Overcoming Membrane Protein Challenges with Computational Methods
A Special Issue of International Journal of Molecular Sciences (ISSN 1422-0067) belonging to the section "Macromolecules".
Deadline for manuscript submissions: 31 October 2026 | Viewed by 185
Editor
Interests: molecular modeling; peptide design; protein structure; transmembrane channel and protein; oncogenic proteins; potential of mean force
Special Issues, Collections and Topics in MDPI journals
Special Issue Information
Dear Colleagues,
Membrane proteins are embedded or bound to biological membranes, therefore participating in crucial cellular processes such as signal transduction, transmembrane molecular/ion transport, energy conversion, and cellular adhesion. Because of these functions, they are major targets for more than half of current therapeutic drugs. Membrane proteins can be functionally and structurally categorized into several groups, including receptors (e.g., G protein-coupled receptors, receptor tyrosine kinases), ion channels, transporters and pumps, enzymes associated with membranes, and membrane-anchored signaling proteins (e.g., post-translationally modified proteins).
Nonetheless, their study by experimental means can be quite challenging (including structural determination). Their structural and functional properties are strongly influenced by the surrounding lipid environment, which can modulate protein conformation, oligomerization, and activity. In addition, many membrane proteins exhibit substantial conformational flexibility and transient interactions with other proteins or lipids. Experimental characterization is further complicated by difficulties in protein expression, purification, and stabilization outside of their native membrane environment. These challenges often lead to incomplete structural information, limited resolution of dynamic states, and gaps in our understanding of membrane-associated molecular mechanisms.
By integrating structural prediction, molecular modeling, and large-scale simulations, computational approaches offer powerful complementary methods that can address experimental limitations by probing membrane protein structure, dynamics, and interactions in environments that closely mimic biological membranes. Such approaches can be used in revealing conformational transitions, protein–lipid interactions, and transient binding interfaces that are often difficult to capture experimentally. Moreover, computational modeling enables systematic exploration of mutation effects, lipid composition, and membrane curvature on protein function, providing mechanistic insights that can guide experimental design.
In this Special Issue, we encourage the submission of articles and reviews that use a range of computational methods, such as: (i) molecular dynamics (atomistic or coarse-grained) in explicit membrane models, to enable investigation of protein motions, interactions, and lipid-mediated regulation; (ii) various free energy calculation approaches (e.g., non-equilibrium methods, metadynamics, umbrella sampling, replica-exchange, etc.), to provide insights into the energetic landscapes and to explore rare conformational states; (iii) AI-based methods for structural predictions; (iv) computational docking and drug design approaches, to identify ligand-binding sites or protein–protein interfaces, suitable for therapeutic targeting. We encourage the combination of multiple in silico strategies with complementary experimental methods.
Dr. Lorant Janosi
Guest Editor
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Keywords
- membrane protein
- structural and functional properties
- computational approaches
- molecular dynamics
- free energy calculations
- computational docking and drug design approaches
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