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Unraveling the structure and dynamics of the human DNAJB6b chaperone by NMR reveals insights into Hsp40-mediated proteostasis. Proc Natl Acad Sci U S A 2019; 116:21529-21538. [PMID: 31591220 DOI: 10.1073/pnas.1914999116] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
J-domain chaperones are involved in the efficient handover of misfolded/partially folded proteins to Hsp70 but also function independently to protect against cell death. Due to their high flexibility, the mechanism by which they regulate the Hsp70 cycle and how specific substrate recognition is performed remains unknown. Here we focus on DNAJB6b, which has been implicated in various human diseases and represents a key player in protection against neurodegeneration and protein aggregation. Using a variant that exists mainly in a monomeric form, we report the solution structure of an Hsp40 containing not only the J and C-terminal substrate binding (CTD) domains but also the functionally important linkers. The structure reveals a highly dynamic protein in which part of the linker region masks the Hsp70 binding site. Transient interdomain interactions via regions crucial for Hsp70 binding create a closed, autoinhibited state and help retain the monomeric form of the protein. Detailed NMR analysis shows that the CTD (but not the J domain) self-associates to form an oligomer comprising ∼35 monomeric units, revealing an intricate balance between intramolecular and intermolecular interactions. The results shed light on the mechanism of autoregulation of the Hsp70 cycle via conserved parts of the linker region and reveal the mechanism of DNAJB6b oligomerization and potentially antiaggregation.
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Abstract
Xplor-NIH is a popular software package for biomolecular structure determination from NMR (and other) experimental data. This chapter illustrates its use with the de novo structure determination of the B1 domain of streptococcal protein G (GB1), based on distances from nuclear Overhauser effects, torsion angles from scalar couplings, and bond-vector orientations from residual dipolar couplings. Including Xplor-NIH's latest developments, a complete structure calculation script is discussed in detail, and is intended to serve as a basis for other applications.
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3
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Delhommel F, Cordier F, Bardiaux B, Bouvier G, Colcombet-Cazenave B, Brier S, Raynal B, Nouaille S, Bahloul A, Chamot-Rooke J, Nilges M, Petit C, Wolff N. Structural Characterization of Whirlin Reveals an Unexpected and Dynamic Supramodule Conformation of Its PDZ Tandem. Structure 2017; 25:1645-1656.e5. [PMID: 28966015 DOI: 10.1016/j.str.2017.08.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/26/2017] [Accepted: 08/18/2017] [Indexed: 10/18/2022]
Abstract
Hearing relies on the transduction of sound-evoked vibrations into electric signals, occurring in the stereocilia bundle of hair cells. The bundle is organized in a staircase pattern formed by rows of packed stereocilia. This architecture is pivotal to transduction and involves a network of scaffolding proteins with hitherto uncharacterized features. Key interactions in this network are mediated by PDZ domains. Here, we describe the architecture of the first two PDZ domains of whirlin, a protein involved in these assemblies and associated with congenital deaf-blindness. C-terminal hairpin extensions of the PDZ domains mediate the transient supramodular assembly, which improves the binding capacity of the first domain. We determined a detailed structural model of the closed conformation of the PDZ tandem and characterized its equilibrium with an ensemble of open conformations. The structural and dynamic behavior of this PDZ tandem provides key insights into the regulatory mechanisms involved in the hearing machinery.
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Affiliation(s)
- Florent Delhommel
- Sorbonne Universités, UPMC Université Paris 06, Complexité du Vivant, 75005 Paris, France; CNRS, UMR 3528, 75015 Paris, France; Unité de Résonance Magnétique Nucléaire des Biomolécules, Institut Pasteur, 75015 Paris, France
| | - Florence Cordier
- CNRS, UMR 3528, 75015 Paris, France; Unité de Résonance Magnétique Nucléaire des Biomolécules, Institut Pasteur, 75015 Paris, France
| | - Benjamin Bardiaux
- CNRS, UMR 3528, 75015 Paris, France; Unité de Bio-Informatique Structurale, Institut Pasteur, 75015 Paris, France
| | - Guillaume Bouvier
- CNRS, UMR 3528, 75015 Paris, France; Unité de Bio-Informatique Structurale, Institut Pasteur, 75015 Paris, France
| | - Baptiste Colcombet-Cazenave
- CNRS, UMR 3528, 75015 Paris, France; Unité de Résonance Magnétique Nucléaire des Biomolécules, Institut Pasteur, 75015 Paris, France
| | - Sébastien Brier
- CNRS, UMR 3528, 75015 Paris, France; Unité de Spectrométrie de Masse Structurale et Protéomique, Institut Pasteur, 75015 Paris, France
| | - Bertrand Raynal
- CNRS, UMR 3528, 75015 Paris, France; Plateforme de Biophysique Moléculaire, Institut Pasteur, 75015 Paris, France
| | - Sylvie Nouaille
- Sorbonne Universités, UPMC Université Paris 06, Complexité du Vivant, 75005 Paris, France; Unité de Génétique et physiologie de l'audition, Institut Pasteur, 75015 Paris, France; Unité Mixte de Recherche, UMRS 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), 75015 Paris, France
| | - Amel Bahloul
- Sorbonne Universités, UPMC Université Paris 06, Complexité du Vivant, 75005 Paris, France; Unité de Génétique et physiologie de l'audition, Institut Pasteur, 75015 Paris, France; Unité Mixte de Recherche, UMRS 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), 75015 Paris, France
| | - Julia Chamot-Rooke
- CNRS, UMR 3528, 75015 Paris, France; Unité de Spectrométrie de Masse Structurale et Protéomique, Institut Pasteur, 75015 Paris, France
| | - Michael Nilges
- CNRS, UMR 3528, 75015 Paris, France; Unité de Bio-Informatique Structurale, Institut Pasteur, 75015 Paris, France
| | - Christine Petit
- Sorbonne Universités, UPMC Université Paris 06, Complexité du Vivant, 75005 Paris, France; Unité de Génétique et physiologie de l'audition, Institut Pasteur, 75015 Paris, France; Unité Mixte de Recherche, UMRS 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), 75015 Paris, France; Collège de France, 75005 Paris, France
| | - Nicolas Wolff
- CNRS, UMR 3528, 75015 Paris, France; Unité de Résonance Magnétique Nucléaire des Biomolécules, Institut Pasteur, 75015 Paris, France.
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Schwieters CD, Bermejo GA, Clore GM. Xplor-NIH for molecular structure determination from NMR and other data sources. Protein Sci 2017; 27:26-40. [PMID: 28766807 DOI: 10.1002/pro.3248] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 07/28/2017] [Indexed: 11/10/2022]
Abstract
Xplor-NIH is a popular software package for biomolecular structure determination from nuclear magnetic resonance (NMR) and other data sources. Here, some of Xplor-NIH's most useful data-associated energy terms are reviewed, including newer alternative options for using residual dipolar coupling data in structure calculations. Further, we discuss new developments in the implementation of strict symmetry for the calculation of symmetric homo-oligomers, and in the representation of the system as an ensemble of structures to account for motional effects. Finally, the different available force fields are presented, among other Xplor-NIH capabilities.
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Affiliation(s)
- Charles D Schwieters
- Imaging Sciences Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, Maryland, 20892-5624
| | - Guillermo A Bermejo
- Imaging Sciences Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, Maryland, 20892-5624
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520
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5
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Cole CA, Mukhopadhyay R, Omar H, Hennig M, Valafar H. Structure Calculation and Reconstruction of Discrete-State Dynamics from Residual Dipolar Couplings. J Chem Theory Comput 2016; 12:1408-22. [PMID: 26984680 DOI: 10.1021/acs.jctc.5b01091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Residual dipolar couplings (RDCs) acquired by nuclear magnetic resonance (NMR) spectroscopy are an indispensable source of information in investigation of molecular structures and dynamics. Here, we present a comprehensive strategy for structure calculation and reconstruction of discrete-state dynamics from RDC data that is based on the singular value decomposition (SVD) method of order tensor estimation. In addition to structure determination, we provide a mechanism of producing an ensemble of conformations for the dynamical regions of a protein from RDC data. The developed methodology has been tested on simulated RDC data with ±1 Hz of error from an 83 residue α protein (PDB ID 1A1Z ) and a 213 residue α/β protein DGCR8 (PDB ID 2YT4 ). In nearly all instances, our method reproduced the structure of the protein including the conformational ensemble to within less than 2 Å. On the basis of our investigations, arc motions with more than 30° of rotation are identified as internal dynamics and are reconstructed with sufficient accuracy. Furthermore, states with relative occupancies above 20% are consistently recognized and reconstructed successfully. Arc motions with a magnitude of 15° or relative occupancy of less than 10% are consistently unrecognizable as dynamical regions within the context of ±1 Hz of error.
