How is a water-soluble globular protein able to spontaneously cross a cellular membrane? It is commonly accepted that it undergoes significant structural rearrangements on the lipid-water interface, thus acquiring membrane binding and penetration ability. In this study molecular dynamics (MD) simulations have been used to explore large-scale conformational changes of the globular viscumin A chain in a complex environment – comprising urea and chloroform/methanol (CHCl3/MeOH) mixture. Being well-packed in aqueous solution, viscumin A undergoes global structural rearrangements in both organic media. In urea, the protein is “swelling” and gradually loses its long-distance contacts, thus resembling the “molten globule” state. In CHCl3/MeOH, viscumin A is in effect turned “inside out”. This is accompanied with strengthening of the secondary structure and surface exposure of hydrophobic epitopes originally buried inside the globule. Resulting solvent-adapted models were further subjected to Monte Carlo simulations with an implicit hydrophobic slab membrane. In contrast to only a few point surface contacts in water and two short regions with weak protein-lipid interactions in urea, MD-derived structures in CHCl3/MeOH reveal multiple determinants of membrane interaction. Consequently it is now possible to propose a specific pathway for the structural adaptation of viscumin A with respect to the cell membrane – a probable first step of its translocation into cytoplasmic targets.
Transmembrane α-helical domains are common structural elements in membrane proteins structure. They are involved into functioning of receptors and ion channels. Protein-protein interactions in lipid environment underlie the function of the most membrane systems. The properties of lipid environment can modulate the activity of membrane proteins, such as receptor tyrosine kinases. Glycophorin A is a glycoprotein that forms a very stable dimer. Its transmembrane domain is known as a good model system to study dimerization of α-helices. The major mechanism of the disturbance of a dimer by point mutations is thought to be a change of protein-protein contacts, but the role of the membrane is not well understood. In present work we study the behavior of transmembrane segment of human glycophorin A and two mutant forms G83A and T87V using molecular dynamics simulations in lipid environment. The free energy of dimerization has been estimated and the analysis of lipid properties was done. We propose different mechanisms for each mutation: T87V strongly changes protein-protein contacts. For G83A we demonstrate with the decomposition approach the major contribution of non-favorable protein-lipid contacts coupled with the redistribution interfacial protein-protein interactions. For monomers and dimers of all three forms of glycophorin A we found lipid binding sites near the interface of dimerization in the hydrophobic region of the bilayer. Surprisingly, in the case of monomers lipid acyl chains bind to the interfacial residues. Thus, the membrane plays an active role in dimer formation.
Helical segments are common structural elements of membrane proteins. Dimerization and oligomerization of transmembrane (TM) α-helices provides the framework for spatial structure formation and protein-protein interactions. The membrane itself also takes part in the protein functioning. There are some examples of the mutual influence of the lipid bilayer properties and embedded membrane proteins. This work aims at the detail investigation of protein-lipid interactions using model systems: TM peptides corresponding to native protein segments. Three peptides were considered corresponding to TM domains of human glycophorin A (GpA), epidermal growth factor receptor (EGFR) and proposed TM-segment of human neuraminidase-1 (Neu1). A computational analysis of structural and dynamical properties was performed using molecular dynamics method. Monomers of peptides were considered incorporated into hydrated lipid bilayers. It was confirmed, that all these TM peptides have stable helical conformation in lipid environment, and the mutual adaptation of peptides and membrane was observed. It was shown that incorporation of the peptide into membrane results in the modulation of local and mean structural properties of the bilayer. Each peptide interacts with lipid acyl chains having special binding sites on the surface of central part of α-helix that exist for at least 200 ns. However, lipid acyl chains substitute each other faster occupying the same site. The formation of a special pattern of protein-lipid interactions may modulate the association of TM domains of membrane proteins, so membrane environment should be considered when proposing new substances targeting cell receptors.
Transmembrane (TM) α-helical domains are common structural elements of membrane proteins. They play an important role in functioning of membrane receptors and ion channels, so protein-protein interactions in the lipid environment are involved into the functioning of the most vital membrane systems. Here we study dimerization of glycophorin A and its two mutant forms G83A and T87V in lipid environment using molecular dynamics simulations. It was found that the dimerization displays prominent entropic character, and the membrane plays an important role in the association of TM α-helices of glycophorin A. We conclude that selected mutations utilize two different mechanisms of the dimer weakening. It was also shown that both monomers and dimers of all three forms of glycophorin A have lipid binding sites in the hydrophobic region of the bilayer. These interactions with lipid acyl chains are involved in the process of TM domains interactions, as we found that monomers “feel” each other in terms of changes of interaction free energy on large distances. Thus, the lipid membrane plays an active role in dimer formation.
Today, recombinant proteins are quite widely used in biomedical and biotechnological applications. At the same time, the question about their full equivalence to the native analogues remains unanswered. To gain additional insight into this problem, intimate atomistic details of a relatively simple protein, small and structurally rigid recombinant cardiotoxin I (CTI) from cobra Naja oxiana venom, were characterized using nuclear magnetic resonance (NMR) spectroscopy and atomistic molecular dynamics (MD) simulations in water. Compared to the natural protein, it contains an additional Met residue at the N-terminus. In this work, the NMR-derived spatial structure of uniformly 13C- and 15N-labeled CTI and its dynamic behavior were investigated and subjected to comparative analysis with the corresponding data for the native toxin. The differences were found in dihedral angles of only a single residue, adjacent to the N-terminal methionine. Microsecond-long MD traces of the toxins reveal an increased flexibility in the residues spatially close to the N-Met. As the detected structural and dynamic changes of the two CTI models do not result in substantial differences in their cytotoxicities, we assume that the recombinant protein can be used for many purposes as a reasonable surrogate of the native one. In addition, we discuss general features of the spatial organization of cytotoxins, implied by the results of the current combined NMR and MD study.