutic purposes with reduced insulin resistance.
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Affiliation(s)
- Raheleh Torabi
- Laboratory of Microanalysis
- Institute of Biochemistry & Biophysics
- University of Tehran
- Tehran
- Iran
| | - Kowsar Bagherzadeh
- Razi Drug Research Center
- Iran University of Medical Sciences
- Tehran
- Iran
- Department of Medicinal Chemistry
| | - Hedayatollah Ghourchian
- Laboratory of Microanalysis
- Institute of Biochemistry & Biophysics
- University of Tehran
- Tehran
- Iran
| | - Massoud Amanlou
- Department of Medicinal Chemistry
- Faculty of Pharmacy and Drug Design and Development Research Center
- Tehran University of Medical Sciences
- Tehran
- Iran
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169
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Huang T, Hinck AP. Production, Isolation, and Structural Analysis of Ligands and Receptors of the TGF-β Superfamily. Methods Mol Biol 2016; 1344:63-92. [PMID: 26520118 PMCID: PMC4846357 DOI: 10.1007/978-1-4939-2966-5_4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The ability to understand the molecular mechanisms by which secreted signaling proteins of the TGF-β superfamily assemble their cell surface receptors into complexes to initiate downstream signaling is dependent upon the ability to determine atomic-resolution structures of the signaling proteins, the ectodomains of the receptors, and the complexes that they form. The structures determined to date have revealed major differences in the overall architecture of the signaling complexes formed by the TGF-βs and BMPs, which has provided insights as to how they have evolved to fulfill their distinct functions. Such studies, have however, only been applied to a few members of the TGF-β superfamily, which is largely due to the difficulty of obtaining milligram-scale quantities of highly homogenous preparations of the disulfide-rich signaling proteins and receptor ectodomains of the superfamily. Here we describe methods used to produce signaling proteins and receptor ectodomains of the TGF-β superfamily using bacterial and mammalian expression systems and procedures to purify them to homogeneity.
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Affiliation(s)
- Tao Huang
- Protein Chemistry, Novo Nordisk Research Center China, 20 Life Science Park Rd, Bldg 2, Beijing, 102206, China
| | - Andrew P Hinck
- Protein Chemistry, Novo Nordisk Research Center China, 20 Life Science Park Rd, Bldg 2, Beijing, 102206, China.
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170
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Sudhakar DR, P. K, Subbarao N. Docking and molecular dynamics simulation study of EGFR1 with EGF-like peptides to understand molecular interactions. MOLECULAR BIOSYSTEMS 2016; 12:1987-95. [DOI: 10.1039/c6mb00032k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Epidermal growth factor receptors (EGFRs) are oncogenes, which regulate the expression of genes in various pathways, allowing cells to grow and divide.
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Affiliation(s)
- D. Raja Sudhakar
- School of Computational and Integrative Sciences
- Jawaharlal Nehru University
- New Delhi-110067
- India
| | - Kalaiarasan P.
- National Centre of Applied Human Genetics
- School of Life Sciences
- Jawaharlal Nehru University
- New Delhi
- India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences
- Jawaharlal Nehru University
- New Delhi-110067
- India
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171
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Zhang L, Jiang H, Sheong F, Pardo-Avila F, Cheung PH, Huang X. Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and Their Recognition with Ligands. Methods Enzymol 2016; 578:343-71. [DOI: 10.1016/bs.mie.2016.05.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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172
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Muthu K, Panneerselvam M, Topno NS, Ramadas K. Structural transition of ETS1 from an auto-inhibited to functional state upon association with the p16INK4anative and mutated promoter region. RSC Adv 2016. [DOI: 10.1039/c5ra24525g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Detailed elucidation of structural changes invoked on transcriptional factors and their target genes upon their association is pivotal for understanding the genetic level regulations imposed in several diseases including ovarian cancer.
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Affiliation(s)
- Kannan Muthu
- Centre for Bioinformatics
- Pondicherry University
- Puducherry
- India-605014
| | | | | | - Krishna Ramadas
- Centre for Bioinformatics
- Pondicherry University
- Puducherry
- India-605014
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173
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Sepuru KM, Rajarathnam K. CXCL1/MGSA Is a Novel Glycosaminoglycan (GAG)-binding Chemokine: STRUCTURAL EVIDENCE FOR TWO DISTINCT NON-OVERLAPPING BINDING DOMAINS. J Biol Chem 2015; 291:4247-55. [PMID: 26721883 DOI: 10.1074/jbc.m115.697888] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Indexed: 12/12/2022] Open
Abstract
In humans, the chemokine CXCL1/MGSA (hCXCL1) plays fundamental and diverse roles in pathophysiology, from microbial killing to cancer progression, by orchestrating the directed migration of immune and non-immune cells. Cellular trafficking is highly regulated and requires concentration gradients that are achieved by interactions with sulfated glycosaminoglycans (GAGs). However, very little is known regarding the structural basis underlying hCXCL1-GAG interactions. We addressed this by characterizing the binding of GAG heparin oligosaccharides to hCXCL1 using NMR spectroscopy. Binding experiments under conditions at which hCXCL1 exists as monomers and dimers indicate that the dimer is the high-affinity GAG ligand. NMR experiments and modeling studies indicate that lysine and arginine residues mediate binding and that they are located in two non-overlapping domains. One domain, consisting of N-loop and C-helical residues (defined as α-domain) has also been identified previously as the GAG-binding domain for the related chemokine CXCL8/IL-8. The second domain, consisting of residues from the N terminus, 40s turn, and third β-strand (defined as β-domain) is novel. Eliminating β-domain binding by mutagenesis does not perturb α-domain binding, indicating two independent GAG-binding sites. It is known that N-loop and N-terminal residues mediate receptor activation, and we show that these residues are also involved in extensive GAG interactions. We also show that the GAG-bound hCXCL1 completely occlude receptor binding. We conclude that hCXCL1-GAG interactions provide stringent control over regulating chemokine levels and receptor accessibility and activation, and that chemotactic gradients mediate cellular trafficking to the target site.
