151
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Abdullin D, Florin N, Hagelueken G, Schiemann O. EPR-Based Approach for the Localization of Paramagnetic Metal Ions in Biomolecules. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410396] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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152
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Gaffney BJ. Connecting lipoxygenase function to structure by electron paramagnetic resonance. Acc Chem Res 2014; 47:3588-95. [PMID: 25341190 PMCID: PMC4270396 DOI: 10.1021/ar500290r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Indexed: 01/09/2023]
Abstract
CONSPECTUS: Lipoxygenase enzymes insert oxygen in a polyunsaturated lipid, yielding a hydroperoxide product. When the acyl chain is arachidonate, with three cis-pentadiene units, 12 positionally and stereochemically different products might result. The plant lipids, linoleate and linolenate, have, respectively, four and eight potential oxygen insertion sites. The puzzle of how specificity is achieved in these reactions grows as more and more protein structures confirm the conservation of a lipoxygenase protein fold in plants, animals, and bacteria. Lipoxygenases are large enough (60-100 kDa) that they provide a protein shell completely surrounding an active site cavity that has the shape of a long acyl chain and contains a catalytic metal (usually iron). This Account summarizes electron paramagnetic resonance (EPR) spectroscopic, and other, experiments designed to bridge the gap between lipid-lipoxygenase interactions in solution and crystal structures. Experiments with spin-labeled lipids give a picture of bound lipids tethered to protein by an acyl chain, but with a polar end emerging from the cavity to solvent exposure, where the headgroup is highly flexible. The location of a spin on the polar end of a lysolecithin was determined by pulsed, dipolar EPR measurements, by representing the protein structure as a five-point grid of spin-labels with coordinates derived from 10 distance determinations between spin pairs. Distances from the lipid spin to each grid site completed a six-point representation of the enzyme with a bound lipid. Insight into the dynamics that allow substrate/product to enter/exit the cavity was obtained with a different set of spin-labeled protein mutants. Once substrate enters the cavity, the rate-limiting step of catalysis involves redox cycling at the metal center. Here, a mononuclear iron cycles between ferric and ferrous (high-spin) forms. Two helices provide pairs of side-chain ligands to the iron, resulting in characteristic EPR signals. Quantitative comparison of EPR spectra of plant and bacterial lipoxygenases has suggested conservation of a unique geometry of lipoxygenase iron centers. High frequency (94 GHz) EPR is consistent with a similar metal center in a manganese version of lipoxygenase. Overall, established and emerging EPR experiments have been developed and applied to the lipoxygenase family of enzymes to elucidate changes in the solution structures that are related to function.
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Affiliation(s)
- Betty J. Gaffney
- Department
of Biological
Science, Florida State University, Tallahassee, Florida 32306-4295, United States
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153
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Tsai CJ, Liu S, Hung CL, Jhong SR, Sung TC, Chiang YW. BAX-induced apoptosis can be initiated through a conformational selection mechanism. Structure 2014; 23:139-148. [PMID: 25497728 DOI: 10.1016/j.str.2014.10.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 10/23/2014] [Accepted: 10/29/2014] [Indexed: 02/01/2023]
Abstract
BAX protein plays a key role in the mitochondria-mediated apoptosis. However, it remains unclear by what mechanism BAX is triggered to initiate apoptosis. Here, we reveal the mechanism using electron spin resonance (ESR) techniques. An inactive BAX monomer was found to exhibit conformational heterogeneity and exist at equilibrium in two conformations, one of which has never been reported. We show that upon apoptotic stimulus by BH3-only peptides, BAX can be induced to convert into either a ligand-bound monomer or an oligomer through a conformational selection mechanism. The kinetics of reaction is studied by means of time-resolved ESR, allowing a direct in situ observation for the transformation of BAX from the native to the bound states. In vitro mitochondrial assays provide further discrimination between the proposed BAX states, thereby revealing a population-shift allosteric mechanism in the process. BAX's apoptotic function is shown to critically depend on excursions between different structural conformations.
