1
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Marze NA, Jeliazkov JR, Roy Burman SS, Boyken SE, DiMaio F, Gray JJ. Modeling oblong proteins and water-mediated interfaces with RosettaDock in CAPRI rounds 28-35. Proteins 2017; 85:479-486. [PMID: 27667482 PMCID: PMC5710743 DOI: 10.1002/prot.25168] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/01/2016] [Accepted: 09/26/2016] [Indexed: 12/27/2022]
Abstract
The 28th-35th rounds of the Critical Assessment of PRotein Interactions (CAPRI) served as a practical benchmark for our RosettaDock protein-protein docking protocols, highlighting strengths and weaknesses of the approach. We achieved acceptable or better quality models in three out of 11 targets. For the two α-repeat protein-green fluorescent protein (αrep-GFP) complexes, we used a novel ellipsoidal partial-global docking method (Ellipsoidal Dock) to generate models with 2.2 Å/1.5 Å interface RMSD, capturing 49%/42% of the native contacts, for the 7-/5-repeat αrep complexes. For the DNase-immunity protein complex, we used a new predictor of hydrogen-bonding networks, HBNet with Bridging Waters, to place individual water models at the complex interface; models were generated with 1.8 Å interface RMSD and 12% native water contacts recovered. The targets for which RosettaDock failed to create an acceptable model were typically difficult in general, as six had no acceptable models submitted by any CAPRI predictor. The UCH-L5-RPN13 and UCH-L5-INO80G de-ubiquitinating enzyme-inhibitor complexes comprised inhibitors undergoing significant structural changes upon binding, with the partners being highly interwoven in the docked complexes. Our failure to predict the nucleosome-enzyme complex in Target 95 was largely due to tight constraints we placed on our model based on sparse biochemical data suggesting two specific cross-interface interactions, preventing the correct structure from being sampled. While RosettaDock's three successes show that it is a state-of-the-art docking method, the difficulties with highly flexible and multi-domain complexes highlight the need for better flexible docking and domain-assembly methods. Proteins 2017; 85:479-486. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Nicholas A. Marze
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Jeliazko R. Jeliazkov
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Shourya S. Roy Burman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Scott E. Boyken
- Department of Biochemistry, University of Washington, Seattle, Washington
- Institute for Protein Design, University of Washington, Seattle, Washington
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, Washington
- Institute for Protein Design, University of Washington, Seattle, Washington
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland
- Johns Hopkins School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
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2
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Morten MJ, Gamsjaeger R, Cubeddu L, Kariawasam R, Peregrina J, Penedo JC, White MF. High-affinity RNA binding by a hyperthermophilic single-stranded DNA-binding protein. Extremophiles 2017; 21:369-379. [PMID: 28074284 PMCID: PMC5346138 DOI: 10.1007/s00792-016-0910-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/19/2016] [Indexed: 12/30/2022]
Abstract
Single-stranded DNA-binding proteins (SSBs), including replication protein A (RPA) in eukaryotes, play a central role in DNA replication, recombination, and repair. SSBs utilise an oligonucleotide/oligosaccharide-binding (OB) fold domain to bind DNA, and typically oligomerise in solution to bring multiple OB fold domains together in the functional SSB. SSBs from hyperthermophilic crenarchaea, such as Sulfolobus solfataricus, have an unusual structure with a single OB fold coupled to a flexible C-terminal tail. The OB fold resembles those in RPA, whilst the tail is reminiscent of bacterial SSBs and mediates interaction with other proteins. One paradigm in the field is that SSBs bind specifically to ssDNA and much less strongly to RNA, ensuring that their functions are restricted to DNA metabolism. Here, we use a combination of biochemical and biophysical approaches to demonstrate that the binding properties of S. solfataricus SSB are essentially identical for ssDNA and ssRNA. These features may represent an adaptation to a hyperthermophilic lifestyle, where DNA and RNA damage is a more frequent event.
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Affiliation(s)
- Michael J Morten
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Roland Gamsjaeger
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, 2006, Australia
| | - Liza Cubeddu
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, 2006, Australia
| | - Ruvini Kariawasam
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, 2006, Australia
| | - Jose Peregrina
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - J Carlos Penedo
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK.