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Affiliation(s)
- Krishna Mohan Sepuru
- From the Department of Biochemistry and Molecular Biology and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555
| | - Krishna Rajarathnam
- From the Department of Biochemistry and Molecular Biology and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555
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174
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Rosenzweig R, Kay LE. Solution NMR Spectroscopy Provides an Avenue for the Study of Functionally Dynamic Molecular Machines: The Example of Protein Disaggregation. J Am Chem Soc 2015; 138:1466-77. [PMID: 26651836 DOI: 10.1021/jacs.5b11346] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Solution-based NMR spectroscopy has been an important tool for studying the structure and dynamics of relatively small proteins and protein complexes with aggregate molecular masses under approximately 50 kDa. The development of new experiments and labeling schemes, coupled with continued improvements in hardware, has significantly reduced this size limitation, enabling atomic-resolution studies of molecular machines in the 1 MDa range. In this Perspective, some of the important advances are highlighted in the context of studies of molecular chaperones involved in protein disaggregation. New insights into the structural biology of disaggregation obtained from NMR studies are described, focusing on the unique capabilities of the methodology for obtaining atomic-resolution descriptions of dynamic systems.
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Affiliation(s)
- Rina Rosenzweig
- Departments of Molecular Genetics, Biochemistry, and Chemistry, The University of Toronto , Toronto, Ontario, Canada M5S 1A8
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry, and Chemistry, The University of Toronto , Toronto, Ontario, Canada M5S 1A8.,Program in Molecular Structure and Function, Hospital for Sick Children , 555 University Avenue, Toronto, Ontario, Canada M5G 1X8
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175
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Topno NS, Kannan M, Krishna R. Interacting mechanism of ID3 HLH domain towards E2A/E12 transcription factor - An Insight through molecular dynamics and docking approach. Biochem Biophys Rep 2015; 5:180-190. [PMID: 28955822 PMCID: PMC5600450 DOI: 10.1016/j.bbrep.2015.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 11/24/2015] [Accepted: 12/01/2015] [Indexed: 10/29/2022] Open
Abstract
Inhibitor of DNA binding protein 3 (ID3) has long been characterized as an oncogene that implicates its functional role through its Helix-Loop-Helix (HLH) domain upon protein-protein interaction. An insight into the dimerization brought by this domain helps in identifying the key residues that favor the mechanism behind it. Molecular dynamics (MD) simulations were performed for the HLH proteins ID3 and Transcription factor E2-alpha (E2A/E12) and their ensemble complex (ID3-E2A/E12) to gather information about the HLH domain region and its role in the interaction process. Further evaluation of the results by Principal Component Analysis (PCA) and Free Energy Landscape (FEL) helped in revealing residues of E2A/E12: Lys570, Ala595, Val598, and Ile599 and ID3: Glu53, Gln63, and Gln66 buried in their HLH motifs imparting key roles in dimerization process. Furthermore the T-pad analysis results helped in identifying the key fluctuations and conformational transitions using the intrinsic properties of the residues present in the domain region of the proteins thus specifying their crucial role towards molecular recognition. The study provides an insight into the interacting mechanism of the ID3-E2A/E12 complex and maps the structural transitions arising in the essential conformational space indicating the key structural changes within the helical regions of the motif. It thereby describes how the internal dynamics of the proteins might regulate their intrinsic structural features and its subsequent functionality.
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Affiliation(s)
- Nishith Saurav Topno
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Muthu Kannan
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Ramadas Krishna
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India
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176
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Akbal-Delibas B, Farhoodi R, Pomplun M, Haspel N. Accurate refinement of docked protein complexes using evolutionary information and deep learning. J Bioinform Comput Biol 2015; 14:1642002. [PMID: 26846813 DOI: 10.1142/s0219720016420026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
One of the major challenges for protein docking methods is to accurately discriminate native-like structures from false positives. Docking methods are often inaccurate and the results have to be refined and re-ranked to obtain native-like complexes and remove outliers. In a previous work, we introduced AccuRefiner, a machine learning based tool for refining protein-protein complexes. Given a docked complex, the refinement tool produces a small set of refined versions of the input complex, with lower root-mean-square-deviation (RMSD) of atomic positions with respect to the native structure. The method employs a unique ranking tool that accurately predicts the RMSD of docked complexes with respect to the native structure. In this work, we use a deep learning network with a similar set of features and five layers. We show that a properly trained deep learning network can accurately predict the RMSD of a docked complex with 1.40 Å error margin on average, by approximating the complex relationship between a wide set of scoring function terms and the RMSD of a docked structure. The network was trained on 35000 unbound docking complexes generated by RosettaDock. We tested our method on 25 different putative docked complexes produced also by RosettaDock for five proteins that were not included in the training data. The results demonstrate that the high accuracy of the ranking tool enables AccuRefiner to consistently choose the refinement candidates with lower RMSD values compared to the coarsely docked input structures.
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Affiliation(s)
- Bahar Akbal-Delibas
- 1 Department of Computer Science, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA 02125, USA
| | - Roshanak Farhoodi
- 1 Department of Computer Science, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA 02125, USA
| | - Marc Pomplun
- 1 Department of Computer Science, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA 02125, USA
| | - Nurit Haspel
- 1 Department of Computer Science, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA 02125, USA
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177
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Transient Interactions of a Cytosolic Protein with Macromolecular and Vesicular Cosolutes: Unspecific and Specific Effects. Chembiochem 2015; 16:2633-45. [DOI: 10.1002/cbic.201500451] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Indexed: 01/04/2023]
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178
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Asgari S, Mirzahoseini H, Karimipour M, Rahimi H, Ebrahim-Habibi A. Rational design of stable and functional hirudin III mutants with lower antigenicity. Biologicals 2015; 43:479-91. [DOI: 10.1016/j.biologicals.2015.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 07/12/2015] [Accepted: 07/23/2015] [Indexed: 12/25/2022] Open
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179
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Zhao Y, Marcink TC, Sanganna Gari RR, Marsh BP, King GM, Stawikowska R, Fields GB, Van Doren SR. Transient collagen triple helix binding to a key metalloproteinase in invasion and development. Structure 2015; 23:257-69. [PMID: 25651059 DOI: 10.1016/j.str.2014.11.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/30/2014] [Accepted: 11/17/2014] [Indexed: 12/17/2022]
Abstract
Skeletal development and invasion by tumor cells depends on proteolysis of collagen by the pericellular metalloproteinase MT1-MMP. Its hemopexin-like (HPX) domain binds to collagen substrates to facilitate their digestion. Spin labeling and paramagnetic nuclear magnetic resonance (NMR) detection have revealed how the HPX domain docks to collagen I-derived triple helix. Mutations impairing triple-helical peptidase activity corroborate the interface. Saturation transfer difference NMR suggests rotational averaging around the longitudinal axis of the triple-helical peptide. Part of the interface emerges as unique and potentially targetable for selective inhibition. The triple helix crosses the junction of blades I and II at a 45° angle to the symmetry axis of the HPX domain, placing the scissile Gly∼Ile bond near the HPX domain and shifted ∼25 Å from MMP-1 complexes. This raises the question of the MT1-MMP catalytic domain folding over the triple helix during catalysis, a possibility accommodated by the flexibility between domains suggested by atomic force microscopy images.
