Special Issue "Recent Advances in Protein Crystallography"

A special issue of Crystals (ISSN 2073-4352). This special issue belongs to the section "Biomolecular Crystals".

Deadline for manuscript submissions: 31 December 2017

Special Issue Editor

Guest Editor
Dr. Albert Guskov

Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
Website | E-Mail
Interests: membrane proteins; protein crystallography; protein crystallization

Special Issue Information

Dear Colleagues,

The field of the structural biology is thriving owing to several so-called “revolutions”, such as the advent of X-ray Free Electron Lasers, remarkable improvements in detectors’ resolution for Cryo-electron Microscopy and many other important developments in all aspects of the field: Protein expression, purification, crystallization, data processing and analysis, and so on. We decided to compile this Special Issue on “Recent advances in Protein Crystallography” to summarize the current progress and the state-of-the-art of the structural biology. Authors are encouraged to submit their manuscripts covering topics expressed in the keywords below. The additional goal of this issue is to provide the growing community of scientists interested in structural biology with an excellent reference material. Additionally we will compile the subsection on protein structures, thus manuscripts describing new structures with the structural-functional analysis or “old” structures but with a new twist are also welcome.

Dr. Albert Guskov
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Crystals is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Structural biology
  • Protein crystallography
  • Membrane proteins
  • Protein crystallization
  • X-ray Free Electron Laser
  • Cryo-Electron Microscopy
  • Protein Expression and purification
  • Data processing and analysis
  • Refinement and validation
  • Biophysical characterization

Published Papers (6 papers)

