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Application of Computational Studies for Elucidation of Protein Structure and...
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Application of Computational Studies for Elucidation of Protein Structure and Function

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: 30 September 2025 | Viewed by 1662

Special Issue Editor

Dr. Takeshi Kikuchi

E-Mail Website
Guest Editor
College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu 525-8577, Shiga, Japan
Interests: computational chemistry; biophysics; bioinformatics; protein structure
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Nowadays, computational techniques are widely applied to various problems including biological systems. In particular, many computer simulation techniques are applied to protein dynamics and folding. Bioinformatics techniques are also applied to extract various information from amino acid sequences and evolutional results. Artificial intelligence techniques have been developed in the field of protein structure prediction. Thus, we are planning this Special Issue regarding new applications of various computational techniques to solve problems related to protein structures and functions. It should be noted that pure theoretical works are important to solve protein problems. We are also interested in very complicated protein systems and drug discovery.

Dr. Takeshi Kikuchi
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. Molecules is an international peer-reviewed open access semimonthly 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

  • simulation
  • artificial intelligence
  • bioinformatics
  • sequence analysis
  • protein assembly
  • drug discovery
  • theory

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Published Papers (2 papers)

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Research

13 pages, 1495 KiB  
Article
A Simple Analysis of the Second (Extra) Disulfide Bridge of VHHs
by Carla Martins, Fabrice Gardebien, Aravindan Arun Nadaradjane, Julien Diharce and Alexandre G. de Brevern
Molecules 2024, 29(20), 4863; https://doi.org/10.3390/molecules29204863 - 14 Oct 2024
Viewed by 560
Abstract
Camelids produce a special type of antibody, known as VHHs, that has lost the VL domain, providing a more optimised VH domain. This particular highly stable antibody domain has interesting properties for biotechnological development. Ordinarily, those molecules possess only [...] Read more.
Camelids produce a special type of antibody, known as VHHs, that has lost the VL domain, providing a more optimised VH domain. This particular highly stable antibody domain has interesting properties for biotechnological development. Ordinarily, those molecules possess only one disulphide bridge, but surprisingly, at least a quarter of these VHHs have a second one. Curiously, this does not seem to be essential for the stability and the function of this domain. In an attempt to characterise precisely the role and impact of this disulphide bridge at the molecular level, several in silico mutants of a VHH were created to disrupt this second disulphide bridge and those systems were submitted to molecular dynamics simulation. The loss of the second disulphide bridge leads to an increase in the flexibility of CDR1 and CDR3 and an unexpected rigidification of CDR2. Local conformational analysis shows local differences in the observed protein conformations. However, in fact, there is no exploration of new conformations but a change in the equilibrium between the different observed conformations. This explains why the interaction of VHHs is not really affected by the presence or absence of this second bridge, but their rigidity is slightly reduced. Therefore, the additional disulphide bridge does not seem to be an essential part of VHHs function. Full article
(This article belongs to the Special Issue Application of Computational Studies for Elucidation of Protein Structure and Function)
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12 pages, 2564 KiB  
Article
Testing the Capability of Embedding-Based Alignments on the GST Superfamily Classification: The Role of Protein Length
by Gabriele Vazzana, Castrense Savojardo, Pier Luigi Martelli and Rita Casadio
Molecules 2024, 29(19), 4616; https://doi.org/10.3390/molecules29194616 - 29 Sep 2024
Viewed by 653
Abstract
In order to shed light on the usage of protein language model-based alignment procedures, we attempted the classification of Glutathione S-transferases (GST; EC 2.5.1.18) and compared our results with the ARBA/UNI rule-based annotation in UniProt. GST is a protein superfamily involved in cellular [...] Read more.
In order to shed light on the usage of protein language model-based alignment procedures, we attempted the classification of Glutathione S-transferases (GST; EC 2.5.1.18) and compared our results with the ARBA/UNI rule-based annotation in UniProt. GST is a protein superfamily involved in cellular detoxification from harmful xenobiotics and endobiotics, widely distributed in prokaryotes and eukaryotes. What is particularly interesting is that the superfamily is characterized by different classes, comprising proteins from different taxa that can act in different cell locations (cytosolic, mitochondrial and microsomal compartments) with different folds and different levels of sequence identity with remote homologs. For this reason, GST functional annotation in a specific class is problematic: unless a structure is released, the protein can be classified only on the basis of sequence similarity, which excludes the annotation of remote homologs. Here, we adopt an embedding-based alignment to classify 15,061 GST proteins automatically annotated by the UniProt-ARBA/UNI rules. Embedding is based on the Meta ESM2-15b protein language. The embedding-based alignment reaches more than a 99% rate of perfect matching with the UniProt automatic procedure. Data analysis indicates that 46% of the UniProt automatically classified proteins do not conserve the typical length of canonical GSTs, whose structure is known. Therefore, 46% of the classified proteins do not conserve the template/s structure required for their family classification. Our approach finds that 41% of 64,207 GST UniProt proteins not yet assigned to any class can be classified consistently with the structural template length. Full article
(This article belongs to the Special Issue Application of Computational Studies for Elucidation of Protein Structure and Function)
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