Abstract:
:A substantial time savings in the collection of multidimensional NMR data can be achieved by coupling the evolution of nuclei in the indirect dimensions. In order to save time, the sampling of the indirect dimensions is inherently incomplete. Therefore, many algorithms and samplings schemes have been developed aimed at separating the coevolved frequencies into analyzable data with limited artifacts. This paper extends the use of circulant matrices to describe coupled evolution with convolutions. By understanding the data in terms of convolutions, there is an exact solution to the inversion problem of extracting the orthogonal vectors from the coupled dimensions. Previously, this inversion problem has been solved using peak coordinates extracted from spectra. In contrast, the method described here uses spectra directly. This solution suggests a simple sampling scheme of collecting N orthogonal spectra, and N + 1 projections at specific projection angles, however, the theory developed can be extended generally to arbitrary projection angles. The circulant matrix methodology is demonstrated for simulated and real data. Further, an algorithm for separating overlapped signals in the detected dimension is presented. The algorithm involves the forward calculation of the coupled spectra from the orthogonal spectra, followed by back calculation of the orthogonal spectra from the coupled spectra, thus permitting rigorous cross-validation. This algorithm is shown to be robust in that erroneous solutions give rise to large artifacts.
journal_name
J Biomol NMRjournal_title
Journal of biomolecular NMRauthors
Mueller GAdoi
10.1007/s10858-009-9309-zsubject
Has Abstractpub_date
2009-05-01 00:00:00pages
13-23issue
1eissn
0925-2738issn
1573-5001journal_volume
44pub_type
杂志文章abstract::Calmodulin is a two-domain protein which in solution can adopt a variety of conformations upon reorientation of its domains. The maximum occurrence (MO) of a set of calmodulin conformations that are representative of the overall conformational space possibly sampled by the protein, has been calculated from the paramag...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-011-9532-2
更新日期:2011-11-01 00:00:00
abstract::It is proposed to obtain effective Lipari-Szabo order parameters and local correlation times for relaxation vectors of protein (13)CO nuclei by carrying out a (13)CO-R(1) auto relaxation experiment, a transverse (13)CO CSA/13CO-13Calpha CSA/dipolar cross correlation and a transverse (13)CO CSA/(13)CO-(15)N CSA/dipolar...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-006-9047-4
更新日期:2006-10-01 00:00:00
abstract::Cytochrome c552 from the thermophilic bacterium Hydrogenobacter thermophilus is a typical c-type cytochrome which binds heme covalently via two thioether bonds between the two heme vinyl groups and two cysteine thiol groups in a CXXCH sequence motif. This protein was converted to a b-type cytochrome by substitution of...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-015-9938-3
更新日期:2015-06-01 00:00:00
abstract::The first reconstitution of an Fe2S2 ferredoxin with a diamagnetic prosthetic group was recently described [Kazanis et al. (1995) J. Am. Chem. Soc., 117, 6625-6626]. The replacement of the iron-sulfur cluster of the bacterial ferredoxin putidaredoxin (Pdx) by gallium (Ga3+) renders the protein diamagnetic and permits ...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1018369721091
更新日期:1997-06-01 00:00:00
abstract::Recently we have shown that HMQC spectra of protonated methyl groups in high molecular weight, highly deuterated proteins have large enhancements in sensitivity and resolution relative to HSQC-generated data sets. These enhancements derive from a TROSY effect in which complete cancellation of intra-methyl (1)H-(1)H an...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/B:JNMR.0000013824.93994.1f
更新日期:2004-02-01 00:00:00
abstract::TROSY-based triple resonance experiments are essential for protein backbone assignment of large biomolecular systems by solution NMR spectroscopy. In a survey of the current Bruker pulse sequence library for TROSY-based experiments we found that several sequences were plagued by artifacts that affect spectral quality ...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-017-0133-6
更新日期:2017-09-01 00:00:00
abstract::The NMR spectra of the complex between the DNA-binding domain of the Dead ringer protein (DRI-DBD, Gly262-Gly398) and its DNA binding site (DRI-DBD:DNA, 26 kDa) have been optimized by biochemical and spectroscopic means. First, we demonstrate the utility of a modified 2D [F1,F2] 13C-filtered NOESY experiment that empl...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1011296112710
更新日期:2001-03-01 00:00:00
