151
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Carneiro MG, Koharudin LMI, Ban D, Sabo TM, Trigo-Mourino P, Mazur A, Griesinger C, Gronenborn AM, Lee D. Sampling of Glycan-Bound Conformers by the Anti-HIV Lectin Oscillatoria agardhii agglutinin in the Absence of Sugar. Angew Chem Int Ed Engl 2015; 54:6462-5. [PMID: 25873445 DOI: 10.1002/anie.201500213] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/16/2015] [Indexed: 02/01/2023]
Abstract
Lectins from different sources have been shown to interfere with HIV infection by binding to the sugars of viral-envelope glycoproteins. Three-dimensional atomic structures of a number of HIV-inactivating lectins have been determined, both as free proteins and in glycan-bound forms. However, details on the mechanism of recognition and binding to sugars are elusive. Herein we focus on the anti-HIV lectin OAA from Oscillatoria agardhii: We show that in the absence of sugars in solution, both the sugar-free and sugar-bound protein conformations that were observed in the X-ray crystal structures exist as conformational substates. Our results suggest that glycan recognition occurs by conformational selection within the ground state; this model differs from the popular "excited-state" model. Our findings provide further insight into molecular recognition of the major receptor on the HIV virus by OAA. These details can potentially be used for the optimization and/or development of preventive anti-HIV therapeutics.
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Affiliation(s)
- Marta G Carneiro
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany)
| | - Leonardus M I Koharudin
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1050 Biomedical Science Tower 3, 3501 5th Avenue, Pittsburgh, PA 15260 (USA)
| | - David Ban
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany).,Present address: St. Jude Children's Research Hospital, Department of Structural Biology, 262 Danny Thomas Place, Memphis, TN 38105 (USA)
| | - T Michael Sabo
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany)
| | - Pablo Trigo-Mourino
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany)
| | - Adam Mazur
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany).,Present address: Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel (Switzerland)
| | - Christian Griesinger
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany)
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1050 Biomedical Science Tower 3, 3501 5th Avenue, Pittsburgh, PA 15260 (USA)
| | - Donghan Lee
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany).
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152
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Yun JH, Kim M, Kim K, Lee D, Jung Y, Oh D, Ko YJ, Cho AE, Cho HS, Lee W. Solution structure of the transmembrane 2 domain of the human melanocortin-4 receptor in sodium dodecyl sulfate (SDS) micelles and the functional implication of the D90N mutant. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1294-302. [PMID: 25753114 DOI: 10.1016/j.bbamem.2015.02.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 02/03/2015] [Accepted: 02/27/2015] [Indexed: 10/23/2022]
Abstract
The melanocortin receptors (MCRs) are members of the G protein-coupled receptor (GPCR) 1 superfamily with seven transmembrane (TM) domains. Among them, the melanocortin-4 receptor (MC4R) subtype has been highlighted recently by genetic studies in obese humans. In particular, in a patient with severe early-onset obesity, a novel heterozygous mutation in the MC4R gene was found in an exchange of Asp to Asn in the 90th amino acid residue located in the TM 2 domain (MC4RD90N). Mutations in the MC4R gene are the most frequent monogenic causes of severe obesity and are described as heterozygous with loss of function. We determine solution structures of the TM 2 domain of MC4R (MC4RTM2) and compared secondary structure of Asp90 mutant (MC4RTM2-D90N) in a micelle environment by nuclear magnetic resonance (NMR) spectroscopy. NMR structure shows that MC4RTM2 forms a long α-helix with a kink at Gly98. Interestingly, the structure of MC4RTM2-D90N is similar to that of MC4RTM2 based on data from CD and NMR spectrum. However, the thermal stability and homogeneity of MC4RD90N is quite different from those of MC4R. The structure from molecular modeling suggests that Asp90(2.50) plays a key role in allosteric sodium ion binding. Our data suggest that the sodium ion interaction of Asp90(2.50) in the allosteric pocket of MC4R is essential to its function, explaining the loss of function of the MC4RD90N mutant.
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Affiliation(s)
- Ji-Hye Yun
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Minsup Kim
- Department of Bioinformatics, Korea University, Sejong 136-701, Republic of Korea
| | - Kuglae Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Dongju Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Youngjin Jung
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Daeseok Oh
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Yoon-Joo Ko
- National Center for Inter-University Research Facilities, Seoul National University, Seoul 151-747, Republic of Korea
| | - Art E Cho
- Department of Bioinformatics, Korea University, Sejong 136-701, Republic of Korea
| | - Hyun-Soo Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Weontae Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea.
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153
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Torres IO, Kuchenbecker KM, Nnadi CI, Fletterick RJ, Kelly MJS, Fujimori DG. Histone demethylase KDM5A is regulated by its reader domain through a positive-feedback mechanism. Nat Commun 2015; 6:6204. [PMID: 25686748 DOI: 10.1038/ncomms7204] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 01/05/2015] [Indexed: 12/13/2022] Open
Abstract
The retinoblastoma binding protein KDM5A removes methyl marks from lysine 4 of histone H3 (H3K4). Misregulation of KDM5A contributes to the pathogenesis of lung and gastric cancers. In addition to its catalytic jumonji C domain, KDM5A contains three PHD reader domains, commonly recognized as chromatin recruitment modules. It is unknown whether any of these domains in KDM5A have functions beyond recruitment and whether they regulate the catalytic activity of the demethylase. Here using biochemical and nuclear magnetic resonance (NMR)-based structural studies, we show that the PHD1 preferentially recognizes unmethylated H3K4 histone tail, product of KDM5A-mediated demethylation of tri-methylated H3K4 (H3K4me3). Binding of unmodified H3 peptide to the PHD1 stimulates catalytic domain-mediated removal of methyl marks from H3K4me3 peptide and nucleosome substrates. This positive-feedback mechanism--enabled by the functional coupling between a reader and a catalytic domain in KDM5A--suggests a model for the spread of demethylation on chromatin.
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Affiliation(s)
- Idelisse Ortiz Torres
- 1] Department of Cellular and Molecular Pharmacology, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA [2] Chemistry and Chemical Biology Graduate Program, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA
| | - Kristopher M Kuchenbecker
- 1] Department of Biochemistry and Biophysics, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA [2] Biophysics Graduate Program, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA
| | - Chimno I Nnadi
- 1] Department of Cellular and Molecular Pharmacology, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA [2] Chemistry and Chemical Biology Graduate Program, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA [3] UCSF Medical Scientist Training Program, University of California, 513 Parnassus Avenue, San Francisco, California 94143, USA
| | - Robert J Fletterick
- Department of Biochemistry and Biophysics, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA
| | - Mark J S Kelly
- Department of Pharmaceutical Chemistry, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA
| | - Danica Galonić Fujimori
- 1] Department of Cellular and Molecular Pharmacology, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA [2] Department of Pharmaceutical Chemistry, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA
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154
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Fizil Á, Gáspári Z, Barna T, Marx F, Batta G. "Invisible" conformers of an antifungal disulfide protein revealed by constrained cold and heat unfolding, CEST-NMR experiments, and molecular dynamics calculations. Chemistry 2015; 21:5136-44. [PMID: 25676351 PMCID: PMC4464532 DOI: 10.1002/chem.201404879] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Indexed: 12/12/2022]
Abstract
Transition between conformational states in proteins is being recognized as a possible key factor of function. In support of this, hidden dynamic NMR structures were detected in several cases up to populations of a few percent. Here, we show by two- and three-state analysis of thermal unfolding, that the population of hidden states may weight 20-40 % at 298 K in a disulfide-rich protein. In addition, sensitive (15) N-CEST NMR experiments identified a low populated (0.15 %) state that was in slow exchange with the folded PAF protein. Remarkably, other techniques failed to identify the rest of the NMR "dark matter". Comparison of the temperature dependence of chemical shifts from experiments and molecular dynamics calculations suggests that hidden conformers of PAF differ in the loop and terminal regions and are most similar in the evolutionary conserved core. Our observations point to the existence of a complex conformational landscape with multiple conformational states in dynamic equilibrium, with diverse exchange rates presumably responsible for the completely hidden nature of a considerable fraction.
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Affiliation(s)
- Ádám Fizil
- Department of Organic Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen (Hungary)
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155
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De Simone A, Aprile FA, Dhulesia A, Dobson CM, Vendruscolo M. Structure of a low-population intermediate state in the release of an enzyme product. eLife 2015; 4:e02777. [PMID: 25575179 PMCID: PMC4383205 DOI: 10.7554/elife.02777] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 12/16/2014] [Indexed: 11/18/2022] Open
Abstract
Enzymes can increase the rate of biomolecular reactions by several orders of magnitude. Although the steps of substrate capture and product release are essential in the enzymatic process, complete atomic-level descriptions of these steps are difficult to obtain because of the transient nature of the intermediate conformations, which makes them largely inaccessible to standard structure determination methods. We describe here the determination of the structure of a low-population intermediate in the product release process by human lysozyme through a combination of NMR spectroscopy and molecular dynamics simulations. We validate this structure by rationally designing two mutations, the first engineered to destabilise the intermediate and the second to stabilise it, thus slowing down or speeding up, respectively, product release. These results illustrate how product release by an enzyme can be facilitated by the presence of a metastable intermediate with transient weak interactions between the enzyme and product.
