Methyl Groups as Probes of Structure and Dynamics in NMR Studies of High-Molecular-Weight Proteins

ChemBioChem ◽  
2005 ◽  
Vol 6 (9) ◽  
pp. 1567-1577 ◽  
Author(s):  
Vitali Tugarinov ◽  
Lewis E. Kay
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
Methyl Groups ◽  
Nmr Studies ◽  
Structure And Dynamics ◽  
High Molecular Weight Proteins

scholarly journals A methyl-TROSY approach for NMR studies of high-molecular-weight DNA with application to the nucleosome core particle

2020 ◽  
Vol 117 (23) ◽  
pp. 12836-12846 ◽  
Author(s):  
Gili Abramov ◽  
Algirdas Velyvis ◽  
Enrico Rennella ◽  
Leo E. Wong ◽  
Lewis E. Kay
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
Methyl Groups ◽  
Core Particle ◽  
Nucleosome Core Particle ◽  
Nmr Studies ◽  
High Molecular Weight Dna ◽  
Nucleosome Core ◽  
Structure And Dynamics ◽  
Methyl Trosy

The development of methyl-transverse relaxation-optimized spectroscopy (methyl-TROSY)–based NMR methods, in concert with robust strategies for incorporation of methyl-group probes of structure and dynamics into the protein of interest, has facilitated quantitative studies of high-molecular-weight protein complexes. Here we develop a one-pot in vitro reaction for producing NMR quantities of methyl-labeled DNA at the C5 and N6 positions of cytosine (5mC) and adenine (6mA) nucleobases, respectively, enabling the study of high-molecular-weight DNA molecules using TROSY approaches originally developed for protein applications. Our biosynthetic strategy exploits the large number of naturally available methyltransferases to specifically methylate DNA at a desired number of sites that serve as probes of structure and dynamics. We illustrate the methodology with studies of the 153-base pair Widom DNA molecule that is simultaneously methyl-labeled at five sites, showing that high-quality13C-1H spectra can be recorded on 100 μM samples in a few minutes. NMR spin relaxation studies of labeled methyl groups in both DNA and the H2B histone protein component of the 200-kDa nucleosome core particle (NCP) establish that methyl groups at 5mC and 6mA positions are, in general, more rigid than Ile, Leu, and Val methyl probes in protein side chains. Studies focusing on histone H2B of NCPs wrapped with either wild-type DNA or DNA methylated at all 26 CpG sites highlight the utility of NMR in investigating the structural dynamics of the NCP and how its histone core is affected through DNA methylation, an important regulator of transcription.

scholarly journals Specific labeling and assignment strategies of valine methyl groups for NMR studies of high molecular weight proteins

2013 ◽  
Vol 57 (3) ◽  
pp. 251-262 ◽  
Author(s):  
Guillaume Mas ◽  
Elodie Crublet ◽  
Olivier Hamelin ◽  
Pierre Gans ◽  
Jérôme Boisbouvier
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
Methyl Groups ◽  
Nmr Studies ◽  
High Molecular Weight Proteins

scholarly journals Stereospecific Isotopic Labeling of Methyl Groups for NMR Spectroscopic Studies of High-Molecular-Weight Proteins

2010 ◽  
Vol 49 (11) ◽  
pp. 1958-1962 ◽  
Author(s):  
Pierre Gans ◽  
Olivier Hamelin ◽  
Remy Sounier ◽  
Isabel Ayala ◽  
M. Asunción Durá ◽  
...  
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
Isotopic Labeling ◽  
Spectroscopic Studies ◽  
Methyl Groups ◽  
High Molecular Weight Proteins

Sequence-Specific Assignments of Methyl Groups in High-Molecular Weight Proteins

2004 ◽  
Vol 126 (12) ◽  
pp. 3710-3711 ◽  
Author(s):  
Daiwen Yang ◽  
Yu Zheng ◽  
Dingjiang Liu ◽  
Daniel F. Wyss
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
Methyl Groups ◽  
High Molecular Weight Proteins

scholarly journals An optimized isotopic labelling strategy of isoleucine-γ2methyl groups for solution NMR studies of high molecular weight proteins

2012 ◽  
Vol 48 (10) ◽  
pp. 1434-1436 ◽  
Author(s):  
Isabel Ayala ◽  
Olivier Hamelin ◽  
Carlos Amero ◽  
Ombeline Pessey ◽  
Michael J. Plevin ◽  
...  
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
Solution Nmr ◽  
Isotopic Labelling ◽  
Nmr Studies ◽  
High Molecular Weight Proteins
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