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Yu B, Pletka CC, Iwahara J. Protein Electrostatics Investigated through Paramagnetic NMR for Nonpolar Groups. J Phys Chem B 2022; 126:2196-2202. [PMID: 35266708 PMCID: PMC8973454 DOI: 10.1021/acs.jpcb.1c10930] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Experimental validation of theoretical models for protein electrostatics remains rare. Recently, we have developed a paramagnetic NMR-based method for de novo determination of effective near-surface electrostatic potentials, which allows for straightforward examination of electrostatic models for biomolecules. In the current work, we expand this method and demonstrate that effective near-surface electrostatic potentials can readily be determined from 1H paramagnetic relaxation enhancement (PRE) data for protein CαH and CH3 groups. The experimental data were compared with those predicted from the Poisson-Boltzmann theory. The impact of structural dynamics on the effective near-surface electrostatic potentials was also assessed. The agreement between the experimental and theoretical data was particularly good for methyl 1H nuclei. Compared to the conventional pKa-based validation, our paramagnetic NMR-based approach can provide a far larger number of experimental data that can directly be used to examine the validity of theoretical electrostatic models for proteins.
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2
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Hong SH, Lee G, Park C, Koo J, Kim EH, Bae E, Suh JY. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2363-2376. [PMID: 35166843 PMCID: PMC8887544 DOI: 10.1093/nar/gkac096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/28/2022] [Accepted: 02/01/2022] [Indexed: 12/02/2022] Open
Abstract
Bacteria and archaea use the CRISPR-Cas system to fend off invasions of bacteriophages and foreign plasmids. In response, bacteriophages encode anti-CRISPR (Acr) proteins that potently inhibit host Cas proteins to suppress CRISPR-mediated immunity. AcrIE4-F7, which was isolated from Pseudomonas citronellolis, is a fused form of AcrIE4 and AcrIF7 that inhibits both type I-E and type I-F CRISPR-Cas systems. Here, we determined the structure of AcrIE4-F7 and identified its Cas target proteins. The N-terminal AcrIE4 domain adopts a novel α-helical fold that targets the PAM interaction site of the type I-E Cas8e subunit. The C-terminal AcrIF7 domain exhibits an αβ fold like native AcrIF7, which disables target DNA recognition by the PAM interaction site in the type I-F Cas8f subunit. The two Acr domains are connected by a flexible linker that allows prompt docking onto their cognate Cas8 targets. Conserved negative charges in each Acr domain are required for interaction with their Cas8 targets. Our results illustrate a common mechanism by which AcrIE4-F7 inhibits divergent CRISPR-Cas types.
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Affiliation(s)
| | | | - Changkon Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Jasung Koo
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Eun-Hee Kim
- Bio-Chemical Analysis Team, Korea Basic Science Institute, Ochang 28119, Korea
| | - Euiyoung Bae
- Correspondence may also be addressed to Euiyoung Bae. Tel: +82 2 880 4648; Fax: +82 2 873 3112;
| | - Jeong-Yong Suh
- To whom correspondence should be addressed. Tel: +82 2 880 4879; Fax: +82 2 877 4906;
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3
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Abstract
Electrostatic potentials computed from three-dimensional structures of biomolecules by solving the Poisson-Boltzmann equation are widely used in molecular biophysics, structural biology, and medicinal chemistry. Despite the approximate nature of the Poisson-Boltzmann theory, validation of the computed electrostatic potentials around biological macromolecules is rare and methodologically limited. Here, we present a unique and powerful NMR method that allows for straightforward and extensive comparison with electrostatic models for biomolecules and their complexes. This method utilizes paramagnetic relaxation enhancement arising from analogous cationic and anionic cosolutes whose spatial distributions around biological macromolecules reflect electrostatic potentials. We demonstrate that this NMR method enables de novo determination of near-surface electrostatic potentials for individual protein residues without using any structural information. We applied the method to ubiquitin and the Antp homeodomain-DNA complex. The experimental data agreed well with predictions from the Poisson-Boltzmann theory. Thus, our experimental results clearly support the validity of the theory for these systems. However, our experimental study also illuminates certain weaknesses of the Poisson-Boltzmann theory. For example, we found that the theory predicts stronger dependence of near-surface electrostatic potentials on ionic strength than observed in the experiments. Our data also suggest that conformational flexibility or structural uncertainties may cause large errors in theoretical predictions of electrostatic potentials, particularly for highly charged systems. This NMR-based method permits extensive assessment of near-surface electrostatic potentials for various regions around biological macromolecules and thereby may facilitate improvement of the computational approaches for electrostatic potentials.
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4
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Abstract
The molecular properties of proteins are influenced by various ions present in the same solution. While site-specific strong interactions between multivalent metal ions and proteins are well characterized, the behavior of other ions that are only weakly interacting with proteins remains elusive. In the current study, using NMR spectroscopy, we have investigated anion-protein interactions for three proteins that are similar in size but differ in overall charge. Using a unique NMR-based approach, we quantified anions accumulated around the proteins. The determined numbers of anions that are electrostatically attracted to the charged proteins were notably smaller than the overall charge valences and were consistent with predictions from the Poisson-Boltzmann theory. This NMR-based approach also allowed us to measure ionic diffusion and characterize the anions interacting with the positively charged proteins. Our data show that these anions rapidly diffuse while bound to the proteins. Using the same experimental approach, we observed the release of the anions from the protein surface upon the formation of the Antp homeodomain-DNA complex. Using paramagnetic relaxation enhancement (PRE), we visualized the spatial distribution of anions around the free proteins and the Antp homeodomain-DNA complex. The obtained PRE data revealed the localization of anions in the vicinity of the highly positively charged regions of the free Antp homeodomain and provided further evidence of the release of anions from the protein surface upon the protein-DNA association. This study sheds light on the dynamic behavior of anions that electrostatically interact with proteins.
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5
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Kim I, Koo J, An SY, Hong S, Ka D, Kim EH, Bae E, Suh JY. Structural and mechanistic insights into the CRISPR inhibition of AcrIF7. Nucleic Acids Res 2020; 48:9959-9968. [PMID: 32810226 PMCID: PMC7515697 DOI: 10.1093/nar/gkaa690] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
The CRISPR–Cas system provides adaptive immunity for bacteria and archaea to combat invading phages and plasmids. Phages evolved anti-CRISPR (Acr) proteins to neutralize the host CRISPR–Cas immune system as a counter-defense mechanism. AcrIF7 in Pseudomonas aeruginosa prophages strongly inhibits the type I-F CRISPR–Cas system. Here, we determined the solution structure of AcrIF7 and identified its target, Cas8f of the Csy complex. AcrIF7 adopts a novel β1β2α1α2β3 fold and interacts with the target DNA binding site of Cas8f. Notably, AcrIF7 competes with AcrIF2 for the same binding interface on Cas8f without common structural motifs. AcrIF7 binding to Cas8f is driven mainly by electrostatic interactions that require position-specific surface charges. Our findings suggest that Acrs of divergent origin may have acquired specificity to a common target through convergent evolution of their surface charge configurations.
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Affiliation(s)
- Iktae Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Jasung Koo
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - So Young An
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Suji Hong
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Donghyun Ka
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Eun-Hee Kim
- Protein Structure Research Team, Korea Basic Science Institute, Ochang 28119, Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Jeong-Yong Suh
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
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6
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An SY, Ka D, Kim I, Kim EH, Kim NK, Bae E, Suh JY. Intrinsic disorder is essential for Cas9 inhibition of anti-CRISPR AcrIIA5. Nucleic Acids Res 2020; 48:7584-7594. [PMID: 32544231 PMCID: PMC7367191 DOI: 10.1093/nar/gkaa512] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 12/22/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins provide adaptive immunity to prokaryotes against invading phages and plasmids. As a countermeasure, phages have evolved anti-CRISPR (Acr) proteins that neutralize the CRISPR immunity. AcrIIA5, isolated from a virulent phage of Streptococcus thermophilus, strongly inhibits diverse Cas9 homologs, but the molecular mechanism underlying the Cas9 inhibition remains unknown. Here, we report the solution structure of AcrIIA5, which features a novel α/β fold connected to an N-terminal intrinsically disordered region (IDR). Remarkably, truncation of the N-terminal IDR abrogates the inhibitory activity against Cas9, revealing that the IDR is essential for Cas9 inhibition by AcrIIA5. Progressive truncations and mutations of the IDR illustrate that the disordered region not only modulates the association between AcrIIA5 and Cas9-sgRNA, but also alters the catalytic efficiency of the inhibitory complex. The length of IDR is critical for the Cas9-sgRNA recognition by AcrIIA5, whereas the charge content of IDR dictates the inhibitory activity. Conformational plasticity of IDR may be linked to the broad-spectrum inhibition of Cas9 homologs by AcrIIA5. Identification of the IDR as the main determinant for Cas9 inhibition expands the inventory of phage anti-CRISPR mechanisms.
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Affiliation(s)
- So Young An
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Donghyun Ka
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Iktae Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Eun-Hee Kim
- Protein Structure Research Team, Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang, Chungbuk 28119, South Korea
| | - Nak-Kyoon Kim
- Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Jeong-Yong Suh
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea.,Institute for Biomedical Sciences, Shinshu University, Minamiminowa, Nagano 399-4598, Japan
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7
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Karamanos TK, Tugarinov V, Clore GM. Determining methyl sidechain conformations in a CS-ROSETTA model using methyl 1H- 13C residual dipolar couplings. JOURNAL OF BIOMOLECULAR NMR 2020; 74:111-118. [PMID: 31950428 PMCID: PMC7083688 DOI: 10.1007/s10858-019-00294-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/17/2019] [Indexed: 05/12/2023]
Abstract
Modelling of protein structures based on backbone chemical shifts, using programs such as CS-ROSETTA, is becoming increasingly popular, especially for systems where few restraints are available or where homologous structures are already known. While the reliability of CS-ROSETTA calculations can be improved by incorporation of some additional backbone NMR data such as those afforded by residual dipolar couplings or minimal NOE data sets involving backbone amide protons, the sidechain conformations are largely modelled by statistical energy terms. Here, we present a simple method based on methyl residual dipolar couplings that can be used to determine the rotameric state of the threefold symmetry axis of methyl groups that occupy a single rotamer, determine rotameric distributions, and identify regions of high flexibility. The method is demonstrated for methyl side chains of a deletion variant of the human chaperone DNAJB6b.
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Affiliation(s)
- Theodoros K Karamanos
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
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8
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Vasquez JK, Tal-Gan Y, Cornilescu G, Tyler KA, Blackwell HE. Simplified AIP-II Peptidomimetics Are Potent Inhibitors of Staphylococcus aureus AgrC Quorum Sensing Receptors. Chembiochem 2017; 18:413-423. [PMID: 28006082 DOI: 10.1002/cbic.201600516] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Indexed: 01/13/2023]
Abstract
The bacterial pathogen Staphylococcus aureus controls many aspects of virulence by using the accessory gene regulator (agr) quorum sensing (QS) system. The agr system is activated by a macrocyclic peptide signal known as an autoinducing peptide (AIP). We sought to develop structurally simplified mimetics of AIPs for use as chemical tools to study QS in S. aureus. Herein, we report new peptidomimetic AgrC receptor inhibitors based on a tail-truncated AIP-II peptide that have almost analogous inhibitory activities to the parent peptide. Structural comparison of one of these peptidomimetics to the parent peptide and a highly potent, all-peptide-derived, S. aureus agr inhibitor (AIP-III D4A) revealed a conserved hydrophobic motif and overall amphipathic nature. Our results suggest that the AIP scaffold is amenable to structural mimicry and minimization for the development of synthetic agr inhibitors.
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Affiliation(s)
- Joseph K Vasquez
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA
| | - Yftah Tal-Gan
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA.,Present address: Department of Chemistry, University of Nevada, 1664 N. Virginia Street, Reno, NV, 89557, USA
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Kimberly A Tyler
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA
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9
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Bermejo GA, Clore GM, Schwieters CD. Improving NMR Structures of RNA. Structure 2016; 24:806-815. [PMID: 27066747 DOI: 10.1016/j.str.2016.03.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/26/2016] [Accepted: 03/04/2016] [Indexed: 01/27/2023]
Abstract
Here, we show that modern solution nuclear magnetic resonance (NMR) structures of RNA exhibit more steric clashes and conformational ambiguities than their crystallographic X-ray counterparts. To tackle these issues, we developed RNA-ff1, a new force field for structure calculation with Xplor-NIH. Using seven published NMR datasets, RNA-ff1 improves covalent geometry and MolProbity validation criteria for clashes and backbone conformation in most cases, relative to both the previous Xplor-NIH force field and the original structures associated with the experimental data. In addition, with smaller base-pair step rises in helical stems, RNA-ff1 structures enjoy more favorable base stacking. Finally, structural accuracy improves in the majority of cases, as supported by complete residual dipolar coupling cross-validation. Thus, the reported advances show great promise in bridging the quality gap that separates NMR and X-ray structures of RNA.
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Affiliation(s)
- Guillermo A Bermejo
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-5624, USA
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Charles D Schwieters
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-5624, USA.
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10
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Dissecting the structural basis of MEIG1 interaction with PACRG. Sci Rep 2016; 6:18278. [PMID: 26726850 PMCID: PMC4698733 DOI: 10.1038/srep18278] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/16/2015] [Indexed: 11/21/2022] Open
Abstract
The product of the meiosis-expressed gene 1 (MEIG1) is found in the cell bodies of spermatocytes and recruited to the manchette, a structure unique to elongating spermatids, by Parkin co-regulated gene (PACRG). This complex is essential for targeting cargo to the manchette during sperm flagellum assembly. Here we show that MEIG1 adopts a unique fold that provides a large surface for interacting with other proteins. We mutated 12 exposed and conserved amino acids and show that four of these mutations (W50A, K57E, F66A, Y68A) dramatically reduce binding to PACRG. These four amino acids form a contiguous hydrophobic patch on one end of the protein. Furthermore, each of these four mutations diminishes the ability of MEIG1 to stabilize PACRG when expressed in bacteria. Together these studies establish the unique structure and key interaction surface of MEIG1 and provide a framework to explore how MEIG1 recruits proteins to build the sperm tail.
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11
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Tal-Gan Y, Ivancic M, Cornilescu G, Blackwell HE. Characterization of structural elements in native autoinducing peptides and non-native analogues that permit the differential modulation of AgrC-type quorum sensing receptors in Staphylococcus aureus. Org Biomol Chem 2015; 14:113-21. [PMID: 26416476 DOI: 10.1039/c5ob01735a] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Staphylococcus aureus uses short macrocyclic peptides (i.e., autoinducing peptides, or AIPs) to assess its local population density in a cell-cell signaling mechanism called quorum sensing (QS). At high cell numbers, this pathogen can initiate many virulent behaviors that allow for the establishment of infection. Binding of the AIP signal to its cognate transmembrane AgrC-type receptor is a critical event in the QS signaling cascade; consequently, interference of AIP:receptor interactions may have the potential to prevent and eradicate certain S. aureus infections. To date, four pairs of AIP:AgrC receptors have been identified in S. aureus, each pair being utilized by a specific S. aureus group (I-IV). Other staphylococcal species also use closely related, but distinct, AIP:AgrC pairs to control QS. We seek to develop non-native ligands capable of intercepting AIP:AgrC binding in each S. aureus group and in related species. As these bacteria may use their respective AIP signal to attenuate the QS systems of other groups/species, such ligands would provide valuable chemical tools to probe possible interference mechanisms in a range of contexts. In the current study, we used solution-phase NMR techniques to characterize the 3-D structures of a set of known native and non-native peptides that have differential modulatory activity in certain AgrC receptors. Analysis of these structures revealed several distinct structural motifs that belay differential activity in selected S. aureus AgrC receptors (i.e., AgrC-I, AgrC-II, and AgrC-III). The results of this study can be leveraged for the design of new synthetic ligands with enhanced selectivities and potencies for these AgrC receptors.
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Affiliation(s)
- Yftah Tal-Gan
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
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12
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Sjodt M, Macdonald R, Spirig T, Chan AH, Dickson CF, Fabian M, Olson JS, Gell DA, Clubb RT. The PRE-Derived NMR Model of the 38.8-kDa Tri-Domain IsdH Protein from Staphylococcus aureus Suggests That It Adaptively Recognizes Human Hemoglobin. J Mol Biol 2015; 428:1107-1129. [PMID: 25687963 DOI: 10.1016/j.jmb.2015.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 01/31/2015] [Accepted: 02/07/2015] [Indexed: 01/11/2023]
Abstract
Staphylococcus aureus is a medically important bacterial pathogen that, during infections, acquires iron from human hemoglobin (Hb). It uses two closely related iron-regulated surface determinant (Isd) proteins to capture and extract the oxidized form of heme (hemin) from Hb, IsdH and IsdB. Both receptors rapidly extract hemin using a conserved tri-domain unit consisting of two NEAT (near iron transporter) domains connected by a helical linker domain. To gain insight into the mechanism of extraction, we used NMR to investigate the structure and dynamics of the 38.8-kDa tri-domain IsdH protein (IsdH(N2N3), A326-D660 with a Y642A mutation that prevents hemin binding). The structure was modeled using long-range paramagnetic relaxation enhancement (PRE) distance restraints, dihedral angle, small-angle X-ray scattering, residual dipolar coupling and inter-domain NOE nuclear Overhauser effect data. The receptor adopts an extended conformation wherein the linker and N3 domains pack against each other via a hydrophobic interface. In contrast, the N2 domain contacts the linker domain via a hydrophilic interface and, based on NMR relaxation data, undergoes inter-domain motions enabling it to reorient with respect to the body of the protein. Ensemble calculations were used to estimate the range of N2 domain positions compatible with the PRE data. A comparison of the Hb-free and Hb-bound forms reveals that Hb binding alters the positioning of the N2 domain. We propose that binding occurs through a combination of conformational selection and induced-fit mechanisms that may promote hemin release from Hb by altering the position of its F helix.
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Affiliation(s)
- Megan Sjodt
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA; University of California, Los Angeles-Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
| | - Ramsay Macdonald
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA; University of California, Los Angeles-Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
| | - Thomas Spirig
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
| | - Albert H Chan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA; University of California, Los Angeles-Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
| | - Claire F Dickson
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Marian Fabian
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251, USA
| | - John S Olson
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251, USA
| | - David A Gell
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Robert T Clubb
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA; University of California, Los Angeles-Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA.
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13
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Han M, Park Y, Kim I, Kim EH, Yu TK, Rhee S, Suh JY. Structural basis for the auxin-induced transcriptional regulation by Aux/IAA17. Proc Natl Acad Sci U S A 2014; 111:18613-8. [PMID: 25512488 PMCID: PMC4284525 DOI: 10.1073/pnas.1419525112] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Auxin is the central hormone that regulates plant growth and organ development. Transcriptional regulation by auxin is mediated by the auxin response factor (ARF) and the repressor, AUX/IAA. Aux/IAA associates with ARF via domain III-IV for transcriptional repression that is reversed by auxin-induced Aux/IAA degradation. It has been known that Aux/IAA and ARF form homo- and hetero-oligomers for the transcriptional regulation, but what determines their association states is poorly understood. Here we report, to our knowledge, the first solution structure of domain III-IV of Aux/IAA17 (IAA17), and characterize molecular interactions underlying the homotypic and heterotypic oligomerization. The structure exhibits a compact β-grasp fold with a highly dynamic insert helix that is unique in Aux/IAA family proteins. IAA17 associates to form a heterogeneous ensemble of front-to-back oligomers in a concentration-dependent manner. IAA17 and ARF5 associate to form homo- or hetero-oligomers using a common scaffold and binding interfaces, but their affinities vary significantly. The equilibrium dissociation constants (KD) for homo-oligomerization are 6.6 μM and 0.87 μM for IAA17 and ARF5, respectively, whereas hetero-oligomerization reveals a ∼ 10- to ∼ 100-fold greater affinity (KD = 73 nM). Thus, individual homo-oligomers of IAA17 and ARF5 spontaneously exchange their subunits to form alternating hetero-oligomers for transcriptional repression. Oligomerization is mainly driven by electrostatic interactions, so that charge complementarity at the interface determines the binding affinity. Variable binding affinity by surface charge modulation may effectively regulate the complex interaction network between Aux/IAA and ARF family proteins required for the transcriptional control of auxin-response genes.
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Affiliation(s)
- Mookyoung Han
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul 151-921, Republic of Korea; and
| | - Yangshin Park
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul 151-921, Republic of Korea; and
| | - Iktae Kim
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul 151-921, Republic of Korea; and
| | - Eun-Hee Kim
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chungbuk 363-883, Republic of Korea
| | - Tae-Kyung Yu
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul 151-921, Republic of Korea; and
| | - Sangkee Rhee
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul 151-921, Republic of Korea; and
| | - Jeong-Yong Suh
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul 151-921, Republic of Korea; and
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14
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Walavalkar NM, Cramer JM, Buchwald WA, Scarsdale JN, Williams DC. Solution structure and intramolecular exchange of methyl-cytosine binding domain protein 4 (MBD4) on DNA suggests a mechanism to scan for mCpG/TpG mismatches. Nucleic Acids Res 2014; 42:11218-32. [PMID: 25183517 PMCID: PMC4176167 DOI: 10.1093/nar/gku782] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Unlike other members of the methyl-cytosine binding domain (MBD) family, MBD4 serves as a potent DNA glycosylase in DNA mismatch repair specifically targeting mCpG/TpG mismatches arising from spontaneous deamination of methyl-cytosine. The protein contains an N-terminal MBD (MBD4MBD) and a C-terminal glycosylase domain (MBD4GD) separated by a long linker. This arrangement suggests that the MBD4MBD either directly augments enzymatic catalysis by the MBD4GD or targets the protein to regions enriched for mCpG/TpG mismatches. Here we present structural and dynamic studies of MBD4MBD bound to dsDNA. We show that MBD4MBD binds with a modest preference formCpG as compared to mismatch, unmethylated and hydroxymethylated DNA. We find that while MBD4MBD exhibits slow exchange between molecules of DNA (intermolecular exchange), the domain exhibits fast exchange between two sites in the same molecule of dsDNA (intramolecular exchange). Introducing a single-strand defect between binding sites does not greatly reduce the intramolecular exchange rate, consistent with a local hopping mechanism for moving along the DNA. These results support a model in which the MBD4MBD4 targets the intact protein to mCpG islands and promotes scanning by rapidly exchanging between successive mCpG sites which facilitates repair of nearby mCpG/TpG mismatches by the glycosylase domain.
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Affiliation(s)
- Ninad M Walavalkar
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jason M Cramer
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - William A Buchwald
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - J Neel Scarsdale
- Institute of Structural Biology and Drug Discovery, Center for the Study of Biological Complexity and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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15
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Berntsen KRM, Vriend G. Anomalies in the refinement of isoleucine. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1037-49. [PMID: 24699648 PMCID: PMC3975889 DOI: 10.1107/s139900471400087x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 01/14/2014] [Indexed: 11/11/2022]
Abstract
A study of isoleucines in protein structures solved using X-ray crystallography revealed a series of systematic trends for the two side-chain torsion angles χ1 and χ2 dependent on the resolution, secondary structure and refinement software used. The average torsion angles for the nine rotamers were similar in high-resolution structures solved using either the REFMAC, CNS or PHENIX software. However, at low resolution these programs often refine towards somewhat different χ1 and χ2 values. Small systematic differences can be observed between refinement software that uses molecular dynamics-type energy terms (for example CNS) and software that does not use these terms (for example REFMAC). Detailing the standard torsion angles used in refinement software can improve the refinement of protein structures. The target values in the molecular dynamics-type energy functions can also be improved.
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Affiliation(s)
- Karen R. M. Berntsen
- CMBI, Radboud University Medical Center, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands
| | - Gert Vriend
- CMBI, Radboud University Medical Center, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands
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16
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Cramer JM, Scarsdale JN, Walavalkar NM, Buchwald WA, Ginder GD, Williams DC. Probing the dynamic distribution of bound states for methylcytosine-binding domains on DNA. J Biol Chem 2013; 289:1294-302. [PMID: 24307175 DOI: 10.1074/jbc.m113.512236] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although highly homologous to other methylcytosine-binding domain (MBD) proteins, MBD3 does not selectively bind methylated DNA, and thus the functional role of MBD3 remains in question. To explore the structural basis of its binding properties and potential function, we characterized the solution structure and binding distribution of the MBD3 MBD on hydroxymethylated, methylated, and unmethylated DNA. The overall fold of this domain is very similar to other MBDs, yet a key loop involved in DNA binding is more disordered than previously observed. Specific recognition of methylated DNA constrains the structure of this loop and results in large chemical shift changes in NMR spectra. Based on these spectral changes, we show that MBD3 preferentially localizes to methylated and, to a lesser degree, unmethylated cytosine-guanosine dinucleotides (CpGs), yet does not distinguish between hydroxymethylated and unmethylated sites. Measuring residual dipolar couplings for the different bound states clearly shows that the MBD3 structure does not change between methylation-specific and nonspecific binding modes. Furthermore, residual dipolar couplings measured for MBD3 bound to methylated DNA can be described by a linear combination of those for the methylation and nonspecific binding modes, confirming the preferential localization to methylated sites. The highly homologous MBD2 protein shows similar but much stronger localization to methylated as well as unmethylated CpGs. Together, these data establish the structural basis for the relative distribution of MBD2 and MBD3 on genomic DNA and their observed occupancy at active and inactive CpG-rich promoters.
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Affiliation(s)
- Jason M Cramer
- From the Department of Biochemistry and Molecular Biology
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17
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Tal-Gan Y, Ivancic M, Cornilescu G, Cornilescu CC, Blackwell HE. Structural characterization of native autoinducing peptides and abiotic analogues reveals key features essential for activation and inhibition of an AgrC quorum sensing receptor in Staphylococcus aureus. J Am Chem Soc 2013; 135:18436-44. [PMID: 24219181 DOI: 10.1021/ja407533e] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Staphylococcus aureus is a major human pathogen that uses quorum sensing (QS) to control virulence. Its QS system is regulated by macrocyclic peptide signals (or autoinducing peptides (AIPs)) and their cognate transmembrane receptors (AgrCs). Four different specificity groups of S. aureus have been identified to date (groups I-IV), each of which uses a different AIP:AgrC pair. Non-native ligands capable of intercepting AIP:AgrC binding, and thereby QS, in S. aureus have attracted considerable interest as chemical tools to study QS pathways and as possible antivirulence strategies for the treatment of infection. We recently reported a set of analogues of the group-III AIP that are capable of strongly modulating the activity of all four AgrC receptors. Critical to the further development of such ligands is a detailed understanding of the structural features of both native AIPs and non-native analogues that are essential for activity. Herein, we report the first three-dimensional structural analysis of the known native AIP signals (AIPs-I-IV) and several AIP-III analogues with varied biological activities using NMR spectroscopy. Integration of these NMR studies with the known agonism and antagonism profiles of these peptides in AgrC-III revealed two key structural elements that control AIP-III (and non-native peptide) activity: (1) a tri-residue hydrophobic "knob" essential for both activation and inhibition and (2) a fourth anchor point on the exocyclic tail needed for receptor activation. These results provide strong structural support for a mechanism of AIP-mediated AgrC activation and inhibition in S. aureus , and should facilitate the design of new AgrC ligands with enhanced activities (as agonists or antagonists) and simplified chemical structures.
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Affiliation(s)
- Yftah Tal-Gan
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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18
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Cornilescu CC, Cornilescu G, Rao H, Porter SF, Tonelli M, DeRider ML, Markley JL, Assadi-Porter FM. Temperature-dependent conformational change affecting Tyr11 and sweetness loops of brazzein. Proteins 2013; 81:919-25. [PMID: 23349025 PMCID: PMC3982881 DOI: 10.1002/prot.24259] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 01/11/2013] [Indexed: 10/27/2022]
Abstract
The sweet protein brazzein, a member of the Csβα fold family, contains four disulfide bonds that lend a high degree of thermal and pH stability to its structure. Nevertheless, a variable temperature study has revealed that the protein undergoes a local, reversible conformational change between 37 and 3°C with a midpoint about 27°C that changes the orientations and side-chain hydrogen bond partners of Tyr8 and Tyr11. To test the functional significance of this effect, we used NMR saturation transfer to investigate the interaction between brazzein and the amino terminal domain of the sweet receptor subunit T1R2; the results showed a stronger interaction at 7°C than at 37°C. Thus the low temperature conformation, which alters the orientations of two loops known to be critical for the sweetness of brazzein, may represent the bound state of brazzein in the complex with the human sweet receptor.
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Affiliation(s)
- Claudia C. Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Wisconsin 53706
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Wisconsin 53706
| | - Hongyu Rao
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Sarah F. Porter
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Wisconsin 53706
| | - Michele L. DeRider
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - John L. Markley
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Wisconsin 53706
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Fariba M. Assadi-Porter
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Wisconsin 53706
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
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19
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Tang M, Nesbitt AE, Sperling LJ, Berthold DA, Schwieters CD, Gennis RB, Rienstra CM. Structure of the disulfide bond generating membrane protein DsbB in the lipid bilayer. J Mol Biol 2013; 425:1670-82. [PMID: 23416557 PMCID: PMC3670690 DOI: 10.1016/j.jmb.2013.02.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 01/11/2013] [Accepted: 02/08/2013] [Indexed: 12/16/2022]
Abstract
The integral membrane protein DsbB in Escherichia coli is responsible for oxidizing the periplasmic protein DsbA, which forms disulfide bonds in substrate proteins. We have developed a high-resolution structural model by combining experimental X-ray and solid-state NMR with molecular dynamics (MD) simulations. We embedded the high-resolution DsbB structure, derived from the joint calculation with X-ray reflections and solid-state NMR restraints, into the lipid bilayer and performed MD simulations to provide a mechanistic view of DsbB function in the membrane. Further, we revealed the membrane topology of DsbB by selective proton spin diffusion experiments, which directly probe the correlations of DsbB with water and lipid acyl chains. NMR data also support the model of a flexible periplasmic loop and an interhelical hydrogen bond between Glu26 and Tyr153.
