1
|
Paramagnetic NMR Spectroscopy Is a Tool to Address Reactivity, Structure, and Protein–Protein Interactions of Metalloproteins: The Case of Iron–Sulfur Proteins. MAGNETOCHEMISTRY 2020. [DOI: 10.3390/magnetochemistry6040046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The study of cellular machineries responsible for the iron–sulfur (Fe–S) cluster biogenesis has led to the identification of a large number of proteins, whose importance for life is documented by an increasing number of diseases linked to them. The labile nature of Fe–S clusters and the transient protein–protein interactions, occurring during the various steps of the maturation process, make their structural characterization in solution particularly difficult. Paramagnetic nuclear magnetic resonance (NMR) has been used for decades to characterize chemical composition, magnetic coupling, and the electronic structure of Fe–S clusters in proteins; it represents, therefore, a powerful tool to study the protein–protein interaction networks of proteins involving into iron–sulfur cluster biogenesis. The optimization of the various NMR experiments with respect to the hyperfine interaction will be summarized here in the form of a protocol; recently developed experiments for measuring longitudinal and transverse nuclear relaxation rates in highly paramagnetic systems will be also reviewed. Finally, we will address the use of extrinsic paramagnetic centers covalently bound to diamagnetic proteins, which contributed over the last twenty years to promote the applications of paramagnetic NMR well beyond the structural biology of metalloproteins.
Collapse
|
2
|
Guin D, Gruebele M. Weak Chemical Interactions That Drive Protein Evolution: Crowding, Sticking, and Quinary Structure in Folding and Function. Chem Rev 2019; 119:10691-10717. [PMID: 31356058 DOI: 10.1021/acs.chemrev.8b00753] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In recent years, better instrumentation and greater computing power have enabled the imaging of elusive biomolecule dynamics in cells, driving many advances in understanding the chemical organization of biological systems. The focus of this Review is on interactions in the cell that affect both biomolecular stability and function and modulate them. The same protein or nucleic acid can behave differently depending on the time in the cell cycle, the location in a specific compartment, or the stresses acting on the cell. We describe in detail the crowding, sticking, and quinary structure in the cell and the current methods to quantify them both in vitro and in vivo. Finally, we discuss protein evolution in the cell in light of current biophysical evidence. We describe the factors that drive protein evolution and shape protein interaction networks. These interactions can significantly affect the free energy, ΔG, of marginally stable and low-population proteins and, due to epistasis, direct the evolutionary pathways in an organism. We finally conclude by providing an outlook on experiments to come and the possibility of collaborative evolutionary biology and biophysical efforts.
Collapse
Affiliation(s)
- Drishti Guin
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States
| | - Martin Gruebele
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States.,Department of Physics , University of Illinois , Urbana , Illinois 61801 , United States.,Center for Biophysics and Quantitative Biology , University of Illinois , Urbana , Illinois 61801 , United States
| |
Collapse
|
3
|
Fatty acid synthase cooperates with protrudin to facilitate membrane outgrowth of cellular protrusions. Sci Rep 2017; 7:46569. [PMID: 28429738 PMCID: PMC5399442 DOI: 10.1038/srep46569] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/17/2017] [Indexed: 01/02/2023] Open
Abstract
Cellular protrusion formation capacity is a key feature of developing neurons and many eukaryotic cells. However, the mechanisms underlying membrane growth in protrusion formation are largely unclear. In this study, photo-reactive unnatural amino acid 3-(3-methyl-3H-diazirin-3-yl)-propamino-carbonyl-Nε-l-lysine was incorporated by a genetic code expansion strategy into protrudin, a protein localized in acidic endosomes and in the endoplasmic reticulum, that induces cellular protrusion and neurite formation. The modified protrudin was used for covalent trapping of protrudin-interacting proteins in living cells. Fatty acid synthase (FASN), which synthesizes free fatty acids, was identified to transiently interact with protrudin. Further characterization revealed a unique cooperation mechanism in which protrudin cooperates with FASN to facilitate cellular protrusion formation. This work reveals a novel mechanism involved in protrusion formation that is dependent on transient interaction between FASN and protrudin, and establishes a creative strategy to investigate transient protein-protein interactions in mammalian cells.
