Symmetry in Protein Function and Structure

A special issue of Symmetry (ISSN 2073-8994). This special issue belongs to the section "Life Sciences".

Deadline for manuscript submissions: 30 September 2024 | Viewed by 6717

Special Issue Editors


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Dipartimento di Medicina Sperimentale, Università di Roma Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
Interests: biophysics
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Dipartimento di Medicina Sperimentale, Università di Roma Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
Interests: protein folding; protein-membrane interaction; protein structure-to-function relationship; protein fluorescence
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The study of the relationship between protein structure and function is a primary focus in structural biology, with important implications in such diverse fields as biophysics, molecular biology, genetics, biochemistry, protein engineering, and bioinformatics. The stunning diversity of molecular functions performed by naturally evolved proteins is made possible by their finely tuned three-dimensional structures, which are in turn determined by their genetically encoded amino acid sequences. Furthermore, protein structures often have a certain degree of intrinsic symmetry. In fact, the visual inspection of common structural motifs reveals that many of them are symmetric. Therefore, it has been suggested that in early evolution, proteins might have been assembled from multiple identical polypeptide chains. These were then replaced by single polypeptide chains encoding multiple repeats, which fold more reliably and efficiently.

To understand the structure–function paradigm, particularly useful structural information comes from the primary amino acid sequences and the associated tertiary structures. Several recent developments in the analysis of the “protein universe” at the tertiary and quaternary structural level have provided important criteria for understanding the range of family folds that exist and some of the evolutionary relationships associated with them.

Altogether, the great number of protein sequences and structures, spectroscopical techniques, and computational strategies can now support the understanding of the fundamental relationships between protein structure and function.

The aim of this Special Issue of Symmetry is to collect original and review articles on all aspects of protein folding motifs related to protein function.

Dr. Almerinda Di Venere
Prof. Dr. Giampiero Mei
Guest Editors

Manuscript Submission Information

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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. Symmetry 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 2400 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 folding
  • protein assembly
  • protein symmetry
  • structure–function relationship
  • misfolding
  • computational analysis
  • spectroscopy

Published Papers (3 papers)

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Research

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12 pages, 3793 KiB  
Article
One for All, All for One: The Peculiar Dynamics of TNF-Receptor-Associated Factor (TRAF2) Subunits
by Velia Minicozzi, Almerinda Di Venere, Anna Maria Caccuri, Giampiero Mei and Luisa Di Paola
Symmetry 2022, 14(4), 720; https://doi.org/10.3390/sym14040720 - 02 Apr 2022
Cited by 3 | Viewed by 1241
Abstract
TNF Receptor-Associated Factor 2 (TRAF2) is a homo-trimer belonging to the TNF-receptor-associated factor family (TRAFs). The TRAF2 oligomeric state is crucial for receptor binding, the interaction with other proteins (involved in the TNFR signaling), and the interaction with biological membranes. In this study, [...] Read more.
TNF Receptor-Associated Factor 2 (TRAF2) is a homo-trimer belonging to the TNF-receptor-associated factor family (TRAFs). The TRAF2 oligomeric state is crucial for receptor binding, the interaction with other proteins (involved in the TNFR signaling), and the interaction with biological membranes. In this study, we present a computational analysis of the Molecular Dynamics of TRAF2-C (a truncated and soluble TRAF2 form) to identify patterns in the interactions between the three chains. We have performed a canonical analysis of the motion applied to molecular dynamics starting from the available crystal structure to identify correlated motions in TRAF2 dynamics. We have computed the displacement matrix, providing a frame-by-frame displacement for each residue in the dynamic. We provide the results in terms of the correlation matrix, which represents a detailed map of the correlated motions of residues. Eventually, we computed the so-called dynamical clusters, based on the Principal Component Analysis (PCA) of the motion (displacement) and the k means application on the first two principal components space. The results clearly indicate that, most of the time, two chains move in a strongly correlated motion, while the third chain follows a freer motion. A detailed analysis of the correlation matrix also shows that a few specific interface residues characterize the interaction of the more independent subunit with the other two. These findings suggest that the equilibrium between the trimer and the dissociated species (dimers and monomers) might be finely tuned by controlling a few critical residues in the protein quaternary structure, probably facilitating the regulation of oligomerization and dissociation in vivo. Full article
(This article belongs to the Special Issue Symmetry in Protein Function and Structure)
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15 pages, 3639 KiB  
Article
Symmetric versus Asymmetric Features of Homologous Homodimeric Amine Oxidases: When Water and Cavities Make the Difference
by Eleonora Nicolai, Velia Minicozzi, Luisa Di Paola, Rosaria Medda, Francesca Pintus, Giampiero Mei and Almerinda Di Venere
Symmetry 2022, 14(3), 522; https://doi.org/10.3390/sym14030522 - 03 Mar 2022
Cited by 1 | Viewed by 2097
Abstract
Symmetry is an intrinsic property of homo-oligomers. Amine oxidases are multidomain homodimeric enzymes that contain one catalytic site per subunit, and that share a high homology degree. In this paper, we investigated, by fluorescence spectroscopy measurements, the conformational dynamics and resiliency in solutions [...] Read more.
Symmetry is an intrinsic property of homo-oligomers. Amine oxidases are multidomain homodimeric enzymes that contain one catalytic site per subunit, and that share a high homology degree. In this paper, we investigated, by fluorescence spectroscopy measurements, the conformational dynamics and resiliency in solutions of two amine oxidases, one from lentil seedlings, and one from Euphorbia characias latex, of which the crystallographic structure is still unknown. The data demonstrate that slight but significant differences exist at the level of the local tridimensional structure, which arise from the presence of large internal cavities, which are characterized by different hydration extents. Molecular dynamics and a contact network methodology were also used to further explore, in silico, the structural features of the two proteins. The analysis demonstrates that the two proteins show similar long-range symmetrical connectivities, but that they differ in their local (intra-subunit) contact networks, which appear mostly asymmetric. These features have been interpreted to suggest a new rationale for the functioning of amino oxidases as obligate homodimers. Full article
(This article belongs to the Special Issue Symmetry in Protein Function and Structure)
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Review