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Affiliation(s)
- Ming Tang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Anna E. Nesbitt
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Lindsay J. Sperling
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Deborah A. Berthold
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Charles D. Schwieters
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert B. Gennis
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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20
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Kim TR, Yang JS, Shin S, Lee J. Statistical torsion angle potential energy functions for protein structure modeling: a bicubic interpolation approach. Proteins 2013; 81:1156-65. [PMID: 23408564 DOI: 10.1002/prot.24265] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Revised: 01/20/2013] [Accepted: 01/24/2013] [Indexed: 11/09/2022]
Abstract
A set of grid type knowledge-based energy functions is introduced for ϕ-χ₁ , ψ-χ₁ , ϕ-ψ, and χ₁ -χ₂ torsion angle combinations. Boltzmann distribution is assumed for the torsion angle populations from protein X-ray structures, and the functions are named as statistical torsion angle potential energy functions. The grid points around periodic boundaries are duplicated to force periodicity, and the remedy relieves the derivative discontinuity problem. The devised functions rapidly improve the quality of model structures. The potential bias in the functions and the usefulness of additional secondary structure information are also investigated. The proposed guiding functions are expected to facilitate protein structure modeling, such as protein structure prediction, protein design, and structure refinement.
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Affiliation(s)
- Tae-Rae Kim
- Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea
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21
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Yu X, Wu X, Bermejo GA, Brooks BR, Taraska JW. Accurate high-throughput structure mapping and prediction with transition metal ion FRET. Structure 2012; 21:9-19. [PMID: 23273426 DOI: 10.1016/j.str.2012.11.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 11/15/2012] [Accepted: 11/17/2012] [Indexed: 11/28/2022]
Abstract
Mapping the landscape of a protein's conformational space is essential to understanding its functions and regulation. The limitations of many structural methods have made this process challenging for most proteins. Here, we report that transition metal ion FRET (tmFRET) can be used in a rapid, highly parallel screen, to determine distances from multiple locations within a protein at extremely low concentrations. The distances generated through this screen for the protein maltose binding protein (MBP) match distances from the crystal structure to within a few angstroms. Furthermore, energy transfer accurately detects structural changes during ligand binding. Finally, fluorescence-derived distances can be used to guide molecular simulations to find low energy states. Our results open the door to rapid, accurate mapping and prediction of protein structures at low concentrations, in large complex systems, and in living cells.
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Affiliation(s)
- Xiaozhen Yu
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiongwu Wu
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Guillermo A Bermejo
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Justin W Taraska
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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22
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Bermejo GA, Clore GM, Schwieters CD. Smooth statistical torsion angle potential derived from a large conformational database via adaptive kernel density estimation improves the quality of NMR protein structures. Protein Sci 2012; 21:1824-36. [PMID: 23011872 DOI: 10.1002/pro.2163] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/14/2012] [Accepted: 09/17/2012] [Indexed: 11/09/2022]
Abstract
Statistical potentials that embody torsion angle probability densities in databases of high-quality X-ray protein structures supplement the incomplete structural information of experimental nuclear magnetic resonance (NMR) datasets. By biasing the conformational search during the course of structure calculation toward highly populated regions in the database, the resulting protein structures display better validation criteria and accuracy. Here, a new statistical torsion angle potential is developed using adaptive kernel density estimation to extract probability densities from a large database of more than 10⁶ quality-filtered amino acid residues. Incorporated into the Xplor-NIH software package, the new implementation clearly outperforms an older potential, widely used in NMR structure elucidation, in that it exhibits simultaneously smoother and sharper energy surfaces, and results in protein structures with improved conformation, nonbonded atomic interactions, and accuracy.
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Affiliation(s)
- Guillermo A Bermejo
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892-5624, USA
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23
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Jung YS, Cai M, Clore GM. Solution structure of the IIAChitobiose-HPr complex of the N,N'-diacetylchitobiose branch of the Escherichia coli phosphotransferase system. J Biol Chem 2012; 287:23819-29. [PMID: 22593574 DOI: 10.1074/jbc.m112.371492] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The solution structure of the complex of enzyme IIA of the N,N'-diacetylchitobiose (Chb) transporter with the histidine phosphocarrier protein HPr has been solved by NMR. The IIA(Chb)-HPr complex completes the structure elucidation of representative cytoplasmic complexes for all four sugar branches of the bacterial phosphoryl transfer system (PTS). The active site His-89 of IIA(Chb) was mutated to Glu to mimic the phosphorylated state. IIA(Chb)(H89E) and HPr form a weak complex with a K(D) of ~0.7 mM. The interacting binding surfaces, concave for IIA(Chb) and convex for HPr, complement each other in terms of shape, residue type, and charge distribution, with predominantly hydrophobic residues, interspersed by some uncharged polar residues, located centrally, and polar and charged residues at the periphery. The active site histidine of HPr, His-15, is buried within the active site cleft of IIA(Chb) formed at the interface of two adjacent subunits of the IIA(Chb) trimer, thereby coming into close proximity with the active site residue, H89E, of IIA(Chb). A His89-P-His-15 pentacoordinate phosphoryl transition state can readily be modeled without necessitating any significant conformational changes, thereby facilitating rapid phosphoryl transfer. Comparison of the IIA(Chb)-HPr complex with the IIA(Chb)-IIB(Chb) complex, as well as with other cytoplasmic complexes of the PTS, highlights a unifying mechanism for recognition of structurally diverse partners. This involves generating similar binding surfaces from entirely different underlying structural elements, large interaction surfaces coupled with extensive redundancy, and side chain conformational plasticity to optimize diverse sets of intermolecular interactions.
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Affiliation(s)
- Young-Sang Jung
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
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24
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Anthis NJ, Doucleff M, Clore GM. Transient, sparsely populated compact states of apo and calcium-loaded calmodulin probed by paramagnetic relaxation enhancement: interplay of conformational selection and induced fit. J Am Chem Soc 2011; 133:18966-74. [PMID: 21999431 PMCID: PMC3218299 DOI: 10.1021/ja2082813] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Calmodulin (CaM) is the universal calcium sensor in eukaryotes, regulating the function of numerous proteins. Crystallography and NMR show that free CaM-4Ca(2+) exists in an extended conformation with significant interdomain separation, but clamps down upon target peptides to form a highly compact structure. NMR has revealed substantial interdomain motions in CaM-4Ca(2+), enabled by a flexible linker. In one instance, CaM-4Ca(2+) has been crystallized in a compact configuration; however, no direct evidence for transient interdomain contacts has been observed in solution, and little is known about how large-scale interdomain motions contribute to biological function. Here, we use paramagnetic relaxation enhancement (PRE) to characterize transient compact states of free CaM that are too sparsely populated to observe by traditional NMR methods. We show that unbound CaM samples a range of compact structures, populated at 5-10%, and that Ca(2+) dramatically alters the distribution of these configurations in favor of states resembling the peptide-bound structure. In the absence of Ca(2+), the target peptide binds only to the C-terminal domain, and the distribution of compact states is similar with and without peptide. These data suggest an alternative pathway of CaM action in which CaM remains associated with its kinase targets even in the resting state. Only CaM-4Ca(2+), however, shows an innate propensity to form the physiologically active compact structures, suggesting that Ca(2+) activates CaM not only through local structural changes within each domain but also through more global remodeling of interdomain interactions. Thus, these findings illustrate the subtle interplay between conformational selection and induced fit.
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Affiliation(s)
- Nicholas J. Anthis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, U.S.A
| | | | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, U.S.A
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25
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Venditti V, Fawzi NL, Clore GM. Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methyl-methyl nuclear Overhauser enhancement spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2011; 51:319-28. [PMID: 21935714 PMCID: PMC3212433 DOI: 10.1007/s10858-011-9559-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 08/07/2011] [Indexed: 05/20/2023]
Abstract
Methyl-transverse relaxation optimized spectroscopy is rapidly becoming the preferred NMR technique for probing structure and dynamics of very large proteins up to ~1 MDa in molecular size. Data interpretation, however, necessitates assignment of methyl groups which still presents a very challenging and time-consuming process. Here we demonstrate that, in combination with a known 3D structure, paramagnetic relaxation enhancement (PRE), induced by nitroxide spin-labels incorporated at only a few surface-exposed engineered cysteines, provides fast, straightforward and robust access to methyl group resonance assignments, including stereoassignments for the methyl groups of leucine and valine. Neither prior assignments, including backbone assignments, for the protein, nor experiments that transfer magnetization between methyl groups and the protein backbone, are required. PRE-derived assignments are refined by 4D methyl-methyl nuclear Overhauser enhancement data, eliminating ambiguities and errors that may arise due to the high sensitivity of PREs to the potential presence of sparsely-populated transient states.
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Affiliation(s)
- Vincenzo Venditti
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Nicolas L. Fawzi
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
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26
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Ultrahigh resolution protein structures using NMR chemical shift tensors. Proc Natl Acad Sci U S A 2011; 108:16974-9. [PMID: 21969532 DOI: 10.1073/pnas.1103728108] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
NMR chemical shift tensors (CSTs) in proteins, as well as their orientations, represent an important new restraint class for protein structure refinement and determination. Here, we present the first determination of both CST magnitudes and orientations for (13)Cα and (15)N (peptide backbone) groups in a protein, the β1 IgG binding domain of protein G from Streptococcus spp., GB1. Site-specific (13)Cα and (15)N CSTs were measured using synchronously evolved recoupling experiments in which (13)C and (15)N tensors were projected onto the (1)H-(13)C and (1)H-(15)N vectors, respectively, and onto the (15)N-(13)C vector in the case of (13)Cα. The orientations of the (13)Cα CSTs to the (1)H-(13)C and (13)C-(15)N vectors agreed well with the results of ab initio calculations, with an rmsd of approximately 8°. In addition, the measured (15)N tensors exhibited larger reduced anisotropies in α-helical versus β-sheet regions, with very limited variation (18 ± 4°) in the orientation of the z-axis of the (15)N CST with respect to the (1)H-(15)N vector. Incorporation of the (13)Cα CST restraints into structure calculations, in combination with isotropic chemical shifts, transferred echo double resonance (13)C-(15)N distances and vector angle restraints, improved the backbone rmsd to 0.16 Å (PDB ID code 2LGI) and is consistent with existing X-ray structures (0.51 Å agreement with PDB ID code 2QMT). These results demonstrate that chemical shift tensors have considerable utility in protein structure refinement, with the best structures comparable to 1.0-Å crystal structures, based upon empirical metrics such as Ramachandran geometries and χ(1)/χ(2) distributions, providing solid-state NMR with a powerful tool for de novo structure determination.