abstract::A simple spectroscopic filtering technique is presented that may aid the assignment of (13)C and (15)N resonances of methyl-containing amino-acids in solid-state magic-angle spinning (MAS) NMR. A filtering block that selects methyl resonances is introduced in two-dimensional (2D) (13)C-homonuclear and (15)N-(13)C hete...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-006-9078-x
更新日期:2006-11-01 00:00:00
abstract::Sample solubility is essential for structural studies of proteins by solution NMR. Attachment of a solubility enhancement tag, such as GB1, MBP and thioredoxin, to a target protein has been used for this purpose. However, signal overlap of the tag with the target protein often made the spectral analysis difficult. Her...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-008-9296-5
更新日期:2009-03-01 00:00:00
abstract::Protein molecules sample different conformations in solution and characterizing these conformations is crucial to understanding protein function. 15N CEST experiments are now routinely used to study slow conformational exchange of protein molecules between a 'visible' major state and 'invisible' minor states. These ex...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-018-00223-3
更新日期:2019-02-01 00:00:00
abstract::Although dynamic nuclear polarization (DNP) has dramatically enhanced solid-state NMR spectral sensitivities of many synthetic materials and some biological macromolecules, recent studies of membrane-protein DNP using exogenously doped paramagnetic radicals as polarizing agents have reported varied and sometimes surpr...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-016-0023-3
更新日期:2016-03-01 00:00:00
abstract::HNCO/HNCACO type correlation experiments are an alternative for assignment of backbone resonances in extensively deuterated proteins in the solid-state, given the fact that line widths on the order of 14-17 Hz are achieved in the carbonyl dimension without the need of high power decoupling. The achieved resolution dem...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-010-9404-1
更新日期:2010-05-01 00:00:00
abstract::Extensive resonance overlap exacerbates assignment of intrinsically disordered proteins (IDPs). This issue can be circumvented by utilizing (15)N, (13)C' and (1)H(N) spins, where the chemical shift dispersion is mainly dictated by the characteristics of consecutive amino acid residues. Especially (15)N and (13)C' spin...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-011-9470-z
更新日期:2011-02-01 00:00:00
abstract::The efficiency of cell-free protein synthesis combined with combinatorial selective 15N-labelling provides a method for the rapid assignment of 15N-HSQC cross-peaks to the 19 different non-proline amino-acid types from five 15N-HSQC spectra. This strategy was explored with two different constructs of the C-terminal do...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-005-5021-9
更新日期:2006-01-01 00:00:00
abstract::Nearly complete backbone 1H, 15N and 13C signal assignments are reported for beta-hydroxydecanoyl thiol ester dehydrase, a 39-kDa homodimer containing 342 amino acids. Although 15N relaxation data show that the protein has a rotational correlation time of 18 ns, assignments were derived from triple-resonance experimen...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/BF00200435
更新日期:1996-06-01 00:00:00
abstract::During the past three years it has become possible to compute ab initio the 13C, 15N and 19F NMR chemical shifts of many sites in native proteins. Chemical shifts are beginning to become a useful supplement to more established methods of solution structure determination, and may find utility in solid-state analysis as...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章,评审
doi:10.1007/BF00211749
更新日期:1995-04-01 00:00:00
abstract::An improved version of the three-dimensional HCCH-COSY NMR experiment is described that correlates the resonances of geminal and vicinal proton pairs with the chemical shift of the 13C nucleus attached to one of the protons. The experiment uses constant-time evolution of transverse 13C magnetization which optimizes tr...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/BF01875522
更新日期:1991-09-01 00:00:00
abstract::We present and test two methods to use quantum chemical calculations to improve standard protein structure refinement by molecular dynamics simulations restrained to experimental NMR data. In the first, we replace the molecular mechanics force field (employed in standard refinement to supplement experimental data) for...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-004-6729-7
更新日期:2005-02-01 00:00:00
abstract::An approach to the determination of the 2-(13)C' chemical shift (CS) tensor orientation in pyrimidine bases via heteronuclear MAS NMR spectroscopy is presented. Considering a dipolar coupled spin 1/2 network of the type S1-I-S2 consisting of directly bonded heteronuclear spins, we have carried out numerical simulation...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1008318530946
