1
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Aute R, Waghela N, Deshmukh MV. Key arginine residues in R2D2 dsRBD1 and dsRBD2 lead the siRNA recognition in Drosophila melanogaster RNAi pathway. Biophys Chem 2024; 310:107247. [PMID: 38663122 DOI: 10.1016/j.bpc.2024.107247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/04/2024] [Accepted: 04/16/2024] [Indexed: 05/23/2024]
Abstract
In Drosophila melanogaster, Dcr-2:R2D2 heterodimer binds to the 21 nucleotide siRNA duplex to form the R2D2/Dcr-2 Initiator (RDI) complex, which is critical for the initiation of siRNA-induced silencing complex (RISC) assembly. During RDI complex formation, R2D2, a protein that contains three dsRNA binding domains (dsRBD), senses two aspects of the siRNA: thermodynamically more stable end (asymmetry sensing) and the 5'-phosphate (5'-P) recognition. Despite several detailed studies to date, the molecular determinants arising from R2D2 for performing these two tasks remain elusive. In this study, we have performed structural, biophysical, and biochemical characterization of R2D2 dsRBDs. We found that the solution NMR-derived structure of R2D2 dsRBD1 yielded a canonical α1-β1-β2-β3-α2 fold, wherein two arginine salt bridges provide additional stability to the R2D2 dsRBD1. Furthermore, we show that R2D2 dsRBD1 interacts with thermodynamically asymmetric siRNA duplex independent of its 5'-phosphorylation state, whereas R2D2 dsRBD2 prefers to interact with 5'-P siRNA duplex. The mutation of key arginine residues, R53 and R101, in concatenated dsRBDs of R2D2 results in a significant loss of siRNA duplex recognition. Our study deciphers the active roles of R2D2 dsRBDs by showing that dsRBD1 initiates siRNA recognition, whereas dsRBD2 senses 5'-phosphate as an authentic mark on functional siRNA.
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Affiliation(s)
- Ramdas Aute
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Nilam Waghela
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mandar V Deshmukh
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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2
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Schneider T, Sawade K, Berner F, Peter C, Kovermann M. Specifying conformational heterogeneity of multi-domain proteins at atomic resolution. Structure 2023; 31:1259-1274.e10. [PMID: 37557171 DOI: 10.1016/j.str.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/02/2023] [Accepted: 07/14/2023] [Indexed: 08/11/2023]
Abstract
The conformational landscape of multi-domain proteins is inherently linked to their specific functions. This also holds for polyubiquitin chains that are assembled by two or more ubiquitin domains connected by a flexible linker thus showing a large interdomain mobility. However, molecular recognition and signal transduction are associated with particular conformational substates that are populated in solution. Here, we apply high-resolution NMR spectroscopy in combination with dual-scale MD simulations to explore the conformational space of K6-, K29-, and K33-linked diubiquitin molecules. The conformational ensembles are evaluated utilizing a paramagnetic cosolute reporting on solvent exposure plus a set of complementary NMR parameters. This approach unravels a conformational heterogeneity of diubiquitins and explains the diversity of structural models that have been determined for K6-, K29-, and K33-linked diubiquitins in free and ligand-bound states so far. We propose a general application of the approach developed here to demystify multi-domain proteins occurring in nature.
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Affiliation(s)
- Tobias Schneider
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Kevin Sawade
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Graduate School Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Frederic Berner
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany.
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3
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Morse PT, Pérez-Mejías G, Wan J, Turner AA, Márquez I, Kalpage HA, Vaishnav A, Zurek MP, Huettemann PP, Kim K, Arroum T, De la Rosa MA, Chowdhury DD, Lee I, Brunzelle JS, Sanderson TH, Malek MH, Meierhofer D, Edwards BFP, Díaz-Moreno I, Hüttemann M. Cytochrome c lysine acetylation regulates cellular respiration and cell death in ischemic skeletal muscle. Nat Commun 2023; 14:4166. [PMID: 37443314 PMCID: PMC10345088 DOI: 10.1038/s41467-023-39820-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Skeletal muscle is more resilient to ischemia-reperfusion injury than other organs. Tissue specific post-translational modifications of cytochrome c (Cytc) are involved in ischemia-reperfusion injury by regulating mitochondrial respiration and apoptosis. Here, we describe an acetylation site of Cytc, lysine 39 (K39), which was mapped in ischemic porcine skeletal muscle and removed by sirtuin5 in vitro. Using purified protein and cellular double knockout models, we show that K39 acetylation and acetylmimetic K39Q replacement increases cytochrome c oxidase (COX) activity and ROS scavenging while inhibiting apoptosis via decreased binding to Apaf-1, caspase cleavage and activity, and cardiolipin peroxidase activity. These results are discussed with X-ray crystallography structures of K39 acetylated (1.50 Å) and acetylmimetic K39Q Cytc (1.36 Å) and NMR dynamics. We propose that K39 acetylation is an adaptive response that controls electron transport chain flux, allowing skeletal muscle to meet heightened energy demand while simultaneously providing the tissue with robust resilience to ischemia-reperfusion injury.
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Affiliation(s)
- Paul T Morse
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Gonzalo Pérez-Mejías
- Instituto de Investigaciones Químicas, Universidad de Sevilla - CSIC, 41092, Sevilla, Spain
| | - Junmei Wan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Alice A Turner
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Inmaculada Márquez
- Instituto de Investigaciones Químicas, Universidad de Sevilla - CSIC, 41092, Sevilla, Spain
| | - Hasini A Kalpage
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Asmita Vaishnav
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Matthew P Zurek
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Philipp P Huettemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Katherine Kim
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Tasnim Arroum
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA
| | - Miguel A De la Rosa
- Instituto de Investigaciones Químicas, Universidad de Sevilla - CSIC, 41092, Sevilla, Spain
| | - Dipanwita Dutta Chowdhury
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Icksoo Lee
- College of Medicine, Dankook University, Cheonan-si, Chungcheongnam-do 31116, Republic of Korea
| | - Joseph S Brunzelle
- Life Sciences Collaborative Access Team, Northwestern University, Center for Synchrotron Research, Argonne, IL, 60439, USA
| | - Thomas H Sanderson
- Department of Emergency Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Moh H Malek
- Department of Health Care Sciences, Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Brian F P Edwards
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas, Universidad de Sevilla - CSIC, 41092, Sevilla, Spain.
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, 48201, USA.
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, 48201, USA.
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4
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Hollmann NM, Jagtap PKA, Linse JB, Ullmann P, Payr M, Murciano B, Simon B, Hub JS, Hennig J. Upstream of N-Ras C-terminal cold shock domains mediate poly(A) specificity in a novel RNA recognition mode and bind poly(A) binding protein. Nucleic Acids Res 2023; 51:1895-1913. [PMID: 36688322 PMCID: PMC9976900 DOI: 10.1093/nar/gkac1277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/24/2023] Open
Abstract
RNA binding proteins (RBPs) often engage multiple RNA binding domains (RBDs) to increase target specificity and affinity. However, the complexity of target recognition of multiple RBDs remains largely unexplored. Here we use Upstream of N-Ras (Unr), a multidomain RBP, to demonstrate how multiple RBDs orchestrate target specificity. A crystal structure of the three C-terminal RNA binding cold-shock domains (CSD) of Unr bound to a poly(A) sequence exemplifies how recognition goes beyond the classical ππ-stacking in CSDs. Further structural studies reveal several interaction surfaces between the N-terminal and C-terminal part of Unr with the poly(A)-binding protein (pAbp). All interactions are validated by mutational analyses and the high-resolution structures presented here will guide further studies to understand how both proteins act together in cellular processes.
