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 the use of high-resolution NMR methods to identify resonances near the metal binding site. We now describe structural features of the metal binding site that are not observable by standard NMR methods in native Pdx due to paramagnetic line broadening. These results provide the first example of high-resolution NMR-derived structural data concerning the metal binding domain of an Fe2S2 ferredoxin, and the first structural information of any sort for the metal binding site of a ferredoxin from this class, which includes adrenodoxin, placental ferredoxin and terpredoxin. Assignments were obtained by applying multidimensional NMR methods to a series of selectively and nonselectively 15N- and 13C/15N-labeled GaPdx samples. For most experiments, a mutant of Pdx was used in which a nonligating Cys85 is replaced by serine. All of the major structural features that were identified in native Pdx are conserved in GaPdx. The overall protein dynamics is considerably faster in GaPdx than in the native protein, as reflected by amide proton exchange rates. The C-terminal residue, Trp106, also exhibits considerable mobility, as indicated by 15N[1H] NOE and 15N T1 values of the C-terminal residue of the protein.
journal_name
J Biomol NMRjournal_title
Journal of biomolecular NMRauthors
Kazanis S,Pochapsky TCdoi
10.1023/a:1018369721091subject
Has Abstractpub_date
1997-06-01 00:00:00pages
337-46issue
4eissn
0925-2738issn
1573-5001journal_volume
9pub_type
杂志文章abstract：:Extensive spectral overlap presents a major problem for the NMR study of large RNAs. Here we present NMR techniques for resolution enhancement and spectral simplification of fully 13C labelled RNA. High-resolution 1H-13C correlation spectra are obtained by combining TROSY-type experiments with multiple-band-selective ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1008340210079
更新日期：2001-02-01 00:00:00
abstract：:The use of pulsed field gradients in multiple-pulse NMR experiments has many advantages, including the possibility of obtaining excellent water suppression without the need for selective presaturation. In such gradient experiments the water magnetization is dephased deliberately; exchange between the saturated protons...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00211750
更新日期：1995-04-01 00:00:00
abstract：:Protein-ligand titrations can readily be monitored with a trimethylsilyl (TMS) tag. Owing to the intensity, narrow line shape and unique chemical shift of a TMS group, dissociation constants can be determined from straightforward 1D 1H-NMR spectra not only in the fast but also in the slow exchange limit. The tag is ea...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-018-0173-6
更新日期：2018-04-01 00:00:00
abstract：:The ability to simultaneously measure many long-range distances is critical to efficient and accurate determination of protein structures by solid-state NMR (SSNMR). So far, the most common distance constraints for proteins are 13C-15N distances, which are usually measured using the rotational-echo double-resonance (R...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-018-0187-0
更新日期：2018-05-01 00:00:00
abstract：:Detection of (15)N in multidimensional NMR experiments of proteins has sparsely been utilized because of the low gyromagnetic ratio (γ) of nitrogen and the presumed low sensitivity of such experiments. Here we show that selecting the TROSY components of proton-attached (15)N nuclei (TROSY (15)NH) yields high quality s...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-015-9991-y
更新日期：2015-12-01 00:00:00
abstract：:Segmental isotopic labeling can facilitate NMR studies of large proteins, multi-domain proteins, and proteins with repetitive sequences by alleviating NMR signal overlaps. Segmental isotopic labeling also allows us to investigate an individual domain in the context of a full-length protein by NMR. Several established ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-018-0175-4
更新日期：2018-08-01 00:00:00
abstract：:Resonance assignment is a prerequisite for almost any NMR-based study of proteins. It can be very challenging in some cases, however, due to the nature of the protein under investigation. This is the case with intrinsically disordered proteins, for example, whose NMR spectra suffer from low chemical shifts dispersion ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-016-0024-2
更新日期：2016-03-01 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：:Joint refinement, i.e., the simultaneous refinement of a structure against both nuclear magnetic resonance (NMR) spectroscopic and X-ray crystallographic data, was performed on the HU protein from Bacillus stearothermophilus (HUBst). The procedure was aimed at investigating the compatibility of the two data sets and a...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1012927325963
更新日期：2001-11-01 00:00:00
abstract：:Understanding of the molecular mechanisms of protein function requires detailed insight into the conformational landscape accessible to the protein. Conformational changes can be crucial for biological processes, such as ligand binding, protein folding, and catalysis. NMR spectroscopy is exquisitely sensitive to such ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-018-0193-2
更新日期：2018-06-01 00:00:00
abstract：:Limitations in the applicability, accuracy, and precision of individual structure characterization methods can sometimes be overcome via an integrative modeling approach that relies on information from all available sources, including all available experimental data and prior models. The open-source Integrative Modeli...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-019-00264-2
更新日期：2019-07-01 00:00:00