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Affiliation(s)
- Casey A Cole
- Department of Computer Science & Engineering, University of South Carolina , Columbia, South Carolina 29208, United States
| | - Rishi Mukhopadhyay
- Department of Computer Science & Engineering, University of South Carolina , Columbia, South Carolina 29208, United States
| | - Hanin Omar
- Department of Computer Science & Engineering, University of South Carolina , Columbia, South Carolina 29208, United States
| | - Mirko Hennig
- Nutrition Research Institute, University of North Carolina at Chapel Hill , Kannapolis, North Carolina 27514, United States
| | - Homayoun Valafar
- Department of Computer Science & Engineering, University of South Carolina , Columbia, South Carolina 29208, United States
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6
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Simin M, Irausquin S, Cole CA, Valafar H. Improvements to REDCRAFT: a software tool for simultaneous characterization of protein backbone structure and dynamics from residual dipolar couplings. JOURNAL OF BIOMOLECULAR NMR 2014; 60:241-264. [PMID: 25403759 DOI: 10.1007/s10858-014-9871-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 10/30/2014] [Indexed: 06/04/2023]
Abstract
Within the past two decades, there has been an increase in the acquisition of residual dipolar couplings (RDC) for investigations of biomolecular structures. Their use however is still not as widely adopted as the traditional methods of structure determination by NMR, despite their potential for extending the limits in studies that examine both the structure and dynamics of biomolecules. This is in part due to the difficulties associated with the analysis of this information-rich data type. The software analysis tool REDCRAFT was previously introduced to address some of these challenges. Here we describe and evaluate a number of additional features that have been incorporated in order to extend its computational and analytical capabilities. REDCRAFT's more traditional enhancements integrate a modified steric collision term, as well as structural refinement in the rotamer space. Other, non-traditional improvements include: the filtering of viable structures based on relative order tensor estimates, decimation of the conformational space based on structural similarity, and forward/reverse folding of proteins. Utilizing REDCRAFT's newest features we demonstrate de-novo folding of proteins 1D3Z and 1P7E to within less than 1.6 Å of the corresponding X-ray structures, using as many as four RDCs per residue and as little as two RDCs per residue, in two alignment media. We also show the successful folding of a structure to less than 1.6 Å of the X-ray structure using {C(i-1)-N(i), N(i)-H(i), and C(i-1)-H(i)} RDCs in one alignment medium, and only {N(i)-H(i)} in the second alignment medium (a set of data which can be collected on deuterated samples). The program is available for download from our website at http://ifestos.cse.sc.edu .
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Affiliation(s)
- Mikhail Simin
- Department of Computer Science and Engineering, University of South Carolina, Columbia, SC, 29208, USA
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7
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Eriksson ESE, Joshi L, Billeter M, Eriksson LA. De novo tertiary structure prediction using RNA123--benchmarking and application to Macugen. J Mol Model 2014; 20:2389. [PMID: 25107358 DOI: 10.1007/s00894-014-2389-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 07/22/2014] [Indexed: 11/26/2022]
Abstract
The present benchmarking study utilizes the RNA123 program for de novo prediction of tertiary structures of a set of 50 RNA molecules for which X-ray/NMR structures are available, based on the nucleic acid sequence only. All molecules contain a hairpin loop motif and a helical structure of canonical and non-canonical base pairs, interrupted by bulges and internal loops to various degrees. RNA molecules with double helices made up purely by canonical base pairing, and molecules containing symmetric internal loops of non-canonical base pairing are, overall, very well predicted. Structures containing bulges and asymmetric internal loops, and more complex structures containing multiple bulges and internal loops in the same molecule, result in larger deviations from their X-ray/NMR predicted structures due to higher degree of flexibility of the nucleotide bases in these regions. In a majority of the molecules included herein, the RNA123 program was, however, able to predict the tertiary structure with a heavy atom RMSD of less than 5 Å to the X-ray/NMR structure, and the models were in most cases structurally closer to the X-ray/NMR structures than models predicted by MC-Fold and MC-Sym. A set of RNA molecules containing pseudoknot tertiary structure motifs were included, but neither of the programs was able to predict the folding of the single-stranded stem onto the helix without additional structural input. The RNA123 program was then applied to predict the tertiary structure of the RNA segment of Macugen®, the first RNA aptamer approved for clinical use, and for which no tertiary structure has yet been solved. Four possible tertiary structures were predicted for this 27-nucleic-acid-long RNA molecule, which will be used in constructing a full model of the PEGylated aptamer and its interaction with the vascular endothelial growth factor target.
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Affiliation(s)
- Emma S E Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30, Göteborg, Sweden,
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8
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Schmidt C, Irausquin SJ, Valafar H. Advances in the REDCAT software package. BMC Bioinformatics 2013; 14:302. [PMID: 24098943 PMCID: PMC3840585 DOI: 10.1186/1471-2105-14-302] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 09/13/2013] [Indexed: 12/24/2022] Open
Abstract
Background Residual Dipolar Couplings (RDCs) have emerged in the past two decades as an informative source of experimental restraints for the study of structure and dynamics of biological macromolecules and complexes. The REDCAT software package was previously introduced for the analysis of molecular structures using RDC data. Here we report additional features that have been included in this software package in order to expand the scope of its analyses. We first discuss the features that enhance REDCATs user-friendly nature, such as the integration of a number of analyses into one single operation and enabling convenient examination of a structural ensemble in order to identify the most suitable structure. We then describe the new features which expand the scope of RDC analyses, performing exercises that utilize both synthetic and experimental data to illustrate and evaluate different features with regard to structure refinement and structure validation. Results We establish the seamless interaction that takes place between REDCAT, VMD, and Xplor-NIH in demonstrations that utilize our newly developed REDCAT-VMD and XplorGUI interfaces. These modules enable visualization of RDC analysis results on the molecular structure displayed in VMD and refinement of structures with Xplor-NIH, respectively. We also highlight REDCAT’s Error-Analysis feature in reporting the localized fitness of a structure to RDC data, which provides a more effective means of recognizing local structural anomalies. This allows for structurally sound regions of a molecule to be identified, and for any refinement efforts to be focused solely on locally distorted regions. Conclusions The newly engineered REDCAT software package, which is available for download via the WWW from http://ifestos.cse.sc.edu, has been developed in the Object Oriented C++ environment. Our most recent enhancements to REDCAT serve to provide a more complete RDC analysis suite, while also accommodating a more user-friendly experience, and will be of great interest to the community of researchers and developers since it hides the complications of software development.
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Affiliation(s)
- Chris Schmidt
- Department of Computer Science & Engineering, University of South Carolina, Columbia, SC 29208, USA.
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Guttman M, Komives EA. The structure, dynamics, and binding of the LA45 module pair of the low-density lipoprotein receptor suggest an important role for LA4 in ligand release. Biochemistry 2011; 50:11001-8. [PMID: 22091758 DOI: 10.1021/bi2014486] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The low-density lipoprotein receptor (LDLR), the primary receptor for cholesterol uptake, binds ligands through its seven LDL-A modules (LAs). We present nuclear magnetic resonance (NMR) and ligand binding measurements on the fourth and fifth modules of the LDLR (LA45), the modules critical for ApoE binding, at physiological pH. Unlike LA5 and all other modules in LDLR, LA4 has a very weak calcium affinity, which probably plays a critical role in endosomal ligand release. The NMR solution structure of each module in the LA45 pair only showed minor differences compared to the analogous domains in previously determined crystal structures. The 12-residue linker connecting the modules, though slightly structured through an interaction with LA4, is highly flexible. Although no intermodule nuclear Overhauser effects were detected, chemical shift perturbations and backbone dynamics suggest cross talk between the two modules. The ligand affinity of both modules is enhanced when the two are linked. LA4 is more flexible than LA5 and remains so even in the module pair, which likely is related to its weaker calcium binding affinity.
