151
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Brutscher B, Felli IC, Gil-Caballero S, Hošek T, Kümmerle R, Piai A, Pierattelli R, Sólyom Z. NMR Methods for the Study of Instrinsically Disordered Proteins Structure, Dynamics, and Interactions: General Overview and Practical Guidelines. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:49-122. [PMID: 26387100 DOI: 10.1007/978-3-319-20164-1_3] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Thanks to recent improvements in NMR instrumentation, pulse sequence design, and sample preparation, a panoply of new NMR tools has become available for atomic resolution characterization of intrinsically disordered proteins (IDPs) that are optimized for the particular chemical and spectroscopic properties of these molecules. A wide range of NMR observables can now be measured on increasingly complex IDPs that report on their structural and dynamic properties in isolation, as part of a larger complex, or even inside an entire living cell. Herein we present basic NMR concepts, as well as optimised tools available for the study of IDPs in solution. In particular, the following sections are discussed hereafter: a short introduction to NMR spectroscopy and instrumentation (Sect. 3.1), the effect of order and disorder on NMR observables (Sect. 3.2), particular challenges and bottlenecks for NMR studies of IDPs (Sect. 3.3), 2D HN and CON NMR experiments: the fingerprint of an IDP (Sect. 3.4), tools for overcoming major bottlenecks of IDP NMR studies (Sect. 3.5), 13C detected experiments (Sect. 3.6), from 2D to 3D: from simple snapshots to site-resolved characterization of IDPs (Sect. 3.7), sequential NMR assignment: 3D experiments (Sect. 3.8), high-dimensional NMR experiments (nD, with n>3) (Sect. 3.9) and conclusions and perspectives (Sect. 3.10).
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Affiliation(s)
- Bernhard Brutscher
- Institut de Biologie Structurale, Université Grenoble 1, CNRS, CEA, 71 avenue des Martyrs, 38044, Grenoble Cedex 9, France.
| | - Isabella C Felli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, 50019, Via Luigi Sacconi 6, Sesto Fiorentino, Florence, Italy.
| | | | - Tomáš Hošek
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, 50019, Via Luigi Sacconi 6, Sesto Fiorentino, Florence, Italy
| | - Rainer Kümmerle
- Bruker BioSpin AG, Industriestrasse 26, 8117, Fällanden, Switzerland
| | - Alessandro Piai
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, 50019, Via Luigi Sacconi 6, Sesto Fiorentino, Florence, Italy
| | - Roberta Pierattelli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, 50019, Via Luigi Sacconi 6, Sesto Fiorentino, Florence, Italy.
| | - Zsófia Sólyom
- Institut de Biologie Structurale, Université Grenoble 1, CNRS, CEA, 71 avenue des Martyrs, 38044, Grenoble Cedex 9, France
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152
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Protein structural information derived from NMR chemical shift with the neural network program TALOS-N. Methods Mol Biol 2015; 1260:17-32. [PMID: 25502373 DOI: 10.1007/978-1-4939-2239-0_2] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Chemical shifts are obtained at the first stage of any protein structural study by NMR spectroscopy. Chemical shifts are known to be impacted by a wide range of structural factors, and the artificial neural network based TALOS-N program has been trained to extract backbone and side-chain torsion angles from (1)H, (15)N, and (13)C shifts. The program is quite robust and typically yields backbone torsion angles for more than 90 % of the residues and side-chain χ 1 rotamer information for about half of these, in addition to reliably predicting secondary structure. The use of TALOS-N is illustrated for the protein DinI, and torsion angles obtained by TALOS-N analysis from the measured chemical shifts of its backbone and (13)C(β) nuclei are compared to those seen in a prior, experimentally determined structure. The program is also particularly useful for generating torsion angle restraints, which then can be used during standard NMR protein structure calculations.
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153
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Skinner SP, Goult BT, Fogh RH, Boucher W, Stevens TJ, Laue ED, Vuister GW. Structure calculation, refinement and validation using CcpNmr Analysis. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:154-61. [PMID: 25615869 PMCID: PMC4304695 DOI: 10.1107/s1399004714026662] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 12/04/2014] [Indexed: 02/02/2023]
Abstract
CcpNmr Analysis provides a streamlined pipeline for both NMR chemical shift assignment and structure determination of biological macromolecules. In addition, it encompasses tools to analyse the many additional experiments that make NMR such a pivotal technique for research into complex biological questions. This report describes how CcpNmr Analysis can seamlessly link together all of the tasks in the NMR structure-determination process. It details each of the stages from generating NMR restraints [distance, dihedral, hydrogen bonds and residual dipolar couplings (RDCs)], exporting these to and subsequently re-importing them from structure-calculation software (such as the programs CYANA or ARIA) and analysing and validating the results obtained from the structure calculation to, ultimately, the streamlined deposition of the completed assignments and the refined ensemble of structures into the PDBe repository. Until recently, such solution-structure determination by NMR has been quite a laborious task, requiring multiple stages and programs. However, with the new enhancements to CcpNmr Analysis described here, this process is now much more intuitive and efficient and less error-prone.
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Affiliation(s)
- Simon P. Skinner
- Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
| | - Benjamin T. Goult
- Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
| | - Rasmus H. Fogh
- Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, England
| | - Wayne Boucher
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, England
| | - Tim J. Stevens
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
| | - Ernest D. Laue
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, England
| | - Geerten W. Vuister
- Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
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154
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Karp JM, Erylimaz E, Cowburn D. Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2015; 61:35-45. [PMID: 25416617 PMCID: PMC4715900 DOI: 10.1007/s10858-014-9879-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 11/17/2014] [Indexed: 06/04/2023]
Abstract
There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not consistently improve prediction accuracy over use of a static X-ray crystal structure. This appears to result from the complex conformational ensemble of the disordered protein segments. We show that using accelerated molecular dynamics (aMD) simulations improves chemical shift prediction, suggesting that methods which better sample the conformational ensemble like aMD are more appropriate tools for use in chemical shift prediction for proteins with disordered regions. Moreover, our study suggests that data accurately reflecting protein dynamics must be used as input for chemical shift prediction in order to correctly predict chemical shifts in systems with disorder.
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Affiliation(s)
- Jerome M. Karp
- Department of Biochemistry, Albert Einstein College of, Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Ertan Erylimaz
- Department of Biochemistry, Albert Einstein College of, Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of, Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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155
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Chen YC, Cheng CS, Tjong SC, Yin HS, Sue SC. Case study of hydrogen bonding in a hydrophobic cavity. J Phys Chem B 2014; 118:14602-11. [PMID: 25412145 DOI: 10.1021/jp5097053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein internal hydrogen bonds and hydrophobicity determine protein folding and structure stabilization, and the introduction of a hydrogen bond has been believed to represent a better interaction for consolidating protein structure. We observed an alternative example for chicken IL-1β. The native IL-1β contains a hydrogen bond between the Y157 side-chain OηH and I133 backbone CO, whereby the substitution from Tyr to Phe abolishes the connection and the mutant without the hydrogen bond is more stable. An attempt to explain the energetic view of the presence of the hydrogen bond fails when only considering the nearly identical X-ray structures. Here, we resolve the mechanism by monitoring the protein backbone dynamics and interior hydrogen bond network. IL-1β contains a hydrophobic cavity in the protein interior, and Y157 is one of the surrounding residues. The Y157 OηH group introduces an unfavorable energy in the hydrophobic cavity, therefore sequestering itself by forming a hydrogen bond with the proximate residue I133. The hydrogen bonding confines Y157 orientation but exerts a force to disrupt the hydrogen bond network surrounding the cavity. The effect propagates over the entire protein and reduces the stability, as reflected in the protein backbone dynamics observed by an NMR hydrogen-deuterium (H/D) exchange experiment. We describe the particular case in which a hydrogen bond does not necessarily confer enhanced protein stability while the disruption of hydrophobicity must be integrally considered.
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Affiliation(s)
- Yi-Chen Chen
- Institute of Bioinformatics and Structural Biology and Department of Life Science, National Tsing Hua University , Hsinchu 30013, Taiwan
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156
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Long D, Sekhar A, Kay LE. Triple resonance-based ¹³C(α) and ¹³C(β) CEST experiments for studies of ms timescale dynamics in proteins. JOURNAL OF BIOMOLECULAR NMR 2014; 60:203-208. [PMID: 25348177 DOI: 10.1007/s10858-014-9868-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/13/2014] [Indexed: 06/04/2023]
Abstract
A pair of triple resonance based CEST pulse schemes are presented for measuring ¹³C(α) and ¹³C(β) chemical shifts of sparsely populated and transiently formed conformers that are invisible to traditional NMR experiments. CEST profiles containing dips at resonance positions of ¹³C(α) or ¹³C(β) spins of major (ground) and minor (excited) conformers are obtained in a pseudo 3rd dimension that is generated by quantifying modulations of cross peaks in ¹⁵N, ¹H(N) correlation spectra. An application to the folding reaction of a G48A mutant of the Fyn SH3 domain is presented, illustrating and validating the methodology.