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27
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Fawzi NL, Fleissner MR, Anthis NJ, Kálai T, Hideg K, Hubbell WL, Clore GM. A rigid disulfide-linked nitroxide side chain simplifies the quantitative analysis of PRE data. JOURNAL OF BIOMOLECULAR NMR 2011; 51:105-14. [PMID: 21947919 PMCID: PMC3489005 DOI: 10.1007/s10858-011-9545-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 06/22/2011] [Indexed: 05/03/2023]
Abstract
The measurement of (1)H transverse paramagnetic relaxation enhancement (PRE) has been used in biomolecular systems to determine long-range distance restraints and to visualize sparsely-populated transient states. The intrinsic flexibility of most nitroxide and metal-chelating paramagnetic spin-labels, however, complicates the quantitative interpretation of PREs due to delocalization of the paramagnetic center. Here, we present a novel, disulfide-linked nitroxide spin label, R1p, as an alternative to these flexible labels for PRE studies. When introduced at solvent-exposed α-helical positions in two model proteins, calmodulin (CaM) and T4 lysozyme (T4L), EPR measurements show that the R1p side chain exhibits dramatically reduced internal motion compared to the commonly used R1 spin label (generated by reacting cysteine with the spin labeling compound often referred to as MTSL). Further, only a single nitroxide position is necessary to account for the PREs arising from CaM S17R1p, while an ensemble comprising multiple conformations is necessary for those observed for CaM S17R1. Together, these observations suggest that the nitroxide adopts a single, fixed position when R1p is placed at solvent-exposed α-helical positions, greatly simplifying the interpretation of PRE data by removing the need to account for the intrinsic flexibility of the spin label.
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Affiliation(s)
- Nicolas L. Fawzi
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MA 20892-0520, USA
| | - Mark R. Fleissner
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Nicholas J. Anthis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MA 20892-0520, USA
| | - Tamás Kálai
- Institute of Organic and Medicinal Chemistry, University of Pécs, Szigeti str. 12, 7624 Pécs, Hungary
| | - Kálmán Hideg
- Institute of Organic and Medicinal Chemistry, University of Pécs, Szigeti str. 12, 7624 Pécs, Hungary
| | - Wayne L. Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MA 20892-0520, USA
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28
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Bulek K, Liu C, Swaidani S, Wang L, Page RC, Gulen MF, Herjan T, Abbadi A, Qian W, Sun D, Lauer M, Hascall V, Misra S, Chance MR, Aronica M, Hamilton T, Li X. The inducible kinase IKKi is required for IL-17-dependent signaling associated with neutrophilia and pulmonary inflammation. Nat Immunol 2011; 12:844-52. [PMID: 21822257 DOI: 10.1038/ni.2080] [Citation(s) in RCA: 150] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 06/28/2011] [Indexed: 02/06/2023]
Abstract
Interleukin 17 (IL-17) is critical in the pathogenesis of inflammatory and autoimmune diseases. Here we report that Act1, the key adaptor for the IL-17 receptor (IL-7R), formed a complex with the inducible kinase IKKi after stimulation with IL-17. Through the use of IKKi-deficient mice, we found that IKKi was required for IL-17-induced expression of genes encoding inflammatory molecules in primary airway epithelial cells, neutrophilia and pulmonary inflammation. IKKi deficiency abolished IL-17-induced formation of the complex of Act1 and the adaptors TRAF2 and TRAF5, activation of mitogen-activated protein kinases (MAPKs) and mRNA stability, whereas the Act1-TRAF6-transcription factor NF-κB axis was retained. IKKi was required for IL-17-induced phosphorylation of Act1 on Ser311, adjacent to a putative TRAF-binding motif. Substitution of the serine at position 311 with alanine impaired the IL-17-mediated Act1-TRAF2-TRAF5 interaction and gene expression. Thus, IKKi is a kinase newly identified as modulating IL-17 signaling through its effect on Act1 phosphorylation and consequent function.
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Affiliation(s)
- Katarzyna Bulek
- Department of Immunology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
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29
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Scarsdale JN, Webb HD, Ginder GD, Williams DC. Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target-methylated DNA sequence. Nucleic Acids Res 2011; 39:6741-52. [PMID: 21531701 PMCID: PMC3159451 DOI: 10.1093/nar/gkr262] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The epigenetic code of DNA methylation is interpreted chiefly by methyl cytosine binding domain (MBD) proteins which in turn recruit multiprotein co-repressor complexes. We previously isolated one such complex, MBD2-NuRD, from primary erythroid cells and have shown it contributes to embryonic/fetal β-type globin gene silencing during development. This complex has been implicated in silencing tumor suppressor genes in a variety of human tumor cell types. Here we present structural details of chicken MBD2 bound to a methylated DNA sequence from the ρ-globin promoter to which it binds in vivo and mediates developmental transcriptional silencing in normal erythroid cells. While previous studies have failed to show sequence specificity for MBD2 outside of the symmetric mCpG, we find that this domain binds in a single orientation on the ρ-globin target DNA sequence. Further, we show that the orientation and affinity depends on guanine immediately following the mCpG dinucleotide. Dynamic analyses show that DNA binding stabilizes the central β-sheet, while the N- and C-terminal regions of the protein maintain mobility. Taken together, these data lead to a model in which DNA binding stabilizes the MBD2 structure and that binding orientation and affinity is influenced by the DNA sequence surrounding the central mCpG.
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Affiliation(s)
- J Neel Scarsdale
- Institute of Structural Biology and Drug Design, Virginia Commonwealth University, Richmond, VA 23298-0035, USA
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30
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Ryabov Y, Schwieters CD, Clore GM. Impact of 15N R2/R1 relaxation restraints on molecular size, shape, and bond vector orientation for NMR protein structure determination with sparse distance restraints. J Am Chem Soc 2011; 133:6154-7. [PMID: 21462982 DOI: 10.1021/ja201020c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
(15)N R(2)/R(1) relaxation data contain information on molecular shape and size as well as on bond vector orientations relative to the diffusion tensor. Since the diffusion tensor can be directly calculated from the molecular coordinates, direct inclusion of (15)N R(2)/R(1) restraints in NMR structure calculations without any a priori assumptions is possible. Here we show that (15)N R(2)/R(1) restraints are particularly valuable when only sparse distance restraints are available. Using three examples of proteins of varying size, namely, GB3 (56 residues), ubiquitin (76 residues), and the N-terminal domain of enzyme I (EIN, 249 residues), we show that incorporation of (15)N R(2)/R(1) restraints results in large and significant increases in coordinate accuracy that can make the difference between being able or unable to determine an approximate global fold. For GB3 and ubiquitin, good coordinate accuracy was obtained using only backbone hydrogen-bond restraints supplemented by (15)N R(2)/R(1) relaxation restraints. For EIN, the global fold could be determined using sparse nuclear Overhauser enhancement (NOE) distance restraints involving only NH and methyl groups in conjunction with (15)N R(2)/R(1) restraints. These results are of practical significance in the study of larger and more complex systems, where the increasing spectral complexity and number of chemical shift degeneracies reduce the number of unambiguous NOE assignments that can be readily obtained, resulting in progressively reduced NOE coverage as the size of the protein increases.
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Affiliation(s)
- Yaroslav Ryabov
- Division of Computational Bioscience, Building 12A, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892-5624, USA
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31
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Takayama Y, Schwieters CD, Grishaev A, Ghirlando R, Clore GM. Combined use of residual dipolar couplings and solution X-ray scattering to rapidly probe rigid-body conformational transitions in a non-phosphorylatable active-site mutant of the 128 kDa enzyme I dimer. J Am Chem Soc 2010; 133:424-7. [PMID: 21162528 DOI: 10.1021/ja109866w] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The first component of the bacterial phosphotransferase system, enzyme I (EI), is a multidomain 128 kDa dimer that undergoes large rigid-body conformational transitions during the course of its catalytic cycle. Here we investigate the solution structure of a non-phosphorylatable active-site mutant in which the active-site histidine is substituted by glutamine. We show that perturbations in the relative orientations and positions of the domains and subdomains can be rapidly and reliably determined by conjoined rigid-body/torsion angle/Cartesian simulated annealing calculations driven by orientational restraints from residual dipolar couplings and shape and translation information afforded by small- and wide-angle X-ray scattering. Although histidine and glutamine are isosteric, the conformational space available to a Gln side chain is larger than that for the imidazole ring of His. An additional hydrogen bond between the side chain of Gln189 located on the EIN(α/β) subdomain and an aspartate (Asp129) on the EIN(α) subdomain results in a small (∼9°) reorientation of the EIN(α) and EIN(α/β) subdomains that is in turn propagated to a larger reorientation (∼26°) of the EIN domain relative to the EIC dimerization domain, illustrating the positional sensitivity of the EIN domain and its constituent subdomains to small structural perturbations.
