Structure, Dynamics, and Function of Protein Tunnels and Channels
Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 3177
Interests: structural bioinformatics; computational protein design; biophysics; molecular modeling; drug design and discovery; ligand transport
Special Issues, Collections and Topics in MDPI journals
Interests: computational chemistry, bioinformatics, protein dynamics, protein engineering, drug design, proteins evolution, new methods development
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
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- protein tunnel
- protein channel
- ligand transport
- molecular gating
- protein dynamics