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3
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Schindler CEM, Chauvot de Beauchêne I, de Vries SJ, Zacharias M. Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI. Proteins 2016; 85:391-398. [PMID: 27785830 DOI: 10.1002/prot.25196] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/13/2016] [Accepted: 09/27/2016] [Indexed: 11/06/2022]
Abstract
The ATTRACT coarse-grained docking approach in combination with various types of atomistic, flexible refinement methods has been applied to predict protein-protein and peptide-protein complexes in CAPRI rounds 28-36. For a large fraction of CAPRI targets (12 out of 18), at least one model of acceptable or better quality was generated, corresponding to a success rate of 67%. In particular, for several peptide-protein complexes excellent predictions were achieved. In several cases, a combination of template-based modeling and extensive molecular dynamics-based refinement yielded medium and even high quality solutions. In one particularly challenging case, the structure of an ubiquitylation enzyme bound to the nucleosome was correctly predicted as a set of acceptable quality solutions. Based on the experience with the CAPRI targets, new interface refinement approaches and methods for ab-initio peptide-protein docking have been developed. Failures and possible improvements of the docking method with respect to scoring and protein flexibility will also be discussed. Proteins 2017; 85:391-398. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Christina E M Schindler
- Physics Department T38, Technische Universität München, Garching, 85748, Germany.,Center for Integrated Protein Science Munich, München, 81377, Germany
| | | | - Sjoerd J de Vries
- Physics Department T38, Technische Universität München, Garching, 85748, Germany
| | - Martin Zacharias
- Physics Department T38, Technische Universität München, Garching, 85748, Germany.,Center for Integrated Protein Science Munich, München, 81377, Germany
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4
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Fuxreiter M, Tóth-Petróczy Á, Kraut DA, Matouschek AT, Lim RYH, Xue B, Kurgan L, Uversky VN. Disordered proteinaceous machines. Chem Rev 2014; 114:6806-43. [PMID: 24702702 PMCID: PMC4350607 DOI: 10.1021/cr4007329] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Monika Fuxreiter
- MTA-DE
Momentum Laboratory of Protein Dynamics, Department of Biochemistry
and Molecular Biology, University of Debrecen, Nagyerdei krt. 98, H-4032 Debrecen, Hungary
| | - Ágnes Tóth-Petróczy
- Department
of Biological Chemistry, Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Daniel A. Kraut
- Department
of Chemistry, Villanova University, 800 East Lancaster Avenue, Villanova, Pennsylvania 19085, United States
| | - Andreas T. Matouschek
- Section
of Molecular Genetics and Microbiology, Institute for Cellular &
Molecular Biology, The University of Texas
at Austin, 2506 Speedway, Austin, Texas 78712, United States
| | - Roderick Y. H. Lim
- Biozentrum
and the Swiss Nanoscience Institute, University
of Basel, Klingelbergstrasse
70, CH-4056 Basel, Switzerland
| | - Bin Xue
- Department of Cell Biology,
Microbiology and Molecular Biology, College
of Fine Arts and Sciences, and Department of Molecular Medicine and USF Health
Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Lukasz Kurgan
- Department
of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Vladimir N. Uversky
- Department of Cell Biology,
Microbiology and Molecular Biology, College
of Fine Arts and Sciences, and Department of Molecular Medicine and USF Health
Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Institute
for Biological Instrumentation, Russian
Academy of Sciences, 142290 Pushchino, Moscow Region 119991, Russia
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5
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Kolesnikova O, Back R, Graille M, Séraphin B. Identification of the Rps28 binding motif from yeast Edc3 involved in the autoregulatory feedback loop controlling RPS28B mRNA decay. Nucleic Acids Res 2013; 41:9514-23. [PMID: 23956223 PMCID: PMC3814365 DOI: 10.1093/nar/gkt607] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In the yeast Saccharomyces cerevisiae, the Edc3 protein was previously reported to participate in the auto-regulatory feedback loop controlling the level of the RPS28B messenger RNA (mRNA). We show here that Edc3 binds directly and tightly to the globular core of Rps28 ribosomal protein. This binding occurs through a motif that is present exclusively in Edc3 proteins from yeast belonging to the Saccharomycetaceae phylum. Functional analyses indicate that the ability of Edc3 to interact with Rps28 is not required for its general function and for its role in the regulation of the YRA1 pre-mRNA decay. In contrast, this interaction appears to be exclusively required for the auto-regulatory mechanism controlling the RPS28B mRNA decay. These observations suggest a plausible model for the evolutionary appearance of a Rps28 binding motif in Edc3.
