Lorant Janosi

Lipid-Modulated Sequence-Specific Association of Glycophorin A in Membranes

Protein association in lipid membranes is a complex process with thermodynamics directed by a multitude of different factors. Amino-acid sequence is a molecular parameter that affects dimerization as shown by limited directed mutations along the transmembrane domains. Membrane-mediated interactions are also important although details of such contributions remain largely unclear. In this study, we probe directly the free energy of association of Glycophorin A by means of extensive parallel Monte Carlo simulations with recently developed methods and a model that accounts for sequence-specificity while representing lipid membranes faithfully. We find that lipid-induced interactions are significant both at short and intermediate separations. The ability of molecules to tilt in a specific hydrophobic environment extends their accessible interfaces, leading to intermittent contacts during protein recognition. The dimer with the lowest free energy is largely determined by the favorable lipid-induced attractive interactions at the closest distance. Finally, the coarse-grained model employed herein, together with the extensive sampling performed, provides estimates of the free energy of association that are in excellent agreement with existing data.

The Gating Mechanism of the Human Aquaporin 5 Revealed by Molecular Dynamics Simulations

Aquaporins are protein channels located across the cell membrane with the role of conducting water or other small sugar alcohol molecules (aquaglyceroporins). The high-resolution X-ray structure of the human aquaporin 5 (HsAQP5) shows that HsAQP5, as all the other known aquaporins, exhibits tetrameric structure. By means of molecular dynamics simulations we analyzed the role of spontaneous fluctuations on the structural behavior of the human AQP5. We found that different conformations within the tetramer lead to a distribution of monomeric channel structures, which can be characterized as open or closed. The switch between the two states of a channel is a tap-like mechanism at the cytoplasmic end which regulates the water passage through the pore. The channel is closed by a translation of the His67 residue inside the pore. Moreover, water permeation rate calculations revealed that the selectivity filter, located at the other end of the channel, regulates the flow rate of water molecules when the channel is open, by locally modifying the orientation of His173. Furthermore, the calculated permeation rates of a fully open channel are in good agreement with the reported experimental value.

Self-Association of Models of Transmembrane Domains of ErbB Receptors in a Lipid Bilayer

Association of transmembrane (TM) helices is facilitated by the close packing of small residues present along the amino-acid sequence. Extensive studies have established the role of such small residue motifs (GxxxG) in the dimerization of Glycophorin A (GpA) and helped to elucidate the association of TM domains in the epidermal growth factor family of receptors (ErbBs). Although membrane-mediated interactions are known to contribute under certain conditions to the dimerization of proteins, their effect is often considered nonspecific, and any potential dependence on protein sequence has not been thoroughly investigated. We recently reported that the association of GpA is significantly assisted by membrane-induced contributions as quantified in different lipid bilayers. Herein we extend our studies to explore the origin of these effects and quantify their magnitude using different amino-acid sequences in the same lipid environment. Using a coarse-grained model that accounts for amino-acid specificity, we perform extensive parallel Monte Carlo simulations of ErbB homodimerization in dipalmitoyl-phosphatidylcholine lipid bilayers. A detailed characterization of dimer formation and estimates of the free energy of association reveal that the TM domains show a significant affinity to self-associate in lipid bilayers, in qualitative agreement with experimental findings. The presence of GxxxG motifs enhances favorable protein-protein interactions at short separations. However, the lipid-induced attraction presents a more complex character than anticipated. Depending on the interfacial residues, lipid-entropic contributions support a decrease of separation or a parallel orientation to the membrane normal, with important implications for protein function.

GxxxG Motifs, Phenylalanine, and Cholesterol Guide the Self-Association of Transmembrane Domains of ErbB2 Receptors

GxxxG motifs are common in transmembrane domains of membrane proteins and are often introduced to artificial peptides to inhibit or promote association to stable structures. The transmembrane domain of ErbB2 presents two separate such motifs that are proposed to be connected to stability and activity of the dimer. Using molecular simulations, we show that these sequences play a critical role during the recognition stage, forming transient complexes that lead to stable dimers. In pure phospholipid bilayers association occurs by contacts formed at the C-terminus promoted by the presence of phenylalanine residues. Helices subsequently rotate to eventually pack at short separations favored by lipid entropic contributions. In contrast, at intermediate cholesterol concentrations, a different pathway is followed that involves dimers with a weaker interface toward the N-terminus. However, at high cholesterol content, a switch toward the C-terminus is observed with an overall nonmonotonic change of the dimerization affinity. This conformational switch modulated by cholesterol has important implications on the thermodynamic, structural, and kinetic characteristics of helix-helix association in lipid membranes.

Modulating Effect of Histidine on Short Arginine- and Tryptophan-Based Antimicrobial Peptides

Antimicrobial peptides (AMPs) are short sequences of aminoacids that organisms use as defense mechanism against foreign bodies. The selectivity of interaction with bacterial cells over mammalian cells underlines their significant potential in developing AMP-based drugs against antibiotics resistant bacteria. We started from a tryptophan- and arginine-rich peptide (RRWWRWWRR) which showed good antimicrobial efficacy. Seven new analogs were design by substitution of tryptophan or arginine residues with histidine residues.

Aquaporins within a Tetramer Exhibit Different Structural Conformations: An in Silico Study of the Human Aquaporin 5

Aquaporins are protein channels located across the cell membrane with the role of conducting water or other small sugar alcohol molecules (aquaglyceroporins). The high-resolution X-ray structure of the human aquaporin 5 (HsAQP5) exhibits an important feature: the entire tetramer is crystallized, i.e., the tetramer is not obtained by rotating the monomeric structure around the main axis of the tetramer. Hence, by means of molecular dynamics simulations we conducted a study on the importance of the protein-protein coupling within an aquaporin tetrameric structure and characterized the structural behavior of the human AQP5. We found that different conformations within the tetramer lead to a distribution of monomeric channel structures, which can be characterized as “open” and “closed”. Both the extracellular (where the selectivity filter is located) and the cytoplasmic ends of a channel sample “closed” states. In the former region, this can be characterized by a strong narrowing and much lower water permeation rates. In the cytoplasmic ends “closed” state water passage is completely blocked by a gating mechanism characterized by the translation of the His67 residue inside the pore. While removing the crystallographic lipid occluding the central pore of the tetramer has no influence on the gating system, the protein-protein coupling might play an important role in regulating its mechanism. Furthermore, our calculated permeation rate of a fully “open” channel was found to be in very good agreement with the experimental value.