1
|
Heinrich F, Van QN, Jean-Francois F, Stephen AG, Lösche M. Membrane-bound KRAS approximates an entropic ensemble of configurations. Biophys J 2021; 120:4055-4066. [PMID: 34384763 DOI: 10.1016/j.bpj.2021.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/08/2021] [Accepted: 08/04/2021] [Indexed: 11/27/2022] Open
Abstract
KRAS4B is a membrane-anchored signaling protein and a primary target in cancer research. Predictions from molecular dynamics simulations that have previously shaped our mechanistic understanding of KRAS signaling disagree with recent experimental results from neutron reflectometry, NMR, and thermodynamic binding studies. To gain insight into these discrepancies, we compare this body of biophysical data to back-calculated experimental results from a series of molecular simulations that implement different subsets of molecular interactions. Our results show that KRAS4B approximates an entropic ensemble of configurations at model membranes containing 30% phosphatidylserine lipids, which is not significantly shaped by interactions between the globular G-domain of KRAS4B and the lipid membrane. These findings revise our understanding of KRAS signaling and promote a model in which the protein samples the accessible conformational space in a near-uniform manner while being available to bind to effector proteins.
Collapse
Affiliation(s)
- Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania; Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland.
| | - Que N Van
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Frantz Jean-Francois
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Andrew G Stephen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania; Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland
| |
Collapse
|
2
|
Affiliation(s)
- Frank Weinhold
- Theoretical Chemistry and Department of Chemistry University of Wisconsin Madison Wisconsin 53706 USA
| |
Collapse
|
3
|
Wittmann T, Mondal A, Tschense CBL, Wittmann JJ, Klimm O, Siegel R, Corzilius B, Weber B, Kaupp M, Senker J. Probing Interactions of N-Donor Molecules with Open Metal Sites within Paramagnetic Cr-MIL-101: A Solid-State NMR Spectroscopic and Density Functional Theory Study. J Am Chem Soc 2018; 140:2135-2144. [DOI: 10.1021/jacs.7b10148] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Thomas Wittmann
- Inorganic
Chemistry III, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Arobendo Mondal
- Institute
of Chemistry, Theoretical Chemistry/Quantum Chemistry, Technical University of Berlin, Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Carsten B. L. Tschense
- Inorganic
Chemistry III, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Johannes J. Wittmann
- Institute
of Physical and Theoretical Chemistry and Institute of Biophysical
Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 7-9, 60438 Frankfurt am Main, Germany
| | - Ottokar Klimm
- Inorganic
Chemistry II, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Renée Siegel
- Inorganic
Chemistry III, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Björn Corzilius
- Institute
of Physical and Theoretical Chemistry and Institute of Biophysical
Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 7-9, 60438 Frankfurt am Main, Germany
| | - Birgit Weber
- Inorganic
Chemistry II, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Martin Kaupp
- Institute
of Chemistry, Theoretical Chemistry/Quantum Chemistry, Technical University of Berlin, Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Juergen Senker
- Inorganic
Chemistry III, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| |
Collapse
|
4
|
Bren KL. Going with the Electron Flow: Heme Electronic Structure and Electron Transfer in Cytochrome
c. Isr J Chem 2016. [DOI: 10.1002/ijch.201600021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Kara L. Bren
- Department of Chemistry University of Rochester Rochester NY 14627-0216 USA
| |
Collapse
|
5
|
Novikov VV, Pavlov AA, Belov AS, Vologzhanina AV, Savitsky A, Voloshin YZ. Transition Ion Strikes Back: Large Magnetic Susceptibility Anisotropy in Cobalt(II) Clathrochelates. J Phys Chem Lett 2014; 5:3799-803. [PMID: 26278750 DOI: 10.1021/jz502011z] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Transition-metal complexes are rarely considered as paramagnetic tags for NMR spectroscopy due to them generally having relatively low magnetic anisotropy. Here we report cobalt(II) cage complexes with the largest (among the transition-metal complexes) axial anisotropy of magnetic susceptibility, reaching as high as 12.6 × 10(-32) m(3) at room temperature. This remarkable anisotropy, which results from an unusual trigonal prismatic geometry of the complexes and translates into large negative value of the zero-field splitting energy, is high enough to promote reliable paramagnetic pseudocontact shifts at the distance beyond 2 nm. Our finding paves the way toward the applications of cobalt(II) clathrochelates as future paramagnetic tags. Given the incredible stability and functionalization versatility of clathrochelates, the fine-tuning of the caging ligand may lead to new chemically stable mononuclear single-molecule magnets, for which magnetic anisotropy is of importance.
