Literature DB >> 16807015

Revisiting the initial rate approximation in kinetic NOE measurements.

Haitao Hu1, Krish Krishnamurthy.   

Abstract

The nuclear Overhauser effect (NOE) is undoubtedly one of the most useful tools in NMR spectroscopy and is widely used in solving structural and conformational problems of small organic molecules and macromolecular systems alike. In particular, measurement of the kinetics of the NOE, often facilitated by selective 1D NOE buildup experiments, can generate invaluable quantitative distance information for the molecule being investigated. In practice, analysis of such kinetic NOE data routinely assumes a first-order approximation of the initial buildup rate. However, often times such an approximation holds true only for the shortest mixing times. As shown by Macura and others, the linear range of the NOE buildup obtained from 2D NOESY and exchange experiments can be substantially extended by simply scaling the NOE cross-peaks against the corresponding diagonal peaks. In this note, we demonstrate through a detailed analysis that the same approach can be applied to the analysis of 1D NOE data obtained with the DPFGSE NOE pulse sequence, one of the most widely used selective 1D NOE experiments today. We show that this approach allows the inclusion of data points acquired with much longer mixing times in the analysis and thus considerably improves the accuracy of the measured cross-relaxation rates and internuclear distances, while considerably simplifying the data analysis. Similar results can be obtained for the rotating frame DPFGSE ROE experiment.

Entities:  

Year:  2006        PMID: 16807015     DOI: 10.1016/j.jmr.2006.06.009

Source DB:  PubMed          Journal:  J Magn Reson        ISSN: 1090-7807            Impact factor:   2.229


  16 in total

1.  Exploiting Uniformly 13C-Labeled Carbohydrates for Probing Carbohydrate-Protein Interactions by NMR Spectroscopy.

Authors:  Gustav Nestor; Taigh Anderson; Stefan Oscarson; Angela M Gronenborn
Journal:  J Am Chem Soc       Date:  2017-04-21       Impact factor: 15.419

2.  Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations.

Authors:  Mingjun Yang; Thibault Angles d'Ortoli; Elin Säwén; Madhurima Jana; Göran Widmalm; Alexander D MacKerell
Journal:  Phys Chem Chem Phys       Date:  2016-06-27       Impact factor: 3.676

3.  Thiolactomycin-based β-ketoacyl-AcpM synthase A (KasA) inhibitors: fragment-based inhibitor discovery using transient one-dimensional nuclear overhauser effect NMR spectroscopy.

Authors:  Kanishk Kapilashrami; Gopal R Bommineni; Carl A Machutta; Pilho Kim; Cheng-Tsung Lai; Carlos Simmerling; Francis Picart; Peter J Tonge
Journal:  J Biol Chem       Date:  2013-01-10       Impact factor: 5.157

4.  Importance of Binding Site Hydration and Flexibility Revealed When Optimizing a Macrocyclic Inhibitor of the Keap1-Nrf2 Protein-Protein Interaction.

Authors:  Fabio Begnini; Stefan Geschwindner; Patrik Johansson; Lisa Wissler; Richard J Lewis; Emma Danelius; Andreas Luttens; Pierre Matricon; Jens Carlsson; Stijn Lenders; Beate König; Anna Friedel; Peter Sjö; Stefan Schiesser; Jan Kihlberg
Journal:  J Med Chem       Date:  2022-02-02       Impact factor: 7.446

5.  Structure elucidation of β-cyclodextrin-xylazine complex by a combination of quantitative (1)H-(1)H ROESY and molecular dynamics studies.

Authors:  Syed Mashhood Ali; Kehkeshan Fatma; Snehal Dhokale
Journal:  Beilstein J Org Chem       Date:  2013-09-23       Impact factor: 2.883

Review 6.  Modern Technologies of Solution Nuclear Magnetic Resonance Spectroscopy for Three-dimensional Structure Determination of Proteins Open Avenues for Life Scientists.

Authors:  Toshihiko Sugiki; Naohiro Kobayashi; Toshimichi Fujiwara
Journal:  Comput Struct Biotechnol J       Date:  2017-04-13       Impact factor: 7.271

7.  Host-guest complexes between cryptophane-C and chloromethanes revisited.

Authors:  Z Takacs; M Soltesova; J Kowalewski; J Lang; T Brotin; J-P Dutasta
Journal:  Magn Reson Chem       Date:  2012-11-07       Impact factor: 2.447

8.  Bacterial Autoimmune Drug Metabolism Transforms an Immunomodulator into Structurally and Functionally Divergent Antibiotics.

Authors:  Hyun Bong Park; Tyler N Goddard; Joonseok Oh; Jaymin Patel; Zheng Wei; Corey E Perez; Brandon Q Mercado; Rurun Wang; Thomas P Wyche; Grazia Piizzi; Richard A Flavell; Jason M Crawford
Journal:  Angew Chem Int Ed Engl       Date:  2020-03-17       Impact factor: 16.823

9.  NMR investigation of chloromethane complexes of cryptophane-A and its analogue with butoxy groups.

Authors:  Z Takacs; E Steiner; J Kowalewski; T Brotin
Journal:  J Phys Chem B       Date:  2014-02-12       Impact factor: 2.991

10.  Conformational properties of α- or β-(1→6)-linked oligosaccharides: Hamiltonian replica exchange MD simulations and NMR experiments.

Authors:  Dhilon S Patel; Robert Pendrill; Sairam S Mallajosyula; Göran Widmalm; Alexander D MacKerell
Journal:  J Phys Chem B       Date:  2014-03-05       Impact factor: 2.991

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.