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Special Issue "Frontier of Protein Crystallography"

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: 31 July 2019

Special Issue Editor

Guest Editor
Prof. Dr. Silvano Geremia

CEB Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, Trieste, Italy
E-Mail
Interests: crystallography; structural biology; vitamin B12 proteins; redox-proteins; drug delivery; diagnostics; metals in medicine; bioinorganic chemistry; supramolecular chemistry; nanostructures

Special Issue Information

Dear Colleagues,

Structural biology is a relatively young science, initiated about 60 years ago with the elucidation of the first three-dimensional crystal structure of myoglobin. Protein crystallography continues to develop vigorously and today there are over 120,000 structures deposited at the Protein Data Bank (PDB), 90% of which are from X-ray data. The technological developments behind this rapid growth involves all crucial steps of the pipeline “from gene to structure”: from the developments of wet lab technologies, including recombinant DNA techniques, protein purification and crystallization; to innovative hardware technology, for example brilliant light sources such as synchrotrons and X-ray free electron lasers (XFEL) together with high-frame-rate and ultra-sensitive detectors. An important impetus to protein crystallography has also been provided by soft technology: theoretical foundations, computational algorithm, and software development. The bio-crystallography integrated with cryo-electron microscopy is a major research trend in structural biology and the present Special Issue is aimed at covering frontier technologies and methodologies in protein crystallography, as well as their novel applications.

Prof. Dr. Silvano Geremia
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. Molecules 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 1800 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

  • X-ray crystallography
  • recombinant protein overexpression
  • protein purification
  • protein crystallization
  • cryo-crystallography
  • radiation sources
  • X-ray detectors
  • structural biology software
  • high-throughput crystallography
  • structural biology

Published Papers (1 paper)

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Review

Open AccessReview A Brief History of Charcot-Leyden Crystal Protein/Galectin-10 Research
Molecules 2018, 23(11), 2931; https://doi.org/10.3390/molecules23112931
Received: 12 October 2018 / Revised: 8 November 2018 / Accepted: 8 November 2018 / Published: 9 November 2018
PDF Full-text (2536 KB) | HTML Full-text | XML Full-text
Abstract
Eosinophils are present in tissues, such as the respiratory tract, spleen, lymph nodes and blood vessels. The significant presence of eosinophils in these tissues are associated with various diseases, including asthma, allergies, acute myeloid leukemia, etc. Charcot-Leyden crystal protein/galectin-10 is overexpressed in eosinophils
[...] Read more.
Eosinophils are present in tissues, such as the respiratory tract, spleen, lymph nodes and blood vessels. The significant presence of eosinophils in these tissues are associated with various diseases, including asthma, allergies, acute myeloid leukemia, etc. Charcot-Leyden crystal protein/galectin-10 is overexpressed in eosinophils and has also been identified in basophils and macrophages. In human body, this protein could spontaneously form Charcot-Leyden crystal in lymphocytes or in the lysates of lymphocytes. At present, the role of Charcot-Leyden crystal protein/galectin-10 in lymphocytes is not fully understood. This review summarizes research progress on Charcot-Leyden crystal protein/galectin-10, with emphasis on its history, cellular distributions, relations to diseases, structures and ligand binding specificity. Full article
(This article belongs to the Special Issue Frontier of Protein Crystallography)
Figures

Figure 1

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 MX: current knowledge and new questions
Authors: Elspeth Garman and Martin Weik
Affiliation: Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
Email:
Abstract: Eighteen years of published research on radiation damage to samples held around 100 K during X-ray crystallography has resulted in thorough characterisation of the phenomenon. However, there are still perplexing questions left to be answered in terms of understanding some of the documented effects, and before crystal clear guidance can be given to experimenters on how to minimise them.
This short review will summarise the main observations and remaining issues to be investigated, as well as some new developments coming into main-line diffraction experimental methods at synchrotrons to optimise the information that can be obtained from protein crystals.