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Affiliation(s)
- Miklos Guttman
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0378, United States
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10
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Shealy P, Liu Y, Simin M, Valafar H. Backbone resonance assignment and order tensor estimation using residual dipolar couplings. JOURNAL OF BIOMOLECULAR NMR 2011; 50:357-69. [PMID: 21667298 PMCID: PMC4071608 DOI: 10.1007/s10858-011-9521-5] [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: 02/25/2011] [Accepted: 05/19/2011] [Indexed: 05/23/2023]
Abstract
An NMR investigation of proteins with known X-ray structures is of interest in a number of endeavors. Performing these studies through nuclear magnetic resonance (NMR) requires the costly step of resonance assignment. The prevalent assignment strategy does not make use of existing structural information and requires uniform isotope labeling. Here we present a rapid and cost-effective method of assigning NMR data to an existing structure-either an X-ray or computationally modeled structure. The presented method, Exhaustively Permuted Assignment of RDCs (EPAR), utilizes unassigned residual dipolar coupling (RDC) data that can easily be obtained by NMR spectroscopy. The algorithm uses only the backbone N-H RDCs from multiple alignment media along with the amino acid type of the RDCs. It is inspired by previous work from Zweckstetter and provides several extensions. We present results on 13 synthetic and experimental datasets from 8 different structures, including two homodimers. Using just two alignment media, EPAR achieves an average assignment accuracy greater than 80%. With three media, the average accuracy is higher than 94%. The algorithm also outputs a prediction of the assignment accuracy, which has a correlation of 0.77 to the true accuracy. This prediction score can be used to establish the needed confidence in assignment accuracy.
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Affiliation(s)
- Paul Shealy
- Department of Computer Science and Engineering, University of South Carolina, 315 Main Street, Columbia, SC 29208, USA
| | - Yizhou Liu
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30603, USA
| | - Mikhail Simin
- Department of Computer Science and Engineering, University of South Carolina, 315 Main Street, Columbia, SC 29208, USA
| | - Homayoun Valafar
- Department of Computer Science and Engineering, University of South Carolina, 315 Main Street, Columbia, SC 29208, USA
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11
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Shi L, Traaseth NJ, Verardi R, Gustavsson M, Gao J, Veglia G. Paramagnetic-based NMR restraints lift residual dipolar coupling degeneracy in multidomain detergent-solubilized membrane proteins. J Am Chem Soc 2011; 133:2232-41. [PMID: 21287984 DOI: 10.1021/ja109080t] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Residual dipolar couplings (RDCs) are widely used as orientation-dependent NMR restraints to improve the resolution of the NMR conformational ensemble of biomacromolecules and define the relative orientation of multidomain proteins and protein complexes. However, the interpretation of RDCs is complicated by the intrinsic degeneracy of analytical solutions and protein dynamics that lead to ill-defined orientations of the structural domains (ghost orientations). Here, we illustrate how restraints from paramagnetic relaxation enhancement (PRE) experiments lift the orientational ambiguity of multidomain membrane proteins solubilized in detergent micelles. We tested this approach on monomeric phospholamban (PLN), a 52-residue membrane protein, which is composed of two helical domains connected by a flexible loop. We show that the combination of classical solution NMR restraints (NOEs and dihedral angles) with RDC and PRE constraints resolves topological ambiguities, improving the convergence of the PLN structural ensemble and giving the depth of insertion of the protein within the micelle. The combination of RDCs with PREs will be necessary for improving the accuracy and precision of membrane protein conformational ensembles, where three-dimensional structures are dictated by interactions with the membrane-mimicking environment rather than compact tertiary folds common in globular proteins.
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Affiliation(s)
- Lei Shi
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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12
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Wang X, Tash B, Flanagan JM, Tian F. RDC derived protein backbone resonance assignment using fragment assembly. JOURNAL OF BIOMOLECULAR NMR 2011; 49:85-98. [PMID: 21191805 PMCID: PMC6936109 DOI: 10.1007/s10858-010-9467-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 12/15/2010] [Indexed: 05/23/2023]
Abstract
Experimental residual dipolar couplings (RDCs) in combination with structural models have the potential for accelerating the protein backbone resonance assignment process because RDCs can be measured accurately and interpreted quantitatively. However, this application has been limited due to the need for very high-resolution structural templates. Here, we introduce a new approach to resonance assignment based on optimal agreement between the experimental and calculated RDCs from a structural template that contains all assignable residues. To overcome the inherent computational complexity of such a global search, we have adopted an efficient two-stage search algorithm and included connectivity data from conventional assignment experiments. In the first stage, a list of strings of resonances (CA-links) is generated via exhaustive searches for short segments of sequentially connected residues in a protein (local templates), and then ranked by the agreement of the experimental (13)C(α) chemical shifts and (15)N-(1)H RDCs to the predicted values for each local template. In the second stage, the top CA-links for different local templates in stage I are combinatorially connected to produce CA-links for all assignable residues. The resulting CA-links are ranked for resonance assignment according to their measured RDCs and predicted values from a tertiary structure. Since the final RDC ranking of CA-links includes all assignable residues and the assignment is derived from a "global minimum", our approach is far less reliant on the quality of experimental data and structural templates. The present approach is validated with the assignments of several proteins, including a 42 kDa maltose binding protein (MBP) using RDCs and structural templates of varying quality. Since backbone resonance assignment is an essential first step for most of biomolecular NMR applications and is often a bottleneck for large systems, we expect that this new approach will improve the efficiency of the assignment process for small and medium size proteins and will extend the size limits assignable by current methods for proteins with structural models.
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Affiliation(s)
- Xingsheng Wang
- Department of Biochemistry and Molecular Biology, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
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13
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Nicastro G, Masino L, Esposito V, Menon RP, De Simone A, Fraternali F, Pastore A. Josephin domain of ataxin-3 contains two distinct ubiquitin-binding sites. Biopolymers 2009; 91:1203-14. [DOI: 10.1002/bip.21210] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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14
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Martino L, He Y, Hands-Taylor KLD, Valentine ER, Kelly G, Giancola C, Conte MR. The interaction of the Escherichia coli protein SlyD with nickel ions illuminates the mechanism of regulation of its peptidyl-prolyl isomerase activity. FEBS J 2009; 276:4529-44. [PMID: 19645725 DOI: 10.1111/j.1742-4658.2009.07159.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The sensitive to lysis D (SlyD) protein from Escherichia coli is related to the FK506-binding protein family, and it harbours both peptidyl-prolyl cis-trans isomerase (PPIase) and chaperone-like activity, preventing aggregation and promoting the correct folding of other proteins. Whereas a functional role of SlyD as a protein-folding catalyst in vivo remains unclear, SlyD has been shown to be an essential component for [Ni-Fe]-hydrogenase metallocentre assembly in bacteria. Interestingly, the isomerase activity of SlyD is uniquely modulated by nickel ions, which possibly regulate its functions in response to external stimuli. In this work, we investigated the solution structure of SlyD and its interaction with nickel ions, enabling us to gain insights into the molecular mechanism of this regulation. We have revealed that the PPIase module of SlyD contains an additional C-terminal alpha-helix packed against the catalytic site of the domain; unexpectedly, our results show that the interaction of SlyD with nickel ions entails participation of the novel structural features of the PPIase domain, eliciting structural alterations of the catalytic pocket. We suggest that such conformational rearrangements upon metal binding underlie the ability of nickel ions to regulate the isomerase activity of SlyD.