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Affiliation(s)
- Nele Merret Hollmann
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany
| | - Pravin Kumar Ankush Jagtap
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
| | - Johanna-Barbara Linse
- Theoretical Physics, Saarland University, 66123 Saarbrücken, Germany.,Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Philip Ullmann
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Marco Payr
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany
| | - Brice Murciano
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Bernd Simon
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jochen S Hub
- Theoretical Physics, Saarland University, 66123 Saarbrücken, Germany.,Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
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5
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Conformational Dynamics of Phytoglobin BvPgb1.2 from Beta vulgaris ssp. vulgaris. Int J Mol Sci 2023; 24:ijms24043973. [PMID: 36835381 PMCID: PMC9961634 DOI: 10.3390/ijms24043973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/09/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023] Open
Abstract
Plant hemoglobins, often referred to as phytoglobins, play important roles in abiotic stress tolerance. Several essential small physiological metabolites can be bound to these heme proteins. In addition, phytoglobins can catalyze a range of different oxidative reactions in vivo. These proteins are often oligomeric, but the degree and relevance of subunit interactions are largely unknown. In this study, we delineate which residues are involved in dimer formation of a sugar beet phytoglobin type 1.2 (BvPgb1.2) using NMR relaxation experiments. E. coli cells harboring a phytoglobin expression vector were cultivated in isotope-labeled (2H, 13C and 15N) M9 medium. The triple-labeled protein was purified to homogeneity using two chromatographic steps. Two forms of BvPgb1.2 were examined, the oxy-form and the more stable cyanide-form. Using three-dimensional triple-resonance NMR experiments, sequence-specific assignments for CN-bound BvPgb1.2 were achieved for 137 backbone amide cross-peaks in the 1H-15N TROSY spectrum, which amounts to 83% of the total number of 165 expected cross-peaks. A large proportion of the non-assigned residues are located in α-helixes G and H, which are proposed to be involved in protein dimerization. Such knowledge around dimer formation will be instrumental for developing a better understanding of phytoglobins' roles in planta.
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6
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Bonin JP, Sapienza PJ, Lee AL. Dynamic allostery in substrate binding by human thymidylate synthase. eLife 2022; 11:79915. [PMID: 36200982 PMCID: PMC9536839 DOI: 10.7554/elife.79915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/31/2022] [Indexed: 11/25/2022] Open
Abstract
Human thymidylate synthase (hTS) is essential for DNA replication and therefore a therapeutic target for cancer. Effective targeting requires knowledge of the mechanism(s) of regulation of this 72 kDa homodimeric enzyme. Here, we investigate the mechanism of binding cooperativity of the nucleotide substrate. We have employed exquisitely sensitive methyl-based CPMG and CEST NMR experiments enabling us to identify residues undergoing bifurcated linear 3-state exchange, including concerted switching between active and inactive conformations in the apo enzyme. The inactive state is populated to only ~1.3%, indicating that conformational selection contributes negligibly to the cooperativity. Instead, methyl rotation axis order parameters, determined by 2H transverse relaxation rates, suggest that rigidification of the enzyme upon substrate binding is responsible for the entropically-driven cooperativity. Lack of the rigidification in product binding and substrate binding to an N-terminally truncated enzyme, both non-cooperative, support this idea. In addition, the lack of this rigidification in the N-terminal truncation indicates that interactions between the flexible N-terminus and the rest of the protein, which are perturbed by substrate binding, play a significant role in the cooperativity—a novel mechanism of dynamic allostery. Together, these findings yield a rare depth of insight into the substrate binding cooperativity of an essential enzyme.
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Affiliation(s)
- Jeffrey P Bonin
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina
| | - Paul J Sapienza
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina
| | - Andrew L Lee
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina
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7
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Taiwo KM, Nam H, LeBlanc RM, Longhini AP, Dayie TK. Cross-correlated relaxation rates provide facile exchange signature in selectively labeled RNA. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 342:107245. [PMID: 35908529 DOI: 10.1016/j.jmr.2022.107245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Gerhard Wagner has made numerous contributions to NMR spectroscopy, particularly his developments in the field of spin-relaxation stand out in directly mapping the spectral density functions of proteins. He and his group developed experimental techniques to reveal the importance of dynamics to protein biological function and drug discovery. On his 75th birthday, we take this opportunity to highlight how some of those seminal ideas developed for proteins are being extended to RNAs. The role of dynamics in the structure and function of RNA has been a major interest in drug design and therapeutics. Here we present the use of cross-correlated relaxation rates (ηxy) from anti-TROSY (R2α) and TROSY (R2β) to rapidly obtain qualitative information about the chemical exchange taking place within the bacterial and human A-site RNA system while reducing the sets of relaxation experiments required to map dynamics. We show that ηxy correlates with the order parameter which gives information on how flexible or rigid a residue is. We further show R2β/ηxy can rapidly be used to probe chemical exchange as seen from its agreement with Rex. In addition, we report the ability of R2β/ηxy to determine chemical exchange taking place within the bacterial A-site RNA during structural transitions at pH 6.2 and 6.5. Finally, comparison of the R2β/ηxy ratios indicates bacterial A-site has greater R2β/ηxy values for G19 (1.34 s-1), A20 (1.38 s-1), U23 (1.63 s-1) and C24 (1.51 s-1) than human A-site [A19 (0.76 s-1), A20 (1.01 s-1), U23 (0.74 s-1) and C24 (0.71 s-1)]. Taken together, we have shown that the chemical exchange can quickly be analyzed for RNA systems from cross-correlated relaxation rates.
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Affiliation(s)
- Kehinde M Taiwo
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, United States.
| | - Hyeyeon Nam
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, United States
| | - Regan M LeBlanc
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, United States
| | - Andrew P Longhini
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, United States
| | - Theodore K Dayie
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, United States.
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8
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Olenginski LT, Kasprzak WK, Bergonzo C, Shapiro BA, Dayie TK. Conformational Dynamics of the Hepatitis B Virus Pre-genomic RNA on Multiple Time Scales: Implications for Viral Replication. J Mol Biol 2022; 434:167633. [PMID: 35595167 DOI: 10.1016/j.jmb.2022.167633] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/28/2022] [Accepted: 05/07/2022] [Indexed: 12/30/2022]
Abstract
Human hepatitis B virus (HBV) replication is initiated by the binding of the viral polymerase (P) to epsilon (ε), an ≈85-nucleotide (nt) cis-acting regulatory stem-loop RNA located at the 5'-end of the pre-genomic RNA (pgRNA). This interaction triggers P and pgRNA packaging and protein-primed reverse transcription and is therefore an attractive therapeutic target. Our recent nuclear magnetic resonance (NMR) structure of ε provides a useful starting point toward a detailed understanding of HBV replication, and hints at the functional importance of ε dynamics. Here, we present a detailed description of ε motions on the ps to ns and μs to ms time scales by NMR spin relaxation and relaxation dispersion, respectively. We also carried out molecular dynamics simulations to provide additional insight into ε conformational dynamics. These data outline a series of complex motions on multiple time scales within ε. Moreover, these motions occur in mostly conserved nucleotides from structural regions (i.e., priming loop, pseudo-triloop, and U43 bulge) that biochemical and mutational studies have shown to be essential for P binding, P-pgRNA packaging, protein-priming, and DNA synthesis. Taken together, our work implicates RNA dynamics as an integral feature that governs HBV replication.
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Affiliation(s)
- Lukasz T Olenginski
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Wojciech K Kasprzak
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Christina Bergonzo
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and University of Maryland, Rockville, MD 20850, USA
| | - Bruce A Shapiro
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Theodore K Dayie
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.
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9
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Macošek J, Simon B, Linse JB, Jagtap PKA, Winter SL, Foot J, Lapouge K, Perez K, Rettel M, Ivanović MT, Masiewicz P, Murciano B, Savitski MM, Loedige I, Hub JS, Gabel F, Hennig J. Structure and dynamics of the quaternary hunchback mRNA translation repression complex. Nucleic Acids Res 2021; 49:8866-8885. [PMID: 34329466 PMCID: PMC8421216 DOI: 10.1093/nar/gkab635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/05/2021] [Accepted: 07/27/2021] [Indexed: 01/02/2023] Open
Abstract
A key regulatory process during Drosophila development is the localized suppression of the hunchback mRNA translation at the posterior, which gives rise to a hunchback gradient governing the formation of the anterior-posterior body axis. This suppression is achieved by a concerted action of Brain Tumour (Brat), Pumilio (Pum) and Nanos. Each protein is necessary for proper Drosophila development. The RNA contacts have been elucidated for the proteins individually in several atomic-resolution structures. However, the interplay of all three proteins during RNA suppression remains a long-standing open question. Here, we characterize the quaternary complex of the RNA-binding domains of Brat, Pum and Nanos with hunchback mRNA by combining NMR spectroscopy, SANS/SAXS, XL/MS with MD simulations and ITC assays. The quaternary hunchback mRNA suppression complex comprising the RNA binding domains is flexible with unoccupied nucleotides functioning as a flexible linker between the Brat and Pum-Nanos moieties of the complex. Moreover, the presence of the Pum-HD/Nanos-ZnF complex has no effect on the equilibrium RNA binding affinity of the Brat RNA binding domain. This is in accordance with previous studies, which showed that Brat can suppress mRNA independently and is distributed uniformly throughout the embryo.
