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Hydrogen-bond network and pH sensitivity in transthyretin: Neutron crystal structure of human transthyretin.

Yokoyama T, Mizuguchi M, Nabeshima Y, Kusaka K, Yamada T, Hosoya T, Ohhara T, Kurihara K, Tomoyori K, Tanaka I, Niimura N
J Struct Biol 177 283-90 (2012)
Cited: 25 times
EuropePMC logo PMID: 22248451

Abstract

Transthyretin (TTR) is a tetrameric protein associated with human amyloidosis. In vitro, the formation of amyloid fibrils by TTR is known to be promoted by low pH. Here we show the neutron structure of TTR, focusing on the hydrogen bonds, protonation states and pH sensitivities. A large crystal was prepared at pD 7.4 for neutron protein crystallography. Neutron diffraction studies were conducted using the IBARAKI Biological Crystal Diffractometer with the time-of-flight method. The neutron structure solved at 2.0Å resolution revealed the protonation states of His88 and the detailed hydrogen-bond network depending on the protonation states of His88. This hydrogen-bond network is composed of Thr75, Trp79, His88, Ser112, Pro113, Thr118-B and four water molecules, and is involved in both monomer-monomer and dimer-dimer interactions, suggesting that the double protonation of His88 by acidification breaks the hydrogen-bond network and causes the destabilization of the TTR tetramer. In addition, the comparison with X-ray structure at pH 4.0 indicated that the protonation occurred to Asp74, His88 and Glu89 at pH 4.0. Our neutron model provides insights into the molecular stability of TTR related to the hydrogen-bond network, the pH sensitivity and the CH···O weak hydrogen bond.

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  3. Neutron crystallographic refinement with REFMAC5 from the CCP4 suite. Catapano L, Long F, Yamashita K, Nicholls RA, Steiner RA, Murshudov GN. Acta Crystallogr D Struct Biol 79 1056-1070 (2023)


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  1. Molecular mechanisms of disease-causing missense mutations. Stefl S, Nishi H, Petukh M, Panchenko AR, Alexov E. J Mol Biol 425 3919-3936 (2013)
  2. Carbon-oxygen hydrogen bonding in biological structure and function. Horowitz S, Trievel RC. J Biol Chem 287 41576-41582 (2012)
  3. Considering protonation as a posttranslational modification regulating protein structure and function. Schönichen A, Webb BA, Jacobson MP, Barber DL. Annu Rev Biophys 42 289-314 (2013)
  4. Neutron protein crystallography: A complementary tool for locating hydrogens in proteins. O'Dell WB, Bodenheimer AM, Meilleur F. Arch Biochem Biophys 602 48-60 (2016)
  5. Diagnostic and Treatment Approaches Involving Transthyretin in Amyloidogenic Diseases. Park GY, Jamerlan A, Shim KH, An SSA. Int J Mol Sci 20 E2982 (2019)
  6. Molecular Mechanisms of Cardiac Amyloidosis. Saito Y, Nakamura K, Ito H. Int J Mol Sci 23 25 (2021)
  7. Modulation of the Mechanisms Driving Transthyretin Amyloidosis. Bezerra F, Saraiva MJ, Almeida MR. Front Mol Neurosci 13 592644 (2020)
  8. Transthyretin Misfolding, A Fatal Structural Pathogenesis Mechanism. Si JB, Kim B, Kim JH. Int J Mol Sci 22 4429 (2021)

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  2. Amyloid-β oligomers are captured by the DNAJB6 chaperone: Direct detection of interactions that can prevent primary nucleation. Österlund N, Lundqvist M, Ilag LL, Gräslund A, Emanuelsson C. J Biol Chem 295 8135-8144 (2020)
  3. Impact of Deuteration on the Assembly Kinetics of Transthyretin Monitored by Native Mass Spectrometry and Implications for Amyloidoses. Yee AW, Moulin M, Breteau N, Haertlein M, Mitchell EP, Cooper JB, Boeri Erba E, Forsyth VT. Angew Chem Int Ed Engl 55 9292-9296 (2016)
  4. The putative role of some conserved water molecules in the structure and function of human transthyretin. Banerjee A, Dasgupta S, Mukhopadhyay BP, Sekar K. Acta Crystallogr D Biol Crystallogr 71 2248-2266 (2015)
  5. Understanding the microscopic binding mechanism of hydroxylated and sulfated polybrominated diphenyl ethers with transthyretin by molecular docking, molecular dynamics simulations and binding free energy calculations. Cao H, Sun Y, Wang L, Zhao C, Fu J, Zhang A. Mol Biosyst 13 736-749 (2017)
  6. Quaternary structure, aggregation and cytotoxicity of transthyretin. Mizuguchi M, Yokoyama T, Nabeshima Y, Kawano K, Tanaka I, Niimura N. Amyloid 19 Suppl 1 5-7 (2012)
  7. Neutron scattering techniques and applications in structural biology. Ankner JF, Heller WT, Herwig KW, Meilleur F, Myles DA. Curr Protoc Protein Sci Chapter 17 Unit17.16 (2013)
  8. Letter Stability and crystal structures of His88 mutant human transthyretins. Yokoyama T, Hanawa Y, Obita T, Mizuguchi M. FEBS Lett 591 1862-1871 (2017)
  9. Crystallization and preliminary neutron diffraction experiment of human farnesyl pyrophosphate synthase complexed with risedronate. Yokoyama T, Ostermann A, Mizuguchi M, Niimura N, Schrader TE, Tanaka I. Acta Crystallogr F Struct Biol Commun 70 470-472 (2014)
  10. Thermodynamic study of transthyretin association (wild-type and senile forms) with heparan sulfate proteoglycan: pH effect and implication of the reactive histidine residue. Geneste A, André C, Magy-Bertrand N, Lethier L, Tijani G, Guillaume YC. Biomed Chromatogr 29 514-522 (2015)
  11. Layer-by-layer supramolecular assemblies based on linear and star-shaped poly(glycerol methacrylate)s for doxorubicin delivery. Sun Y, Gao H, Yang YW, Wang A, Wu G, Wang Y, Fan Y, Ma J. J Biomed Mater Res A 101 2164-2173 (2013)
  12. The Taste-Masking Mechanism of Chitosan at the Molecular Level on Bitter Drugs of Alkaloids and Flavonoid Glycosides from Traditional Chinese Medicine. Xu Y, Sun Q, Chen W, Han Y, Gao Y, Ye J, Wang H, Gao L, Liu Y, Yang Y. Molecules 27 7455 (2022)
  13. The mechanism and conformational changes of polybrominated diphenyl ethers to TTR by fluorescence spectroscopy, molecular simulation, and quantum chemistry. Xu J, Wei Y, Yang W, Yang L, Yi Z. Analyst 143 4662-4673 (2018)


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