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Affiliation(s)
- Luigi Martino
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
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Mukhopadhyay R, Miao X, Shealy P, Valafar H. Efficient and accurate estimation of relative order tensors from lambda-maps. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 198:236-247. [PMID: 19345125 PMCID: PMC4071621 DOI: 10.1016/j.jmr.2009.02.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 02/17/2009] [Accepted: 02/27/2009] [Indexed: 05/25/2023]
Abstract
The rapid increase in the availability of RDC data from multiple alignment media in recent years has necessitated the development of more sophisticated analyses that extract the RDC data's full information content. This article presents an analysis of the distribution of RDCs from two media (2D-RDC data), using the information obtained from a lambda-map. This article also introduces an efficient algorithm, which leverages these findings to extract the order tensors for each alignment medium using unassigned RDC data in the absence of any structural information. The results of applying this 2D-RDC analysis method to synthetic and experimental data are reported in this article. The relative order tensor estimates obtained from the 2D-RDC analysis are compared to order tensors obtained from the program REDCAT after using assignment and structural information. The final comparisons indicate that the relative order tensors estimated from the unassigned 2D-RDC method very closely match the results from methods that require assignment and structural information. The presented method is successful even in cases with small datasets. The results of analyzing experimental RDC data for the protein 1P7E are presented to demonstrate the potential of the presented work in accurately estimating the principal order parameters from RDC data that incompletely sample the RDC space. In addition to the new algorithm, a discussion of the uniqueness of the solutions is presented; no more than two clusters of distinct solutions have been shown to satisfy each lambda-map.
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16
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Feng H, Cai S, Chen Z, Lin M, Feng J. Application of the forward linear prediction on high-resolution NMR spectra in inhomogeneous fields. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2008; 71:1027-1031. [PMID: 18417415 DOI: 10.1016/j.saa.2008.02.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Revised: 02/24/2008] [Accepted: 02/28/2008] [Indexed: 05/26/2023]
Abstract
In homogeneous fields, the advantages of forward linear prediction (LP) for processing 2D NMR data sets have long been recognized. In this paper, the forward LP method was employed to obtain high-resolution NMR spectra in inhomogeneous fields. Intermolecular multiple-quantum coherence (iMQC) signals are caused by intermolecular dipolar interactions and can be used to obtain 1D high-resolution NMR spectra from the 2D iMQC spectra acquired in inhomogeneous fields. However, when the 2D spectra are acquired with insufficient increments to save experimental time, wiggles around strong peaks and bad resolution will occur. Extending the data set by forward LP in the indirect dimension is a good way to improve spectral resolution. Compared to normal discrete Fourier transform, the forward LP method can shorten experimental time by a factor of four or more at the same level of sensitivity and resolution.
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Affiliation(s)
- Hai Feng
- Department of Physics, State Key Laboratory of Physical Chemistry of Solid Surface, Xiamen University, Xiamen, Fujian 361005, China
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17
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Abstract
Orientational restraints such as residual dipolar couplings promise to overcome many of the problems that traditionally limited liquid-state nuclear magnetic resonance spectroscopy. Recently, we developed methods to predict a molecular alignment tensor and thus residual dipolar couplings for a given molecular structure. This provides many new opportunities for the study of the structure and dynamics of proteins, nucleic acids, oligosaccharides and small molecules. This protocol details the use of the software PALES (Prediction of AlignmEnt from Structure) for prediction of an alignment tensor from a known three-dimensional (3D) coordinate file of a solute. The method is applicable to alignment of molecules in many neutral and charged orienting media and takes into account the molecular shape and 3D charge distribution of the molecule.
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18
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Canlas CG, Ma D, Tang P, Xu Y. Residual dipolar coupling measurements of transmembrane proteins using aligned low-q bicelles and high-resolution magic angle spinning NMR spectroscopy. J Am Chem Soc 2008; 130:13294-300. [PMID: 18788737 PMCID: PMC2704097 DOI: 10.1021/ja802578z] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bicelles are a major medium form to produce weak alignment of soluble proteins for residual dipolar coupling (RDC) measurements. The obstacle to using the same type of bicelles for transmembrane proteins with solution-state NMR spectroscopy is the loss of signals due to the adhesion or penetration of the proteins into large bicelles, resulting in slow protein tumbling. In this study, weak alignment of the second and third transmembrane domains (TM23) of the human glycine receptor (GlyR) was achieved in low-q bicelles (q = DMPC/DHPC). Although protein-free bicelles with such low q would likely show isotropic properties, the insertion of TM23 induced weakly preferred orientations so that the RDC of the embedded protein can be measured. The extent of the alignment increased but the TM23 signal intensity decreased when q was varied from 0.19 to 0.60. A q of 0.50 was found to be an optimal compromise between alignment and the signal-to-noise ratio. In each pair of NMR experiments for RDC measurements, the same sample and pulse sequence were used, with one being performed at high-resolution magic-angle spinning to obtain pure J-couplings without RDC. A meaningful structure refinement in bicelles was possible by iteratively fitting the experimental RDCs to the back-calculated RDCs using the high-resolution NMR structure of GlyR TM23 in trifluoroethanol as the starting template. Combination of this method with the conventional high-resolution NMR in membrane mimicking mixtures of water and organic solvents offers an attractive way to derive structural information for membrane proteins in their native environment.
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Affiliation(s)
- Christian G. Canlas
- Departments of Anesthesiology, Pharmacology, and Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260
| | - Dejian Ma
- Departments of Anesthesiology, Pharmacology, and Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260
| | - Pei Tang
- Departments of Anesthesiology, Pharmacology, and Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260
| | - Yan Xu
- Departments of Anesthesiology, Pharmacology, and Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260
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19
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Miao X, Mukhopadhyay R, Valafar H. Estimation of relative order tensors, and reconstruction of vectors in space using unassigned RDC data and its application. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 194:202-11. [PMID: 18692422 PMCID: PMC2669903 DOI: 10.1016/j.jmr.2008.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Revised: 06/27/2008] [Accepted: 07/02/2008] [Indexed: 05/11/2023]
Abstract
Advances in NMR instrumentation and pulse sequence design have resulted in easier acquisition of Residual Dipolar Coupling (RDC) data. However, computational and theoretical analysis of this type of data has continued to challenge the international community of investigators because of their complexity and rich information content. Contemporary use of RDC data has required a-priori assignment, which significantly increases the overall cost of structural analysis. This article introduces a novel algorithm that utilizes unassigned RDC data acquired from multiple alignment media (nD-RDC, n3) for simultaneous extraction of the relative order tensor matrices and reconstruction of the interacting vectors in space. Estimation of the relative order tensors and reconstruction of the interacting vectors can be invaluable in a number of endeavors. An example application has been presented where the reconstructed vectors have been used to quantify the fitness of a template protein structure to the unknown protein structure. This work has other important direct applications such as verification of the novelty of an unknown protein and validation of the accuracy of an available protein structure model in drug design. More importantly, the presented work has the potential to bridge the gap between experimental and computational methods of structure determination.
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Affiliation(s)
- Xijiang Miao
- Computer Science and Engineering, Swearingen Engineering Center, University of South Carolina, Columbia, SC 29308, USA
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20
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Bansal S, Miao X, Adams MWW, Prestegard JH, Valafar H. Rapid classification of protein structure models using unassigned backbone RDCs and probability density profile analysis (PDPA). JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 192:60-8. [PMID: 18321742 PMCID: PMC2699457 DOI: 10.1016/j.jmr.2008.01.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Revised: 01/19/2008] [Accepted: 01/29/2008] [Indexed: 05/22/2023]
Abstract
A method of identifying the best structural model for a protein of unknown structure from a list of structural candidates using unassigned 15N1H residual dipolar coupling (RDC) data and probability density profile analysis (PDPA) is described. Ten candidate structures have been obtained for the structural genomics target protein PF2048.1 using ROBETTA. 15N1H residual dipolar couplings have been measured from NMR spectra of the protein in two alignment media and these data have been analyzed using PDPA to rank the models in terms of their ability to represent the actual structure. A number of advantages in using this method to characterize a protein structure become apparent. RDCs can easily and rapidly be acquired, and without the need for assignment, the cost and duration of data acquisition is greatly reduced. The approach is quite robust with respect to imprecise and missing data. In the case of PF2048.1, a 79 residue protein, only 58 and 55 of the total RDC data were observed. The method can accelerate structure determination at higher resolution using traditional NMR spectroscopy by providing a starting point for the addition of NOEs and other NMR structural data.