更新日期:2000-10-01 00:00:00
abstract::Four novel amino acid type-selective triple resonance experiments to identify the backbone amino proton and nitrogen resonances of Arg and Lys and of their sequential neighbors in (13C,15N)-labeled proteins are presented: the R(i+1)-HSQC and R(i,i+1)-HSQC select signals originating from Arg side chains, the K(i+1)-HSQ...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1011206131623
更新日期:2001-08-01 00:00:00
abstract::We recently engineered encodable lanthanide binding tags (LBTs) into proteins and demonstrated their applicability in Nuclear Magnetic Resonance (NMR) spectroscopy, X-ray crystallography and luminescence studies. Here, we engineered two-loop-LBTs into the model protein interleukin-1β (IL1β) and measured (1)H, (15)N-ps...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-015-9984-x
更新日期:2015-11-01 00:00:00
abstract::Great theoretical and methodological advances are pushing the limits of resolution and sensitivity in solid state NMR (SSNMR). However, sample preparation remains a critical issue for the success of an experiment. The factors affecting spectral quality in SSNMR samples are discussed, examining cases encountered in the...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-013-9776-0
更新日期:2013-10-01 00:00:00
abstract::The interference between conformational exchange-induced time-dependent variations of chemical shifts in a pair of scalar coupled 1H and 15N spins is used to construct novel TROSY-type NMR experiments to suppress NMR signal loss in [15N,1H]-correlation spectra of a 14-mer DNA duplex free in solution and complexed with...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1011208109853
更新日期:2001-07-01 00:00:00
abstract::The biological environment in which a protein performs its function is a crowded milieu containing millions of molecules that can potentially lead to a great many transient, non-specific interactions. NMR spectroscopy is especially well suited to study these weak molecular contacts. Here, non-specific interactions bet...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-013-9705-2
更新日期:2013-03-01 00:00:00
abstract::Two new techniques offering considerable improvements in the quality of 1H photo-CIDNP spectra of proteins are demonstrated. Both focus on the problem of progressive photo-degradation of the flavin dye used to generate polarization in exposed tryptophan, tyrosine and histidine side-chains. One approach uses rapid addi...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1008351128089
更新日期:2000-03-01 00:00:00
abstract::Residual dipolar couplings provide complementary information to the nuclear Overhauser effect measurements that are traditionally used in biomolecular structure determination by NMR. In a de novo structure determination, however, lack of knowledge about the degree and orientation of molecular alignment complicates the...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-007-9215-1
更新日期:2008-02-01 00:00:00
abstract::In our previous work, we proposed a new way to represent protein native states, using ensembles of a small number of conformations with relative Populations, or ESP in short. Using Ubiquitin as an example, we showed that using a small number of conformations could greatly reduce the potential of overfitting and assign...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-015-9993-9
更新日期:2015-12-01 00:00:00
abstract::Simple pulse schemes are presented for the measurement of methyl (13)C and (1)H CSA values from (1)H-(13)C dipole/(13)C CSA and (1)H-(13)C dipole/(1)H CSA cross-correlated relaxation. The methodology is applied to protein L and malate synthase G. Average (13)C CSA values are considerably smaller for Ile than Leu/Val (...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-004-4349-x
更新日期:2004-12-01 00:00:00
abstract::13CHD2 methyl isotopomers are particularly useful to study methyl dynamics in proteins because, as compared with other methyl isotopomers, the 13C relaxation mechanism for this isotopomer is straightforward. However, in the case of proteins, where (omega tau)2 > 1, the refocused INEPT pulse sequence does not completel...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1012482426306
更新日期:2001-10-01 00:00:00
abstract::We present heteronuclear three-dimensional gradient-NMR techniques for the resonanceassignment of exchangeable (-OH and -NH) protons in uniformly 13C isotopically enrichedoligosaccharides and for the measurement of 1H-1H nuclear Overhauser enhancementsinvolving these protons. These techniques are derived from conventi...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/A:1018671517876
更新日期:1997-01-01 00:00:00