Collapse
Affiliation(s)
- Valentin V Novikov
- †Nesmeyanov Institute of Organoelement Compounds, RAS, Vavilova str. 28, 119991 Moscow, Russia
| | - Alexander A Pavlov
- †Nesmeyanov Institute of Organoelement Compounds, RAS, Vavilova str. 28, 119991 Moscow, Russia
| | - Alexander S Belov
- †Nesmeyanov Institute of Organoelement Compounds, RAS, Vavilova str. 28, 119991 Moscow, Russia
| | - Anna V Vologzhanina
- †Nesmeyanov Institute of Organoelement Compounds, RAS, Vavilova str. 28, 119991 Moscow, Russia
| | - Anton Savitsky
- ‡Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Yan Z Voloshin
- †Nesmeyanov Institute of Organoelement Compounds, RAS, Vavilova str. 28, 119991 Moscow, Russia
| |
Collapse
|
6
|
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
|
7
|
Hansen DF, Westler WM, Kunze MBA, Markley JL, Weinhold F, Led JJ. Accurate structure and dynamics of the metal-site of paramagnetic metalloproteins from NMR parameters using natural bond orbitals. J Am Chem Soc 2012; 134:4670-82. [PMID: 22329704 PMCID: PMC3303200 DOI: 10.1021/ja209348p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
A natural bond orbital (NBO) analysis of unpaired electron
spin
density in metalloproteins is presented, which allows a fast and robust
calculation of paramagnetic NMR parameters. Approximately 90% of the
unpaired electron spin density occupies metal–ligand NBOs,
allowing the majority of the density to be modeled by only a few NBOs
that reflect the chemical bonding environment. We show that the paramagnetic
relaxation rate of protons can be calculated accurately using only
the metal–ligand NBOs and that these rates are in good agreement
with corresponding rates measured experimentally. This holds, in particular,
for protons of ligand residues where the point-dipole approximation
breaks down. To describe the paramagnetic relaxation of heavy nuclei,
also the electron spin density in the local orbitals must be taken
into account. Geometric distance restraints for 15N can
be derived from the paramagnetic relaxation enhancement and the Fermi
contact shift when local NBOs are included in the analysis. Thus,
the NBO approach allows us to include experimental paramagnetic NMR
parameters of 15N nuclei as restraints in a structure optimization
protocol. We performed a molecular dynamics simulation and structure
determination of oxidized rubredoxin using the experimentally obtained
paramagnetic NMR parameters of 15N. The corresponding structures
obtained are in good agreement with the crystal structure of rubredoxin.
Thus, the NBO approach allows an accurate description of the geometric
structure and the dynamics of metalloproteins, when NMR parameters
are available of nuclei in the immediate vicinity of the metal-site.
Collapse
Affiliation(s)
- D Flemming Hansen
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, United Kingdom.
| | | | | | | | | | | |
Collapse
|
8
|
Lin IJ, Xia B, King DS, Machonkin TE, Westler WM, Markley JL. Hyperfine-shifted (13)C and (15)N NMR signals from Clostridium pasteurianum rubredoxin: extensive assignments and quantum chemical verification. J Am Chem Soc 2010; 131:15555-63. [PMID: 19799419 PMCID: PMC2766250 DOI: 10.1021/ja905928x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Stable isotope-labeling methods, coupled with novel techniques for detecting fast-relaxing NMR signals, now permit detailed investigations of paramagnetic centers of metalloproteins. We have utilized these advances to carry out comprehensive assignments of the hyperfine-shifted 13C and 15N signals of the rubredoxin from Clostridium pasteurianum (CpRd) in both its oxidized and reduced states. We used residue-specific labeling (by chemical synthesis) and residue-type-selective labeling (by biosynthesis) to assign signals detected by one-dimensional 15N NMR spectroscopy, to nitrogen atoms near the iron center. We refined and extended these 15N assignments to the adjacent carbonyl carbons by means of one-dimensional 13C[15N] decoupling difference experiments. We collected paramagnetic-optimized SuperWEFT 13C[13C] constant time COSY (SW-CT-COSY) data to complete the assignment of 13C signals of reduced CpRd. By following these 13C signals as the protein was gradually oxidized, we transferred these assignments to carbons in the oxidized state. We have compared these assignments with hyperfine chemical shifts calculated from available X-ray structures of CpRd in its oxidized and reduced forms. The results allow the evaluation of the X-ray structural models as representative of the solution structure of the protein, and they provide a framework for future investigation of the active site of this protein. The methods developed here should be applicable to other proteins that contain a paramagnetic center with high spin and slow electron exchange.