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Affiliation(s)
- Sonal Bansal
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602
| | - Xijiang Miao
- Computer Science and Engineering, University of South Carolina, Columbia SC 29308, USA
| | | | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602
| | - Homayoun Valafar
- Computer Science and Engineering, University of South Carolina, Columbia SC 29308, USA
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21
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Yao L, Vögeli B, Torchia DA, Bax A. Simultaneous NMR study of protein structure and dynamics using conservative mutagenesis. J Phys Chem B 2008; 112:6045-56. [PMID: 18358021 DOI: 10.1021/jp0772124] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel iterative procedure is described that allows both the orientation and dynamics of internuclear bond vectors to be determined from direct interpretation of NMR dipolar couplings, measured under at least three orthogonal alignment conditions. If five orthogonal alignments are available, the approach also yields information on the degree of motional anisotropy and the direction in which the largest amplitude internal motion of each bond vector takes place. The method is demonstrated for the backbone (15)N-(1)H, (13)C(alpha)-(1)H(alpha), and (13)C(alpha)-13C' interactions in the previously well-studied protein domain GB3, dissolved in a liquid crystalline suspension of filamentous phage Pf1. Alignment variation is achieved by using conservative mutations of charged surface residues. Results indicate remarkably uniform backbone dynamics, with amplitudes that agree well with those of previous (15)N relaxation studies for most residues involved in elements of secondary structure, but larger amplitude dynamics than those found by (15)N relaxation for residues in loop and turn regions. In agreement with a previous analysis of dipolar couplings, the N-H bonds in the second beta-strand, which is involved in antibody recognition, show elevated dynamics with largest amplitudes orthogonal to the chain direction.
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Affiliation(s)
- Lishan Yao
- Laboratory of Chemical Physics, NIDDK, and National Institute of Dental and Cranofacial Research, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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22
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Habeck M, Nilges M, Rieping W. A unifying probabilistic framework for analyzing residual dipolar couplings. JOURNAL OF BIOMOLECULAR NMR 2008; 40:135-44. [PMID: 18095170 PMCID: PMC2758374 DOI: 10.1007/s10858-007-9215-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2007] [Revised: 11/21/2007] [Accepted: 11/26/2007] [Indexed: 05/11/2023]
Abstract
Residual dipolar couplings provide complementary information to the nuclear Overhauser effect measurements that are traditionally used in biomolecular structure determination by NMR. In a de novo structure determination, however, lack of knowledge about the degree and orientation of molecular alignment complicates the analysis of dipolar coupling data. We present a probabilistic framework for analyzing residual dipolar couplings and demonstrate that it is possible to estimate the atomic coordinates, the complete molecular alignment tensor, and the error of the couplings simultaneously. As a by-product, we also obtain estimates of the uncertainty in the coordinates and the alignment tensor. We show that our approach encompasses existing methods for determining the alignment tensor as special cases, including least squares estimation, histogram fitting, and elimination of an explicit alignment tensor in the restraint energy.
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Affiliation(s)
- Michael Habeck
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, Spemannstr. 35, 72076 Tubingen, Germany
- Department of Empirical Inference, Max-Planck-Institute for Biological Cybernetics, Spemannstr. 38, 72076 Tubingen, Germany
| | - Michael Nilges
- Unité de Bioinformatique Structurale, Institut Pasteur, 25-28 Rue du Dr. Roux, 75724 Paris CEDEX 15, France
| | - Wolfgang Rieping
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
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23
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Shankar N, Xia T, Kennedy SD, Krugh TR, Mathews DH, Turner DH. NMR reveals the absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA. Biochemistry 2007; 46:12665-78. [PMID: 17929882 DOI: 10.1021/bi700802s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
NMR studies provide insights into structural features of internal loops. These insights can be combined with thermodynamic studies to generate models for predicting structure and energetics. The tandem mismatch internal loop, 5'GUGG3'(3'CUAC5'), has been studied by NMR. The NMR structure reveals an internal loop with no hydrogen bonding between the loop bases and with the G in the AG mismatch flipped out of the helix. The sequence of this internal loop is highly conserved in rRNA. The loop is located in the large ribosomal subunit and is part of a conserved 58-nt fragment that is the binding domain of ribosomal protein L11. Structural comparisons between variants of this internal loop in crystal structures of the 58-nt domain complexed with L11 protein and of the large ribosomal subunit (LSU) suggest that this thermodynamically destabilizing internal loop is partially preorganized for tertiary interactions and for binding L11. A model for predicting the base pairing and free energy of 2 x 2 nucleotide internal loops with a purine-purine mismatch next to a pyrimidine-pyrimidine mismatch is proposed on the basis of the present NMR structure and previously reported thermodynamics.
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Affiliation(s)
- Neelaabh Shankar
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642, USA
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24
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DeSilva TM, Veglia G, Opella SJ. Solution structures of the reduced and Cu(I) bound forms of the first metal binding sequence of ATP7A associated with Menkes disease. Proteins 2006; 61:1038-49. [PMID: 16211579 DOI: 10.1002/prot.20639] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The coding sequence for the first N-terminal copper binding motif of the human Menkes disease protein (MNK1; residues 2-79) was synthesized, cloned, and expressed in bacteria for biochemical and structural studies. MNK1 adopts the betaalphabetabetaalphabeta fold common to all the metal binding sequences (MBS) found in other metal transport systems (e.g., the yeast copper chaperone for superoxide dismutase CCS, the yeast copper chaperone ATX1 bound to Hg(II), and most recently Cu(I), the bacterial copper binding protein, CopZ, and the bacterial Hg(II) binding protein MerP), although substantial differences were found in the metal binding loop. Similar to ATX1, MNK1 binds Cu(I) in a distorted linear bicoordinate geometry. As with MerP, MNK1 has a high affinity for both Hg(II) and Cu(I), although it displays a marked preference for Cu(I). In addition, we found that F71 is a key residue in the compact folding of MNK1, and its mutation to alanine results in an unfolded structure. The homologous residue in MerP has also been mutated with similar results. Finally, to understand the relationship between protein folding and metal affinity and specificity, we expressed a chimeric MBS with the MNK1 protein carrying the binding motif of MerP (CAAC-MNK1); this chimeric protein showed differences in structure and the dynamics of the binding site that may account for metal specificity.
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Affiliation(s)
- Tara M DeSilva
- Department of Neurology, Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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25
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Seetharaman M, Eldho NV, Padgett RA, Dayie KT. Structure of a self-splicing group II intron catalytic effector domain 5: parallels with spliceosomal U6 RNA. RNA (NEW YORK, N.Y.) 2006; 12:235-47. [PMID: 16428604 PMCID: PMC1370903 DOI: 10.1261/rna.2237806] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2005] [Accepted: 11/03/2005] [Indexed: 05/06/2023]
Abstract
Domain 5 (D5) is absolutely required for all catalytic functions of group II introns. Here we describe the solution NMR structure, electrostatic calculations, and detailed magnesium ion-binding surface of D5 RNA from the Pylaiella littoralis large ribosomal RNA intron (D5-PL). The overall structure consists of a hairpin capped by a GNRA tetraloop. The stem is divided into lower and upper helices of 8 and 5 bp, respectively, separated by an internal bulge. The D5-PL internal bulge nucleotides stack into the helical junction, resulting in a coupling between the bulge A25 and the closing base pair (G8-C27) of the lower helix. Comparison of the D5-PL structure to previously reported related structures indicates that our structure is most similar, in the helical regions, to the crystal structure of D5 from yeast Ai5gamma (D5-Ai5gamma) and the NMR structure of the U6 snRNA stem-loop region. Our structure differs in many respects from both the NMR and X-ray structures of D5-Ai5gamma in the bulge region. Electrostatic calculations and NMR chemical shift perturbation analyses reveal magnesium ion-binding sites in the tetraloop, internal bulge, and the AGC triad in the lower stem. Our results suggest that the structure, electrostatic environment, and the magnesium ion-binding sites within the tetraloop, bulge, and triad regions are conserved features of the splicing machinery of both the group II introns and the spliceosome that are likely key for catalytic function.
