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Crystals
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Macromolecular Serial Crystallography (Volume II)
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Macromolecular Serial Crystallography (Volume II)

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

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 12644

Special Issue Editor

Dr. Jose Manuel Martin Garcia

E-Mail Website
Guest Editor
Department of Crystallography & Structural Biology, Institute of Physical Chemistry Blas Cabrera (IQF-BC), CSIC Serrano 119, 28006 Madrid, Spain
Interests: macromolecular serial crystallography at synchrotrons radiation sources and X-ray free electron lasers (XFELs); structural biology; protein dynamics; drug discovery; development of protein micro-crystallization and sample delivery methods for serial crystallography
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

After the publication of the first volume of the Special Issue “Macromolecular Serial Crystallography” in Crystals (https://0-www-mdpi-com.brum.beds.ac.uk/journal/crystals/special_issues/Macromolecular_Serial_Crystallography), we are now delighted to announce the launch of the second volume on this topic. Room temperature macromolecular serial crystallography started to gain popularity about ten years ago when the first serial femtosecond crystallography experiment was performed at the first X-ray free-electron laser (XFEL) ever built. This cutting-edge technology has enabled structural biologists access to previously restricted scientific areas (e.g., macromolecular dynamics) for conventional macromolecular crystallography. Until recently, the number of structural biologists using these facilities was limited to just a few groups. However, this number has increased notably in the past 3–4 years due to 1) the appearance of XFEL facilities with advanced technology, allowing for higher data collection rates (megahertz, MHz) and improved data processing pipelines, 2) improved sample efficiency methods, which allows for collecting full data sets at much lower sample consumption, and 3) the successful adaptation of serial crystallography strategies at most 3rd generation synchrotron facilities, allowing a fruitful synergy between synchrotrons and XFELs that have accelerated the access and impact to an even larger community.

Thus, the main goal of this Special Issue “Macromolecular Serial Crystallography II” will be to gather both research and review articles from experts in the filed (chemists, biologists, physicists, and structural biologists), with the ultimate goal of creating an international platform that provides rich and reference information on the latest advances and exciting discoveries in the still-emerging technology of serial crystallography at XFELs and its adaptation to 3rd generation synchrotron radiation sources.

Dr. José Manuel Martín-García
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 submissions that pass pre-check are 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 2600 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

  • Protein structure and dynamics
  • Drug discovery science
  • Serial femtosecond crystallography
  • X-ray free electron lasers
  • Synchrotron radiation sources
  • Sample delivery techniques
  • Data Processing and analysis for serial crystallography

Published Papers (5 papers)

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Editorial

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2 pages, 169 KiB  
Editorial
Macromolecular Serial Crystallography (Volume II)
by Jose M. Martin-Garcia
Crystals 2022, 12(6), 768; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst12060768 - 26 May 2022
Cited by 1 | Viewed by 1018
Abstract
The successful adaptation of the serial macromolecular crystallography approach at most 3rd generation synchrotron facilities allows a fruitful synergy between synchrotrons and XFELs that have accelerated the access and impact of this approach to an even larger community [...] Full article
(This article belongs to the Special Issue Macromolecular Serial Crystallography (Volume II))

