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Title: Design of an expression system to enhance MBP-mediated crystallization

Abstract

Crystallization chaperones have been used to facilitate the crystallization of challenging proteins. Even though the maltose-binding protein (MBP) is one of the most commonly used crystallization chaperones, the design of optimal expression constructs for crystallization of MBP fusion proteins remains a challenge. To increase the success rate of MBP-facilitated crystallization, a series of expression vectors have been designed with either a short flexible linker or a set of rigid helical linkers. Seven death domain superfamily members were tested for crystallization with this set of vectors, six of which had never been crystallized before. All of the seven targets were crystallized, and their structures were determined using at least one of the vectors. Our successful crystallization of all of the targets demonstrates the validity of our approach and expands the arsenal of the crystallization chaperone toolkit, which may be applicable to crystallization of other difficult protein targets, as well as to other crystallization chaperones.

Authors:
 [1];  [2];  [2];  [3];  [3];  [3];  [2];  [2];  [4]
  1. Univ. of Science and Technology of China, Hefei (China); National Inst. of Health (NIH), Bethesda, MD (United States)
  2. National Inst. of Health (NIH), Bethesda, MD (United States)
  3. Univ. of Science and Technology of China, Hefei (China)
  4. Case Western Reserve Univ., Cleveland, OH (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Cancer Inst.; National Inst. of General Medical Sciences; China Postdoctoral Science Foundation
OSTI Identifier:
1357647
Grant/Contract Number:  
AC02-98CH10886; Y1-CO-1020; Y1-GM-1104; 2015M582007
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; X-ray crystallography

Citation Formats

Jin, Tengchuan, Chuenchor, Watchalee, Jiang, Jiansheng, Cheng, Jinbo, Li, Yajuan, Fang, Kang, Huang, Mo, Smith, Patrick, and Xiao, Tsan Sam. Design of an expression system to enhance MBP-mediated crystallization. United States: N. p., 2017. Web. doi:10.1038/srep40991.
Jin, Tengchuan, Chuenchor, Watchalee, Jiang, Jiansheng, Cheng, Jinbo, Li, Yajuan, Fang, Kang, Huang, Mo, Smith, Patrick, & Xiao, Tsan Sam. Design of an expression system to enhance MBP-mediated crystallization. United States. doi:https://doi.org/10.1038/srep40991
Jin, Tengchuan, Chuenchor, Watchalee, Jiang, Jiansheng, Cheng, Jinbo, Li, Yajuan, Fang, Kang, Huang, Mo, Smith, Patrick, and Xiao, Tsan Sam. Mon . "Design of an expression system to enhance MBP-mediated crystallization". United States. doi:https://doi.org/10.1038/srep40991. https://www.osti.gov/servlets/purl/1357647.
@article{osti_1357647,
title = {Design of an expression system to enhance MBP-mediated crystallization},
author = {Jin, Tengchuan and Chuenchor, Watchalee and Jiang, Jiansheng and Cheng, Jinbo and Li, Yajuan and Fang, Kang and Huang, Mo and Smith, Patrick and Xiao, Tsan Sam},
abstractNote = {Crystallization chaperones have been used to facilitate the crystallization of challenging proteins. Even though the maltose-binding protein (MBP) is one of the most commonly used crystallization chaperones, the design of optimal expression constructs for crystallization of MBP fusion proteins remains a challenge. To increase the success rate of MBP-facilitated crystallization, a series of expression vectors have been designed with either a short flexible linker or a set of rigid helical linkers. Seven death domain superfamily members were tested for crystallization with this set of vectors, six of which had never been crystallized before. All of the seven targets were crystallized, and their structures were determined using at least one of the vectors. Our successful crystallization of all of the targets demonstrates the validity of our approach and expands the arsenal of the crystallization chaperone toolkit, which may be applicable to crystallization of other difficult protein targets, as well as to other crystallization chaperones.},
doi = {10.1038/srep40991},
journal = {Scientific Reports},
number = 1,
volume = 7,
place = {United States},
year = {2017},
month = {1}
}

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Works referenced in this record:

Bax Crystal Structures Reveal How BH3 Domains Activate Bax and Nucleate Its Oligomerization to Induce Apoptosis
journal, January 2013


The Fas–FADD death domain complex structure unravels signalling by receptor clustering
journal, December 2008

  • Scott, Fiona L.; Stec, Boguslaw; Pop, Cristina
  • Nature, Vol. 457, Issue 7232
  • DOI: 10.1038/nature07606

