scholarly journals Measuring fast hydrogen exchange rates by NMR spectroscopy

2007 ◽  
Vol 184 (1) ◽  
pp. 108-113 ◽  
Author(s):  
Fatiha Kateb ◽  
Philippe Pelupessy ◽  
Geoffrey Bodenhausen
Keyword(s):  
Nmr Spectroscopy ◽  
Exchange Rates ◽  
Hydrogen Exchange

Measurement of hydrogen exchange rates using 2D NMR spectroscopy

1986 ◽  
Vol 69 (2) ◽  
pp. 201-209 ◽  
Author(s):  
Christopher M Dobson ◽  
Lu-Yun Lian ◽  
Christina Redfield ◽  
Karen D Topping
Keyword(s):  
Nmr Spectroscopy ◽  
Exchange Rates ◽  
Hydrogen Exchange ◽  
2D Nmr ◽  
2D Nmr Spectroscopy

scholarly journals Base-Pair Opening Dynamics Study of Fluoride Riboswitch in the Bacillus cereus CrcB Gene

2021 ◽  
Vol 22 (6) ◽  
pp. 3234
Author(s):  
Juhyun Lee ◽  
Si-Eun Sung ◽  
Janghyun Lee ◽  
Jin Young Kang ◽  
Joon-Hwa Lee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Nmr Spectroscopy ◽  
Bacillus Cereus ◽  
Base Pair ◽  
Noncoding Rna ◽  
Hydrogen Exchange ◽  
Magnesium Ion ◽  
Fluoride Ion ◽  
Base Pair Opening

Riboswitches are segments of noncoding RNA that bind with metabolites, resulting in a change in gene expression. To understand the molecular mechanism of gene regulation in a fluoride riboswitch, a base-pair opening dynamics study was performed with and without ligands using the Bacillus cereus fluoride riboswitch. We demonstrate that the structural stability of the fluoride riboswitch is caused by two steps depending on ligands. Upon binding of a magnesium ion, significant changes in a conformation of the riboswitch occur, resulting in the greatest increase in their stability and changes in dynamics by a fluoride ion. Examining hydrogen exchange dynamics through NMR spectroscopy, we reveal that the stabilization of the U45·A37 base-pair due to the binding of the fluoride ion, by changing the dynamics while maintaining the structure, results in transcription regulation. Our results demonstrate that the opening dynamics and stabilities of a fluoride riboswitch in different ion states are essential for the genetic switching mechanism.

Determination of amide hydrogen exchange rates in peptides by mass spectrometry

1992 ◽  
Vol 64 (20) ◽  
pp. 2456-2458 ◽  
Author(s):  
Geraldine. Thevenon-Emeric ◽  
John. Kozlowski ◽  
Zhongqi. Zhang ◽  
David L. Smith
Keyword(s):  
Mass Spectrometry ◽  
Exchange Rates ◽  
Hydrogen Exchange ◽  
Amide Hydrogen ◽  
Amide Hydrogen Exchange

scholarly journals NMR Hydrogen Exchange and Relaxation Reveal Positions Stabilized by p53 Rescue Mutants N239Y and N235K

2021 ◽  
Author(s):  
Jenaro Soto ◽  
Colleen Moody ◽  
Ali Alhoshani ◽  
Marilyn Sanchez-Bonilla ◽  
Daisy Martinon ◽  
...  
Keyword(s):  
Exchange Rates ◽  
Protein Dynamics ◽  
Protein Sequence ◽  
Hydrogen Exchange ◽  
Cancer Therapeutics ◽  
Drug Efficacy ◽  
Dna Binding Domain ◽  
Protein Sequence Analysis ◽  
Stabilizing Effect ◽  
Folding Dynamics

Inactivation of p53 is found in over 50% of all cancers; p53 disfunction is often caused by a single missense mutation localized in the DNA binding domain (DBD). Rescue mutants N235K and N239Y stabilize and restore function to multiple p53 cancer mutants. Here, we use NMR to compare protein dynamics between WT and rescue mutants to understand the mechanism of stabilization. We measured and compared folding dynamics by calculating protection factors (PFs) from NMR hydrogen exchange rates of backbone amides. We find that both rescue mutants impose a global stabilizing effect that dampens their motions compared to WT DBD, predominantly in the beta-sandwich. However, a few regions become more flexible in rescue mutants. Notably, positions that have increased PFs map to cancer mutants rescued by each mutant. We also compared relaxation results to obtain flexibility information in the ps to ns timescale regime. Protein sequence analysis was used to determine the occurrence of these rescue mutants in nature and showed that 235K is found in mice and rats, but there is no evidence of 239Y occurring naturally in any species. Understanding the mechanism by which stabilizing mutants rescue p53 may reveal novel avenues for the development of cancer therapeutics. Our findings suggest that cancer therapeutics aimed at restoring p53 function could consider protein dynamics as a metric of drug efficacy.

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