Robust and versatile interpretation of spectra with coupled evolution periods using multi-way decomposition

Malmodin, Daniel; Billeter, Martin

doi:10.1002/mrc.1824

Cited by 24 publications

(19 citation statements)

References 31 publications

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“…To overcome the inherent time limitation of 2D NMR spectroscopy, two conceptually different approaches can be envisaged. First, the number of scans required to sample the multidimensional time space may be reduced by using spectral aliasing, nonlinear data sampling techniques, spatial frequency encoding, or Hadamard-type frequency-space spectroscopy (7,8). Second, accelerating the recovery of spin polarization between scans by means of optimized pulse sequences (9)(10)(11) or the addition of relaxation agents to the solution (12, 13) allows higher repetition rates of the pulse sequence.…”

Section: Resultsmentioning

confidence: 99%

Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy

Schanda

Forge

Brutscher

2007

Proc. Natl. Acad. Sci. U.S.A.

152

151

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Atom-resolved real-time studies of kinetic processes in proteins have been hampered in the past by the lack of experimental techniques that yield sufficient temporal and atomic resolution. Here we present band-selective optimized flip-angle short transient (SOFAST) real-time 2D NMR spectroscopy, a method that allows simultaneous observation of reaction kinetics for a large number of nuclear sites along the polypeptide chain of a protein with an unprecedented time resolution of a few seconds. SOFAST real-time 2D NMR spectroscopy combines fast NMR data acquisition techniques with rapid sample mixing inside the NMR magnet to initiate the kinetic event. We demonstrate the use of SOFAST real-time 2D NMR to monitor the conformational transition of ␣-lactalbumin from a molten globular to the native state for a large number of amide sites along the polypeptide chain. The kinetic behavior observed for the disappearance of the molten globule and the appearance of the native state is monoexponential and uniform along the polypeptide chain. This observation confirms previous findings that a single transition state ensemble controls folding of ␣-lactalbumin from the molten globule to the native state. In a second application, the spontaneous unfolding of native ubiquitin under nondenaturing conditions is characterized by amide hydrogen exchange rate constants measured at high pH by using SOFAST real-time 2D NMR. Our data reveal that ubiquitin unfolds in a gradual manner with distinct unfolding regimes.hydrogen/deuterium exchange ͉ molecular kinetics ͉ ␣-lactalbumin ͉ ubiquitin A detailed description of the structural changes occurring during the folding and unfolding of proteins still remains a challenging objective in biophysics. The understanding of the fundamental mechanisms of the folding process will also shed light on the factors leading to protein misfolding responsible for neurodegenerative diseases such as Alzheimer's and Parkinson's diseases (1). The ideal method to study protein folding/unfolding provides structural information at atomic resolution and is sensitive to changes occurring on time scales ranging from microseconds to minutes, a task that no single technique is able to fulfill. NMR spectroscopy is especially well adapted to obtain detailed atomistic information about the mechanisms, kinetics, and energetics of the folding/unfolding process for virtually every nuclear site in the protein. NMR methods are sensitive to molecular dynamics occurring over a wide range of time scales (Fig. 1a). Although steady-state NMR methods are well suited to characterize equilibrium molecular dynamics occurring on a subsecond time scale (2, 3), unidirectional processes are best studied by real-time NMR (4, 5), where a series of NMR spectra is recorded during the reaction (Fig. 1b). Two difficulties have so far hampered the widespread application of real-time NMR to the study of protein folding. The first problem is the low intrinsic sensitivity of NMR at ambient temperature, a consequence of the small transition energies ...

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Section: Resultsmentioning

confidence: 99%

Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy

Schanda

Forge

Brutscher

2007

Proc. Natl. Acad. Sci. U.S.A.

152

151

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“…A major breakthrough for the application of real-time NMR to atom-resolved studies of protein folding has been the introduction of fast and ultrafast multidimensional NMR techniques (9,10). In particular, the SOFAST-HMQC (11-13) and ultraSOFAST-HMQC (14,15) experiments allow the recording of two-dimensional 1 H- 15 N correlation spectra of proteins at ϳ0.1-1 s Ϫ1 repetition rates, thus providing the required time resolution for the study of kinetic molecular processes occurring on the seconds-to-minutes time scale.…”

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confidence: 99%

Native-unlike Long-lived Intermediates along the Folding Pathway of the Amyloidogenic Protein β2-Microglobulin Revealed by Real-time Two-dimensional NMR