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Affiliation(s)
- Chia-Jung Tsai
- Department of Chemistry and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Sophia Liu
- Department of Chemistry and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chien-Lun Hung
- Department of Chemistry and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Siao-Ru Jhong
- Department of Chemistry and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Tai-Ching Sung
- Department of Chemistry and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan.
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154
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Iyalomhe O, Herrick DZ, Cafiso DS, Maloney PC. Closure of the cytoplasmic gate formed by TM5 and TM11 during transport in the oxalate/formate exchanger from Oxalobacter formigenes. Biochemistry 2014; 53:7735-44. [PMID: 25409483 PMCID: PMC4270380 DOI: 10.1021/bi5012173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
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OxlT, the oxalate/formate exchanger
of Oxalobacter
formigenes, is a member of the major facilitator superfamily
of transporters. In the present work, substrate (oxalate) was found
to enhance the reactivity of the cysteine mutant S336C on the cytoplasmic
end of helix 11 to methanethiosulfonate ethyl carboxylate. In addition,
S336C is found to spontaneously cross-link to S143C in TM5 in either
native or reconstituted membranes under conditions that support transport.
Continuous wave EPR measurements are consistent with this result and
indicate that positions 143 and 336 are in close proximity in the
presence of substrate. These two residues are localized within helix
interacting GxxxG-like motifs (G140LASG144 and
S336DIFG340) at the cytoplasmic poles of TM5
and TM11. Pulse EPR measurements were used to determine distances
and distance distributions across the cytoplasmic or periplasmic ends
of OxlT and were compared with the predictions of an inside-open homology
model. The data indicate that a significant population of transporter
is in an outside-open configuration in the presence of substrate;
however, each end of the transporter exhibits significant conformational
heterogeneity, where both inside-open and outside-open configurations
are present. These data indicate that TM5 and TM11, which form part
of the transport pathway, transiently close during transport and that
there is a conformational equilibrium between inside-open and outside-open
states of OxlT in the presence of substrate.
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Affiliation(s)
- Osigbemhe Iyalomhe
- Department of Physiology, The Johns Hopkins University, School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205, United States
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155
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Hammond CM, Owen-Hughes T, Norman DG. Modelling multi-protein complexes using PELDOR distance measurements for rigid body minimisation experiments using XPLOR-NIH. Methods 2014; 70:139-53. [PMID: 25448300 PMCID: PMC4274318 DOI: 10.1016/j.ymeth.2014.10.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 10/23/2014] [Accepted: 10/27/2014] [Indexed: 10/25/2022] Open
Abstract
Crystallographic and NMR approaches have provided a wealth of structural information about protein domains. However, often these domains are found as components of larger multi domain polypeptides or complexes. Orienting domains within such contexts can provide powerful new insight into their function. The combination of site specific spin labelling and Pulsed Electron Double Resonance (PELDOR) provide a means of obtaining structural measurements that can be used to generate models describing how such domains are oriented. Here we describe a pipeline for modelling the location of thio-reactive nitroxyl spin locations to engineered sties on the histone chaperone Vps75. We then use a combination of experimentally determined measurements and symmetry constraints to model the orientation in which homodimers of Vps75 associate to form homotetramers using the XPLOR-NIH platform. This provides a working example of how PELDOR measurements can be used to generate a structural model.
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Affiliation(s)
- Colin M Hammond
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, UK
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, UK.
| | - David G Norman
- Nucleic Acids Structure Research Group, University of Dundee, Dundee DD1 5EH, UK.