Collapse
|
4
|
Zhao L, Ehrt C, Koch O, Wu YW. One-Pot N2C/C2C/N2N Ligation To Trap Weak Protein-Protein Interactions. Angew Chem Int Ed Engl 2016; 55:8129-33. [PMID: 27213482 DOI: 10.1002/anie.201601299] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/13/2016] [Indexed: 01/19/2023]
Abstract
Weak transient protein-protein interactions (PPIs) play an essential role in cellular dynamics. However, it is challenging to obtain weak protein complexes owing to their short lifetime. Herein we present a general and facile method for trapping weak PPIs in an unbiased manner using proximity-induced ligations. To expand the chemical ligation spectrum, we developed novel N2N (N-terminus to N-terminus) and C2C (C-terminus to C-terminus) ligation approaches. By using N2C (N-terminus to C-terminus), N2N, and C2C ligations in one pot, the interacting proteins were linked. The weak Ypt1:GDI interaction drove C2C ligation with t1/2 of 4.8 min and near quantitative conversion. The Ypt1-GDI conjugate revealed that binding of Ypt1 G-domain causes opening of the lipid-binding site of GDI, which can accommodate one prenyl group, giving insights into Rab membrane recycling. Moreover, we used this strategy to trap the KRas homodimer, which plays an important role in Ras signaling.
Collapse
Affiliation(s)
- Lei Zhao
- Chemical Genomics Center of the Max Planck Society, Otto-Hahn-Strasse 15, 44227, Dortmund, Germany
| | - Christiane Ehrt
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Oliver Koch
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Yao-Wen Wu
- Chemical Genomics Center of the Max Planck Society, Otto-Hahn-Strasse 15, 44227, Dortmund, Germany.
| |
Collapse
|
5
|
Zhao L, Ehrt C, Koch O, Wu YW. Eintopf-N2C/C2C/N2N-Proteinligationsstrategien zur Analyse schwacher Protein-Protein-Wechselwirkungen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Lei Zhao
- Chemical Genomics Center der Max-Planck-Gesellschaft; Otto-Hahn-Straße 15 44227 Dortmund Deutschland
| | - Christiane Ehrt
- Technische Universität Dortmund; Fakultät für Chemie und Chemische Biologie; Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Oliver Koch
- Technische Universität Dortmund; Fakultät für Chemie und Chemische Biologie; Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Yao-Wen Wu
- Chemical Genomics Center der Max-Planck-Gesellschaft; Otto-Hahn-Straße 15 44227 Dortmund Deutschland
| |
Collapse
|
6
|
Shi J, Liu Y, Guo R, Li X, He A, Gao Y, Wei Y, Liu C, Zhao Y, Xu Y, Noda I, Wu J. Design of a New Concentration Series for the Orthogonal Sample Design Approach and Estimation of the Number of Reactions in Chemical Systems. APPLIED SPECTROSCOPY 2015; 69:1229-1242. [PMID: 26647046 DOI: 10.1366/14-07759] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A new concentration series is proposed for the construction of a two-dimensional (2D) synchronous spectrum for orthogonal sample design analysis to probe intermolecular interaction between solutes dissolved in the same solutions. The obtained 2D synchronous spectrum possesses the following two properties: (1) cross peaks in the 2D synchronous spectra can be used to reflect intermolecular interaction reliably, since interference portions that have nothing to do with intermolecular interaction are completely removed, and (2) the two-dimensional synchronous spectrum produced can effectively avoid accidental collinearity. Hence, the correct number of nonzero eigenvalues can be obtained so that the number of chemical reactions can be estimated. In a real chemical system, noise present in one-dimensional spectra may also produce nonzero eigenvalues. To get the correct number of chemical reactions, we classified nonzero eigenvalues into significant nonzero eigenvalues and insignificant nonzero eigenvalues. Significant nonzero eigenvalues can be identified by inspecting the pattern of the corresponding eigenvector with help of the Durbin-Watson statistic. As a result, the correct number of chemical reactions can be obtained from significant nonzero eigenvalues. This approach provides a solid basis to obtain insight into subtle spectral variations caused by intermolecular interaction.
