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Biomolecules
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Protein Structural Landscapes: From Structure to Function through Correlative Structural...
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Protein Structural Landscapes: From Structure to Function through Correlative Structural Biology

A special issue of Biomolecules (ISSN 2218-273X).

Deadline for manuscript submissions: closed (1 August 2019) | Viewed by 9630

Special Issue Editor

Dr. Vito Calderone

E-Mail Website1 Website2
Guest Editor
Magnetic Resonance Center and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
Interests: X-ray protein crystallography; mitochondrial proteins; metalloproteins; structure-based drug design; protein–protein complexes; structural biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The determination of the structure of proteins is crucial to discovering how these biomolecules work. Detailed structures may not only unravel how a protein interacts with other structures, but also how cells work in reality. The process of determining a precise molecular structure can be very long and difficult. As of today, the most common route for determining a protein’s structure is to crystallize it and determine its 3D structure from its X-ray diffraction data. Nevertheless, these images of the protein do not fully represent how the protein really looks, as it is in fact dynamic and more indistinct. Moreover, some proteins are very hard if not impossible to crystallize.

Other methods, such as solution or solid-state NMR, cryo-electron microscopy, electron tomography or mass spectroscopy, provide different points of view of proteins at different scales. The integration of the structural data derived from such different technologies helps our understanding of how proteins, protein complexes or whole pathogens interact dynamically with their functional environment. This fundamental understanding will in turn allow us to provide new therapeutics to tackle the main challenges of a continuously ageing society, public health and global pandemics.

This Special Issue will therefore welcome (but is not limited to) papers dealing with an integration of the abovementioned techniques and showing a synergistic approach to biological problems; all of this within the more comprehensive frame of addressing human pathologies along with the elucidation of cellular processes.

Dr. Vito Calderone
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. Biomolecules 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 2700 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
  • solution and solid-state NMR
  • bioinformatics
  • cryo-EM
  • integrated structural biology
  • metalloproteins
  • structure–function relationship
  • structure-based drug design

Published Papers (2 papers)

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16 pages, 3977 KiB  
Article
The Structural Versatility of the BTB Domains of KCTD Proteins and Their Recognition of the GABAB Receptor
by Nicole Balasco, Giovanni Smaldone and Luigi Vitagliano
Biomolecules 2019, 9(8), 323; https://doi.org/10.3390/biom9080323 - 31 Jul 2019
Cited by 8 | Viewed by 3514
Abstract
Several recent investigations have demonstrated that members of the KCTD (Potassium Channel Tetramerization Domain) protein family are involved in fundamental processes. However, the paucity of structural data available on these proteins has frequently prevented the definition of their biochemical role(s). Fortunately, this scenario [...] Read more.
Several recent investigations have demonstrated that members of the KCTD (Potassium Channel Tetramerization Domain) protein family are involved in fundamental processes. However, the paucity of structural data available on these proteins has frequently prevented the definition of their biochemical role(s). Fortunately, this scenario is rapidly changing as, in very recent years, several crystallographic structures have been reported. Although these investigations have provided very important insights into the function of KCTDs, they have also raised some puzzling issues. One is related to the observation that the BTB (broad-complex, tramtrack, and bric-à-brac) domain of these proteins presents a remarkable structural versatility, being able to adopt a variety of oligomeric states. To gain insights into this intriguing aspect, we performed extensive molecular dynamics simulations on several BTB domains of KCTD proteins in different oligomeric states (monomers, dimers, tetramers, and open/close pentamers). These studies indicate that KCTD-BTB domains are stable in the simulation timescales, even in their monomeric forms. Moreover, simulations also show that the dynamic behavior of open pentameric states is strictly related to their functional roles and that different KCTDs may form stable hetero-oligomers. Molecular dynamics (MD) simulations also provided a dynamic view of the complex formed by KCTD16 and the GABAB2 receptor, whose structure has been recently reported. Finally, simulations carried out on the isolated fragment of the GABAB2 receptor that binds KCTD16 indicate that it is able to assume the local conformation required for the binding to KCTD. Full article
(This article belongs to the Special Issue Protein Structural Landscapes: From Structure to Function through Correlative Structural Biology)
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Review

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12 pages, 2033 KiB  
Review
Integrative Approaches in Structural Biology: A More Complete Picture from the Combination of Individual Techniques
by Linda Cerofolini, Marco Fragai, Enrico Ravera, Christoph A. Diebolder, Ludovic Renault and Vito Calderone
Biomolecules 2019, 9(8), 370; https://doi.org/10.3390/biom9080370 - 14 Aug 2019
Cited by 20 | Viewed by 5430
Abstract
With the recent technological and computational advancements, structural biology has begun to tackle more and more difficult questions, including complex biochemical pathways and transient interactions among macromolecules. This has demonstrated that, to approach the complexity of biology, one single technique is largely insufficient [...] Read more.
With the recent technological and computational advancements, structural biology has begun to tackle more and more difficult questions, including complex biochemical pathways and transient interactions among macromolecules. This has demonstrated that, to approach the complexity of biology, one single technique is largely insufficient and unable to yield thorough answers, whereas integrated approaches have been more and more adopted with successful results. Traditional structural techniques (X-ray crystallography and Nuclear Magnetic Resonance (NMR)) and the emerging ones (cryo-electron microscopy (cryo-EM), Small Angle X-ray Scattering (SAXS)), together with molecular modeling, have pros and cons which very nicely complement one another. In this review, three examples of synergistic approaches chosen from our previous research will be revisited. The first shows how the joint use of both solution and solid-state NMR (SSNMR), X-ray crystallography, and cryo-EM is crucial to elucidate the structure of polyethylene glycol (PEG)ylated asparaginase, which would not be obtainable through any of the techniques taken alone. The second deals with the integrated use of NMR, X-ray crystallography, and SAXS in order to elucidate the catalytic mechanism of an enzyme that is based on the flexibility of the enzyme itself. The third one shows how it is possible to put together experimental data from X-ray crystallography and NMR restraints in order to refine a protein model in order to obtain a structure which simultaneously satisfies both experimental datasets and is therefore closer to the ‘real structure’. Full article
(This article belongs to the Special Issue Protein Structural Landscapes: From Structure to Function through Correlative Structural Biology)
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