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Affiliation(s)
- Yingchu Zhao
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA
| | - Thomas C Marcink
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA
| | | | - Brendan P Marsh
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
| | - Gavin M King
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA; Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
| | - Roma Stawikowska
- Torrey Pines Institute for Molecular Studies, 11350 Southwest Village Parkway, Port Saint Lucie, FL 34987, USA
| | - Gregg B Fields
- Torrey Pines Institute for Molecular Studies, 11350 Southwest Village Parkway, Port Saint Lucie, FL 34987, USA
| | - Steven R Van Doren
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA.
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180
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Shahid SA, Nagaraj M, Chauhan N, Franks TW, Bardiaux B, Habeck M, Orwick-Rydmark M, Linke D, van Rossum BJ. Festkörper-NMR-Studien an der Membrananker-Domäne von YadA in der bakteriellen Außenmembran. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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181
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Li Y, Wong YL, Ng FM, Liu B, Wong YX, Poh ZY, Then SW, Lee MY, Ng HQ, Hung AW, Cherian J, Hill J, Keller TH, Kang C. Characterization of the interaction between Escherichia coli topoisomerase IV E subunit and an ATP competitive inhibitor. Biochem Biophys Res Commun 2015; 467:961-6. [PMID: 26471301 DOI: 10.1016/j.bbrc.2015.10.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 10/07/2015] [Indexed: 10/22/2022]
Abstract
Bacterial topoisomerase IV (ParE) is essential for DNA replication and serves as an attractive target for antibacterial drug development. The X-ray structure of the N-terminal 24 kDa ParE, responsible for ATP binding has been solved. Due to the accessibility of structural information of ParE, many potent ParE inhibitors have been discovered. In this study, a pyridylurea lead molecule against ParE of Escherichia coli (eParE) was characterized with a series of biochemical and biophysical techniques. More importantly, solution NMR analysis of compound binding to eParE provides better understanding of the molecular interactions between the inhibitor and eParE.
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Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Ying Lei Wong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Fui Mee Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Boping Liu
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Yun Xuan Wong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Zhi Ying Poh
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Siew Wen Then
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Michelle Yueqi Lee
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Hui Qi Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Alvin W Hung
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Joseph Cherian
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - Thomas H Keller
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, 138669, Singapore.
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182
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van Zundert GCP, Rodrigues JPGLM, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond ASJ, van Dijk M, de Vries SJ, Bonvin AMJJ. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. J Mol Biol 2015; 428:720-725. [PMID: 26410586 DOI: 10.1016/j.jmb.2015.09.014] [Citation(s) in RCA: 1758] [Impact Index Per Article: 195.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/16/2015] [Accepted: 09/17/2015] [Indexed: 11/25/2022]
Abstract
The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2.
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Affiliation(s)
- G C P van Zundert
- Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands
| | - J P G L M Rodrigues
- Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands
| | - M Trellet
- Centre National de la Recherche Scientifique Laboratoire d'Informatique pour la Mécanique et les Sciences de l'Ingénieur, rue John Von Neumann, 91403 Orsay, France
| | - C Schmitz
- Instaclustr Level 5, 1 Moore Street, Canberra ACT 2600, Australia
| | - P L Kastritis
- European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - E Karaca
- European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - A S J Melquiond
- Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - M van Dijk
- Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, the Netherlands
| | - S J de Vries
- Physik-Department, Technische Universität München, James-Franck-Strasse 1, 85748 Garching, Germany
| | - A M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands
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183
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In situ structural analysis of the human nuclear pore complex. Nature 2015; 526:140-143. [PMID: 26416747 PMCID: PMC4886846 DOI: 10.1038/nature15381] [Citation(s) in RCA: 266] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 08/07/2015] [Indexed: 12/12/2022]
Abstract
Nuclear pore complexes are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Determining their 110-megadalton structure imposes a formidable challenge and requires in situ structural biology approaches. Of approximately 30 nucleoporins (Nups), 15 are structured and form the Y and inner-ring complexes. These two major scaffolding modules assemble in multiple copies into an eight-fold rotationally symmetric structure that fuses the inner and outer nuclear membranes to form a central channel of ~60 nm in diameter. The scaffold is decorated with transport-channel Nups that often contain phenylalanine-repeat sequences and mediate the interaction with cargo complexes. Although the architectural arrangement of parts of the Y complex has been elucidated, it is unclear how exactly it oligomerizes in situ. Here we combine cryo-electron tomography with mass spectrometry, biochemical analysis, perturbation experiments and structural modelling to generate, to our knowledge, the most comprehensive architectural model of the human nuclear pore complex to date. Our data suggest previously unknown protein interfaces across Y complexes and to inner-ring complex members. We show that the transport-channel Nup358 (also known as Ranbp2) has a previously unanticipated role in Y-complex oligomerization. Our findings blur the established boundaries between scaffold and transport-channel Nups. We conclude that, similar to coated vesicles, several copies of the same structural building block--although compositionally identical--engage in different local sets of interactions and conformations.