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Affiliation(s)
- Yuki Takayama
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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32
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Schwieters CD, Suh JY, Grishaev A, Ghirlando R, Takayama Y, Clore GM. Solution structure of the 128 kDa enzyme I dimer from Escherichia coli and its 146 kDa complex with HPr using residual dipolar couplings and small- and wide-angle X-ray scattering. J Am Chem Soc 2010; 132:13026-45. [PMID: 20731394 PMCID: PMC2955445 DOI: 10.1021/ja105485b] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The solution structures of free Enzyme I (EI, ∼128 kDa, 575 × 2 residues), the first enzyme in the bacterial phosphotransferase system, and its complex with HPr (∼146 kDa) have been solved using novel methodology that makes use of prior structural knowledge (namely, the structures of the dimeric EIC domain and the isolated EIN domain both free and complexed to HPr), combined with residual dipolar coupling (RDC), small- (SAXS) and wide- (WAXS) angle X-ray scattering and small-angle neutron scattering (SANS) data. The calculational strategy employs conjoined rigid body/torsion/Cartesian simulated annealing, and incorporates improvements in calculating and refining against SAXS/WAXS data that take into account complex molecular shapes in the description of the solvent layer resulting in a better representation of the SAXS/WAXS data. The RDC data orient the symmetrically related EIN domains relative to the C(2) symmetry axis of the EIC dimer, while translational, shape, and size information is provided by SAXS/WAXS. The resulting structures are independently validated by SANS. Comparison of the structures of the free EI and the EI-HPr complex with that of the crystal structure of a trapped phosphorylated EI intermediate reveals large (∼70-90°) hinge body rotations of the two subdomains comprising the EIN domain, as well as of the EIN domain relative to the dimeric EIC domain. These large-scale interdomain motions shed light on the structural transitions that accompany the catalytic cycle of EI.
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Affiliation(s)
- Charles D. Schwieters
- Division of Computational Biosciences, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-5624
| | - Jeong-Yong Suh
- Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, U.S.A
| | - Alexander Grishaev
- Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, U.S.A
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of health, Bethesda, MD 20892-0530, U.S.A
| | - Yuki Takayama
- Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, U.S.A
| | - G. Marius Clore
- Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, U.S.A
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33
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Bermejo GA, Strub MP, Ho C, Tjandra N. Ligand-free open-closed transitions of periplasmic binding proteins: the case of glutamine-binding protein. Biochemistry 2010; 49:1893-902. [PMID: 20141110 PMCID: PMC2831130 DOI: 10.1021/bi902045p] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The ability to undergo large-scale domain rearrangements is essential for the substrate-binding function of periplasmic binding proteins (PBPs), which are indispensable for nutrient uptake in Gram-negative bacteria. Crystal structures indicate that PBPs typically adopt either an "open" unliganded configuration or a "closed" liganded one. However, it is not clear whether, as a general rule, PBPs remain open until ligand-induced interdomain closure or are in equilibrium with a minor population of unliganded, closed species. Evidence for the latter has been recently reported on maltose-binding protein (MBP) in aqueous solution [Tang, C., et al. (2007) Nature 449, 1078-1082] via paramagnetic relaxation enhancement (PRE), a technique able to probe lowly populated regions of conformational space. Here, we use PRE to study the unliganded open-closed transition of another PBP: glutamine-binding protein (GlnBP). Through a combination of domain structure knowledge and intermolecular and concentration dependence PRE experiments, a set of surface residues was found to be involved in intermolecular interactions. Barring such residues, PRE data on ligand-free GlnBP, paramagnetically labeled at two sites (one at a time), could be appropriately explained by the unliganded, open crystal structure in that it both yielded a good PRE fit and was not significantly affected by PRE-based refinement. Thus, contrary to MBP, our data did not particularly suggest the coexistence of a minor closed conformer. Several possibilities were explored to explain the observed differences in such closely structurally related systems; among them, a particularly interesting one arises from close inspection of the interdomain "hinge" region of various PBPs: strong hydrogen bond interactions discourage large-scale interdomain dynamics.
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Affiliation(s)
- Guillermo A. Bermejo
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Marie-Paule Strub
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Chien Ho
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Nico Tjandra
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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34
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Jung YS, Cai M, Clore GM. Solution structure of the IIAChitobiose-IIBChitobiose complex of the N,N'-diacetylchitobiose branch of the Escherichia coli phosphotransferase system. J Biol Chem 2010; 285:4173-4184. [PMID: 19959833 PMCID: PMC2823556 DOI: 10.1074/jbc.m109.080937] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 11/30/2009] [Indexed: 11/06/2022] Open
Abstract
The solution structure of the IIA-IIB complex of the N,N'-diacetylchitobiose (Chb) transporter of the Escherichia coli phosphotransferase system has been solved by NMR. The active site His-89 of IIA(Chb) was mutated to Glu to mimic the phosphorylated state and the active site Cys-10 of IIB(Chb) was substituted by serine to prevent intermolecular disulfide bond formation. Binding is weak with a K(D) of approximately 1.3 mm. The two complementary interaction surfaces are largely hydrophobic, with the protruding active site loop (residues 9-16) of IIB(Chb) buried deep within the active site cleft formed at the interface of two adjacent subunits of the IIA(Chb) trimer. The central hydrophobic portion of the interface is surrounded by a ring of polar and charged residues that provide a relatively small number of electrostatic intermolecular interactions that serve to correctly align the two proteins. The conformation of the active site loop in unphosphorylated IIB(Chb) is inconsistent with the formation of a phosphoryl transition state intermediate because of steric hindrance, especially from the methyl group of Ala-12 of IIB(Chb). Phosphorylation of IIB(Chb) is accompanied by a conformational change within the active site loop such that its path from residues 11-13 follows a mirror-like image relative to that in the unphosphorylated state. This involves a transition of the phi/psi angles of Gly-13 from the right to left alpha-helical region, as well as smaller changes in the backbone torsion angles of Ala-12 and Met-14. The resulting active site conformation is fully compatible with the formation of the His-89-P-Cys-10 phosphoryl transition state without necessitating any change in relative translation or orientation of the two proteins within the complex.
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Affiliation(s)
- Young-Sang Jung
- From the Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Mengli Cai
- From the Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - G Marius Clore
- From the Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892.
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35
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Ryabov Y, Suh JY, Grishaev A, Clore GM, Schwieters CD. Using the experimentally determined components of the overall rotational diffusion tensor to restrain molecular shape and size in NMR structure determination of globular proteins and protein-protein complexes. J Am Chem Soc 2009; 131:9522-31. [PMID: 19537713 DOI: 10.1021/ja902336c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper describes an approach for making use of the components of the experimentally determined rotational diffusion tensor derived from NMR relaxation measurements in macromolecular structure determination. The parameters of the rotational diffusion tensor describe the shape and size of the macromolecule or macromolecular complex, and are therefore complementary to traditional NMR restraints. The structural information contained in the rotational diffusion tensor is not dissimilar to that present in the small-angle region of solution X-ray scattering profiles. We demonstrate the utility of rotational diffusion tensor restraints for protein structure refinement using the N-terminal domain of enzyme I (EIN) as an example and validate the results by solution small-angle X-ray scattering. We also show how rotational diffusion tensor restraints can be used for docking complexes using the dimeric HIV-1 protease and the EIN-HPr complexes as examples. In the former case, the rotational diffusion tensor restraints are sufficient in their own right to determine the position of one subunit relative to another. In the latter case, rotational diffusion tensor restraints complemented by highly ambiguous distance restraints derived from chemical shift perturbation mapping and a hydrophobic contact potential are sufficient to correctly dock EIN to HPr. In each case, the cluster containing the lowest-energy structure corresponds to the correct solution.
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Affiliation(s)
- Yaroslav Ryabov
- Division of Computational Bioscience, Building 12A, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892-5624, USA
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36
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Bermejo GA, Strub MP, Ho C, Tjandra N. Determination of the solution-bound conformation of an amino acid binding protein by NMR paramagnetic relaxation enhancement: use of a single flexible paramagnetic probe with improved estimation of its sampling space. J Am Chem Soc 2009; 131:9532-7. [PMID: 19583434 PMCID: PMC2720827 DOI: 10.1021/ja902436g] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate the feasibility of elucidating the bound ("closed") conformation of a periplasmic binding protein, the glutamine-binding protein (GlnBP), in solution, using paramagnetic relaxation enhancements (PREs) arising from a single paramagnetic group. GlnBP consists of two globular domains connected by a hinge. Using the ligand-free ("open") conformation as a starting point, conjoined rigid-body/torsion-angle simulated annealing calculations were performed using backbone (1)H(N)-PREs as a major source of distance information. Paramagnetic probe flexibility was accounted for via a multiple-conformer representation. A conventional approach where the entire PRE data set is enforced at once during simulated annealing yielded poor results due to inappropriate conformational sampling of the probe. On the other hand, significant improvements in coordinate accuracy were obtained by estimating the probe sampling space prior to structure calculation. Such sampling is achieved by refining the ensemble of probe conformers with intradomain PREs only, keeping the protein backbone fixed in the open form. Subsequently, while constraining the probe to the previously found conformations, the domains are allowed to move relative to each other under the influence of the non-intradomain PREs, giving the hinge region torsional degrees of freedom. Thus, by partitioning the protocol into "probe sampling" and "backbone sampling" stages, structures significantly closer to the X-ray structure of ligand-bound GlnBP were obtained.
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Affiliation(s)
- Guillermo A. Bermejo
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Marie-Paule Strub
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Chien Ho
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Nico Tjandra
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
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37
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Wylie BJ, Schwieters CD, Oldfield E, Rienstra CM. Protein structure refinement using 13C alpha chemical shift tensors. J Am Chem Soc 2009; 131:985-92. [PMID: 19123862 DOI: 10.1021/ja804041p] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have obtained the (13)C alpha chemical shift tensors for each amino acid in the protein GB1. We then developed a CST force field and incorporated this into the Xplor-NIH structure determination program. GB1 structures obtained by using CST restraints had improved precision over those obtained in the absence of CST restraints and were also more accurate. When combined with isotropic chemical shifts, distance, and vector angle restraints, the root-mean squared error with respect to existing X-ray structures was better than approximately 1.0 A. These results are of broad general interest since they show that chemical shift tensors can be used in protein structure refinement, improving both structural accuracy and precision, opening up the way to accurate de novo structure determination.