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Affiliation(s)
- Mahadevan Seetharaman
- Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
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26
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de Chiara C, Menon RP, Adinolfi S, de Boer J, Ktistaki E, Kelly G, Calder L, Kioussis D, Pastore A. The AXH Domain Adopts Alternative Folds. Structure 2005; 13:743-53. [PMID: 15893665 DOI: 10.1016/j.str.2005.02.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2005] [Revised: 02/20/2005] [Accepted: 02/22/2005] [Indexed: 11/24/2022]
Abstract
AXH is a protein module identified in two unrelated families that comprise the transcriptional repressor HBP1 and ataxin-1 (ATX1), the protein responsible for spinocerebellar ataxia type-1 (SCA1). SCA1 is a neurodegenerative disorder associated with protein misfolding and formation of toxic intranuclear aggregates. We have solved the structure in solution of monomeric AXH from HBP1. The domain adopts a nonclassical permutation of an OB fold and binds nucleic acids, a function previously unidentified for this region of HBP1. Comparison of HBP1 AXH with the crystal structure of dimeric ATX1 AXH indicates that, despite the significant sequence homology, the two proteins have different topologies, suggesting that AXH has chameleon properties. We further demonstrate that HBP1 AXH remains monomeric, whereas the ATX1 dimer spontaneously aggregates and forms fibers. Our results describe an entirely novel, to our knowledge, example of a chameleon fold and suggest a link between these properties and the SCA1 pathogenesis.
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Affiliation(s)
- Cesira de Chiara
- National Institute for Medical Research, The Ridgeway, London, United Kingdom
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27
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Prestegard JH, Mayer KL, Valafar H, Benison GC. Determination of protein backbone structures from residual dipolar couplings. Methods Enzymol 2005; 394:175-209. [PMID: 15808221 PMCID: PMC1808351 DOI: 10.1016/s0076-6879(05)94007-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
There are a number of circumstances in which a focus on determination of the backbone structure of a protein, as opposed to a complete all-atom structure, may be appropriate. This is particularly the case for structures determined as a part of a structural genomics initiative in which computational modeling of many sequentially related structures from the backbone of a single family representative is anticipated. It is, however, also the case when the backbone may be a stepping-stone to more targeted studies of ligand interaction or protein-protein interaction. Here an NMR protocol is described that can produce a backbone structure of a protein without the need for extensive experiments directed at side chain resonance assignment or the collection of structural information on side chains. The procedure relies primarily on orientational constraints from residual dipolar couplings as opposed to distance constraints from NOEs. Procedures for sample preparation, data acquisition, and data analysis are described, along with examples from application to small target proteins of a structural genomics project.
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Affiliation(s)
- J H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens 30602, USA
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28
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Mascioni A, Eggimann BL, Veglia G. Determination of helical membrane protein topology using residual dipolar couplings and exhaustive search algorithm: application to phospholamban. Chem Phys Lipids 2004; 132:133-44. [PMID: 15530454 DOI: 10.1016/j.chemphyslip.2004.09.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Dipolar waves are distinct hallmarks of both the secondary and tertiary structures of alpha-helical proteins that are immobilized in membrane bilayers or embedded in anisotropic media. We present a simple, semi-empirical approach that exploits the modulation of the amplitude and average of dipolar waves to determine the topology of alpha-helical proteins. Moreover, we describe the application of this method for the structural determination of a detergent solubilized membrane protein, phospholamban (PLB) that is involved in calcium regulation of cardiac muscle. When combined with high-resolution solid-state NMR data, this method can serve as a fast route for determining the topology of helical membrane proteins solubilized in detergent micelles.
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Affiliation(s)
- Alessandro Mascioni
- Department of Chemistry, University of Minnesota, 207 Pleasant St. S.E. Minneapolis, MN 55455, USA
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29
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Di Lello P, Benison GC, Valafar H, Pitts KE, Summers AO, Legault P, Omichinski JG. NMR structural studies reveal a novel protein fold for MerB, the organomercurial lyase involved in the bacterial mercury resistance system. Biochemistry 2004; 43:8322-32. [PMID: 15222745 DOI: 10.1021/bi049669z] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mercury resistant bacteria have developed a system of two enzymes (MerA and MerB), which allows them to efficiently detoxify both ionic and organomercurial compounds. The organomercurial lyase (MerB) catalyzes the protonolysis of the carbon-mercury bond resulting in the formation of ionic mercury and a reduced hydrocarbon. The ionic mercury [Hg(II)] is subsequently reduced to the less reactive elemental mercury [Hg(0)] by a specific mercuric reductase (MerA). To better understand MerB's unique enzymatic activity, we used nuclear magnetic resonance (NMR) spectroscopy to determine the structure of the free enzyme. MerB is characterized by a novel protein fold consisting of three noninteracting antiparallel beta-sheets surrounded by six alpha-helices. By comparing the NMR data of free MerB and the MerB/Hg/DTT complex, we identified a set of residues that likely define a Hg/DTT binding site. These residues cluster around two cysteines (C(96) and C(159)) that are crucial to MerB's catalytic activity. A detailed analysis of the structure revealed the presence of an extensive hydrophobic groove adjacent to this Hg/DTT binding site. This extensive hydrophobic groove has the potential to interact with the hydrocarbon moiety of a wide variety of substrates and may explain the broad substrate specificity of MerB.
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Affiliation(s)
- Paola Di Lello
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
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30
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Abstract
Residual dipolar couplings (RDCs) have recently emerged as a new tool in nuclear magnetic resonance (NMR) with which to study macromolecular structure and function in a solution environment. RDCs are complementary to the more conventional use of NOEs to provide structural information. While NOEs are local-distance restraints, RDCs provide long-range orientational information. RDCs are now widely utilized in structure calculations. Increasingly, they are being used in novel applications to address complex issues in structural biology such as the accurate determination of the global structure of oligonucleotides and the relative orientation of protein domains. This review briefly describes the theory and methods for obtaining RDCs and then describes the range of biological applications where RDCs have been used.
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Affiliation(s)
- Rebecca S Lipsitz
- Laboratory of Biophysical Chemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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31
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Alfano C, Sanfelice D, Babon J, Kelly G, Jacks A, Curry S, Conte MR. Structural analysis of cooperative RNA binding by the La motif and central RRM domain of human La protein. Nat Struct Mol Biol 2004; 11:323-9. [PMID: 15004549 DOI: 10.1038/nsmb747] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2004] [Accepted: 02/19/2004] [Indexed: 11/08/2022]
Abstract
The La protein is a conserved component of eukaryotic ribonucleoprotein complexes that binds the 3' poly(U)-rich elements of nascent RNA polymerase III (pol III) transcripts to assist folding and maturation. This specific recognition is mediated by the N-terminal domain (NTD) of La, which comprises a La motif and an RNA recognition motif (RRM). We have determined the solution structures of both domains and show that the La motif adopts an alpha/beta fold that comprises a winged-helix motif elaborated by the insertion of three helices. Chemical shift mapping experiments show that these insertions are involved in RNA interactions. They further delineate a distinct surface patch on each domain-containing both basic and aromatic residues-that interacts with RNA and accounts for the cooperative binding of short oligonucleotides exhibited by the La NTD.