Collapse
Affiliation(s)
- I-Jin Lin
- Graduate Program in Biophysics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
| | | | | | | | | | | |
Collapse
|
9
|
An NMR structural study of nickel-substituted rubredoxin. J Biol Inorg Chem 2009; 15:409-20. [PMID: 19997764 DOI: 10.1007/s00775-009-0613-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2009] [Accepted: 11/10/2009] [Indexed: 10/20/2022]
Abstract
The Ni(II) and Zn(II) derivatives of Desulfovibrio vulgaris rubredoxin (DvRd) have been studied by NMR spectroscopy to probe the structure at the metal centre. The beta CH(2) proton pairs from the cysteines that bind the Ni(II) atom have been identified using 1D nuclear Overhauser enhancement (NOE) difference spectra and sequence specifically assigned via NOE correlations to neighbouring protons and by comparison with the published X-ray crystal structure of a Ni(II) derivative of Clostridium pasteurianum rubredoxin. The solution structures of DvRd(Zn) and DvRd(Ni) have been determined and the paramagnetic form refined using pseudocontact shifts. The determination of the magnetic susceptibility anisotropy tensor allowed the contact and pseudocontact contributions to the observed chemical shifts to be obtained. Analysis of the pseudocontact and contact chemical shifts of the cysteine H beta protons and backbone protons close to the metal centre allowed conclusions to be drawn as to the geometry and hydrogen-bonding pattern at the metal binding site. The importance of NH-S hydrogen bonds at the metal centre for the delocalization of electron spin density is confirmed for rubredoxins and can be extrapolated to metal centres in Cu proteins: amicyanin, plastocyanin, stellacyanin, azurin and pseudoazurin.
Collapse
|
10
|
Rastrelli F, Bagno A. Predicting the NMR Spectra of Paramagnetic Molecules by DFT: Application to Organic Free Radicals and Transition-Metal Complexes. Chemistry 2009; 15:7990-8004. [DOI: 10.1002/chem.200802443] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
11
|
Hrobárik P, Reviakine R, Arbuznikov AV, Malkina OL, Malkin VG, Köhler FH, Kaupp M. Density functional calculations of NMR shielding tensors for paramagnetic systems with arbitrary spin multiplicity: validation on 3d metallocenes. J Chem Phys 2007; 126:024107. [PMID: 17228943 DOI: 10.1063/1.2423003] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The calculation of nuclear shieldings for paramagnetic molecules has been implemented in the ReSpect program, which allows the use of modern density functional methods with accurate treatments of spin-orbit effects for all relevant terms up to order Omicron(alpha4) in the fine structure constant. Compared to previous implementations, the methodology has been extended to compounds of arbitrary spin multiplicity. Effects of zero-field splittings in high-spin systems are approximately accounted for. Validation of the new implementation is carried out for the 13C and 1H NMR signal shifts of the 3d metallocenes 4VCp2, 3CrCp2, 2MnCp2, 6MnCp2, 2CoCp2, and 3NiCp2. Zero-field splitting effects on isotropic shifts tend to be small or negligible. Agreement with experimental isotropic shifts is already good with the BP86 gradient-corrected functional and is further improved by admixture of Hartree-Fock exchange in hybrid functionals. Decomposition of the shieldings confirms the dominant importance of the Fermi-contact shifts, but contributions from spin-orbit dependent terms are frequently also non-negligible. Agreement with 13C NMR shift tensors from solid-state experiments is of similar quality as for isotropic shifts.