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Affiliation(s)
- Dong Long
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, ON, M5S 1A8, Canada
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157
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Solanas C, Herrero S, Dasari A, Plaza GR, Llorca J, Pérez-Rigueiro J, Elices M, Guinea GV. Insights into the production and characterization of electrospun fibers from regenerated silk fibroin. Eur Polym J 2014. [DOI: 10.1016/j.eurpolymj.2014.08.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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158
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Molecular insights into the interaction between Plasmodium falciparum apical membrane antigen 1 and an invasion-inhibitory peptide. PLoS One 2014; 9:e109674. [PMID: 25343578 PMCID: PMC4208761 DOI: 10.1371/journal.pone.0109674] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 09/03/2014] [Indexed: 11/28/2022] Open
Abstract
Apical membrane antigen 1 (AMA1) of the human malaria parasite Plasmodium falciparum has been implicated in invasion of the host erythrocyte. It interacts with malarial rhoptry neck (RON) proteins in the moving junction that forms between the host cell and the invading parasite. Agents that block this interaction inhibit invasion and may serve as promising leads for anti-malarial drug development. The invasion-inhibitory peptide R1 binds to a hydrophobic cleft on AMA1, which is an attractive target site for small molecules that block parasite invasion. In this work, truncation and mutational analyses show that Phe5-Phe9, Phe12 and Arg15 in R1 are the most important residues for high affinity binding to AMA1. These residues interact with two well-defined binding hot spots on AMA1. Computational solvent mapping reveals that one of these hot spots is suitable for small molecule targeting. We also confirm that R1 in solution binds to AMA1 with 1∶1 stoichiometry and adopts a secondary structure consistent with the major form of R1 observed in the crystal structure of the complex. Our results provide a basis for designing high affinity inhibitors of the AMA1-RON2 interaction.
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159
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Künze G, Theisgen S, Huster D. Backbone ¹H, ¹⁵N, and ¹³C and side chain ¹³Cβ NMR chemical shift assignment of murine interleukin-10. BIOMOLECULAR NMR ASSIGNMENTS 2014; 8:375-8. [PMID: 23982919 DOI: 10.1007/s12104-013-9521-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 08/16/2013] [Indexed: 05/22/2023]
Abstract
Almost complete assignment of backbone (1)H, (13)C, (15)N and side chain (13)Cβ resonances for the immune-regulatory cytokine IL-10 is reported. The protein was overexpressed in Escherichia coli and was refolded from inclusion bodies. The point mutation C149Y was introduced to suppress incorrect disulfide bond formation and to improve protein refolding.
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Affiliation(s)
- Georg Künze
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstraße 16/18, 04107, Leipzig, Germany,
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160
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Singh H, Rao BJ, Chary KVR. ¹H, ¹³C and ¹⁵N NMR assignments of a mutant of UV inducible transcript (S55A-UVI31+) from Chlamydomonas reinhardtii. BIOMOLECULAR NMR ASSIGNMENTS 2014; 8:371-374. [PMID: 23979961 DOI: 10.1007/s12104-013-9520-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/16/2013] [Indexed: 06/02/2023]
Abstract
Almost complete sequence specific (1)H, (13)C and (15)N resonance assignments of a mutant of UV inducible transcript (S55A-UVI31+) from Chlamydomonas reinhardtii are reported, as a prelude to its structural and functional characterization. Site-directed mutagenesis of uvi31+ was carried out using complementary mutation harbouring oligonucleotides for S55A mutant. The resulting mutant was sequenced and then S55A mutant of uvi31+ cDNA were expressed in E. coli, and purification were carried out from where the protein was purified to high homogeneity. The point mutation S55A in UVI31+ results in a significant enhancement in its DNA endonuclease activity as compared to its wild type protein.
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Affiliation(s)
- Himanshu Singh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, 1, Homi Bhabha Road, Colaba, Mumbai, 400005, India
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161
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Hayat M, Iqbal N. Discriminating protein structure classes by incorporating Pseudo Average Chemical Shift to Chou's general PseAAC and Support Vector Machine. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2014; 116:184-192. [PMID: 24997484 DOI: 10.1016/j.cmpb.2014.06.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 06/09/2014] [Accepted: 06/13/2014] [Indexed: 06/03/2023]
Abstract
Proteins control all biological functions in living species. Protein structure is comprised of four major classes including all-α class, all-β class, α+β, and α/β. Each class performs different function according to their nature. Owing to the large exploration of protein sequences in the databanks, the identification of protein structure classes is difficult through conventional methods with respect to cost and time. Looking at the importance of protein structure classes, it is thus highly desirable to develop a computational model for discriminating protein structure classes with high accuracy. For this purpose, we propose a silco method by incorporating Pseudo Average Chemical Shift and Support Vector Machine. Two feature extraction schemes namely Pseudo Amino Acid Composition and Pseudo Average Chemical Shift are used to explore valuable information from protein sequences. The performance of the proposed model is assessed using four benchmark datasets 25PDB, 1189, 640 and 399 employing jackknife test. The success rates of the proposed model are 84.2%, 85.0%, 86.4%, and 89.2%, respectively on the four datasets. The empirical results reveal that the performance of our proposed model compared to existing models is promising in the literature so far and might be useful for future research.
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Affiliation(s)
- Maqsood Hayat
- Department of Computer Science, Abdul Wali Khan University Mardan, Pakistan.
| | - Nadeem Iqbal
- Department of Computer Science, Abdul Wali Khan University Mardan, Pakistan
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162
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Wiedemann C, Ohlenschläger O, Medagli B, Onesti S, Görlach M. ¹H, ¹⁵N, and ¹³C chemical shift assignments for the winged helix domains of two archeal MCM C-termini. BIOMOLECULAR NMR ASSIGNMENTS 2014; 8:357-360. [PMID: 23934138 DOI: 10.1007/s12104-013-9516-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 08/01/2013] [Indexed: 06/02/2023]
Abstract
High-fidelity replication guarantees the stable inheritance of genetic information stored in the DNA of living organisms. The minichromosome maintenance (MCM) complex functions as replicative DNA-unwinding helicase and has been identified as one key player in the replication process of archea and eukarya. Despite the availability of considerable structural information on archeal MCMs, such information was missing for their C-terminal domain. In order to obtain more detailed structural information, we assigned the NMR chemical shifts for backbone and side chain nuclei for the MCM C-terminal winged helix domains of the archeal species Methanothermobacter thermautrophicus and Sulfolobus solfataricus.
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Affiliation(s)
- Christoph Wiedemann
- Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research-Fritz Lipman Institute, Beutenbergstr. 11, 07745, Jena, Germany,
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163
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Inhibition of the human respiratory syncytial virus small hydrophobic protein and structural variations in a bicelle environment. J Virol 2014; 88:11899-914. [PMID: 25100835 DOI: 10.1128/jvi.00839-14] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The small hydrophobic (SH) protein is a 64-amino-acid polypeptide encoded by the human respiratory syncytial virus (hRSV). SH protein has a single α-helical transmembrane (TM) domain that forms pentameric ion channels. Herein, we report the first inhibitor of the SH protein channel, pyronin B, and we have mapped its binding site to a conserved surface of the RSV SH pentamer, at the C-terminal end of the transmembrane domain. The validity of the SH protein structural model used has been confirmed by using a bicellar membrane-mimicking environment. However, in bicelles the α-helical stretch of the TM domain extends up to His-51, and by comparison with previous models both His-22 and His-51 adopt an interhelical/lumenal orientation relative to the channel pore. Neither His residue was found to be essential for channel activity although His-51 protonation reduced channel activity at low pH, with His-22 adopting a more structural role. The latter results are in contrast with previous patch clamp data showing channel activation at low pH, which could not be reproduced in the present work. Overall, these results establish a solid ground for future drug development targeting this important viroporin. Importance: The human respiratory syncytial virus (hRSV) is responsible for 64 million reported cases of infection and 160,000 deaths each year. Lack of adequate antivirals fuels the search for new targets for treatment. The small hydrophobic (SH) protein is a 64-amino-acid polypeptide encoded by hRSV and other paramyxoviruses, and its absence leads to viral attenuation in vivo and early apoptosis in infected cells. SH protein forms pentameric ion channels that may constitute novel drug targets, but no inhibitor for this channel activity has been reported so far. A small-molecule inhibitor, pyronin B, can reduce SH channel activity, and its likely binding site on the SH protein channel has been identified. Black lipid membrane (BLM) experiments confirm that protonation of both histidine residues reduces stability and channel activity. These results contrast with previous patch clamp data that showed low-pH activation, which we have not been able to reproduce.
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164
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acACS: improving the prediction accuracy of protein subcellular locations and protein classification by incorporating the average chemical shifts composition. ScientificWorldJournal 2014; 2014:864135. [PMID: 25110749 PMCID: PMC4106170 DOI: 10.1155/2014/864135] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 06/15/2014] [Accepted: 06/16/2014] [Indexed: 11/17/2022] Open
Abstract
The chemical shift is sensitive to changes in the local environments and can report the structural changes. The structure information of a protein can be represented by the average chemical shifts (ACS) composition, which has been broadly applied for enhancing the prediction accuracy in protein subcellular locations and protein classification. However, different kinds of ACS composition can solve different problems. We established an online web server named acACS, which can convert secondary structure into average chemical shift and then compose the vector for representing a protein by using the algorithm of auto covariance. Our solution is easy to use and can meet the needs of users.
