New Advances in Protein Crystallography

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

Deadline for manuscript submissions: closed (10 December 2023) | Viewed by 895

Special Issue Editors

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
Institute of Crystallography, National Research Council of Italy, Via Amendola 122/O, 70126 Bari, Italy
Interests: phasing methods; crystal structure determination; protein crystallography; software development

Special Issue Information

Dear Colleagues,

The structural knowledge about the tridimensional arrangements of biological macromolecules is of paramount importance in many fields and can help us to overcome the main problems that afflict humanity, such as diseases and environmental pollution. Nowadays, different techniques can allow us to gain such knowledge, each having their pros and cons: X-ray diffraction (DRX), cryogenic electron microscopy (cryo-EM), and nuclear magnetic resonance (NMR). Each of them has experienced relevant advances in the experimental and computational sides, which allowed us to push forward the efficiency of the structural determination process and improve the data resolution. The present Special Issue aims to present state-of-the-art scientific developments in data collection and data analysis in these techniques, and their application to some topic proteins of medical, biological, biopharmaceutic, or biotechnological interest. Studies that combine different techniques in the framework of integrative structural biology will be considered as a priority. The topics of interest include, but are not limited to, the following:

  • New methods to improve protein crystallization;
  • New strategies for data collection;
  • In situ and time-resolved experiments;
  • Room-temperature X-ray diffraction and diffuse scattering;
  • Novel phasing algorithms;
  • Model building and refinement;
  • Advanced validation criteria.

Special attention will be devoted to papers highlighting the role of artificial intelligence in data analysis, with specific reference to the interplay between structural predictions, model validation, and experimental data analysis.

Dr. Rocco Caliandro
Dr. Benedetta Carrozzini
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 2600 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

  • protein crystallography
  • X-ray diffraction
  • cryo-EM
  • NMR
  • phasing methods
  • crystal structure determination
  • computational modeling
  • artificial intelligence
  • integrative structural biology

Published Papers (1 paper)

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Research

13 pages, 2792 KiB  
Article
Dynamics–Function Correlation in Photosystem II: Molecular Dynamics in Solution
Crystals 2023, 13(10), 1441; https://doi.org/10.3390/cryst13101441 - 28 Sep 2023
Viewed by 516
Abstract
A detailed comprehension of protein function requires information on the spatial structure of the protein, which is often gathered from X-ray crystallography. However, conformational dynamics often also plays an important functional role in proteins and can be directly investigated by complementary quasielastic neutron [...] Read more.
A detailed comprehension of protein function requires information on the spatial structure of the protein, which is often gathered from X-ray crystallography. However, conformational dynamics often also plays an important functional role in proteins and can be directly investigated by complementary quasielastic neutron scattering. A classic example for dynamics–function correlations is Photosystem II, which is a multimeric pigment–protein complex responsible for catalyzing the light-induced photosynthetic water splitting into protons and oxygen. Several functional subprocesses of photosynthetic electron transfer and water splitting are strongly dependent on temperature and hydration, two factors also known to affect protein dynamics. Photosystem II is often investigated in the form of membrane fragments, where the protein complex remains embedded into its native lipid environment. However, experiments on protein function are often carried out in solution state, while direct investigations of molecular dynamics by quasielastic neutron scattering are mainly performed using specifically hydrated membrane fragments only. The present study provides the first quasielastic neutron scattering investigation of the molecular dynamics of Photosystem II membrane fragments (PSIImf) in solution over a wide temperature range from 50 to 300 K. At physiological temperatures above the melting point of water, we observed that the dynamics of PSIImf are significantly activated, leading to larger atomic mean square displacement values compared to those of specifically hydrated membrane stacks. The QENS data can be described by two dynamical components: a fast one, most probably corresponding to methyl group rotation; and a slower one, representing localized conformational dynamics. The latter component could be fitted by a jump-diffusion model at 300 K. The dynamics observed characterize the level of flexibility necessary for the proper PS II functionality under physiological conditions. In contrast, we observe a severe restriction of molecular dynamics upon freezing of the solvent below ~276 K. We associate this unexpected suppression of dynamics with a substantial aggregation of PSIImf caused by ice formation. Full article
(This article belongs to the Special Issue New Advances in Protein Crystallography)
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