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Affiliation(s)
- Jakub Macošek
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Johanna-Barbara Linse
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
| | - Pravin Kumar Ankush Jagtap
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Sophie L Winter
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Jaelle Foot
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Karine Lapouge
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Kathryn Perez
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Mandy Rettel
- Proteomics Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Miloš T Ivanović
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
| | - Pawel Masiewicz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Brice Murciano
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Mikhail M Savitski
- Proteomics Core Facility, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Inga Loedige
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
| | - Frank Gabel
- Institut Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Heidelberg 69117, Germany.,Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
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10
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Aggarwal P, Bhavesh NS. Hinge like domain motion facilitates human RBMS1 protein binding to proto-oncogene c-myc promoter. Nucleic Acids Res 2021; 49:5943-5955. [PMID: 33999211 PMCID: PMC8191779 DOI: 10.1093/nar/gkab363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 04/02/2021] [Accepted: 04/24/2021] [Indexed: 01/07/2023] Open
Abstract
DNA binding proteins recognize DNA specifically or non-specifically using direct and indirect readout mechanisms like sliding, hopping, and diffusion. However, a common difficulty in explicitly elucidating any particular mechanism of site-specific DNA-protein recognition is the lack of knowledge regarding target sequences and inadequate account of non-specific interactions, in general. Here, we decipher the structural basis of target search performed by the key regulator of expression of c-myc proto-oncogene, the human RBMS1 protein. In this study, we have shown the structural reorganization of this multi-domain protein required for recognizing the specific c-myc promoter sequence. The results suggest that a synergy between structural re-organization and thermodynamics is necessary for the recognition of target sequences. The study presents another perspective of looking at the DNA-protein interactions.
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Affiliation(s)
- Priyanka Aggarwal
- Transcription Regulation group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Neel Sarovar Bhavesh
- Transcription Regulation group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
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11
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Olenginski LT, Dayie TK. Quantifying the effects of long-range 13C- 13C dipolar coupling on measured relaxation rates in RNA. JOURNAL OF BIOMOLECULAR NMR 2021; 75:203-211. [PMID: 33914223 PMCID: PMC8131303 DOI: 10.1007/s10858-021-00368-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
Selective stable isotope labeling has transformed structural and dynamics analysis of RNA by NMR spectroscopy. These methods can remove 13C-13C dipolar couplings that complicate 13C relaxation analyses. While these phenomena are well documented for sites with adjacent 13C nuclei (e.g. ribose C1'), less is known about so-called isolated sites (e.g. adenosine C2). To investigate and quantify the effects of long-range (> 2 Å) 13C-13C dipolar interactions on RNA dynamics, we simulated adenosine C2 relaxation rates in uniformly [U-13C/15N]-ATP or selectively [2-13C]-ATP labeled RNAs. Our simulations predict non-negligible 13C-13C dipolar contributions from adenosine C4, C5, and C6 to C2 longitudinal (R1) relaxation rates in [U-13C/15N]-ATP labeled RNAs. Moreover, these contributions increase at higher magnetic fields and molecular weights to introduce discrepancies that exceed 50%. This will become increasingly important at GHz fields. Experimental R1 measurements in the 61 nucleotide human hepatitis B virus encapsidation signal ε RNA labeled with [U-13C/15N]-ATP or [2-13C]-ATP corroborate these simulations. Thus, in the absence of selectively labeled samples, long-range 13C-13C dipolar contributions must be explicitly taken into account when interpreting adenosine C2 R1 rates in terms of motional models for large RNAs.
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Affiliation(s)
- Lukasz T Olenginski
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Theodore K Dayie
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA.
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12
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Namitz KEW, Zheng T, Canning AJ, Alicea-Velazquez NL, Castañeda CA, Cosgrove MS, Hanes SD. Structure analysis suggests Ess1 isomerizes the carboxy-terminal domain of RNA polymerase II via a bivalent anchoring mechanism. Commun Biol 2021; 4:398. [PMID: 33767358 PMCID: PMC7994582 DOI: 10.1038/s42003-021-01906-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/24/2021] [Indexed: 01/07/2023] Open
Abstract
Accurate gene transcription in eukaryotes depends on isomerization of serine-proline bonds within the carboxy-terminal domain (CTD) of RNA polymerase II. Isomerization is part of the "CTD code" that regulates recruitment of proteins required for transcription and co-transcriptional RNA processing. Saccharomyces cerevisiae Ess1 and its human ortholog, Pin1, are prolyl isomerases that engage the long heptad repeat (YSPTSPS)26 of the CTD by an unknown mechanism. Here, we used an integrative structural approach to decipher Ess1 interactions with the CTD. Ess1 has a rigid linker between its WW and catalytic domains that enforces a distance constraint for bivalent interaction with the ends of long CTD substrates (≥4-5 heptad repeats). Our binding results suggest that the Ess1 WW domain anchors the proximal end of the CTD substrate during isomerization, and that linker divergence may underlie evolution of substrate specificity.
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Affiliation(s)
- Kevin E. W. Namitz
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA ,grid.29857.310000 0001 2097 4281Present Address: Department of Chemistry, Pennsylvania State University, University Park, PA USA
| | - Tongyin Zheng
- grid.264484.80000 0001 2189 1568Departments of Biology and Chemistry, Syracuse University, Syracuse, NY USA
| | - Ashley J. Canning
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA
| | - Nilda L. Alicea-Velazquez
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA ,grid.247980.00000 0001 2184 3689Present Address: Department of Chemistry and Biochemistry, Central Connecticut State University, New Britain, CT USA
| | - Carlos A. Castañeda
- grid.264484.80000 0001 2189 1568Departments of Biology and Chemistry, Syracuse University, Syracuse, NY USA
| | - Michael S. Cosgrove
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA
| | - Steven D. Hanes
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA
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13
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Smith AA, Bolik-Coulon N, Ernst M, Meier BH, Ferrage F. How wide is the window opened by high-resolution relaxometry on the internal dynamics of proteins in solution? JOURNAL OF BIOMOLECULAR NMR 2021; 75:119-131. [PMID: 33759077 PMCID: PMC8018934 DOI: 10.1007/s10858-021-00361-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
The dynamics of molecules in solution is usually quantified by the determination of timescale-specific amplitudes of motions. High-resolution nuclear magnetic resonance (NMR) relaxometry experiments-where the sample is transferred to low fields for longitudinal (T1) relaxation, and back to high field for detection with residue-specific resolution-seeks to increase the ability to distinguish the contributions from motion on timescales slower than a few nanoseconds. However, tumbling of a molecule in solution masks some of these motions. Therefore, we investigate to what extent relaxometry improves timescale resolution, using the "detector" analysis of dynamics. Here, we demonstrate improvements in the characterization of internal dynamics of methyl-bearing side chains by carbon-13 relaxometry in the small protein ubiquitin. We show that relaxometry data leads to better information about nanosecond motions as compared to high-field relaxation data only. Our calculations show that gains from relaxometry are greater with increasing correlation time of rotational diffusion.
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Affiliation(s)
- Albert A Smith
- Institut für Medizinische Physik und Biophysik, Universität Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany.
- Physical Chemistry ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Nicolas Bolik-Coulon
- Laboratoire des biomolécules, LBM, Département de Chimie, École normale superieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Matthias Ernst
- Physical Chemistry ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Beat H Meier
- Physical Chemistry ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Fabien Ferrage
- Laboratoire des biomolécules, LBM, Département de Chimie, École normale superieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.