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Affiliation(s)
- Caterina Alfano
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, St. Michael's Building, Portsmouth PO1 2DT, UK
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32
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Sigel RKO, Sashital DG, Abramovitz DL, Palmer AG, Butcher SE, Pyle AM. Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif. Nat Struct Mol Biol 2004; 11:187-92. [PMID: 14745440 DOI: 10.1038/nsmb717] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2003] [Accepted: 10/29/2003] [Indexed: 11/08/2022]
Abstract
Domain 5 (D5) is the central core of group II intron ribozymes. Many base and backbone substituents of this highly conserved hairpin participate in catalysis and are crucial for binding to other intron domains. We report the solution structures of the 34-nucleotide D5 hairpin from the group II intron ai5 gamma in the absence and presence of divalent metal ions. The bulge region of D5 adopts a novel fold, where G26 adopts a syn conformation and flips down into the major groove of helix 1, close to the major groove face of the catalytic AGC triad. The backbone near G26 is kinked, exposing the base plane of the adjacent A-U pair to the solvent and causing bases of the bulge to stack intercalatively. Metal ion titrations reveal strong Mg(2+) binding to a minor groove shelf in the D5 bulge. Another distinct metal ion-binding site is observed along the minor groove side of the catalytic triad, in a manner consistent with metal ion binding in the ribozyme active site.
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Affiliation(s)
- Roland K O Sigel
- Department of Chemistry, Winterthurerstrasse 190, University of Zürich, CH-8057 Zürich, Switzerland
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33
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Jacobs DM, Saxena K, Vogtherr M, Bernado P, Pons M, Fiebig KM. Peptide binding induces large scale changes in inter-domain mobility in human Pin1. J Biol Chem 2003; 278:26174-82. [PMID: 12686540 DOI: 10.1074/jbc.m300796200] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pin1 is a peptidyl-prolyl cis/trans isomerase (PPIase) essential for cell cycle regulation. Pin1-catalyzed peptidyl-prolyl isomerization provides a key conformational switch to activate phosphorylation sites with the common phospho-Ser/Thr-Pro sequence motif. This motif is ubiquitously exploited in cellular response to a variety of signals. Pin1 is able to bind phospho-Ser/Thr-Pro-containing sequences at two different sites that compete for the same substrate. One binding site is located within the N-terminal WW domain, which is essential for protein targeting and localization. The other binding site is located in the C-terminal catalytic domain, which is structural homologous to the FK506-binding protein (FKBP) class of PPIases. A flexible linker of 12 residues connects the WW and catalytic domain. To characterize the structure and dynamics of full-length Pin1 in solution, high resolution NMR methods have been used to map the nature of interactions between the two domains of Pin1. In addition, the influence of target peptides on domain interactions has been investigated. The studies reveal a dynamic picture of the domain interactions. 15N spin relaxation data, differential chemical shift mapping, and residual dipolar coupling data indicate that Pin1 can either behave as two independent domains connected by the flexible linker or as a single intact domain with some amount of hinge bending motion depending on the sequence of the bound peptide. The functional importance of the modulation of relative domain flexibility in light of the multitude of interaction partners of Pin1 is discussed.
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Affiliation(s)
- Doris M Jacobs
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Marie-Curie Strasse 11, 60439 Frankfurt, Germany.
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Jacks A, Babon J, Kelly G, Manolaridis I, Cary PD, Curry S, Conte MR. Structure of the C-terminal domain of human La protein reveals a novel RNA recognition motif coupled to a helical nuclear retention element. Structure 2003; 11:833-43. [PMID: 12842046 DOI: 10.1016/s0969-2126(03)00121-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The La protein is an important component of ribonucleoprotein complexes that acts mainly as an RNA chaperone to facilitate correct processing and maturation of RNA polymerase III transcripts, but can also stimulate translation initiation. We report here the structure of the C-terminal domain of human La, which comprises an atypical RNA recognition motif (La225-334) and a long unstructured C-terminal tail. The central beta sheet of La225-334 reveals novel features: the putative RNA binding surface is formed by a five-stranded beta sheet and, strikingly, is largely obscured by a long C-terminal alpha helix that encompasses a recently identified nuclear retention element. Contrary to previous observations, we find that the La protein does not contain a dimerization domain.
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Affiliation(s)
- Amanda Jacks
- Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, St Michael's Building, PO1 2DT, Portsmouth, United
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35
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Abstract
RNA motifs are directed and ordered stacked arrays of non-Watson-Crick base pairs forming distinctive foldings of the phosphodiester backbones of the interacting RNA strands. They correspond to the 'loops' - hairpin, internal and junction - that intersperse the Watson-Crick two-dimensional helices as seen in two-dimensional representations of RNA structure. RNA motifs mediate the specific interactions that induce the compact folding of complex RNAs. RNA motifs also constitute specific protein or ligand binding sites. A given motif is characterized by all the sequences that fold into essentially identical three-dimensional structures with the same ordered array of isosteric non-Watson-Crick base pairs. It is therefore crucial, when analyzing a three-dimensional RNA structure in order to identify and compare motifs, to first classify its non-Watson-Crick base pairs geometrically.
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Affiliation(s)
- Neocles B Leontis
- Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA.
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36
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Reiter NJ, Nikstad LJ, Allmann AM, Johnson RJ, Butcher SE. Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification. RNA (NEW YORK, N.Y.) 2003; 9:533-42. [PMID: 12702812 PMCID: PMC1370419 DOI: 10.1261/rna.2199103] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2002] [Accepted: 01/29/2003] [Indexed: 05/20/2023]
Abstract
Phosphorothioate-substitution experiments are often used to elucidate functionally important metal ion-binding sites on RNA. All previous experiments with S(P)-phosphorothioate-substituted RNAs have been done in the absence of structural information for this particular diastereomer. Yeast U6 RNA contains a metal ion-binding site that is essential for spliceosome function and includes the pro-S(P) oxygen 5' of U(80). S(P)-phosphorothioate substitution at this location creates spliceosomes dependent on thiophilic ions for the first step of splicing. We have determined the solution structure of the U(80) S(P)-phosphorothioate-substituted U6 intramolecular stem-loop (ISL), and also report the refined NMR structure of the unmodified U6 ISL. Both structures were determined with inclusion of (1)H-(13)C residual dipolar couplings. The precision of the structures with and without phosphorothioate (RMSD = 1.05 and 0.79 A, respectively) allows comparison of the local and long-range structural effect of the modification. We find that the U6-ISL structure is unperturbed by the phosphorothioate. Additionally, the thermodynamic stability of the U6 ISL is dependent on the protonation state of the A(79)-C(67) wobble pair and is not affected by the adjacent phosphorothioate. These results indicate that a single S(P)-phosphorothioate substitution can be structurally benign, and further validate the metal ion rescue experiments used to identify the essential metal-binding site(s) in the spliceosome.
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Affiliation(s)
- Nicholas J Reiter
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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37
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McCallum SA, Pardi A. Refined solution structure of the iron-responsive element RNA using residual dipolar couplings. J Mol Biol 2003; 326:1037-50. [PMID: 12589752 DOI: 10.1016/s0022-2836(02)01431-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The iron-responsive element (IRE) is a 30nt RNA motif located in the non-coding regions of mRNAs of proteins involved in iron regulation. In humans, the IRE plays a direct role in the control of iron levels by post-transcriptional regulation of the ferritin and transferrin receptor proteins through highly specific recognition by IRE-binding proteins. The IRE fold is representative of many RNA motifs that contain helical domains separated by a bulge or internal loop. The global structures of such extended multi-domain RNAs are not well defined by conventional NMR-distance and torsion angle structural restraints. Residual dipolar couplings (RDCs) are employed here to better define the global structure of the IRE RNA in solution. RDCs contain valuable long-range structural information that compliments the short-range structural data derived from standard NOE-distance and torsion angle restraints. Several approaches for estimating alignment tensor parameters and incorporating RDCs into RNA structure determinations are compared. Both the local and global structure of the IRE are improved significantly by refinement with RDCs. These RDC refinements provide insight on the conformational dynamics of the IRE. These studies highlight some issues that need to be addressed when incorporating RDCs in solution structure determinations of nucleic acids. The approach used here should prove valuable for structure determinations of various multi-domain systems.