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184
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Solution NMR characterization of chemokine CXCL8/IL-8 monomer and dimer binding to glycosaminoglycans: structural plasticity mediates differential binding interactions. Biochem J 2015; 472:121-33. [PMID: 26371375 PMCID: PMC4692082 DOI: 10.1042/bj20150059] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 09/11/2015] [Indexed: 01/05/2023]
Abstract
Structural plasticity plays a major role in determining differential binding of CXCL8 monomer and dimer to glycosaminoglycans (GAGs) and that dimer is the high-affinity GAG ligand. We propose that these properties play important roles in orchestrating in vivo chemokine-mediated neutrophil function. Chemokine CXCL8/interleukin-8 (IL-8) plays a crucial role in directing neutrophils and oligodendrocytes to combat infection/injury and tumour cells in metastasis development. CXCL8 exists as monomers and dimers and interaction of both forms with glycosaminoglycans (GAGs) mediate these diverse cellular processes. However, very little is known regarding the structural basis underlying CXCL8–GAG interactions. There are conflicting reports on the affinities, geometry and whether the monomer or dimer is the high-affinity GAG ligand. To resolve these issues, we characterized the binding of a series of heparin-derived oligosaccharides [heparin disaccharide (dp2), heparin tetrasaccharide (dp4), heparin octasaccharide (dp8) and heparin 14-mer (dp14)] to the wild-type (WT) dimer and a designed monomer using solution NMR spectroscopy. The pattern and extent of binding-induced chemical shift perturbation (CSP) varied between dimer and monomer and between longer and shorter oligosaccharides. NMR-based structural models show that different interaction modes coexist and that the nature of interactions varied between monomer and dimer and oligosaccharide length. MD simulations indicate that the binding interface is structurally plastic and provided residue-specific details of the dynamic nature of the binding interface. Binding studies carried out under conditions at which WT CXCL8 exists as monomers and dimers provide unambiguous evidence that the dimer is the high-affinity GAG ligand. Together, our data indicate that a set of core residues function as the major recognition/binding site, a set of peripheral residues define the various binding geometries and that the structural plasticity of the binding interface allows multiplicity of binding interactions. We conclude that structural plasticity most probably regulates in vivo CXCL8 monomer/dimer–GAG interactions and function.
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185
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Bochicchio A, Rossetti G, Tabarrini O, Krauβ S, Carloni P. Molecular view of ligands specificity for CAG repeats in anti-Huntington therapy. J Chem Theory Comput 2015; 11:4911-22. [PMID: 26574279 DOI: 10.1021/acs.jctc.5b00208] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Huntington's disease is a fatal and devastating neurodegenerative genetic disorder for which there is currently no cure. It is characterized by Huntingtin protein's mRNA transcripts with 36 or more CAG repeats. Inhibiting the formation of pathological complexes between these expanded transcripts and target proteins may be a valuable strategy against the disease. Yet, the rational design of molecules specifically targeting the expanded CAG repeats is limited by the lack of structural information. Here, we use well-tempered metadynamics-based free energy calculations to investigate pose and affinity of two ligands targeting CAG repeats for which affinities have been previously measured. The first consists of two 4-guanidinophenyl rings linked by an ester group. It is the most potent ligand identified so far, with Kd = 60(30) nM. The second consists of a 4-phenyl dihydroimidazole and 4-1H-indole dihydroimidazole connected by a C-C bond (Kd = 700(80) nM). Our calculations reproduce the experimental affinities and uncover the recognition pattern between ligands' and their RNA target. They also provide a molecular basis for the markedly different affinity of the two ligands for CAG repeats as observed experimentally. These findings may pave the way for a structure-based hit-to-lead optimization to further improve ligand selectivity toward CAG repeat-containing mRNAs.
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Affiliation(s)
| | - Giulia Rossetti
- Department of Oncology, Hematology and Stem Cell Transplantation, RWTH Aachen University , D-52074 Aachen, North Rhine-Westphalia, Germany
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, Università di Perugia , Via del Liceo 1, I-06123 Perugia, Perugia, Italy
| | - Sybille Krauβ
- German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Strasse 25, D-53127 Bonn, North Rhine-Westphalia, Germany
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186
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Shahid SA, Nagaraj M, Chauhan N, Franks TW, Bardiaux B, Habeck M, Orwick-Rydmark M, Linke D, van Rossum BJ. Solid-state NMR Study of the YadA Membrane-Anchor Domain in the Bacterial Outer Membrane. Angew Chem Int Ed Engl 2015; 54:12602-6. [PMID: 26332158 DOI: 10.1002/anie.201505506] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 07/17/2015] [Indexed: 12/12/2022]
Abstract
MAS-NMR was used to study the structure and dynamics at ambient temperatures of the membrane-anchor domain of YadA (YadA-M) in a pellet of the outer membrane of E. coli in which it was expressed. YadA is an adhesin from the pathogen Yersinia enterocolitica that is involved in interactions with the host cell, and it is a model protein for studying the autotransport process. Existing assignments were sucessfully transferred to a large part of the YadA-M protein in the E. coli lipid environment by using (13) C-(13) C DARR and PDSD spectra at different mixing times. The chemical shifts in most regions of YadA-M are unchanged relative to those in microcrystalline YadA-M preparations from which a structure has previously been solved, including the ASSA region that is proposed to be involved in transition-state hairpin formation for transport of the soluble domain. Comparisons of the dynamics between the microcrystalline and membrane-embedded samples indicate greater flexibility of the ASSA region in the outer-membrane preparation at physiological temperatures. This study will pave the way towards MAS-NMR structure determination of membrane proteins, and a better understanding of functionally important dynamic residues in native membrane environments.
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Affiliation(s)
- Shakeel A Shahid
- Max-Planck-Institute for Developmental Biology, Department 1, Tübingen (Germany).,Leibniz-Institut für Molekulare Pharmakologie FMP, Robert-Rössle-Str. 10, 13125 Berlin (Germany)
| | - Madhu Nagaraj
- Leibniz-Institut für Molekulare Pharmakologie FMP, Robert-Rössle-Str. 10, 13125 Berlin (Germany)
| | - Nandini Chauhan
- University of Oslo, Department of Biosciences, POBox 1066 Blindern, 0316 Oslo (Norway)
| | - Trent W Franks
- Leibniz-Institut für Molekulare Pharmakologie FMP, Robert-Rössle-Str. 10, 13125 Berlin (Germany)
| | - Benjamin Bardiaux
- Unité de Bioinformatique Structurale, CNRS UMR3528, Institut Pasteur, Paris (France)
| | - Michael Habeck
- Felix-Bernstein Institute for Mathematical Statistics, Georg-August-Universität Göttingen (Germany).,Max Planck Institute for Biophysical Chemistry, Göttingen (Germany)
| | | | - Dirk Linke
- Max-Planck-Institute for Developmental Biology, Department 1, Tübingen (Germany). .,University of Oslo, Department of Biosciences, POBox 1066 Blindern, 0316 Oslo (Norway).
| | - Barth-J van Rossum
- Leibniz-Institut für Molekulare Pharmakologie FMP, Robert-Rössle-Str. 10, 13125 Berlin (Germany).