Collapse
Affiliation(s)
- Jiajia Shi
- College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang 050024, China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Johansson H, Jensen MR, Gesmar H, Meier S, Vinther JM, Keeler C, Hodsdon ME, Led JJ. Specific and nonspecific interactions in ultraweak protein-protein associations revealed by solvent paramagnetic relaxation enhancements. J Am Chem Soc 2014; 136:10277-86. [PMID: 24969589 PMCID: PMC4111215 DOI: 10.1021/ja503546j] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
Weak
and transient protein–protein interactions underlie
numerous biological processes. However, the location of the interaction
sites of the specific complexes and the effect of transient, nonspecific
protein–protein interactions often remain elusive. We have
investigated the weak self-association of human growth hormone (hGH, KD = 0.90 ± 0.03 mM) at neutral pH by the
paramagnetic relaxation enhancement (PRE) of the amide protons induced
by the soluble paramagnetic relaxation agent, gadodiamide (Gd(DTPA-BMA)).
Primarily, it was found that the PREs are in agreement with the general
Hwang-Freed model for relaxation by translational diffusion (J. Chem. Phys.1975, 63, 4017–4025),
only if crowding effects on the diffusion in the protein solution
are taken into account. Second, by measuring the PREs of the amide
protons at increasing hGH concentrations and a constant concentration
of the relaxation agent, it is shown that a distinction can be made
between residues that are affected only by transient, nonspecific
protein–protein interactions and residues that are involved
in specific protein–protein associations. Thus, the PREs of
the former residues increase linearly with the hGH concentration in
the entire concentration range because of a reduction of the diffusion
caused by the transient, nonspecific protein–protein interactions,
while the PREs of the latter residues increase only at the lower hGH
concentrations but decrease at the higher concentrations because of
specific protein–protein associations that impede the access
of gadodiamide to the residues of the interaction surface. Finally,
it is found that the ultraweak aggregation of hGH involves several
interaction sites that are located in patches covering a large part
of the protein surface.
Collapse
Affiliation(s)
- Helle Johansson
- Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | | | | | | | | | | | | | | |
Collapse
|
8
|
Tierney DL. Jahn-Teller dynamics in a series of high-symmetry Co(II) chelates determine paramagnetic relaxation enhancements. J Phys Chem A 2012; 116:10959-72. [PMID: 23095055 DOI: 10.1021/jp309245e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
NMR paramagnetic relaxation enhancements (PREs) of a series of structurally characterized, trigonal bis-trispyrazolylborate (Tp) chelates of high-spin Co(II), spanning 100-850 MHz in field, are reported. Prior knowledge of the metal-nucleus distances allows numerical extraction of position-dependent electron spin relaxation rates (τ(c)(-1)) from direct measurement of the individual PREs of the four symmetry distinct protons in Co(Tp)(2), using available closed-form expressions. The data for this electronically complex system where spin-orbit coupling defines the ground state electronic structure are analyzed in terms of the Solomon-Bloembergen-Morgan (SBM) relations, as well as available zero-field splitting limit theories. A simple angular correction is shown to be sufficient to reconcile the individual τ(c)(T) data for the four classes of protons. The data identify a previously unrecognized dynamic Jahn-Teller effect in these historically important complexes, with a barrier of ~230 cm(-1), pointing to a level of dynamics in trispyrazolylborate chemistry that has not been described before, and further show that it is the Jahn-Teller that is responsible for the PREs in fluid solution. A field-dependent component is also identified for the two protons nearest g(//), which is suggested to arise due to Zeeman mixing of excited state character into the ground level.
