High-pressure-induced water penetration into 3-isopropylmalate dehydrogenase.

Acta Crystallographica. Section D, Biological Crystallography
Takayuki NagaeNobuhisa Watanabe

Abstract

Hydrostatic pressure induces structural changes in proteins, including denaturation, the mechanism of which has been attributed to water penetration into the protein interior. In this study, structures of 3-isopropylmalate dehydrogenase (IPMDH) from Shewanella oneidensis MR-1 were determined at about 2 Å resolution under pressures ranging from 0.1 to 650 MPa using a diamond anvil cell (DAC). Although most of the protein cavities are monotonically compressed as the pressure increases, the volume of one particular cavity at the dimer interface increases at pressures over 340 MPa. In parallel with this volume increase, water penetration into the cavity could be observed at pressures over 410 MPa. In addition, the generation of a new cleft on the molecular surface accompanied by water penetration could also be observed at pressures over 580 MPa. These water-penetration phenomena are considered to be initial steps in the pressure-denaturation process of IPMDH.

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Citations

Oct 15, 2013·Journal of Synchrotron Radiation·Leonard Michel Gabriel ChavasNaohiro Matsugaki
Mar 24, 2012·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Takayuki NagaeNobuhisa Watanabe
May 30, 2014·The Protein Journal·Roghayeh Abedi KarjibanMohd Basyaruddin Abdul Rahman
Sep 11, 2012·Current Opinion in Structural Biology·Roger FourmeKazuyuki Akasaka
Apr 8, 2015·Acta Crystallographica. Section D, Biological Crystallography·Hiroyuki YamadaNobuhisa Watanabe
Apr 20, 2012·Journal of Synchrotron Radiation·L M G ChavasS Wakatsuki
Sep 11, 2018·Acta Crystallographica. Section D, Structural Biology·Takayuki NagaeNobuhisa Watanabe
Mar 17, 2021·Nature Communications·Marie Luise GrünbeinIlme Schlichting
Jul 3, 2020·Journal of Bioscience and Bioengineering·Masahiko OkaiMasami Ishida
Feb 28, 2021·Annual Review of Biophysics·Nozomi AndoMaxwell B Watkins

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Methods Mentioned

BETA
NMR
gel-filtration
X-­ray
X-ray

Software Mentioned

PyMOL
CASTp
MOLREP
SSM
CCP
2000
HKL
REFMAC
VOIDOO
Coot

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