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14
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Leeb S, Yang F, Oliveberg M, Danielsson J. Connecting Longitudinal and Transverse Relaxation Rates in Live-Cell NMR. J Phys Chem B 2020; 124:10698-10707. [PMID: 33179918 PMCID: PMC7735724 DOI: 10.1021/acs.jpcb.0c08274] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/22/2020] [Indexed: 12/26/2022]
Abstract
In the cytosolic environment, protein crowding and Brownian motions result in numerous transient encounters. Each such encounter event increases the apparent size of the interacting molecules, leading to slower rotational tumbling. The extent of transient protein complexes formed in live cells can conveniently be quantified by an apparent viscosity, based on NMR-detected spin-relaxation measurements, that is, the longitudinal (T1) and transverse (T2) relaxation. From combined analysis of three different proteins and surface mutations thereof, we find that T2 implies significantly higher apparent viscosity than T1. At first sight, the effect on T1 and T2 seems thus nonunifiable, consistent with previous reports on other proteins. We show here that the T1 and T2 deviation is actually not a inconsistency but an expected feature of a system with fast exchange between free monomers and transient complexes. In this case, the deviation is basically reconciled by a model with fast exchange between the free-tumbling reporter protein and a transient complex with a uniform 143 kDa partner. The analysis is then taken one step further by accounting for the fact that the cytosolic content is by no means uniform but comprises a wide range of molecular sizes. Integrating over the complete size distribution of the cytosolic interaction ensemble enables us to predict both T1 and T2 from a single binding model. The result yields a bound population for each protein variant and provides a quantification of the transient interactions. We finally extend the approach to obtain a correction term for the shape of a database-derived mass distribution of the interactome in the mammalian cytosol, in good accord with the existing data of the cellular composition.
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Affiliation(s)
- Sarah Leeb
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, Stockholm 106 91, Sweden
| | - Fan Yang
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, Stockholm 106 91, Sweden
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, Stockholm 106 91, Sweden
| | - Jens Danielsson
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, Stockholm 106 91, Sweden
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15
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Nam H, Becette O, LeBlanc RM, Oh D, Case DA, Dayie TK. Deleterious effects of carbon-carbon dipolar coupling on RNA NMR dynamics. JOURNAL OF BIOMOLECULAR NMR 2020; 74:321-331. [PMID: 32363430 DOI: 10.1007/s10858-020-00315-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/18/2020] [Indexed: 06/11/2023]
Abstract
Many regulatory RNAs undergo dynamic exchanges that are crucial for their biological functions and NMR spectroscopy is a versatile tool for monitoring dynamic motions of biomolecules. Meaningful information on biomolecular dynamics requires an accurate measurement of relaxation parameters such as longitudinal (R1) rates, transverse (R2) rates and heteronuclear Overhauser effect (hNOE). However, earlier studies have shown that the large 13C-13C interactions complicate analysis of the carbon relaxation parameters. To investigate the effect of 13C-13C interactions on RNA dynamic studies, we performed relaxation measurements on various RNA samples with different labeling patterns and compared these measurements with the computational simulations. For uniformly labeled samples, contributions of the neighboring carbon to R1 measurements were observed. These contributions increased with increasing magnetic field and overall correlation time ([Formula: see text]) for R1 rates, necessitating more careful analysis for uniformly labeled large RNAs. In addition, the hNOE measurements were also affected by the adjacent carbon nuclei. Unlike R1 rates, R1ρ rates showed relatively good agreement between uniformly- and site-selectively labeled samples, suggesting no dramatic effect from their attached carbon, in agreement with previous observations. Overall, having more accurate rate measurements avoids complex analysis and will be a key for interpreting 13C relaxation rates for molecular motion that can provide valuable insights into cellular molecular recognition events.
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Affiliation(s)
- Hyeyeon Nam
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Owen Becette
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Regan M LeBlanc
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Daniel Oh
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Theodore K Dayie
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA.
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16
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Marcellini M, Nguyen MH, Martin M, Hologne M, Walker O. Accurate Prediction of Protein NMR Spin Relaxation by Means of Polarizable Force Fields. Application to Strongly Anisotropic Rotational Diffusion. J Phys Chem B 2020; 124:5103-5112. [DOI: 10.1021/acs.jpcb.0c01922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Moreno Marcellini
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon1, Lyon, France
| | - Minh-Ha Nguyen
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon1, Lyon, France
| | - Marie Martin
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon1, Lyon, France
| | - Maggy Hologne
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon1, Lyon, France
| | - Olivier Walker
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon1, Lyon, France
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17
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Anderson JS, Hernández G, LeMaster DM. 13C NMR Relaxation Analysis of Protein GB3 for the Assessment of Side Chain Dynamics Predictions by Current AMBER and CHARMM Force Fields. J Chem Theory Comput 2020; 16:2896-2913. [PMID: 32268062 DOI: 10.1021/acs.jctc.0c00050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Molecular simulations with seven current AMBER- and CHARMM-based force fields yield markedly differing internal bond vector autocorrelation function predictions for many of the 223 methine and methylene H-C bonds of the 56-residue protein GB3. To enable quantification of accuracy, 13C R1, R2, and heteronuclear NOE relaxation rates have been determined for the methine and stereochemically assigned methylene Cα and Cβ positions. With only three experimental relaxation values for each bond vector, central to this analysis is the accuracy with which MD-derived autocorrelation curves can be represented by a 3-parameter equation which, in turn, maps onto the NMR relaxation values. In contrast to the more widely used extended Lipari-Szabo order parameter representation, 95% of these MD-derived internal autocorrelation curves for GB3 can be fitted to within 1.0% rmsd over the time frame from 30 ps to 4 ns by a biexponential Larmor frequency-selective representation (LF-S2). Applying the LF-S2 representation to the experimental relaxation rates and uncertainties serves to determine the boundary range for the autocorrelation function of each bond vector consistent with the experimental data. Not surprisingly, all seven force fields predict the autocorrelation functions for the more motionally restricted 1Hα-13Cα and 1Hβ-13Cβ bond vectors with reasonable accuracy. However, for the 1Hβ-13Cβ bond vectors exhibiting aggregate order parameter S2 values less than 0.85, only 1% of the MD-derived predictions lie with 1 σ of the experimentally determined autocorrelation functions and only 7% within 2 σ. On the other hand, substantial residue type-specific improvements in predictive performance were observed among the recent AMBER force fields. This analysis indicates considerable potential for the use of 13C relaxation measurements in guiding the optimization of the side chain dynamics characteristics of protein molecular simulations.
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Affiliation(s)
- Janet S Anderson
- Department of Chemistry, Union College, Schenectady, New York 12308, United States
| | - Griselda Hernández
- Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, New York 12201, United States
| | - David M LeMaster
- Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, New York 12201, United States
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18
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Houston P, Macro N, Kang M, Chen L, Yang J, Wang L, Wu Z, Zhong D. Ultrafast Dynamics of Water-Protein Coupled Motions around the Surface of Eye Crystallin. J Am Chem Soc 2020; 142:3997-4007. [PMID: 31991083 PMCID: PMC7261499 DOI: 10.1021/jacs.9b13506] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Water dynamics on the protein surface mediate both protein structure and function. However, many questions remain about the role of the protein hydration layers in protein fluctuations and how the dynamics of these layers relate to specific protein properties. The fish eye lens protein γM7-crystallin (γM7) is found in vivo at extremely high concentrations nearing the packing limit, corresponding to only a few water layers between adjacent proteins. In this study, we conducted a site-specific probing of hydration water motions and side-chain dynamics at nine selected sites around the surface of γM7 using a tryptophan scan with femtosecond spectroscopy and NMR nuclear spin relaxation (NSR). We observed correlated fluctuations between hydration water and protein side chains on the time scales of a few picoseconds and hundreds of picoseconds, corresponding to local reorientations and network restructuring, respectively. These motions are heterogeneous over the protein surface and relate to the various steric and chemical properties of the local protein environment. Overall, we found that γM7 has relatively slower water dynamics within the hydration shell than a similar β-sheet protein, which may contribute to the high packing limit of this unique protein.
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Affiliation(s)
- Patrick Houston
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus Ohio, 43210, USA
| | - Nicolas Macro
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus Ohio, 43210, USA
| | - Minhee Kang
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus Ohio, 43210, USA
| | - Long Chen
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus Ohio, 43210, USA
| | - Jin Yang
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus Ohio, 43210, USA
| | - Lijuan Wang
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus Ohio, 43210, USA
| | - Zhengrong Wu
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus Ohio, 43210, USA
| | - Dongping Zhong
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus Ohio, 43210, USA
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19
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Marušič M, Schlagnitweit J, Petzold K. RNA Dynamics by NMR Spectroscopy. Chembiochem 2019; 20:2685-2710. [PMID: 30997719 PMCID: PMC6899578 DOI: 10.1002/cbic.201900072] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/12/2019] [Indexed: 12/22/2022]
Abstract
An ever-increasing number of functional RNAs require a mechanistic understanding. RNA function relies on changes in its structure, so-called dynamics. To reveal dynamic processes and higher energy structures, new NMR methods have been developed to elucidate these dynamics in RNA with atomic resolution. In this Review, we provide an introduction to dynamics novices and an overview of methods that access most dynamic timescales, from picoseconds to hours. Examples are provided as well as insight into theory, data acquisition and analysis for these different methods. Using this broad spectrum of methodology, unprecedented detail and invisible structures have been obtained and are reviewed here. RNA, though often more complicated and therefore neglected, also provides a great system to study structural changes, as these RNA structural changes are more easily defined-Lego like-than in proteins, hence the numerous revelations of RNA excited states.