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Affiliation(s)
- Alfonso De Simone
- Department of Life
Sciences, Imperial College London,
London, United Kingdom
| | - Francesco A Aprile
- Department of
Chemistry, University of Cambridge,
Cambridge, United Kingdom
| | - Anne Dhulesia
- Department of
Chemistry, University of Cambridge,
Cambridge, United Kingdom
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156
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Brutscher B, Felli IC, Gil-Caballero S, Hošek T, Kümmerle R, Piai A, Pierattelli R, Sólyom Z. NMR Methods for the Study of Instrinsically Disordered Proteins Structure, Dynamics, and Interactions: General Overview and Practical Guidelines. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:49-122. [PMID: 26387100 DOI: 10.1007/978-3-319-20164-1_3] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Thanks to recent improvements in NMR instrumentation, pulse sequence design, and sample preparation, a panoply of new NMR tools has become available for atomic resolution characterization of intrinsically disordered proteins (IDPs) that are optimized for the particular chemical and spectroscopic properties of these molecules. A wide range of NMR observables can now be measured on increasingly complex IDPs that report on their structural and dynamic properties in isolation, as part of a larger complex, or even inside an entire living cell. Herein we present basic NMR concepts, as well as optimised tools available for the study of IDPs in solution. In particular, the following sections are discussed hereafter: a short introduction to NMR spectroscopy and instrumentation (Sect. 3.1), the effect of order and disorder on NMR observables (Sect. 3.2), particular challenges and bottlenecks for NMR studies of IDPs (Sect. 3.3), 2D HN and CON NMR experiments: the fingerprint of an IDP (Sect. 3.4), tools for overcoming major bottlenecks of IDP NMR studies (Sect. 3.5), 13C detected experiments (Sect. 3.6), from 2D to 3D: from simple snapshots to site-resolved characterization of IDPs (Sect. 3.7), sequential NMR assignment: 3D experiments (Sect. 3.8), high-dimensional NMR experiments (nD, with n>3) (Sect. 3.9) and conclusions and perspectives (Sect. 3.10).
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Affiliation(s)
- Bernhard Brutscher
- Institut de Biologie Structurale, Université Grenoble 1, CNRS, CEA, 71 avenue des Martyrs, 38044, Grenoble Cedex 9, France.
| | - Isabella C Felli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, 50019, Via Luigi Sacconi 6, Sesto Fiorentino, Florence, Italy.
| | | | - Tomáš Hošek
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, 50019, Via Luigi Sacconi 6, Sesto Fiorentino, Florence, Italy
| | - Rainer Kümmerle
- Bruker BioSpin AG, Industriestrasse 26, 8117, Fällanden, Switzerland
| | - Alessandro Piai
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, 50019, Via Luigi Sacconi 6, Sesto Fiorentino, Florence, Italy
| | - Roberta Pierattelli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, 50019, Via Luigi Sacconi 6, Sesto Fiorentino, Florence, Italy.
| | - Zsófia Sólyom
- Institut de Biologie Structurale, Université Grenoble 1, CNRS, CEA, 71 avenue des Martyrs, 38044, Grenoble Cedex 9, France
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157
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Kragelj J, Blackledge M, Jensen MR. Ensemble Calculation for Intrinsically Disordered Proteins Using NMR Parameters. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:123-47. [PMID: 26387101 DOI: 10.1007/978-3-319-20164-1_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Intrinsically disordered proteins (IDPs) perform their function despite their lack of well-defined tertiary structure. Residual structure has been observed in IDPs, commonly described as transient/dynamic or expressed in terms of fractional populations. In order to understand how the protein primary sequence dictates the dynamic and structural properties of IDPs and in general to understand how IDPs function, atomic-level descriptions are needed. Nuclear magnetic resonance spectroscopy provides information about local and long-range structure in IDPs at amino acid specific resolution and can be used in combination with ensemble descriptions to represent the dynamic nature of IDPs. In this chapter we describe sample-and-select approaches for ensemble modelling of local structural propensities in IDPs with specific emphasis on validation of these ensembles.
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Affiliation(s)
- Jaka Kragelj
- IBS, University Grenoble Alpes, 38044, Grenoble, France.,IBS, CNRS, 38044, Grenoble, France.,IBS, CEA, 38044, Grenoble, France
| | - Martin Blackledge
- IBS, University Grenoble Alpes, 38044, Grenoble, France.,IBS, CNRS, 38044, Grenoble, France.,IBS, CEA, 38044, Grenoble, France
| | - Malene Ringkjøbing Jensen
- IBS, University Grenoble Alpes, 38044, Grenoble, France. .,IBS, CNRS, 38044, Grenoble, France. .,IBS, CEA, 38044, Grenoble, France.
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158
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Vahdati L, Fanelli R, Bernadat G, Correia I, Lequin O, Ongeri S, Piarulli U. Synthesis and conformational studies of a stable peptidomimetic β-hairpin based on a bifunctional diketopiperazine turn inducer. NEW J CHEM 2015. [DOI: 10.1039/c4nj01437e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new β-hairpin mimic foldamer based on the assembly of a reverse turn inducer, a peptidomimetic strand, and a tetrapeptide sequence was prepared, and its conformation in solution was assessed by NMR and computational investigations.
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Affiliation(s)
- Leila Vahdati
- Università degli Studi dell'Insubria
- Dipartimento di Scienza e Alta Tecnologia
- I-22100 Como
- Italy
- Molécules Fluorées et Chimie Médicinale
| | - Roberto Fanelli
- Università degli Studi dell'Insubria
- Dipartimento di Scienza e Alta Tecnologia
- I-22100 Como
- Italy
| | - Guillaume Bernadat
- Molécules Fluorées et Chimie Médicinale
- BioCIS UMR-CNRS 8076
- LabEx LERMIT
- Université Paris-Sud
- Faculté de Pharmacie
| | - Isabelle Correia
- Sorbonne Universités – UPMC Univ Paris 06
- Ecole Normale Supérieure – PSL Research University
- CNRS UMR 7203 LBM
- 75252 Paris Cedex 05
- France
| | - Olivier Lequin
- Sorbonne Universités – UPMC Univ Paris 06
- Ecole Normale Supérieure – PSL Research University
- CNRS UMR 7203 LBM
- 75252 Paris Cedex 05
- France
| | - Sandrine Ongeri
- Molécules Fluorées et Chimie Médicinale
- BioCIS UMR-CNRS 8076
- LabEx LERMIT
- Université Paris-Sud
- Faculté de Pharmacie
| | - Umberto Piarulli
- Università degli Studi dell'Insubria
- Dipartimento di Scienza e Alta Tecnologia
- I-22100 Como
- Italy
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159
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Geudens N, De Vleeschouwer M, Fehér K, Rokni-Zadeh H, Ghequire MGK, Madder A, De Mot R, Martins JC, Sinnaeve D. Impact of a stereocentre inversion in cyclic lipodepsipeptides from the viscosin group: a comparative study of the viscosinamide and pseudodesmin conformation and self-assembly. Chembiochem 2014; 15:2736-46. [PMID: 25382202 DOI: 10.1002/cbic.201402389] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Indexed: 01/21/2023]
Abstract
The viscosin group covers a series of cyclic lipodepsipeptides (CLPs) produced by Pseudomonas bacteria, with a range of biological functions and antimicrobial activities. Their oligopeptide moieties are composed of both L- and D-amino acids. Remarkably, the Leu5 amino acid-centrally located in the nonapeptide sequence-is the sole residue found to possess either an L or D configuration, depending on the producing strain. The impact of this D/L switch on the solution conformation was investigated by NMR-restrained molecular modelling of the epimers pseudodesmin A and viscosinamide A. Although the backbone fold remained unaffected, the D/L switch adjusted the segregation between hydrophobic and hydrophilic residues, and thus the amphipathicity. It also influenced the self-assembly capacity in organic solvents. Additionally, several new minor variants of viscosinamide A from Pseudomonas fluorescens DR54 were identified, and an NMR assay is proposed to assess the presence of either an L- or D-Leu5.
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Affiliation(s)
- Niels Geudens
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, 9000 Ghent (Belgium)
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160
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Kulkarni AK, Ojha RP. Conformations of a model cyclic hexapeptide, CYIQNC: (1)H-NMR and molecular dynamics studies. J Biomol Struct Dyn 2014; 33:1850-65. [PMID: 25375824 DOI: 10.1080/07391102.2014.975283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Solution conformation of the cyclic hexapeptide sequence, [cyclo-S-Cys-Tyr-Ile-Gln-Asn-Cys-S] (CYIQNC) - a disulfide-linked fragment of a neurohypophyseal peptide hormone oxytocin (OT) - has been investigated by high-field one-dimensional (1D) and two-dimensional (2D) NMR spectroscopic methods and compared with the results obtained from computer simulation studies. (1)H-NMR results based on temperature dependence of amide proton chemical shifts and nuclear Overhauser effect indicate that peptide in solution populates different conformations, characterized by two fused β-turns. The segment Ile(3)-Gln(4)-Asn(5)-Cys(6) yields a preferred type-III β-turn at residues 4, 5 (HB, 3HN → 6CO), while the segment Cys(6), Cys(1)-Tyr(2)-Ile(3) exhibits inherently weaker, flexible β-turn either of type I/II'/III/half-turn at residues 1, 2 (HB, 6HN → 3CO). The computer simulation studies using a mixed protocol of distance geometry-simulated annealing followed by constrained minimization, restrained molecular dynamics, and energy minimization showed the possibility of existence of additional conformations with the hydrogen bonds, (a) 5HN → 3CO and (b) 2HN → 6CO. These results, therefore, indicate that the additional conformations obtained from both NMR and simulation studies can also be possible to the peptide. These additional conformations might have very small population in the solution and did not show their signatures in these conditions. These findings will be helpful in designing more analogs with modifications in the cyclic moiety of OT.