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Affiliation(s)
- Benjamin J Wylie
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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38
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Tang C, Louis JM, Aniana A, Suh JY, Clore GM. Visualizing transient events in amino-terminal autoprocessing of HIV-1 protease. Nature 2008; 455:693-6. [PMID: 18833280 PMCID: PMC2798589 DOI: 10.1038/nature07342] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Accepted: 08/12/2008] [Indexed: 11/09/2022]
Abstract
HIV-1 protease processes the Gag and Gag-Pol polyproteins into mature structural and functional proteins, including itself, and is therefore indispensable for viral maturation. The mature protease is active only as a dimer with each subunit contributing catalytic residues. The full-length transframe region protease precursor appears to be monomeric yet undergoes maturation via intramolecular cleavage of a putative precursor dimer, concomitant with the appearance of mature-like catalytic activity. How such intramolecular cleavage can occur when the amino and carboxy termini of the mature protease are part of an intersubunit beta-sheet located distal from the active site is unclear. Here we visualize the early events in N-terminal autoprocessing using an inactive mini-precursor with a four-residue N-terminal extension that mimics the transframe region protease precursor. Using paramagnetic relaxation enhancement, a technique that is exquisitely sensitive to the presence of minor species, we show that the mini-precursor forms highly transient, lowly populated (3-5%) dimeric encounter complexes that involve the mature dimer interface but occupy a wide range of subunit orientations relative to the mature dimer. Furthermore, the occupancy of the mature dimer configuration constitutes a very small fraction of the self-associated species (accounting for the very low enzymatic activity of the protease precursor), and the N-terminal extension makes transient intra- and intersubunit contacts with the substrate binding site and is therefore available for autocleavage when the correct dimer orientation is sampled within the encounter complex ensemble.
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Affiliation(s)
- Chun Tang
- Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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39
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Wang X, Weldeghiorghis T, Zhang G, Imperiali B, Prestegard JH. Solution structure of Alg13: the sugar donor subunit of a yeast N-acetylglucosamine transferase. Structure 2008; 16:965-75. [PMID: 18547528 DOI: 10.1016/j.str.2008.03.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Revised: 03/07/2008] [Accepted: 03/13/2008] [Indexed: 10/22/2022]
Abstract
The solution structure of Alg13, the glycosyl donor-binding domain of an important bipartite glycosyltransferase in the yeast Saccharomyces cerevisiae, is presented. This glycosyltransferase is unusual in that it is active only in the presence of a binding partner, Alg14. Alg13 is found to adopt a unique topology among glycosyltransferases. Rather than the conventional Rossmann fold found in all GT-B enzymes, the N-terminal half of the protein is a Rossmann-like fold with a mixed parallel and antiparallel beta sheet. The Rossmann fold of the C-terminal half of Alg13 is conserved. However, although conventional GT-B enzymes usually possess three helices at the C terminus, only two helices are present in Alg13. Titration of Alg13 with both UDP-GlcNAc, the native glycosyl donor, and a paramagnetic mimic, UDP-TEMPO, shows that the interaction of Alg13 with the sugar donor is primarily through the residues in the C-terminal half of the protein.
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Affiliation(s)
- Xu Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
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40
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Kuszewski JJ, Thottungal RA, Clore GM, Schwieters CD. Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm. JOURNAL OF BIOMOLECULAR NMR 2008; 41:221-39. [PMID: 18668206 PMCID: PMC2575051 DOI: 10.1007/s10858-008-9255-1] [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: 05/09/2008] [Accepted: 07/02/2008] [Indexed: 05/05/2023]
Abstract
We report substantial improvements to the previously introduced automated NOE assignment and structure determination protocol known as PASD (Kuszewski et al. (2004) J Am Chem Soc 26:6258-6273). The improved protocol includes extensive analysis of input spectral data to create a low-resolution contact map of residues expected to be close in space. This map is used to obtain reasonable initial guesses of NOE assignment likelihoods which are refined during subsequent structure calculations. Information in the contact map about which residues are predicted to not be close in space is applied via conservative repulsive distance restraints which are used in early phases of the structure calculations. In comparison with the previous protocol, the new protocol requires significantly less computation time. We show results of running the new PASD protocol on six proteins and demonstrate that useful assignment and structural information is extracted on proteins of more than 220 residues. We show that useful assignment information can be obtained even in the case in which a unique structure cannot be determined.
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Affiliation(s)
- John J Kuszewski
- Imaging Sciences Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-5624, USA
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41
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Hu J, Hu K, Williams DC, Komlosh ME, Cai M, Clore GM. Solution NMR structures of productive and non-productive complexes between the A and B domains of the cytoplasmic subunit of the mannose transporter of the Escherichia coli phosphotransferase system. J Biol Chem 2008; 283:11024-37. [PMID: 18270202 PMCID: PMC2447639 DOI: 10.1074/jbc.m800312200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Indexed: 11/06/2022] Open
Abstract
Solution structures of complexes between the isolated A (IIA(Man)) and B (IIB(Man)) domains of the cytoplasmic component of the mannose transporter of Escherichia coli have been solved by NMR. The complex of wild-type IIA(Man) and IIB(Man) is a mixture of two species comprising a productive, phosphoryl transfer competent complex and a non-productive complex with the two active site histidines, His-10 of IIA(Man) and His-175 of IIB(Man), separated by approximately 25A. Mutation of the active site histidine, His-10, of IIA(Man) to a glutamate, to mimic phosphorylation, results in the formation of a single productive complex. The apparent equilibrium dissociation constants for the binding of both wild-type and H10E IIA(Man) to IIB(Man) are approximately the same (K(D) approximately 0.5 mM). The productive complex can readily accommodate a transition state involving a pentacoordinate phosphoryl group with trigonal bipyramidal geometry bonded to the Nepsilon2 atom of His-10 of IIA(Man) and the Ndelta1 atom of His-175 of IIB(Man) with negligible (<0.2A) local backbone conformational changes in the immediate vicinity of the active site. The non-productive complex is related to the productive one by a approximately 90 degrees rotation and approximately 37A translation of IIB(Man) relative to IIA(Man), leaving the active site His-175 of IIB(Man) fully exposed to solvent in the non-productive complex. The interaction surface on IIA(Man) for the non-productive complex comprises a subset of residues used in the productive complex and in both cases involves both subunits of IIA(Man). The selection of the productive complex by IIA(Man)(H10E) can be attributed to neutralization of the positively charged Arg-172 of IIB(Man) at the center of the interface. The non-productive IIA(Man)-IIB(Man) complex may possibly be relevant to subsequent phosphoryl transfer from His-175 of IIB(Man) to the incoming sugar located on the transmembrane IIC(Man)-IID(Man) complex.
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Affiliation(s)
- Jun Hu
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
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Bermejo GA, Llinás M. Deuterated protein folds obtained directly from unassigned nuclear overhauser effect data. J Am Chem Soc 2008; 130:3797-805. [PMID: 18318535 DOI: 10.1021/ja074836e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate the feasibility of determining the global fold of a highly deuterated protein from unassigned experimental NMR nuclear Overhauser effect (NOE) data only. The method relies on the calculation of a spatial configuration of covalently unconnected protons-a "cloud"-directly from unassigned distance restraints derived from 13C- and 15N-edited NOESY spectra. Each proton in the cloud, labeled by its chemical shift and that of the directly bound 13C or 15N, is subsequently mapped to specific atoms in the protein. This is achieved via graph-theoretical protocols that search for connectivities in graphs that encode the structural information within the cloud. The peptidyl HN chain is traced by seeking for all possible routes and selecting the one that yields the minimal sum of sequential distances. Complete proton identification in the cloud is achieved by linking the side-chain protons to proximal main-chain HNs via bipartite graph matching. The identified protons automatically yield the NOE assignments, which in turn are used for structure calculation with RosettaNMR, a protocol that incorporates structural bias derived from protein databases. The method, named Sparse-Constraint CLOUDS, was applied to experimental NOESY data on the 58-residue Z domain of staphylococcal protein A. The generated structures are of similar accuracy to those previously reported, which were derived via a conventional approach involving a larger NMR data set. Additional tests were performed on seven reported protein structures of various folds, using restraint lists simulated from the known atomic coordinates.
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Affiliation(s)
- Guillermo A Bermejo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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43
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Schwieters CD, Clore GM. A Pseudopotential for Improving the Packing of Ellipsoidal Protein Structures Determined from NMR Data. J Phys Chem B 2007; 112:6070-3. [DOI: 10.1021/jp076244o] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Charles D. Schwieters
- Imaging Sciences Laboratory, Center for Information Technology, National Institutes of Health, Building 12A, Bethesda, Maryland 20892-5624, and Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Bethesda, Maryland 20892-0510
| | - G. Marius Clore
- Imaging Sciences Laboratory, Center for Information Technology, National Institutes of Health, Building 12A, Bethesda, Maryland 20892-5624, and Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Bethesda, Maryland 20892-0510
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44
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Tang C, Schwieters CD, Clore GM. Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR. Nature 2007; 449:1078-82. [PMID: 17960247 DOI: 10.1038/nature06232] [Citation(s) in RCA: 335] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Accepted: 09/07/2007] [Indexed: 11/09/2022]
Abstract
Large-scale domain rearrangements in proteins have long been recognized to have a critical function in ligand binding and recognition, catalysis and regulation. Crystal structures have provided a static picture of the apo (usually open) and holo usually closed) states. The general question arises as to whether the apo state exists as a single species in which the closed state is energetically inaccessible and interdomain rearrangement is induced by ligand or substrate binding, or whether the predominantly open form already coexists in rapid equilibrium with a minor closed species. The maltose-binding protein (MBP), a member of the bacterial periplasmic binding protein family, provides a model system for investigating this problem because it has been the subject of extensive studies by crystallography, NMR and other biophysical techniques. Here we show that although paramagnetic relaxation enhancement (PRE) data for the sugar-bound form are consistent with the crystal structure of holo MBP, the PRE data for the apo state are indicative of a rapidly exchanging mixture (ns to mus regime) of a predominantly ( approximately 95%) open form (represented by the apo crystal structure) and a minor (approximately 5%) partially closed species. Using ensemble simulated annealing refinement against the PRE data we are able to determine a <r(-6)> ensemble average structure of the minor apo species and show that it is distinct from the sugar-bound state.