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156
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Ward R, Pliotas C, Branigan E, Hacker C, Rasmussen A, Hagelueken G, Booth IR, Miller S, Lucocq J, Naismith JH, Schiemann O. Probing the structure of the mechanosensitive channel of small conductance in lipid bilayers with pulsed electron-electron double resonance. Biophys J 2014; 106:834-42. [PMID: 24559986 PMCID: PMC3944623 DOI: 10.1016/j.bpj.2014.01.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 01/03/2014] [Accepted: 01/07/2014] [Indexed: 01/16/2023] Open
Abstract
Mechanosensitive channel proteins are important safety valves against osmotic shock in bacteria, and are involved in sensing touch and sound waves in higher organisms. The mechanosensitive channel of small conductance (MscS) has been extensively studied. Pulsed electron-electron double resonance (PELDOR or DEER) of detergent-solubilized protein confirms that as seen in the crystal structure, the outer ring of transmembrane helices do not pack against the pore-forming helices, creating an apparent void. The relevance of this void to the functional form of MscS in the bilayer is the subject of debate. Here, we report PELDOR measurements of MscS reconstituted into two lipid bilayer systems: nanodiscs and bicelles. The distance measurements from multiple mutants derived from the PELDOR data are consistent with the detergent-solution arrangement of the protein. We conclude, therefore, that the relative positioning of the transmembrane helices is preserved in mimics of the cell bilayer, and that the apparent voids are not an artifact of detergent solution but a property of the protein that will have to be accounted for in any molecular mechanism of gating.
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Affiliation(s)
- Richard Ward
- Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland
| | - Christos Pliotas
- Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland
| | - Emma Branigan
- Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland
| | - Christian Hacker
- School of Medicine, University of St. Andrews, St. Andrews, Scotland
| | - Akiko Rasmussen
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland
| | - Gregor Hagelueken
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Ian R Booth
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland
| | - Samantha Miller
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland
| | - John Lucocq
- School of Medicine, University of St. Andrews, St. Andrews, Scotland
| | - James H Naismith
- Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland.
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany; Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland.
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157
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Cafiso DS. Identifying and quantitating conformational exchange in membrane proteins using site-directed spin labeling. Acc Chem Res 2014; 47:3102-9. [PMID: 25152957 PMCID: PMC4204925 DOI: 10.1021/ar500228s] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Protein structures are not static but sample different conformations
over a range of amplitudes and time scales. These fluctuations may
involve relatively small changes in bond angles or quite large rearrangements
in secondary structure and tertiary fold. The equilibrium between
discrete structural substates on the microsecond to millisecond time
scale is sometimes termed conformational exchange. Protein dynamics
and conformational exchange are believed to provide the basis for
many important activities, such as protein–protein and protein–ligand
interactions, enzymatic activity and protein allostery; however, for
many proteins, the dynamics and conformational exchange that lead
to function are poorly defined. Spectroscopic methods, such
as NMR, are among the most important
methods to explore protein dynamics and conformational exchange; however,
they are difficult to implement in some systems and with some types
of exchange events. Site-directed spin labeling (SDSL) is an EPR based
approach that is particularly well-suited to high molecular-weight
systems such as membrane proteins. Because of the relatively fast
time scale for EPR spectroscopy, it is an excellent method to examine
exchange. Conformations that are in exchange are captured as distinct
populations in the EPR spectrum, and this feature when combined with
the use of methods that can shift the free energy of conformational
substates allows one to identify regions of proteins that are in dynamic
exchange. In addition, modern pulse EPR methods have the ability to
examine conformational heterogeneity, resolve discrete protein states,
and identify the substates in exchange. Protein crystallography
has provided high-resolution models for
a number of membrane proteins; but because of conformational exchange,
these models do not always reflect the structures that are present
when the protein is in a native bilayer environment. In the case of
the Escherichia coli vitamin B12 transporter,
BtuB, the energy coupling segment of this protein undergoes a substrate-dependent
unfolding, which acts to couple this outer-membrane protein to the
inner-membrane protein TonB. EPR spectroscopy demonstrates that the
energy coupling segment is in equilibrium between ordered and disordered
states, and that substrate binding shifts this equilibrium to favor
an unfolded state. However, in crystal structures of BtuB, this segment
is resolved and folded within the protein, and neither the presence
of this equilibrium nor the substrate-induced change is revealed.
This is a result of the solute environment and the crystal lattice,
both of which act to stabilize one conformational substate of the
transporter. Using SDSL, it can be shown that conformational
exchange is present
in other regions of BtuB and in other members of this transporter
family. Conformational exchange has also been examined in systems
such as the plasma membrane SNARE protein, syntaxin 1A, where dynamics
are controlled by regulatory proteins such as munc18. Regulating the
microsecond to millisecond time scale dynamics in the neuronal SNAREs
is likely to be a key feature that regulates assembly of the SNAREs
and neurotransmitter release.