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Affiliation(s)
- Scott A McCallum
- Department of Chemistry and Biochemistry, 215 UCB, University of Colorado, Boulder, CO 80309-0215, USA
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38
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Sashital DG, Allmann AM, Van Doren SR, Butcher SE. Structural basis for a lethal mutation in U6 RNA. Biochemistry 2003; 42:1470-7. [PMID: 12578359 PMCID: PMC3124365 DOI: 10.1021/bi027137h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
U6 RNA is essential for nuclear pre-mRNA splicing and has been implicated directly in catalysis of intron removal. The U80G mutation at the essential magnesium binding site of the U6 3' intramolecular stem-loop region (ISL) is lethal in yeast. To further understand the structure and function of the U6 ISL, we have investigated the structural basis for the lethal U80G mutation by NMR and optical spectroscopy. The NMR structure reveals that the U80G mutation causes a structural rearrangement within the ISL resulting in the formation of a new Watson-Crick base pair (C67 x G80), and disrupts a protonated C67 x A79 wobble pair that forms in the wild-type structure. Despite the structural change, the accessibility of the metal binding site is unperturbed, and cadmium titration produces similar phosphorus chemical shift changes for both the U80G mutant and wild-type RNAs. The thermodynamic stability of the U80G mutant is significantly increased (Delta Delta G(fold) = -3.6 +/- 1.9 kcal/mol), consistent with formation of the Watson-Crick pair. Our structural and thermodynamic data, in combination with previous genetic data, suggest that the lethal basis for the U80G mutation is stem-loop hyperstabilization. This hyperstabilization may prevent the U6 ISL melting and rearrangement necessary for association with U4.
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Affiliation(s)
| | | | | | - Samuel E. Butcher
- To whom correspondence should be addressed: 433 Babcock Dr., Madison, WI 53706.
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Nair M, McIntosh PB, Frenkiel TA, Kelly G, Taylor IA, Smerdon SJ, Lane AN. NMR structure of the DNA-binding domain of the cell cycle protein Mbp1 from Saccharomyces cerevisiae. Biochemistry 2003; 42:1266-73. [PMID: 12564929 DOI: 10.1021/bi0205247] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The three-dimensional solution structure of the DNA-binding domain of Mlu-1 box binding protein (Mbp1) has been determined by multidimensional NMR spectroscopy. Mbp1 is a cell cycle transcription factor from Saccharomyces cerevisiae and consists of an N-terminal DNA-binding domain, a series of ankyrin repeats, and a heterodimerization domain at the C-terminus. A set of conformers comprising 19 refined structures was calculated via a molecular dynamics simulated annealing protocol using distance, dihedral angle, and residual dipolar coupling restraints derived from either double or triple resonance NMR experiments. The solution structure consists of a six-stranded beta-sheet segment folded against two pairs of alpha-helices in the topology of the winged helix-turn-helix family of proteins and is in agreement with the X-ray structures. In addition, the solution structure shows that the C-terminal tail region of this domain folds back and makes specific interactions with the N-terminal beta-strand of the protein. This C-terminal region is essential for full DNA-binding activity but appears in the X-ray structure to be disordered. The fold-back structure extends the region of positive electrostatic potential, and this may enhance the nonspecific contribution to binding by favorable electrostatic interactions with the DNA backbone.
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Affiliation(s)
- Margie Nair
- Division of Molecular Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
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40
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Gronenborn AM. The importance of being ordered: improving NMR structures using residual dipolar couplings. C R Biol 2002; 325:957-66. [PMID: 12481689 DOI: 10.1016/s1631-0691(02)01512-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Residual dipolar couplings arise from small degrees of alignment of molecules in a magnetic field. Most biomolecules lack sufficient intrinsic magnetic susceptibility anisotropies for practical purposes; however, alignment can be achieved using dilute aqueous phospholipid mixtures, colloidal suspensions of rod-shaped viruses, complex phases of surfactant systems and strained gels. The stability of the liquid crystalline phases varies with respect to temperature range, pH variation and time and is critically dependent on sample composition and experimental conditions. The magnitude of the residual dipolar couplings depends upon the degree of ordering and allows the determination of the corresponding inter-nuclear vectors with respect to the molecule's alignment frame. Inclusion of dipolar constraints into NMR structure calculations leads to improved precision and accuracy of the resulting structures, especially in cases where the information content provided by traditional NOE constraints is limited. In addition, rapid evaluation of backbone protein folds and determination of the relative orientations of individual components in multi-molecular complexes have become feasible. Dipolar coupling based strategies may well emerge as the most critical developments, in establishing NMR as a valuable and competitive methodology in the structural genomics initiative.
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Affiliation(s)
- Angela M Gronenborn
- Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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41
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Dangi B, Dobrodumov AV, Louis JM, Gronenborn AM. Solution structure and dynamics of the human-Escherichia coli thioredoxin chimera: insights into thermodynamic stability. Biochemistry 2002; 41:9376-88. [PMID: 12135359 DOI: 10.1021/bi0258501] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have determined the high-resolution solution structure of the oxidized form of a chimeric human and Escherichia coli thioredoxin (TRX(HE)) by NMR. The overall structure is well-defined with a rms difference for the backbone atoms of 0.27 +/- 0.06 A. The topology of the protein is identical to those of the human and E. coli parent proteins, consisting of a central five-stranded beta-sheet surrounded by four alpha-helices. Analysis of the interfaces between the two domains derived from the human and E. coli sequences reveals that the general hydrophobic packing is unaltered and only subtle changes in the details of side chain interactions are observed. The packing of helix alpha(4) with helix alpha(2) across the hybrid interface is less optimal than in the parent molecules, and electrostatic interactions between polar side chains are missing. In particular, lysine-glutamate salt bridges between residues on helices alpha(2) and alpha(4), which were observed in both human and E. coli proteins, are not present in the chimeric protein. The origin of the known reduced thermodynamic stability of TRX(HE) was probed by mutagenesis on the basis of these structural findings. Two mutants of TRX(HE), S44D and S44E, were created, and their thermal and chemical stabilities were examined. Improved stability toward chaotropic agents was observed for both mutants, but no increase in the denaturation temperature was seen compared to that of TRX(HE). In addition to the structural analysis, the backbone dynamics of TRX(HE) were investigated by (15)N NMR relaxation measurements. Analysis using the model free approach reveals that the protein is fairly rigid with an average S(2) of 0.88. Increased mobility is primarily present in two external loop regions comprising residues 72-74 and 92-94 that contain glycine and proline residues.
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Affiliation(s)
- Bindi Dangi
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0560, USA
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42
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Hus JC, Prompers JJ, Brüschweiler R. Assignment strategy for proteins with known structure. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2002; 157:119-123. [PMID: 12202140 DOI: 10.1006/jmre.2002.2569] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In protein NMR the assignment of nuclear spin resonances is a prerequisite for all subsequent applications, such as studies of ligand binding, protein-DNA interactions, and dynamics. Resonance assignment is a time consuming step even when the 3D x-ray structure of the protein is available. A new strategy is presented to solve the "inverse" assignment problem, which is the determination of the NMR resonance assignment from a known 3D protein structure. The protocol employs NMR data in the form of residual dipolar couplings and chemical shifts, while it does not require any sequential NMR connectivity information. The assignment problem is mathematically formulated in terms of a weighted matching problem that can be computationally efficiently solved by a combinatorial optimization algorithm. The protocol is applied to ubiquitin using two or three residual dipolar couplings per amino acid measured in Pfl phage medium together with chemical shift information. The algorithm yields for more than 90% of the protein backbone resonances the correct assignment.
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Affiliation(s)
- Jean-Christophe Hus
- Carlson School of Chemistry and Biochemistry, Clark University, Worcester, Massachusetts 01610, USA
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Clore GM, Schwieters CD. Theoretical and computational advances in biomolecular NMR spectroscopy. Curr Opin Struct Biol 2002; 12:146-53. [PMID: 11959490 DOI: 10.1016/s0959-440x(02)00302-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Recent developments in experimental and computational aspects of NMR spectroscopy have had a significant impact on the accuracy and speed of macromolecular structure determination in solution, particularly with regard to systems of high complexity (such as protein complexes). These include experiments designed to provide long-range orientational and translational restraints, improvements in internal coordinate dynamics used for simulated annealing, and the development of database potentials of mean force to improve the description of the non-bonded contacts.
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Affiliation(s)
- G Marius Clore
- Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0510, USA.
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