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Affiliation(s)
- Olga Kolesnikova
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé et de la Recherche Médicale (INSERM) U964/Université de Strasbourg, 67404 Illkirch, France, Ecole Polytechnique, Laboratoire de Biochimie, CNRS UMR7654, 91128 Palaiseau Cedex, France and Institut de Biochimie et Biophysique Moléculaire et Cellulaire (IBBMC), CNRS, UMR8619, Bat 430, Université Paris Sud, 91405 Orsay Cedex, France
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6
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A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome. CELLULAR AND MOLECULAR LIFE SCIENCES : CMLS 2013. [PMID: 23942625 DOI: 10.1007/s00018‐013‐1446‐6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intrinsic disorder (i.e., lack of a unique 3-D structure) is a common phenomenon, and many biologically active proteins are disordered as a whole, or contain long disordered regions. These intrinsically disordered proteins/regions constitute a significant part of all proteomes, and their functional repertoire is complementary to functions of ordered proteins. In fact, intrinsic disorder represents an important driving force for many specific functions. An illustrative example of such disorder-centric functional class is RNA-binding proteins. In this study, we present the results of comprehensive bioinformatics analyses of the abundance and roles of intrinsic disorder in 3,411 ribosomal proteins from 32 species. We show that many ribosomal proteins are intrinsically disordered or hybrid proteins that contain ordered and disordered domains. Predicted globular domains of many ribosomal proteins contain noticeable regions of intrinsic disorder. We also show that disorder in ribosomal proteins has different characteristics compared to other proteins that interact with RNA and DNA including overall abundance, evolutionary conservation, and involvement in protein-protein interactions. Furthermore, intrinsic disorder is not only abundant in the ribosomal proteins, but we demonstrate that it is absolutely necessary for their various functions.
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7
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Peng Z, Oldfield CJ, Xue B, Mizianty MJ, Dunker AK, Kurgan L, Uversky VN. A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome. Cell Mol Life Sci 2013; 71:1477-504. [PMID: 23942625 PMCID: PMC7079807 DOI: 10.1007/s00018-013-1446-6] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 07/29/2013] [Accepted: 07/31/2013] [Indexed: 01/01/2023]
Abstract
Intrinsic disorder (i.e., lack of a unique 3-D structure) is a common phenomenon, and many biologically active proteins are disordered as a whole, or contain long disordered regions. These intrinsically disordered proteins/regions constitute a significant part of all proteomes, and their functional repertoire is complementary to functions of ordered proteins. In fact, intrinsic disorder represents an important driving force for many specific functions. An illustrative example of such disorder-centric functional class is RNA-binding proteins. In this study, we present the results of comprehensive bioinformatics analyses of the abundance and roles of intrinsic disorder in 3,411 ribosomal proteins from 32 species. We show that many ribosomal proteins are intrinsically disordered or hybrid proteins that contain ordered and disordered domains. Predicted globular domains of many ribosomal proteins contain noticeable regions of intrinsic disorder. We also show that disorder in ribosomal proteins has different characteristics compared to other proteins that interact with RNA and DNA including overall abundance, evolutionary conservation, and involvement in protein–protein interactions. Furthermore, intrinsic disorder is not only abundant in the ribosomal proteins, but we demonstrate that it is absolutely necessary for their various functions.