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165
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Kosicka I, Kristensen T, Bjerring M, Thomsen K, Scavenius C, Enghild JJ, Nielsen NC. Preparation of uniformly 13C,15N-labeled recombinant human amylin for solid-state NMR investigation. Protein Expr Purif 2014; 99:119-30. [DOI: 10.1016/j.pep.2014.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 04/01/2014] [Accepted: 04/02/2014] [Indexed: 11/29/2022]
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166
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Aoto PC, Nishimura C, Dyson HJ, Wright PE. Probing the non-native H helix translocation in apomyoglobin folding intermediates. Biochemistry 2014; 53:3767-80. [PMID: 24857522 PMCID: PMC4067146 DOI: 10.1021/bi500478m] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Apomyoglobin folds via sequential
helical intermediates that are
formed by rapid collapse of the A, B, G, and H helix regions. An equilibrium
molten globule with a similar structure is formed near pH 4. Previous
studies suggested that the folding intermediates are kinetically trapped
states in which folding is impeded by non-native packing of the G
and H helices. Fluorescence spectra of mutant proteins in which cysteine
residues were introduced at several positions in the G and H helices
show differential quenching of W14 fluorescence, providing direct
evidence of translocation of the H helix relative to helices A and
G in both the kinetic and equilibrium intermediates. Förster
resonance energy transfer measurements show that a 5-({2-[(acetyl)amino]ethyl}amino)naphthalene-1-sulfonic
acid acceptor coupled to K140C (helix H) is closer to Trp14 (helix
A) in the equilibrium molten globule than in the native state, by
a distance that is consistent with sliding of the H helix in an N-terminal
direction by approximately one helical turn. Formation of an S108C–L135C
disulfide prevents H helix translocation in the equilibrium molten
globule by locking the G and H helices into their native register.
By enforcing nativelike packing of the A, G, and H helices, the disulfide
resolves local energetic frustration and facilitates transient docking
of the E helix region onto the hydrophobic core but has only a small
effect on the refolding rate. The apomyoglobin folding landscape is
highly rugged, with several energetic bottlenecks that frustrate folding;
relief of any one of the major identified bottlenecks is insufficient
to speed progression to the transition state.
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Affiliation(s)
- Phillip C Aoto
- Department of Molecular Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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167
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Chow WY, Rajan R, Muller KH, Reid DG, Skepper JN, Wong WC, Brooks RA, Green M, Bihan D, Farndale RW, Slatter DA, Shanahan CM, Duer MJ. NMR spectroscopy of native and in vitro tissues implicates polyADP ribose in biomineralization. Science 2014; 344:742-6. [PMID: 24833391 DOI: 10.1126/science.1248167] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is useful to determine molecular structure in tissues grown in vitro only if their fidelity, relative to native tissue, can be established. Here, we use multidimensional NMR spectra of animal and in vitro model tissues as fingerprints of their respective molecular structures, allowing us to compare the intact tissues at atomic length scales. To obtain spectra from animal tissues, we developed a heavy mouse enriched by about 20% in the NMR-active isotopes carbon-13 and nitrogen-15. The resulting spectra allowed us to refine an in vitro model of developing bone and to probe its detailed structure. The identification of an unexpected molecule, poly(adenosine diphosphate ribose), that may be implicated in calcification of the bone matrix, illustrates the analytical power of this approach.
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Affiliation(s)
- W Ying Chow
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Rakesh Rajan
- Orthopaedic Research Unit, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Karin H Muller
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3DY, UK
| | - David G Reid
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Jeremy N Skepper
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3DY, UK
| | - Wai Ching Wong
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Roger A Brooks
- Orthopaedic Research Unit, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Maggie Green
- Central Biomedical Resources, University of Cambridge, School of Clinical Medicine, West Forvie Building, Forvie Site, Robinson Way, Cambridge CB2 0SZ, UK
| | - Dominique Bihan
- Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK
| | - Richard W Farndale
- Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK
| | - David A Slatter
- Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK
| | - Catherine M Shanahan
- British Heart Foundation Centre of Research Excellence, Cardiovascular Division, James Black Centre, King's College London, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Melinda J Duer
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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168
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Casu F, Duggan BM, Hennig M. The arginine-rich RNA-binding motif of HIV-1 Rev is intrinsically disordered and folds upon RRE binding. Biophys J 2014; 105:1004-17. [PMID: 23972852 DOI: 10.1016/j.bpj.2013.07.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 06/19/2013] [Accepted: 07/02/2013] [Indexed: 11/17/2022] Open
Abstract
Arginine-rich motifs (ARMs) capable of binding diverse RNA structures play critical roles in transcription, translation, RNA trafficking, and RNA packaging. The regulatory HIV-1 protein Rev is essential for viral replication and belongs to the ARM family of RNA-binding proteins. During the early stages of the HIV-1 life cycle, incompletely spliced and full-length viral mRNAs are very inefficiently recognized by the splicing machinery of the host cell and are subject to degradation in the cell nucleus. These transcripts harbor the Rev Response Element (RRE), which orchestrates the interaction with the Rev ARM and the successive Rev-dependent mRNA export pathway. Based on established criteria for predicting intrinsic disorder, such as hydropathy, combined with significant net charge, the very basic primary sequences of ARMs are expected to adopt coil-like structures. Thus, we initiated this study to investigate the conformational changes of the Rev ARM associated with RNA binding. We used multidimensional NMR and circular dichroism spectroscopy to monitor the observed structural transitions, and described the conformational landscapes using statistical ensemble and molecular-dynamics simulations. The combined spectroscopic and simulated results imply that the Rev ARM is intrinsically disordered not only as an isolated peptide but also when it is embedded into an oligomerization-deficient Rev mutant. RRE recognition triggers a crucial coil-to-helix transition employing an induced-fit mechanism.
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Affiliation(s)
- Fabio Casu
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
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169
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Singh H, Raghavan V, Shukla M, Rao BJ, Chary KVR. ¹H, ¹³C and ¹⁵N resonance assignments of S114A mutant of UVI31+ from Chlamydomonas reinhardtii. BIOMOLECULAR NMR ASSIGNMENTS 2014; 8:71-74. [PMID: 23266947 PMCID: PMC3955482 DOI: 10.1007/s12104-012-9455-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Accepted: 12/13/2012] [Indexed: 06/01/2023]
Abstract
Almost complete sequence specific (1)H, (13)C and (15)N resonance assignments of S114A mutant of UVI31+ from Chlamydomonas reinhardtii are reported. The cDNA of S114A mutant of UVI31+ was cloned from a eukaryotic green algae (C. reinhardtii) and overexpressed in E.coli from where the protein was purified to homogeneity. The point mutation S114A in UVI31+ reduces its DNA endonuclease activity substantially as compared with its wild type. As a prelude to the structural characterization of S114A mutant of UVI31+, we report here complete sequence-specific (1)H, (13)C and (15)N NMR assignments.
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Affiliation(s)
- Himanshu Singh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, 1, Homi Bhabha Road, Colaba, Mumbai, 400005 India
| | - Vandana Raghavan
- Department of Biological Sciences, Tata Institute of Fundamental Research, 1, Homi Bhabha Road, Colaba, Mumbai, 400005 India
| | - Manish Shukla
- Department of Biological Sciences, Tata Institute of Fundamental Research, 1, Homi Bhabha Road, Colaba, Mumbai, 400005 India
| | - Basuthkar J. Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, 1, Homi Bhabha Road, Colaba, Mumbai, 400005 India
| | - Kandala V. R. Chary
- Department of Chemical Sciences, Tata Institute of Fundamental Research, 1, Homi Bhabha Road, Colaba, Mumbai, 400005 India
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170
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Li Y, Surya W, Claudine S, Torres J. Structure of a conserved Golgi complex-targeting signal in coronavirus envelope proteins. J Biol Chem 2014; 289:12535-49. [PMID: 24668816 PMCID: PMC4007446 DOI: 10.1074/jbc.m114.560094] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Coronavirus envelope (CoV E) proteins are ∼100-residue polypeptides with at least one channel-forming α-helical transmembrane (TM) domain. The extramembrane C-terminal tail contains a completely conserved proline, at the center of a predicted β-coil-β motif. This hydrophobic motif has been reported to constitute a Golgi-targeting signal or a second TM domain. However, no structural data for this or other extramembrane domains in CoV E proteins is available. Herein, we show that the E protein in the severe acute respiratory syndrome virus has only one TM domain in micelles, whereas the predicted β-coil-β motif forms a short membrane-bound α-helix connected by a disordered loop to the TM domain. However, complementary results suggest that this motif is potentially poised for conformational change or in dynamic exchange with other conformations.