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Affiliation(s)
- Ashok Kumar Kulkarni
- a Department of Physiology , MediCiti Institute of Medical Sciences , Ghanpur, Medchal Mandal, R. R. Dist., Hyderabad 501401 , India
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161
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Xu L, Chen Y, Wang X. Dual effects of familial Alzheimer's disease mutations (D7H, D7N, and H6R) on amyloid β peptide: Correlation dynamics and zinc binding. Proteins 2014; 82:3286-97. [DOI: 10.1002/prot.24669] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 07/17/2014] [Accepted: 08/11/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Liang Xu
- School of Chemistry; Dalian University of Technology; Dalian China
| | - Yonggang Chen
- Network and Information Center, Dalian University of Technology; Dalian China
| | - Xiaojuan Wang
- School of Chemical Machinery, Dalian University of Technology; Dalian China
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162
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Fujiyama S, Abe Y, Tani J, Urabe M, Sato K, Aramaki T, Katayama T, Ueda T. Structure and mechanism of the primosome protein DnaT- functional structures for homotrimerization, dissociation of ssDNA from the PriB·ssDNA complex, and formation of the DnaT·ssDNA complex. FEBS J 2014; 281:5356-70. [DOI: 10.1111/febs.13080] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 09/20/2014] [Accepted: 09/24/2014] [Indexed: 12/31/2022]
Affiliation(s)
- Saki Fujiyama
- Department of Protein Structure, Function and Design; Graduate School of Pharmaceutical Sciences; Kyushu University; Fukuoka Japan
| | - Yoshito Abe
- Department of Protein Structure, Function and Design; Graduate School of Pharmaceutical Sciences; Kyushu University; Fukuoka Japan
| | - Junya Tani
- Department of Protein Structure, Function and Design; Graduate School of Pharmaceutical Sciences; Kyushu University; Fukuoka Japan
| | - Masashi Urabe
- Department of Protein Structure, Function and Design; Graduate School of Pharmaceutical Sciences; Kyushu University; Fukuoka Japan
| | - Kenji Sato
- Department of Protein Structure, Function and Design; Graduate School of Pharmaceutical Sciences; Kyushu University; Fukuoka Japan
| | - Takahiko Aramaki
- Department of Protein Structure, Function and Design; Graduate School of Pharmaceutical Sciences; Kyushu University; Fukuoka Japan
| | - Tsutomu Katayama
- Department of Molecular Biology; Graduate School of Pharmaceutical Sciences; Kyushu University; Fukuoka Japan
| | - Tadashi Ueda
- Department of Protein Structure, Function and Design; Graduate School of Pharmaceutical Sciences; Kyushu University; Fukuoka Japan
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163
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Yedvabny E, Nerenberg PS, So C, Head-Gordon T. Disordered structural ensembles of vasopressin and oxytocin and their mutants. J Phys Chem B 2014; 119:896-905. [PMID: 25231121 DOI: 10.1021/jp505902m] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Vasopressin and oxytocin are intrinsically disordered cyclic nonapeptides belonging to a family of neurohypophysial hormones. Although unique in their functions, these peptides differ only by two residues and both feature a tocin ring formed by the disulfide bridge between first and sixth cysteine residues. This sequence and structural similarity are experimentally linked to oxytocin agonism at vasopressin receptors and vasopressin antagonism at oxytocin receptors. Yet single- or double-residue mutations in both peptides have been shown to have drastic impacts on their activities at either receptor, and possibly the ability to bind to their neurophysin carrier protein. In this study we perform molecular dynamics simulations of the unbound native and mutant sequences of the oxytocin and vasopressin hormones to characterize their structural ensembles. We classify the subpopulations of these structural ensembles on the basis of the distributions of radius of gyration and secondary structure and hydrogen-bonding features of the canonical tocin ring and disordered tail region. We then relate the structural changes observed in the unbound form of the different hormone sequences to experimental information about peptide receptor binding, and more indirectly, carrier protein binding affinity, receptor activity, and protease degradation. This study supports the hypothesis that the structural characteristics of the unbound form of an IDP can be used to predict structural or functional preferences of its functional bound form.
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Affiliation(s)
- Eugene Yedvabny
- Department of Chemistry, ‡Department of Bioengineering, and §Department of Chemical and Biomolecular Engineering, University of California , Berkeley, California 94720-3220, United States
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164
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Yun JH, Lee WK, Kim H, Kim E, Cheong C, Cho MH, Lee W. Solution structure of telomere binding domain of AtTRB2 derived from Arabidopsis thaliana. Biochem Biophys Res Commun 2014; 452:436-42. [DOI: 10.1016/j.bbrc.2014.08.095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 08/19/2014] [Indexed: 10/24/2022]
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165
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Pandey AK, Thomas KM, Forbes C, Zondlo NJ. Tunable control of polyproline helix (PPII) structure via aromatic electronic effects: an electronic switch of polyproline helix. Biochemistry 2014; 53:5307-14. [PMID: 25075447 PMCID: PMC4139158 DOI: 10.1021/bi500696k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/28/2014] [Indexed: 01/10/2023]
Abstract
Aromatic rings exhibit defined interactions via the unique aromatic π face. Aromatic amino acids interact favorably with proline residues via both the hydrophobic effect and aromatic-proline interactions, C-H/π interactions between the aromatic π face and proline ring C-H bonds. The canonical aromatic amino acids Trp, Tyr, and Phe strongly disfavor a polyproline helix (PPII) when they are present in proline-rich sequences because of the large populations of cis amide bonds induced by favorable aromatic-proline interactions (aromatic-cis-proline and proline-cis-proline-aromatic interactions). We demonstrate the ability to tune polyproline helix conformation and cis-trans isomerism in proline-rich sequences using aromatic electronic effects. Electron-rich aromatic residues strongly disfavor polyproline helix and exhibit large populations of cis amide bonds, while electron-poor aromatic residues exhibit small populations of cis amide bonds and favor polyproline helix. 4-Aminophenylalanine is a pH-dependent electronic switch of polyproline helix, with cis amide bonds favored as the electron-donating amine, but trans amide bonds and polyproline helix preferred as the electron-withdrawing ammonium. Peptides with block proline-aromatic PPXPPXPPXPP sequences exhibited electronically switchable pH-dependent structures. Electron-poor aromatic amino acids provide special capabilities to integrate aromatic residues into polyproline helices and to serve as the basis of aromatic electronic switches to change structure.
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Affiliation(s)
- Anil K. Pandey
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Krista M. Thomas
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Christina
R. Forbes
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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166
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Tsuda K, Kuwasako K, Nagata T, Takahashi M, Kigawa T, Kobayashi N, Güntert P, Shirouzu M, Yokoyama S, Muto Y. Novel RNA recognition motif domain in the cytoplasmic polyadenylation element binding protein 3. Proteins 2014; 82:2879-86. [PMID: 25066254 DOI: 10.1002/prot.24651] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/03/2014] [Accepted: 07/15/2014] [Indexed: 11/06/2022]
Abstract
The family of cytoplasmic polyadenylation element binding proteins CPEB1, CPEB2, CPEB3, and CPEB4 binds to the 3'-untranslated region (3'-UTR) of mRNA, and plays significant roles in mRNA metabolism and translation regulation. They have a common domain organization, involving two consecutive RNA recognition motif (RRM) domains followed by a zinc finger domain in the C-terminal region. We solved the solution structure of the first RRM domain (RRM1) of human CPEB3, which revealed that CPEB3 RRM1 exhibits structural features distinct from those of the canonical RRM domain. Our structural data provide important information about the RNA binding ability of CPEB3 RRM1.
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Affiliation(s)
- Kengo Tsuda
- RIKEN Systems and Structural Biology Center, Tsurumi-ku, Yokohama, 230-0045, Japan; Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Tsurumi-ku, Yokohama, 230-0045, Japan
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167
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Daubner GM, Brümmer A, Tocchini C, Gerhardy S, Ciosk R, Zavolan M, Allain FHT. Structural and functional implications of the QUA2 domain on RNA recognition by GLD-1. Nucleic Acids Res 2014; 42:8092-105. [PMID: 24838563 PMCID: PMC4081071 DOI: 10.1093/nar/gku445] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 05/04/2014] [Accepted: 05/06/2014] [Indexed: 01/13/2023] Open
Abstract
The STAR family comprises ribonucleic acid (RNA)-binding proteins that play key roles in RNA-regulatory processes. RNA recognition is achieved by a KH domain with an additional α-helix (QUA2) that seems to extend the RNA-binding surface to six nucleotides for SF1 (Homo sapiens) and seven nucleotides for GLD-1 (Caenorhabditis elegans). To understand the structural basis of this probable difference in specificity, we determined the solution structure of GLD-1 KH-QUA2 with the complete consensus sequence identified in the tra-2 gene. Compared to SF1, the GLD-1 KH-QUA2 interface adopts a different conformation resulting indeed in an additional sequence-specific binding pocket for a uracil at the 5'end. The functional relevance of this binding pocket is emphasized by our bioinformatics analysis showing that GLD-1 binding sites with this 5'end uracil are more predictive for the functional response of the messenger RNAs to gld-1 knockout. We further reveal the importance of the KH-QUA2 interface in vitro and that its alteration in vivo affects the level of translational repression dependent on the sequence of the GLD-1 binding motif. In conclusion, we demonstrate that the QUA2 domain distinguishes GLD-1 from other members of the STAR family and contributes more generally to the modulation of RNA-binding affinity and specificity of KH domain containing proteins.