Corazza

Rennella

Schanda

et al. 2010

Journal of Biological Chemistry

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␤2-microglobulin (␤2m), the light chain of class I major histocompatibility complex, is responsible for the dialysis-related amyloidosis and, in patients undergoing long term dialysis, the full-length and chemically unmodified ␤2m converts into amyloid fibrils. The protein, belonging to the immunoglobulin superfamily, in common to other members of this family, experiences during its folding a long-lived intermediate associated to the trans-to-cis isomerization of Pro-32 that has been addressed as the precursor of the amyloid fibril formation. In this respect, previous studies on the W60G ␤2m mutant, showing that the lack of Trp-60 prevents fibril formation in mild aggregating condition, prompted us to reinvestigate the refolding kinetics of wild type and W60G ␤2m at atomic resolution by real-time NMR. The analysis, conducted at ambient temperature by the band selective flip angle short transient real-time two-dimensional NMR techniques and probing the ␤2m states every 15 s, revealed a more complex folding energy landscape than previously reported for wild type ␤2m, involving more than a single intermediate species, and shedding new light into the fibrillogenic pathway. Moreover, a significant difference in the kinetic scheme previously characterized by optical spectroscopic methods was discovered for the W60G ␤2m mutant.Among the amyloidogenic proteins that have been most frequently studied over the last years, there is ␤ 2 -microglobulin (␤2m) 4 that is responsible for dialysis-related amyloidosis.␤2m, the non-polymorphic light chain of class I major histocompatibility complex, is a small protein that converts into fibrils without the necessity of any chemical modification. Fibril formation occurs in vitro, and most probably also in vivo, through the intact protein. This allows extending experimental conclusions from in vitro studies to the natural process. More importantly, ␤2m recapitulates exquisitely the paradigm of the partially unfolded intermediate, bridging the native fold and the fibrillar conformation, as traditionally invoked to explain the conformational transition from the native fold to the amyloid. Therefore, a detailed characterization of all intermediate states occurring along the folding pathway is of great importance to understand the process of fibril formation. A kinetic scheme of ␤2m refolding entailing two fast steps, burst phase and fast phase, prior to reaching a slow conversion phase from the intermediate to the native state, was first reported by Chiti et al. (1). This long-lived ␤2m refolding intermediate, termed I 2 or I T by different authors, has long been recognized as an effective fibril-competent species, formerly regarded as an ensemble of species (1) and later as a single species (2-4). It has been shown that I T contains a non-native trans peptide bond between His-31 and Pro-32 that slowly converts into cis conformation during the final refolding step (3). The isomerization occurs with minor rearrangements of the protein toward the native structure from an already native-lik...

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“…The time gain for recording 30 2D projections of the size shown in Fig.2 instead of a corresponding set of at least three 4D spectra is about 1500. Additional advantages of the method include optimal results with respect to signal-to-noise as well as resolution (due to aliasing, see Fig.2B) [3].…”

Section: Discussionmentioning

confidence: 99%

“…The projected spectra become (after Fourier transform t → ω, t M → ω M ; denotes convolutions): Multi-way decomposition takes a set of projections P (ω, ω M ) as input, delivering the shapes F k i as output ( Fig.1) [2][3]. PRODECOMP is an implementation of multi-way decomposition relying on the FNNLS algorithm [4].…”

Section: Algorithmmentioning

confidence: 99%

“…Multi-way decomposition with the program PRODECOMP [2][3] is illustrated on a set of 30 projections recorded for the protein ubiquitin. The NMR input projections correspond to a 9-dimensional conventional spectrum; thus, the output components consist of nine shapes F k i , which describe resonance frequenices of all nitrogens, carbons and hydrogens in protein fragments of type CβH n − CαH − CO − NH − CαH − CβH n .…”

Section: Applicationmentioning

confidence: 99%

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Multi‐way decomposition of projected spectra obtained in protein NMR

Billeter

Staykova

Fredriksson

et al. 2007

Proc Appl Math and Mech

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Multidimensional nuclear magnetic resonance spectroscopy is a highly versatile tool in protein research. Experimental limitations prohibit spectra with ≥ 5 dimensions. However, similar information can be obtained by recording 2-dimensional projections. A decomposition-based approach for analyzing projections is presented and applied to a protein. The resulting resonance identification is a prerequisite for further characterization of structure, dynamics and interactions of proteins.

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Robust and versatile interpretation of spectra with coupled evolution periods using multi-way decomposition

Cited by 24 publications

References 31 publications

Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy

Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy

Native-unlike Long-lived Intermediates along the Folding Pathway of the Amyloidogenic Protein β2-Microglobulin Revealed by Real-time Two-dimensional NMR

Multi‐way decomposition of projected spectra obtained in protein NMR

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