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Affiliation(s)
- Maja Marušič
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetSolnavägen 917177StockholmSweden
| | - Judith Schlagnitweit
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetSolnavägen 917177StockholmSweden
| | - Katja Petzold
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetSolnavägen 917177StockholmSweden
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20
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Molecular recognition of ubiquitin and Lys63-linked diubiquitin by STAM2 UIM-SH3 dual domain: the effect of its linker length and flexibility. Sci Rep 2019; 9:14645. [PMID: 31601934 PMCID: PMC6787221 DOI: 10.1038/s41598-019-51182-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/25/2019] [Indexed: 11/09/2022] Open
Abstract
Multidomain proteins represent a broad spectrum of the protein landscape and are involved in various interactions. They could be considered as modular building blocks assembled in distinct fashion and connected by linkers of varying lengths and sequences. Due to their intrinsic flexibility, these linkers provide proteins a subtle way to modulate interactions and explore a wide range of conformational space. In the present study, we are seeking to understand the effect of the flexibility and dynamics of the linker involved in the STAM2 UIM-SH3 dual domain protein with respect to molecular recognition. We have engineered several constructs of UIM-SH3 with different length linkers or domain deletion. By means of SAXS and NMR experiments, we have shown that the modification of the linker modifies the flexibility and the dynamics of UIM-SH3. Indeed, the global tumbling of both the UIM and SH3 domain is different but not independent from each other while the length of the linker has an impact on the ps-ns time scale dynamics of the respective domains. Finally, the modification of the flexibility and dynamics of the linker has a drastic effect on the interaction of UIM-SH3 with Lys63-linked diubiquitin with a roughly eight-time weaker dissociation constant.
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21
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Moretto L, Heylen R, Holroyd N, Vance S, Broadhurst RW. Modular type I polyketide synthase acyl carrier protein domains share a common N-terminally extended fold. Sci Rep 2019; 9:2325. [PMID: 30787330 PMCID: PMC6382882 DOI: 10.1038/s41598-019-38747-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/15/2018] [Indexed: 11/09/2022] Open
Abstract
Acyl carrier protein (ACP) domains act as interaction hubs within modular polyketide synthase (PKS) systems, employing specific protein-protein interactions to present acyl substrates to a series of enzyme active sites. Many domains from the multimodular PKS that generates the toxin mycolactone display an unusually high degree of sequence similarity, implying that the few sites which vary may do so for functional reasons. When domain boundaries based on prior studies were used to prepare two isolated ACP segments from this system for studies of their interaction properties, one fragment adopted the expected tertiary structure, but the other failed to fold, despite sharing a sequence identity of 49%. Secondary structure prediction uncovered a previously undetected helical region (H0) that precedes the canonical helix-bundle ACP topology in both cases. This article reports the NMR solution structures of two N-terminally extended mycolactone mACP constructs, mH0ACPa and mH0ACPb, both of which possess an additional α-helix that behaves like a rigid component of the domain. The interactions of these species with a phosphopantetheinyl transferase and a ketoreductase domain are unaffected by the presence of H0, but a shorter construct that lacks the H0 region is shown to be substantially less thermostable than mH0ACPb. Bioinformatics analysis suggests that the extended H0-ACP motif is present in 98% of type I cis-acyltransferase PKS chain-extension modules. The polypeptide linker that connects an H0-ACP motif to the preceding domain must therefore be ~12 residues shorter than previously thought, imposing strict limits on ACP-mediated substrate delivery within and between PKS modules.
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Affiliation(s)
- Luisa Moretto
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Smålandsgatan-24, 392 34, Kalmar, Sweden
| | - Rachel Heylen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Natalie Holroyd
- Department of Medical Physics and Bioengineering, University College London, London, WC1E 6BT, UK
| | - Steven Vance
- Crescendo Biologics Ltd, Meditrina Building 260, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - R William Broadhurst
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
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22
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Wright CM, Whitaker RH, Onuiri JE, Blackburn T, McGarity S, Bjornsti MA, Placzek WJ. UBC9 Mutant Reveals the Impact of Protein Dynamics on Substrate Selectivity and SUMO Chain Linkages. Biochemistry 2019; 58:621-632. [PMID: 30574775 DOI: 10.1021/acs.biochem.8b01045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
SUMO, a conserved ubiquitin-like protein, is conjugated to a multitude of cellular proteins to maintain genomic integrity and resist genotoxic stress. Studies of the SUMO E2 conjugating enzyme mutant, UBC9P123L, suggested that altered substrate specificity enhances cell sensitivity to DNA damaging agents. Using nuclear magnetic resonance chemical shift studies, we confirm that the mutation does not alter the core globular fold of UBC9, while 15N relaxation measurements demonstrate mutant-induced stabilization of distinct chemical states in residues near the active site cysteine and substrate recognition motifs. We further demonstrate that the P123L substitution induces a switch from the preferential addition of SUMO to lysine residues in unstructured sites to acceptor lysines embedded in secondary structures, thereby also inducing alterations in SUMO chain linkages. Our results provide new insights regarding the impact that structural dynamics of UBC9 have on substrate selection and specifically SUMO chain formation. These findings highlight the potential contribution of nonconsensus SUMO targets and/or alternative SUMO chain linkages on DNA damage response and chemotherapeutic sensitivity.
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23
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Yoo S, Lee S, Park CJ. Backbone Dynamics and Model-Free Analysis of the RecQ C-Terminal Domain of Bloom Syndrome Protein. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Sooji Yoo
- Department of Chemistry; Gwangju Institute of Science and Technology; Gwangju 61005 Korea
| | - Sungjin Lee
- Department of Chemistry; Gwangju Institute of Science and Technology; Gwangju 61005 Korea
| | - Chin-Ju Park
- Department of Chemistry; Gwangju Institute of Science and Technology; Gwangju 61005 Korea
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24
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Morimoto D, Walinda E, Iwakawa N, Nishizawa M, Kawata Y, Yamamoto A, Shirakawa M, Scheler U, Sugase K. High-Sensitivity Rheo-NMR Spectroscopy for Protein Studies. Anal Chem 2017; 89:7286-7290. [PMID: 28665116 DOI: 10.1021/acs.analchem.7b01816] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Shear stress can induce structural deformation of proteins, which might result in aggregate formation. Rheo-NMR spectroscopy has the potential to monitor structural changes in proteins under shear stress at the atomic level; however, existing Rheo-NMR methodologies have insufficient sensitivity to probe protein structure and dynamics. Here we present a simple and versatile approach to Rheo-NMR, which maximizes sensitivity by using a spectrometer equipped with a cryogenic probe. As a result, the sensitivity of the instrument ranks highest among the Rheo-NMR spectrometers reported so far. We demonstrate that the newly developed Rheo-NMR instrument can acquire high-quality relaxation data for a protein under shear stress and can trace structural changes in a protein during fibril formation in real time. The described approach will facilitate rheological studies on protein structural deformation, thereby aiding a physical understanding of shear-induced amyloid fibril formation.