New surface contacts formed upon reductive lysine methylation: Improving the probability of protein crystallization: Lysine Methylation
journal, May 2010

  • Sledz, Pawel; Zheng, Heping; Murzyn, Krzysztof
  • Protein Science, Vol. 19, Issue 7
  • DOI: 10.1002/pro.420

Structural basis of procaspase-9 recruitment by the apoptotic protease-activating factor 1
journal, June 1999

  • Qin, Hongxu; Srinivasula, Srinivasa M.; Wu, Geng
  • Nature, Vol. 399, Issue 6736
  • DOI: 10.1038/21124

A Maltose-Binding Protein Fusion Construct Yields a Robust Crystallography Platform for MCL1
journal, April 2015


Crystal structure of human IPS-1/MAVS/VISA/Cardif caspase activation recruitment domain
journal, January 2008

  • Potter, Jane A.; Randall, Richard E.; Taylor, Garry L.
  • BMC Structural Biology, Vol. 8, Issue 1
  • DOI: 10.1186/1472-6807-8-11

Application of protein engineering to enhance crystallizability and improve crystal properties
journal, April 2010

  • Derewenda, Zygmunt S.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 5
  • DOI: 10.1107/S090744491000644X

It's all in the crystals…
journal, March 2011

  • Derewenda, Zygmunt S.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444911007797

Mass spectrometry guided in situ proteolysis to obtain crystals for X-ray structure determination
journal, October 2010

  • Gheyi, Tarun; Rodgers, Logan; Romero, Richard
  • Journal of the American Society for Mass Spectrometry, Vol. 21, Issue 10
  • DOI: 10.1016/j.jasms.2010.06.015

Escherichia coli maltose-binding protein is uncommonly effective at promoting the solubility of polypeptides to which it is fused
journal, January 1999

  • Kapust, Rachel B.; Waugh, David S.
  • Protein Science, Vol. 8, Issue 8, p. 1668-1674
  • DOI: 10.1110/ps.8.8.1668

Fusion Partner Toolchest for the Stabilization and Crystallization of G Protein-Coupled Receptors
journal, June 2012


Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions
journal, July 2012


Structural insights for engineering binding proteins based on non-antibody scaffolds
journal, August 2012


GPCR Engineering Yields High-Resolution Structural Insights into  2-Adrenergic Receptor Function
journal, October 2007


Crystallization and improvement of crystal quality for X-ray diffraction of maltooligosyl trehalose synthase by reductive methylation of lysine residues
journal, April 1999

  • Kobayashi, Masanori; Kubota, Michio; Matsuura, Yoshiki
  • Acta Crystallographica Section D Biological Crystallography, Vol. 55, Issue 4
  • DOI: 10.1107/S0907444999002115

Structure of the human smoothened receptor bound to an antitumour agent
journal, May 2013

  • Wang, Chong; Wu, Huixian; Katritch, Vsevolod
  • Nature, Vol. 497, Issue 7449
  • DOI: 10.1038/nature12167

Easy mammalian expression and crystallography of maltose-binding protein-fused human proteins
journal, April 2016

  • Bokhove, Marcel; Sadat Al Hosseini, Hamed; Saito, Takako
  • Journal of Structural Biology, Vol. 194, Issue 1
  • DOI: 10.1016/j.jsb.2016.01.016

Crystal structure of peroxisomal targeting signal-2 bound to its receptor complex Pex7p–Pex21p
journal, June 2013

  • Pan, Dongqing; Nakatsu, Toru; Kato, Hiroaki
  • Nature Structural & Molecular Biology, Vol. 20, Issue 8
  • DOI: 10.1038/nsmb.2618

The Fas–FADD death domain complex structure reveals the basis of DISC assembly and disease mutations
journal, October 2010

  • Wang, Liwei; Yang, Jin Kuk; Kabaleeswaran, Venkataraman
  • Nature Structural & Molecular Biology, Vol. 17, Issue 11
  • DOI: 10.1038/nsmb.1920

Thioredoxin as a fusion tag for carrier‐driven crystallization
journal, December 2008

  • Corsini, Lorenzo; Hothorn, Michael; Scheffzek, Klaus
  • Protein Science, Vol. 17, Issue 12
  • DOI: 10.1110/ps.037564.108

Structure of the caspase-recruitment domain from a zebrafish guanylate-binding protein
journal, July 2013

  • Jin, Tengchuan; Huang, Mo; Smith, Patrick
  • Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 69, Issue 8
  • DOI: 10.1107/S1744309113015558