Collapse
Affiliation(s)
- David L Tierney
- Department of Chemistry and Chemical Biology, The University of New Mexico, Albuquerque, New Mexico 87131, United States.
| |
Collapse
|
9
|
Clore GM, Iwahara J. Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes. Chem Rev 2009; 109:4108-39. [PMID: 19522502 DOI: 10.1021/cr900033p] [Citation(s) in RCA: 588] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- G Marius Clore
- Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
| | | |
Collapse
|
10
|
Zhang C, Huang K, Li H, Chen J, Liu S, Zhao Y, Wang D, Xu Y, Wu J, Noda I, Ozaki Y. Double Orthogonal Sample Design Scheme and Corresponding Basic Patterns in Two-Dimensional Correlation Spectra for Probing Subtle Spectral Variations Caused by Intermolecular Interactions. J Phys Chem A 2009; 113:12142-56. [DOI: 10.1021/jp9005185] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chengfeng Zhang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Engineering Plastics, Joint Laboratory of Polymer Science and Materials, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, PR China, Graduate School of Chinese Academy of Sciences, Beijing 100190, China, College of Chemistry and Environmental Science, Henan Normal
| | - Kun Huang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Engineering Plastics, Joint Laboratory of Polymer Science and Materials, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, PR China, Graduate School of Chinese Academy of Sciences, Beijing 100190, China, College of Chemistry and Environmental Science, Henan Normal
| | - Huizhen Li
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Engineering Plastics, Joint Laboratory of Polymer Science and Materials, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, PR China, Graduate School of Chinese Academy of Sciences, Beijing 100190, China, College of Chemistry and Environmental Science, Henan Normal
| | - Jing Chen
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Engineering Plastics, Joint Laboratory of Polymer Science and Materials, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, PR China, Graduate School of Chinese Academy of Sciences, Beijing 100190, China, College of Chemistry and Environmental Science, Henan Normal
| | - Shaoxuan Liu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Engineering Plastics, Joint Laboratory of Polymer Science and Materials, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, PR China, Graduate School of Chinese Academy of Sciences, Beijing 100190, China, College of Chemistry and Environmental Science, Henan Normal
| | - Ying Zhao
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Engineering Plastics, Joint Laboratory of Polymer Science and Materials, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, PR China, Graduate School of Chinese Academy of Sciences, Beijing 100190, China, College of Chemistry and Environmental Science, Henan Normal
| | - Dujin Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Engineering Plastics, Joint Laboratory of Polymer Science and Materials, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, PR China, Graduate School of Chinese Academy of Sciences, Beijing 100190, China, College of Chemistry and Environmental Science, Henan Normal
| | - Yizhuang Xu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Engineering Plastics, Joint Laboratory of Polymer Science and Materials, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, PR China, Graduate School of Chinese Academy of Sciences, Beijing 100190, China, College of Chemistry and Environmental Science, Henan Normal
| | - Jinguang Wu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Engineering Plastics, Joint Laboratory of Polymer Science and Materials, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, PR China, Graduate School of Chinese Academy of Sciences, Beijing 100190, China, College of Chemistry and Environmental Science, Henan Normal
| | - Isao Noda
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Engineering Plastics, Joint Laboratory of Polymer Science and Materials, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, PR China, Graduate School of Chinese Academy of Sciences, Beijing 100190, China, College of Chemistry and Environmental Science, Henan Normal
| | - Yukihiro Ozaki
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Engineering Plastics, Joint Laboratory of Polymer Science and Materials, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, PR China, Graduate School of Chinese Academy of Sciences, Beijing 100190, China, College of Chemistry and Environmental Science, Henan Normal
| |
Collapse
|
11
|
Jensen MR, Kristensen SM, Keeler C, Christensen HEM, Hodsdon ME, Led JJ. Weak self-association of human growth hormone investigated by nitrogen-15 NMR relaxation. Proteins 2009; 73:161-72. [PMID: 18409193 DOI: 10.1002/prot.22039] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The self-association of human growth hormone(hGH) was investigated using 15N NMR relaxation.The investigation relies on the 15N R1 and R2 relaxation rates and the heteronuclear{1H}-15N NOEs of the backbone amide groups at multiple protein concentrations. It is shown that the rotational correlation time of hGH in solution depends strongly on its concentration, indicating a significant degree of self-association.The self-association is reversible and the monomers in the aggregates are noncovalently linked. Extrapolation of the relaxation data to zero concentration predicts a correlation time of 13.4 ns and a rotational diffusion anisotropy of 1.26 for monomeric hGH, in agreement with the rotational diffusion properties estimated by hydrodynamic calculations. Moreover, the extrapolation allows characterization of the backbone dynamics of monomeric hGH without interference from self-association phenomena, and it is found that hGH is considerably more flexible than originally thought. A concerted least-squares analysis of the 15N relaxations and their concentration dependence reveals that the self-association goes beyond a simple monomer-dimer equilibrium, and that tetramers or other multimeric states co-exist in fast exchange with the monomeric and dimeric hGH at sub-millimolar concentrations. Small changes in the 1H and 15N amide chemical shifts suggest that a region around the C-terminus is involved in the oligomer formation.