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Affiliation(s)
- David S. Cafiso
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia 22904-4319, United States
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158
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Kerry PS, Turkington HL, Ackermann K, Jameison SA, Bode BE. Analysis of influenza A virus NS1 dimer interfaces in solution by pulse EPR distance measurements. J Phys Chem B 2014; 118:10882-8. [PMID: 25148246 PMCID: PMC4191058 DOI: 10.1021/jp508386r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
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Pulsed electron–electron double
resonance (PELDOR) is an
electron paramagnetic resonance (EPR) spectroscopy technique for nanometer
distance measurements between paramagnetic centers such as radicals.
PELDOR has been recognized as a valuable tool to approach structural
questions in biological systems. In this manuscript, we demonstrate
the value of distance measurements for differentiating competing structural
models on the dimerization of the effector domain (ED) of the non-structural
protein 1 (NS1) of the influenza A virus. Our results show NS1 to
be well amenable to nanometer distance measurements by EPR, yielding
high quality data. In combination with mutants perturbing protein
dimerization and in silico prediction based on crystal
structures, we can exclude one of two potential dimerization interfaces.
Furthermore, our results lead to a viable hypothesis of a NS1 ED:ED
interface which is flexible through rotation around the vector interconnecting
the two native cysteines. These results prove the high value of pulse
EPR as a complementary method for structural biology.
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Affiliation(s)
- Philip S Kerry
- Biomedical Sciences Research Complex, University of St Andrews , St Andrews, Fife, KY16 9ST, U.K
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159
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Florin N, Schiemann O, Hagelueken G. High-resolution crystal structure of spin labelled (T21R1) azurin from Pseudomonas aeruginosa: a challenging structural benchmark for in silico spin labelling algorithms. BMC STRUCTURAL BIOLOGY 2014; 14:16. [PMID: 24884565 PMCID: PMC4055355 DOI: 10.1186/1472-6807-14-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/08/2014] [Indexed: 01/23/2023]
Abstract
Background EPR-based distance measurements between spin labels in proteins have become a valuable tool in structural biology. The direct translation of the experimental distances into structural information is however often impaired by the intrinsic flexibility of the spin labelled side chains. Different algorithms exist that predict the approximate conformation of the spin label either by using pre-computed rotamer libraries of the labelled side chain (rotamer approach) or by simply determining its accessible volume (accessible volume approach). Surprisingly, comparisons with many experimental distances have shown that both approaches deliver the same distance prediction accuracy of about 3 Å. Results Here, instead of comparing predicted and experimental distances, we test the ability of both approaches to predict the actual conformations of spin labels found in a new high-resolution crystal structure of spin labelled azurin (T21R1). Inside the crystal, the label is found in two very different environments which serve as a challenging test for the in silico approaches. Conclusions Our results illustrate why simple and more sophisticated programs lead to the same prediciton error. Thus, a more precise treatment of the complete environment of the label and also its interactions with the environment will be needed to increase the accuracy of in silico spin labelling algorithms.
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Affiliation(s)
| | | | - Gregor Hagelueken
- Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr, 12, Bonn, NRW 53115, Germany.
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160
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Bowman A, Hammond CM, Stirling A, Ward R, Shang W, El-Mkami H, Robinson DA, Svergun DI, Norman DG, Owen-Hughes T. The histone chaperones Vps75 and Nap1 form ring-like, tetrameric structures in solution. Nucleic Acids Res 2014; 42:6038-51. [PMID: 24688059 PMCID: PMC4027167 DOI: 10.1093/nar/gku232] [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: 11/15/2022] Open
Abstract
NAP-1 fold histone chaperones play an important role in escorting histones to and from sites of nucleosome assembly and disassembly. The two NAP-1 fold histone chaperones in budding yeast, Vps75 and Nap1, have previously been crystalized in a characteristic homodimeric conformation. In this study, a combination of small angle X-ray scattering, multi angle light scattering and pulsed electron–electron double resonance approaches were used to show that both Vps75 and Nap1 adopt ring-shaped tetrameric conformations in solution. This suggests that the formation of homotetramers is a common feature of NAP-1 fold histone chaperones. The tetramerisation of NAP-1 fold histone chaperones may act to shield acidic surfaces in the absence of histone cargo thus providing a ‘self-chaperoning’ type mechanism.
