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

Nagae T, Kawamura T, Chavas LM, Niwa K, Hasegawa M, Kato C, Watanabe N
Acta Crystallogr D Biol Crystallogr 68 300-9 (2012)
Related entries: 3vl2, 3vl3, 3vl4, 3vl6, 3vl7

Cited: 10 times
EuropePMC logo PMID: 22349232

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.

Articles - 3vkz mentioned but not cited (2)

  1. High-pressure-induced water penetration into 3-isopropylmalate dehydrogenase. Nagae T, Kawamura T, Chavas LM, Niwa K, Hasegawa M, Kato C, Watanabe N. Acta Crystallogr D Biol Crystallogr 68 300-309 (2012)
  2. Structural analysis of 3-isopropylmalate dehydrogenase from the obligate piezophile Shewanella benthica DB21MT-2 and the nonpiezophile Shewanella oneidensis MR-1. Nagae T, Kato C, Watanabe N. Acta Crystallogr Sect F Struct Biol Cryst Commun 68 265-268 (2012)


Reviews citing this publication (3)

  1. High-pressure macromolecular crystallography and NMR: status, achievements and prospects. Fourme R, Girard E, Akasaka K. Curr Opin Struct Biol 22 636-642 (2012)
  2. High Pressure Processing Applications in Plant Foods. Houška M, Silva FVM, Evelyn, Buckow R, Terefe NS, Tonello C. Foods 11 223 (2022)
  3. Molecular dynamics of thermoenzymes at high temperature and pressure: a review. Abedi Karjiban R, Lim WZ, Basri M, Abdul Rahman MB. Protein J 33 369-376 (2014)

Articles citing this publication (5)

  1. An electroporation strategy to synthesize the membrane-coated nanoparticles for enhanced anti-inflammation therapy in bone infection. Shi M, Shen K, Yang B, Zhang P, Lv K, Qi H, Wang Y, Li M, Yuan Q, Zhang Y. Theranostics 11 2349-2363 (2021)
  2. Effect of X-ray free-electron laser-induced shockwaves on haemoglobin microcrystals delivered in a liquid jet. Grünbein ML, Gorel A, Foucar L, Carbajo S, Colocho W, Gilevich S, Hartmann E, Hilpert M, Hunter M, Kloos M, Koglin JE, Lane TJ, Lewandowski J, Lutman A, Nass K, Nass Kovacs G, Roome CM, Sheppard J, Shoeman RL, Stricker M, van Driel T, Vetter S, Doak RB, Boutet S, Aquila A, Decker FJ, Barends TRM, Stan CA, Schlichting I. Nat Commun 12 1672 (2021)
  3. Effects of Pressure and Temperature on the Atomic Fluctuations of Dihydrofolate Reductase from a Psychropiezophile and a Mesophile. Huang Q, Rodgers JM, Hemley RJ, Ichiye T. Int J Mol Sci 20 E1452 (2019)
  4. On 3LEZ, a deep-sea halophilic protein with in vitro class-a β-lactamase activity: molecular-dynamics, docking, and reactivity simulations. Pietra F. Chem Biodivers 9 2659-2684 (2012)
  5. Pressure Adaptations in Deep-Sea Moritella Dihydrofolate Reductases: Compressibility versus Stability. Penhallurick RW, Ichiye T. Biology (Basel) 10 1211 (2021)


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