Collapse
Affiliation(s)
- Malene Ringkjøbing Jensen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | | | | | | | | | | |
Collapse
|
12
|
Lindfors HE, de Koning PE, Drijfhout JW, Venezia B, Ubbink M. Mobility of TOAC spin-labelled peptides binding to the Src SH3 domain studied by paramagnetic NMR. JOURNAL OF BIOMOLECULAR NMR 2008; 41:157-67. [PMID: 18560762 PMCID: PMC2480485 DOI: 10.1007/s10858-008-9248-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Accepted: 05/13/2008] [Indexed: 05/15/2023]
Abstract
Paramagnetic relaxation enhancement provides a tool for studying the dynamics as well as the structure of macromolecular complexes. The application of side-chain coupled spin-labels is limited by the mobility of the free radical. The cyclic, rigid amino acid spin-label TOAC (2,2,6,6-Tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid), which can be incorporated straightforwardly by peptide synthesis, provides an attractive alternative. In this study, TOAC was incorporated into a peptide derived from focal adhesion kinase (FAK), and the interaction of the peptide with the Src homology 3 (SH3) domain of Src kinase was studied, using paramagnetic NMR. Placing TOAC within the binding motif of the peptide has a considerable effect on the peptide-protein binding, lowering the affinity substantially. When the TOAC is positioned just outside the binding motif, the binding constant remains nearly unaffected. Although the SH3 domain binds weakly and transiently to proline-rich peptides from FAK, the interaction is not very dynamic and the relative position of the spin-label to the protein is well-defined. It is concluded that TOAC can be used to generate reliable paramagnetic NMR restraints.
Collapse
Affiliation(s)
- Hanna E. Lindfors
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Peter E. de Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, Leiden, The Netherlands
| | - Jan Wouter Drijfhout
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, Leiden, The Netherlands
| | - Brigida Venezia
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| |
Collapse
|
13
|
Qi J, Li H, Huang K, Chen H, Liu S, Yang L, Zhao Y, Zhang C, Li W, Wu J, Xu D, Xu Y, Noda I. Orthogonal sample design scheme for two-dimensional synchronous spectroscopy and its application in probing intermolecular interactions. APPLIED SPECTROSCOPY 2007; 61:1359-1365. [PMID: 18198029 DOI: 10.1366/000370207783291993] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
This paper introduces a new approach to probing intermolecular interactions based on a framework of two-dimensional (2D) synchronous spectroscopy. Mathematical analysis performed on 2D synchronous spectra using variable concentration as an external perturbation shows that the cross-peaks are composed of two parts. The first part reflects intermolecular interactions that manifest in the form of deviation from the Beer-Lambert law. The second part is related simply to the concentration variations of the solutes and is responsible for the generation of interfering cross-peaks not related to the intermolecular interactions in the system. It is the second part that prevents the reliable identification of intermolecular interactions. We propose a way of selecting the concentrations of solutes so that the resultant dynamic concentration vectors of different solutes become orthogonal to one another. Therefore, the contribution of the second part to the cross-peaks can be effectively removed by the dot product of orthogonal vectors. Our new approach has been tested on a simulated chemical system and a real chemical system. The results demonstrate that interfering cross-peaks can be successfully removed from a 2D synchronous spectrum so that the cross-peaks can be used as a reliable tool to characterize or probe intermolecular interactions.
