Special Issue "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

Guest Editor
Dr. Rocco Caliandro

Institute of Crystallography, CNR, Bari, Italy
Website | E-Mail
Interests: protein crystallography; phasing algorithms; molecular dynamics

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

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Keywords

•    Phasing methods
•    Structural refinement
•    Protein crystallography

Published Papers (2 papers)

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Research

Open AccessArticle A Novel Approach to Data Collection for Difficult Structures: Data Management for Large Numbers of Crystals with the BLEND Software
Crystals 2017, 7(8), 242; doi:10.3390/cryst7080242
Received: 11 July 2017 / Revised: 26 July 2017 / Accepted: 31 July 2017 / Published: 4 August 2017
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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
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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
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Open AccessArticle Analysis of Diffracted Intensities from Finite Protein Crystals with Incomplete Unit Cells
Crystals 2017, 7(7), 220; doi:10.3390/cryst7070220
Received: 31 May 2017 / Revised: 7 July 2017 / Accepted: 8 July 2017 / Published: 14 July 2017
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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
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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
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