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Affiliation(s)
- Andrew Bowman
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, DD1 5EH, UK
| | - Colin M Hammond
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, DD1 5EH, UK
| | - Andrew Stirling
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, DD1 5EH, UK
| | - Richard Ward
- Nucleic Acids Structure Research Group, University of Dundee, Dundee, DD1 5EH, UK
| | - Weifeng Shang
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Hassane El-Mkami
- School of Physics and Astronomy, University of St Andrews, St Andrews FE2 4KM, UK
| | - David A Robinson
- Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, DD1 5EH, UK
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | - David G Norman
- Nucleic Acids Structure Research Group, University of Dundee, Dundee, DD1 5EH, UK
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, DD1 5EH, UK
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161
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Lemmin T, Dimitrov M, Fraering PC, Dal Peraro M. Perturbations of the straight transmembrane α-helical structure of the amyloid precursor protein affect its processing by γ-secretase. J Biol Chem 2014; 289:6763-6774. [PMID: 24469457 PMCID: PMC3945338 DOI: 10.1074/jbc.m113.470781] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Revised: 01/14/2014] [Indexed: 01/30/2023] Open
Abstract
The amyloid precursor protein (APP) is a widely expressed type I transmembrane (TM) glycoprotein present at the neuronal synapse. The proteolytic cleavage by γ-secretase of its C-terminal fragment produces amyloid-β (Aβ) peptides of different lengths, the deposition of which is an early indicator of Alzheimer disease. At present, there is no consensus on the conformation of the APP-TM domain at the biological membrane. Although structures have been determined by NMR in detergent micelles, their conformation is markedly different. Here we show by using molecular simulations that the APP-TM region systematically prefers a straight α-helical conformation once embedded in a membrane bilayer. However, APP-TM is highly flexible, and its secondary structure is strongly influenced by the surrounding lipid environment, as when enclosed in detergent micelles. This behavior is confirmed when analyzing in silico the atomistic APP-TM population observed by residual dipolar couplings and double electron-electron resonance spectroscopy. These structural and dynamic features are critical in the proteolytic processing of APP by the γ-secretase enzyme, as suggested by a series of Gly(700) mutants. Affecting the hydration and flexibility of APP-TM, these mutants invariantly show an increase in the production of Aβ38 compared with Aβ40 peptides, which is reminiscent of the effect of γ-secretase modulators inhibitors.
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Affiliation(s)
- Thomas Lemmin
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Mitko Dimitrov
- Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Patrick C Fraering
- Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
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162
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Ji M, Ruthstein S, Saxena S. Paramagnetic metal ions in pulsed ESR distance distribution measurements. Acc Chem Res 2014; 47:688-95. [PMID: 24289139 DOI: 10.1021/ar400245z] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The use of pulsed electron spin resonance (ESR) to measure interspin distance distributions has advanced biophysical research. The three major techniques that use pulsed ESR are relaxation rate based distance measurements, double quantum coherence (DQC), and double electron electron resonance (DEER). Among these methods, the DEER technique has become particularly popular largely because it is easy to implement on commercial instruments and because programs are available to analyze experimental data. Researchers have widely used DEER to measure the structure and conformational dynamics of molecules labeled with the methanethiosulfonate spin label (MTSSL). Recently, researchers have exploited endogenously bound paramagnetic metal ions as spin probes as a way to determine structural constraints in metalloproteins. In this context Cu(2+) has served as a useful paramagnetic metal probe at X-band for DEER based distance measurements. Sample preparation is simple, and a coordinated-Cu(2+) ion offers limited spatial flexibility, making it an attractive probe for DEER experiments. On the other hand, Cu(2+) has a broad absorption ESR spectrum at low temperature, which leads to two potential complications. First, the Cu(2+)-based DEER time domain data has lower signal to noise ratio compared with MTSSL. Second, accurate distance distribution analysis often requires high-quality experimental data at different external magnetic fields or with different frequency offsets. In this Account, we summarize characteristics of Cu(2+)-based DEER distance distribution measurements and data analysis methods. We highlight a novel application of such measurements in a protein-DNA complex to identify the metal ion binding site and to elucidate its chemical mechanism of function. We also survey the progress of research on other metal ions in high frequency DEER experiments.