Collapse
Affiliation(s)
- Jian Qi
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, PR China
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Clore GM, Tang C, Iwahara J. Elucidating transient macromolecular interactions using paramagnetic relaxation enhancement. Curr Opin Struct Biol 2007; 17:603-16. [PMID: 17913493 PMCID: PMC2134839 DOI: 10.1016/j.sbi.2007.08.013] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Accepted: 08/18/2007] [Indexed: 11/25/2022]
Abstract
Recent advances in the use of paramagnetic relaxation enhancement (PRE) in structure refinement and in the analysis of transient dynamic processes involved in macromolecular complex formation are presented. In the slow exchange regime, we show, using the SRY/DNA complex as an example, that the PRE provides a powerful tool that can lead to significant increases in the reliability and accuracy of NMR structure determinations. Refinement necessitates the use of an ensemble representation of the paramagnetic center and a model-free extension of the Solomon-Bloembergen equations. In the fast exchange regime, the PRE provides insight into dynamic processes and the existence of transient, low population intermediate species. The PRE allows one to characterize dynamic nonspecific binding of a protein to DNA; to directly demonstrate that the search process whereby a transcription factor locates its specific DNA target site involves both intramolecular (sliding) and intermolecular (hopping and intersegment transfer) translocation; and to detect and visualize the distribution of an ensemble of transient encounter complexes in protein-protein association.
Collapse
Affiliation(s)
- 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.
| | | | | |
Collapse
|
15
|
Wang X, Srisailam S, Yee AA, Lemak A, Arrowsmith C, Prestegard JH, Tian F. Domain-domain motions in proteins from time-modulated pseudocontact shifts. JOURNAL OF BIOMOLECULAR NMR 2007; 39:53-61. [PMID: 17657568 DOI: 10.1007/s10858-007-9174-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2007] [Revised: 06/18/2007] [Accepted: 06/19/2007] [Indexed: 05/14/2023]
Abstract
In recent years paramagnetic NMR derived structural constraints have become increasingly popular for the study of biomolecules. Some of these are based on the distance and angular dependences of pseudo contact shifts (PCSs). When modulated by internal motions PCSs also become sensitive reporters on molecular dynamics. We present here an investigation of the domain-domain motion in a two domain protein (PA0128) through time-modulation of PCSs. PA0128 is a protein of unknown function from Pseudomonas aeruginosa (PA) and contains a Zn(2+) binding site in the N-terminal domain. When substituted with Co(2+) in the binding site, several resonances from the C-terminal domain showed severe line broadening along the (15)N dimension. Relaxation compensated CPMG experiments revealed that the dramatic increase in the (15)N linewidth came from contributions of chemical exchange. Since several sites with perturbed relaxation are localized to a single beta-strand region, and since extracted timescales of motion for the perturbed sites are identical, and since the magnitude of the chemical exchange contributions is consistent with PCSs, the observed rate enhancements are interpreted as the result of concerted domain motion on the timescale of a few milliseconds. Given the predictability of PCS differences and the easy interpretation of the experimental results, we suggest that these effects might be useful in the study of molecular processes occurring on the millisecond to microsecond timescale.
Collapse
Affiliation(s)
- X Wang
- Southeast Collaboratory for Biomolecular NMR, Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | | | | | | | | | | | | |
Collapse
|
16
|
Vlasie MD, Comuzzi C, van den Nieuwendijk AMCH, Prudêncio M, Overhand M, Ubbink M. Long-Range-Distance NMR Effects in a Protein Labeled with a Lanthanide–DOTA Chelate. Chemistry 2007; 13:1715-23. [PMID: 17115462 DOI: 10.1002/chem.200600916] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A two-thiol reactive lanthanide-DOTA (1,4,7,10-tetraazacyclododecane-N,N',N'',N'''-tetraacetic acid) chelate, CLaNP-3 (CLaNP=caged lanthanide NMR probe), was synthesized for the rigid attachment to cysteine groups on a protein surface, and used to obtain long-range-distance information from the {15N,1H} HSQC spectra of the protein-lanthanide complex. The DOTA ring exhibits several isomers that are in exchange; however, single resonances were observed for most amide groups in the protein, allowing determination of a single, apparent magnetic-susceptibility tensor. Pseudocontact shifts caused by Yb-containing CLaNP-3 were observed for atoms at 15-35 A from the metal. By using Gd-containing CLaNP-3, relaxation effects were observed, allowing distances up to 30 A from the paramagnetic center to be determined accurately. Similar results were obtained with a Gd-DTPA (diethylene-triaminepentaacetic acid) chelate, CLaNP-1, bound in the same bidentate manner to the protein. This study demonstrates that bidentate attachment of a paramagnetic probe enables determination of long-range distances.