abstract：:The systematic difference between T2 values obtained from CPMG and T1p experiments was observed for backbone 15N nuclei of bacterial ribonuclease barnase. Theoretical consideration suggests that the observed difference is caused by off-resonance effects of 180 degree pulses of the CPMG pulse train. Namely, at off-reso...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1008348827208
更新日期：2000-07-01 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：: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：:NMR spectra of ubiquitin in the presence of bicelles at a concentration of 32% w/v have been recorded at 700 MHz under sample spinning conditions at the magic angle (54.7 degrees ) and at an angle of 45.5 degrees . At the magic angle, the 1H-15N HSQC spectrum of ubiquitin in bicelles is virtually indistinguishable fro...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-005-3210-1
更新日期：2005-11-01 00:00:00
abstract：:We report here the backbone 1HN, 15N, 13C alpha, 13CO, and 1H alpha NMR assignments for the catalytic domain of human fibroblast collagenase (HFC). Three independent assignment pathways (matching 1H, 13C alpha, and 13CO resonances) were used to establish sequential connections. The connections using 13C alpha resonanc...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1018615400129
更新日期：1997-01-01 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：:NMR relaxometry plays crucial role in studies of protein dynamics. The measurement of longitudinal and transverse relaxation rates of [Formula: see text]N is the main source of information on backbone motions. However, even the most basic approach exploiting a series of [Formula: see text]N HSQC spectra can require se...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-017-0115-8
更新日期：2017-06-01 00:00:00
abstract：:We describe a new labeling method that allows for full protonation at the backbone Hα position, maintaining protein side chains with a high level of deuteration. We refer to the method as alpha proton exchange by transamination (α-PET) since it relies on transaminase activity demonstrated here using Escherichia coli e...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-019-00230-y
更新日期：2019-02-01 00:00:00
abstract：:Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion NMR experiments are extremely powerful for characterizing millisecond time-scale conformational exchange processes in biomolecules. A large number of such CPMG experiments have now emerged for measuring protein backbone chemical shifts of sparsely populated (>0.5%...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-009-9310-6
更新日期：2009-09-01 00:00:00
abstract：:We have developed a tool for computer-assisted assignments of protein NMR spectra from triple resonance data. The program is designed to resemble established manual assignment procedures as closely as possible. IBIS exports its results in XEASY format. Thus, using IBIS the operator has continuous visual and accounting...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1024078926886
更新日期：2003-08-01 00:00:00
abstract：:Four-dimensional NMR spectroscopy can be speeded up by a large factor by a projection-reconstruction technique related to that used in X-ray tomography. The limited amount of information recorded in a few suitably-tilted projection planes suffices to recreate the entire four-dimensional spectrum. The method is demonst...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/B:JNMR.0000015421.60023.e5
更新日期：2004-04-01 00:00:00
abstract：:Relaxation measurements of side-chain 13CH2-groups of uniformly 13C labeled human ubiquitin were performed at 600 MHz and 800 MHz magnetic field strength at 30 degrees C. Dipole-dipole cross-correlated relaxation effects in T1 experiments were suppressed by the combination of radio-frequency pulses and pulsed field gr...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1023833407515
更新日期：2003-07-01 00:00:00
abstract：:A procedure is presented for automated sequence-specific assignment of NMR resonances of uniformly [(13)C, (15)N]-labeled RNA. The method is based on a suite of four through-bond and two through-space high-dimensional automated projection spectroscopy (APSY) experiments. The approach is exemplified with a 0.3 mM sampl...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-014-9841-3
更新日期：2014-08-01 00:00:00
abstract：:Simulated neural networks are described which aid the assignment of protein NMR spectra. A network trained to recognize amino acid type from TOCSY data was trained on 148 assigned spin systems from E. coli acyl carrier proteins (ACPs) and tested on spin systems from spinach ACP, which has a 37% sequence homology with ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00178334
更新日期：1994-01-01 00:00:00
abstract：:An approach for the efficient implementation of RN(n)(nu) symmetry-based pulse schemes that are often employed for recoupling and decoupling of nuclear spin interactions in biological solid state NMR investigations is demonstrated at high magic-angle spinning frequencies. RF pulse sequences belonging to the RN(n)(nu) ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-009-9335-x
更新日期：2009-08-01 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：: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：:Human ATP-binding cassette, sub-family B, member 6 (ABCB6) is a mitochondrial ABC transporter, and presumably contributes to iron homeostasis. Aimed at understanding the structural basis for the conformational changes accompanying the substrate-transportation cycle, we have studied the C-terminal nucleotide-binding do...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-006-9000-6
更新日期：2006-05-01 00:00:00
abstract：:The (1)H, (13)C and (15)N NMR resonances of the backbone of serine protease PB92 have been assigned. This 269-residue protein is one of the largest monomeric proteins assigned so far. The amount and quality of information available suggest that even larger proteins could be assigned with present methods. Measured chem...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00178340
更新日期：1994-01-01 00:00:00