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Affiliation(s)
- Yan Li
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
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171
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Gupta S, Bhattacharjya S. NMR characterization of the near native and unfolded states of the PTB domain of Dok1: alternate conformations and residual clusters. PLoS One 2014; 9:e90557. [PMID: 24587391 PMCID: PMC3938774 DOI: 10.1371/journal.pone.0090557] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 02/03/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Phosphotyrosine binding (PTB) domains are critically involved in cellular signaling and diseases. PTB domains are categorized into three distinct structural classes namely IRS-like, Shc-like and Dab-like. All PTB domains consist of a core pleckstrin homology (PH) domain with additional structural elements in Shc and Dab groups. The core PH fold of the PTB domain contains a seven stranded β-sheet and a long C-terminal helix. PRINCIPAL FINDINGS In this work, the PTB domain of Dok1 protein has been characterized, by use of NMR spectroscopy, in solutions containing sub-denaturing and denaturing concentrations of urea. We find that the Dok1 PTB domain displays, at sub-denaturing concentrations of urea, alternate conformational states for residues located in the C-terminal helix and in the β5 strand of the β-sheet region. The β5 strand of PTB domain has been found to be experiencing significant chemical shift perturbations in the presence of urea. Notably, many of these residues in the helix and in the β5 strand are also involved in ligand binding. Structural and dynamical analyses at 7 M urea showed that the PTB domain is unfolded with islands of motionally restricted regions in the polypeptide chain. Further, the C-terminal helix appears to be persisted in the unfolded state of the PTB domain. By contrast, residues encompassing β-sheets, loops, and the short N-terminal helix lack any preferred secondary structures. Moreover, these residues demonstrated an intimate contact with the denaturant. SIGNIFICANCE This study implicates existence of alternate conformational states around the ligand binding pocket of the PTB domain either in the native or in the near native conditions. Further, the current study demonstrates that the C-terminal helical region of PTB domain may be considered as a potential site for the initiation of folding.
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Affiliation(s)
- Sebanti Gupta
- School of Biological Sciences, Division of Structural and Computational Biology, Nanyang Technological University, Singapore, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Division of Structural and Computational Biology, Nanyang Technological University, Singapore, Singapore
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172
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Pohl G, Asensio A, Dannenberg JJ. Capping parallel β-sheets of acetyl(Ala)6NH2 with an acetyl(Ala)5ProNH2 can arrest the growth of the sheet, suggesting a potential for curtailing amyloid growth. An ONIOM and density functional theory study. Biochemistry 2014; 53:617-23. [PMID: 24422496 PMCID: PMC3985835 DOI: 10.1021/bi401366w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present ONIOM calculations using B3LYP/d95(d,p) as the high level and AM1 as the medium level on parallel β-sheets containing four strands of Ac-AAAAAA-NH2 capped with either Ac-AAPAAA-NH2 or Ac-AAAPAA-NH2. Because Pro can form H-bonds from only one side of the peptide linkage (that containing the C═O H-bond acceptor), only one of the two Pro-containing strands can favorably add to the sheet on each side. Surprisingly, when the sheet is capped with AAPAAA-NH2 at one edge, the interaction between the cap and sheet is slightly more stabilizing than that of another all Ala strand. Breaking down the interaction enthalpies into H-bonding and distortion energies shows the favorable interaction to be due to lower distortion energies in both the strand and the four-stranded sheet. Because another strand would be inhibited for attachment to the other side of the capping (Pro-containing) strand, we suggest the possible use of Pro residues in peptides designed to arrest the growth of many amyloids.
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Affiliation(s)
- Gabor Pohl
- Department of Chemistry, City University of New York, Hunter College and the Graduate School , 695 Park Avenue, New York, New York 10065, United States
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173
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Mompeán M, Buratti E, Guarnaccia C, Brito RMM, Chakrabartty A, Baralle FE, Laurents DV. "Structural characterization of the minimal segment of TDP-43 competent for aggregation". Arch Biochem Biophys 2014; 545:53-62. [PMID: 24440310 DOI: 10.1016/j.abb.2014.01.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 12/13/2013] [Accepted: 01/07/2014] [Indexed: 12/13/2022]
Abstract
TDP-43 is a nuclear protein whose abnormal aggregates are implicated in ALS and FTLD. Recently, an Asn/Gln rich C-terminal segment of TDP-43 has been shown to produce aggregation in vitro and reproduce most of the protein's pathological hallmarks in cells, but little is known about this segment's structure. Here, CD and 2D heteronuclear NMR spectroscopies provide evidence that peptides corresponding to the wild type and mutated sequences of this segment adopt chiefly disordered conformations that, in the case of the wild type sequence, spontaneously forms a β-sheet rich oligomer. Moreover, MD simulation provides evidence for a structure consisting of two β-strands and a well-defined, yet non-canonical structural element. Furthermore, MD simulations of four pathological mutations (Q343R, N345K, G348V and N352S) occurring in this segment predict that all of them could affect this region's structure. In particular, the Q343R variant tends to stabilize disordered conformers, N345K permits the formation of longer, more stable β-strands, and G348V tends to shorten and destabilize them. Finally, N352S acts to alter the β-stand register and when S352 is phosphorylated, it induces partial unfolding. Our results provide a better understanding of TDP-43 aggregation process and will be useful to design effectors capable to modulate its progression.
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Affiliation(s)
- Miguel Mompeán
- Instituto de Química Física "Rocasolano" CSIC, Serrano 119, E-28006 Madrid, Spain
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, I-34149 Trieste, Italy
| | - Corrado Guarnaccia
- International Centre for Genetic Engineering and Biotechnology, I-34149 Trieste, Italy
| | - Rui M M Brito
- Chemistry Dept., Faculty of Science and Technology & Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Avijit Chakrabartty
- Dept. of Biochemistry, University of Toronto, Toronto Medical Discovery Tower 4-305, MaRS Centre, 101 College St., Toronto, ON M5G 1L7, Canada
| | - Francisco E Baralle
- International Centre for Genetic Engineering and Biotechnology, I-34149 Trieste, Italy.
| | - Douglas V Laurents
- Instituto de Química Física "Rocasolano" CSIC, Serrano 119, E-28006 Madrid, Spain.
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174
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Vila JA, Arnautova YA. 13C Chemical Shifts in Proteins: A Rich Source of Encoded Structural Information. COMPUTATIONAL METHODS TO STUDY THE STRUCTURE AND DYNAMICS OF BIOMOLECULES AND BIOMOLECULAR PROCESSES 2014. [PMCID: PMC7121069 DOI: 10.1007/978-3-642-28554-7_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite the formidable progress in Nuclear Magnetic Resonance (NMR) spectroscopy, quality assessment of NMR-derived structures remains as an important problem. Thus, validation of protein structures is essential for the spectroscopists, since it could enable them to detect structural flaws and potentially guide their efforts in further refinement. Moreover, availability of accurate and efficient validation tools would help molecular biologists and computational chemists to evaluate quality of available experimental structures and to select a protein model which is the most suitable for a given scientific problem. The 13Cα nuclei are ubiquitous in proteins, moreover, their shieldings are easily obtainable from NMR experiments and represent a rich source of encoded structural information that makes 13Cα chemical shifts an attractive candidate for use in computational methods aimed at determination and validation of protein structures. In this chapter, the basis of a novel methodology of computing, at the quantum chemical level of theory, the 13Cα shielding for the amino acid residues in proteins is described. We also identify and examine the main factors affecting the 13Cα-shielding computation. Finally, we illustrate how the information encoded in the 13C chemical shifts can be used for a number of applications, viz., from protein structure prediction of both α-helical and β-sheet conformations, to determination of the fraction of the tautomeric forms of the imidazole ring of histidine in proteins as a function of pH or to accurate detection of structural flaws, at a residue-level, in NMR-determined protein models.
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175
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Adler J, Scheidt HA, Krüger M, Thomas L, Huster D. Local interactions influence the fibrillation kinetics, structure and dynamics of Aβ(1–40) but leave the general fibril structure unchanged. Phys Chem Chem Phys 2014; 16:7461-71. [DOI: 10.1039/c3cp54501f] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Selective point mutations introducing local fields do not alter the overall structure and morphology of Aβ(1–40) fibrils.
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Affiliation(s)
- Juliane Adler
- Institute of Medical Physics and Biophysics
- University of Leipzig
- D-04107 Leipzig, Germany
| | - Holger A. Scheidt
- Institute of Medical Physics and Biophysics
- University of Leipzig
- D-04107 Leipzig, Germany
| | - Martin Krüger
- Institute of Anatomy
- University of Leipzig
- D-04103 Leipzig, Germany
| | - Lars Thomas
- Institute of Medical Physics and Biophysics
- University of Leipzig
- D-04107 Leipzig, Germany
| | - Daniel Huster
- Institute of Medical Physics and Biophysics
- University of Leipzig
- D-04107 Leipzig, Germany
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
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176
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Figueiredo AM, Whittaker SBM, Knowling SE, Radford SE, Moore GR. Conformational dynamics is more important than helical propensity for the folding of the all α-helical protein Im7. Protein Sci 2013; 22:1722-38. [PMID: 24123274 DOI: 10.1002/pro.2372] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/30/2013] [Accepted: 09/04/2013] [Indexed: 11/06/2022]
Abstract
Im7 folds via an on-pathway intermediate that contains three of the four native α-helices. The missing helix, helix III, is the shortest and its failure to be formed until late in the pathway is related to frustration in the structure. Im7H3M3, a 94-residue variant of the 87-residue Im7 in which helix III is the longest of the four native helices, also folds via an intermediate. To investigate the structural basis for this we calculated the frustration in the structure of Im7H3M3 and used NMR to investigate its dynamics. We found that the native state of Im7H3M3 is highly frustrated and in equilibrium with an intermediate state that lacks helix III, similar to Im7. Model-free analysis identified residues with chemical exchange contributions to their relaxation that aligned with the residues predicted to have highly frustrated interactions, also like Im7. Finally, we determined properties of urea-denatured Im7H3M3 and identified four clusters of interacting residues that corresponded to the α-helices of the native protein. In Im7 the cluster sizes were related to the lengths of the α-helices with cluster III being the smallest but in Im7H3M3 cluster III was also the smallest, despite this region forming the longest helix in the native state. These results suggest that the conformational properties of the urea-denatured states promote formation of a three-helix intermediate in which the residues that form helix III remain non-helical. Thus it appears that features of the native structure are formed early in folding linked to collapse of the unfolded state.