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Affiliation(s)
- Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura , Nishikyo-ku, Kyoto 615-8510, Japan
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho , Sakyo-ku, Kyoto 606-8501, Japan
| | - Naoto Iwakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura , Nishikyo-ku, Kyoto 615-8510, Japan
| | - Mayu Nishizawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura , Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yasushi Kawata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University , 4-101 Koyama-cho Minami, Tottori 680-8552, Japan
| | - Akihiko Yamamoto
- Bruker BioSpin K.K. , 3-9 Moriya-cho, Kanagawa-ku, Yokohama, Kanagawa 221-0022, Japan
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura , Nishikyo-ku, Kyoto 615-8510, Japan
| | - Ulrich Scheler
- Leibniz-Institut für Polymerforschung Dresden e.V. , Hohe Strasse 6, D-01069 Dresden, Germany
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura , Nishikyo-ku, Kyoto 615-8510, Japan
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25
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Feilen LP, Haubrich K, Strecker P, Probst S, Eggert S, Stier G, Sinning I, Konietzko U, Kins S, Simon B, Wild K. Fe65-PTB2 Dimerization Mimics Fe65-APP Interaction. Front Mol Neurosci 2017; 10:140. [PMID: 28553201 PMCID: PMC5425604 DOI: 10.3389/fnmol.2017.00140] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/25/2017] [Indexed: 01/21/2023] Open
Abstract
Physiological function and pathology of the Alzheimer’s disease causing amyloid precursor protein (APP) are correlated with its cytosolic adaptor Fe65 encompassing a WW and two phosphotyrosine-binding domains (PTBs). The C-terminal Fe65-PTB2 binds a large portion of the APP intracellular domain (AICD) including the GYENPTY internalization sequence fingerprint. AICD binding to Fe65-PTB2 opens an intra-molecular interaction causing a structural change and altering Fe65 activity. Here we show that in the absence of the AICD, Fe65-PTB2 forms a homodimer in solution and determine its crystal structure at 2.6 Å resolution. Dimerization involves the unwinding of a C-terminal α-helix that mimics binding of the AICD internalization sequence, thus shielding the hydrophobic binding pocket. Specific dimer formation is validated by nuclear magnetic resonance (NMR) techniques and cell-based analyses reveal that Fe65-PTB2 together with the WW domain are necessary and sufficient for dimerization. Together, our data demonstrate that Fe65 dimerizes via its APP interaction site, suggesting that besides intra- also intermolecular interactions between Fe65 molecules contribute to homeostatic regulation of APP mediated signaling.
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Affiliation(s)
- Lukas P Feilen
- Heidelberg University Biochemistry Center (BZH), University of HeidelbergHeidelberg, Germany
| | - Kevin Haubrich
- Heidelberg University Biochemistry Center (BZH), University of HeidelbergHeidelberg, Germany.,European Molecular Biology Laboratory (EMBL), Structural and Computational BiologyHeidelberg, Germany
| | - Paul Strecker
- Division of Human Biology and Human Genetics, University of KaiserslauternKaiserslautern, Germany
| | - Sabine Probst
- Institute for Regenerative Medicine (IREM), University of ZurichZurich, Switzerland
| | - Simone Eggert
- Division of Human Biology and Human Genetics, University of KaiserslauternKaiserslautern, Germany
| | - Gunter Stier
- Heidelberg University Biochemistry Center (BZH), University of HeidelbergHeidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), University of HeidelbergHeidelberg, Germany
| | - Uwe Konietzko
- Institute for Regenerative Medicine (IREM), University of ZurichZurich, Switzerland
| | - Stefan Kins
- Division of Human Biology and Human Genetics, University of KaiserslauternKaiserslautern, Germany
| | - Bernd Simon
- European Molecular Biology Laboratory (EMBL), Structural and Computational BiologyHeidelberg, Germany
| | - Klemens Wild
- Heidelberg University Biochemistry Center (BZH), University of HeidelbergHeidelberg, Germany
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26
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Gonzalez GM, Hardwick SW, Maslen SL, Skehel JM, Holmqvist E, Vogel J, Bateman A, Luisi BF, Broadhurst RW. Structure of the Escherichia coli ProQ RNA-binding protein. RNA (NEW YORK, N.Y.) 2017; 23:696-711. [PMID: 28193673 PMCID: PMC5393179 DOI: 10.1261/rna.060343.116] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 02/03/2017] [Indexed: 05/20/2023]
Abstract
The protein ProQ has recently been identified as a global small noncoding RNA-binding protein in Salmonella, and a similar role is anticipated for its numerous homologs in divergent bacterial species. We report the solution structure of Escherichia coli ProQ, revealing an N-terminal FinO-like domain, a C-terminal domain that unexpectedly has a Tudor domain fold commonly found in eukaryotes, and an elongated bridging intradomain linker that is flexible but nonetheless incompressible. Structure-based sequence analysis suggests that the Tudor domain was acquired through horizontal gene transfer and gene fusion to the ancestral FinO-like domain. Through a combination of biochemical and biophysical approaches, we have mapped putative RNA-binding surfaces on all three domains of ProQ and modeled the protein's conformation in the apo and RNA-bound forms. Taken together, these data suggest how the FinO, Tudor, and linker domains of ProQ cooperate to recognize complex RNA structures and serve to promote RNA-mediated regulation.
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Affiliation(s)
- Grecia M Gonzalez
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Steven W Hardwick
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Sarah L Maslen
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - J Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Erik Holmqvist
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, 75124 Uppsala, Sweden
| | - Jörg Vogel
- RNA Biology Group, Institute of Molecular Infection Biology, University of Würzburg, D-97080 Wurzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), University of Würzburg, D-97080 Wurzburg, Germany
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - R William Broadhurst
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
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27
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Goodrich AC, Meyers DJ, Frueh DP. Molecular impact of covalent modifications on nonribosomal peptide synthetase carrier protein communication. J Biol Chem 2017; 292:10002-10013. [PMID: 28455448 DOI: 10.1074/jbc.m116.766220] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 04/27/2017] [Indexed: 11/06/2022] Open
Abstract
Nonribosomal peptide synthesis involves the interplay between covalent protein modifications, conformational fluctuations, catalysis, and transient protein-protein interactions. Delineating the mechanisms involved in orchestrating these various processes will deepen our understanding of domain-domain communication in nonribosomal peptide synthetases (NRPSs) and lay the groundwork for the rational reengineering of NRPSs by swapping domains handling different substrates to generate novel natural products. Although many structural and biochemical studies of NRPSs exist, few studies have focused on the energetics and dynamics governing the interactions in these systems. Here, we present detailed binding studies of an adenylation domain and its partner carrier protein in apo-, holo-, and substrate-loaded forms. Results from fluorescence anisotropy, isothermal titration calorimetry, and NMR titrations indicated that covalent modifications to a carrier protein modulate domain communication, suggesting that chemical modifications to carrier proteins during NRPS synthesis may impart directionality to sequential NRPS domain interactions. Comparison of the structure and dynamics of an apo-aryl carrier protein with those of its modified forms revealed structural fluctuations induced by post-translational modifications and mediated by modulations of protein dynamics. The results provide a comprehensive molecular description of a carrier protein throughout its life cycle and demonstrate how a network of dynamic residues can propagate the molecular impact of chemical modifications throughout a protein and influence its affinity toward partner domains.
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Affiliation(s)
| | - David J Meyers
- the Department of Pharmacology and Molecular Sciences Synthetic Core Facility, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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28
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Harden BJ, Frueh DP. Molecular Cross-Talk between Nonribosomal Peptide Synthetase Carrier Proteins and Unstructured Linker Regions. Chembiochem 2017; 18:629-632. [PMID: 28120469 PMCID: PMC5380562 DOI: 10.1002/cbic.201700030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Indexed: 11/08/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) employ multiple domains separated by linker regions to incorporate substrates into natural products. During synthesis, substrates are covalently tethered to carrier proteins that translocate between catalytic partner domains. The molecular parameters that govern translocation and associated linker remodeling remain unknown. Here, we used NMR to characterize the structure, dynamics, and invisible states of a peptidyl carrier protein flanked by its linkers. We showed that the N-terminal linker stabilizes and interacts with the protein core while modulating dynamics at specific sites involved in post-translational modifications and/or domain interactions. The results detail the molecular communication between peptidyl carrier proteins and their linkers and could guide efforts in engineering NRPSs to obtain new pharmaceuticals.
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Affiliation(s)
- Bradley J. Harden
- Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205
| | - Dominique P. Frueh
- Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205
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29
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Chen PC, Hologne M, Walker O. Computing the Rotational Diffusion of Biomolecules via Molecular Dynamics Simulation and Quaternion Orientations. J Phys Chem B 2017; 121:1812-1823. [DOI: 10.1021/acs.jpcb.6b11703] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Po-chia Chen
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Maggy Hologne
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Olivier Walker
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
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30
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Ravera E, Sgheri L, Parigi G, Luchinat C. A critical assessment of methods to recover information from averaged data. Phys Chem Chem Phys 2017; 18:5686-701. [PMID: 26565805 DOI: 10.1039/c5cp04077a] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Conformational heterogeneity is key to the function of many biomacromolecules, but only a few groups have tried to characterize it until recently. Now, thanks to the increased throughput of experimental data and the increased computational power, the problem of the characterization of protein structural variability has become more and more popular. Several groups have devoted their efforts in trying to create quantitative, reliable and accurate protocols for extracting such information from averaged data. We analyze here different approaches, discussing strengths and weaknesses of each. All approaches can roughly be clustered into two groups: those satisfying the maximum entropy principle and those recovering ensembles composed of a restricted number of molecular conformations. In the first case, the solution focuses on the features that are common to all the infinite solutions satisfying the experimental data; in the second case, the reconstructed ensemble shows the conformational regions where a large probability can be placed. The upper limits for conformational probabilities (MaxOcc) can also be calculated. We also give an overview of the mainstream experimental observables, with considerations on the assumptions underlying their usage.