Collapse
Affiliation(s)
- Monica D Vlasie
- Leiden Institute of Chemistry, Gorlaeus Laboratories Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | | | | | | | | | | |
Collapse
|
17
|
Jensen MR, Hansen DF, Ayna U, Dagil R, Hass MAS, Christensen HEM, Led JJ. On the use of pseudocontact shifts in the structure determination of metalloproteins. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2006; 44:294-301. [PMID: 16477687 DOI: 10.1002/mrc.1771] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The utility of pseudocontact shifts in the structure refinement of metalloproteins has been evaluated using a native, paramagnetic Cu(2+) metalloprotein, plastocyanin from Anabaena variabilis (A.v.), as a model protein. First, the possibility of detecting signals of nuclei spatially close to the paramagnetic metal ion is investigated using the WEFT pulse sequence in combination with the conventional TOCSY and (1)H-(15)N HSQC sequences. Second, the importance of the electrical charge of the metal ion for the determination of correct pseudocontact shifts from the obtained chemical shifts is evaluated. Thus, using both the Cu(+) plastocyanin and Cd(2+)-substituted plastocyanin as the diamagnetic references, it is found that the Cd(2+)-substituted protein with the same electrical charge of the metal ion as the paramagnetic Cu(2+) plastocyanin provides the most appropriate diamagnetic reference signals. Third, it is found that reliable pseudocontact shifts cannot be obtained from the chemical shifts of the (15)N nuclei in plastocyanin, most likely because these shifts are highly dependent on even minor differences in the structure of the paramagnetic and diamagnetic proteins. Finally, the quality of the obtained (1)H pseudocontact shifts, as well as the possibility of improving the accuracy of the obtained structure, is demonstrated by incorporating the shifts as restraints in a refinement of the solution structure of A.v. plastocyanin. It is found that incorporation of the pseudocontact shifts enhances the precision of the structure in regions with only few NOE restraints and improves the accuracy of the overall structure.
Collapse
Affiliation(s)
- Malene Ringkjøbing Jensen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | | | | | | | | | | | | |
Collapse
|
18
|
Salgueiro CA, Morgado L, Fonseca B, Lamosa P, Catarino T, Turner DL, Louro RO. Binding of ligands originates small perturbations on the microscopic thermodynamic properties of a multicentre redox protein. FEBS J 2005; 272:2251-60. [PMID: 15853810 DOI: 10.1111/j.1742-4658.2005.04649.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
NMR and visible spectroscopy coupled to redox measurements were used to determine the equilibrium thermodynamic properties of the four haems in cytochrome c3 under conditions in which the protein was bound to ligands, the small anion phosphate and the protein rubredoxin with the iron in the active site replaced by zinc. Comparison of these results with data for the isolated cytochrome shows that binding of ligands causes only small changes in the reduction potentials of the haems and their pairwise interactions, and also that the redox-sensitive acid-base centre responsible for the redox-Bohr effect is essentially unaffected. Although neither of the ligands tested is a physiological partner of cytochrome c3, the small changes observed for the thermodynamic properties of cytochrome c3 bound to these ligands vs. the unbound state, indicate that the thermodynamic properties measured for the isolated protein are relevant for a physiological interpretation of the role of this cytochrome in the bioenergetic metabolism of Desulfovibrio.
