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Life
Special Issues
Structure, Dynamics, and Function of Protein Tunnels and Channels
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Structure, Dynamics, and Function of Protein Tunnels and Channels

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Proteins and Proteomics".

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 3465

Special Issue Editors

Prof. Dr. Jan Brezovsky

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Guest Editor
Laboratory of Biomolecular Interactions and Transport, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, & International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland
Interests: structural bioinformatics; computational protein design; biophysics; molecular modeling; drug design and discovery; ligand transport
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Artur Gora

E-Mail Website
Guest Editor
Tunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego 8, 44-100 Gliwice, Poland
Interests: computational chemistry, bioinformatics, protein dynamics, protein engineering, drug design, proteins evolution, new methods development

Special Issue Information

Dear Colleagues,

Protein structures are not perfectly compact but contain a very complex system of voids, some parts of which are essential for protein function by forming transport tunnels and channels. Protein tunnels connect the functional buried cavities with bulk solvent, whereas protein channels enable transport through biological membranes. These transport paths govern the exchange rates of ligands, ions, and water solvent. Detailed knowledge of these paths is critical to understand the mechanisms of protein function, which can be exploited for practical applications. By engineering these structural features, protein variants with improved stability, activity or selectivity can be developed. As a functionally relevant component, protein tunnels and channels represent attractive targets for drug discovery.

However, navigating the voids in proteins is not straightforward, particularly when considering the dynamic nature of proteins. The perpetual conformational changes cause constrictions and expansion of some regions of the space, i.e., gating. The existence of such molecular gates translates into a very fluid behavior of tunnels and channels, frequently resulting in their transient presence. Since the primary source of protein structure information is their crystal structures, many transient tunnels and gates undoubtedly remain to be identified, and their functional roles and to be unveiled.

In this view, the primary goal of this Special Issue of Life is to gather original research articles on exciting discoveries of novel transport paths in proteins, functional characterization of transport paths, engineering of such pathways, and their perturbation by the environment (ligands, drugs, solvents,  membrane, etc.) investigated by experimental and/or computational methods; as well as studies on the development and benchmarking of methods for identification and analyses of transport pathways. Critical reviews focused on specific and timely topics relevant to molecular transport in proteins are also highly welcomed.

Prof. Dr. Jan Brezovsky
Prof. Dr. Artur Gora
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. Life 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 2600 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 tunnel
  • protein channel
  • ligand transport
  • molecular gating
  • protein dynamics

Published Papers (1 paper)

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Research

11 pages, 1325 KiB  
Article
F1099L-CFTR (c.3297C>G) has Impaired Channel Function and Associates with Mild Disease Phenotypes in Two Pediatric Patients
by Xiaoying Zhang, Jaspal S. Hothi, Yanhui H. Zhang, Aixia Ren, Michael J. Rock, Saumini Srinivasan, Dennis C. Stokes, Anjaparavanda P. Naren and Weiqiang Zhang
Life 2021, 11(2), 131; https://doi.org/10.3390/life11020131 - 8 Feb 2021
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Abstract
(1) Background: many rare cystic fibrosistransmembrane conductance regulator (CFTR) mutations remain poorly characterized with regard to functional consequences of the mutation. We present the clinical features of two pediatric cystic fibrosis (CF) subjects who are heterozygous for F1099L (c.3297C>G), one with G551D [...] Read more.
(1) Background: many rare cystic fibrosistransmembrane conductance regulator (CFTR) mutations remain poorly characterized with regard to functional consequences of the mutation. We present the clinical features of two pediatric cystic fibrosis (CF) subjects who are heterozygous for F1099L (c.3297C>G), one with G551D (a class III mutation) and one with 3849 + 10kbC->T (a class V mutation). We also identified the molecular defect(s) that are associated with F1099L mutation to correlate with the clinical features that we observed; (2) Methods: clinical findings and history were extracted from the electronic medical record and de-identified. F1099L-CFTR protein expression level and maturation status, channel function, and the effects of CFTR modulation on these characteristics were investigated using western blotting and iodide efflux assay; (3) Results: these two subjects have mild CF phenotypes when F1099L is combined with two known disease-causing mutations. F1099L-CFTR has a moderate defect in processing and maturation, causing fewer CFTR channels at the cell surface and, therefore, impaired channel activities. These defects could be effectively corrected using VX-809 (lumacaftor); and, (4) Conclusions: our biochemical data correlate with the disease manifestations and suggest that F1099L is potentially a CF-causing mutation. The study expands our knowledge of rare CFTR mutations and may help in developing effective therapies for subjects with F1099L mutation. Full article
(This article belongs to the Special Issue Structure, Dynamics, and Function of Protein Tunnels and Channels)
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