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 complicated and time consuming, in part due to the need for different software at the various analysis steps and for validating the results. Here, we present an integrated, cross-platform and open-source software that is significantly more versatile than the typical line shape fitting application. The software is a completely redesigned version of PINT ( https://pint-nmr.github.io/PINT/ ). It features a graphical user interface and includes functionality for peak picking, editing of peak lists and line shape fitting. In addition, the obtained peak intensities can be used directly to extract, for instance, relaxation rates, heteronuclear NOE values and exchange parameters. In contrast to most available software the entire process from spectral visualization to preparation of publication-ready figures is done solely using PINT and often within minutes, thereby, increasing productivity for users of all experience levels. Unique to the software are also the outstanding tools for evaluating the quality of the fitting results and extensive, but easy-to-use, customization of the fitting protocol and graphical output. In this communication, we describe the features of the new version of PINT and benchmark its performance.
journal_name
J Biomol NMRjournal_title
Journal of biomolecular NMRauthors
Niklasson M,Otten R,Ahlner A,Andresen C,Schlagnitweit J,Petzold K,Lundström Pdoi
10.1007/s10858-017-0141-6subject
Has Abstractpub_date
2017-10-01 00:00:00pages
93-99issue
2eissn
0925-2738issn
1573-5001pii
10.1007/s10858-017-0141-6journal_volume
69pub_type
杂志文章abstract：:Higher sensitivity of NMR spectrometers and novel isotopic labeling schemes have ushered the development of rapid data acquisition methodologies, improving the time resolution with which NMR data can be acquired. For nucleic acids, longitudinal relaxation optimization in conjunction with Ernst angle excitation (SOFAST...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-014-9856-9
更新日期：2014-11-01 00:00:00
abstract：:Silkworms serve as promising bioreactors for the production of recombinant proteins, including glycoproteins and membrane proteins, for structural and functional protein analyses. However, lack of methodology for stable isotope labeling has been a major deterrent to using this expression system for nuclear magnetic re...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-015-9930-y
更新日期：2015-06-01 00:00:00
abstract：:The solvent-exposed regions of (U-13C)ascomycin when bound to its putative target protein, FKBP, have been identified based on the different proton longitudinal relaxation rates (R1 = 1/T1) measured in the absence and presence of the paramagnetic relaxation reagent, 4-hydroxy-2,2,6,6-tetramethyl-piperidinyl-1-oxy (HyT...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF02192797
更新日期：1992-01-01 00:00:00
abstract：:We describe a general computational approach to site-specific resonance assignments in multidimensional NMR studies of uniformly (15)N,(13)C-labeled biopolymers, based on a simple Monte Carlo/simulated annealing (MCSA) algorithm contained in the program MCASSIGN2. Input to MCASSIGN2 includes lists of multidimensional ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-011-9517-1
更新日期：2011-07-01 00:00:00
abstract：:Protein expression in E. coli grown in shaker flasks is a routine and pivotal tool in many research laboratories. To maximize protein yields, cells are normally induced in the middle of the linear growth phase, typically at an OD600 of ≤ 1 for cells grown in Luria-Bertani (LB) medium at 37 °C. We recently showed that ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-019-00285-x
更新日期：2019-12-01 00:00:00
abstract：:The use of dipolar shifts as important constraints in refining molecular structure of paramagnetic metalloproteins by solution NMR is now well established. A crucial initial step in this procedure is the determination of the orientation. of the anisotropic paramagnetic susceptibility tensor in the molecular frame whic...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1008309121949
更新日期：2000-06-01 00:00:00
abstract：:Recent advances in the field of in-cell NMR spectroscopy have made it possible to study proteins in the context of bacterial or mammalian cell extracts or even entire cells. As most mammalian cells are part of a multi-cellular complex, there is a need to develop novel NMR approaches enabling the study of proteins with...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-020-00328-8
更新日期：2020-09-01 00:00:00
abstract：:The key to obtaining the model-free description of the dynamics of a macromolecule is the optimisation of the model-free and Brownian rotational diffusion parameters using the collected R (1), R (2) and steady-state NOE relaxation data. The problem of optimising the chi-squared value is often assumed to be trivial, ho...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-007-9214-2
更新日期：2008-02-01 00:00:00
abstract：:The NMR derived translational diffusion coefficients were performed on unlabeled and uniformly labeled 13C,15N human insulin in water, both in neat, with zinc ions only, and in pharmaceutical formulation, containing only m-cresol as phenolic ligand, glycerol and zinc ions. The results show the dominant role of the pH ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-018-0197-y
更新日期：2018-06-01 00:00:00
abstract：:As part of efforts to develop improved methods for NMR protein sample preparation and structure determination, the Northeast Structural Genomics Consortium (NESG) has implemented an NMR screening pipeline for protein target selection, construct optimization, and buffer optimization, incorporating efficient microscale ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-009-9386-z
更新日期：2010-01-01 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 discuss the optimum experimental conditions to obtain assignment spectra for solid proteins at magic-angle spinning (MAS) frequencies around 100 kHz. We present a systematic examination of the MAS dependence of the amide proton T 2' times and a site-specific comparison of T 2' at 93 kHz versus 60 kHz MAS frequency....