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187
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Kobashigawa Y, Amano S, Yokogawa M, Kumeta H, Morioka H, Inouye M, Schlessinger J, Inagaki F. Structural analysis of the mechanism of phosphorylation of a critical autoregulatory tyrosine residue in FGFR1 kinase domain. Genes Cells 2015; 20:860-70. [DOI: 10.1111/gtc.12277] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 07/10/2015] [Indexed: 12/23/2022]
Affiliation(s)
- Yoshihiro Kobashigawa
- Department of Structural Biology; Faculty of Advanced Life Science; Hokkaido University; Sapporo Hokkaido 060-0810 Japan
- Department of Analytical and Biophysical Chemistry; Faculty of Life Sciences; Kumamoto University; Kumamoto 862-0973 Japan
| | - Shinjiro Amano
- Department of Structural Biology; Faculty of Advanced Life Science; Hokkaido University; Sapporo Hokkaido 060-0810 Japan
| | - Mariko Yokogawa
- Department of Structural Biology; Faculty of Advanced Life Science; Hokkaido University; Sapporo Hokkaido 060-0810 Japan
| | - Hiroyuki Kumeta
- Department of Structural Biology; Faculty of Advanced Life Science; Hokkaido University; Sapporo Hokkaido 060-0810 Japan
| | - Hiroshi Morioka
- Department of Analytical and Biophysical Chemistry; Faculty of Life Sciences; Kumamoto University; Kumamoto 862-0973 Japan
| | - Masayori Inouye
- Center for Advanced Biotechnology and Medicine; Robert Wood Johnson Medical School; Piscataway NJ 08854 USA
| | - Joseph Schlessinger
- Department of Pharmacology; Yale University School of Medicine; New Haven CT 06520 USA
| | - Fuyuhiko Inagaki
- Department of Structural Biology; Faculty of Advanced Life Science; Hokkaido University; Sapporo Hokkaido 060-0810 Japan
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188
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Musiani F, Ciurli S. Evolution of Macromolecular Docking Techniques: The Case Study of Nickel and Iron Metabolism in Pathogenic Bacteria. Molecules 2015; 20:14265-92. [PMID: 26251891 PMCID: PMC6332059 DOI: 10.3390/molecules200814265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/23/2015] [Accepted: 07/28/2015] [Indexed: 11/24/2022] Open
Abstract
The interaction between macromolecules is a fundamental aspect of most biological processes. The computational techniques used to study protein-protein and protein-nucleic acid interactions have evolved in the last few years because of the development of new algorithms that allow the a priori incorporation, in the docking process, of experimentally derived information, together with the possibility of accounting for the flexibility of the interacting molecules. Here we review the results and the evolution of the techniques used to study the interaction between metallo-proteins and DNA operators, all involved in the nickel and iron metabolism of pathogenic bacteria, focusing in particular on Helicobacter pylori (Hp). In the first part of the article we discuss the methods used to calculate the structure of complexes of proteins involved in the activation of the nickel-dependent enzyme urease. In the second part of the article, we concentrate on two applications of protein-DNA docking conducted on the transcription factors HpFur (ferric uptake regulator) and HpNikR (nickel regulator). In both cases we discuss the technical expedients used to take into account the conformational variability of the multi-domain proteins involved in the calculations.
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Affiliation(s)
- Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, Bologna I-40127, Italy.
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, Bologna I-40127, Italy.
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189
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Mazzei L, Dobrovolska O, Musiani F, Zambelli B, Ciurli S. On the interaction of Helicobacter pylori NikR, a Ni(II)-responsive transcription factor, with the urease operator: in solution and in silico studies. J Biol Inorg Chem 2015. [PMID: 26204982 DOI: 10.1007/s00775-015-1284-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Helicobacter pylori (Hp) is a carcinogen that relies on Ni(II) to survive in the extreme pH conditions of the human guts. The regulation of genes coding for Ni(II) enzymes and proteins is effected by the nickel-responsive transcription factor NikR, composed of a DNA-binding domain (DBD) and a metal-binding domain (MBD). The scope of this study is to obtain the molecular details of the HpNikR interaction with the urease operator OP ureA , in solution. The size of the full-length protein prevents the characterization of the HpNikR-OP ureA interaction using NMR. We thus investigated the two separate domains of HpNikR. The conservation of their oligomeric state was established by multiple-angle light scattering. Isothermal calorimetric titrations indicated that the thermodynamics of Ni(II) binding to the isolated MBD is independent of the presence of the adjacent DBDs. The NMR spectra of the isolated DBD support considerable conservation of its structural properties. The spectral perturbations induced on the DBD by OP ureA provided information useful to calculate a structural model of the HpNikR-OP ureA complex using a docking computational protocol. The NMR assignment of the residues involved in the protein-DNA interaction represents a starting point for the development of drugs potentially able to eradicate H. pylori infections. All evidences so far collected, in this and previous studies, consistently indicate that binding of Ni(II) to the MBD increases the HpNikR-DNA affinity by modulating the dynamic, and not the structural, properties of the protein, suggesting that the formation of a stable complex relies upon an induced fit mechanism.
