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Crystals
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X-ray Protein Crystallography
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X-ray Protein Crystallography

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

Deadline for manuscript submissions: 31 December 2024 | Viewed by 5149

Special Issue Editor

Prof. Dr. Ki Hyun Nam

E-Mail Website
Guest Editor
College of General Education, Kookmin University, Seoul 02707, Republic of Korea
Interests: serial crystallography; serial femtosecond crystallography; room temperature structure; X-ray crystallography; molecular dynamics; macromolecular crystallography
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Structural biology research employing X-ray crystallography techniques is a valuable tool for comprehending biological and chemical processes at the atomic level, as well as for gaining insights into the design of new drugs and the engineering of industrially used enzymes. This Special Issue aims to serve as a unique multidisciplinary platform, encompassing a wide spectrum of research articles, reviews, and research prospects associated with X-ray crystallography-based structural biology techniques. We invite papers that address protein structures and functions, traditional X-ray crystallography, serial crystallography, crystallization, data processing, and radiation damage to X-ray crystallography.

Dr. Ki Hyun Nam
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 2100 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 crystallography
  • X-ray crystallography
  • serial crystallography
  • structure determination
  • crys-tallization
  • data processing
  • radiation damage

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Published Papers (4 papers)

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Research

10 pages, 627 KiB  
Article
Structural Insights into Phycocyanin Langmuir–Blodgett Multilayers via Serial Femtosecond Crystallography with X-ray Free-Electron Laser
by Eugenia Pechkova, Fabio Massimo Speranza, Paola Ghisellini, Stefano Fiordoro, Cristina Rando and Roberto Eggenhöffner
Crystals 2024, 14(9), 767; https://doi.org/10.3390/cryst14090767 - 29 Aug 2024
Viewed by 688
Abstract
Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) has revolutionized classical X-ray diffraction experiments by utilizing ultra-short, intense, and coherent X-ray pulses. However, the SFX approach still requires thousands of nearly identical samples, leading to significant protein consumption. We propose utilizing Langmuir–Blodgett [...] Read more.
Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) has revolutionized classical X-ray diffraction experiments by utilizing ultra-short, intense, and coherent X-ray pulses. However, the SFX approach still requires thousands of nearly identical samples, leading to significant protein consumption. We propose utilizing Langmuir–Blodgett protein multilayers, which are characterized by long-range order, thermal stability, and the ability to induce protein crystallization, even in proteins that cannot be crystallized by conventional methods. This study aimed to combine the intrinsic properties of Langmuir–Blodgett multilayers with advanced XFEL techniques at the Linac Coherent Light Source. Since the macromolecule organization can be explored in nano or 2D crystals exploiting the properties of SFX–XFEL radiation that enable the capture of high-resolution diffraction images before radiation damage occurs, we propose Langmuir–Blodgett protein nanofilm technology as a novel approach for direct “on-chip” protein sample preparation. The present study extends previous investigations into Langmuir–Blodgett phycocyanin multilayer nanofilms using synchrotron radiation cryo-EM microscopy and second-order nonlinear imaging of chiral crystal (SONICC) experiments. We also examined the thermal stability of phycocyanin Langmuir–Blodgett multilayered films deposited on Si3N4 membranes to evaluate structural changes occurring at 150 °C compared with room temperature. Phycocyanin Langmuir–Blodgett films are worthy of investigation in view of their suitability for tissue engineering and other applications due to their thermal integrity and stability as the results of the present investigation reveal. Full article
(This article belongs to the Special Issue X-ray Protein Crystallography)
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12 pages, 2347 KiB  
Article
Crystallographic Data Collection Using a Multilayer Monochromator on an Undulator Beamline at the Shanghai Synchrotron Radiation Facility
by Chenyu Zhang, Qin Xu, Weiwei Wang, Miao Liang, Li Yu, Minjun Li, Zhimin Zhu, Liqing Huang, Qianhui Li, Feng Yu, Yuzhu Wang, Huan Zhou and Qisheng Wang
Crystals 2024, 14(2), 199; https://doi.org/10.3390/cryst14020199 - 19 Feb 2024
Viewed by 1462
Abstract
To resolve photons hungry for weak diffraction samples by the crystallographic method, a double-multilayer monochromator (DMM) was employed on an undulator beamline (BL17UM) at the Shanghai Synchrotron Radiation Facility (SSRF) to provide a focused sub-micron beam with high brightness for macromolecular crystallography experiments. [...] Read more.