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Affiliation(s)
- Angelo Miguel Figueiredo
- Centre for Structural and Molecular Biochemistry, School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
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177
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Kimura T, Vukoti K, Lynch DL, Hurst DP, Grossfield A, Pitman MC, Reggio PH, Yeliseev AA, Gawrisch K. Global fold of human cannabinoid type 2 receptor probed by solid-state 13C-, 15N-MAS NMR and molecular dynamics simulations. Proteins 2013; 82:452-65. [PMID: 23999926 DOI: 10.1002/prot.24411] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 08/12/2013] [Accepted: 08/21/2013] [Indexed: 12/12/2022]
Abstract
The global fold of human cannabinoid type 2 (CB2 ) receptor in the agonist-bound active state in lipid bilayers was investigated by solid-state (13)C- and (15)N magic-angle spinning (MAS) NMR, in combination with chemical-shift prediction from a structural model of the receptor obtained by microsecond-long molecular dynamics (MD) simulations. Uniformly (13)C- and (15)N-labeled CB2 receptor was expressed in milligram quantities by bacterial fermentation, purified, and functionally reconstituted into liposomes. (13)C MAS NMR spectra were recorded without sensitivity enhancement for direct comparison of Cα, Cβ, and C=O bands of superimposed resonances with predictions from protein structures generated by MD. The experimental NMR spectra matched the calculated spectra reasonably well indicating agreement of the global fold of the protein between experiment and simulations. In particular, the (13) C chemical shift distribution of Cα resonances was shown to be very sensitive to both the primary amino acid sequence and the secondary structure of CB2. Thus the shape of the Cα band can be used as an indicator of CB2 global fold. The prediction from MD simulations indicated that upon receptor activation a rather limited number of amino acid residues, mainly located in the extracellular Loop 2 and the second half of intracellular Loop 3, change their chemical shifts significantly (≥ 1.5 ppm for carbons and ≥ 5.0 ppm for nitrogens). Simulated two-dimensional (13) Cα(i)-(13)C=O(i) and (13)C=O(i)-(15)NH(i + 1) dipolar-interaction correlation spectra provide guidance for selective amino acid labeling and signal assignment schemes to study the molecular mechanism of activation of CB2 by solid-state MAS NMR.
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Affiliation(s)
- Tomohiro Kimura
- Laboratory of Membrane Biochemistry and Biophysics, NIAAA, NIH, Bethesda, Maryland, 20892
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178
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Martin OA, Arnautova YA, Icazatti AA, Scheraga HA, Vila JA. Physics-based method to validate and repair flaws in protein structures. Proc Natl Acad Sci U S A 2013; 110:16826-31. [PMID: 24082119 PMCID: PMC3801053 DOI: 10.1073/pnas.1315525110] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A method that makes use of information provided by the combination of (13)C(α) and (13)C(β) chemical shifts, computed at the density functional level of theory, enables one to (i) validate, at the residue level, conformations of proteins and detect backbone or side-chain flaws by taking into account an ensemble average of chemical shifts over all of the conformations used to represent a protein, with a sensitivity of ∼90%; and (ii) provide a set of (χ1/χ2) torsional angles that leads to optimal agreement between the observed and computed (13)C(α) and (13)C(β) chemical shifts. The method has been incorporated into the CheShift-2 protein validation Web server. To test the reliability of the provided set of (χ1/χ2) torsional angles, the side chains of all reported conformations of five NMR-determined protein models were refined by a simple routine, without using NOE-based distance restraints. The refinement of each of these five proteins leads to optimal agreement between the observed and computed (13)C(α) and (13)C(β) chemical shifts for ∼94% of the flaws, on average, without introducing a significantly large number of violations of the NOE-based distance restraints for a distance range ≤ 0.5 , in which the largest number of distance violations occurs. The results of this work suggest that use of the provided set of (χ1/χ2) torsional angles together with other observables, such as NOEs, should lead to a fast and accurate refinement of the side-chain conformations of protein models.
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Affiliation(s)
- Osvaldo A. Martin
- Instituto de Matemática Aplicada San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Departamento de Física, Universidad Nacional de San Luis, 5700 San Luis, Argentina
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853; and
| | | | - Alejandro A. Icazatti
- Instituto de Matemática Aplicada San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Departamento de Física, Universidad Nacional de San Luis, 5700 San Luis, Argentina
| | - Harold A. Scheraga
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853; and
| | - Jorge A. Vila
- Instituto de Matemática Aplicada San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Departamento de Física, Universidad Nacional de San Luis, 5700 San Luis, Argentina
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853; and
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179
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Fan GL, Li QZ. Discriminating bioluminescent proteins by incorporating average chemical shift and evolutionary information into the general form of Chou's pseudo amino acid composition. J Theor Biol 2013; 334:45-51. [DOI: 10.1016/j.jtbi.2013.06.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 05/30/2013] [Accepted: 06/03/2013] [Indexed: 01/22/2023]
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180
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Russo L, Raiola L, Campitiello MA, Magrì A, Fattorusso R, Malgieri G, Pappalardo G, La Mendola D, Isernia C. Probing the residual structure in avian prion hexarepeats by CD, NMR and MD techniques. Molecules 2013; 18:11467-84. [PMID: 24043142 PMCID: PMC6270093 DOI: 10.3390/molecules180911467] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/03/2013] [Accepted: 09/09/2013] [Indexed: 02/06/2023] Open
Abstract
Many proteins perform essential biological functions by means of regions that lacking specific organized structure exist as an ensemble of interconverting transient conformers. The characterization of such regions, including the description of their structural propensities, number of conformations and relative populations can provide useful insights. Prion diseases result from the conversion of a normal glycoprotein into a misfolded pathogenic isoform. The structures of mammal and chicken prion proteins show a similar fold with a globular domain and a flexible N-terminal portion that contains different repeated regions: octarepeats (PHGGGWGQ) in mammals and hexarepeats (PHNPGY) in chickens. The higher number of prolines in the hexarepeat region suggests that this region may retain a significant amount of residual secondary structure. Here, we report the CD, NMR and MD characterization of a peptide (2-HexaPY) composed of two hexarepeats. We combine experimental NMR data and MD to investigate at atomic level its ensemble-averaged structural properties, demonstrating how each residue of both repeats has a different quantified PPII propensity that shows a periodicity along the sequence. This feature explains the absence of cooperativity to stabilize a PPII conformation. Nonetheless, such residual structure can play a role in nucleating local structural transitions as well as modulating intra-molecular or inter-molecular interactions.
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Affiliation(s)
- Luigi Russo
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
| | - Luca Raiola
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
| | - Maria Anna Campitiello
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
| | - Antonio Magrì
- CNR-Istituto di Biostrutture e Bioimmagini, viale Doria 6, 95125 Catania, Italy; E-Mails: (A.M.); (G.P.)
| | - Roberto Fattorusso
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
- Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, Università di Napoli “Federico II”, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Gaetano Malgieri
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
| | - Giuseppe Pappalardo
- CNR-Istituto di Biostrutture e Bioimmagini, viale Doria 6, 95125 Catania, Italy; E-Mails: (A.M.); (G.P.)
| | - Diego La Mendola
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno Pisano 6, 56126 Pisa, Italy; E-Mail:
| | - Carla Isernia
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy; E-Mails: (L.R.); (L.R.); (M.A.C.); (R.F.); (G.M.)
- Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, Università di Napoli “Federico II”, Via Mezzocannone 16, 80134 Napoli, Italy
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +39-0823-274-636; Fax: +39-0823-274-605
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181
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Shu I, Scian M, Stewart JM, Kier BL, Andersen NH. 13C structuring shifts for the analysis of model β-hairpins and β-sheets in proteins: diagnostic shifts appear only at the cross-strand H-bonded residues. JOURNAL OF BIOMOLECULAR NMR 2013; 56:313-329. [PMID: 23851979 DOI: 10.1007/s10858-013-9749-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 05/28/2013] [Indexed: 06/02/2023]
Abstract
The present studies have shown that (13)C=O, (13)C(α) and (13)C(β) of H-bonded strand residues in β-hairpins provide additional probes for quantitating the extent of folding in β-hairpins and other β-sheet models. Large differences in the structuring shifts (CSDs) of these (13)C sites in H-bonded versus non-H-bonded sites are observed: the differences between H-bonded and non-H-bonded sites are greater than 1.2 ppm for all three (13)C probes. This prompts us to suggest that efforts to determine the extent of hairpin folding from (13)C shifts should be based exclusively on the observation at the cross-strand H-bonded sites. Furthermore, the statistics suggest the (13)C' and (13)C(β) CSDs will provide the best differentiation with 100%-folded CSD values approaching -2.6 and +3 ppm, respectively, for the H-bonded sites. These conclusions can be extended to edge-strands of protein β-sheets. Our survey of reported (13)C shifts in β-proteins indicates that some of the currently employed random coil values need to be adjusted, particularly for ionization-induced effects.