Title: The progression of Thermofluor assay in modern protein crystallography and drug discovery
Author: Li-Kai Liu
Affiliation: University of Missouri, USA
Email: liulik@missouri.edu
Abstract: Fluorescence-based thermal stability assay TSA (or differential scanning fluorimetry, DSF) is commonly used as a screening method in a laboratory setting to rapidly detect small molecule ligands that bind and stabilize purified proteins. An unfolding temperature (Tm) is measured by an increase in the signal of a fluorescent dye whose spectral properties change upon binding to an unfolded protein. TSA was originally developed for applications in drug discovery to harness universal biophysical properties of ligand-induced protein stability. This original role has been expanded for target characterization, protein crystallography and drug development over the last decade. To summarize what has been achieved in modern drug discovery, we will review some of the recent advances and critical applications of TSA.

Title: Molecular interactions of the antibody drugs targeting PD-1, PD-L1, and CTLA-4 in immuno-oncology
Author:
Yong-Seok Heo
Affiliation:
Department of Chemistry, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea  
Email:
ysheo@konkuk.ac.kr
Abstract:
Cancer cells can evade immune surveillance through the molecular interactions of immune checkpoint proteins, including PD-1, PD-L1, and CTLA-4. Since 2011, the FDA-approved antibody drugs ipilimumab (Yervoy®), nivolumab (Opdivo®), pembrolizumab (Keytruda®), atezolizumab (Tecentriq®), durvalumab (Imfinzi®), and avelumab (Bavencio®), which blocks the immune checkpoint proteins, have developed a significant breakthrough in the treatment of a wide range of cancers, as they can induce durable therapeutic responses. In recent years, crystal structures related to the antibodies against PD-1, PD-L1, and CTLA-4 have been reported. In this review, we describe the latest structural studies of these monoclonal antibodies and their interactions with the immune checkpoint proteins. A comprehensive analysis of the interactions of these immune checkpoint blockers can provide a better understanding of their therapeutic mechanism of action. The accumulation of the structural studies would provide a basis essential for the rational design of next-generation therapies in immuno-oncology.

Title: Protein Crystallography Unravels the Plant Leucine-Rich Repeat Receptor Kinase (LRR-RK) Activation Mechanism
Authors: Sayan Chakraborty1, Krittin Trihemasava2 and Guozhou Xu1
Affiliations: 1 Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
2 National Institute of Health, Bethesda, Maryland, USA
Email: schakr10@ncsu.edu
Abstract: Secreted peptides are essential mediators for intercellular communication that controls a wide range of biological and developmental activities in plants including stem cell homeostasis, cell proliferation, wound healing, hormone secretion, immunological defenses, and symbiosis with other species. Most of the known secreted peptide ligand receptors belong to the leucine-rich repeat receptor kinase (LRR-RK) family of membrane integral proteins. It is estimated that there are more than 200 members of LRR-RK receptors present in Arabidopsis thaliana, making it the largest family of plant receptor kinases. Genetic and biochemical studies have provided significant information about the peptide ligands and LRR-RKs; however, investigation of complex structures at an atomic level is vital to understand the functions of LRR-RKs and how they regulate various biological processes. Structural characterization of essential plant proteins and other macromolecules have been scarce, which severely limits our understanding of certain biological processes in plants. In comparison to biomedical sciences, the application of X-ray crystallography in plant biology has not nearly been as extensive. The field of plant structural biology, specifically the molecular architecture of plant signaling mechanisms, is a relatively nascent field with limited information available regarding the structural components of this particular realm. In this review, we aim to illustrate the insight gained by studying structures and mechanisms of LRR-RK activation induced by secreted post-translationally modified peptide ligands.