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Affiliation(s)
- Enrico Ravera
- Center for Magnetic Resonance (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.
| | - Luca Sgheri
- Istituto per le Applicazioni del Calcolo, Sezione di Firenze, CNR, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.
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31
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Ubiquitylation Directly Induces Fold Destabilization of Proteins. Sci Rep 2016; 6:39453. [PMID: 27991582 PMCID: PMC5172356 DOI: 10.1038/srep39453] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 11/23/2016] [Indexed: 12/24/2022] Open
Abstract
Ubiquitin is a common post-translational modifier and its conjugation is a key signal for proteolysis by the proteasome. Because the molecular mass of ubiquitin is larger than that of other modifiers such as phosphate, acetyl, or methyl groups, ubiquitylation not only influences biochemical signaling, but also may exert physical effects on its substrate proteins by increasing molecular volume and altering shape anisotropy. Here we show that ubiquitylation destabilizes the fold of two proteins, FKBP12 and FABP4, and that elongation of the conjugated ubiquitin chains further enhances this destabilization effect. Moreover, NMR relaxation analysis shows that ubiquitylation induces characteristic structural fluctuations in the backbone of both proteins. These results suggest that the ubiquitylation-driven structural fluctuations lead to fold destabilization of its substrate proteins. Thus, physical destabilization by ubiquitylation may facilitate protein degradation by the proteasome.
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32
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Kilpatrick AM, Honts JE, Sleister HM, Fowler CA. Solution NMR structures of the C-domain of Tetrahymena cytoskeletal protein Tcb2 reveal distinct calcium-induced structural rearrangements. Proteins 2016; 84:1748-1756. [PMID: 27488393 DOI: 10.1002/prot.25111] [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: 04/28/2016] [Revised: 07/08/2016] [Accepted: 07/25/2016] [Indexed: 01/31/2023]
Abstract
Tcb2 is a calcium-binding protein that localizes to the membrane-associated skeleton of the ciliated protozoan Tetrahymena thermophila with hypothesized roles in ciliary movement, cell cortex signaling, and pronuclear exchange. Tcb2 has also been implicated in a unique calcium-triggered, ATP-independent type of contractility exhibited by filamentous networks isolated from the Tetrahymena cytoskeleton. To gain insight into Tcb2's structure-function relationship and contractile properties, we determined solution NMR structures of its C-terminal domain in the calcium-free and calcium-bound states. The overall architecture is similar to other calcium-binding proteins, with paired EF-hand calcium-binding motifs. Comparison of the two structures reveals that Tcb2-C's calcium-induced conformational transition differs from the prototypical calcium sensor calmodulin, suggesting that the two proteins play distinct functional roles in Tetrahymena and likely have different mechanisms of target recognition. Future studies of the full-length protein and the identification of Tcb2 cellular targets will help establish the molecular basis of Tcb2 function and its unique contractile properties. Proteins 2016; 84:1748-1756. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Adina M Kilpatrick
- Department of Physics and Astronomy, Drake University, Des Moines, Iowa, 50311.
| | - Jerry E Honts
- Department, of Biology, Drake University, Des Moines, Iowa, 50311
| | - Heidi M Sleister
- Department, of Biology, Drake University, Des Moines, Iowa, 50311
| | - C Andrew Fowler
- Roy J. and Lucille A. Carver College of Medicine NMR Facility, University of Iowa, Iowa City, Iowa, 52242
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33
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Castañeda CA, Chaturvedi A, Camara CM, Curtis JE, Krueger S, Fushman D. Linkage-specific conformational ensembles of non-canonical polyubiquitin chains. Phys Chem Chem Phys 2016; 18:5771-88. [PMID: 26422168 PMCID: PMC4758893 DOI: 10.1039/c5cp04601g] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Polyubiquitination is a critical protein post-translational modification involved in a variety of processes in eukaryotic cells. The molecular basis for selective recognition of the polyubiquitin signals by cellular receptors is determined by the conformations polyubiquitin chains adopt; this has been demonstrated for K48- and K63-linked chains. Recent studies of the so-called non-canonical chains (linked via K6, K11, K27, K29, or K33) suggest they play important regulatory roles in growth, development, and immune system pathways, but biophysical studies are needed to elucidate the physical/structural basis of their interactions with receptors. A first step towards this goal is characterization of the conformations these chains adopt in solution. We assembled diubiquitins (Ub2) comprised of every lysine linkage. Using solution NMR measurements, small-angle neutron scattering (SANS), and in silico ensemble generation, we determined population-weighted conformational ensembles that shed light on the structure and dynamics of the non-canonical polyubiquitin chains. We found that polyubiquitin is conformationally heterogeneous, and each chain type exhibits unique conformational ensembles. For example, K6-Ub2 and K11-Ub2 (at physiological salt concentration) are in dynamic equilibrium between at least two conformers, where one exhibits a unique Ub/Ub interface, distinct from that observed in K48-Ub2 but similar to crystal structures of these chains. Conformers for K29-Ub2 and K33-Ub2 resemble recent crystal structures in the ligand-bound state. Remarkably, a number of diubiquitins adopt conformers similar to K48-Ub2 or K63-Ub2, suggesting potential overlap of biological function among different lysine linkages. These studies highlight the potential power of determining function from elucidation of conformational states.
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Affiliation(s)
- Carlos A Castañeda
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA.
| | - Apurva Chaturvedi
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA.
| | - Christina M Camara
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA.
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899-8562, USA
| | - Susan Krueger
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899-8562, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA.
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34
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Goodrich AC, Harden BJ, Frueh DP. Solution Structure of a Nonribosomal Peptide Synthetase Carrier Protein Loaded with Its Substrate Reveals Transient, Well-Defined Contacts. J Am Chem Soc 2015; 137:12100-9. [PMID: 26334259 DOI: 10.1021/jacs.5b07772] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are microbial enzymes that produce a wealth of important natural products by condensing substrates in an assembly line manner. The proper sequence of substrates is obtained by tethering them to phosphopantetheinyl arms of holo carrier proteins (CPs) via a thioester bond. CPs in holo and substrate-loaded forms visit NRPS catalytic domains in a series of transient interactions. A lack of structural information on substrate-loaded carrier proteins has hindered our understanding of NRPS synthesis. Here, we present the first structure of an NRPS aryl carrier protein loaded with its substrate via a native thioester bond, together with the structure of its holo form. We also present the first quantification of NRPS CP backbone dynamics. Our results indicate that prosthetic moieties in both holo and loaded forms are in contact with the protein core, but they also sample states in which they are disordered and extend in solution. We observe that substrate loading induces a large conformational change in the phosphopantetheinyl arm, thereby modulating surfaces accessible for binding to other domains. Our results are discussed in the context of NRPS domain interactions.
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Affiliation(s)
- Andrew C Goodrich
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine , Hunterian 701, 725 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Bradley J Harden
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine , Hunterian 701, 725 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Dominique P Frueh
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine , Hunterian 701, 725 North Wolfe Street, Baltimore, Maryland 21205, United States
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35
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Simon B, Masiewicz P, Ephrussi A, Carlomagno T. The structure of the SOLE element of oskar mRNA. RNA (NEW YORK, N.Y.) 2015; 21:1444-53. [PMID: 26089324 PMCID: PMC4509934 DOI: 10.1261/rna.049601.115] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/29/2015] [Indexed: 05/23/2023]
Abstract
mRNA localization by active transport is a regulated process that requires association of mRNPs with protein motors for transport along either the microtubule or the actin cytoskeleton. oskar mRNA localization at the posterior pole of the Drosophila oocyte requires a specific mRNA sequence, termed the SOLE, which comprises nucleotides of both exon 1 and exon 2 and is assembled upon splicing. The SOLE folds into a stem-loop structure. Both SOLE RNA and the exon junction complex (EJC) are required for oskar mRNA transport along the microtubules by kinesin. The SOLE RNA likely constitutes a recognition element for a yet unknown protein, which either belongs to the EJC or functions as a bridge between the EJC and the mRNA. Here, we determine the solution structure of the SOLE RNA by Nuclear Magnetic Resonance spectroscopy. We show that the SOLE forms a continuous helical structure, including a few noncanonical base pairs, capped by a pentanucleotide loop. The helix displays a widened major groove, which could accommodate a protein partner. In addition, the apical helical segment undergoes complex dynamics, with potential functional significance.