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Affiliation(s)
- Irene Shu
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
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182
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Predicting acidic and alkaline enzymes by incorporating the average chemical shift and gene ontology informations into the general form of Chou's PseAAC. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.05.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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183
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Shen Y, Bax A. Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks. JOURNAL OF BIOMOLECULAR NMR 2013; 56:227-41. [PMID: 23728592 PMCID: PMC3701756 DOI: 10.1007/s10858-013-9741-y] [Citation(s) in RCA: 825] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 05/03/2013] [Indexed: 05/05/2023]
Abstract
A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, ≥90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed (ϕ, ψ) torsion angles of ca 12º. TALOS-N also reports sidechain χ(1) rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts.
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Affiliation(s)
- Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 126 NIH, Bethesda, MD 20892-0520, USA
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184
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Iešmantavičius V, Jensen MR, Ozenne V, Blackledge M, Poulsen FM, Kjaergaard M. Modulation of the Intrinsic Helix Propensity of an Intrinsically Disordered Protein Reveals Long-Range Helix–Helix Interactions. J Am Chem Soc 2013; 135:10155-63. [DOI: 10.1021/ja4045532] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - Malene Ringkjøbing Jensen
- Institut de Biologie Structurale Jean-Pierre Ebel, CEA-CNRS-UJF UMR 5075,
41 rue Jules Horowitz, 38027 Grenoble, France
| | - Valéry Ozenne
- Institut de Biologie Structurale Jean-Pierre Ebel, CEA-CNRS-UJF UMR 5075,
41 rue Jules Horowitz, 38027 Grenoble, France
| | - Martin Blackledge
- Institut de Biologie Structurale Jean-Pierre Ebel, CEA-CNRS-UJF UMR 5075,
41 rue Jules Horowitz, 38027 Grenoble, France
| | - Flemming M. Poulsen
- Department
of Biology, University of Copenhagen, 1017
København K, Copenhagen,
Denmark
| | - Magnus Kjaergaard
- Department
of Biology, University of Copenhagen, 1017
København K, Copenhagen,
Denmark
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185
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Barré P, Eliezer D. Structural transitions in tau k18 on micelle binding suggest a hierarchy in the efficacy of individual microtubule-binding repeats in filament nucleation. Protein Sci 2013; 22:1037-48. [PMID: 23740819 DOI: 10.1002/pro.2290] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 05/21/2013] [Accepted: 05/22/2013] [Indexed: 12/31/2022]
Abstract
The protein tau is found in an aggregated filamentous state in the intraneuronal paired helical filament deposits characteristic of Alzheimer's disease and other related dementias and mutations in tau protein and mRNA cause frontotemproal dementia. Tau isoforms include a microtubule-binding domain containing either three or four imperfect tandem microtubule binding repeats that also form the core of tau filaments and contain hexapaptide motifs that are critical for tau aggregation. The tau microtubule-binding domain can also engage in direct interactions with detergents, fatty acids, or membranes, which can greatly facilitate tau aggregation and may also mediate some tau functions. Here, we show that the alternatively spliced second microtubule-binding repeat exhibits significantly different structural characteristics compared with the other three repeats in the context of the intact repeat domain. Most notably, the PHF6* hexapeptide motif located at the N-terminus of repeat 2 has a lower propensity to form strand-like structure than the corresponding PHF6 motif in repeat 3, and unlike PHF6 converts to partially helical structure in the micelle-bound state. Interestingly, the behavior of the Module-B motif, located at the beginning of repeat 4, resembles that of PHF6* rather than PHF6. Our observations, combined with previous results showing that PHF6* and Module-B are both less effective than PHF6 in nucleating tau aggregation, suggest a hierarchy in the efficacy of these motifs in nucleating tau aggregation that originates in differences in their intrinsic propensities for extended strand-like structure and the resistance of these propensities to changes in tau's environment.
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Affiliation(s)
- Patrick Barré
- Department of Biochemistry, Program in Structural Biology, Weill Cornell Medical College, New York, 10065, USA
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186
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Rout AK, Patel S, Somlata, Shukla M, Saraswathi D, Bhattacharya A, Chary KVR. Functional manipulation of a calcium-binding protein from Entamoeba histolytica guided by paramagnetic NMR. J Biol Chem 2013; 288:23473-87. [PMID: 23782698 DOI: 10.1074/jbc.m112.411058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
EhCaBP1, one of the calcium-binding proteins from Entamoeba histolytica, is a two-domain EF-hand protein. The two domains of EhCaBP1 are structurally and functionally different from each other. However, both domains are required for structural stability and a full range of functional diversity. Analysis of sequence and structure of EhCaBP1 and other CaBPs indicates that the C-terminal domain of EhCaBP1 possesses a unique structure compared with other family members. This had been attributed to the absence of a Phe-Phe interaction between highly conserved Phe residues at the -4 position in EF-hand III (F[-4]; Tyr(81)) and at the 13th position in EF-hand IV (F[+13]; Phe(129)) of the C-terminal domain. Against this backdrop, we mutated the Tyr residue at the -4th position of EF III to the Phe residue (Y81F), to bring in the Phe-Phe interaction and understand the nature of structural and functional changes in the protein by NMR spectroscopy, molecular dynamics (MD) simulation, isothermal titration calorimetry (ITC), and biological assays, such as imaging and actin binding. The Y81F mutation in EhCaBP1 resulted in a more compact structure for the C-terminal domain of the mutant as in the case of calmodulin and troponin C. The compact structure is favored by the presence of a π-π interaction between Phe(81) and Phe(129) along with several hydrophobic interactions of Phe(81), which are not seen in the wild-type protein. Furthermore, the biological assays reveal preferential membrane localization of the mutant, loss of its colocalization with actin in the phagocytic cups, whereas retaining its ability to bind G- and F-actin.
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Affiliation(s)
- Ashok K Rout
- Tata Institute of Fundamental Research, Mumbai, India
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187
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Ramírez-Gualito K, Richter M, Matzapetakis M, Singer D, Berger S. Structural characterization by NMR of a double phosphorylated chimeric peptide vaccine for treatment of Alzheimer's disease. Molecules 2013; 18:4929-41. [PMID: 23624647 PMCID: PMC6269680 DOI: 10.3390/molecules18054929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 04/19/2013] [Accepted: 04/22/2013] [Indexed: 11/16/2022] Open
Abstract
Rational design of peptide vaccines becomes important for the treatment of some diseases such as Alzheimer's disease (AD) and related disorders. In this study, as part of a larger effort to explore correlations of structure and activity, we attempt to characterize the doubly phosphorylated chimeric peptide vaccine targeting a hyperphosphorylated epitope of the Tau protein. The 28-mer linear chimeric peptide consists of the double phosphorylated B cell epitope Tau₂₂₉₋₂₃₇[pThr231/pSer235] and the immunomodulatory T cell epitope Ag85B₂₄₁₋₂₅₅ originating from the well-known antigen Ag85B of the Mycobacterium tuberculosis, linked by a four amino acid sequence -GPSL-. NMR chemical shift analysis of our construct demonstrated that the synthesized peptide is essentially unfolded with a tendency to form a β-turn due to the linker. In conclusion, the -GPSL- unit presumably connects the two parts of the vaccine without transferring any structural information from one part to the other. Therefore, the double phosphorylated epitope of the Tau peptide is flexible and accessible.
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Affiliation(s)
- Karla Ramírez-Gualito
- Institute of Analytical Chemistry, University Leipzig, Johannisallee 29, Leipzig 04103, Germany; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +49-341-973-6101; Fax: +49-341-971-1833
| | - Monique Richter
- Institute of Bioanalytical Chemistry, University Leipzig, Deutscher Platz 5, Leipzig 04103, Germany; E-Mails: (M.R.); (D.S.)
| | - Manolis Matzapetakis
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. Av. da República, Oeiras 2780-157, Portugal; E-Mail:
| | - David Singer
- Institute of Bioanalytical Chemistry, University Leipzig, Deutscher Platz 5, Leipzig 04103, Germany; E-Mails: (M.R.); (D.S.)
| | - Stefan Berger
- Institute of Analytical Chemistry, University Leipzig, Johannisallee 29, Leipzig 04103, Germany; E-Mail:
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188
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Abstract
Solution nuclear magnetic resonance (NMR) spectroscopy has come a long way in characterizing the structure and function of biological molecules since the first one-dimensional spectrum of protein was recorded about 30 years ago. To date (September 1, 2012), there are 9,521 solution NMR structures in the Protein Data Bank, compared to 74,009 determined by crystallographic methods. Unlike X-ray and electron microscopy (EM) methods, which are based on the concepts of Fourier optics and image reconstruction, structure determination by NMR involves measuring structural restraints and finding structural solutions that satisfy the restraints. Although the NMR approach is much less direct in a physical sense, it has proven itself over the years to be capable of de novo structure determination at high precision. Moreover, the method is highly versatile and can be used in a variety of ways for addressing mechanistic questions. NMR measurements of protein internal dynamics and protein-protein or protein-ligand interaction are directly relevant to function in vivo because the molecules are often in physiological buffer conditions. The method can also be applied to investigate protein-folding intermediates, conformational changes, as well as intrinsically unfolded proteins. Recently, along with X-ray and EM, solution NMR has entered a state of rapid growth for structural studies of membrane proteins, already demonstrating its feasibility in de novo structure determination of membrane-embedded ion channels and receptors. As the hardware advances rapidly, especially in cryogenic probes that have much higher sensitivity, the sample concentration required for solution NMR investigation is decreasing, hopefully soon to a concentration level at which nonspecific protein aggregation is no longer an issue. After three decades of improvement in spectrometer technology, NMR pulse experiments, isotope labeling schemes, and structure determination software, we believe that solution NMR will truly enter the production phase in the next decade to answer biological questions of high impact, and to become more versatile than ever in complementing X-ray and EM in investigating protein structure and function.