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Research

Jump to: Review

Open AccessArticle Expression, Purification, Crystallization, and X-ray Structural Analysis of CRISPR-Associated Protein Cas6 from Methanocaldococcus jannaschii
Crystals 2017, 7(11), 344; doi:10.3390/cryst7110344
Received: 20 September 2017 / Revised: 7 November 2017 / Accepted: 8 November 2017 / Published: 10 November 2017
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Abstract
The CRISPR-associated protein 6, Cas6 protein, is an endoribonuclease that cleaves precursor CRISPR RNAs within the repeat sequence to release specific invader-targeting RNAs. Cas6 protein can recognize different sequences by their specific scaffold. To investigate its binding mode, we purified and crystallized a
[...] Read more.
The CRISPR-associated protein 6, Cas6 protein, is an endoribonuclease that cleaves precursor CRISPR RNAs within the repeat sequence to release specific invader-targeting RNAs. Cas6 protein can recognize different sequences by their specific scaffold. To investigate its binding mode, we purified and crystallized a His-tagged Cas6 protein from Methanocaldococcus jannaschii (MjCas6) using the sitting-drop vapor-diffusion method. The crystals diffracted to a resolution of 1.85 Å and belonged to monoclinic space group C2, with unit-cell parameters a = 200.84 Å, b = 85.26 Å, c = 100.06 Å, β = 118.47°. The crystals of MjCas6 contain four molecules in the asymmetric unit. The protein fold is similar to the other Cas6 homologues, such as Pyrococcus furiosus Cas6, suggesting functional similarity. Moreover, in the C2 crystal the MjCas6 monomers formed a tandem array, which we hypothesize to possibly correlate with repetitive RNA precursors. Full article
(This article belongs to the Special Issue Recent Advances in Protein Crystallography)
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Open AccessArticle The Use of Size Exclusion Chromatography to Monitor Protein Self-Assembly
Crystals 2017, 7(11), 331; doi:10.3390/cryst7110331
Received: 6 September 2017 / Revised: 20 October 2017 / Accepted: 23 October 2017 / Published: 31 October 2017
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Abstract
High resolution size exclusion chromatography (SEC) coupled with static light scattering (SLS) analyses were conducted to study the effect of the mobile phase ionic strength and protein concentration on the output of SEC experiments. The results highlight the effect of small changes in
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High resolution size exclusion chromatography (SEC) coupled with static light scattering (SLS) analyses were conducted to study the effect of the mobile phase ionic strength and protein concentration on the output of SEC experiments. The results highlight the effect of small changes in the mobile phase composition on the estimation of molar masses estimated from retention time-based calibration curve compared with those obtained from SLS analysis. By comparing the SLS data with the SEC chromatograms, we show that SEC can provide helpful information on the protein aggregation state as macromolecules approach known precipitation points in their phase diagrams. This suggests the potential use of SEC as an easily accessible lab-based scanning methodology to monitor protein self-assembly prior to nucleation and crystallization. Implications for the use of SEC to study protein phase diagrams are discussed. Full article
(This article belongs to the Special Issue Recent Advances in Protein Crystallography)
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Open AccessArticle Crystal Structure of the 23S rRNA Fragment Specific to r-Protein L1 and Designed Model of the Ribosomal L1 Stalk from Haloarcula marismortui
Crystals 2017, 7(2), 37; doi:10.3390/cryst7020037
Received: 13 December 2016 / Accepted: 29 January 2017 / Published: 2 February 2017
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Abstract
The crystal structure of the 92-nucleotide L1-specific fragment of 23S rRNA from Haloarcula marismortui (Hma) has been determined at 3.3 Å resolution. Similar to the corresponding bacterial rRNA fragments, this structure contains joined helix 76-77 topped by an approximately globular structure formed by
[...] Read more.
The crystal structure of the 92-nucleotide L1-specific fragment of 23S rRNA from Haloarcula marismortui (Hma) has been determined at 3.3 Å resolution. Similar to the corresponding bacterial rRNA fragments, this structure contains joined helix 76-77 topped by an approximately globular structure formed by the residual part of the L1 stalk rRNA. The position of HmaL1 relative to the rRNA was found by its docking to the rRNA fragment using the L1-rRNA complex from Thermus thermophilus as a guide model. In spite of the anomalous negative charge of the halophilic archaeal protein, the conformation of the HmaL1-rRNA interface appeared to be very close to that observed in all known L1-rRNA complexes. The designed structure of the L1 stalk was incorporated into the H. marismortui 50S ribosomal subunit. Comparison of relative positions of L1 stalks in 50S subunits from H. marismortui and T. thermophilus made it possible to reveal the site of inflection of rRNA during the ribosome function. Full article
(This article belongs to the Special Issue Recent Advances in Protein Crystallography)
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Open AccessArticle Crystal Structure of the Substrate-Binding Domain from Listeria monocytogenes Bile-Resistance Determinant BilE
Crystals 2016, 6(12), 162; doi:10.3390/cryst6120162
Received: 28 October 2016 / Revised: 29 November 2016 / Accepted: 6 December 2016 / Published: 9 December 2016
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Abstract
BilE has been reported as a bile resistance determinant that plays an important role in colonization of the gastrointestinal tract by Listeria monocytogenes, the causative agent of listeriosis. The mechanism(s) by which BilE mediates bile resistance are unknown. BilE shares significant sequence
[...] Read more.
BilE has been reported as a bile resistance determinant that plays an important role in colonization of the gastrointestinal tract by Listeria monocytogenes, the causative agent of listeriosis. The mechanism(s) by which BilE mediates bile resistance are unknown. BilE shares significant sequence similarity with ATP-binding cassette (ABC) importers that contribute to virulence and stress responses by importing quaternary ammonium compounds that act as compatible solutes. Assays using related compounds have failed to demonstrate transport mediated by BilE. The putative substrate-binding domain (SBD) of BilE was expressed in isolation and the crystal structure solved at 1.5 Å. Although the overall fold is characteristic of SBDs, the binding site varies considerably relative to the well-characterized homologs ProX from Archaeoglobus fulgidus and OpuBC and OpuCC from Bacillus subtilis. This suggests that BilE may bind an as-yet unknown ligand. Elucidation of the natural substrate of BilE could reveal a novel bile resistance mechanism. Full article
(This article belongs to the Special Issue Recent Advances in Protein Crystallography)
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Review