Collapse
Affiliation(s)
- Peter Hrobárik
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84536 Bratislava, Slovakia
| | | | | | | | | | | | | |
Collapse
|
12
|
Hansen DF, Led JJ. Determination of the geometric structure of the metal site in a blue copper protein by paramagnetic NMR. Proc Natl Acad Sci U S A 2006; 103:1738-43. [PMID: 16446449 PMCID: PMC1413626 DOI: 10.1073/pnas.0507179103] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The biological function of metalloproteins is closely tied to the geometric and electronic structures of the metal sites. Here, we show that the geometric structure of the metal site of a metalloprotein in solution can be determined from experimentally measured electron-nuclear spin-spin interactions obtained by NMR. Thus, the geometric metal site structure of plastocyanin from Anabaena variabilis was determined by including the paramagnetic relaxation enhancement of protons close to the copper site as restraints in a conventional NMR structure determination, together with the distribution of the unpaired electron onto the ligand atoms. Also, the interproton distances (nuclear Overhauser enhancements) and dihedral angles (scalar nuclear spin-spin couplings) normally used in NMR structure determinations were included as restraints. The structure calculations were carried out with the program X-PLOR and a module that takes into account the specific characteristics of the paramagnetic restraints. A well defined metal site structure was obtained with the structural characteristics of the blue copper site, including a distorted tetrahedral geometry, a short Cu-Cys S gamma bond, and a long Cu-Met S delta bond. Overall, the agreement of the obtained metal site structure of Anabaena variabilis plastocyanin with those of other plastocyanins obtained by x-ray crystallography confirms the reliability of the approach.
Collapse
Affiliation(s)
- D. Flemming Hansen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Jens J. Led
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| |
Collapse
|
13
|
Yao H, Costache AD, Sem DS. Chemical proteomic tool for ligand mapping of CYP antitargets: an NMR-compatible 3D QSAR descriptor in the Heme-Based Coordinate System. ACTA ACUST UNITED AC 2005; 44:1456-65. [PMID: 15272854 DOI: 10.1021/ci034208q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemical proteomic strategies strive to probe and understand protein-ligand interactions across gene families. One gene family of particular interest in drug and xenobiotic metabolism are the cytochromes P450 (CYPs), the topic of this article. Although numerous tools exist to probe affinity of CYP-ligand interactions, fewer exist for the rapid experimental characterization of the structural nature of these interactions. As a complement to recent advances in X-ray crystallography, NMR methods are being developed that allow for fairly high throughput characterization of protein-ligand interactions. One especially promising NMR approach involves the use of paramagnetic induced relaxation effects to measure distances of ligand atoms from the heme iron in CYP enzymes. Distances obtained from these T(1) relaxation measurements can be used as a direct source of 1-dimensional structural information or to restrain a ligand docking to generate a 3-dimensional data set. To facilitate such studies, we introduce the concept of the Heme-Based Coordinate System and present how it can be used in combination with NMR T(1) relaxation data to derive 3D QSAR descriptors directly or in combination with in silico docking. These descriptors should have application in defining the binding preferences of CYP binding sites using 3D QSAR models. They are especially well-suited for the biasing of fragment assembly and combinatorial chemistry drug design strategies, to avoid fragment or reagent combinations with enhanced affinity for CYP antitargets.
Collapse
Affiliation(s)
- Huili Yao
- Chemical Proteomics Facility at Marquette, Chemistry Department, P.O. Box 1881, Marquette University, Milwaukee, Wisconsin 53201, USA
| | | | | |
Collapse
|
14
|
Yazyev OV, Helm L, Malkin VG, Malkina OL. Quantum Chemical Investigation of Hyperfine Coupling Constants on First Coordination Sphere Water Molecule of Gadolinium(III) Aqua Complexes. J Phys Chem A 2005; 109:10997-1005. [PMID: 16331943 DOI: 10.1021/jp053825+] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hyperfine interactions (HFI) on the nuclei of the first coordination sphere water molecules in a model [Gd(H(2)O)(8)](3+) aqua complex and in the magnetic resonance imaging contrast agent [Gd(DOTA)(H(2)O)](-) were studied theoretically. Density functional theory (DFT) calculations combined with classical molecular dynamics (MD) simulations have been used in order to take into account dynamic effects in aqueous solution. DFT relativistic calculations show a strong spin-polarization of the first coordination sphere water molecules. This spin-polarization leads to a positive (17)O isotropic hyperfine coupling constant (A(iso)((17)O) = 0.58 +/- 0.11 MHz) and to a significant increase of the effective distance (r(eff)(Gd-O) = 2.72 +/- 0.06 A) of dipolar interaction compared to the mean internuclear distance (r(Gd-O) = 2.56 +/- 0.06 A) obtained from the MD trajectory of [Gd(DOTA)(H(2)O)](-) in aqueous solution. The point-dipole model for anisotropic hyperfine interaction overestimates therefore the longitudinal relaxation rate of the (17)O nucleus by approximately 45%. The (1)H isotropic hyperfine coupling constant of the bound water molecule is predicted to be very small (A(iso)((1)H) = 0.03 +/- 0.02 MHz), and the point-dipole approximation for first coordination sphere water protons holds. The calculated hyperfine parameters are in good agreement with available experimental data.
