Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
8.3
5.5
Journals
Biomolecules
Special Issues
Protein Structure and Folding: AlphaFold and Beyond
share announcement

Protein Structure and Folding: AlphaFold and Beyond

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Biomacromolecules: Proteins".

Deadline for manuscript submissions: closed (31 January 2023) | Viewed by 3126

Special Issue Editors

Dr. Luigi Vitagliano

E-Mail Website
Guest Editor
Institute of Biostructures and Bioimaging, CNR, Via Pietro Castellino n. 111, 80131 Napoli, Italy
Interests: protein structure–function; molecular dynamics; computational biology; structural biology; molecular basis of diseases; biophysics
Special Issues, Collections and Topics in MDPI journals
Dr. Nicole Balasco

E-Mail Website
Guest Editor
Institute of Molecular Biology and Pathology, National Research Council (CNR), Department of Chemistry, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
Interests: protein structure–function; molecular modeling; molecular dynamics; molecular interactions; computational biology; structural biology
Special Issues, Collections and Topics in MDPI journals
Dr. Luciana Esposito

E-Mail Website
Guest Editor
Institute of Biostructures and Bioimaging, CNR, Via Pietro Castellino n. 111, 80131 Napoli, Italy
Interests: protein structure–function; molecular modeling; molecular dynamics; computational biology; structural biology; DNA photodamage

Special Issue Information

Dear Colleagues,

The prediction of the three-dimensional structure of proteins from their sequences has represented for decades the Holy Grail of structural biology. For more than half a century, despite intense research activities in this field, the number of successful attempts has been marginal. This situation has rapidly changed in the last couple of years with the development of machine learning approaches culminating in the AlphaFold release by DeepMind. This approach has led to the rapid and generally reliable structure  prediction of the proteome of many highly studied organisms, and it is expected to generate, in the near feature, three-dimensional models for essentially all proteins with a known sequence. Such a huge, and somehow unexpected, scientific triumph will heavily affect the approach of the structural biology community to the problem of protein structure and folding prediction. 

This Special Issue invites reviews and novel research results in which the characterization of protein structure and folding is studied by considering this novel scenario. In particular, studies corroborating AlphaFold models or highlighting discrepancies between newly determined structures with the predicted ones are welcome. Moreover, computational studies describing innovative aspects of protein structure and folding as well as investigations whose findings could be exploited in the future for improving the predictions approach will also be favorably considered.

We look forward to your contributions to this issue.

Dr. Luigi Vitagliano
Dr. Nicole Balasco
Dr. Luciana Esposito
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. 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 structure determination
  • protein folding
  • protein function–structure relationships
  • computational biology
  • data mining
  • protein structure–stability
  • protein structure predictions

Published Papers (2 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

18 pages, 4621 KiB  
Article
Structural Basis of PE_PGRS Polymorphism, a Tool for Functional Modulation
by Eliza Kramarska, Flavio De Maio, Giovanni Delogu and Rita Berisio
Biomolecules 2023, 13(5), 812; https://doi.org/10.3390/biom13050812 - 10 May 2023
Viewed by 1284
Abstract
Background: The mycobacterial PE_PGRS protein family is present only in pathogenic strains of the genus mycobacterium, such as Mtb and members of the MTB complex, suggesting a likely important role of this family in pathogenesis. Their PGRS domains are highly polymorphic and have [...] Read more.
Background: The mycobacterial PE_PGRS protein family is present only in pathogenic strains of the genus mycobacterium, such as Mtb and members of the MTB complex, suggesting a likely important role of this family in pathogenesis. Their PGRS domains are highly polymorphic and have been suggested to cause antigenic variations and facilitate pathogen survival. The availability of AlphaFold2.0 offered us a unique opportunity to better understand structural and functional properties of these domains and a role of polymorphism in Mtb evolution and dissemination. Methods: We made extensive use of AlphaFold2.0 computations and coupled them with sequence distribution phylogenetic and frequency analyses, and antigenic predictions. Results: Modeling of several polymorphic forms of PE_PGRS33, the prototype of the PE_PGRS family and sequence analyses allowed us to predict the structural impact of mutations/deletions/insertions present in the most frequent variants. These analyses well correlate with the observed frequency and with the phenotypic features of the described variants. Conclusions: Here, we provide a thorough description of structural impacts of the observed polymorphism of PE_PGRS33 protein and we correlate predicted structures to the known fitness of strains containing specific variants. Finally, we also identify protein variants associated with bacterial evolution, showing sophisticated modifications likely endowed with a gain-of-function role during bacterial evolution. Full article
(This article belongs to the Special Issue Protein Structure and Folding: AlphaFold and Beyond)
►▼ Show Figures

Figure 1

18 pages, 3524 KiB  
Article
Local Backbone Geometry Plays a Critical Role in Determining Conformational Preferences of Amino Acid Residues in Proteins
by Nicole Balasco, Luciana Esposito, Alfonso De Simone and Luigi Vitagliano
Biomolecules 2022, 12(9), 1184; https://doi.org/10.3390/biom12091184 - 26 Aug 2022
Cited by 2 | Viewed by 1397
Abstract
The definition of the structural basis of the conformational preferences of the genetically encoded amino acid residues is an important yet unresolved issue of structural biology. In order to gain insights into this intricate topic, we here determined and compared the amino acid [...] Read more.
The definition of the structural basis of the conformational preferences of the genetically encoded amino acid residues is an important yet unresolved issue of structural biology. In order to gain insights into this intricate topic, we here determined and compared the amino acid propensity scales for different (φ, ψ) regions of the Ramachandran plot and for different secondary structure elements. These propensities were calculated using the Chou–Fasman approach on a database of non-redundant protein chains retrieved from the Protein Data Bank. Similarities between propensity scales were evaluated by linear regression analyses. One of the most striking and unexpected findings is that distant regions of the Ramachandran plot may exhibit significantly similar propensity scales. On the other hand, contiguous regions of the Ramachandran plot may present anticorrelated propensities. In order to provide an interpretative background to these results, we evaluated the role that the local variability of protein backbone geometry plays in this context. Our analysis indicates that (dis)similarities of propensity scales between different regions of the Ramachandran plot are coupled with (dis)similarities in the local geometry. The concept that similarities of the propensity scales are dictated by the similarity of the NCαC angle and not necessarily by the similarity of the (φ, ψ) conformation may have far-reaching implications in the field. Full article
(This article belongs to the Special Issue Protein Structure and Folding: AlphaFold and Beyond)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-2
Back to TopTop