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Affiliation(s)
- Zhenling Peng
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, T6G 2V4, Canada
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8
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Knee KM, Goulet DR, Zhang J, Chen B, Chiu W, King JA. The group II chaperonin Mm-Cpn binds and refolds human γD crystallin. Protein Sci 2011; 20:30-41. [PMID: 20981710 DOI: 10.1002/pro.531] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chaperonins assist in the folding of nascent and misfolded proteins, though the mechanism of folding within the lumen of the chaperonin remains poorly understood. The archeal chaperonin from Methanococcus marapaludis, Mm-Cpn, shares the eightfold double barrel structure with other group II chaperonins, including the eukaryotic TRiC/CCT, required for actin and tubulin folding. However, Mm-Cpn is composed of a single species subunit, similar to group I chaperonin GroEL, rather than the eight subunit species needed for TRiC/CCT. Features of the β-sheet fold have been identified as sites of recognition by group II chaperonins. The crystallins, the major components of the vertebrate eye lens, are β-sheet proteins with two homologous Greek key domains. During refolding in vitro a partially folded intermediate is populated, and partitions between productive folding and off-pathway aggregation. We report here that in the presence of physiological concentrations of ATP, Mm-Cpn suppressed the aggregation of HγD-Crys by binding the partially folded intermediate. The complex was sufficiently stable to permit recovery by size exclusion chromatography. In the presence of ATP, Mm-Cpn promoted the refolding of the HγD-Crys intermediates to the native state. The ability of Mm-Cpn to bind and refold a human β-sheet protein suggests that Mm-Cpn may be useful as a simplified model for the substrate recognition mechanism of TRiC/CCT.
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Affiliation(s)
- Kelly M Knee
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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9
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Bermejo GA, Llinás M. Structure-oriented methods for protein NMR data analysis. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 56:311-28. [PMID: 20633357 PMCID: PMC2944251 DOI: 10.1016/j.pnmrs.2010.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Accepted: 02/09/2010] [Indexed: 05/29/2023]
Affiliation(s)
| | - Miguel Llinás
- Department of Chemistry, Carnegie Mellon University, Pittsburgh PA 15213, USA
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10
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Sacan A, Toroslu IH, Ferhatosmanoglu H. Integrated search and alignment of protein structures. Bioinformatics 2008; 24:2872-9. [PMID: 18945684 DOI: 10.1093/bioinformatics/btn545] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Identification and comparison of similar three-dimensional (3D) protein structures has become an even greater challenge in the face of the rapidly growing structure databases. Here, we introduce Vorometric, a new method that provides efficient search and alignment of a query protein against a database of protein structures. Voronoi contacts of the protein residues are enriched with the secondary structure information and a metric substitution matrix is developed to allow efficient indexing. The contact hits obtained from a distance-based indexing method are extended to obtain high-scoring segment pairs, which are then used to generate structural alignments. RESULTS Vorometric is the first to address both search and alignment problems in the protein structure databases. The experimental results show that Vorometric is simultaneously effective in retrieving similar protein structures, producing high-quality structure alignments, and identifying cross-fold similarities. Vorometric outperforms current structure retrieval methods in search accuracy, while requiring com-parable running times. Furthermore, the structural superpositions produced are shown to have better quality and coverage, when compared with those of the popular structure alignment tools. AVAILABILITY Vorometric is available as a web service at http://bio.cse.ohio-state.edu/Vorometric
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Affiliation(s)
- Ahmet Sacan
- Department of Computer Engineering, Middle East Technical University, Ankara, Turkey.
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11
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Lemak A, Steren CA, Arrowsmith CH, Llinás M. Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach. JOURNAL OF BIOMOLECULAR NMR 2008; 41:29-41. [PMID: 18458824 DOI: 10.1007/s10858-008-9238-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Accepted: 04/08/2008] [Indexed: 05/26/2023]
Abstract
ABACUS [Grishaev et al. (2005) Proteins 61:36-43] is a novel protocol for automated protein structure determination via NMR. ABACUS starts from molecular fragments defined by unassigned J-coupled spin-systems and involves a Monte Carlo stochastic search in assignment space, probabilistic sequence selection, and assembly of fragments into structures that are used to guide the stochastic search. Here, we report further development of the two main algorithms that increase the flexibility and robustness of the method. Performance of the BACUS [Grishaev and Llinás (2004) J Biomol NMR 28:1-101] algorithm was significantly improved through use of sequential connectivities available from through-bond correlated 3D-NMR experiments, and a new set of likelihood probabilities derived from a database of 56 ultra high resolution X-ray structures. A Multicanonical Monte Carlo procedure, Fragment Monte Carlo (FMC), was developed for sequence-specific assignment of spin-systems. It relies on an enhanced assignment sampling and provides the uncertainty of assignments in a quantitative manner. The efficiency of the protocol was validated on data from four proteins of between 68-116 residues, yielding 100% accuracy in sequence specific assignment of backbone and side chain resonances.