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Affiliation(s)
- Ming Ji
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sharon Ruthstein
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Chemistry, Faculty of Exact Science, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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163
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Giannoulis A, Ward R, Branigan E, Naismith JH, Bode BE. PELDOR in rotationally symmetric homo-oligomers. Mol Phys 2013; 111:2845-2854. [PMID: 24954956 PMCID: PMC4056887 DOI: 10.1080/00268976.2013.798697] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 04/12/2013] [Indexed: 12/24/2022]
Abstract
Nanometre distance measurements by pulsed electron-electron double resonance (PELDOR) spectroscopy have become an increasingly important tool in structural biology. The theoretical underpinning of the experiment is well defined for systems containing two nitroxide spin-labels (spin pairs); however, recently experiments have been reported on homo-oligomeric membrane proteins consisting of up to eight spin-labelled monomers. We have explored the theory behind these systems by examining model systems based on multiple spins arranged in rotationally symmetric polygons. The results demonstrate that with a rising number of spins within the test molecule, increasingly strong distortions appear in distance distributions obtained from an analysis based on the simple spin pair approach. These distortions are significant over a range of system sizes and remain so even when random errors are introduced into the symmetry of the model. We present an alternative approach to the extraction of distances on such systems based on a minimisation that properly treats multi-spin correlations. We demonstrate the utility of this approach on a spin-labelled mutant of the heptameric Mechanosensitive Channel of Small Conductance of E. coli.
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Affiliation(s)
- Angeliki Giannoulis
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
| | - Richard Ward
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
| | - Emma Branigan
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
| | - James H. Naismith
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
| | - Bela E. Bode
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
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164
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Matalon E, Huber T, Hagelueken G, Graham B, Frydman V, Feintuch A, Otting G, Goldfarb D. Gadolinium(III) Spin Labels for High-Sensitivity Distance Measurements in Transmembrane Helices. Angew Chem Int Ed Engl 2013; 52:11831-4. [DOI: 10.1002/anie.201305574] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 08/14/2013] [Indexed: 12/28/2022]
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165
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Matalon E, Huber T, Hagelueken G, Graham B, Frydman V, Feintuch A, Otting G, Goldfarb D. Gadolinium(III) Spin Labels for High-Sensitivity Distance Measurements in Transmembrane Helices. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305574] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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166
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Alexander NS, Stein RA, Koteiche HA, Kaufmann KW, Mchaourab HS, Meiler J. RosettaEPR: rotamer library for spin label structure and dynamics. PLoS One 2013; 8:e72851. [PMID: 24039810 PMCID: PMC3764097 DOI: 10.1371/journal.pone.0072851] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 07/15/2013] [Indexed: 11/18/2022] Open
Abstract
An increasingly used parameter in structural biology is the measurement of distances between spin labels bound to a protein. One limitation to these measurements is the unknown position of the spin label relative to the protein backbone. To overcome this drawback, we introduce a rotamer library of the methanethiosulfonate spin label (MTSSL) into the protein modeling program Rosetta. Spin label rotamers were derived from conformations observed in crystal structures of spin labeled T4 lysozyme and previously published molecular dynamics simulations. Rosetta’s ability to accurately recover spin label conformations and EPR measured distance distributions was evaluated against 19 experimentally determined MTSSL labeled structures of T4 lysozyme and the membrane protein LeuT and 73 distance distributions from T4 lysozyme and the membrane protein MsbA. For a site in the core of T4 lysozyme, the correct spin label conformation (Χ1 and Χ2) is recovered in 99.8% of trials. In surface positions 53% of the trajectories agree with crystallized conformations in Χ1 and Χ2. This level of recovery is on par with Rosetta performance for the 20 natural amino acids. In addition, Rosetta predicts the distance between two spin labels with a mean error of 4.4 Å. The width of the experimental distance distribution, which reflects the flexibility of the two spin labels, is predicted with a mean error of 1.3 Å. RosettaEPR makes full-atom spin label modeling available to a wide scientific community in conjunction with the powerful suite of modeling methods within Rosetta.
