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Crystals
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Novel Structural Studies of Coronavirus Proteins
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Novel Structural Studies of Coronavirus Proteins

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

Deadline for manuscript submissions: closed (31 August 2022) | Viewed by 7509

Special Issue Editors

Prof. Dr. Marc Messerschmidt

E-Mail Website
Guest Editor
Biodesign Institute, Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, USA
Interests: chemistry; crystallography; time resolved diffraction; free electron lasers; synchrotron radiation
Dr. Jeney Wierman

E-Mail Website
Guest Editor
Structural Molecular Biology Group, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA
Interests: serial crystallography; time-resolved dynamics; metalloenzymes; crystallography methods; room temperature crystallography
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,

During the past year, the COVID-19 pandemic’s severity refocused many scientific efforts to research related to SARS-CoV-2. Large facilities worldwide, such as synchrotrons and XFELs, dedicated overwhelming time and energy to this exceptional and ongoing story. The focused timeline and scope of COVID-19 related research will certainly be remembered as an historic effort across many scientific fields, including that of structural biology. Structural studies have shown to be critical in identifying important features for COVID-19 research, and highlighting these studies is a particular motivation for this Special Issue of Crystals. We hope that this serves as a celebration of the contributions from crystallographers worldwide to COVID-19-related research.

Thus, the main goal of this Special Issue, “Novel Structural Studies of Coronavirus Proteins”, will be to gather both research and review articles from experts in the field (chemists, biologists, physicists, and structural biologists), with the ultimate goal of creating an international platform that provides with rich and reference information on the latest advances and exciting discoveries in the field of X-ray crystallography at synchrotrons and XFELs towards understanding the functioning of SARS-CoV-2 to advance develop new drug treatments and vaccines against the ongoing COVID-19 pandemic.

Prof. Dr. Marc Messerschmidt
Dr. Jeney Wierman
Dr. José Manuel Martín-García
Guest Editors

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

  • Coronavirus
  • SArs-CoV-2
  • Novel structures
  • Crystals
  • Time resolved structures
  • X-ray crystallography
  • Structure-based drug discovery
  • X-ray free electron lasers
  • Synchrotrons

Published Papers (2 papers)

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Research

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14 pages, 29402 KiB  
Article
Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography
by Omur Guven, Mehmet Gul, Esra Ayan, J Austin Johnson, Baris Cakilkaya, Gozde Usta, Fatma Betul Ertem, Nurettin Tokay, Busra Yuksel, Oktay Gocenler, Cengizhan Buyukdag, Sabine Botha, Gihan Ketawala, Zhen Su, Brandon Hayes, Frederic Poitevin, Alexander Batyuk, Chun Hong Yoon, Christopher Kupitz, Serdar Durdagi, Raymond G. Sierra and Hasan DeMirciadd Show full author list remove Hide full author list
Crystals 2021, 11(12), 1579; https://doi.org/10.3390/cryst11121579 - 17 Dec 2021
Cited by 7 | Viewed by 3592
Abstract
Since early 2020, COVID-19 has grown to affect the lives of billions globally. A worldwide investigation has been ongoing for characterizing the virus and also for finding an effective drug and developing vaccines. As time has been of the essence, a crucial part [...] Read more.
Since early 2020, COVID-19 has grown to affect the lives of billions globally. A worldwide investigation has been ongoing for characterizing the virus and also for finding an effective drug and developing vaccines. As time has been of the essence, a crucial part of this research has been drug repurposing; therefore, confirmation of in silico drug screening studies have been carried out for this purpose. Here we demonstrated the possibility of screening a variety of drugs efficiently by leveraging a high data collection rate of 120 images/second with the new low-noise, high dynamic range ePix10k2M Pixel Array Detector installed at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Linac Coherent Light Source (LCLS). The X-ray Free-Electron Laser (XFEL) is used for remote high-throughput data collection for drug repurposing of the main protease (Mpro) of SARS-CoV-2 at ambient temperature with mitigated X-ray radiation damage. We obtained multiple structures soaked with nine drug candidate molecules in two crystal forms. Although our drug binding attempts failed, we successfully established a high-throughput Serial Femtosecond X-ray crystallographic (SFX) data collection protocol. Full article
(This article belongs to the Special Issue Novel Structural Studies of Coronavirus Proteins)
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Review

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16 pages, 2315 KiB  
Review
Understanding Cysteine Chemistry Using Conventional and Serial X-ray Protein Crystallography
by Nathan Smith and Mark A. Wilson
Crystals 2022, 12(11), 1671; https://doi.org/10.3390/cryst12111671 - 19 Nov 2022
Viewed by 2528
Abstract
Proteins that use cysteine residues for catalysis or regulation are widely distributed and intensively studied, with many biomedically important examples. Enzymes where cysteine is a catalytic nucleophile typically generate covalent catalytic intermediates whose structures are important for understanding mechanism and for designing targeted [...] Read more.
Proteins that use cysteine residues for catalysis or regulation are widely distributed and intensively studied, with many biomedically important examples. Enzymes where cysteine is a catalytic nucleophile typically generate covalent catalytic intermediates whose structures are important for understanding mechanism and for designing targeted inhibitors. The formation of catalytic intermediates can change enzyme conformational dynamics, sometimes activating protein motions that are important for catalytic turnover. However, these transiently populated intermediate species have been challenging to structurally characterize using traditional crystallographic approaches. This review describes the use and promise of new time-resolved serial crystallographic methods to study cysteine-dependent enzymes, with a focus on the main (Mpro) and papain-like (PLpro) cysteine proteases of SARS-CoV-2, as well as on other examples. We review features of cysteine chemistry that are relevant for the design and execution of time-resolved serial crystallography experiments. In addition, we discuss emerging X-ray techniques, such as time-resolved sulfur X-ray spectroscopy, that may be able to detect changes in sulfur charge states and covalency during catalysis or regulatory modification. In summary, cysteine-dependent enzymes have features that make them especially attractive targets for new time-resolved serial crystallography approaches, which can reveal both changes to enzyme structures and dynamics during catalysis in crystalline samples. Full article
(This article belongs to the Special Issue Novel Structural Studies of Coronavirus Proteins)
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