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Affiliation(s)
- James J Chou
- Jack and Eileen Connors Structural Biology Laboratory, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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189
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Meng W, Luan B, Lyle N, Pappu RV, Raleigh DP. The Denatured State Ensemble Contains Significant Local and Long-Range Structure under Native Conditions: Analysis of the N-Terminal Domain of Ribosomal Protein L9. Biochemistry 2013; 52:2662-71. [DOI: 10.1021/bi301667u] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wenli Meng
- Department
of Chemistry, Stony Brook University, Stony
Brook, New York 11794-3400,
United States
| | - Bowu Luan
- Department
of Chemistry, Stony Brook University, Stony
Brook, New York 11794-3400,
United States
| | - Nicholas Lyle
- Department
of Biomedical Engineering, Washington University in St. Louis, One Brookings Drive,
Campus Box 1097, St. Louis, Missouri 63130-4899, United States
| | - Rohit V. Pappu
- Department
of Biomedical Engineering, Washington University in St. Louis, One Brookings Drive,
Campus Box 1097, St. Louis, Missouri 63130-4899, United States
| | - Daniel P. Raleigh
- Department
of Chemistry, Stony Brook University, Stony
Brook, New York 11794-3400,
United States
- Graduate Program in Biochemistry
and Structural Biology and Graduate Program in Biophysics, Stony Brook University, Stony Brook, New York 11794,
United States
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190
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Endres NF, Das R, Smith AW, Arkhipov A, Kovacs E, Huang Y, Pelton JG, Shan Y, Shaw DE, Wemmer DE, Groves JT, Kuriyan J. Conformational coupling across the plasma membrane in activation of the EGF receptor. Cell 2013; 152:543-56. [PMID: 23374349 PMCID: PMC3718647 DOI: 10.1016/j.cell.2012.12.032] [Citation(s) in RCA: 376] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 09/28/2012] [Accepted: 12/11/2012] [Indexed: 01/01/2023]
Abstract
How the epidermal growth factor receptor (EGFR) activates is incompletely understood. The intracellular portion of the receptor is intrinsically active in solution, and to study its regulation, we measured autophosphorylation as a function of EGFR surface density in cells. Without EGF, intact EGFR escapes inhibition only at high surface densities. Although the transmembrane helix and the intracellular module together suffice for constitutive activity even at low densities, the intracellular module is inactivated when tethered on its own to the plasma membrane, and fluorescence cross-correlation shows that it fails to dimerize. NMR and functional data indicate that activation requires an N-terminal interaction between the transmembrane helices, which promotes an antiparallel interaction between juxtamembrane segments and release of inhibition by the membrane. We conclude that EGF binding removes steric constraints in the extracellular module, promoting activation through N-terminal association of the transmembrane helices.
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Affiliation(s)
- Nicholas F Endres
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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191
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Hansen AL, Bouvignies G, Kay LE. Probing slowly exchanging protein systems via ¹³Cα-CEST: monitoring folding of the Im7 protein. JOURNAL OF BIOMOLECULAR NMR 2013; 55:279-289. [PMID: 23386228 DOI: 10.1007/s10858-013-9711-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 01/20/2013] [Indexed: 06/01/2023]
Abstract
A¹³C(α) chemical exchange saturation transfer based experiment is presented for the study of protein systems undergoing slow interconversion between an 'observable' ground state and one or more 'invisible' excited states. Here a labeling strategy whereby [2-(13)C]-glucose is the sole carbon source is exploited, producing proteins with ¹³C at the C(α) position, while the majority of residues remain unlabeled at CO or C(β). The new experiment is demonstrated with an application to the folding reaction of the Im7 protein that involves an on-pathway excited state. The obtained excited state (13)C(α) chemical shifts are cross validated by comparison to values extracted from analysis of CPMG relaxation dispersion profiles, establishing the utility of the methodology.
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Affiliation(s)
- Alexandar L Hansen
- Department of Molecular Genetics, The University of Toronto, Toronto, ON, M5S 1A8, Canada
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192
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Mithu VS, Bakthavatsalam S, Madhu PK. (13)C-(13)c homonuclear recoupling in solid-state nuclear magnetic resonance at a moderately high magic-angle-spinning frequency. PLoS One 2013; 8:e50504. [PMID: 23326308 PMCID: PMC3542364 DOI: 10.1371/journal.pone.0050504] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 10/22/2012] [Indexed: 11/18/2022] Open
Abstract
Two-dimensional (13)C-(13)C correlation experiments are widely employed in structure determination of protein assemblies using solid-state nuclear magnetic resonance. Here, we investigate the process of (13)C-(13)C magnetisation transfer at a moderate magic-angle-spinning frequency of 30 kHz using some of the prominent second-order dipolar recoupling schemes. The effect of isotropic chemical-shift difference and spatial distance between two carbons and amplitude of radio frequency on (1)H channel on the magnetisation transfer efficiency of these schemes is discussed in detail.
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Affiliation(s)
- Venus Singh Mithu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India
| | - Subha Bakthavatsalam
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India
| | - Perunthiruthy K. Madhu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India
- * E-mail:
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193
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High-pressure NMR reveals close similarity between cold and alcohol protein denaturation in ubiquitin. Proc Natl Acad Sci U S A 2013; 110:E368-76. [PMID: 23284170 DOI: 10.1073/pnas.1212222110] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proteins denature not only at high, but also at low temperature as well as high pressure. These denatured states are not easily accessible for experiment, because usually heat denaturation causes aggregation, whereas cold or pressure denaturation occurs at temperatures well below the freezing point of water or pressures above 5 kbar, respectively. Here we have obtained atomic details of the pressure-assisted, cold-denatured state of ubiquitin at 2,500 bar and 258 K by high-resolution NMR techniques. Under these conditions, a folded, native-like and a disordered state exist in slow exchange. Secondary chemical shifts show that the disordered state has structural propensities for a native-like N-terminal β-hairpin and α-helix and a nonnative C-terminal α-helix. These propensities are very similar to the previously described alcohol-denatured (A-)state. Similar to the A-state, (15)N relaxation data indicate that the secondary structure elements move as independent segments. The close similarity of pressure-assisted, cold-denatured, and alcohol-denatured states with native and nonnative secondary elements supports a hierarchical mechanism of folding and supports the notion that similar to alcohol, pressure and cold reduce the hydrophobic effect. Indeed, at nondenaturing concentrations of methanol, a complete transition from the native to the A-state can be achieved at ambient temperature by varying the pressure from 1 to 2,500 bar. The methanol-assisted pressure transition is completely reversible and can also be induced in protein G. This method should allow highly detailed studies of protein-folding transitions in a continuous and reversible manner.
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194
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Mittal J, Yoo TH, Georgiou G, Truskett TM. Structural ensemble of an intrinsically disordered polypeptide. J Phys Chem B 2012. [PMID: 23205890 DOI: 10.1021/jp308984e] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Intrinsically disordered proteins (IDPs), which play key roles in cell signaling and regulation, do not display specific tertiary structure when isolated in solution. Instead, they dynamically explore an ensemble of unfolded configurations, adopting more stable, ordered structures only after binding to their ligands. Whether ligands induce IDP structural changes upon binding or simply bind to pre-existing conformers that are populated within the IDP's structural ensemble is not well understood. Molecular simulations can provide information with the spatiotemporal resolution necessary to resolve these issues. Here, we report on the conformational ensemble of a 15-residue wild-type p53 fragment from the TAD domain and its mutant (TAD-P27L) obtained by replica exchange molecular dynamics simulation using an optimized (fully atomistic, explicit solvent) protein model and the experimental validation of the simulation results. We use a clustering method based on structural similarity to identify conformer states populated by the peptides in solution from the simulated ensemble. We show that p53 populates solution structures that strongly resemble the ligand (MDM2)-bound structure, but at the same time, the conformational free-energy landscape is relatively flat in the absence of the ligand.
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Affiliation(s)
- Jeetain Mittal
- Department of Chemical Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States.