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Affiliation(s)
- Nathan S. Alexander
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Richard A. Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Hanane A. Koteiche
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Kristian W. Kaufmann
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Hassane S. Mchaourab
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
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167
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Hubbell WL, López CJ, Altenbach C, Yang Z. Technological advances in site-directed spin labeling of proteins. Curr Opin Struct Biol 2013; 23:725-33. [PMID: 23850140 DOI: 10.1016/j.sbi.2013.06.008] [Citation(s) in RCA: 232] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 06/12/2013] [Indexed: 12/23/2022]
Abstract
Molecular flexibility over a wide time range is of central importance to the function of many proteins, both soluble and membrane. Revealing the modes of flexibility, their amplitudes, and time scales under physiological conditions is the challenge for spectroscopic methods, one of which is site-directed spin labeling EPR (SDSL-EPR). Here we provide an overview of some recent technological advances in SDSL-EPR related to investigation of structure, structural heterogeneity, and dynamics of proteins. These include new classes of spin labels, advances in measurement of long range distances and distance distributions, methods for identifying backbone and conformational fluctuations, and new strategies for determining the kinetics of protein motion.
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Affiliation(s)
- Wayne L Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, United States.
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168
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Jeschke G. Conformational dynamics and distribution of nitroxide spin labels. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 72:42-60. [PMID: 23731861 DOI: 10.1016/j.pnmrs.2013.03.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 03/26/2013] [Accepted: 03/27/2013] [Indexed: 06/02/2023]
Abstract
Long-range distance measurements based on paramagnetic relaxation enhancement (PRE) in NMR, quantification of surface water dynamics near biomacromolecules by Overhauser dynamic nuclear polarization (DNP) and sensitivity enhancement by solid-state DNP all depend on introducing paramagnetic species into an otherwise diamagnetic NMR sample. The species can be introduced by site-directed spin labeling, which offers precise control for positioning the label in the sequence of a biopolymer. However, internal flexibility of the spin label gives rise to dynamic processes that potentially influence PRE and DNP behavior and leads to a spatial distribution of the electron spin even in solid samples. Internal dynamics of spin labels and their static conformational distributions have been studied mainly by electron paramagnetic resonance spectroscopy and molecular dynamics simulations, with a large body of results for the most widely applied methanethiosulfonate spin label MTSL. These results are critically discussed in a unifying picture based on rotameric states of the group that carries the spin label. Deficiencies in our current understanding of dynamics and conformations of spin labeled groups and of their influence on NMR observables are highlighted and directions for further research suggested.
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Affiliation(s)
- Gunnar Jeschke
- ETH Zürich, Laboratory Physical Chemistry, Zürich, Switzerland.
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169
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Hagelueken G, Abdullin D, Ward R, Schiemann O. mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL. Mol Phys 2013; 111:2757-2766. [PMID: 24954955 PMCID: PMC4056886 DOI: 10.1080/00268976.2013.809804] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 05/18/2013] [Indexed: 01/07/2023]
Abstract
Nanometer distance measurements based on electron paramagnetic resonance methods in combination with site-directed spin labelling are powerful tools for the structural analysis of macromolecules. The software package mtsslSuite provides scientists with a set of tools for the translation of experimental distance distributions into structural information. The package is based on the previously published mtsslWizard software for in silico spin labelling. The mtsslSuite includes a new version of MtsslWizard that has improved performance and now includes additional types of spin labels. Moreover, it contains applications for the trilateration of paramagnetic centres in biomolecules and for rigid-body docking of subdomains of macromolecular complexes. The mtsslSuite is tested on a number of challenging test cases and its strengths and weaknesses are evaluated.