Collapse
Affiliation(s)
- Oleg V Yazyev
- Laboratoire de Chimie Inorganique et Bioinorganique, Ecole Polytechnique Fédérale de Lausanne, EPFL-BCH, CH-1015 Lausanne, Switzerland
| | | | | | | |
Collapse
|
15
|
Machonkin TE, Westler WM, Markley JL. Paramagnetic NMR spectroscopy and density functional calculations in the analysis of the geometric and electronic structures of iron-sulfur proteins. Inorg Chem 2005; 44:779-97. [PMID: 15859246 DOI: 10.1021/ic048624j] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Paramagnetic NMR spectroscopy has been underutilized in the study of metalloproteins. One difficulty of the technique is that paramagnetic relaxation broadens signals from nuclei near paramagnetic centers. In systems with low electronic relaxation rates, this makes such signals difficult to observe or impossible to assign by traditional methods. We show how the challenges of detecting and assigning signals from nuclei near the metal center can be overcome through the combination of uniform and selective 2H, 13C, and 15N isotopic labeling with NMR experiments that utilize direct one-dimensional (2H, 13C, and 15N) and two-dimensional (13C-X) detection. We have developed methods for calculating NMR chemical shifts and relaxation rates by density functional theory (DFT) approaches. We use the correspondence between experimental NMR parameters and those calculated from structural models of iron-sulfur clusters derived from X-ray crystallography to validate the computational approach and to investigate how structural differences are manifested in these values. We have applied this strategy to three iron-sulfur proteins: Clostridium pasteurianum rubredoxin, Anabaena [2Fe-2S] ferredoxin, and human [2Fe-2S] ferredoxin. Provided that an accurate structural model of the iron-sulfur cluster and surrounding residues is available from diffraction data, our results show that DFT calculations can return NMR observables with excellent accuracy. This suggests that it might be possible to use calculations to refine structures or to generate structural models of active sites when crystal structures are unavailable. The approach has yielded insights into the electronic structures of these iron-sulfur proteins. In rubredoxin, the results show that substantial unpaired electron spin is delocalized across NH...S hydrogen bonds and that the reduction potential can be changed by 77 mV simply by altering the strength of one of these hydrogen bonds. In reduced [2Fe-2S] ferredoxins, hyperfine shift data have provided quantitative information on the degree of valence trapping. The approach described here for iron-sulfur proteins offers new avenues for detailed studies of these and other metalloprotein systems.