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Affiliation(s)
- Alexander Lemak
- The Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada M5G 2M9.
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12
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Wu B, Yee A, Huang YJ, Ramelot TA, Cort JR, Semesi A, Jung JW, Lee W, Montelione GT, Kennedy MA, Arrowsmith CH. The solution structure of ribosomal protein S17E from Methanobacterium thermoautotrophicum: a structural homolog of the FF domain. Protein Sci 2008; 17:583-8. [PMID: 18218711 PMCID: PMC2248302 DOI: 10.1110/ps.073272208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Revised: 11/19/2007] [Accepted: 11/20/2007] [Indexed: 10/22/2022]
Abstract
The ribosomal protein S17E from the archaeon Methanobacterium thermoautotrophicum is a component of the 30S ribosomal subunit. S17E is a 62-residue protein conserved in archaea and eukaryotes and has no counterparts in bacteria. Mammalian S17E is a phosphoprotein component of eukaryotic ribosomes. Archaeal S17E proteins range from 59 to 79 amino acids, and are about half the length of the eukaryotic homologs which have an additional C-terminal region. Here we report the three-dimensional solution structure of S17E. S17E folds into a small three-helix bundle strikingly similar to the FF domain of human HYPA/FBP11, a novel phosphopeptide-binding fold. S17E bears a conserved positively charged surface acting as a robust scaffold for molecular recognition. The structure of M. thermoautotrophicum S17E provides a template for homology modeling of eukaryotic S17E proteins in the family.
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Affiliation(s)
- Bin Wu
- Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, Toronto, Ontario M5G 2M9, Canada
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13
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Acidic C-terminal tail of the ssDNA-binding protein of bacteriophage T7 and ssDNA compete for the same binding surface. Proc Natl Acad Sci U S A 2008; 105:1855-60. [PMID: 18238893 DOI: 10.1073/pnas.0711919105] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
ssDNA-binding proteins are key components of the machinery that mediates replication, recombination, and repair. Prokaryotic ssDNA-binding proteins share a conserved DNA-binding fold and an acidic C-terminal tail. It has been proposed that in the absence of ssDNA, the C-terminal tail contacts the ssDNA-binding cleft, therefore predicting that the binding of ssDNA and the C-terminal tail is mutually exclusive. Using chemical cross-linking, competition studies, and NMR chemical-shift mapping, we demonstrate that: (i) the C-terminal peptide of the gene 2.5 protein cross-links to the core of the protein only in the absence of ssDNA, (ii) the cross-linked species fails to bind to ssDNA, and (iii) a C-terminal peptide and ssDNA bind to the same overall surface of the protein. We propose that the protection of the DNA-binding cleft by the electrostatic shield of the C-terminal tail observed in prokaryotic ssDNA-binding proteins, ribosomal proteins, and high-mobility group proteins is an evolutionarily conserved mechanism. This mechanism prevents random binding of charged molecules to the nucleic acid-binding pocket and coordinates nucleic acid-protein and protein-protein interactions.
