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

Authors:
;  [1]
  1. NIAID
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
NIHNIAID
OSTI Identifier:
1247349
Resource Type:
Journal Article
Resource Relation:
Journal Name: Federation of European Biochemical Societies (FEBS) Journal; Journal Volume: 281; Journal Issue: (18) ; 09, 2014
Country of Publication:
United States
Language:
ENGLISH

Citation Formats

Lu, Jinghua, and Sun, Peter D. A rapid and rational approach to generating isomorphous heavy-atom phasing derivatives. United States: N. p., 2016. Web. doi:10.1111/febs.12910.
Lu, Jinghua, & Sun, Peter D. A rapid and rational approach to generating isomorphous heavy-atom phasing derivatives. United States. doi:10.1111/febs.12910.
Lu, Jinghua, and Sun, Peter D. Tue . "A rapid and rational approach to generating isomorphous heavy-atom phasing derivatives". United States. doi:10.1111/febs.12910.
@article{osti_1247349,
title = {A rapid and rational approach to generating isomorphous heavy-atom phasing derivatives},
author = {Lu, Jinghua and Sun, Peter D.},
abstractNote = {},
doi = {10.1111/febs.12910},
journal = {Federation of European Biochemical Societies (FEBS) Journal},
number = (18) ; 09, 2014,
volume = 281,
place = {United States},
year = {Tue Apr 12 00:00:00 EDT 2016},
month = {Tue Apr 12 00:00:00 EDT 2016}
}
  • No abstract prepared.
  • Using idealized known RNA secondary-structural fragments, it is demonstrated that it is possible to solve novel complex RNA structures without resort to heavy-atom phasing methods. The crystallographic phase problem [Muirhead & Perutz (1963 ▶), Nature (London), 199, 633–638] remains the single major impediment to obtaining a three-dimensional structure of a macromolecule once suitable crystals have been obtained. Recently, it was found that it was possible to solve the structure of a 142-nucleotide L1 ligase ribozyme heterodimer that possesses no noncrystallographic symmetry without heavy-atom derivatives, anomalous scattering atoms or other modifications and without a model of the tertiary structure of themore » ribozyme [Robertson & Scott (2007 ▶), Science, 315, 1549–1553]. Using idealized known RNA secondary-structural fragments such as A-form helices and GNRA tetraloops in an iterative molecular-replacement procedure, it was possible to obtain an estimated phase set that, when subjected to solvent flattening, yielded an interpretable electron-density map with minimized model bias, allowing the tertiary structure of the ribozyme to be solved. This approach has also proven successful with other ribozymes, structured RNAs and RNA–protein complexes.« less
  • In order to overcome the difficulties associated with the ‘classical’ heavy-atom derivatization procedure, an attempt has been made to develop a rational crystal-free heavy-atom-derivative screening method and a quick-soak derivatization procedure which allows heavy-atom compound identification. Despite the development in recent times of a range of techniques for phasing macromolecules, the conventional heavy-atom derivatization method still plays a significant role in protein structure determination. However, this method has become less popular in modern high-throughput oriented crystallography, mostly owing to its trial-and-error nature, which often results in lengthy empirical searches requiring large numbers of well diffracting crystals. In addition, the phasingmore » power of heavy-atom derivatives is often compromised by lack of isomorphism or even loss of diffraction. In order to overcome the difficulties associated with the ‘classical’ heavy-atom derivatization procedure, an attempt has been made to develop a rational crystal-free heavy-atom derivative-screening method and a quick-soak derivatization procedure which allows heavy-atom compound identification. The method includes three basic steps: (i) the selection of likely reactive compounds for a given protein and specific crystallization conditions based on pre-defined heavy-atom compound reactivity profiles, (ii) screening of the chosen heavy-atom compounds for their ability to form protein adducts using mass spectrometry and (iii) derivatization of crystals with selected heavy-metal compounds using the quick-soak method to maximize diffraction quality and minimize non-isomorphism. Overall, this system streamlines the process of heavy-atom compound identification and minimizes the problem of non-isomorphism in phasing.« less
  • Heavy-atom derivatization is routinely used in protein structure determination and is thus of critical importance in structural biology. In order to replace the current trial-and-error heavy-atom derivative screening with a knowledge-based rational derivative-selection method, the reactivity of more than 40 heavy-atom compounds over a wide range of buffer and pH values was systematically examined using peptides which contained a single reactive amino-acid residue. Heavy-atom derivatization is routinely used in protein structure determination and is thus of critical importance in structural biology. In order to replace the current trial-and-error heavy-atom derivative screening with a knowledge-based rational derivative-selection method, the reactivity ofmore » more than 40 heavy-atom compounds over a wide range of buffer and pH values was systematically examined using peptides which contained a single reactive amino-acid residue. Met-, Cys- and His-containing peptides were derivatized against Hg, Au and Pt compounds, while Tyr-, Glu-, Asp-, Asn- and Gln-containing peptides were assessed against Pb compounds. A total of 1668 reactive conditions were examined using mass spectrometry and were compiled into heavy-atom reactivity tables. The results showed that heavy-atom derivatization reactions are highly linked to buffer and pH, with the most accommodating buffer being MES at pH 6. A group of 21 compounds were identified as most successful irrespective of ligand or buffer/pH conditions. To assess the applicability of the peptide heavy-atom reactivity to proteins, lysozyme crystals were derivatized with a list of peptide-reactive compounds that included both known and new compounds for lysozyme derivatization. The results showed highly consistent heavy-atom reactivities between the peptides and lysozyme.« less
  • This paper describes the use of barium chloride to produce a heavy-atom derivative of xylanase II crystals from Trichoderma longibrachiatum, which was obtained either by cocrystallization or soaking. SAD phasing led to interpretable electron-density maps that allowed unambiguous chain tracing. In the best case, with a data set collected at 9.5 keV, 88% of the residues were built, with 83% of the side chains assigned. The barium ions are found to mainly interact with main-chain carbonyl groups and water molecules. It is suggested that barium ions could also be used as a potential anomalous scatterer in the quick cryosoaking proceduremore » for phasing.« less