Literature DB >> 23657843

PINT: a software for integration of peak volumes and extraction of relaxation rates.

Alexandra Ahlner1, Mats Carlsson, Bengt-Harald Jonsson, Patrik Lundström.   

Abstract

We present the software Peak INTegration (PINT), designed to perform integration of peaks in NMR spectra. The program is very simple to run, yet powerful enough to handle complicated spectra. Peaks are integrated by fitting predefined line shapes to experimental data and the fitting can be customized to deal with, for instance, heavily overlapped peaks. The results can be inspected visually, which facilitates systematic optimization of the line shape fitting. Finally, integrated peak volumes can be used to extract parameters such as relaxation rates and information about low populated states. The utility of PINT is demonstrated by applications to the 59 residue SH3 domain of the yeast protein Abp1p and the 289 residue kinase domain of murine EphB2.

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Year:  2013        PMID: 23657843     DOI: 10.1007/s10858-013-9737-7

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  11 in total

1.  The design of a hyperstable mutant of the Abp1p SH3 domain by sequence alignment analysis.

Authors:  A Rath; A R Davidson
Journal:  Protein Sci       Date:  2000-12       Impact factor: 6.725

2.  MUNIN: application of three-way decomposition to the analysis of heteronuclear NMR relaxation data.

Authors:  D M Korzhneva; I V Ibraghimov; M Billeter; V Y Orekhov
Journal:  J Biomol NMR       Date:  2001-11       Impact factor: 2.835

Review 3.  New tools provide new insights in NMR studies of protein dynamics.

Authors:  Anthony Mittermaier; Lewis E Kay
Journal:  Science       Date:  2006-04-14       Impact factor: 47.728

4.  An improved 15N relaxation dispersion experiment for the measurement of millisecond time-scale dynamics in proteins.

Authors:  D Flemming Hansen; Pramodh Vallurupalli; Lewis E Kay
Journal:  J Phys Chem B       Date:  2007-11-15       Impact factor: 2.991

5.  Fractional volume integration in two-dimensional NMR spectra: CAKE, a Monte Carlo approach.

Authors:  Rocco Romano; Debora Paris; Fausto Acernese; Fabrizio Barone; Andrea Motta
Journal:  J Magn Reson       Date:  2008-03-21       Impact factor: 2.229

6.  Automated peak picking and peak integration in macromolecular NMR spectra using AUTOPSY.

Authors:  R Koradi; M Billeter; M Engeli; P Güntert; K Wüthrich
Journal:  J Magn Reson       Date:  1998-12       Impact factor: 2.229

7.  Eph receptors and ligands comprise two major specificity subclasses and are reciprocally compartmentalized during embryogenesis.

Authors:  N W Gale; S J Holland; D M Valenzuela; A Flenniken; L Pan; T E Ryan; M Henkemeyer; K Strebhardt; H Hirai; D G Wilkinson; T Pawson; S Davis; G D Yancopoulos
Journal:  Neuron       Date:  1996-07       Impact factor: 17.173

8.  Evidence for physical and functional interactions among two Saccharomyces cerevisiae SH3 domain proteins, an adenylyl cyclase-associated protein and the actin cytoskeleton.

Authors:  T Lila; D G Drubin
Journal:  Mol Biol Cell       Date:  1997-02       Impact factor: 4.138

9.  Homology of a yeast actin-binding protein to signal transduction proteins and myosin-I.

Authors:  D G Drubin; J Mulholland; Z M Zhu; D Botstein
Journal:  Nature       Date:  1990-01-18       Impact factor: 49.962

10.  NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

Authors:  F Delaglio; S Grzesiek; G W Vuister; G Zhu; J Pfeifer; A Bax
Journal:  J Biomol NMR       Date:  1995-11       Impact factor: 2.835

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  29 in total

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Authors:  Ashish Kabra; Efsita Rumpa; Ying Li
Journal:  J Biol Chem       Date:  2020-02-18       Impact factor: 5.157

2.  Fractional enrichment of proteins using [2-(13)C]-glycerol as the carbon source facilitates measurement of excited state 13Cα chemical shifts with improved sensitivity.

Authors:  Alexandra Ahlner; Cecilia Andresen; Shahid N Khan; Lewis E Kay; Patrik Lundström
Journal:  J Biomol NMR       Date:  2015-05-20       Impact factor: 2.835

3.  Measuring the signs of the methyl 1H chemical shift differences between major and 'invisible' minor protein conformational states using methyl 1H multi-quantum spectroscopy.

Authors:  Anusha B Gopalan; Pramodh Vallurupalli
Journal:  J Biomol NMR       Date:  2018-03-21       Impact factor: 2.835

4.  A methyl 1H double quantum CPMG experiment to study protein conformational exchange.

Authors:  Anusha B Gopalan; Tairan Yuwen; Lewis E Kay; Pramodh Vallurupalli
Journal:  J Biomol NMR       Date:  2018-10-01       Impact factor: 2.835

5.  Structural features of Argonaute-GW182 protein interactions.

Authors:  Janina Pfaff; Janosch Hennig; Franz Herzog; Ruedi Aebersold; Michael Sattler; Dierk Niessing; Gunter Meister
Journal:  Proc Natl Acad Sci U S A       Date:  2013-09-16       Impact factor: 11.205

6.  Pre-Anchoring of Pin1 to Unphosphorylated c-Myc in a Fuzzy Complex Regulates c-Myc Activity.

Authors:  Sara Helander; Meri Montecchio; Robert Pilstål; Yulong Su; Jacob Kuruvilla; Malin Elvén; Javed M E Ziauddin; Madhanagopal Anandapadamanaban; Susana Cristobal; Patrik Lundström; Rosalie C Sears; Björn Wallner; Maria Sunnerhagen
Journal:  Structure       Date:  2015-11-19       Impact factor: 5.006

7.  Structure and dynamics of the platelet integrin-binding C4 domain of von Willebrand factor.

Authors:  Emma-Ruoqi Xu; Sören von Bülow; Po-Chia Chen; Peter J Lenting; Katra Kolšek; Camilo Aponte-Santamaría; Bernd Simon; Jaelle Foot; Tobias Obser; Reinhard Schneppenheim; Frauke Gräter; Cécile V Denis; Matthias Wilmanns; Janosch Hennig
Journal:  Blood       Date:  2018-10-10       Impact factor: 22.113

8.  Dynamic ion pair behavior stabilizes single α-helices in proteins.

Authors:  Matthew Batchelor; Marcin Wolny; Emily G Baker; Emanuele Paci; Arnout P Kalverda; Michelle Peckham
Journal:  J Biol Chem       Date:  2018-12-28       Impact factor: 5.157

9.  Conformational Dynamics of Deubiquitinase A and Functional Implications.

Authors:  Ashish Kabra; Ying Li
Journal:  Biochemistry       Date:  2021-01-08       Impact factor: 3.162

10.  Probing the Transition State in Enzyme Catalysis by High-Pressure NMR Dynamics.

Authors:  John B Stiller; S Jordan Kerns; Marc Hoemberger; Young-Jin Cho; Renee Otten; Michael F Hagan; Dorothee Kern
Journal:  Nat Catal       Date:  2019-06-24
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