Helical assembly in the MyD88–IRAK4–IRAK2 complex in TLR/IL-1R signalling
journal, May 2010


XDS
journal, January 2010

  • Kabsch, Wolfgang
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
  • DOI: 10.1107/S0907444909047337

Toward rational protein crystallization: A Web server for the design of crystallizable protein variants
journal, August 2007

  • Goldschmidt, Lukasz; Cooper, David R.; Derewenda, Zygmunt S.
  • Protein Science, Vol. 16, Issue 8
  • DOI: 10.1110/ps.072914007

N-Terminal T4 Lysozyme Fusion Facilitates Crystallization of a G Protein Coupled Receptor
journal, October 2012


Crystallization of a trimeric human T cell leukemia virus type 1 gp21 ectodomain fragment as a chimera with maltose-binding protein
journal, July 1998

  • Center, Rob J.; Kobe, Bostjan; Wilson, Kirilee A.
  • Protein Science, Vol. 7, Issue 7
  • DOI: 10.1002/pro.5560070715

An approach to crystallizing proteins by metal-mediated synthetic symmetrization
journal, September 2011

  • Laganowsky, Arthur; Zhao, Minglei; Soriaga, Angela B.
  • Protein Science, Vol. 20, Issue 11
  • DOI: 10.1002/pro.727

Crystal Structure of the Maltose Transporter in a Pretranslocation Intermediate State
journal, May 2011


Solution structure of the tumor necrosis factor receptor-1 death domain
journal, July 2001

  • Sukits, Steven F.; Lin, Lih-Ling; Hsu, Sang
  • Journal of Molecular Biology, Vol. 310, Issue 4
  • DOI: 10.1006/jmbi.2001.4790

Processive Steps in the Reverse Direction Require Uncoupling of the Lead Head Lever Arm of Myosin VI
journal, October 2012


In situ proteolysis for protein crystallization and structure determination
journal, November 2007

  • Dong, Aiping; Xu, Xiaohui; Edwards, Aled M.
  • Nature Methods, Vol. 4, Issue 12
  • DOI: 10.1038/nmeth1118

Chapter 16 Tagging for Protein Expression
book, January 2009

  • Malhotra, Arun; Burgess, Richard R.; Deutscher, Murray P.
  • Guide to Protein Purification, 2nd Edition, Vol. 463, p. 239-258
  • DOI: 10.1016/S0076-6879(09)63016-0

Structure of the NLRP1 caspase recruitment domain suggests potential mechanisms for its association with procaspase-1: 2.0 Å Crystal Structure of the NLRP1 CARD
journal, April 2013

  • Jin, Tengchuan; Curry, James; Smith, Patrick
  • Proteins: Structure, Function, and Bioinformatics, Vol. 81, Issue 7
  • DOI: 10.1002/prot.24287

Overview of tag protein fusions: from molecular and biochemical fundamentals to commercial systems
journal, January 2003


Enhanced Crystallizability by Protein Engineering Approaches: A General Overview
journal, May 2012

  • Ruggiero, Alessia; Smaldone, Giovanni; Squeglia, Flavia
  • Protein & Peptide Letters, Vol. 19, Issue 7
  • DOI: 10.2174/092986612800793172

MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009

  • Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
  • DOI: 10.1107/S0907444909042073

Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

The structure of the CARD8 caspase-recruitment domain suggests its association with the FIIND domain and procaspases through adjacent surfaces
journal, April 2013

  • Jin, Tengchuan; Huang, Mo; Smith, Patrick
  • Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 69, Issue 5
  • DOI: 10.1107/S1744309113010075

Polymer-driven crystallization
journal, November 2007

  • Nauli, Sehat; Farr, Saman; Lee, Yueh-Jung
  • Protein Science, Vol. 16, Issue 11
  • DOI: 10.1110/ps.073074207

The death-fold superfamily of homotypic interaction motifs
journal, October 2011

  • Kersse, Kristof; Verspurten, Jelle; Berghe, Tom Vanden
  • Trends in Biochemical Sciences, Vol. 36, Issue 10
  • DOI: 10.1016/j.tibs.2011.06.006

Structure-function analyses of the human SIX1–EYA2 complex reveal insights into metastasis and BOR syndrome
journal, February 2013

  • Patrick, Aaron N.; Cabrera, Joshua H.; Smith, Anna L.
  • Nature Structural & Molecular Biology, Vol. 20, Issue 4
  • DOI: 10.1038/nsmb.2505

Basis for a ubiquitin-like protein thioester switch toggling E1–E2 affinity
journal, January 2007

