Literature DB >> 25129623

Effective strategy to assign ¹H- ¹⁵N heteronuclear correlation NMR signals from lysine side-chain NH3₃⁺ groups of proteins at low temperature.

Alexandre Esadze1, Levani Zandarashvili, Junji Iwahara.   

Abstract

Recent studies have shown that lysine side-chain NH3(+) groups are excellent probes for NMR investigations of dynamics involving hydrogen bonds and ion pairs relevant to protein function. However, due to rapid hydrogen exchange, observation of (1)H-(15)N NMR cross peaks from lysine NH3(+) groups often requires use of a relatively low temperature, which renders difficulty in resonance assignment. Here we present an effective strategy to assign (1)H and (15)N resonances of NH3(+) groups at low temperatures. This strategy involves two new (1)H/(13)C/(15)N triple-resonance experiments for lysine side chains. Application to a protein-DNA complex is demonstrated.

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Year:  2014        PMID: 25129623      PMCID: PMC4160661          DOI: 10.1007/s10858-014-9854-y

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


  19 in total

1.  Domain packing and dynamics in the DNA complex of the N-terminal zinc fingers of TFIIIA.

Authors:  M P Foster; D S Wuttke; I Radhakrishnan; D A Case; J M Gottesfeld; P E Wright
Journal:  Nat Struct Biol       Date:  1997-08

Review 2.  NMR studies on the dynamics of hydrogen bonds and ion pairs involving lysine side chains of proteins.

Authors:  Levani Zandarashvili; Alexandre Esadze; Junji Iwahara
Journal:  Adv Protein Chem Struct Biol       Date:  2013       Impact factor: 3.507

3.  Short selective pulses for biochemical applications.

Authors:  E Kupce; J Boyd; I D Campbell
Journal:  J Magn Reson B       Date:  1995-03

4.  CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data.

Authors:  Jing Huang; Alexander D MacKerell
Journal:  J Comput Chem       Date:  2013-07-06       Impact factor: 3.376

5.  Stopped-flow fluorescence kinetic study of protein sliding and intersegment transfer in the target DNA search process.

Authors:  Alexandre Esadze; Junji Iwahara
Journal:  J Mol Biol       Date:  2013-09-25       Impact factor: 5.469

6.  Heteronuclear NMR spectroscopy for lysine NH(3) groups in proteins: unique effect of water exchange on (15)N transverse relaxation.

Authors:  Junji Iwahara; Young-Sang Jung; G Marius Clore
Journal:  J Am Chem Soc       Date:  2007-02-15       Impact factor: 15.419

7.  Unambiguous determination of the ionization state of a glycoside hydrolase active site lysine by 1H-15N heteronuclear correlation spectroscopy.

Authors:  David K Y Poon; Mario Schubert; Jason Au; Mark Okon; Stephen G Withers; Lawrence P McIntosh
Journal:  J Am Chem Soc       Date:  2006-12-06       Impact factor: 15.419

8.  Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions.

Authors:  M Piotto; V Saudek; V Sklenár
Journal:  J Biomol NMR       Date:  1992-11       Impact factor: 2.835

9.  Residue-specific pKa determination of lysine and arginine side chains by indirect 15N and 13C NMR spectroscopy: application to apo calmodulin.

Authors:  Ingemar André; Sara Linse; Frans A A Mulder
Journal:  J Am Chem Soc       Date:  2007-11-29       Impact factor: 15.419

10.  Positive and negative impacts of nonspecific sites during target location by a sequence-specific DNA-binding protein: origin of the optimal search at physiological ionic strength.

Authors:  Alexandre Esadze; Catherine A Kemme; Anatoly B Kolomeisky; Junji Iwahara
Journal:  Nucleic Acids Res       Date:  2014-05-16       Impact factor: 16.971

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  13 in total

1.  Balancing between affinity and speed in target DNA search by zinc-finger proteins via modulation of dynamic conformational ensemble.

Authors:  Levani Zandarashvili; Alexandre Esadze; Dana Vuzman; Catherine A Kemme; Yaakov Levy; Junji Iwahara
Journal:  Proc Natl Acad Sci U S A       Date:  2015-08-31       Impact factor: 11.205

2.  Direct detection of lysine side chain NH3+ in protein-heparin complexes using NMR spectroscopy.

Authors:  Krishna Mohan Sepuru; Junji Iwahara; Krishna Rajarathnam
Journal:  Analyst       Date:  2018-01-02       Impact factor: 4.616

3.  pH-dependent random coil (1)H, (13)C, and (15)N chemical shifts of the ionizable amino acids: a guide for protein pK a measurements.

Authors:  Gerald Platzer; Mark Okon; Lawrence P McIntosh
Journal:  J Biomol NMR       Date:  2014-09-20       Impact factor: 2.835

Review 4.  NMR Methods for Characterizing the Basic Side Chains of Proteins: Electrostatic Interactions, Hydrogen Bonds, and Conformational Dynamics.

Authors:  Dan Nguyen; Chuanying Chen; B Montgomery Pettitt; Junji Iwahara
Journal:  Methods Enzymol       Date:  2018-09-27       Impact factor: 1.600

5.  A chemical approach for site-specific identification of NMR signals from protein side-chain NH₃⁺ groups forming intermolecular ion pairs in protein-nucleic acid complexes.

Authors:  Kurtis M Anderson; Dan Nguyen; Alexandre Esadze; Levani Zandrashvili; David G Gorenstein; Junji Iwahara
Journal:  J Biomol NMR       Date:  2015-02-19       Impact factor: 2.835

6.  Site-Specific Detection and Characterization of Ubiquitin Carbamylation.

Authors:  Westley Pawloski; Teppei Komiyama; Christos Kougentakis; Ananya Majumdar; David Fushman
Journal:  Biochemistry       Date:  2022-04-05       Impact factor: 3.321

7.  Conformational Dynamics and the Binding of Specific and Nonspecific DNA by the Autoinhibited Transcription Factor Ets-1.

Authors:  Geneviève Desjardins; Mark Okon; Barbara J Graves; Lawrence P McIntosh
Journal:  Biochemistry       Date:  2016-07-15       Impact factor: 3.162

8.  Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate.

Authors:  Levani Zandarashvili; Dan Nguyen; Kurtis M Anderson; Mark A White; David G Gorenstein; Junji Iwahara
Journal:  Biophys J       Date:  2015-09-01       Impact factor: 4.033

9.  Changes in conformational dynamics of basic side chains upon protein-DNA association.

Authors:  Alexandre Esadze; Chuanying Chen; Levani Zandarashvili; Sourav Roy; B Montgometry Pettitt; Junji Iwahara
Journal:  Nucleic Acids Res       Date:  2016-06-10       Impact factor: 16.971

Review 10.  Physicochemical Properties of Ion Pairs of Biological Macromolecules.

Authors:  Junji Iwahara; Alexandre Esadze; Levani Zandarashvili
Journal:  Biomolecules       Date:  2015-09-30
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