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Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40127, Italy
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190
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Jiang H, Sheong FK, Zhu L, Gao X, Bernauer J, Huang X. Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement. PLoS Comput Biol 2015; 11:e1004404. [PMID: 26181723 PMCID: PMC4504477 DOI: 10.1371/journal.pcbi.1004404] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/16/2015] [Indexed: 01/17/2023] Open
Abstract
Argonaute (Ago) proteins and microRNAs (miRNAs) are central components in RNA interference, which is a key cellular mechanism for sequence-specific gene silencing. Despite intensive studies, molecular mechanisms of how Ago recognizes miRNA remain largely elusive. In this study, we propose a two-step mechanism for this molecular recognition: selective binding followed by structural re-arrangement. Our model is based on the results of a combination of Markov State Models (MSMs), large-scale protein-RNA docking, and molecular dynamics (MD) simulations. Using MSMs, we identify an open state of apo human Ago-2 in fast equilibrium with partially open and closed states. Conformations in this open state are distinguished by their largely exposed binding grooves that can geometrically accommodate miRNA as indicated in our protein-RNA docking studies. miRNA may then selectively bind to these open conformations. Upon the initial binding, the complex may perform further structural re-arrangement as shown in our MD simulations and eventually reach the stable binary complex structure. Our results provide novel insights in Ago-miRNA recognition mechanisms and our methodology holds great potential to be widely applied in the studies of other important molecular recognition systems. In RNA interference, Argonaute proteins and microRNAs together form the functional core that regulates the gene expression with high sequence specificity. Elucidating the detailed mechanism of molecular recognition between Argonaute proteins and microRNAs is thus important not only for the fundamental understanding of RNA interference, but also for the further development of microRNA-based therapeutic application. In this work, we propose a two-step model to understand the mechanism of microRNA loading into human Argonaute-2: selective binding followed by structural re-arrangement. Our model is based on the results from a combined approach of molecular dynamics simulations, Markov State Models and protein-RNA docking. In particular, we identify a metastable open state of apo hAgo2 in rapid equilibrium with other states. Some of conformations in this open state have largely exposed RNA binding groove that can accommodate microRNA. We further show that the initial Argonaute-microRNA binding complex undergoes structural re-arrangement to reach stable binary crystal structure. These results provide novel insights into the underlying mechanism of Argonaute-microRNA recognition. In addition, our method is readily applicable to the investigation of other complex molecular recognition events such as protein-protein interactions and protein-ligand binding.
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Affiliation(s)
- Hanlun Jiang
- Bioengineering Graduate Program, Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- The HKUST Shenzhen Research Institute, Shenzhen, China
| | - Fu Kit Sheong
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Lizhe Zhu
- The HKUST Shenzhen Research Institute, Shenzhen, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Center of Systems Biology and Human Health, School of Science and Institute for Advance Study, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xin Gao
- Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Julie Bernauer
- Inria Saclay-Île de France, Bâtiment Alan Turing, Campus de l’École Polytechnique, Palaiseau, France
- Laboratoire d’Informatique de l’École Polytechnique (LIX), CNRS UMR 7161, École Polytechnique, Palaiseau, France
- * E-mail: (JB); (XH)
| | - Xuhui Huang
- Bioengineering Graduate Program, Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- The HKUST Shenzhen Research Institute, Shenzhen, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Center of Systems Biology and Human Health, School of Science and Institute for Advance Study, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- * E-mail: (JB); (XH)
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191
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Tan TC, Kracher D, Gandini R, Sygmund C, Kittl R, Haltrich D, Hällberg BM, Ludwig R, Divne C. Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation. Nat Commun 2015; 6:7542. [PMID: 26151670 PMCID: PMC4507011 DOI: 10.1038/ncomms8542] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 05/19/2015] [Indexed: 02/06/2023] Open
Abstract
A new paradigm for cellulose depolymerization by fungi focuses on an oxidative mechanism involving cellobiose dehydrogenases (CDH) and copper-dependent lytic polysaccharide monooxygenases (LPMO); however, mechanistic studies have been hampered by the lack of structural information regarding CDH. CDH contains a haem-binding cytochrome (CYT) connected via a flexible linker to a flavin-dependent dehydrogenase (DH). Electrons are generated from cellobiose oxidation catalysed by DH and shuttled via CYT to LPMO. Here we present structural analyses that provide a comprehensive picture of CDH conformers, which govern the electron transfer between redox centres. Using structure-based site-directed mutagenesis, rapid kinetics analysis and molecular docking, we demonstrate that flavin-to-haem interdomain electron transfer (IET) is enabled by a haem propionate group and that rapid IET requires a closed CDH state in which the propionate is tightly enfolded by DH. Following haem reduction, CYT reduces LPMO to initiate oxygen activation at the copper centre and subsequent cellulose depolymerization.
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Affiliation(s)
- Tien-Chye Tan
- School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 21, Stockholm S-10691, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelelaboratoriet, Scheeles väg 2, Stockholm S-17177, Sweden
| | - Daniel Kracher
- Food Biotechnology Laboratory, Department of Food Science and Technology, Vienna Institute of Biotechnology (VIBT), BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - Rosaria Gandini
- School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 21, Stockholm S-10691, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelelaboratoriet, Scheeles väg 2, Stockholm S-17177, Sweden
| | - Christoph Sygmund
- Food Biotechnology Laboratory, Department of Food Science and Technology, Vienna Institute of Biotechnology (VIBT), BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - Roman Kittl
- Food Biotechnology Laboratory, Department of Food Science and Technology, Vienna Institute of Biotechnology (VIBT), BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, Department of Food Science and Technology, Vienna Institute of Biotechnology (VIBT), BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - B. Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm S-17177, Sweden
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg 22603, Germany; and Centre for Structural Systems Biology (CSSB), DESY-Campus, Hamburg 22603, Germany
| | - Roland Ludwig
- Food Biotechnology Laboratory, Department of Food Science and Technology, Vienna Institute of Biotechnology (VIBT), BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - Christina Divne
- School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 21, Stockholm S-10691, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelelaboratoriet, Scheeles väg 2, Stockholm S-17177, Sweden
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192
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Computational approaches for designing potent and selective analogs of peptide toxins as novel therapeutics. Future Med Chem 2015; 6:1645-58. [PMID: 25406005 DOI: 10.4155/fmc.14.98] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Peptide toxins provide valuable therapeutic leads for many diseases. As they bind to their targets with high affinity, potency is usually ensured. However, toxins also bind to off-target receptors, causing potential side effects. Thus, a major challenge in generating drugs from peptide toxins is ensuring their specificity for their intended targets. Computational methods can play an important role in solving such design problems through construction of accurate models of receptor-toxin complexes and calculation of binding free energies. Here we review the computational methods used for this purpose and their application to toxins targeting ion channels. We describe ShK and HsTX1 toxins, high-affinity blockers of the voltage-gated potassium channel Kv1.3, which could be developed as therapeutic agents for autoimmune diseases.