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Affiliation(s)
- Gerrit M Daubner
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Anneke Brümmer
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Cristina Tocchini
- Friedrich Miescher Institute for Biomedical Research, 4002 Basel, Switzerland
| | - Stefan Gerhardy
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Rafal Ciosk
- Friedrich Miescher Institute for Biomedical Research, 4002 Basel, Switzerland
| | | | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
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168
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Kusunoki H, Tanaka T, Kohno T, Wakamatsu K, Hamaguchi I. Structural characterization of the BH3-like motif of hepatitis B virus X protein. Biochem Biophys Res Commun 2014; 450:741-5. [PMID: 24950407 DOI: 10.1016/j.bbrc.2014.06.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 06/10/2014] [Indexed: 01/26/2023]
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169
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Jiang F, Zhou CY, Wu YD. Residue-Specific Force Field Based on the Protein Coil Library. RSFF1: Modification of OPLS-AA/L. J Phys Chem B 2014; 118:6983-98. [DOI: 10.1021/jp5017449] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Fan Jiang
- Laboratory
of Computational Chemistry and Drug Design, Laboratory of Chemical
Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Chen-Yang Zhou
- College
of Chemistry, Peking University, Beijing 100871, China
| | - Yun-Dong Wu
- Laboratory
of Computational Chemistry and Drug Design, Laboratory of Chemical
Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- College
of Chemistry, Peking University, Beijing 100871, China
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170
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Casu F, Duggan BM, Hennig M. The arginine-rich RNA-binding motif of HIV-1 Rev is intrinsically disordered and folds upon RRE binding. Biophys J 2014; 105:1004-17. [PMID: 23972852 DOI: 10.1016/j.bpj.2013.07.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 06/19/2013] [Accepted: 07/02/2013] [Indexed: 11/17/2022] Open
Abstract
Arginine-rich motifs (ARMs) capable of binding diverse RNA structures play critical roles in transcription, translation, RNA trafficking, and RNA packaging. The regulatory HIV-1 protein Rev is essential for viral replication and belongs to the ARM family of RNA-binding proteins. During the early stages of the HIV-1 life cycle, incompletely spliced and full-length viral mRNAs are very inefficiently recognized by the splicing machinery of the host cell and are subject to degradation in the cell nucleus. These transcripts harbor the Rev Response Element (RRE), which orchestrates the interaction with the Rev ARM and the successive Rev-dependent mRNA export pathway. Based on established criteria for predicting intrinsic disorder, such as hydropathy, combined with significant net charge, the very basic primary sequences of ARMs are expected to adopt coil-like structures. Thus, we initiated this study to investigate the conformational changes of the Rev ARM associated with RNA binding. We used multidimensional NMR and circular dichroism spectroscopy to monitor the observed structural transitions, and described the conformational landscapes using statistical ensemble and molecular-dynamics simulations. The combined spectroscopic and simulated results imply that the Rev ARM is intrinsically disordered not only as an isolated peptide but also when it is embedded into an oligomerization-deficient Rev mutant. RRE recognition triggers a crucial coil-to-helix transition employing an induced-fit mechanism.
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Affiliation(s)
- Fabio Casu
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
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171
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Jensen MR, Zweckstetter M, Huang JR, Blackledge M. Exploring free-energy landscapes of intrinsically disordered proteins at atomic resolution using NMR spectroscopy. Chem Rev 2014; 114:6632-60. [PMID: 24725176 DOI: 10.1021/cr400688u] [Citation(s) in RCA: 214] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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172
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Elbaum MB, Zondlo NJ. OGlcNAcylation and phosphorylation have similar structural effects in α-helices: post-translational modifications as inducible start and stop signals in α-helices, with greater structural effects on threonine modification. Biochemistry 2014; 53:2242-60. [PMID: 24641765 PMCID: PMC4004263 DOI: 10.1021/bi500117c] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
OGlcNAcylation
and phosphorylation are the major competing intracellular
post-translational modifications of serine and threonine residues.
The structural effects of both post-translational modifications on
serine and threonine were examined within Baldwin model α-helical
peptides (Ac-AKAAAAKAAAAKAAGY-NH2 or Ac-YGAKAAAAKAAAAKAA-NH2). At the N-terminus of an α-helix, both phosphorylation
and OGlcNAcylation stabilized the α-helix relative to the free
hydroxyls, with a larger induced structure for phosphorylation than
for OGlcNAcylation, for the dianionic phosphate than for the monoanionic
phosphate, and for modifications on threonine than for modifications
on serine. Both phosphoserine and phosphothreonine resulted in peptides
more α-helical than alanine at the N-terminus, with dianionic
phosphothreonine the most α-helix-stabilizing residue here.
In contrast, in the interior of the α-helix, both post-translational
modifications were destabilizing with respect to the α-helix,
with the greatest destabilization seen for threonine OGlcNAcylation
at residue 5 and threonine phosphorylation at residue 10, with peptides
containing either post-translational modification existing as random
coils. At the C-terminus, both OGlcNAcylation and phosphorylation
were destabilizing with respect to the α-helix, though the induced
structural changes were less than in the interior of the α-helix.
In general, the structural effects of modifications on threonine were
greater than the effects on serine, because of both the lower α-helical
propensity of Thr and the more defined induced structures upon modification
of threonine than serine, suggesting threonine residues are particularly
important loci for structural effects of post-translational modifications.
The effects of serine and threonine post-translational modifications
are analogous to the effects of proline on α-helices, with the
effects of phosphothreonine being greater than those of proline throughout
the α-helix. These results provide a basis for understanding
the context-dependent structural effects of these competing protein
post-translational modifications.
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Affiliation(s)
- Michael B Elbaum
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
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173
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Berkut AA, Usmanova DR, Peigneur S, Oparin PB, Mineev KS, Odintsova TI, Tytgat J, Arseniev AS, Grishin EV, Vassilevski AA. Structural similarity between defense peptide from wheat and scorpion neurotoxin permits rational functional design. J Biol Chem 2014; 289:14331-40. [PMID: 24671422 DOI: 10.1074/jbc.m113.530477] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
In this study, we present the spatial structure of the wheat antimicrobial peptide (AMP) Tk-AMP-X2 studied using NMR spectroscopy. This peptide was found to adopt a disulfide-stabilized α-helical hairpin fold and therefore belongs to the α-hairpinin family of plant defense peptides. Based on Tk-AMP-X2 structural similarity to cone snail and scorpion potassium channel blockers, a mutant molecule, Tk-hefu, was engineered by incorporating the functionally important residues from κ-hefutoxin 1 onto the Tk-AMP-X2 scaffold. The designed peptide contained the so-called essential dyad of amino acid residues significant for channel-blocking activity. Electrophysiological studies showed that although the parent peptide Tk-AMP-X2 did not present any activity against potassium channels, Tk-hefu blocked Kv1.3 channels with similar potency (IC50 ∼ 35 μm) to κ-hefutoxin 1 (IC50 ∼ 40 μm). We conclude that α-hairpinins are attractive in their simplicity as structural templates, which may be used for functional engineering and drug design.
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Affiliation(s)
- Antonina A Berkut
- From the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia, Moscow Institute of Physics and Technology (State University), Moscow 117303, Russia
| | - Dinara R Usmanova
- From the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia, Moscow Institute of Physics and Technology (State University), Moscow 117303, Russia
| | - Steve Peigneur
- Laboratory of Toxicology and Pharmacology, University of Leuven, Leuven 3000, Belgium, and
| | - Peter B Oparin
- From the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Konstantin S Mineev
- From the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Tatyana I Odintsova
- N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Jan Tytgat
- Laboratory of Toxicology and Pharmacology, University of Leuven, Leuven 3000, Belgium, and
| | - Alexander S Arseniev
- From the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Eugene V Grishin
- From the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Alexander A Vassilevski
- From the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia,
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174
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Brister M, Pandey AK, Bielska AA, Zondlo NJ. OGlcNAcylation and phosphorylation have opposing structural effects in tau: phosphothreonine induces particular conformational order. J Am Chem Soc 2014; 136:3803-16. [PMID: 24559475 PMCID: PMC4004249 DOI: 10.1021/ja407156m] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Indexed: 01/12/2023]
Abstract
Phosphorylation and OGlcNAcylation are dynamic intracellular protein post-translational modifications that frequently are alternatively observed on the same serine and threonine residues. Phosphorylation and OGlcNAcylation commonly occur in natively disordered regions of proteins, and often have opposing functional effects. In the microtubule-associated protein tau, hyperphosphorylation is associated with protein misfolding and aggregation as the neurofibrillary tangles of Alzheimer's disease, whereas OGlcNAcylation stabilizes the soluble form of tau. A series of peptides derived from the proline-rich domain (residues 174-251) of tau was synthesized, with free Ser/Thr hydroxyls, phosphorylated Ser/Thr (pSer/pThr), OGlcNAcylated Ser/Thr, and diethylphosphorylated Ser/Thr. Phosphorylation and OGlcNAcylation were found by CD and NMR to have opposing structural effects on polyproline helix (PPII) formation, with phosphorylation favoring PPII, OGlcNAcylation opposing PPII, and the free hydroxyls intermediate in structure, and with phosphorylation structural effects greater than OGlcNAcylation. For tau196-209, phosphorylation and OGlcNAcylation had similar structural effects, opposing a nascent α-helix. Phosphomimic Glu exhibited PPII-favoring structural effects. Structural changes due to Thr phosphorylation were greater than those of Ser phosphorylation or Glu, with particular conformational restriction as the dianion, with mean (3)JαN = 3.5 Hz (pThr) versus 5.4 Hz (pSer), compared to 7.2, 6.8, and 6.2 Hz for Thr, Ser, and Glu, respectively, values that correlate with the backbone torsion angle ϕ. Dianionic phosphothreonine induced strong phosphothreonine amide protection and downfield amide chemical shifts (δmean = 9.63 ppm), consistent with formation of a stable phosphate-amide hydrogen bond. These data suggest potentially greater structural importance of threonine phosphorylation than serine phosphorylation due to larger induced structural effects.
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Affiliation(s)
| | | | - Agata A. Bielska
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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175
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Ball KA, Wemmer DE, Head-Gordon T. Comparison of structure determination methods for intrinsically disordered amyloid-β peptides. J Phys Chem B 2014; 118:6405-16. [PMID: 24410358 PMCID: PMC4066902 DOI: 10.1021/jp410275y] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Intrinsically disordered proteins (IDPs) represent a new frontier in structural biology since the primary characteristic of IDPs is that structures need to be characterized as diverse ensembles of conformational substates. We compare two general but very different ways of combining NMR spectroscopy with theoretical methods to derive structural ensembles for the disease IDPs amyloid-β 1-40 and amyloid-β 1-42, which are associated with Alzheimer's Disease. We analyze the performance of de novo molecular dynamics and knowledge-based approaches for generating structural ensembles by assessing their ability to reproduce a range of NMR experimental observables. In addition to the comparison of computational methods, we also evaluate the relative value of different types of NMR data for refining or validating the IDP structural ensembles for these important disease peptides.