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17 pages, 2701 KiB  
Review
Cytochrome c Interaction with Cardiolipin Plays a Key Role in Cell Apoptosis: Implications for Human Diseases
by Laura Fiorucci, Fulvio Erba, Roberto Santucci and Federica Sinibaldi
Symmetry 2022, 14(4), 767; https://doi.org/10.3390/sym14040767 - 07 Apr 2022
Cited by 9 | Viewed by 2458
Abstract
In the cell cytochrome, c performs different functions depending on the environment in which it acts; therefore, it has been classified as a multifunction protein. When anchored to the outer side of the inner mitochondrial membrane, native cytochrome c acts as a Schweitzer-StennerSchweitzer-Stenner [...] Read more.
In the cell cytochrome, c performs different functions depending on the environment in which it acts; therefore, it has been classified as a multifunction protein. When anchored to the outer side of the inner mitochondrial membrane, native cytochrome c acts as a Schweitzer-StennerSchweitzer-Stenner that transfers electrons from cytochrome c reductase to cytochrome c oxidase in the respiratory chain. On the other hand, to interact with cardiolipin (one of the phospholipids making up the mitochondrial membrane) and form the cytochrome c/cardiolipin complex in the apoptotic process, the protein reorganizes its structure into a non-native state characterized by different asymmetry. The formation of the cytochrome c/cardiolipin complex is a fundamental step of the apoptotic pathway, since the structural rearrangement induces peroxidase activity in cytochrome c, the subsequent permeabilization of the membrane, and the release of the free protein into the cytoplasm, where cytochrome c activates the apoptotic process. Apoptosis is closely related to the pathogenesis of neoplastic, neurodegenerative and cardiovascular diseases; in this contest, the biosynthesis and remodeling of cardiolipin are crucial for the regulation of the apoptotic process. Since the role of cytochrome c as a promoter of apoptosis strictly depends on the non-native conformation(s) that the protein acquires when bound to the cardiolipin and such event leads to cytochrome c traslocation into the cytosol, the structural and functional properties of the cytochrome c/cardiolipin complex in cell fate will be the focus of the present review. Full article
(This article belongs to the Special Issue Symmetry in Protein Function and Structure)
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