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Open AccessReview An Overview of the Top Ten Detergents Used for Membrane Protein Crystallization
Crystals 2017, 7(7), 197; doi:10.3390/cryst7070197
Received: 7 June 2017 / Revised: 26 June 2017 / Accepted: 28 June 2017 / Published: 1 July 2017
Cited by 1 | PDF Full-text (5018 KB) | HTML Full-text | XML Full-text
Abstract
To study integral membrane proteins, one has to extract them from the membrane—the step that is typically achieved by the application of detergents. In this mini-review, we summarize the top 10 detergents used for the structural analysis of membrane proteins based on the
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To study integral membrane proteins, one has to extract them from the membrane—the step that is typically achieved by the application of detergents. In this mini-review, we summarize the top 10 detergents used for the structural analysis of membrane proteins based on the published results. The aim of this study is to provide the reader with an overview of the main properties of available detergents (critical micelle concentration (CMC) value, micelle size, etc.) and provide an idea of what detergents to may merit further study. Furthermore, we briefly discuss alternative solubilization and stabilization agents, such as polymers. Full article
(This article belongs to the Special Issue Recent Advances in Protein Crystallography)
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Open AccessReview The Synergetic Effects of Combining Structural Biology and EPR Spectroscopy on Membrane Proteins
Crystals 2017, 7(4), 117; doi:10.3390/cryst7040117
Received: 14 February 2017 / Revised: 9 April 2017 / Accepted: 12 April 2017 / Published: 20 April 2017
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Abstract
Protein structures as provided by structural biology such as X-ray crystallography, cryo-electron microscopy and NMR spectroscopy are key elements to understand the function of a protein on the molecular level. Nonetheless, they might be error-prone due to crystallization artifacts or, in particular in
[...] Read more.
Protein structures as provided by structural biology such as X-ray crystallography, cryo-electron microscopy and NMR spectroscopy are key elements to understand the function of a protein on the molecular level. Nonetheless, they might be error-prone due to crystallization artifacts or, in particular in case of membrane-imbedded proteins, a mostly artificial environment. In this review, we will introduce different EPR spectroscopy methods as powerful tools to complement and validate structural data gaining insights in the dynamics of proteins and protein complexes such that functional cycles can be derived. We will highlight the use of EPR spectroscopy on membrane-embedded proteins and protein complexes ranging from receptors to secondary active transporters as structural information is still limited in this field and the lipid environment is a particular challenge. Full article
(This article belongs to the Special Issue Recent Advances in Protein Crystallography)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Radiation Damage in Macromolecular Crystallography
Authors: Helena Taberman
Affiliation: Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom

Title: State-of-the Art Behavioral Characterizations of the PB2cap Binding Domain Accelerate Inhibitor Design
Authors: Amanda Constantinides, Chelsea Severin, Ryan Gummper, Xiaofeng Zheng and Ming Luo
Abstract: Influenza A and B’s evolutionary adaptations are no match for modern visualization technology. X-ray crystallographic structural determinations of Influenza A’s PB2 cap binding domain (PB2cap) have dynamically improved the behavioral characterization of Influenza’s RNA-dependent RNA polymerase machinery (PA, PB2, and PB1). Structurally resembling the human hand by the catalytic PB1 subunit, PA lies near the finger region, and PB2 lies near the thumb region. PB2 “cap-snatches” the host cell’s pre-mRNA, while PA’s endonuclease cuts it 10-13 nucleotides downstream and transfers it to PB1, where viral mRNA is synthesized (Tarendeau et al., 2007). Precisely targeting the PB2cap binding domain with a small molecule inhibitor will halt viral proliferation via interference with cap-snatching behavior. Unliganded wild-type, liganded, and unliganded mutant PB2cap from A/California/07/2009 H1N1 was expressed in Escherichia coli, purified by Nickel Affinity and Size Exclusion chromatography, crystallized, and subjected to X-ray diffraction experiments. Structures were solved by the molecular replacement method, refined, and deposited in the Protein Data Bank (PDB). Structural determinations revealed the functions of Glu361, Lys376, His357, Phe404, Phe323, Lys339, His432, Asn429, Gln406, and Met401 in the Influenza A PB2cap binding domain (Severin et al., 2016) and the dissociation of the Influenza A PB2cap C-terminal domain (residues 446-479) upon ligand binding (Constantinides et al., 2017). Understanding the behavior of these residues will aid in the ultimate development of a small-molecule inhibitor that binds both Influenza A and B PB2cap.

Title: High-resolution crystal structure of RpoS fragment including a partial region 1.2 and region 2 from the intracellular pathogen Legionella pneumophila
Authors:
Nannan Zhang, Xiaofang Chen, Xiaojian Gong, Honghua Ge*
Affiliation:
Institute of Health Sciences, Anhui University, Hefei, Anhui 230601, China
Abstract:
Legionella pneumophila RpoS (LpRpoS) is an alternative sigma factor of RNA polymerase (RNAP) essential for virulence and stress resistance. To investigate the mechanism of RpoS in the intracellular pathogen L. pneumophila, we determined the high-resolution crystal structure of the LpRpoS (residues 95-194) containing a partial region 1.2 and region 2 at 1.6 A resolution. The structure reveals that the conserved residues are critical for promoter melting, DNA and core RNAP binding. The differences in regulatory factor binding sites between Escherichia coli RpoS and LpRpoS suggest that LpRpoS may employ a distinct mechanism to recruit alternative regulatory factors controlling transcription initiation.

 

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