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Affiliation(s)
- K Aurelia Ball
- Graduate Group in Biophysics , Berkeley, California 94720, United States
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176
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Popovic M, Wienk H, Coglievina M, Boelens R, Pongor S, Pintar A. The basic helix-loop-helix region of the transcriptional repressor hairy and enhancer of split 1 is preorganized to bind DNA. Proteins 2014; 82:537-45. [DOI: 10.1002/prot.24507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 12/19/2013] [Accepted: 01/06/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Matija Popovic
- Protein Structure and Bioinformatics Group; International Centre for Genetic Engineering and Biotechnology (ICGEB); AREA Science Park I-34149 Trieste Italy
| | - Hans Wienk
- Bijvoet Center for Biomolecular Research, Utrecht University; 3584 CH Utrecht the Netherlands
| | - Maristella Coglievina
- Protein Structure and Bioinformatics Group; International Centre for Genetic Engineering and Biotechnology (ICGEB); AREA Science Park I-34149 Trieste Italy
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, Utrecht University; 3584 CH Utrecht the Netherlands
| | - Sándor Pongor
- Protein Structure and Bioinformatics Group; International Centre for Genetic Engineering and Biotechnology (ICGEB); AREA Science Park I-34149 Trieste Italy
| | - Alessandro Pintar
- Protein Structure and Bioinformatics Group; International Centre for Genetic Engineering and Biotechnology (ICGEB); AREA Science Park I-34149 Trieste Italy
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177
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Differences in β-strand populations of monomeric Aβ40 and Aβ42. Biophys J 2014; 104:2714-24. [PMID: 23790380 DOI: 10.1016/j.bpj.2013.04.056] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 04/24/2013] [Accepted: 04/26/2013] [Indexed: 11/20/2022] Open
Abstract
Using homonuclear (1)H NOESY spectra, with chemical shifts, (3)JH(N)H(α) scalar couplings, residual dipolar couplings, and (1)H-(15)N NOEs, we have optimized and validated the conformational ensembles of the amyloid-β 1-40 (Aβ40) and amyloid-β 1-42 (Aβ42) peptides generated by molecular dynamics simulations. We find that both peptides have a diverse set of secondary structure elements including turns, helices, and antiparallel and parallel β-strands. The most significant difference in the structural ensembles of the two peptides is the type of β-hairpins and β-strands they populate. We find that Aβ42 forms a major antiparallel β-hairpin involving the central hydrophobic cluster residues (16-21) with residues 29-36, compatible with known amyloid fibril forming regions, whereas Aβ40 forms an alternative but less populated antiparallel β-hairpin between the central hydrophobic cluster and residues 9-13, that sometimes forms a β-sheet by association with residues 35-37. Furthermore, we show that the two additional C-terminal residues of Aβ42, in particular Ile-41, directly control the differences in the β-strand content found between the Aβ40 and Aβ42 structural ensembles. Integrating the experimental and theoretical evidence accumulated over the last decade, it is now possible to present monomeric structural ensembles of Aβ40 and Aβ42 consistent with available information that produce a plausible molecular basis for why Aβ42 exhibits greater fibrillization rates than Aβ40.
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178
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Moon S, Lee YW, Kim WT, Lee W. Solution structure of CEH-37 homeodomain of the nematode Caenorhabditis elegans. Biochem Biophys Res Commun 2014; 443:370-5. [PMID: 24361878 DOI: 10.1016/j.bbrc.2013.11.133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 11/18/2013] [Indexed: 11/28/2022]
Abstract
The nematode Caenorhabditis elegans protein CEH-37 belongs to the paired OTD/OTX family of homeobox-containing homeodomain proteins. CEH-37 shares sequence similarity with homeodomain proteins, although it specifically binds to double-stranded C. elegans telomeric DNA, which is unusual to homeodomain proteins. Here, we report the solution structure of CEH-37 homeodomain and molecular interaction with double-stranded C. elegans telomeric DNA using nuclear magnetic resonance (NMR) spectroscopy. NMR structure shows that CEH-37 homeodomain is composed of a flexible N-terminal region and three α-helices with a helix-turn-helix (HTH) DNA binding motif. Data from size-exclusion chromatography and fluorescence spectroscopy reveal that CEH-37 homeodomain interacts strongly with double-stranded C. elegans telomeric DNA. NMR titration experiments identified residues responsible for specific binding to nematode double-stranded telomeric DNA. These results suggest that C. elegans homeodomain protein, CEH-37 could play an important role in telomere function via DNA binding.
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Affiliation(s)
- Sunjin Moon
- Structural Biochemistry and Molecular Biophysics Lab, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Yong Woo Lee
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Woo Taek Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Weontae Lee
- Structural Biochemistry and Molecular Biophysics Lab, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea.
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179
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Thestrup T, Litzlbauer J, Bartholomäus I, Mues M, Russo L, Dana H, Kovalchuk Y, Liang Y, Kalamakis G, Laukat Y, Becker S, Witte G, Geiger A, Allen T, Rome LC, Chen TW, Kim DS, Garaschuk O, Griesinger C, Griesbeck O. Optimized ratiometric calcium sensors for functional in vivo imaging of neurons and T lymphocytes. Nat Methods 2014; 11:175-82. [DOI: 10.1038/nmeth.2773] [Citation(s) in RCA: 253] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 11/29/2013] [Indexed: 01/20/2023]
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180
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Fedechkin SO, Brockerman J, Pfaff DA, Burns L, Webb T, Nelson A, Zhang F, Sabantsev AV, Melnikov AS, McKnight CJ, Smirnov SL. Gelsolin-like activation of villin: calcium sensitivity of the long helix in domain 6. Biochemistry 2013; 52:7890-900. [PMID: 24070253 DOI: 10.1021/bi400699s] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Villin is a gelsolin-like cytoskeleton regulator localized in the brush border at the apical end of epithelial cells. Villin regulates microvilli by bundling F-actin at low calcium levels and severing it at high calcium levels. The villin polypeptide consists of six gelsolin-like repeats (V1-V6) and the unique, actin binding C-terminal headpiece domain (HP). Villin modular fragment V6-HP requires calcium to stay monomeric and bundle F-actin. Our data show that isolated V6 is monomeric and does not bind F-actin at any level of calcium. We propose that the 40-residue unfolded V6-to-HP linker can be a key regulatory element in villin's functions such as its interactions with F-actin. Here we report a calcium-bound solution nuclear magnetic resonance (NMR) structure of V6, which has a gelsolin-like fold with the long α-helix in the extended conformation. Intrinsic tryptophan fluorescence quenching reveals two-Kd calcium binding in V6 (Kd1 of 22 μM and Kd2 of 2.8 mM). According to our NMR data, the conformation of V6 responds the most to micromolar calcium. We show that the long α-helix and the adjacent residues form the calcium-sensitive elements in V6. These observations are consistent with the calcium activation of F-actin severing by villin analogous to the gelsolin helix-straightening mechanism.
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Affiliation(s)
- Stanislav O Fedechkin
- Department of Chemistry, Western Washington University , 516 High Street, Bellingham, Washington 98225-9150, United States
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181
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Munyuki G, Jackson GE, Venter GA, Kövér KE, Szilágyi L, Rautenbach M, Spathelf BM, Bhattacharya B, van der Spoel D. β-Sheet Structures and Dimer Models of the Two Major Tyrocidines, Antimicrobial Peptides from Bacillus aneurinolyticus. Biochemistry 2013; 52:7798-806. [DOI: 10.1021/bi401363m] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gadzikano Munyuki
- Department
of Chemistry, University of Cape Town, P Bag X3, Rondebosch, Cape Town, South Africa 7701
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box
596, SE-751 24 Uppsala, Sweden
| | - Graham E. Jackson
- Department
of Chemistry, University of Cape Town, P Bag X3, Rondebosch, Cape Town, South Africa 7701
| | - Gerhard A. Venter
- Department
of Chemistry, University of Cape Town, P Bag X3, Rondebosch, Cape Town, South Africa 7701
| | - Katalin E. Kövér
- Department
of Chemistry, University of Debrecen, H-4010 Debrecen, Egyetem tér 1, Pf. 20, Hungary
| | - László Szilágyi
- Department
of Chemistry, University of Debrecen, H-4010 Debrecen, Egyetem tér 1, Pf. 20, Hungary
| | - Marina Rautenbach
- BIOPEP
Peptide group, Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa 7600
| | - Barbara M. Spathelf
- BIOPEP
Peptide group, Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa 7600
| | - Bhaswati Bhattacharya
- BIOPEP
Peptide group, Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa 7600
| | - David van der Spoel
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box
596, SE-751 24 Uppsala, Sweden
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182
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Inhibition of human neutrophil activity by an RNA aptamer bound to interleukin-8. Biomaterials 2013; 35:578-89. [PMID: 24129312 DOI: 10.1016/j.biomaterials.2013.09.107] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 09/26/2013] [Indexed: 02/04/2023]
Abstract
Interleukin-8 (IL-8) is a proinflammatory CXC chemokine that has been associated with the promotion of neutrophil chemotaxis, degranulation, and the pathogenesis of several neutrophil-infiltrating chronic inflammatory diseases. In the current study, we generated and characterized a 2'-fluoro-pyrimidine modified RNA aptamer (8A-35) against human IL-8. The 8A-35 aptamer binds to IL-8 with high specificity and affinity, yielding an estimated K(D) of 1.72 pM. NMR data revealed that the residues of Lys8, Leu10, Val63, Val66, Lys69 and Ala74 of IL-8 interact with aptamer. Moreover, the 8A-35 aptamer has a potent IL-8-neutralizing activity that can modulate multiple biological activities of IL-8 in human neutrophils, including migration, intracellular signaling, and intracellular Ca(2+) mobilization. Our results suggest that the 8A-35 aptamer has great potential to be a lead structure in the development of effective therapeutic agents against inflammatory diseases.