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14
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Huang YJ, Tejero R, Powers R, Montelione GT. A topology-constrained distance network algorithm for protein structure determination from NOESY data. Proteins 2006; 62:587-603. [PMID: 16374783 DOI: 10.1002/prot.20820] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This article formulates the multidimensional nuclear Overhauser effect spectroscopy (NOESY) interpretation problem using graph theory and presents a novel, bottom-up, topology-constrained distance network analysis algorithm for NOESY cross peak interpretation using assigned resonances. AutoStructure is a software suite that implements this topology-constrained distance network analysis algorithm and iteratively generates structures using the three-dimensional (3D) protein structure calculation programs XPLOR/CNS or DYANA. The minimum input for AutoStructure includes the amino acid sequence, a list of resonance assignments, and lists of 2D, 3D, and/or 4D-NOESY cross peaks. AutoStructure can also analyze homodimeric proteins when X-filtered NOESY experiments are available. The quality of input data and final 3D structures is evaluated using recall, precision, and F-measure (RPF) scores, a statistical measure of goodness of fit with the input data. AutoStructure has been tested on three protein NMR data sets for which high-quality structures have previously been solved by an expert, and yields comparable high-quality distance constraint lists and 3D protein structures in hours. We also compare several protein structures determined using AutoStructure with corresponding homologous proteins determined with other independent methods. The program has been used in more than two dozen protein structure determinations, several of which have already been published.
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Affiliation(s)
- Yuanpeng Janet Huang
- Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854-5638, USA
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15
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Gaspar JA, Liu C, Vassall KA, Meglei G, Stephen R, Stathopulos PB, Pineda-Lucena A, Wu B, Yee A, Arrowsmith CH, Meiering EM. A novel member of the YchN-like fold: solution structure of the hypothetical protein Tm0979 from Thermotoga maritima. Protein Sci 2005; 14:216-23. [PMID: 15608123 PMCID: PMC2253327 DOI: 10.1110/ps.041068605] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We report herein the NMR structure of Tm0979, a structural proteomics target from Thermotoga maritima. The Tm0979 fold consists of four beta/alpha units, which form a central parallel beta-sheet with strand order 1234. The first three helices pack toward one face of the sheet and the fourth helix packs against the other face. The protein forms a dimer by adjacent parallel packing of the fourth helices sandwiched between the two beta-sheets. This fold is very interesting from several points of view. First, it represents the first structure determination for the DsrH family of conserved hypothetical proteins, which are involved in oxidation of intracellular sulfur but have no defined molecular function. Based on structure and sequence analysis, possible functions are discussed. Second, the fold of Tm0979 most closely resembles YchN-like folds; however the proteins that adopt these folds differ in secondary structural elements and quaternary structure. Comparison of these proteins provides insight into possible mechanisms of evolution of quaternary structure through a simple mechanism of hydrophobicity-changing mutations of one or two residues. Third, the Tm0979 fold is found to be similar to flavodoxin-like folds and beta/alpha barrel proteins, and may provide a link between these very abundant folds and putative ancestral half-barrel proteins.
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Affiliation(s)
- Joe A Gaspar
- Guelph-Waterloo Centre for Graduate Studies in Chemistry and Biochemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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16
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Aramini JM, Huang YJ, Cort JR, Goldsmith-Fischman S, Xiao R, Shih LY, Ho CK, Liu J, Rost B, Honig B, Kennedy MA, Acton TB, Montelione GT. Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii. Protein Sci 2003; 12:2823-30. [PMID: 14627742 PMCID: PMC2366990 DOI: 10.1110/ps.03359003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2003] [Revised: 08/08/2003] [Accepted: 08/18/2003] [Indexed: 10/26/2022]
Abstract
We report NMR assignments and solution structure of the 71-residue 30S ribosomal protein S28E from the archaean Pyrococcus horikoshii, target JR19 of the Northeast Structural Genomics Consortium. The structure, determined rapidly with the aid of automated backbone resonance assignment (AutoAssign) and automated structure determination (AutoStructure) software, is characterized by a four-stranded beta-sheet with a classic Greek-key topology and an oligonucleotide/oligosaccharide beta-barrel (OB) fold. The electrostatic surface of S28E exhibits positive and negative patches on opposite sides, the former constituting a putative binding site for RNA. The 13 C-terminal residues of the protein contain a consensus sequence motif constituting the signature of the S28E protein family. Surprisingly, this C-terminal segment is unstructured in solution.
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Affiliation(s)
- James M Aramini
- Northeast Structural Genomics Consortium Center for Advanced Biotechnology and Medicine (CABM), Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
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