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195
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Marianski M, Asensio A, Dannenberg JJ. Comparison of some dispersion-corrected and traditional functionals as applied to peptides and conformations of cyclohexane derivatives. J Chem Phys 2012; 137:044109. [PMID: 22852599 DOI: 10.1063/1.4737517] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We compare the energetic and structural properties of fully optimized α-helical and antiparallel β-sheet polyalanines and the energetic differences between axial and equatorial conformations of three cyclohexane derivatives (methyl, fluoro, and chloro) as calculated using several functionals designed to treat dispersion (B97-D, ωB97x-D, M06, M06L, and M06-2X) with other traditional functionals not specifically parametrized to treat dispersion (B3LYP, X3LYP, and PBE1PBE) and with experimental results. Those functionals developed to treat dispersion significantly overestimate interaction enthalpies of folding for the α-helix and predict unreasonable structures that contain Ramachandran φ and ψ and C = O...N H-bonding angles that are out of the bounds of databases compiled the β-sheets. These structures are consistent with overestimation of the interaction energies. For the cyclohexanes, these functionals overestimate the stabilities of the axial conformation, especially when used with smaller basis sets. Their performance improves when the basis set is improved from D95∗∗ to aug-cc-pVTZ (which would not be possible with systems as large as the peptides).
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Affiliation(s)
- Mateusz Marianski
- Department of Chemistry, City University of New York - Hunter College and the Graduate School, 695 Park Avenue, New York, New York 10065, USA
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196
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Chen K, Piszczek G, Carter C, Tjandra N. The maturational refolding of the β-hairpin motif of equine infectious anemia virus capsid protein extends its helix α1 at capsid assembly locus. J Biol Chem 2012. [PMID: 23184932 PMCID: PMC3548464 DOI: 10.1074/jbc.m112.425140] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
A retroviral capsid (CA) protein consists of two helical domains, CAN and CAC, which drive hexamer and dimer formations, respectively, to form a capsid lattice. The N-terminal 13 residues of CA refold to a β-hairpin motif upon processing from its precursor polyprotein Gag. The β-hairpin is essential for correct CA assembly but unexpectedly it is not within any CA oligomeric interfaces. To understand the β-hairpin function we studied the full-length CA protein from equine infectious anemia virus (EIAV), a lentivirus sharing the same cone-shaped capsid core as HIV-1. Solution NMR spectroscopy is perfectly suited to study EIAV-CA that dimerizes weaker than HIV-1-CA. Comparison between the wild-type (wt) EIAV-CA and a variant lacking the β-hairpin structure demonstrated that folding of the β-hairpin specifically extended the N terminus of helix α1 from Tyr20 to Pro17. This coil to helix transition involves the conserved sequence of Thr16-Pro17-Arg18 (Ser16-Pro17-Arg18 in HIV-1-CA). The extended region of helix α1 constituted an expanded EIAV-CAN oligomeric interface and overlapped with the HIV-1-CA hexamer-core residue Arg18, helical in structure and pivotal in assembly. Therefore we propose the function of the maturational refolding of the β-hairpin in CA assembly is to extend helix α1 at the N terminus to enhance the CAN oligomerization along the capsid assembly core interface. In addition, NMR resonance line broadening indicated the presence of micro-millisecond exchange kinetics due to the EIAV-CAN domain oligomerization, independent to the faster EIAV-CAC domain dimerization.
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Affiliation(s)
- Kang Chen
- Laboratory of Molecular Biophysics, NHLBI, National Institutes of Health, Bethesda, Maryland 20892, USA
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197
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Penk A, Förster Y, Scheidt HA, Nimptsch A, Hacker MC, Schulz-Siegmund M, Ahnert P, Schiller J, Rammelt S, Huster D. The pore size of PLGA bone implants determines the de novo formation of bone tissue in tibial head defects in rats. Magn Reson Med 2012; 70:925-35. [PMID: 23165861 DOI: 10.1002/mrm.24541] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/04/2012] [Accepted: 10/04/2012] [Indexed: 12/20/2022]
Abstract
PURPOSE The influence of the pore size of biodegradable poly(lactic-co-glycolic acid) scaffolds on bone regeneration was investigated. METHODS Cylindrical poly(lactic-co-glycolic acid) scaffolds were implanted into a defect in the tibial head of rats. Pore sizes of 100-300, 300-500, and 500-710 μm were tested and compared to untreated defects as control. Two and four weeks after implantation, the specimens were explanted and defect regeneration and de novo extracellular matrix generation were investigated by MRI, quantitative solid-state NMR, and mass spectrometry. RESULTS The pore size of the scaffolds had a pronounced influence on the quantity of the extracellular matrix synthesized in the graft; most collagen was synthesized within the first 2 weeks of implantation, while the amount of hydroxyapatite increased in the second 2 weeks. After 4 weeks, the scaffolds contained large quantities of newly formed lamellar bone while the control defects were filled by inhomogenous woven bone. Best results were obtained for scaffolds of a pore size of 300-500 μm. CONCLUSION Our analysis showed that the structure and dynamics of the regenerated extracellular matrix was very similar to that of the native bone, suggesting that biomineralization was significantly enhanced by the choice of the most appropriate implant material.
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Affiliation(s)
- Anja Penk
- Institute of Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
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198
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Tian Y, Opella SJ, Marassi FM. Improved chemical shift prediction by Rosetta conformational sampling. JOURNAL OF BIOMOLECULAR NMR 2012; 54:237-243. [PMID: 23007199 PMCID: PMC3484222 DOI: 10.1007/s10858-012-9677-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 09/16/2012] [Indexed: 06/01/2023]
Abstract
Chemical shift frequencies represent a time-average of all the conformational states populated by a protein. Thus, chemical shift prediction programs based on sequence and database analysis yield higher accuracy for rigid rather than flexible protein segments. Here we show that the prediction accuracy can be significantly improved by averaging over an ensemble of structures, predicted solely from amino acid sequence with the Rosetta program. This approach to chemical shift and structure prediction has the potential to be useful for guiding resonance assignments, especially in solid-state NMR structural studies of membrane proteins in proteoliposomes.
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Affiliation(s)
- Ye Tian
- Sanford Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0307, USA
| | - Stanley J. Opella
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0307, USA
| | - Francesca M. Marassi
- Sanford Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
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199
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Krejcirikova A, Tugarinov V. 3D-TROSY-based backbone and ILV-methyl resonance assignments of a 319-residue homodimer from a single protein sample. JOURNAL OF BIOMOLECULAR NMR 2012; 54:135-43. [PMID: 22960997 DOI: 10.1007/s10858-012-9667-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 08/29/2012] [Indexed: 05/20/2023]
Abstract
The feasibility of practically complete backbone and ILV methyl chemical shift assignments from a single [U-(2)H,(15)N,(13)C; Ileδ1-{(13)CH(3)}; Leu,Val-{(13)CH(3)/(12)CD(3)}]-labeled protein sample of the truncated form of ligand-free Bst-Tyrosyl tRNA Synthetase (Bst-ΔYRS), a 319-residue predominantly helical homodimer, is established. Protonation of ILV residues at methyl positions does not appreciably detract from the quality of TROSY triple resonance data. The assignments are performed at 40 °C to improve the sensitivity of the measurements and alleviate the overlap of (1)H-(15)N correlations in the abundant α-helical segments of the protein. A number of auxiliary approaches are used to assist in the assignment process: (1) selection of (1)H-(15)N amide correlations of certain residue types (Ala, Thr/Ser) that simplifies 2D (1)H-(15)N TROSY spectra, (2) straightforward identification of ILV residue types from the methyl-detected 'out-and-back' HMCM(CG)CBCA experiment, and (3) strong sequential HN-HN NOE connectivities in the helical regions. The two subunits of Bst-YRS were predicted earlier to exist in two different conformations in the absence of ligands. In agreement with our earlier findings (Godoy-Ruiz in J Am Chem Soc 133:19578-195781, 2011), no evidence of dimer asymmetry has been observed in either amide- or methyl-detected experiments.
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Affiliation(s)
- Anna Krejcirikova
- Department of Chemistry and Biochemistry, University of Maryland, Biomolecular Sci. Bldg./CBSO, College Park, MD 20742, USA
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200
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Allison JR. Assessing and refining molecular dynamics simulations of proteins with nuclear magnetic resonance data. Biophys Rev 2012; 4:189-203. [PMID: 28510078 DOI: 10.1007/s12551-012-0087-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Accepted: 06/12/2012] [Indexed: 11/28/2022] Open
Abstract
The sophistication of the force fields, algorithms and hardware used for molecular dynamics (MD) simulations of proteins is continuously increasing. No matter how advanced the methodology, however, it is essential to evaluate the appropriateness of the structures sampled in a simulation by comparison with quantitative experimental data. Solution nuclear magnetic resonance (NMR) data are particularly useful for checking the quality of protein simulations, as they provide both structural and dynamic information on a variety of temporal and spatial scales. Here, various features and implications of using NMR data to validate and bias MD simulations are outlined, including an overview of the different types of NMR data that report directly on structural properties and of relevant simulation techniques. The focus throughout is on how to properly account for conformational averaging, particularly within the context of the assumptions inherent in the relationships that link NMR data to structural properties.
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Affiliation(s)
- Jane R Allison
- Centre for Theoretical Chemistry and Physics, Institute of Natural Sciences, Massey University Albany, Albany Highway, Auckland, 0632, New Zealand.
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