To resolve photons hungry for weak diffraction samples by the crystallographic method, a double-multilayer monochromator (DMM) was employed on an undulator beamline (BL17UM) at the Shanghai Synchrotron Radiation Facility (SSRF) to provide a focused sub-micron beam with high brightness for macromolecular crystallography experiments. High-quality crystallographic datasets from model protein crystal samples were collected and processed by an existing crystallographic program for structure solution and refinement. The data quality was compared with datasets from a normal silicon crystal monochromator to evaluate the bandwidth of the DMM effect on these crystallographic data. This experiment demonstrates that multilayer optics on an undulator beamline may play a valuable role in satisfying the demands of structure-related research, which requires novel methods. Full article
(This article belongs to the Special Issue X-ray Protein Crystallography)
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12 pages, 3460 KiB  
Article
Fixed-Target Pink-Beam Serial Synchrotron Crystallography at Pohang Light Source II
by Yongsam Kim and Ki Hyun Nam
Crystals 2023, 13(11), 1544; https://doi.org/10.3390/cryst13111544 - 27 Oct 2023
Cited by 4 | Viewed by 1303
Abstract
Serial crystallography (SX) enables the determination of the structure of macromolecules or small molecules with minimal radiation damage. In particular, biomolecule structures determined using the SX technique have the advantage of providing room-temperature crystal structures with high biological relevance. The SX technique requires [...] Read more.
Serial crystallography (SX) enables the determination of the structure of macromolecules or small molecules with minimal radiation damage. In particular, biomolecule structures determined using the SX technique have the advantage of providing room-temperature crystal structures with high biological relevance. The SX technique requires numerous crystals to be collected to complete three-dimensional structural information. To minimize crystal sample consumption, we introduced SX data collection with fixed-target (FT) pink-beam serial synchrotron crystallography (SSX) at the 1C beamline of Pohang Light Source II. A new sample holder consisting of a magnetic frame with a nylon mesh was developed for easy sample handling. The FT-pink-SSX diffraction data were collected by continuously scanning X-rays using a stepping motor. The room-temperature structures of glucose isomerase and lysozyme were successfully determined at a resolution of 1.7 and 2.2 Å, respectively. The use of pink-beam FT-SSX in experimental applications and data acquisition for large beam sizes is discussed. Our results provide useful information for future pink-beam SSX and SX data collection using large X-ray beams. Full article
(This article belongs to the Special Issue X-ray Protein Crystallography)
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11 pages, 3099 KiB  
Article
Crystal Structure and Sequence Analysis of N5, N10-Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase Enzyme from Porphyromonas gingivalis
by Sehyeok Im, Hackwon Do, Jisub Hwang, Youn-Soo Shim and Jun Hyuck Lee
Crystals 2023, 13(10), 1489; https://doi.org/10.3390/cryst13101489 - 13 Oct 2023
Viewed by 1219
Abstract
The methylenetetrahydrofolate dehydrogenase–cyclohydrolase (FolD) enzyme has a dual activity of N5,N10-methylenetetrahydrofolate dehydrogenase and cyclohydrolase. This enzyme plays a critical role in the chemical modification of tetrahydrofolate, which is an important coenzyme involved in the synthesis of DNA, RNA, and amino acids. Therefore, bacterial [...] Read more.
The methylenetetrahydrofolate dehydrogenase–cyclohydrolase (FolD) enzyme has a dual activity of N5,N10-methylenetetrahydrofolate dehydrogenase and cyclohydrolase. This enzyme plays a critical role in the chemical modification of tetrahydrofolate, which is an important coenzyme involved in the synthesis of DNA, RNA, and amino acids. Therefore, bacterial FolD has been studied as a potential drug target for the development of antibiotics. Here, we determined the crystal structure of FolD (PgFolD) from the oral pathogen Porphyromonas gingivalis at 2.05 Å resolution using the molecular replacement method. The crystal structure of PgFolD was successfully refined to a crystallographic R-factor of 21.4% (Rfree = 23.8%). The crystals belong to the space group of P4322 with the unit cell parameters of a = 110.7 Å, b = 110.7 Å, and c = 69.8 Å, containing one subunit in the asymmetric unit. Our analytical size-exclusion chromatography results indicated that PgFolD forms a stable dimer in solution. Additionally, structural and sequence comparison studies with previously known FolDs revealed that PgFolD has a different substrate-binding site residue composition. These findings provide valuable insights for the structure-based development of specific inhibitors against the Porphyromonas gingivalis pathogen. Full article
(This article belongs to the Special Issue X-ray Protein Crystallography)
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