Literature DB >> 25040395

A rapid and rational approach to generating isomorphous heavy-atom phasing derivatives.

Jinghua Lu1, Peter D Sun.   

Abstract

In attempts to replace the conventional trial-and-error heavy-atom derivative search method with a rational approach, we previously defined heavy metal compound reactivity against peptide ligands. Here, we assembled a composite pH- and buffer-dependent peptide reactivity profile for each heavy metal compound to guide rational heavy-atom derivative search. When knowledge of the best-reacting heavy-atom compound is combined with mass spectrometry assisted derivatization, and with a quick-soak method to optimize phasing, it is likely that the traditional heavy-atom compounds could meet the demand of modern high-throughput X-ray crystallography. As an example, we applied this rational heavy-atom phasing approach to determine a previously unknown mouse serum amyloid A2 crystal structure. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Entities:  

Keywords:  heavy-atom reactivity profiles; mass spectrometry-assisted heavy-atom derivatization; quick-soaking method; rational heavy-atom screen

Mesh:

Substances:

Year:  2014        PMID: 25040395      PMCID: PMC4169333          DOI: 10.1111/febs.12910

Source DB:  PubMed          Journal:  FEBS J        ISSN: 1742-464X            Impact factor:   5.542


  14 in total

1.  Mass-spectrometry assisted heavy-atom derivative screening of human Fc gamma RIII crystals.

Authors:  P D Sun; C H Hammer
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2000-02

2.  HAD, a data bank of heavy-atom binding sites in protein crystals: a resource for use in multiple isomorphous replacement and anomalous scattering.

Authors:  S A Islam; D Carvin; M J Sternberg; T L Blundell
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1998-11-01

3.  Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0.

Authors:  G Bricogne; C Vonrhein; C Flensburg; M Schiltz; W Paciorek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2003-10-23

4.  Generating isomorphous heavy-atom derivatives by a quick-soak method. Part II: phasing of new structures.

Authors:  Peter D Sun; Sergei Radaev
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2002-06-20

5.  Generating isomorphous heavy-atom derivatives by a quick-soak method. Part I: test cases.

Authors:  Peter D Sun; Sergei Radaev; Michael Kattah
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2002-06-20

6.  Heavy-atom Database System: a tool for the preparation of heavy-atom derivatives of protein crystals based on amino-acid sequence and crystallization conditions.

Authors:  Michihiro Sugahara; Yukuhiko Asada; Haruhiko Ayama; Hisashi Ukawa; Hideyuki Taka; Naoki Kunishima
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-08-16

Review 7.  Current state and prospects of macromolecular crystallography.

Authors:  Zbigniew Dauter
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-12-14

Review 8.  The preparation of isomorphous derivatives.

Authors:  C C Blake
Journal:  Adv Protein Chem       Date:  1968

9.  Novel approach to phasing proteins: derivatization by short cryo-soaking with halides.

Authors:  Z Dauter; M Dauter; K R Rajashankar
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2000-02

10.  The magic triangle goes MAD: experimental phasing with a bromine derivative.

Authors:  Tobias Beck; Tim Gruene; George M Sheldrick
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24
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  3 in total

1.  Introduction: celebrating the international year of crystallography: introduction.

Authors:  Mariusz Jaskolski; Alexander Wlodawer
Journal:  FEBS J       Date:  2014-09       Impact factor: 5.542

Review 2.  An overview of heavy-atom derivatization of protein crystals.

Authors:  Ashley C W Pike; Elspeth F Garman; Tobias Krojer; Frank von Delft; Elisabeth P Carpenter
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-03-01       Impact factor: 7.652

3.  High-throughput in situ experimental phasing.

Authors:  Joshua M Lawrence; Julien Orlans; Gwyndaf Evans; Allen M Orville; James Foadi; Pierre Aller
Journal:  Acta Crystallogr D Struct Biol       Date:  2020-07-28       Impact factor: 7.652

  3 in total

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