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183
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Martínez-Lumbreras S, Santiveri C, Mirassou Y, Zorrilla S, Pérez-Cañadillas J. Two Singular Types of CCCH Tandem Zinc Finger in Nab2p Contribute to Polyadenosine RNA Recognition. Structure 2013; 21:1800-11. [DOI: 10.1016/j.str.2013.07.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 07/22/2013] [Accepted: 07/23/2013] [Indexed: 01/09/2023]
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184
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Russo L, Raiola L, Campitiello MA, Magrì A, Fattorusso R, Malgieri G, Pappalardo G, La Mendola D, Isernia C. Probing the residual structure in avian prion hexarepeats by CD, NMR and MD techniques. Molecules 2013; 18:11467-84. [PMID: 24043142 PMCID: PMC6270093 DOI: 10.3390/molecules180911467] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/03/2013] [Accepted: 09/09/2013] [Indexed: 02/06/2023] Open
Abstract
Many proteins perform essential biological functions by means of regions that lacking specific organized structure exist as an ensemble of interconverting transient conformers. The characterization of such regions, including the description of their structural propensities, number of conformations and relative populations can provide useful insights. Prion diseases result from the conversion of a normal glycoprotein into a misfolded pathogenic isoform. The structures of mammal and chicken prion proteins show a similar fold with a globular domain and a flexible N-terminal portion that contains different repeated regions: octarepeats (PHGGGWGQ) in mammals and hexarepeats (PHNPGY) in chickens. The higher number of prolines in the hexarepeat region suggests that this region may retain a significant amount of residual secondary structure. Here, we report the CD, NMR and MD characterization of a peptide (2-HexaPY) composed of two hexarepeats. We combine experimental NMR data and MD to investigate at atomic level its ensemble-averaged structural properties, demonstrating how each residue of both repeats has a different quantified PPII propensity that shows a periodicity along the sequence. This feature explains the absence of cooperativity to stabilize a PPII conformation. Nonetheless, such residual structure can play a role in nucleating local structural transitions as well as modulating intra-molecular or inter-molecular interactions.
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Affiliation(s)
- Luigi Russo
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
| | - Luca Raiola
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
| | - Maria Anna Campitiello
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
| | - Antonio Magrì
- CNR-Istituto di Biostrutture e Bioimmagini, viale Doria 6, 95125 Catania, Italy; E-Mails: (A.M.); (G.P.)
| | - Roberto Fattorusso
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
- Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, Università di Napoli “Federico II”, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Gaetano Malgieri
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
| | - Giuseppe Pappalardo
- CNR-Istituto di Biostrutture e Bioimmagini, viale Doria 6, 95125 Catania, Italy; E-Mails: (A.M.); (G.P.)
| | - Diego La Mendola
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno Pisano 6, 56126 Pisa, Italy; E-Mail:
| | - Carla Isernia
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
- Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, Università di Napoli “Federico II”, Via Mezzocannone 16, 80134 Napoli, Italy
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +39-0823-274-636; Fax: +39-0823-274-605
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185
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Gerben SR, Lemkul JA, Brown AM, Bevan DR. Comparing atomistic molecular mechanics force fields for a difficult target: a case study on the Alzheimer’s amyloid β-peptide. J Biomol Struct Dyn 2013; 32:1817-32. [DOI: 10.1080/07391102.2013.838518] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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186
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Popovic M, Zlatev V, Hodnik V, Anderluh G, Felli IC, Pongor S, Pintar A. Flexibility of the PDZ-binding motif in the micelle-bound form of Jagged-1 cytoplasmic tail. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1818:1706-16. [PMID: 22465068 DOI: 10.1016/j.bbamem.2012.03.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 01/07/2023]
Abstract
Human Jagged-1, one of the ligands of Notch receptors, is a transmembrane protein composed of a large extracellular region and a 125-residue cytoplasmic tail which bears a C-terminal PDZ recognition motif. To investigate the interaction between Jagged-1 cytoplasmic tail and the inner leaflet of the plasma membrane we determined, by solution NMR, the secondary structure and dynamics of the recombinant protein corresponding to the intracellular region of Jagged-1, J1_tmic, bound to negatively charged lysophospholipid micelles. NMR showed that the PDZ binding motif is preceded by four alpha-helical segments and that, despite the extensive interaction between J1_tmic and the micelle, the PDZ binding motif remains highly flexible. Binding of J1_tmic to negatively charged, but not to zwitterionic vesicles, was confirmed by surface plasmon resonance. To study the PDZ binding region in more detail, we prepared a peptide corresponding to the last 24 residues of Jagged-1, J1C24, and different phosphorylated variants of it. J1C24 displays a marked helical propensity and undergoes a coil-helix transition in the presence of negatively charged, but not zwitterionic, lysophospholipid micelles. Phosphorylation at different positions drastically decreases the helical propensity of the peptides and abolishes the coil-helix transition triggered by lysophospholipid micelles. We propose that phosphorylation of residues upstream of the PDZ binding motif may shift the equilibrium from an ordered, membrane-bound, interfacial form of Jagged-1 C-terminal region to a more disordered form with an increased accessibility of the PDZ recognition motif, thus playing an indirect role in the interaction between Jagged-1 and the PDZ-containing target protein.
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Affiliation(s)
- Matija Popovic
- International Centre for Genetic Engineering and Biotechnology, AREA Science Park Padriciano 99, 1-34149 Trieste, Italy
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187
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Ullah A, Kemp G, Lee B, Alves C, Young H, Sykes BD, Fliegel L. Structural and functional analysis of transmembrane segment IV of the salt tolerance protein Sod2. J Biol Chem 2013; 288:24609-24. [PMID: 23836910 DOI: 10.1074/jbc.m113.483065] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Sod2 is the plasma membrane Na(+)/H(+) exchanger of the fission yeast Schizosaccharomyces pombe. It provides salt tolerance by removing excess intracellular sodium (or lithium) in exchange for protons. We examined the role of amino acid residues of transmembrane segment IV (TM IV) ((126)FPQINFLGSLLIAGCITSTDPVLSALI(152)) in activity by using alanine scanning mutagenesis and examining salt tolerance in sod2-deficient S. pombe. Two amino acids were critical for function. Mutations T144A and V147A resulted in defective proteins that did not confer salt tolerance when reintroduced into S. pombe. Sod2 protein with other alanine mutations in TM IV had little or no effect. T144D and T144K mutant proteins were inactive; however, a T144S protein was functional and provided lithium, but not sodium, tolerance and transport. Analysis of sensitivity to trypsin indicated that the mutations caused a conformational change in the Sod2 protein. We expressed and purified TM IV (amino acids 125-154). NMR analysis yielded a model with two helical regions (amino acids 128-142 and 147-154) separated by an unwound region (amino acids 143-146). Molecular modeling of the entire Sod2 protein suggested that TM IV has a structure similar to that deduced by NMR analysis and an overall structure similar to that of Escherichia coli NhaA. TM IV of Sod2 has similarities to TM V of the Zygosaccharomyces rouxii Na(+)/H(+) exchanger and TM VI of isoform 1 of mammalian Na(+)/H(+) exchanger. TM IV of Sod2 is critical to transport and may be involved in cation binding or conformational changes of the protein.
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Affiliation(s)
- Asad Ullah
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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188
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Rosenman DJ, Connors CR, Chen W, Wang C, García AE. Aβ monomers transiently sample oligomer and fibril-like configurations: ensemble characterization using a combined MD/NMR approach. J Mol Biol 2013; 425:3338-59. [PMID: 23811057 DOI: 10.1016/j.jmb.2013.06.021] [Citation(s) in RCA: 182] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 05/15/2013] [Accepted: 06/12/2013] [Indexed: 12/24/2022]
Abstract
Amyloid β (Aβ) peptides are a primary component of fibrils and oligomers implicated in the etiology of Alzheimer's disease (AD). However, the intrinsic flexibility of these peptides has frustrated efforts to investigate the secondary and tertiary structure of Aβ monomers, whose conformational landscapes directly contribute to the kinetics and thermodynamics of Aβ aggregation. In this work, de novo replica exchange molecular dynamics (REMD) simulations on the microseconds-per-replica timescale are used to characterize the structural ensembles of Aβ42, Aβ40, and M35-oxidized Aβ42, three physiologically relevant isoforms with substantially different aggregation properties. J-coupling data calculated from the REMD trajectories were compared to corresponding NMR-derived values acquired through two different pulse sequences, revealing that all simulations converge on the order of hundreds of nanoseconds-per-replica toward ensembles that yield good agreement with experiment. Though all three Aβ species adopt highly heterogeneous ensembles, these are considerably more structured compared to simulations on shorter timescales. Prominent in the C-terminus are antiparallel β-hairpins between L17-A21, A30-L36, and V39-I41, similar to oligomer and fibril intrapeptide models that expose these hydrophobic side chains to solvent and may serve as hotspots for self-association. Compared to reduced Aβ42, the absence of a second β-hairpin in Aβ40 and the sampling of alternate β topologies by M35-oxidized Aβ42 may explain the reduced aggregation rates of these forms. A persistent V24-K28 bend motif, observed in all three species, is stabilized by buried backbone to side-chain hydrogen bonds with D23 and a cross-region salt bridge between E22 and K28, highlighting the role of the familial AD-linked E22 and D23 residues in Aβ monomer folding. These characterizations help illustrate the conformational landscapes of Aβ monomers at atomic resolution and provide insight into the early stages of Aβ aggregation pathways.