Title: Structure-Based Design of Antivirulence Drugs: Therapeutics for the Post-Antibiotic Era
Author: Zongchao Jia
Affiliation: Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
Email: jia@queensu.ca
Abstract: The alarming rise of bacterial strains that are resistant to available antibiotics, coupled with decades of stagnation in the field of antibiotic development, necessitates exploration of new therapeutic approaches to treat bacterial infections. Targeting bacterial virulence is an attractive alternative to antimicrobial therapy in that this approach disarms pathogens of processes that cause human disease, without placing immediate selective pressure on the target bacterium. The growing number of validated virulence targets for which structural information has been obtained, along with advances in computational power, make the rational design of antivirulence drugs a promising avenue to explore. Here, we review the principles of structure-based drug design and the exciting opportunities this technique presents for antivirulence drug discovery.

Title: High-throughput Crystallization Pipeline at the Crystallography Platform of the Institut Pasteur
Author: Ahmed Haouz
Affiliation: Institut Pasteur, Plateforme de Cristallographie, CNRS‐UMR 3528, Paris, France
Email: ahmed.haouz@pasteur.fr
Abstract: The availability of whole genome sequence data, made possible by significant advances in DNA sequencing technology, led to the emergence of structural genomics projects. These projects have not only greatly increased the number of 3-D structures deposited in the Protein Data Bank during the last two decades, but also influenced the strategy used by the crystallographic community by introducing automation in most stages of the structure-determination pipeline (cloning, expression, purification, crystallization and synchrotron X-ray data collection). Today, dedicated crystallization facilities, many of them open to the general user community, are capable of setting up thousands of screening trials per day. We present here a review of current methods for high-throughput crystallization and procedures to obtain suitable crystals for X-ray diffraction studies. An overview of our results and current technologies available in the crystallography platform at the Institut Pasteur (Paris) is presented as an example.

Title: Structural insights into the regulation mechanism of small GTPase by GEFs
Authors: Sachiko Toma-Fukai1 and Toshiyuki Shimizu2
Affiliations: 1Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan; 2Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
Emails: shimizu@mol.f.u-tokyo.ac.jp; toma@ms.naist.jp
Abstract: Small GTPases are key regulators in cellular events, and their dysfunction causes many types of cancer. The core domain of small GTPases, the G-domain, is composed of three conserved motifs: the phosphate-binding loop (P-loop), switch I, and switch II. These three motifs cooperatively recognize guanine nucleotides and are responsible for GTPase activity. The intrinsic GTP hydrolysis activities of small GTPases are generally low, and they are accelerated by GTPase-activating proteins (GAPs). Guanine-nucleotide exchange factors (GEFs) promote GDP dissociation from small GTPases so that they can bind GTP. When GDP is released from small GTPases and GTP binds to them, a conformational rearrangement of switch I and switch II regions that allows binding to the gamma phosphate occurs and enables small GTPase to interact with downstream effectors. The GTPase switch is turned on by GEF and turned off by GAP. For several decades, crystal structures of many GEFs and GAP have been reported and have shown structural diversity of them. Recently several atypical GEF structures had been reported and reveal their ingenious GEF mechanism. In this review, we focused of the latest structural studies of GEF. To know the variety of GEF mechanism based on atomic resolution structure would provide us the new approach to drug discovery.

Title: Protein Crystallography and Drug Discovery
Authors: Laurent Maveyraud and Lionel Mourey
Affiliation: Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
Email: laurent.maveyraud@ipbs.fr
Abstract: With the advent of structural biology in the drug discovery process, medicinal chemists gained the opportunity to use detailed structural information in order to progress screening hits into leads or drug candidates. X-ray crystallography has proven to be an invaluable tool in this respect, as it is able to provide exquisitely comprehensive structural information about the interaction of a ligand with a pharmacological target. As fragment-based drug discovery emerged in the recent years, X-ray crystallography has also become a powerful screening technology, able to provide structural information on complexes involving low-molecular weight compounds, despite weak binding affinities. Given the low numbers of compounds needed in a fragment library, compared to the hundreds of thousand usually present in drug-like compound libraries, it now becomes feasible to screen a whole fragment library using X-ray crystallography, providing a wealth of structural details that will fuel the fragment to drug process. Here, we review theoretical and practical aspects as well as the pros and cons of using X-crystallography in the drug discovery process.

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