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Crystals
Special Issues
Macromolecular Crystallography: Progress and Prospects
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Macromolecular Crystallography: Progress and Prospects

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

Deadline for manuscript submissions: closed (15 September 2023) | Viewed by 4751

Special Issue Editors

Dr. Vasundara Srinivasan

E-Mail Website
Guest Editor
Laboratory for Structural Biology of Infection and Inflammation, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Universität Hamburg, Build. 22a, c/o DESY, 22607 Hamburg, Germany
Interests: structural biology; membrane proteins; SARS-CoV-2; mechanistic enzymology; structure-based drug discovery; time-resolved serial crystallography
Special Issues, Collections and Topics in MDPI journals
Dr. Santosh Panjikar

E-Mail Website
Guest Editor
1. ANSTO, Australian Synchrotron, 800 Blackburn Road, Clayton 3168, Australia
2. Department of Molecular Biology and Biochemistry, Monash University, Clayton, Australia
Interests: structural biology; graphene-based biosensor; structural determination of macromolecules and software development in crystallography

Special Issue Information

Dear Colleagues,

X-ray diffraction is a prime technique to reveal the three-dimensional structures of biological molecules (proteins, viruses, and nucleic acids) to atomic resolution (~1-3 Å). Static crystallographic snapshots have been used in revealing the detailed mechanisms by which macromolecules carry out their functions. Recent technical developments have made it possible to observe the structural dynamics of macromolecules and their complexes through various diffraction techniques available at third- or fourth-generation synchrotrons.

We invite researchers to contribute to this Special Issue on “Macromolecular Crystallography: Progress and Prospects”, which is intended to serve as a unique forum covering broad aspects and the current status in macromolecular crystallography.

Dr. Vasundara Srinivasan
Dr. Santosh Panjikar
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 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

  • time-resolved serial crystallography at XFEL and synchrotrons (SFX, SSX)
  • pink-beam crystallography
  • small-angle X-ray scattering (SAXS)
  • structural-based drug discovery
  • mechanistic enzymology
  • membrane proteins
  • macromolecular complexes
  • software developments for macromolecular crystallography
  • deep learning and artificial intelligence

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Further information on MDPI's Special Issue polices can be found here.

Published Papers (3 papers)

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Research

13 pages, 3228 KiB  
Article
Refining Protein Envelopes with a Transition Region for Enhanced Direct Phasing in Protein Crystallography
by Ruijiang Fu, Wu-Pei Su and Hongxing He
Crystals 2024, 14(1), 85; https://doi.org/10.3390/cryst14010085 - 16 Jan 2024
Viewed by 1062
Abstract
In protein crystallography, the determination of an accurate protein envelope is of paramount importance for ab initio phasing of diffraction data. In our previous work, we introduced an approach to ascertain the protein envelope by seeking an optimal cutoff value on a weighted-average [...] Read more.
In protein crystallography, the determination of an accurate protein envelope is of paramount importance for ab initio phasing of diffraction data. In our previous work, we introduced an approach to ascertain the protein envelope by seeking an optimal cutoff value on a weighted-average density map. In this paper, we present a significant advancement in our approach by focusing on identifying a transition region that demarcates the boundary between the protein and solvent regions, rather than relying solely on a single cutoff value. Within this transition region, we conducted a meticulous search for the protein envelope using a finer map and our proposed transition hybrid input–output (THIO) algorithm. Through this improvement, we achieved a refined protein envelope even when starting from random phases, enabling us to determine protein structures with irregular envelopes and successfully phase crystals with reduced solvent contents. To validate the efficacy of our method, we conducted tests using real diffraction data from five protein crystals, each containing solvent contents ranging from 60% to 65%. Solving these structures through conventional direct methods proved difficult due to the limited solvent content. The mean phase error obtained through our proposed method was about 30°. The reconstructed model matched with the structure in the protein data bank with a root mean square deviation (r.m.s.d.) of about 1 Å. These results serve as compelling evidence that the utilization of the proposed transition region in conjunction with the THIO algorithm contributes significantly to the construction of a reliable protein envelope. This, in turn, becomes indispensable for the direct phasing of protein crystals with lower solvent contents. Full article
(This article belongs to the Special Issue Macromolecular Crystallography: Progress and Prospects)
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11 pages, 897 KiB  
Communication
Ethoxylate Polymer-Based 96-Well Screen for Protein Crystallization
by Ulrike Demmer, Olivier N. Lemaire, Mélissa Belhamri and Ulrich Ermler
Crystals 2023, 13(10), 1519; https://doi.org/10.3390/cryst13101519 - 19 Oct 2023
Viewed by 1325
Abstract
Crystallization is the limiting step in X-ray structure determination of biological macromolecules. As crystallization experiments can be largely automatized, the diversity of precipitant solutions is often the determinant factor to obtain crystals of high quality. Here, we introduce a 96-well screening kit of [...] Read more.
Crystallization is the limiting step in X-ray structure determination of biological macromolecules. As crystallization experiments can be largely automatized, the diversity of precipitant solutions is often the determinant factor to obtain crystals of high quality. Here, we introduce a 96-well screening kit of crystallization conditions, centered on three ethoxylate-based organic polymers as precipitants and various additional compounds to promote crystal formation. This crystallization screen was tested on various non-standard proteins from bacteria and archaea. Structure determination succeeded for seven out of thirteen targets based on crystals that frequently diffracted to a higher resolution than those obtained with commercially available screening kits. Crystallization hits were rarely similar among the three ethoxylate-based organic polymers and, in comparison, with already available crystallization screens. Hence, the presented crystallization screen is an efficient tool to complement other screens and increase the likelihood of growing crystals suitable for X-ray structure determination. Full article
(This article belongs to the Special Issue Macromolecular Crystallography: Progress and Prospects)
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14 pages, 5669 KiB  
Article
3D Printed Microfluidic Cell for SAXS Time-Resolved Measurements of the Structure of Protein Crystallization Solutions
by Margarita A. Marchenkova, Sergei V. Chapek, Petr V. Konarev, Ksenia B. Ilina, Georgy S. Peters, Yury V. Pisarevsky, Vladimir A. Shishkov, Alexander V. Soldatov and Mikhail V. Kovalchuk
Crystals 2023, 13(6), 938; https://doi.org/10.3390/cryst13060938 - 11 Jun 2023
Cited by 2 | Viewed by 1796
Abstract
A multichannel microfluidic cell (MFC) obtained using 3D printing for studying the structure of complex solutions by small-angle X-ray scattering (SAXS) is described. MFC was tested at the BioMUR beamline of the Kurchatov synchrotron. A comparative analysis of SAXS signal from the standard [...] Read more.
A multichannel microfluidic cell (MFC) obtained using 3D printing for studying the structure of complex solutions by small-angle X-ray scattering (SAXS) is described. MFC was tested at the BioMUR beamline of the Kurchatov synchrotron. A comparative analysis of SAXS signal from the standard capillary and from the developed MFC was carried out, with MFC showing significant advantages. The dynamics of SAXS scattering curves for lysozyme solutions with NaCl precipitant were studied when the protein and precipitant concentrations changed. The obtained time series of data are well consistent with the known data for the lysozyme solution. Full article
(This article belongs to the Special Issue Macromolecular Crystallography: Progress and Prospects)
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