Literature DB >> 22248451

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

Takeshi Yokoyama1, Mineyuki Mizuguchi, Yuko Nabeshima, Katsuhiro Kusaka, Taro Yamada, Takaaki Hosoya, Takashi Ohhara, Kazuo Kurihara, Katsuaki Tomoyori, Ichiro Tanaka, Nobuo Niimura.   

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. Copyright Â
© 2012 Elsevier Inc. All rights reserved.

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Year:  2012        PMID: 22248451     DOI: 10.1016/j.jsb.2011.12.022

Source DB:  PubMed          Journal:  J Struct Biol        ISSN: 1047-8477            Impact factor:   2.867


  15 in total

Review 1.  Carbon-oxygen hydrogen bonding in biological structure and function.

Authors:  Scott Horowitz; Raymond C Trievel
Journal:  J Biol Chem       Date:  2012-10-09       Impact factor: 5.157

Review 2.  Considering protonation as a posttranslational modification regulating protein structure and function.

Authors:  André Schönichen; Bradley A Webb; Matthew P Jacobson; Diane L Barber
Journal:  Annu Rev Biophys       Date:  2013-02-28       Impact factor: 12.981

Review 3.  Molecular mechanisms of disease-causing missense mutations.

Authors:  Shannon Stefl; Hafumi Nishi; Marharyta Petukh; Anna R Panchenko; Emil Alexov
Journal:  J Mol Biol       Date:  2013-07-16       Impact factor: 5.469

4.  Neutron diffraction studies towards deciphering the protonation state of catalytic residues in the bacterial KDN9P phosphatase.

Authors:  Tyrel Bryan; Javier M González; John P Bacik; Nicholas J DeNunzio; Clifford J Unkefer; Tobias E Schrader; Andreas Ostermann; Debra Dunaway-Mariano; Karen N Allen; S Zoë Fisher
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2013-08-19

5.  Direct observation of hydrogen atom dynamics and interactions by ultrahigh resolution neutron protein crystallography.

Authors:  Julian C-H Chen; B Leif Hanson; S Zoë Fisher; Paul Langan; Andrey Y Kovalevsky
Journal:  Proc Natl Acad Sci U S A       Date:  2012-09-04       Impact factor: 11.205

6.  Crystallization and preliminary neutron diffraction experiment of human farnesyl pyrophosphate synthase complexed with risedronate.

Authors:  Takeshi Yokoyama; Andreas Ostermann; Mineyuki Mizuguchi; Nobuo Niimura; Tobias E Schrader; Ichiro Tanaka
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2014-03-25       Impact factor: 1.056

Review 7.  Transthyretin Misfolding, A Fatal Structural Pathogenesis Mechanism.

Authors:  Jin-Beom Si; Bokyung Kim; Jin Hae Kim
Journal:  Int J Mol Sci       Date:  2021-04-23       Impact factor: 5.923

8.  Hydrogen-bond network and pH sensitivity in human transthyretin.

Authors:  Takeshi Yokoyama; Mineyuki Mizuguchi; Yuko Nabeshima; Katsuhiro Kusaka; Taro Yamada; Takaaki Hosoya; Takashi Ohhara; Kazuo Kurihara; Ichiro Tanaka; Nobuo Niimura
Journal:  J Synchrotron Radiat       Date:  2013-09-29       Impact factor: 2.616

9.  Fluorotryptophan Incorporation Modulates the Structure and Stability of Transthyretin in a Site-Specific Manner.

Authors:  Xun Sun; H Jane Dyson; Peter E Wright
Journal:  Biochemistry       Date:  2017-09-28       Impact factor: 3.162

10.  Binding site asymmetry in human transthyretin: insights from a joint neutron and X-ray crystallographic analysis using perdeuterated protein.

Authors:  Melina Haupt; Matthew P Blakeley; Stuart J Fisher; Sax A Mason; Jon B Cooper; Edward P Mitchell; V Trevor Forsyth
Journal:  IUCrJ       Date:  2014-10-21       Impact factor: 4.769

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