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193
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Ucisik MN, Chakravorty DK, Merz KM. Models for the Metal Transfer Complex of the N-Terminal Region of CusB and CusF. Biochemistry 2015; 54:4226-35. [PMID: 26079272 DOI: 10.1021/acs.biochem.5b00195] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The tripartite CusCFBA pump in Escherichia coli is a very effective heavy metal extrusion system specific for Cu(I) and Ag(I). The N-terminal region of the membrane fusion protein CusB (CusB-NT) is highly disordered, and hence, experimentally characterizing its structure is challenging. In a previous study, this disorder was confirmed with molecular dynamics simulations, although some key structural elements were determined. It was experimentally shown that CusB-NT is fully functional in transferring the metal from the metallochaperone CusF. In this study, we docked these two entities together and formed two representative metal coordination modes, which consist of residues from both proteins. In this way, we created two potential CusB-NT/CusF complexes that share coordination of Cu(I) and thereby represent structural models for the metal transfer process. Each model complex was simulated for 4 μs. The previously observed structural disorder in CusB-NT disappeared upon complexation with CusF. The only differences between the two models occurred in the M21-M36 loop region of CusB-NT and the open flap of CusF: we observed the model with two CusB-NT methionine residues and a CusF methionine as the metal coordination site (termed "MMM") to be more stable than the model with a CusB-NT methionine, a CusF methionine, and a CusF histidine ligating the metal (termed "MMH"). The observed stability of the MMM model was probed for an additional 2 μs, yielding a total simulation time of 6 μs. We hypothesize that both MMM and MMH configurations might take part in the metal exchange process in which the MMH configuration would appear first and would be followed by the MMM configuration. Given the experimental finding of comparable binding affinities of CusB-NT and CusF, the increased stability of the MMM configuration might be a determinant for the transfer from CusF to CusB-NT. The metal would be transferred from the more CusF-dominated metal binding environment (MMH model) to a more CusB-dominated one (MMM model) in which the coordination environment is more stable. From the MMM model, the metal ion would ultimately be coordinated by the CusB methionines only, which would complete the Cu(I) transfer process.
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Affiliation(s)
- Melek N Ucisik
- †Department of Chemistry and Quantum Theory Project, University of Florida, 2328 New Physics Building, P.O. Box 118435, Gainesville, Florida 32611-8435, United States.,‡Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801-3364, United States
| | - Dhruva K Chakravorty
- §Department of Chemistry, University of New Orleans, 2000 Lake Shore Drive, New Orleans, Louisiana 70148, United States
| | - Kenneth M Merz
- ∥Institute for Cyber Enabled Research, Department of Chemistry, and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824-1322, United States
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194
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Oliva R, Chermak E, Cavallo L. Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps. Molecules 2015; 20:12045-60. [PMID: 26140438 PMCID: PMC6332208 DOI: 10.3390/molecules200712045] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/08/2015] [Accepted: 06/17/2015] [Indexed: 12/24/2022] Open
Abstract
In view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the complex. However, reliably scoring protein-protein docking poses is still an unsolved problem. As a consequence, the screening of many docking models is usually required in the analysis step, to possibly single out the correct ones. Here, making use of exemplary cases, we review our recently introduced methods for the analysis of protein complex structures and for the scoring of protein docking poses, based on the use of inter-residue contacts and their visualization in inter-molecular contact maps. We also show that the ensemble of tools we developed can be used in the context of rational drug design targeting protein-protein interactions.
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Affiliation(s)
- Romina Oliva
- Department of Sciences and Technologies, University "Parthenope" of Naples, Centro Direzionale Isola C4, 80143 Naples, Italy.
| | - Edrisse Chermak
- Kaust Catalysis Center, Physical Sciences and Engineering Division, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Saudi Arabia.
| | - Luigi Cavallo
- Kaust Catalysis Center, Physical Sciences and Engineering Division, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Saudi Arabia.
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195
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Sarkar A, Dai Y, Haque MM, Seeger F, Ghosh A, Garcin ED, Montfort WR, Hazen SL, Misra S, Stuehr DJ. Heat Shock Protein 90 Associates with the Per-Arnt-Sim Domain of Heme-free Soluble Guanylate Cyclase: IMplications for Enzyme Maturation. J Biol Chem 2015; 290:21615-28. [PMID: 26134567 DOI: 10.1074/jbc.m115.645515] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Indexed: 11/06/2022] Open
Abstract
Heat shock protein 90 (hsp90) drives heme insertion into the β1 subunit of soluble guanylate cyclase (sGC) β1, which enables it to associate with a partner sGCα1 subunit and mature into a nitric oxide (NO)-responsive active form. We utilized fluorescence polarization measurements and hydrogen-deuterium exchange mass spectrometry to define molecular interactions between the specific human isoforms hsp90β and apo-sGCβ1. hsp90β and its isolated M domain, but not its isolated N and C domains, bind with low micromolar affinity to a heme-free, truncated version of sGCβ1 (sGCβ1(1-359)-H105F). Surprisingly, hsp90β and its M domain bound to the Per-Arnt-Sim (PAS) domain of apo-sGC-β1(1-359), which lies adjacent to its heme-binding (H-NOX) domain. The interaction specifically involved solvent-exposed regions in the hsp90β M domain that are largely distinct from sites utilized by other hsp90 clients. The interaction strongly protected two regions of the sGCβ1 PAS domain and caused local structural relaxation in other regions, including a PAS dimerization interface and a segment in the H-NOX domain. Our results suggest a means by which the hsp90β interaction could prevent apo-sGCβ1 from associating with its partner sGCα1 subunit while enabling structural changes to assist heme insertion into the H-NOX domain. This mechanism would parallel that in other clients like the aryl hydrocarbon receptor and HIF1α, which also interact with hsp90 through their PAS domains to control protein partner and small ligand binding interactions.
