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Crystals
Special Issues
Development of Computational Methods for Structure Determination of Biological Macromolecules
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Development of Computational Methods for Structure Determination of Biological Macromolecules

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

Deadline for manuscript submissions: closed (31 May 2017)

Special Issue Editor

Dr. Rocco Caliandro

E-Mail Website
Guest Editor
Institute of Crystallography, National Research Council of Italy, Via Amendola 122/O, 70126 Bari, Italy
Interests: protein crystallography; phasing methods; modulated enhanced diffraction; multivariate analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Protein crystallography is today the best and well established technique to obtain structural models at atomic resolution. After having solved the phasing problem for small molecules, computational methods for structure determination are now routinely and successfully applied to solve the crystal structure of biological macromolecules. Nevertheless, new challenges in the field of biological macromolecules need to be faced; for example, the development of pipelines for high-throughput protein crystallography, the solution of very large systems as ribosomes and viruses, the investigation of the fast structural dynamics at XFEL sources, the solution of proteins from powder data, the application of molecular replacement to low homology models, and the ab initio solution of proteins not containing heavy atoms.

The Special Issue on “Development of Computational Methods for Structure Determination of Biological Macromolecules” is intended to provide a unique international forum aimed at covering the latter advancements in the different computational steps of the protein crystal structure determination, namely data reduction, initial phasing, phase refinement, structural refinement, model validation. The volume is especially open to any innovative contributions aiming at solving the above challenges.

Dr. Rocco Caliandro
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

  • Phasing methods
  • Structural refinement
  • Protein crystallography

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Published Papers (3 papers)

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Research

11 pages, 269 KiB  
Article
Probabilistic Estimate of |Foa| from FEL Data
by Carmelo Giacovazzo, Benedetta Carrozzini and Giovanni Luca Cascarano
Crystals 2018, 8(4), 175; https://doi.org/10.3390/cryst8040175 - 18 Apr 2018
Viewed by 2907
Abstract
The method of the joint probability distribution function was applied in order to estimate the normal structure factor amplitudes of the anomalous scatterer substructure in a FEL experiment. The two-wavelength case was examined. In this, the prior knowledge of the moduli [...] Read more.
The method of the joint probability distribution function was applied in order to estimate the normal structure factor amplitudes of the anomalous scatterer substructure in a FEL experiment. The two-wavelength case was examined. In this, the prior knowledge of the moduli | F 1 + | , | F 1 − | , | F 2 + | , | F 2 − | was used to predict the value of | F 0 a | , which is the structure factor amplitude arising from the normal scattering of the heavy atom anomalous scatterers. The mathematical treatment provides a solid theoretical basis for the RIP (Radiation-damage Induced Phasing) method, which was originally proposed in order to take the radiation damage induced by synchrotron radiation sources into account. This was further adapted to exploit FEL data, where the crystal damage is usually more massive. Full article
(This article belongs to the Special Issue Development of Computational Methods for Structure Determination of Biological Macromolecules)
2669 KiB  
Article
A Novel Approach to Data Collection for Difficult Structures: Data Management for Large Numbers of Crystals with the BLEND Software
by Anastasia Mylona, Stephen Carr, Pierre Aller, Isabel Moraes, Richard Treisman, Gwyndaf Evans and James Foadi
Crystals 2017, 7(8), 242; https://doi.org/10.3390/cryst7080242 - 4 Aug 2017
Cited by 6 | Viewed by 5460
Abstract
The present article describes how to use the computer program BLEND to help assemble complete datasets for the solution of macromolecular structures, starting from partial or complete datasets, derived from data collection from multiple crystals. The program is demonstrated on more than two [...] Read more.
The present article describes how to use the computer program BLEND to help assemble complete datasets for the solution of macromolecular structures, starting from partial or complete datasets, derived from data collection from multiple crystals. The program is demonstrated on more than two hundred X-ray diffraction datasets obtained from 50 crystals of a complex formed between the SRF transcription factor, its cognate DNA, and a peptide from the SRF cofactor MRTF-A. This structure is currently in the process of being fully solved. While full details of the structure are not yet available, the repeated application of BLEND on data from this structure, as they have become available, has made it possible to produce electron density maps clear enough to visualise the potential location of MRTF sequences. Full article
(This article belongs to the Special Issue Development of Computational Methods for Structure Determination of Biological Macromolecules)
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1009 KiB  
Article
Analysis of Diffracted Intensities from Finite Protein Crystals with Incomplete Unit Cells
by Sophie R. Williams, Ruben A. Dilanian, Harry M. Quiney and Andrew V. Martin
Crystals 2017, 7(7), 220; https://doi.org/10.3390/cryst7070220 - 14 Jul 2017
Cited by 3 | Viewed by 4354
Abstract
Developments in experimental techniques in micro electron diffraction and serial X-ray crystallography provide the opportunity to collect diffraction data from protein nanocrystals. Incomplete unit cells on the surfaces of protein crystals can affect the distribution of diffracted intensities for crystals with very high [...] Read more.
Developments in experimental techniques in micro electron diffraction and serial X-ray crystallography provide the opportunity to collect diffraction data from protein nanocrystals. Incomplete unit cells on the surfaces of protein crystals can affect the distribution of diffracted intensities for crystals with very high surface-to-volume ratios. The extraction of structure factors from diffraction data for such finite protein crystals sizes is considered here. A theoretical model for the continuous diffracted intensity distribution for data merged from finite crystals with two symmetry-related sub-units of the conventional unit cell is presented. This is used to extend a whole-pattern fitting technique to account for incomplete unit cells in the extraction of structure factor amplitudes. The accuracy of structure factor amplitudes found from this whole-pattern fitting technique and from an integration approach are evaluated. Full article
(This article belongs to the Special Issue Development of Computational Methods for Structure Determination of Biological Macromolecules)
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