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 assigning relative populations to protein ensembles could significantly improve their quality. To demonstrate that ESP indeed is an excellent alternative to represent protein native states, in this work we compare the quality of two ESP ensembles of Ubiquitin with several well-known regular ensembles or average structure representations. Extensive amount of significant experimental data are employed to achieve a thorough assessment. Our results demonstrate that ESP ensembles, though much smaller in size comparing to regular ensembles, perform equally or even better sometimes in all four different types of experimental data used in the assessment, namely, the residual dipolar couplings, residual chemical shift anisotropy, hydrogen exchange rates, and solution scattering profiles. This work further underlines the significance of having relative populations in describing the native states.
journal_name
J Biomol NMRjournal_title
Journal of biomolecular NMRauthors
Vammi V,Song Gdoi
10.1007/s10858-015-9993-9subject
Has Abstractpub_date
2015-12-01 00:00:00pages
341-351issue
4eissn
0925-2738issn
1573-5001pii
10.1007/s10858-015-9993-9journal_volume
63pub_type
杂志文章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：:To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of (13)C(alpha) chemical shifts, we selected the structure of the nucleic acid binding (NAB) protein from the SARS coronavirus determined by NMR in solution (PDB id 2K87). NAB is a 116-residue alpha/beta protein, which contains 9 prolines...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-010-9435-7
更新日期：2010-09-01 00:00:00
abstract：:No matter the source of compounds, drug discovery campaigns focused directly on the target are entirely dependent on a consistent stream of reliable data that reports on how a putative ligand interacts with the protein of interest. The data will derive from many sources including enzyme assays and many types of biophy...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-020-00343-9
更新日期：2020-11-01 00:00:00
abstract：:We have developed an approach for simultaneous structure calculation and automatic Nuclear Overhauser Effect (NOE) assignment to solve nuclear magnetic resonance (NMR) structures from unassigned NOESY data. The approach, autoNOE-Rosetta, integrates Resolution Adapted Structural RECombination (RASREC) Rosetta NMR calcu...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-014-9833-3
更新日期：2014-07-01 00:00:00
abstract：:Melittin is a naturally occurring hexacosa peptide which forms an amphiphilic helix in methanol, a random coil in water, and a tetramer of helices at basic pH or in the presence of a high salt concentration. The monomeric structure in methanol has been well characterized by proton NMR (Pastore et al. (1989) Eur. Bioph...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00198369
更新日期：1993-11-01 00:00:00
abstract：:Protein-nucleic acid interactions involve intermolecular ion pairs of protein side-chain and DNA or RNA phosphate groups. Using three protein-DNA complexes, we demonstrate that site-specific oxygen-to-sulfur substitution in phosphate groups allows for identification of NMR signals from the protein side-chain NH3 (+) g...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-015-9909-8
更新日期：2015-05-01 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：:Activated dynamics plays a central role in protein function, where transitions between distinct conformations often underlie the switching between active and inactive states. The characteristic time scales of these transitions typically fall in the microsecond to millisecond range, which is amenable to investigations ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-013-9764-4
更新日期：2013-09-01 00:00:00
abstract：:Protein structure determination by NMR methods has started in the mid-eighties and has been growing steadily since then. Ca. 14% of the protein structures deposited in the PDB have been solved by NMR. The evaluation of the quality of NMR structures however is still lacking a well-established practice. In this work, we...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-008-9228-4
更新日期：2008-04-01 00:00:00
abstract：:The transmembrane protein YuaF from B. subtilis is a member of the NfeD-like clan with a potential role in maintaining membrane integrity during conditions of cellular stress. nfeD-genes are primarily found in highly conserved operon structures together with the gene of another membrane protein belonging to the SPFH s...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-008-9261-3
更新日期：2008-09-01 00:00:00
abstract：:Although beta-lactoglobulin (beta-LG) has been studied extensively for more than 50 years, its physical properties in solution are not yet understood fully in terms of its three-dimensional (3D) structure. For example, despite a recent high-resolution crystal structure, it is still not clear why the two common variant...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1008268528695
更新日期：1998-07-01 00:00:00
abstract：:Accessible surface area (ASA) is the surface area of an atom, amino acid or biomolecule that is exposed to solvent. The calculation of a molecule's ASA requires three-dimensional coordinate data and the use of a "rolling ball" algorithm to both define and calculate the ASA. For polymers such as proteins, the ASA for i...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-015-9957-0
更新日期：2015-07-01 00:00:00
abstract：:A simple triple resonance NMR experiment that leads to the correlation of the backbone amide resonances of each amino acid residue 'i' with that of residues 'i-1' and 'i+1' in ((13)C, (15)N) labelled intrinsically disordered proteins (IDPs) is presented. The experimental scheme, {HN-NCA heteronuclear TOCSY-NH}, exploi...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-015-9976-x
更新日期：2015-10-01 00:00:00