Research

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9 pages, 1063 KiB  
Article
The Gamification of XFEL Education Using XFEL Crystal Blaster
by Fiacre Kabayiza, Sarah B. Woodruff and William J. Bauer
Crystals 2022, 12(5), 671; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst12050671 - 06 May 2022
Cited by 2 | Viewed by 2068
Abstract
Novel groundbreaking techniques, such as serial femtosecond crystallography (SFX), which utilizes X-ray free-electron lasers (XFELs), have led to impressive advances in the field of structural biology. However, educating the next generation of scientists on this complex, advanced, and continuously evolving field can be [...] Read more.
Novel groundbreaking techniques, such as serial femtosecond crystallography (SFX), which utilizes X-ray free-electron lasers (XFELs), have led to impressive advances in the field of structural biology. However, educating the next generation of scientists on this complex, advanced, and continuously evolving field can be challenging. Gamification has been shown to be an effective strategy for engaging new learners and has a positive influence on knowledge acquisition, student satisfaction, and motivation. Here, we present an educational game, XFEL Crystal Blaster, aimed at increasing middle and high school students’ exposure to advanced topics in crystallography. This simple and accessible game is available on multiple platforms, is intuitive for gamers, and requires no prior knowledge of the game’s content. The assessment of students’ experiences with the game suggests that the XFEL Crystal Blaster game is likely to develop some introductory knowledge of XFELs and X-ray crystallography and increase interest in learning more about X-ray crystallography. Both of these outcomes are key to engaging students in the exploration of emerging scientific fields that are potential career pathways. Full article
(This article belongs to the Special Issue Macromolecular Serial Crystallography (Volume II))
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15 pages, 2950 KiB  
Article
Crystallization of ApoA1 and ApoE4 Nanolipoprotein Particles and Initial XFEL-Based Structural Studies
by Megan L. Shelby, Deepshika Gilbile, Thomas D. Grant, William J. Bauer, Brent Segelke, Wei He, Angela C. Evans, Natalia Crespo, Pontus Fischer, Tim Pakendorf, Vincent Hennicke, Mark S. Hunter, Alex Batyuk, Miriam Barthelmess, Alke Meents, Tonya L. Kuhl, Matthias Frank and Matthew A. Coleman
Crystals 2020, 10(10), 886; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst10100886 - 01 Oct 2020
Cited by 6 | Viewed by 3851
Abstract
Nanolipoprotein particles (NLPs), also called “nanodiscs”, are discoidal particles with a patch of lipid bilayer corralled by apolipoproteins. NLPs have long been of interest due to both their utility as membrane-model systems into which membrane proteins can be inserted and solubilized and their [...] Read more.
Nanolipoprotein particles (NLPs), also called “nanodiscs”, are discoidal particles with a patch of lipid bilayer corralled by apolipoproteins. NLPs have long been of interest due to both their utility as membrane-model systems into which membrane proteins can be inserted and solubilized and their physiological role in lipid and cholesterol transport via high-density lipoprotein (HDL) and low-density lipoprotein (LDL) maturation, which are important for human health. Serial femtosecond crystallography (SFX) at X-ray free electron lasers (XFELs) is a powerful approach for structural biology of membrane proteins, which are traditionally difficult to crystallize as large single crystals capable of producing high-quality diffraction suitable for structure determination. To facilitate understanding of the specific role of two apolipoprotein/lipid complexes, ApoA1 and ApoE4, in lipid binding and HDL/LDL particle maturation dynamics, and to develop new SFX methods involving NLP membrane protein encapsulation, we have prepared and crystallized homogeneous populations of ApoA1 and ApoE4 NLPs. Crystallization of empty NLPs yields semi-ordered objects that appear crystalline and give highly anisotropic and diffuse X-ray diffraction, similar to fiber diffraction. Several unit cell parameters were approximately determined for both NLPs from these measurements. Thus, low-background, sample conservative methods of delivery are critical. Here we implemented a fixed target sample delivery scheme utilizing the Roadrunner fast-scanning system and ultra-thin polymer/graphene support films, providing a low-volume, low-background approach to membrane protein SFX. This study represents initial steps in obtaining structural information for ApoA1 and ApoE4 NLPs and developing this system as a supporting scaffold for future structural studies of membrane proteins crystalized in a native lipid environment. Full article
(This article belongs to the Special Issue Macromolecular Serial Crystallography (Volume II))
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9 pages, 1856 KiB  
Article
EM-detwin: A Program for Resolving Indexing Ambiguity in Serial Crystallography Using the Expectation-Maximization Algorithm
by Yingchen Shi and Haiguang Liu
Crystals 2020, 10(7), 588; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst10070588 - 08 Jul 2020
Cited by 3 | Viewed by 2348
Abstract
Serial crystallography (SX), first used as an application of X-ray free-electron lasers (XFELs), is becoming a useful method to determine atomic-resolution structures of proteins from micrometer-sized crystals with bright X-ray sources. Because of unknown orientations of crystals in SX, indexing ambiguity issue arises [...] Read more.
Serial crystallography (SX), first used as an application of X-ray free-electron lasers (XFELs), is becoming a useful method to determine atomic-resolution structures of proteins from micrometer-sized crystals with bright X-ray sources. Because of unknown orientations of crystals in SX, indexing ambiguity issue arises when the symmetry of Bravais lattice is higher than the space group symmetry, making some diffraction signals wrongly merged to the total intensity in twinned orientations. In this research, we developed a program within the CrystFEL framework, the EM-detwin, to resolve this indexing ambiguity problem based on the expectation-maximization algorithm. Testing results on the performance of the EM-detwin have demonstrated its usefulness in correctly indexing diffraction data as a valuable tool for SX data analysis. Full article
(This article belongs to the Special Issue Macromolecular Serial Crystallography (Volume II))
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Review

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16 pages, 3210 KiB  
Review
Insights into Solution Structures of Photosynthetic Protein Complexes from Small-Angle Scattering Methods
by Maksym Golub, Adrian Kölsch, Artem Feoktystov, Athina Zouni and Jörg Pieper
Crystals 2021, 11(2), 203; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst11020203 - 19 Feb 2021
Cited by 10 | Viewed by 2484
Abstract
High-resolution structures of photosynthetic pigment–protein complexes are often determined using crystallography or cryo-electron microscopy (cryo-EM), which are restricted to the use of protein crystals or to low temperatures, respectively. However, functional studies and biotechnological applications of photosystems necessitate the use of proteins isolated [...] Read more.
High-resolution structures of photosynthetic pigment–protein complexes are often determined using crystallography or cryo-electron microscopy (cryo-EM), which are restricted to the use of protein crystals or to low temperatures, respectively. However, functional studies and biotechnological applications of photosystems necessitate the use of proteins isolated in aqueous solution, so that the relevance of high-resolution structures has to be independently verified. In this regard, small-angle neutron and X-ray scattering (SANS and SAXS, respectively) can serve as the missing link because of their capability to provide structural information for proteins in aqueous solution at physiological temperatures. In the present review, we discuss the principles and prototypical applications of SANS and SAXS using the photosynthetic pigment–protein complexes phycocyanin (PC) and Photosystem I (PSI) as model systems for a water-soluble and for a membrane protein, respectively. For example, the solution structure of PSI was studied using SAXS and SANS with contrast matching. A Guinier analysis reveals that PSI in solution is virtually free of aggregation and characterized by a radius of gyration of about 75 Å. The latter value is about 10% larger than expected from the crystal structure. This is corroborated by an ab initio structure reconstitution, which also shows a slight expansion of Photosystem I in buffer solution at room temperature. In part, this may be due to conformational states accessible by thermally activated protein dynamics in solution at physiological temperatures. The size of the detergent belt is derived by comparison with SANS measurements without detergent match, revealing a monolayer of detergent molecules under proper solubilization conditions. Full article
(This article belongs to the Special Issue Macromolecular Serial Crystallography (Volume II))
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