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Affiliation(s)
- Gregor Hagelueken
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Dinar Abdullin
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Richard Ward
- Biomedical Sciences Research Complex, The University of St. Andrews, Fife, UK
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany ; Biomedical Sciences Research Complex, The University of St. Andrews, Fife, UK
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170
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The architecture of EssB, an integral membrane component of the type VII secretion system. Structure 2013; 21:595-603. [PMID: 23499020 PMCID: PMC3694306 DOI: 10.1016/j.str.2013.02.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 02/03/2013] [Accepted: 02/05/2013] [Indexed: 11/22/2022]
Abstract
The membrane-bound EssB is an integral and essential component of the bacterial type VII secretion system that can contribute to pathogenicity. The architecture of Geobacillus thermodenitrificans EssB has been investigated by combining crystallographic and EPR spectroscopic methods. The protein forms a dimer that straddles the cytoplasmic membrane. A helical fold is observed for the C-terminal segment, which is positioned on the exterior of the membrane. This segment contributes most to dimer formation. The N-terminal segment displays a structure related to the pseudokinase fold and may contribute to function by recognizing substrates or secretion system partners. The remaining part of EssB may serve as an anchor point for the secretion apparatus, which is embedded in the cytoplasmic membrane with the C-terminal domain protruding out to interact with partner proteins or components of peptidoglycan.
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171
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Conformational state of the MscS mechanosensitive channel in solution revealed by pulsed electron-electron double resonance (PELDOR) spectroscopy. Proc Natl Acad Sci U S A 2012; 109:E2675-82. [PMID: 23012406 DOI: 10.1073/pnas.1202286109] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The heptameric mechanosensitive channel of small conductance (MscS) provides a critical function in Escherichia coli where it opens in response to increased bilayer tension. Three approaches have defined different closed and open structures of the channel, resulting in mutually incompatible models of gating. We have attached spin labels to cysteine mutants on key secondary structural elements specifically chosen to discriminate between the competing models. The resulting pulsed electron-electron double resonance (PELDOR) spectra matched predicted distance distributions for the open crystal structure of MscS. The fit for the predictions by structural models of MscS derived by other techniques was not convincing. The assignment of MscS as open in detergent by PELDOR was unexpected but is supported by two crystal structures of spin-labeled MscS. PELDOR is therefore shown to be a powerful experimental tool to interrogate the conformation of transmembrane regions of integral membrane proteins.
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172
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Pasi M, Tiberti M, Arrigoni A, Papaleo E. xPyder: a PyMOL plugin to analyze coupled residues and their networks in protein structures. J Chem Inf Model 2012; 52:1865-74. [PMID: 22721491 DOI: 10.1021/ci300213c] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A versatile method to directly identify and analyze short- or long-range coupled or communicating residues in a protein conformational ensemble is of extreme relevance to achieve a complete understanding of protein dynamics and structural communication routes. Here, we present xPyder, an interface between one of the most employed molecular graphics systems, PyMOL, and the analysis of dynamical cross-correlation matrices (DCCM). The approach can also be extended, in principle, to matrices including other indexes of communication propensity or intensity between protein residues, as well as the persistence of intra- or intermolecular interactions, such as those underlying protein dynamics. The xPyder plugin for PyMOL 1.4 and 1.5 is offered as Open Source software via the GPL v2 license, and it can be found, along with the installation package, the user guide, and examples, at http://linux.btbs.unimib.it/xpyder/.
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Affiliation(s)
- Marco Pasi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza 2, 20126 Milan, Italy
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173
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Jeschke G. Characterization of Protein Conformational Changes with Sparse Spin-Label Distance Constraints. J Chem Theory Comput 2012; 8:3854-63. [PMID: 26593026 DOI: 10.1021/ct300113z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The combination of site-directed spin labeling with pulse EPR distance measurements can provide a moderate number of distance constraints on the nanometer length scale for proteins in different states. By adapting an existing algorithm (Zheng, W.; Brooks, B. R. Biophys. J. 2006, 90, 4327) to the problem, we address the question to what extent conformational change can be characterized when the protein structure is known for one of the states, whereas only a sparse set of distance constraints between spin labels is available for the other state. We find that the type and general direction of the conformational change can be recognized, while the amplitude may be uncertain.
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Affiliation(s)
- G Jeschke
- Lab. Phys. Chem., ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland
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