abstract：:Dynamics of large-amplitude conformational motions in proteins are complex and less understood, although these processes are intimately associated with structure, folding, stability, and function of proteins. Here, we use a large set of spectra obtained by cross-relaxation suppressed exchange NMR spectroscopy (EXSY) t...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-007-9186-2
更新日期：2007-11-01 00:00:00
abstract：:NMR spectroscopy is uniquely suited for atomic resolution studies of biomolecules such as proteins, nucleic acids and metabolites, since detailed information on structure and dynamics are encoded in positions and line shapes of peaks in NMR spectra. Unfortunately, accurate determination of these parameters is often co...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-017-0141-6
更新日期：2017-10-01 00:00:00
abstract：:The importance of protein chemical shift values for the determination of three-dimensional protein structure has increased in recent years because of the large databases of protein structures with assigned chemical shift data. These databases have allowed the investigation of the quantitative relationship between chem...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1023060720156
更新日期：2003-05-01 00:00:00
abstract：:Sparse sampling in biomolecular multidimensional NMR offers increased acquisition speed and resolution and, if appropriate conditions are met, an increase in sensitivity. Sparse sampling of indirectly detected time domains combined with the direct truly multidimensional Fourier transform has elicited particular attent...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-011-9584-3
更新日期：2012-01-01 00:00:00
abstract：:The kinetics of lanthanide (III) exchange for calcium(II) in the C-terminal EF-hand of the protein calbindin D9k have been studied by one-dimensional (1D) stopped-flow NMR. By choosing a paramagnetic lanthanide (Ce3+), kinetics in the sub-second range can be easily measured. This is made possible by the fact that (i) ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1020245031235
更新日期：2002-08-01 00:00:00
abstract：:The present study deals with the relevance of using mobility-averaged dipolar couplings for the structure refinement of flexible proteins. The 68-residue protein p8MTCP1 has been chosen as model for this study. Its solution state consists mainly of three alpha-helices. The two N-terminal helices are strapped in a well...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1013821123201
更新日期：2002-01-01 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：:G protein-coupled receptors (GPCRs) are transmembrane signal transducers which regulate many key physiological process. Since their discovery, their analysis has been limited by difficulties in obtaining sufficient amounts of the receptors in high-quality, functional form from heterologous expression hosts. Albeit hig...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-020-00354-6
更新日期：2021-01-27 00:00:00
abstract：:The solution molecular structure of the four-iron ferredoxin (Fd) from the hyperthermophilic archaeon Thermococcus litoralis (Tl) has been investigated by 1H NMR spectroscopy. TOCSY and NOESY experiments in H2O, tailored to detect both weakly and strongly relaxed resonances, together with steady-state NOEs in both H2O...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00190455
更新日期：1996-01-01 00:00:00
abstract：:In order to understand the role of the glycans in glycoproteins in solution, structural information obtained by NMR spectroscopy is obviously required. However, the assignment of the NMR signals from the glycans in larger glycoproteins is still difficult, mainly due to the lack of appropriate methods for the assignmen...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1026776721348
更新日期：2000-12-01 00:00:00
abstract：:Senktide is a highly specific and potent analog of neurokinin B, the natural ligand of the tachykinin receptor NK-3. The membrane-bound conformation of senktide, interacting with negatively charged membrane vesicles composed of perdeuterated phosphatidylcholine and phosphatidylglycerol (70:30), has been investigated u...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00176010
更新日期：1993-07-01 00:00:00
abstract：:We propose a method for the determination of (15)N csa/dipolar cross-correlation rates based on the measurement of the two apparent transverse (or longitudinal) relaxation rates associated with each component of the nitrogen doublet (N(alpha) and N(beta)). This is achieved by inserting a spin state selective scheme in...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/b:jnmr.0000048948.66235.d9
更新日期：2004-10-01 00:00:00
abstract：:1H alpha, 13C alpha, and 15N alpha secondary shifts, defined as the difference between the observed value and the random coil value, have been calculated for interleukin-1 receptor antagonist protein and interleukin-1 beta. Averaging of the secondary chemical shifts with those of adjacent residues was used to smooth o...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF02192848
更新日期：1992-11-01 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：:NMR spectroscopy provides a powerful approach for the characterisation of chemical exchange and molecular interactions by analysis of series of experiments acquired over the course of a titration measurement. The appearance of NMR resonances undergoing chemical exchange depends on the frequency difference relative to ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-019-00297-7
更新日期：2020-01-01 00:00:00
abstract：:The 3D HCCH-TOCSY and HCC(CO)NH-TOCSY experiments provide through bond connectivity and are used for side-chain chemical shift assignment by solution-state NMR. Careful design and implementation of the pulse sequence are key to the successful application of the technique particularly when trying to extract the maximum...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-020-00310-4
更新日期：2020-05-01 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
