Special Issue "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: 31 March 2022.

Special Issue Editor

Dr. José Manuel Martín-García
E-Mail Website1 Website2
Guest Editor
Department of Crystallography & Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, Madrid, Spain
Interests: serial crystallography; X-ray free-electron lasers; time-resolved serial crystallography; protein structure and dynamics; structure-based drug discovery
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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

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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 (3 papers)

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Research

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Article
Crystallization of ApoA1 and ApoE4 Nanolipoprotein Particles and Initial XFEL-Based Structural Studies
Crystals 2020, 10(10), 886; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst10100886 - 01 Oct 2020
Cited by 2 | Viewed by 1380
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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Article
EM-detwin: A Program for Resolving Indexing Ambiguity in Serial Crystallography Using the Expectation-Maximization Algorithm
Crystals 2020, 10(7), 588; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst10070588 - 08 Jul 2020
Cited by 2 | Viewed by 704
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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Review
Insights into Solution Structures of Photosynthetic Protein Complexes from Small-Angle Scattering Methods
Crystals 2021, 11(2), 203; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst11020203 - 19 Feb 2021
Viewed by 868
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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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: Protein crystallography at X-ray Free-Electron Lasers (XFELs)
Author: Wei Liu, Arizona State University
Abstract: Protein crystallography has been successful in structural biology studies for decades. The atomic details solved by XRD of biological macromolecules reveal the mechanism of important biological activity, and therefore facilitate the related drug discovery. However, the protein crystallography is hindered due to the necessity of relatively large size protein crystals. The application of X-ray free electron laser (XFEL) alleviates the uncertain and time-consuming crystal size optimization process. Tens of thousands micron-sized protein crystals are injected to the ultra-brilliant, femtosecond beam and the diffraction patterns from each crystal are merged and processed to build the complete model of the protein. In this paper, the fundamental principle of XFEL is introduced, the successful outcomes of XFEL with protein structure determination and the great potential in time resolved studies are summarized and discussed.
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