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Affiliation(s)
| | - Yue Dai
- From the Departments of Pathobiology
| | | | - Franziska Seeger
- the Department of Chemistry and Biochemistry, University of Maryland at Baltimore County, Baltimore, Maryland 21250, and
| | | | - Elsa D Garcin
- the Department of Chemistry and Biochemistry, University of Maryland at Baltimore County, Baltimore, Maryland 21250, and
| | - William R Montfort
- the Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721
| | | | - Saurav Misra
- Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
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196
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Guan X, Hu X, Cui F, Li Y, Jing X, Xie Z. EGFP-Based Protein Nanoparticles with Cell-Penetrating Peptide for Efficient siRNA Delivery. Macromol Biosci 2015; 15:1484-9. [DOI: 10.1002/mabi.201500163] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 06/08/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Xingang Guan
- State Key Laboratory of Polymer Physics and Chemistry; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
- Life Science Research Center; Beihua University; Jilin 132013 P. R. China
| | - Xiuli Hu
- State Key Laboratory of Polymer Physics and Chemistry; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
| | - Fengchao Cui
- Key Laboratory of Synthetic Rubber; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
| | - Yunqi Li
- Key Laboratory of Synthetic Rubber; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
| | - Xiabing Jing
- State Key Laboratory of Polymer Physics and Chemistry; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
| | - Zhigang Xie
- State Key Laboratory of Polymer Physics and Chemistry; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
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197
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Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors. Molecules 2015; 20:11569-603. [PMID: 26111183 PMCID: PMC6272567 DOI: 10.3390/molecules200611569] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 06/02/2015] [Accepted: 06/15/2015] [Indexed: 02/06/2023] Open
Abstract
Blocking protein-protein interactions (PPI) using small molecules or peptides modulates biochemical pathways and has therapeutic significance. PPI inhibition for designing drug-like molecules is a new area that has been explored extensively during the last decade. Considering the number of available PPI inhibitor databases and the limited number of 3D structures available for proteins, docking and scoring methods play a major role in designing PPI inhibitors as well as stabilizers. Docking methods are used in the design of PPI inhibitors at several stages of finding a lead compound, including modeling the protein complex, screening for hot spots on the protein-protein interaction interface and screening small molecules or peptides that bind to the PPI interface. There are three major challenges to the use of docking on the relatively flat surfaces of PPI. In this review we will provide some examples of the use of docking in PPI inhibitor design as well as its limitations. The combination of experimental and docking methods with improved scoring function has thus far resulted in few success stories of PPI inhibitors for therapeutic purposes. Docking algorithms used for PPI are in the early stages, however, and as more data are available docking will become a highly promising area in the design of PPI inhibitors or stabilizers.
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198
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Cordeiro TN, García J, Bernadó P, Millet O, Pons M. A Three-protein Charge Zipper Stabilizes a Complex Modulating Bacterial Gene Silencing. J Biol Chem 2015; 290:21200-12. [PMID: 26085102 DOI: 10.1074/jbc.m114.630400] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Indexed: 12/31/2022] Open
Abstract
The Hha/YmoA nucleoid-associated proteins help selectively silence horizontally acquired genetic material, including pathogenicity and antibiotic resistance genes and their maintenance in the absence of selective pressure. Members of the Hha family contribute to gene silencing by binding to the N-terminal dimerization domain of H-NS and modifying its selectivity. Hha-like proteins and the H-NS N-terminal domain are unusually rich in charged residues, and their interaction is mostly electrostatic-driven but, nonetheless, highly selective. The NMR-based structural model of the complex between Hha/YmoA and the H-NS N-terminal dimerization domain reveals that the origin of the selectivity is the formation of a three-protein charge zipper with interdigitated complementary charged residues from Hha and the two units of the H-NS dimer. The free form of YmoA shows collective microsecond-millisecond dynamics that can by measured by NMR relaxation dispersion experiments and shows a linear dependence with the salt concentration. The number of residues sensing the collective dynamics and the population of the minor form increased in the presence of H-NS. Additionally, a single residue mutation in YmoA (D43N) abolished H-NS binding and the dynamics of the apo-form, suggesting the dynamics and binding are functionally related.
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Affiliation(s)
- Tiago N Cordeiro
- From the Biomolecular NMR Laboratory, Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain, Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université Montpellier 1 and 2, 34092 Montpellier, France
| | - Jesús García
- Institute for Research in Biomedicine (IRB-Barcelona), 08028 Barcelona, Spain, and
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université Montpellier 1 and 2, 34092 Montpellier, France
| | - Oscar Millet
- the Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC-bioGUNE), 48160 Elexalde, Derio, Spain
| | - Miquel Pons
- From the Biomolecular NMR Laboratory, Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain,
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199
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Structural Insight into the Complex of Ferredoxin and [FeFe] Hydrogenase fromChlamydomonas reinhardtii. Chembiochem 2015; 16:1663-9. [DOI: 10.1002/cbic.201500130] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Indexed: 01/01/2023]
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200
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Yu F, He F, Yao H, Wang C, Wang J, Li J, Qi X, Xue H, Ding J, Zhang P. Structural basis of intramitochondrial phosphatidic acid transport mediated by Ups1-Mdm35 complex. EMBO Rep 2015; 16:813-23. [PMID: 26071601 DOI: 10.15252/embr.201540137] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/15/2015] [Indexed: 01/12/2023] Open
Abstract
Ups1 forms a complex with Mdm35 and is critical for the transport of phosphatidic acid (PA) from the mitochondrial outer membrane to the inner membrane. We report the crystal structure of the Ups1-Mdm35-PA complex and the functional characterization of Ups1-Mdm35 in PA binding and transfer. Ups1 features a barrel-like structure consisting of an antiparallel β-sheet and three α-helices. Mdm35 adopts a three-helical clamp-like structure to wrap around Ups1 to form a stable complex. The β-sheet and α-helices of Ups1 form a long tunnel-like pocket to accommodate the substrate PA, and a short helix α2 acts as a lid to cover the pocket. The hydrophobic residues lining the pocket and helix α2 are critical for PA binding and transfer. In addition, a hydrophilic patch on the surface of Ups1 near the PA phosphate-binding site also plays an important role in the function of Ups1-Mdm35. Our study reveals the molecular basis of the function of Ups1-Mdm35 and sheds new light on the mechanism of intramitochondrial phospholipid transport by the MSF1/PRELI family proteins.
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Affiliation(s)
- Fang Yu
- National Center for Protein Science Shanghai and State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Fangyuan He
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Hongyan Yao
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Chengyuan Wang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Jianchuan Wang
- National Center for Protein Science Shanghai and State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Jianxu Li
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Xiaofeng Qi
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Hongwei Xue
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Jianping Ding
- National Center for Protein Science Shanghai and State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
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