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Affiliation(s)
- Chun Tang
- Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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45
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Lee D, Walsh JD, Migliorini M, Yu P, Cai T, Schwieters CD, Krueger S, Strickland DK, Wang YX. The structure of receptor-associated protein (RAP). Protein Sci 2007; 16:1628-40. [PMID: 17656581 PMCID: PMC2203372 DOI: 10.1110/ps.072865407] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Revised: 05/24/2007] [Accepted: 05/25/2007] [Indexed: 10/23/2022]
Abstract
The receptor-associated protein (RAP) is a molecular chaperone that binds tightly to certain newly synthesized LDL receptor family members in the endoplasmic reticulum (ER) and facilitates their delivery to the Golgi. We have adopted a divide-and-conquer strategy to solve the structures of the individual domains of RAP using NMR spectroscopy. We present here the newly determined structure of domain 2. Based on this structure and the structures of domains 1 and 3, which were solved previously, we utilized experimental small-angle neutron scattering (SANS) data and a novel simulated annealing protocol to characterize the overall structure of RAP. The results reveal that RAP adopts a unique structural architecture consisting of three independent three-helix bundles that are connected by long and flexible linkers. The flexible linkers and the quasi-repetitive structural architecture may allow RAP to adopt various possible conformations when interacting with the LDL receptors, which are also made of repetitive substructure units.
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Affiliation(s)
- Donghan Lee
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland 21702, USA
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46
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Cai M, Huang Y, Suh JY, Louis JM, Ghirlando R, Craigie R, Clore GM. Solution NMR structure of the barrier-to-autointegration factor-Emerin complex. J Biol Chem 2007; 282:14525-35. [PMID: 17355960 DOI: 10.1074/jbc.m700576200] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The barrier-to-autointegration factor BAF binds to the LEM domain (Em(LEM)) of the nuclear envelope protein emerin and plays an essential role in the nuclear architecture of metazoan cells. In addition, the BAF(2) dimer bridges and compacts double-stranded DNA nonspecifically via two symmetry-related DNA binding sites. In this article we present biophysical and structural studies on a complex of BAF(2) and Em(LEM). Light scattering, analytical ultracentrifugation, and NMR indicate a stoichiometry of one molecule of Em(LEM) bound per BAF(2) dimer. The equilibrium dissociation constant (K(d)) for the interaction of the BAF(2) dimer and Em(LEM), determined by isothermal titration calorimetry, is 0.59 +/- 0.03 microm. Z-exchange spectroscopy between corresponding cross-peaks of the magnetically non-equivalent subunits of the BAF(2) dimer in the complex yields a dissociation rate constant of 78 +/- 2s(-1). The solution NMR structure of the BAF(2)-Em(LEM) complex reveals that the LEM and DNA binding sites on BAF(2) are non-overlapping and that both subunits of the BAF(2) dimer contribute approximately equally to the Em(LEM) binding site. The relevance of the implications of the structural and biophysical data on the complex in the context of the interaction between the BAF(2) dimer and Em(LEM) at the nuclear envelope is discussed.
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Affiliation(s)
- Mengli Cai
- Laboratories of Chemical Physics and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892-0520, USA
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47
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Cornilescu G, Hadley EB, Woll MG, Markley JL, Gellman SH, Cornilescu CC. Solution structure of a small protein containing a fluorinated side chain in the core. Protein Sci 2007; 16:14-9. [PMID: 17123960 PMCID: PMC2222841 DOI: 10.1110/ps.062557707] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2006] [Revised: 10/06/2006] [Accepted: 10/10/2006] [Indexed: 10/23/2022]
Abstract
We report the first high-resolution structure for a protein containing a fluorinated side chain. Recently we carried out a systematic evaluation of phenylalanine to pentafluorophenylalanine (Phe --> F(5)-Phe) mutants for the 35-residue chicken villin headpiece subdomain (c-VHP), the hydrophobic core of which features a cluster of three Phe side chains (residues 6, 10, and 17). Phe --> F(5)-Phe mutations are interesting because aryl-perfluoroaryl interactions of optimal geometry are intrinsically more favorable than either aryl-aryl or perfluoroaryl-perfluoroaryl interactions, and because perfluoroaryl units are more hydrophobic than are analogous aryl units. Only one mutation, Phe10 --> F(5)-Phe, was found to provide enhanced tertiary structural stability relative to the native core (by approximately 1 kcal/mol, according to guanidinium chloride denaturation studies). The NMR structure of this mutant, described here, reveals very little variation in backbone conformation or side chain packing relative to the wild type. Thus, although Phe --> F(5)-Phe mutations offer the possibility of greater tertiary structural stability from side chain-side chain attraction and/or side chain desolvation, the constraints associated with the native c-VHP fold apparently prevent the modified polypeptide from taking advantage of this possibility. Our findings are important because they complement several studies that have shown that fluorination of saturated side chain carbon atoms can provide enhanced conformational stability.
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Affiliation(s)
- Gabriel Cornilescu
- NMRFAM, Department of biochemistry, University of Wisconsin, Madison, WI 53706, USA
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48
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Clore GM, Schwieters CD. Concordance of Residual Dipolar Couplings, Backbone Order Parameters and Crystallographic B-factors for a Small α/β Protein: A Unified Picture of High Probability, Fast Atomic Motions in Proteins. J Mol Biol 2006; 355:879-86. [PMID: 16343537 DOI: 10.1016/j.jmb.2005.11.042] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2005] [Revised: 11/03/2005] [Accepted: 11/14/2005] [Indexed: 11/28/2022]
Abstract
Using ensemble refinement of the third immunoglobulin binding domain (GB3) of streptococcal protein G (a small alpha/beta protein of 56 residues), we demonstrate that backbone (N-H, N-C', Calpha-Halpha, Calpha-C') residual dipolar coupling data in five independent alignment media, generalized order parameters from 15N relaxation data, and B-factors from a high-resolution (1.1A), room temperature crystal structure are entirely consistent with one another within experimental error. The optimal ensemble size representation is between four and eight, as assessed by complete cross-validation of the residual dipolar couplings. Thus, in the case of GB3, all three observables reflect the same low-amplitude anisotropic motions arising from fluctuations in backbone phi/psi torsion angles in the picosecond to nanosecond regime in both solution and crystalline environments, yielding a unified picture of fast, high-probability atomic motions in proteins. An understanding of these motions is crucial for understanding the impact of protein dynamics on protein function, since they provide part of the driving force for triggered conformational changes that occur, for example, upon ligand binding, signal transduction and enzyme catalysis.
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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 20892-0520, USA.
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Suh JY, Cai M, Williams DC, Clore GM. Solution structure of a post-transition state analog of the phosphotransfer reaction between the A and B cytoplasmic domains of the mannitol transporter IIMannitol of the Escherichia coli phosphotransferase system. J Biol Chem 2006; 281:8939-49. [PMID: 16443929 DOI: 10.1074/jbc.m513466200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The solution structure of the post-transition state complex between the isolated cytoplasmic A (IIAMtl) and phosphorylated B (phospho-IIBMtl) domains of the mannitol transporter of the Escherichia coli phosphotransferase system has been solved by NMR. The active site His-554 of IIAMtl was mutated to glutamine to block phosphoryl transfer activity, and the active site Cys-384 of IIBMtl (residues of IIBMtl are denoted in italic type) was substituted by serine to permit the formation of a stable phosphorylated form of IIBMtl. The two complementary interaction surfaces are predominantly hydrophobic, and two methionines on IIBMtl, Met-388 and Met-393, serve as anchors by interacting with two deep pockets on the surface of IIAMtl. With the exception of a salt bridge between the conserved Arg-538 of IIAMtl and the phosphoryl group of phospho-IIBMtl, electrostatic interactions between the two proteins are limited to the outer edges of the interface, are few in number, and appear to be weak. This accounts for the low affinity of the complex (Kd approximately 3.7 mm), which is optimally tuned to the intact biological system in which the A and B domains are expressed as a single polypeptide connected by a flexible 21-residue linker. The phosphoryl transition state can readily be modeled with no change in protein-protein orientation and minimal perturbations in both the backbone immediately adjacent to His-554 and Cys-384 and the side chains in close proximity to the phosphoryl group. Comparison with the previously solved structure of the IIAMtl-HPr complex reveals how IIAMtl uses the same interaction surface to recognize two structurally unrelated proteins and explains the much higher affinity of IIAMtl for HPr than IIBMtl.
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Affiliation(s)
- Jeong-Yong Suh
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
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50
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Tang C, Iwahara J, Clore GM. Accurate determination of leucine and valine side-chain conformations using U-[15N/13C/2H]/[1H-(methine/methyl)-Leu/Val] isotope labeling, NOE pattern recognition, and methine Cgamma-Hgamma/Cbeta-Hbeta residual dipolar couplings: application to the 34-kDa enzyme IIA(chitobiose). JOURNAL OF BIOMOLECULAR NMR 2005; 33:105-21. [PMID: 16258829 DOI: 10.1007/s10858-005-1206-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2005] [Accepted: 07/14/2005] [Indexed: 05/05/2023]
Abstract
An isotope labeling scheme is described in which specific protonation of methine and methyl protons of leucine and valine is obtained on a 15N/13C labeled background with uniform deuteration of all other non-exchangeable protons. The presence of a protonated methine group has little effect on the favorable relaxation properties of the methyl protons of Leu and Val. This labeling scheme permits the rotameric state of leucine side-chains to be readily determined by simple inspection of the pattern of Hgamma(i)-H(N)(i) and Hgamma(i)-H(N)(i+1) NOEs in a 3D 15N-separated NOE spectrum free of complications arising from spectral overlap and spin-diffusion. In addition, one-bond residual dipolar couplings for the methine 13C-1H bond vectors of Leu and Val can be accurately determined from an intensity J-modulated constant-time HCCH-COSY experiment and used to accurately orient the side-chains of Leu and Val. Incorporation of these data into structure refinement improves the accuracy with which the conformations of Leu and Val side-chains can be established. This is important to ensure optimal packing both within the protein core and at intermolecular interfaces. The impact of the method on protein structure determination is illustrated by application to enzyme IIA(Chitobiose), a 34 kDa homotrimeric phosphotransferase protein.
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Affiliation(s)
- Chun Tang
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5/B1-30I, Bethesda, MD 20892-0520, USA
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