Detecting O2 binding sites in protein cavities

Scientific Reports
Ryo KitaharaFrans A A Mulder

Abstract

Internal cavities are important elements in protein structure, dynamics, stability and function. Here we use NMR spectroscopy to investigate the binding of molecular oxygen (O2) to cavities in a well-studied model for ligand binding, the L99A mutant of T4 lysozyme. On increasing the O2 concentration to 8.9 mM, changes in (1)H, (15)N, and (13)C chemical shifts and signal broadening were observed specifically for backbone amide and side chain methyl groups located around the two hydrophobic cavities of the protein. O2-induced longitudinal relaxation enhancements for amide and methyl protons could be adequately accounted for by paramagnetic dipolar relaxation. These data provide the first experimental demonstration that O2 binds specifically to the hydrophobic, and not the hydrophilic cavities, in a protein. Molecular dynamics simulations visualized the rotational and translational motions of O2 in the cavities, as well as the binding and egress of O2, suggesting that the channel consisting of helices D, E, G, H, and J could be the potential gateway for ligand binding to the protein. Due to strong paramagnetic relaxation effects, O2 gas-pressure NMR measurements can detect hydrophobic cavities when populated to as little as 1%, an...Continue Reading

References

Mar 1, 1990·Journal of Molecular Graphics·G Vriend
Nov 20, 1965·Nature·B P Schoenborn
Jul 3, 1965·Nature·B P SchoenbornJ C Kendrew
Oct 5, 1980·Journal of Molecular Biology·S E Phillips
Nov 1, 1995·Journal of Biomolecular NMR·F DelaglioA Bax
Jun 1, 1996·Nature Structural Biology·V A FeherF W Dahlquist
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Feb 1, 1996·Journal of Molecular Graphics·R KoradiK Wüthrich
Aug 16, 1996·Journal of Molecular Biology·S J Hubbard, P Argos
Oct 31, 2001·Nature Structural Biology·F A MulderL E Kay
Apr 19, 2002·Journal of the American Chemical Society·Griselda HernándezDavid M LeMaster
Sep 27, 2002·Journal of Magnetic Resonance·Tobias S UlmerJonathan Boyd
Mar 27, 2003·Journal of the American Chemical Society·Lynn McNaughtonDavid M LeMaster
Mar 3, 2004·Biophysical Journal·Ching-Ling Teng, Robert G Bryant
May 3, 2006·Langmuir : the ACS Journal of Surfaces and Colloids·Gaurav Arora, Stanley I Sandler
Jun 6, 2006·Biophysical Journal·Jordi CohenKlaus Schulten
Jul 21, 2006·The Journal of Physical Chemistry. B·Lydia NisiusEike Brunner
Aug 19, 2007·Biophysical Journal·Jordi Cohen, Klaus Schulten
Sep 11, 2008·Proceedings of the National Academy of Sciences of the United States of America·Lijun LiuBrian W Matthews
Mar 15, 2013·The Journal of Chemical Physics·Shinji SaitoBiman Bagchi
Sep 10, 2014·Proceedings of the National Academy of Sciences of the United States of America·Nathaniel V NucciA Joshua Wand

❮ Previous
Next ❯

Citations

Dec 7, 2016·Biochimica Et Biophysica Acta. Biomembranes·Samuel GenhedenAnthony G Lee
Dec 7, 2016·Biochimica Et Biophysica Acta. General Subjects·Baolei JiaChe Ok Jeon
Jan 16, 2019·PLoS Computational Biology·Dheeraj DubeSurajit Sengupta
Oct 2, 2019·Proceedings of the National Academy of Sciences of the United States of America·Mengjun XueFrans A A Mulder
Dec 23, 2017·Protein Science : a Publication of the Protein Society·Ryo KitaharaFrans A A Mulder
May 19, 2018·PLoS Computational Biology·Jagannath MondalPramodh Vallurupalli
Apr 6, 2018·Chemical Science·Yong WangKresten Lindorff-Larsen

❮ Previous
Next ❯

Methods Mentioned

BETA
X-ray
nuclear magnetic resonance
NMR
optical spectroscopy

Software Mentioned

Sparky
LINCS
WHATIF
NMRPipe
GROMACS

Related Concepts

Related Feeds

Bacterial Cell Wall Structure

Bacterial cell walls are made of peptidoglycan (also called murein), which is made from polysaccharide chains cross-linked by unusual peptides containing D-amino acids. Here is the latest research on bacterial cell wall structures.

Bacterial Cell Wall Structure (ASM)

Bacterial cell walls are made of peptidoglycan (also called murein), which is made from polysaccharide chains cross-linked by unusual peptides containing D-amino acids. Here is the latest research on bacterial cell wall structures.