  • Huang, Danny T.; Hunt, Harold W.; Zhuang, Min
  • Nature, Vol. 445, Issue 7126
  • DOI: 10.1038/nature05490

A graphical user interface to the CCP 4 program suite
journal, June 2003

  • Potterton, Elizabeth; Briggs, Peter; Turkenburg, Maria
  • Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 7
  • DOI: 10.1107/S0907444903008126

New concepts and aids to facilitate crystallization
journal, June 2013

  • Bukowska, Magdalena A.; Grütter, Markus G.
  • Current Opinion in Structural Biology, Vol. 23, Issue 3
  • DOI: 10.1016/j.sbi.2013.03.003

Structure of a signal transduction regulator, RACK1, from Arabidopsis thaliana
journal, October 2008

  • Ullah, Hemayet; Scappini, Erica Louise; Moon, Andrea Florence
  • Protein Science, Vol. 17, Issue 10
  • DOI: 10.1110/ps.035121.108

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Combining in-situ proteolysis and microseed matrix screening to promote crystallization of PrPc-nanobody complexes
journal, May 2011

  • Abskharon, R. N. N.; Soror, S. H.; Pardon, E.
  • Protein Engineering Design and Selection, Vol. 24, Issue 9
  • DOI: 10.1093/protein/gzr017

Crystal structures of MBP fusion proteins: Structures of MBP Fusion Proteins
journal, January 2016


Lysine Methylation as a Routine Rescue Strategy for Protein Crystallization
journal, November 2006


Death Domain Assembly Mechanism Revealed by Crystal Structure of the Oligomeric PIDDosome Core Complex
journal, February 2007


Molecular recognition of parathyroid hormone by its G protein-coupled receptor
journal, March 2008

  • Pioszak, Augen A.; Xu, H. Eric
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 13
  • DOI: 10.1073/pnas.0801027105

Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206

A synergistic approach to protein crystallization: Combination of a fixed-arm carrier with surface entropy reduction
journal, January 2010

  • Moon, Andrea F.; Mueller, Geoffrey A.; Zhong, Xuejun
  • Protein Science
  • DOI: 10.1002/pro.368

[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997


    Works referencing / citing this record:

    T4 lysozyme-facilitated crystallization of the human molybdenum cofactor-dependent enzyme mARC
    text, January 2018

    • Kubitza, Christian; Ginsel, Carsten; Bittner, Florian
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/pubdb-2018-03789

    T4 lysozyme-facilitated crystallization of the human molybdenum cofactor-dependent enzyme mARC
    journal, May 2018

    • Kubitza, Christian; Ginsel, Carsten; Bittner, Florian
    • Acta Crystallographica Section F Structural Biology Communications, Vol. 74, Issue 6
    • DOI: 10.1107/s2053230x18006921

    Evaluation of multiple fused partners on enhancing soluble level of prenyltransferase NovQ in Escherichia coli
    journal, November 2018


    Crystal structure of the Streptococcus agalactiae CAMP factor provides insights into its membrane-permeabilizing activity
    journal, June 2018

    • Jin, Tengchuan; Brefo-Mensah, Eric; Fan, Weirong
    • Journal of Biological Chemistry, Vol. 293, Issue 30
    • DOI: 10.1074/jbc.ra118.002336

    Crystal structures of the recombinant β-factor XIIa protease with bound Thr-Arg and Pro-Arg substrate mimetics
    journal, June 2019

    • Pathak, Monika; Manna, Rosa; Li, Chan
    • Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 6
    • DOI: 10.1107/s2059798319006910

    Structure determination of the CAMP factor of Streptococcus agalactiae with the aid of an MBP tag and insights into membrane-surface attachment
    journal, July 2019

    • Li, Yajuan; Zeng, Weihong; Li, Yuelong
    • Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 8
    • DOI: 10.1107/s205979831901057x

    Functional and structural characterization of zebrafish ASC
    journal, June 2018

    • Li, Yajuan; Huang, Yi; Cao, Xiaocong
    • The FEBS Journal, Vol. 285, Issue 14
    • DOI: 10.1111/febs.14514

    Crystal structure and activation mechanism of DR3 death domain
    journal, April 2019

    • Yin, Xueying; Li, Wenqian; Ma, Huan
    • The FEBS Journal, Vol. 286, Issue 13
    • DOI: 10.1111/febs.14834

    Polyionic Tags as Enhancers of Protein Solubility in Recombinant Protein Expression
    journal, May 2018