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-015-9975-y
更新日期：2015-10-01 00:00:00
abstract：:Under the condition that the longitudinal relaxation time of spin I is shorter than the longitudinal relaxation time of spin S the steady-state magnetization in [S,I]-TROSY-type experiments can be enhanced by intermediate storage of a part of the steady-state magnetization of spin I on spin S with a pulse sequence ele...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1012431013082
更新日期：2001-10-01 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：: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：:For biomolecular NMR structures typically only a poor correspondence is observed between statistics derived from the experimental input data and structural quality indicators obtained from the structure ensembles. Here, we investigate the relationship between the amount of available NMR data and structure quality. By ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-005-2826-5
更新日期：2005-10-01 00:00:00
abstract：:Methyl groups have emerged as powerful probes of protein dynamics with timescales from picoseconds to seconds. Typically, studies involving high molecular weight complexes exploit (13)CH3- or (13)CHD2-labeling in otherwise highly deuterated proteins. The (13)CHD2 label offers the unique advantage of providing (13)C, (...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-016-0038-9
更新日期：2016-06-01 00:00:00
abstract：:2D 15N-1H correlation spectra are ideal for measuring backbone amide populations to determine amide exchange protection factors in studies of protein folding or other structural features. Most protein NMR spectroscopists use HSQC, which has been shown to be generally superior to HMQC in both resolution and sensitivity...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00182288
更新日期：1995-06-01 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：:Adiabatic pulses have been widely used for broadband decoupling and spin inversion at high magnetic fields. In this paper we propose adiabatic pulses and supercycles that can be used at high magnetic fields like 800 or 900 MHz to obtain broadband TOCSY sequences with C,C or H,H J-transfer. The new mixing sequences are...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1026785725363
更新日期：2000-11-01 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：: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 discovery of the TROSY effect (Pervushin et al. in Proc Natl Acad Sci USA 94:12366-12371, 1997) for reducing transverse relaxation and line sharpening through selecting pathways in which dipole-dipole and CSA Hamiltonians partially cancel each other had a tremendous impact on solution NMR studies of macromolecules...
journal_title：Journal of biomolecular NMR
pub_type： 信件
doi：10.1007/s10858-016-0075-4
更新日期：2016-12-01 00:00:00
abstract：:Intramolecular correlations among the (18)O-labels of metabolic oligophosphates, mapped by J-decoupled (31)P NMR 2D chemical shift correlation spectroscopy, impart stringent constraints to the (18)O-isotope distributions over the whole oligophosphate moiety. The multiple deduced correlations of isotopic labels enable ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-011-9515-3
更新日期：2011-07-01 00:00:00
abstract：:A new homonuclear Hartmann-Hahn-type mixing scheme is introduced that effects coherence transfer between resonances in two separated frequency bands. The mixing scheme relies on the irradiation of two-band selective shaped pulses that are expanded in an MLEV-16 supercycle. Similar to heteronuclear Hartmann-Hahn experi...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00211162
更新日期：1996-09-01 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：: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：: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：:Based on high-resolution structures of the free molecules accurate determination of structures of protein complexes by NMR spectroscopy is possible using residual dipolar couplings. In order, however, to be able to apply these methods, protein backbone resonances have to be assigned first. This NMR assignment process ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1024768328860
更新日期：2003-09-01 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