Collapse
Affiliation(s)
- Carlos A Salgueiro
- Instituto de Tecnologia Quimica e Biológica, Universidade Nova de Lisboa, Portugal
| | | | | | | | | | | | | |
Collapse
|
19
|
Prudêncio M, Ubbink M. Transient complexes of redox proteins: structural and dynamic details from NMR studies. J Mol Recognit 2004; 17:524-39. [PMID: 15386621 DOI: 10.1002/jmr.686] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Redox proteins participate in many metabolic routes, in particular those related to energy conversion. Protein-protein complexes of redox proteins are characterized by a weak affinity and a short lifetime. Two-dimensional NMR spectroscopy has been applied to many redox protein complexes, providing a wealth of information about the process of complex formation, the nature of the interface and the dynamic properties of the complex. These studies have shown that some complexes are non-specific and exist as a dynamic ensemble of orientations while in other complexes the proteins assume a single orientation. The binding interface in these complexes consists of a small hydrophobic patch for specificity, surrounded by polar, uncharged residues that may enhance dissociation, and, in most complexes, a ring or patch of charged residues that enhances the association by electrostatic interactions. The entry and exit port of the electrons is located within the hydrophobic interaction site, ensuring rapid electron transfer from one redox centre to the next.
Collapse
Affiliation(s)
- Miguel Prudêncio
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, PO Box 9502, 2300 RA Leiden, The Netherlands
| | | |
Collapse
|
20
|
Nomura M, Kobayashi T, Kohno T, Fujiwara K, Tenno T, Shirakawa M, Ishizaki I, Yamamoto K, Matsuyama T, Mishima M, Kojima C. Paramagnetic NMR study of Cu2+
-IDA complex localization on a protein surface and its application to elucidate long distance information. FEBS Lett 2004; 566:157-61. [PMID: 15147887 DOI: 10.1016/j.febslet.2004.04.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2004] [Revised: 04/12/2004] [Accepted: 04/13/2004] [Indexed: 01/08/2023]
Abstract
The paramagnetic metal chelate complex Cu(2+)-iminodiacetic acid (Cu(2+)-IDA) was mixed with ubiquitin, a small globular protein. Quantitative analyses of (1)H and (15)N chemical shift changes and line broadenings induced by the paramagnetic effects indicated that Cu(2+)-IDA was localized to a histidine residue (His68) on the ubiquitin surface. The distances between the backbone amide proton and the Cu(2+) relaxation center were evaluated from the proton transverse relaxation rates enhanced by the paramagnetic effect. These correlated well with the distances calculated from the crystal structure up to 20 A. Here, we show that a Cu(2+)-IDA is the first paramagnetic reagent that specifically localizes to a histidine residue on the protein surface and gives the long-range distance information.
Collapse
Affiliation(s)
- Makoto Nomura
- Laboratory of Biophysics, Graduate School of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Jensen MR, Led JJ. Determination of the electron relaxation rates in paramagnetic metal complexes: applicability of available NMR methods. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2004; 167:169-177. [PMID: 15040973 DOI: 10.1016/j.jmr.2003.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2003] [Revised: 12/03/2003] [Indexed: 05/24/2023]
Abstract
Four different approaches for determining the electron relaxation rates in paramagnetic metallo-proteins are investigated, using a paramagnetic Ni2+ complex of a protein as an example. All four approaches rely on the determination of the longitudinal paramagnetic relaxation enhancements, R1p, of the 1H nuclei and the backbone 15N nuclei. Three of the methods utilize the field dependence of the R1p rates. It is found that the applicability of each of these methods depends on whether the fast-motion condition, omegaS2tau2<<1, applies to the electron relaxation, omegaS being the Larmor frequency of the electron spin S and tau the correlation time of the electron relaxation. If the fast-motion condition is fulfilled, the electron relaxation rate can be obtained from the ratio of the R1p rates of one or more protons at two magnetic field strengths (method A). On the other hand, if the fast-motion condition does not apply, more elaborate methods must be used that, in general, require a determination of the R1p rates over a larger range of magnetic field strengths (method C). However, in the case of paramagnetic metal ions with relatively slow electron relaxation rates only two magnetic field strengths suffice, if the R1p rates of a hetero nucleus are included in the analysis (method B). In the fourth method (method D), the electron relaxation is estimated as a parameter in a structure calculation, using distance constraints derived from proton R1p rates at only one magnetic field strength. In general, only methods B and C give unambiguous electron relaxation rates.
Collapse
Affiliation(s)
- Malene Ringkjøbing Jensen
- Department of Chemistry, University of Copenhagen, The HC Ørsted Institute, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | | |
Collapse
|