Collapse
Affiliation(s)
- Timothy E Machonkin
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642, USA
| | | | | |
Collapse
|
16
|
KOWALEWSKI JOZEF, KRUK DANUTA, PARIGI GIACOMO. NMR RELAXATION IN SOLUTION OF PARAMAGNETIC COMPLEXES: RECENT THEORETICAL PROGRESS FOR S≥1. ADVANCES IN INORGANIC CHEMISTRY 2005. [DOI: 10.1016/s0898-8838(05)57002-8] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
17
|
Goodfellow BJ, Nunes SG, Rusnak F, Moura I, Ascenso C, Moura JJG, Volkman BF, Markley JL. Zinc-substituted Desulfovibrio gigas desulforedoxins: resolving subunit degeneracy with nonsymmetric pseudocontact shifts. Protein Sci 2002; 11:2464-70. [PMID: 12237467 PMCID: PMC2373705 DOI: 10.1110/ps.0208802] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2002] [Revised: 07/09/2002] [Accepted: 07/17/2002] [Indexed: 10/27/2022]
Abstract
Desulfovibrio gigas desulforedoxin (Dx) consists of two identical peptides, each containing one [Fe-4S] center per monomer. Variants with different iron and zinc metal compositions arise when desulforedoxin is produced recombinantly from Escherichia coli. The three forms of the protein, the two homodimers [Fe(III)/Fe(III)]Dx and [Zn(II)/Zn(II)]Dx, and the heterodimer [Fe(III)/Zn(II)]Dx, can be separated by ion exchange chromatography on the basis of their charge differences. Once separated, the desulforedoxins containing iron can be reduced with added dithionite. For NMR studies, different protein samples were prepared labeled with (15)N or (15)N + (13)C. Spectral assignments were determined for [Fe(II)/Fe(II)]Dx and [Fe(II)/Zn(II)]Dx from 3D (15)N TOCSY-HSQC and NOESY-HSQC data, and compared with those reported previously for [Zn(II)/Zn(II)]Dx. Assignments for the (13)C(alpha) shifts were obtained from an HNCA experiment. Comparison of (1)H-(15)N HSQC spectra of [Zn(II)/Zn(II)]Dx, [Fe(II)/Fe(II)]Dx and [Fe(II)/Zn(II)]Dx revealed that the pseudocontact shifts in [Fe(II)/Zn(II)]Dx can be decomposed into inter- and intramonomer components, which, when summed, accurately predict the observed pseudocontact shifts observed for [Fe(II)/Fe(II)]Dx. The degree of linearity observed in the pseudocontact shifts for residues >/=8.5 A from the metal center indicates that the replacement of Fe(II) by Zn(II) produces little or no change in the structure of Dx. The results suggest a general strategy for the analysis of NMR spectra of homo-oligomeric proteins in which a paramagnetic center introduced into a single subunit is used to break the magnetic symmetry and make it possible to obtain distance constraints (both pseudocontact and NOE) between subunits.
Collapse
|
18
|
Piana S, Sebastiani D, Carloni P, Parrinello M. Ab initio molecular dynamics-based assignment of the protonation state of pepstatin A/HIV-1 protease cleavage site. J Am Chem Soc 2001; 123:8730-7. [PMID: 11535077 DOI: 10.1021/ja003145e] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A recent 13C NMR experiment (Smith et al. Nature Struct. Biol. 1996, 3, 946-950) on the Asp 25-Asp25' dyad in pepstatin A/HIV-1 protease measured two separate resonance lines, which were interpreted as being a singly protonated dyad. We address this issue by performing ab initio molecular dynamics calculations on models for this site accompanied by calculations of 13C NMR chemical shifts and isotopic shifts. We find that already on the picosecond time-scale the model proposed by Smith et al. is not stable and evolves toward a different monoprotonated form whose NMR pattern differs from the experimental one. We suggest, instead, a different protonation state in which both aspartic groups are protonated. Despite the symmetric protonation state, the calculated 13C NMR properties are in good agreement with the experiment. We rationalize this result using a simple valence bond model, which explains the chemical inequality of the two C sites. The model calculations, together with our calculations on the complex, allow also the rationalization of 13C NMR properties on other HIV-1 PR/inhibitor complexes. Both putative binding of the substrate to the free enzyme, which has the dyad singly protonated (Piana, S.; Carloni, P. Proteins: Struct., Funct., Genet. 2000, 39, 26-36), and pepstatin A binding to the diprotonated form are consistent with the inverse solvent isotope effect on the onset of inhibition of pepsin by pepstatin and the kinetic iso-mechanism proposed for aspartic proteases (Cho, T.-K.; Rebholz, K.; Northrop, D.B. Biochemistry 1994, 33, 9637-9642).