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Affiliation(s)
- Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, D-69117, Germany
| | - Pawel Masiewicz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, D-69117, Germany
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, D-69117, Germany
| | - Teresa Carlomagno
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, D-69117, Germany Helmholtz Zentrum für Infektionsforschung, Braunschweig, D-38124, Germany
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36
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Simon B, Masiewicz P, Ephrussi A, Carlomagno T. The structure of the SOLE element of oskar mRNA. RNA (NEW YORK, N.Y.) 2015; 21:1444-1453. [PMID: 26089324 DOI: 10.1261/rna.049601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/29/2015] [Indexed: 05/23/2023]
Abstract
mRNA localization by active transport is a regulated process that requires association of mRNPs with protein motors for transport along either the microtubule or the actin cytoskeleton. oskar mRNA localization at the posterior pole of the Drosophila oocyte requires a specific mRNA sequence, termed the SOLE, which comprises nucleotides of both exon 1 and exon 2 and is assembled upon splicing. The SOLE folds into a stem-loop structure. Both SOLE RNA and the exon junction complex (EJC) are required for oskar mRNA transport along the microtubules by kinesin. The SOLE RNA likely constitutes a recognition element for a yet unknown protein, which either belongs to the EJC or functions as a bridge between the EJC and the mRNA. Here, we determine the solution structure of the SOLE RNA by Nuclear Magnetic Resonance spectroscopy. We show that the SOLE forms a continuous helical structure, including a few noncanonical base pairs, capped by a pentanucleotide loop. The helix displays a widened major groove, which could accommodate a protein partner. In addition, the apical helical segment undergoes complex dynamics, with potential functional significance.
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Affiliation(s)
- Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, D-69117, Germany
| | - Pawel Masiewicz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, D-69117, Germany
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, D-69117, Germany
| | - Teresa Carlomagno
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, D-69117, Germany Helmholtz Zentrum für Infektionsforschung, Braunschweig, D-38124, Germany
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37
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Giambaşu GM, York DM, Case DA. Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin. RNA (NEW YORK, N.Y.) 2015; 21:963-74. [PMID: 25805858 PMCID: PMC4408802 DOI: 10.1261/rna.047357.114] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 01/17/2015] [Indexed: 05/16/2023]
Abstract
RNA hairpins are widespread and very stable motifs that contribute decisively to RNA folding and biological function. The GTP1G2C3A4C5U6U7C8G9G10U11G12C13C14 construct (with a central UUCG tetraloop) has been extensively studied by solution NMR, and offers and excellent opportunity to evaluate the structure and dynamical description afforded by molecular dynamics (MD) simulations. Here, we compare average structural parameters and NMR relaxation rates estimated from a series of multiple independent explicit solvent MD simulations using the two most recent RNA AMBER force fields (ff99 and ff10). Predicted overall tumbling times are ∼20% faster than those inferred from analysis of NMR data and follow the same trend when temperature and ionic strength is varied. The Watson-Crick stem and the "canonical" UUCG loop structure are maintained in most simulations including the characteristic syn conformation along the glycosidic bond of G9, although some key hydrogen bonds in the loop are partially disrupted. Our analysis pinpoints G9-G10 backbone conformations as a locus of discrepancies between experiment and simulation. In general the results for the more recent force-field parameters (ff10) are closer to experiment than those for the older ones (ff99). This work provides a comprehensive and detailed comparison of state of the art MD simulations against a wide variety of solution NMR measurements.
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Affiliation(s)
- George M Giambaşu
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Darrin M York
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - David A Case
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
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38
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Wiedemann C, Bellstedt P, Görlach M. PREdator: a python based GUI for data analysis, evaluation and fitting. SOURCE CODE FOR BIOLOGY AND MEDICINE 2014. [PMCID: PMC4179214 DOI: 10.1186/1751-0473-9-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The analysis of a series of experimental data is an essential procedure in virtually every field of research. The information contained in the data is extracted by fitting the experimental data to a mathematical model. The type of the mathematical model (linear, exponential, logarithmic, etc.) reflects the physical laws that underlie the experimental data. Here, we aim to provide a readily accessible, user-friendly python script for data analysis, evaluation and fitting. PREdator is presented at the example of NMR paramagnetic relaxation enhancement analysis.
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Richman DE, Majumdar A, García-Moreno E B. pH dependence of conformational fluctuations of the protein backbone. Proteins 2014; 82:3132-43. [PMID: 25137073 DOI: 10.1002/prot.24673] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 06/25/2014] [Accepted: 08/04/2014] [Indexed: 01/08/2023]
Abstract
Proton binding equilibria (pK(a) values) of ionizable groups in proteins are exquisitely sensitive to their microenvironments. Apparent pK(a) values measured for individual ionizable residues with NMR spectroscopy are actually population-weighted averages of the pK(a) in different conformational microstates. NMR spectroscopy experiments with staphylococcal nuclease were used to test the hypothesis that pK(a) values of surface Glu and Asp residues are affected by pH-sensitive fluctuations of the backbone between folded and locally unfolded conformations. (15)N spin relaxation studies showed that as the pH decreases from the neutral into the acidic range the amplitudes of backbone fluctuations in the ps-ns timescale increase near carboxylic residues. Hydrogen exchange experiments suggested that backbone conformational fluctuations promoted by decreasing pH also reflect slower local or sub-global unfolding near carboxylic groups. This study has implications for structure-based pKa calculations: (1) The timescale of the backbone's response to ionization events in proteins can range from ps to ms, and even longer; (2) pH-sensitive fluctuations of the backbone can be localized to both the segment the ionizable residue is attached to or the one that occludes the ionizable group; (3) Structural perturbations are not necessarily propagated through Coulomb interactions; instead, local fluctuations appear to be coupled through the co-operativity inherent to elements of secondary structure and to networks of hydrogen bonds. These results are consistent with the idea that local conformational fluctuations and stabilities are important determinants of apparent pK(a) values of ionizable residues in proteins.
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Affiliation(s)
- Daniel E Richman
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland, 21218
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Göbl C, Madl T, Simon B, Sattler M. NMR approaches for structural analysis of multidomain proteins and complexes in solution. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 80:26-63. [PMID: 24924266 DOI: 10.1016/j.pnmrs.2014.05.003] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/14/2014] [Indexed: 05/22/2023]
Abstract
NMR spectroscopy is a key method for studying the structure and dynamics of (large) multidomain proteins and complexes in solution. It plays a unique role in integrated structural biology approaches as especially information about conformational dynamics can be readily obtained at residue resolution. Here, we review NMR techniques for such studies focusing on state-of-the-art tools and practical aspects. An efficient approach for determining the quaternary structure of multidomain complexes starts from the structures of individual domains or subunits. The arrangement of the domains/subunits within the complex is then defined based on NMR measurements that provide information about the domain interfaces combined with (long-range) distance and orientational restraints. Aspects discussed include sample preparation, specific isotope labeling and spin labeling; determination of binding interfaces and domain/subunit arrangements from chemical shift perturbations (CSP), nuclear Overhauser effects (NOEs), isotope editing/filtering, cross-saturation, and differential line broadening; and based on paramagnetic relaxation enhancements (PRE) using covalent and soluble spin labels. Finally, the utility of complementary methods such as small-angle X-ray or neutron scattering (SAXS, SANS), electron paramagnetic resonance (EPR) or fluorescence spectroscopy techniques is discussed. The applications of NMR techniques are illustrated with studies of challenging (high molecular weight) protein complexes.
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Affiliation(s)
- Christoph Göbl
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany
| | - Tobias Madl
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Molecular Biology, University of Graz, Graz, Austria.
| | - Bernd Simon
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Michael Sattler
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.
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