Topical Collection "Unveiling Protein Functions, Dynamics and Interactions in Health and Disease Using Experimental and Theoretical Approaches"
Interests: molecular biology; neuroscience; computational chemistry; molecular dynamics; bioinformatics; peptide design; drug design; protein-protein and protein-nucleic acids interaction
Interests: specialized in enzymology and biochemistry of protein synthesis; assay development (in vivo expression, enzymatic activity, UV-vis fluorescence spectroscopy); biochemistry of bacterial translation factors; expression analysis of human eIF5A-2 isoform
2. New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
Interests: digestion and cloning of plasmids; bacterial transformation, recombinant protein expression by bacterial; archaeal and mammalian culture; electrophoretic separation on polyacrylamide gels; western blot, dot-blot; protein purification with chromatographic separation (AKTA, HPLC, FPLC) based on affinity; ion-exchange and size exclusion; high throughput screening; genomic DNA isolation; total RNA isolation; in vitro transcription; sucrose and glycerol gradients preparation; ribosome profiling, protein and RNA immunoprecipitation; PCR and reverse-transcriptase-PCR (RT-PCR); zymogram assay; RNA cleavage assay, radiolabeled of RNA; electrophoresis mobility shift assay (EMSA); pull-down assay
In the last years, important scientific results have been obtained thanks to the application of approaches and techniques coming from the most diverse branches of science, sometimes very far from each other. This is particularly true for the biological sciences, in which, for example, the use of computational techniques to support experimental data, and vice versa, has been a fruitful strategy in a large number of studies. In this scenario, the study of proteins features such as the interplay between their structure/dynamics and function, and their intermolecular interactions, both in health and diseases, acquires a key role.
Frequently, the sole experimental results, even if combining different disciplines, do not provide a clear understanding of a complex biological problem. In particular, in the study of proteins function, some key questions can arise, for instance, concerning the role of mutations or of conformational changes of proteins structure associated with a specific cellular function. The use of standard or advanced theoretical approaches (i.e., classical molecular dynamics, molecular docking or enhanced sampling approaches) can help both the comprehension of experimental data or, in turn, can better guide the design of future experiments.
The aim of this Special Issue is to bridge the gap sometimes existing among different approaches that are exploited for a common purpose, i.e., understanding and describing different functional-dynamical features of proteins in specific physiological and pathological conditions. A multi-disciplinary collection including molecular biology, structural biology, biophysics, biochemistry, bioinformatics and computational chemistry is the scope of this issue.
In this context, this collection aims at reporting current experimental and computational trends in the field of proteins functions, interactions and dynamics. In this Special Issue, original research articles, Reviews, and Perspectives are welcome. Research areas may include (but not limited to) the following:
(i) Understanding the structural, dynamical and functional role of point mutations
(ii) Conformational changes of proteins linked to their function
(iii) Protein-proteins, protein-nucleic acids and protein-ligand interactions in health and diseases
(iv) Protein design and engineering for biomedical applications
I look forward to receiving your contributions.
Dr. Daniele Di Marino
Dr. Cristina Maracci
Dr. Alice Romagnoli
Dr. Stefano Motta
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 collection 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.
- Protein’s structure and dynamics
- Protein-protein interactions
- Point mutations
- Molecular biology
- Molecular modelling
- Molecular dynamics
- Protein-ligand interaction
- Protein-nucleic acids interaction
- Protein’s conformational changes
The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.
Title: A computational approach to investigate TDP-43 C-terminal fragments aggregation in Amyotrophic Lateral Sclerosis
Authors: Greta Grassmann, Mattia Miotto, Lorenzo Di Rienzo, Federico Salaris, Beatrice Silvestri, Elsa Zacco, Alessandro Rosa, Gian Gaetano Tartaglia, Giancarlo Ruocco, and Edoardo Milanetti.
Affiliation: - Università di Bologna, Via Irnerio 46, Bologna I-40126, Italy. - Center for Life Nano-& Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy. - Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy. - Department of Neuroscience and Brain Technologies,Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy. - Centre for Human Technologies, via Enrico Melen, 83, 16152 Genova, Italy. - Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy