State-of-the-Art Protein X-Ray Crystallography

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Biophysics: Structure, Dynamics, and Function".

Deadline for manuscript submissions: 31 August 2025 | Viewed by 656

Special Issue Editors


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Guest Editor
Department of Physics and Texas Center for Superconductivity, University of Houston, Houston, TX 77204, USA
Interests: direct phasing methods for solving the X-ray phase problem in protein crystallography
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Department of Physics, School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
Interests: iterative phasing methods to solve the phase problem of protein crystallography; deep learning methods to solve the phase problem of X-ray diffraction; deep learning methods to reconstruct protein structures from cryo-EM density maps
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

X-ray crystallography stands as the main technique for detailed protein structural determination. A bottleneck of this procedure is the construction of a protein density map from X-ray diffraction data, the so-called phase problem. Traditional solutions, including anomalous scattering, isomorphous replacement, and molecular replacement, are often costly, time-consuming, and may carry model bias, rendering them challenging or even impractical in some cases.

A promising avenue to overcome these challenges involves the application of iterative projection algorithms and deep learning methods to direct phasing. This has led to a significant breakthrough in the last decade. Researchers have recognized that, given sufficient constraints such as high solvent content and the presence of non-crystallographic symmetry, the phase problem has become solvable. Trial calculations utilizing hybrid input–output and difference-map iterative algorithms have demonstrated the feasibility of obtaining high-resolution structures starting from a random electron density. This implies that ab initio phasing, devoid of any model bias, is attainable for a notable fraction of protein crystals.

This Special Issue aims to present an overview of the progress made in the field of direct phasing for protein crystals. Contributions from researchers will explore new ground. Through the exchange of ideas, it is hoped that this Special Issue will promote general knowledge and stimulate further growth of this new and important area of research in protein crystallography.

Prof. Dr. Wu-Pei Su
Dr. Hongxing He
Guest Editors

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Keywords

  • ab initio phasing methods
  • X-ray crystallography
  • protein structural determination
  • image reconstruction from Fourier amplitudes
  • iterative projection algorithms
  • phasing with deep learning methods

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Published Papers (1 paper)

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Research

18 pages, 7501 KiB  
Article
Probing the Active Site of Class 3 L-Asparaginase by Mutagenesis: Mutations of the Ser-Lys Tandems of ReAV
by Kinga Pokrywka, Marta Grzechowiak, Joanna Sliwiak, Paulina Worsztynowicz, Joanna I. Loch, Milosz Ruszkowski, Miroslaw Gilski and Mariusz Jaskolski
Biomolecules 2025, 15(7), 944; https://doi.org/10.3390/biom15070944 - 29 Jun 2025
Viewed by 80
Abstract
The ReAV enzyme from Rhizobium etli, a representative of Class 3 L-asparaginases, is sequentially and structurally different from other known L-asparaginases. This distinctiveness makes ReAV a candidate for novel antileukemic therapies. ReAV is a homodimeric protein, with each subunit containing a highly [...] Read more.
The ReAV enzyme from Rhizobium etli, a representative of Class 3 L-asparaginases, is sequentially and structurally different from other known L-asparaginases. This distinctiveness makes ReAV a candidate for novel antileukemic therapies. ReAV is a homodimeric protein, with each subunit containing a highly specific zinc-binding site created by two cysteines, a lysine, and a water molecule. Two Ser-Lys tandems (Ser48-Lys51, Ser80-Lys263) are located in the close proximity of the metal binding site, with Ser48 hypothesized to be the catalytic nucleophile. To further investigate the catalytic process of ReAV, site-directed mutagenesis was employed to introduce alanine substitutions at residues from the Ser-Lys tandems and at Arg47, located near the Ser48-Lys51 tandem. These mutational studies, along with enzymatic assays and X-ray structure determinations, demonstrated that substitution of each of these highly conserved residues abolished the catalytic activity, confirming their essential role in enzyme mechanism. Full article
(This article belongs to the Special Issue State-of-the-Art Protein X-Ray Crystallography)
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