Collapse
Affiliation(s)
- S Piana
- Scuola Internazionale Superiore di Studi Avanzati and Istituto Nazionale di Fisica della Materia, Via Beirut 2-4, 34014 Trieste, Italy
| | | | | | | |
Collapse
|
19
|
Affiliation(s)
- I Bertini
- Magnetic Resonance Center (CERM), University of Florence, Florence 50019, Italy
| | | | | |
Collapse
|
20
|
Affiliation(s)
- G N La Mar
- Department of Chemistry, University of California, Davis, California 95616, USA
| |
Collapse
|
21
|
Todorović S, Juranić N, Macura S, Rusnak F. Binding of 15N-Labeled Isoniazid to KatG and KatG(S315T): Use of Two-Spin [zz]-Order Relaxation Rate for 15N−Fe Distance Determination. J Am Chem Soc 1999. [DOI: 10.1021/ja9918674] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Smilja Todorović
- Contribution from the Department of Biochemistry and Molecular Biology, Section of Hematology Research, Mayo Clinic and Foundation, Rochester, Minnesota 55905, and Faculty of Physical Chemistry, University of Belgrade, Belgrade, Yugoslavia
| | - Nenad Juranić
- Contribution from the Department of Biochemistry and Molecular Biology, Section of Hematology Research, Mayo Clinic and Foundation, Rochester, Minnesota 55905, and Faculty of Physical Chemistry, University of Belgrade, Belgrade, Yugoslavia
| | - Slobodan Macura
- Contribution from the Department of Biochemistry and Molecular Biology, Section of Hematology Research, Mayo Clinic and Foundation, Rochester, Minnesota 55905, and Faculty of Physical Chemistry, University of Belgrade, Belgrade, Yugoslavia
| | - Frank Rusnak
- Contribution from the Department of Biochemistry and Molecular Biology, Section of Hematology Research, Mayo Clinic and Foundation, Rochester, Minnesota 55905, and Faculty of Physical Chemistry, University of Belgrade, Belgrade, Yugoslavia
| |
Collapse
|
22
|
Volkman BF, Wilkens SJ, Lee AL, Xia B, Westler WM, Beger R, Markley JL. Redox-Dependent Magnetic Alignment of Clostridium pasteurianum Rubredoxin: Measurement of Magnetic Susceptibility Anisotropy and Prediction of Pseudocontact Shift Contributions. J Am Chem Soc 1999. [DOI: 10.1021/ja990079b] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Brian F. Volkman
- Contribution from the National Magnetic Resonance Facility at Madison, Department of Biochemistry, and Graduate Program in Biophysics, University of Wisconsin−Madison, 433 Babcock Drive, Madison, Wisconsin 53706, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6059, and National Center for Toxicological Research, Jefferson, Arkansas 72079
| | - Steven J. Wilkens
- Contribution from the National Magnetic Resonance Facility at Madison, Department of Biochemistry, and Graduate Program in Biophysics, University of Wisconsin−Madison, 433 Babcock Drive, Madison, Wisconsin 53706, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6059, and National Center for Toxicological Research, Jefferson, Arkansas 72079
| | - Andrew L. Lee
- Contribution from the National Magnetic Resonance Facility at Madison, Department of Biochemistry, and Graduate Program in Biophysics, University of Wisconsin−Madison, 433 Babcock Drive, Madison, Wisconsin 53706, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6059, and National Center for Toxicological Research, Jefferson, Arkansas 72079
| | - Bin Xia
- Contribution from the National Magnetic Resonance Facility at Madison, Department of Biochemistry, and Graduate Program in Biophysics, University of Wisconsin−Madison, 433 Babcock Drive, Madison, Wisconsin 53706, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6059, and National Center for Toxicological Research, Jefferson, Arkansas 72079
| | - William M. Westler
- Contribution from the National Magnetic Resonance Facility at Madison, Department of Biochemistry, and Graduate Program in Biophysics, University of Wisconsin−Madison, 433 Babcock Drive, Madison, Wisconsin 53706, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6059, and National Center for Toxicological Research, Jefferson, Arkansas 72079
| | - Richard Beger
- Contribution from the National Magnetic Resonance Facility at Madison, Department of Biochemistry, and Graduate Program in Biophysics, University of Wisconsin−Madison, 433 Babcock Drive, Madison, Wisconsin 53706, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6059, and National Center for Toxicological Research, Jefferson, Arkansas 72079
| | - John L. Markley
- Contribution from the National Magnetic Resonance Facility at Madison, Department of Biochemistry, and Graduate Program in Biophysics, University of Wisconsin−Madison, 433 Babcock Drive, Madison, Wisconsin 53706, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6059, and National Center for Toxicological Research, Jefferson, Arkansas 72079
| |
Collapse
|