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Affiliation(s)
- David J Rosenman
- Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
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189
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Mallajosyula SS, Adams KM, Barchi JJ, MacKerell AD. Conformational determinants of the activity of antiproliferative factor glycopeptide. J Chem Inf Model 2013; 53:1127-37. [PMID: 23627670 DOI: 10.1021/ci400147s] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The antiproliferative factor (APF) involved in interstitial cystitis is a glycosylated nonapeptide (TVPAAVVVA) containing a sialylated core 1 α-O-disaccharide linked to the N-terminal threonine. The chemical structure of APF was deduced using spectroscopic techniques and confirmed using total synthesis. The synthetic APF provided a platform to study amino acid modifications and their effect on APF activity, based on which a structure-activity relationship (SAR) for APF activity was previously proposed. However, this SAR model could not explain the change in activity associated with minor alterations in the peptide sequence. Presented is computational analysis of 14 APF derivatives to identify structural trends from which a more detailed SAR is obtained. The APF activity is found to be dictated by the close interplay between carbohydrate-peptide and peptide-peptide interactions. The former involves hydrogen bond and hydrophobic interactions, and the latter is dominated by hydrophobic interactions. The highly flexible hydrophobic peptide adopts collapsed conformations separated by low energy barriers. APF activity correlates with hydrophobic clustering associated with amino acids 4A, 6V, and 8V. Peptide conformations are highly sensitive to single point mutations, which explain the experimental trends. The presented SAR will act as a guide for lead optimization of more potent APF analogues of potential therapeutic utility.
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Affiliation(s)
- Sairam S Mallajosyula
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
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190
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Sommer LAM, Schaad M, Dames SA. NMR- and circular dichroism-monitored lipid binding studies suggest a general role for the FATC domain as membrane anchor of phosphatidylinositol 3-kinase-related kinases (PIKK). J Biol Chem 2013; 288:20046-63. [PMID: 23671275 DOI: 10.1074/jbc.m113.467233] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The FATC domain is shared by all members of the family of phosphatidylinositol-3 kinase-related kinases (PIKKs). It has been shown that the FATC domain plays an important role for the regulation of each PIKK. However, other than an involvement in protein-protein interactions, a common principle for the action of the FATC domain has not been detected. A detailed characterization of the structure and lipid binding properties of the FATC domain of the Ser/Thr kinase target of rapamycin (TOR) revealed that it contains a redox-sensitive membrane anchor in its C terminus. Because the C-terminal regions of the FATC domains of all known PIKKs are rather hydrophobic and especially rich in aromatic residues, we examined whether the ability to interact with lipids and membranes might be a general property. Here, we present the characterization of the interactions with lipids and different membrane mimetics for the FATC domains of human DNA-PKcs, human ATM, human ATR, human SMG-1, and human TRRAP by NMR and CD spectroscopy. The data indicate that all of these can interact with different membrane mimetics and may have different preferences only for membrane properties such as surface charge, curvature, and lipid packing. The oxidized form of the TOR FATC domain is well structured overall and forms an α-helix that is followed by a disulfide-bonded loop. In contrast, the FATC domains of the other PIKKs are rather unstructured in the isolated form and only significantly populate α-helical secondary structure upon interaction with membrane mimetics.
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Affiliation(s)
- Lisa A M Sommer
- Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
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191
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Abstract
Proline residues have unique roles in protein folding, structure, and function. Proline and the aromatic amino acids comprise the encoded cyclic protein residues. Aromatic protein side chains are defined by their negatively charged π faces, while the faces of the proline ring are partially positively charged. This polarity results from their two-point connection of the side chain to the electron-withdrawing protein backbone, and the lower electronegativity of hydrogen compared to carbon, nitrogen, and oxygen. The hydrogens adjacent to the carbonyl and amide nitrogen, Hα and Hδ, respectively, are the most partially positive. Proline's side chain is also conformationally restricted, allowing for interaction with aromatic residues with minimal entropic or steric penalty. Proline and aromatic residues can interact favorably with each other, due to both the hydrophobic effect and the interaction between the π aromatic face and the polarized C-H bonds, called a CH/π interaction. Aromatic-proline interactions can occur locally, for example, to stabilize cis-amide bonds, and over larger distances, in the tertiary structures of proteins, and intermolecularly in protein-protein interactions. In peptides and proteins, aromatic-proline sequences more readily adopt cis-prolyl amide bonds, where the aromatic ring interacts with the proline ring in the cis conformation. In aromatic-proline sequences, Trp and Tyr are more likely to induce cis-amide bonds than Phe, suggesting an aromatic electronic effect. This result would be expected for a CH/π interaction, in which a more electron-rich aromatic would have a stronger (more cis-stabilizing) interaction with partial positive charges on prolyl hydrogens. In this Account, we describe our investigations into the nature of local aromatic-proline interactions, using peptide models. We synthesized a series of 26 peptides, TXPN, varying X from electron-rich to electron poor aromatic amino acids, and found that the population of cis-amide bond (Ktrans/cis) is tunable by aromatic electronics. With 4-substituted phenylalanines, we observed a Hammett correlation between aromatic electronics and Ktrans/cis, with cis-trans isomerism electronically controllable by 1.0 kcal/mol. All aromatic residues exhibit a higher cis population than Ala or cyclohexylalanine, with Trp showing the strongest aromatic-proline interaction. In addition, proline stereoelectronic effects can modulate cis-trans isomerism by an additional 1.0 kcal/mol. The aromatic-proline interaction is enthalpic, consistent with its description as a CH/π interaction. Proline-aromatic sequences can also promote cis-prolyl bonds, either through interactions of the aromatic ring with the preceding cis-proline or with the Hα prior to cis-proline. Within proline-rich peptides, sequences commonly found in natively disordered proteins, aromatic residues promote multiple cis-amide bonds due to multiple favorable aromatic-proline interactions. Collectively, we found aromatic-proline interactions to be significantly CH/π in nature, tunable by aromatic electronics. We discuss these data in the context of aromatic-proline and aromatic-glycine interactions in local structure, in tertiary structure, in protein-protein interactions, and in protein assemblies.
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Affiliation(s)
- Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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192
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Gerig JT. Investigation of Ethanol–Peptide and Water–Peptide Interactions through Intermolecular Nuclear Overhauser Effects and Molecular Dynamics Simulations. J Phys Chem B 2013; 117:4880-92. [DOI: 10.1021/jp4007526] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- J. T. Gerig
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
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193
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Yoshinaga S, Sato T, Hirakane M, Esaki K, Hamaguchi T, Haga-Yamanaka S, Tsunoda M, Kimoto H, Shimada I, Touhara K, Terasawa H. Structure of the mouse sex peptide pheromone ESP1 reveals a molecular basis for specific binding to the class C G-protein-coupled vomeronasal receptor. J Biol Chem 2013; 288:16064-72. [PMID: 23576433 DOI: 10.1074/jbc.m112.436782] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Exocrine gland-secreting peptide 1 (ESP1) is a sex pheromone that is released in male mouse tear fluids and enhances female sexual receptive behavior. ESP1 is selectively recognized by a specific class C G-protein-coupled receptor (GPCR), V2Rp5, among the hundreds of receptors expressed in vomeronasal sensory neurons (VSNs). The specific sensing mechanism of the mammalian peptide pheromone by the class C GPCR remains to be elucidated. Here we identified the minimal functional region needed to retain VSN-stimulating activity in ESP1 and determined its three-dimensional structure, which adopts a helical fold stabilized by an intramolecular disulfide bridge with extensive charged patches. We then identified the amino acids involved in the activation of VSNs by a structure-based mutational analysis, revealing that the highly charged surface is crucial for the ESP1 activity. We also demonstrated that ESP1 specifically bound to an extracellular region of V2Rp5 by an in vitro pulldown assay. Based on homology modeling of V2Rp5 using the structure of the metabotropic glutamate receptor, we constructed a docking model of the ESP1-V2Rp5 complex in which the binding interface exhibited good electrostatic complementarity. These experimental results, supported by the molecular docking simulations, reveal that charge-charge interactions determine the specificity of ESP1 binding to V2Rp5 in the large extracellular region characteristic of class C GPCRs. The present study provides insights into the structural basis for the narrowly tuned sensing of mammalian peptide pheromones by class C GPCRs.
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Affiliation(s)
- Sosuke Yoshinaga
- Faculty of Life Sciences, Kumamoto University, Chuo-ku, Kumamoto 862-0973, Japan
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194
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Pandey AK, Naduthambi D, Thomas KM, Zondlo NJ. Proline editing: a general and practical approach to the synthesis of functionally and structurally diverse peptides. Analysis of steric versus stereoelectronic effects of 4-substituted prolines on conformation within peptides. J Am Chem Soc 2013; 135:4333-63. [PMID: 23402492 PMCID: PMC4209921 DOI: 10.1021/ja3109664] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Functionalized proline residues have diverse applications. Herein we describe a practical approach, proline editing, for the synthesis of peptides with stereospecifically modified proline residues. Peptides are synthesized by standard solid-phase peptide synthesis to incorporate Fmoc-hydroxyproline (4R-Hyp). In an automated manner, the Hyp hydroxyl is protected and the remainder of the peptide synthesized. After peptide synthesis, the Hyp protecting group is orthogonally removed and Hyp selectively modified to generate substituted proline amino acids, with the peptide main chain functioning to "protect" the proline amino and carboxyl groups. In a model tetrapeptide (Ac-TYPN-NH2), 4R-Hyp was stereospecifically converted to 122 different 4-substituted prolyl amino acids, with 4R or 4S stereochemistry, via Mitsunobu, oxidation, reduction, acylation, and substitution reactions. 4-Substituted prolines synthesized via proline editing include incorporated structured amino acid mimetics (Cys, Asp/Glu, Phe, Lys, Arg, pSer/pThr), recognition motifs (biotin, RGD), electron-withdrawing groups to induce stereoelectronic effects (fluoro, nitrobenzoate), handles for heteronuclear NMR ((19)F:fluoro; pentafluorophenyl or perfluoro-tert-butyl ether; 4,4-difluoro; (77)SePh) and other spectroscopies (fluorescence, IR: cyanophenyl ether), leaving groups (sulfonate, halide, NHS, bromoacetate), and other reactive handles (amine, thiol, thioester, ketone, hydroxylamine, maleimide, acrylate, azide, alkene, alkyne, aryl halide, tetrazine, 1,2-aminothiol). Proline editing provides access to these proline derivatives with no solution-phase synthesis. All peptides were analyzed by NMR to identify stereoelectronic and steric effects on conformation. Proline derivatives were synthesized to permit bioorthogonal conjugation reactions, including azide-alkyne, tetrazine-trans-cyclooctene, oxime, reductive amination, native chemical ligation, Suzuki, Sonogashira, cross-metathesis, and Diels-Alder reactions. These proline derivatives allowed three parallel bioorthogonal reactions to be conducted in one solution.
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Affiliation(s)
- Anil K. Pandey
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
| | - Devan Naduthambi
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
| | - Krista M. Thomas
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
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195
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Anderson KM, Esadze A, Manoharan M, Brüschweiler R, Gorenstein DG, Iwahara J. Direct observation of the ion-pair dynamics at a protein-DNA interface by NMR spectroscopy. J Am Chem Soc 2013; 135:3613-9. [PMID: 23406569 PMCID: PMC3721336 DOI: 10.1021/ja312314b] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Ion pairing is one of the most fundamental chemical interactions and is essential for molecular recognition by biological macromolecules. From an experimental standpoint, very little is known to date about ion-pair dynamics in biological macromolecular systems. Absorption, infrared, and Raman spectroscopic methods were previously used to characterize dynamic properties of ion pairs, but these methods can be applied only to small compounds. Here, using NMR (15)N relaxation and hydrogen-bond scalar (15)N-(31)P J-couplings ((h3)J(NP)), we have investigated the dynamics of the ion pairs between lysine side-chain NH3(+) amino groups and DNA phosphate groups at the molecular interface of the HoxD9 homeodomain-DNA complex. We have determined the order parameters and the correlation times for C-N bond rotation and reorientation of the lysine NH3(+) groups. Our data indicate that the NH3(+) groups in the intermolecular ion pairs are highly dynamic at the protein-DNA interface, which should lower the entropic costs for protein-DNA association. Judging from the C-N bond-rotation correlation times along with experimental and quantum-chemically derived (h3)J(NP) hydrogen-bond scalar couplings, it seems that breakage of hydrogen bonds in the ion pairs occurs on a sub-nanosecond time scale. Interestingly, the oxygen-to-sulfur substitution in a DNA phosphate group was found to enhance the mobility of the NH3(+) group in the intermolecular ion pair. This can partially account for the affinity enhancement of the protein-DNA association by the oxygen-to-sulfur substitution, which is a previously observed but poorly understood phenomenon.
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Affiliation(s)
- Kurtis M. Anderson
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555
- Department of NanoMedicine and Biomedical Engineering, Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77225
| | - Alexandre Esadze
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555
| | - Mariappan Manoharan
- Chemical Sciences Laboratory, Department of Chemistry and Biochemistry, and National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32306
| | - Rafael Brüschweiler
- Chemical Sciences Laboratory, Department of Chemistry and Biochemistry, and National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32306
| | - David G. Gorenstein
- Department of NanoMedicine and Biomedical Engineering, Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77225
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555
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196
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Tommos C, Valentine KG, Martínez-Rivera MC, Liang L, Moorman VR. Reversible phenol oxidation and reduction in the structurally well-defined 2-Mercaptophenol-α₃C protein. Biochemistry 2013; 52:1409-18. [PMID: 23373469 DOI: 10.1021/bi301613p] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
2-Mercaptophenol-α₃C serves as a biomimetic model for enzymes that use tyrosine residues in redox catalysis and multistep electron transfer. This model protein was tailored for electrochemical studies of phenol oxidation and reduction with specific emphasis on the redox-driven protonic reactions occurring at the phenol oxygen. This protein contains a covalently modified 2-mercaptophenol-cysteine residue. The radical site and the phenol compound were specifically chosen to bury the phenol OH group inside the protein. A solution nuclear magnetic resonance structural analysis (i) demonstrates that the synthetic 2-mercaptophenol-α₃C model protein behaves structurally as a natural protein, (ii) confirms the design of the radical site, (iii) reveals that the ligated phenol forms an interhelical hydrogen bond to glutamate 13 (phenol oxygen-carboxyl oxygen distance of 3.2 ± 0.5 Å), and (iv) suggests a proton-transfer pathway from the buried phenol OH (average solvent accessible surface area of 3 ± 5%) via glutamate 13 (average solvent accessible surface area of the carboxyl oxygens of 37 ± 18%) to the bulk solvent. A square-wave voltammetry analysis of 2-mercaptophenol-α₃C further demonstrates that (v) the phenol oxidation-reduction cycle is reversible, (vi) formal phenol reduction potentials can be obtained, and (vii) the phenol-O(•) state is long-lived with an estimated lifetime of ≥180 millisecond. These properties make 2-mercaptophenol-α₃C a unique system for characterizing phenol-based proton-coupled electron transfer in a low-dielectric and structured protein environment.
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Affiliation(s)
- Cecilia Tommos
- Graduate Group in Biochemistry and Molecular Biophysics and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, United States.
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197
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Ozenne V, Bauer F, Salmon L, Huang JR, Jensen MR, Segard S, Bernadó P, Charavay C, Blackledge M. Flexible-meccano: a tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables. Bioinformatics 2013; 28:1463-70. [PMID: 22613562 DOI: 10.1093/bioinformatics/bts172] [Citation(s) in RCA: 267] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Intrinsically disordered proteins (IDPs) represent a significant fraction of the human proteome. The classical structure function paradigm that has successfully underpinned our understanding of molecular biology breaks down when considering proteins that have no stable tertiary structure in their functional form. One convenient approach is to describe the protein in terms of an equilibrium of rapidly inter-converting conformers. Currently, tools to generate such ensemble descriptions are extremely rare, and poorly adapted to the prediction of experimental data. RESULTS We present flexible-meccano-a highly efficient algorithm that generates ensembles of molecules, on the basis of amino acid-specific conformational potentials and volume exclusion. Conformational sampling depends uniquely on the primary sequence, with the possibility of introducing additional local or long-range conformational propensities at an amino acid-specific resolution. The algorithm can also be used to calculate expected values of experimental parameters measured at atomic or molecular resolution, such as nuclear magnetic resonance (NMR) and small angle scattering, respectively. We envisage that flexible-meccano will be useful for researchers who wish to compare experimental data with those expected from a fully disordered protein, researchers who see experimental evidence of deviation from 'random coil' behaviour in their protein, or researchers who are interested in working with a broad ensemble of conformers representing the flexibility of the IDP of interest. AVAILABILITY A fully documented multi-platform executable is provided, with examples, at http://www.ibs.fr/science-213/scientific-output/software/flexible-meccano/ CONTACT martin.blackledge@ibs.fr.
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Affiliation(s)
- Valéry Ozenne
- Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel, 41 Rue Jules Horowitz, Grenoble, France
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198
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Guillière F, Danioux C, Jaubert C, Desnoues N, Delepierre M, Prangishvili D, Sezonov G, Guijarro JI. Solution structure of an archaeal DNA binding protein with an eukaryotic zinc finger fold. PLoS One 2013; 8:e52908. [PMID: 23326363 PMCID: PMC3541406 DOI: 10.1371/journal.pone.0052908] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 11/23/2012] [Indexed: 11/18/2022] Open
Abstract
While the basal transcription machinery in archaea is eukaryal-like, transcription factors in archaea and their viruses are usually related to bacterial transcription factors. Nevertheless, some of these organisms show predicted classical zinc fingers motifs of the C2H2 type, which are almost exclusively found in proteins of eukaryotes and most often associated with transcription regulators. In this work, we focused on the protein AFV1p06 from the hyperthermophilic archaeal virus AFV1. The sequence of the protein consists of the classical eukaryotic C2H2 motif with the fourth histidine coordinating zinc missing, as well as of N- and C-terminal extensions. We showed that the protein AFV1p06 binds zinc and solved its solution structure by NMR. AFV1p06 displays a zinc finger fold with a novel structure extension and disordered N- and C-termini. Structure calculations show that a glutamic acid residue that coordinates zinc replaces the fourth histidine of the C2H2 motif. Electromobility gel shift assays indicate that the protein binds to DNA with different affinities depending on the DNA sequence. AFV1p06 is the first experimentally characterised archaeal zinc finger protein with a DNA binding activity. The AFV1p06 protein family has homologues in diverse viruses of hyperthermophilic archaea. A phylogenetic analysis points out a common origin of archaeal and eukaryotic C2H2 zinc fingers.
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Affiliation(s)
- Florence Guillière
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS UMR 3528, Paris, France
- Université Paris 7 Denis Diderot, Paris, France
| | - Chloé Danioux
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Paris, France
- Université Pierre et Marie Curie, Paris, France
| | - Carole Jaubert
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Paris, France
- Université Pierre et Marie Curie, Paris, France
| | - Nicole Desnoues
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Paris, France
| | - Muriel Delepierre
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
| | - David Prangishvili
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Paris, France
| | - Guennadi Sezonov
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Paris, France
- Université Pierre et Marie Curie, Paris, France
- * E-mail: (JIG); (GS)
| | - J. Iñaki Guijarro
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS UMR 3528, Paris, France
- * E-mail: (JIG); (GS)
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199
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Solution structure and dynamics of C-terminal regulatory domain of Vibrio vulnificus extracellular metalloprotease. Biochem Biophys Res Commun 2013; 430:541-6. [DOI: 10.1016/j.bbrc.2012.11.117] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 11/29/2012] [Indexed: 11/19/2022]
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200
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Chong SH, Yim J, Ham S. Structural heterogeneity in familial Alzheimer's disease mutants of amyloid-beta peptides. MOLECULAR BIOSYSTEMS 2013; 9:997-1003. [DOI: 10.1039/c2mb25457c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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