Specification of binding modes between a transmembrane peptide mimic of ATP6V0C and polytopic E5 of human papillomavirus-16

<p>Interaction of E5 of papillomavirus-16 based on its three transmembrane domains (TMDs) with a peptide mimicking the fourth TMD (TMD-A) of the 16 kDa c subunit of the human vacuolar H⁺-ATPase, ATP6V0C, and one of its mutant is investigated. Docking reveals binding of the peptide between the second and third TMD of E5. A series of hydrophobic residues are responsible for the contact. Estimated weak binding energies based on potential of mean force calculations reveal marginal differences of the estimated binding energies between wild type (WT) and mutant peptide. Also differences in estimated binding energies of dimers of the individual TMDs of E5 with the WT peptide are marginal. Correlation of rotational data derived from coarse-grained molecular dynamics simulations of the peptides and the protein as well as from the principal component analysis reveal that the binding of TMD-A with TMD3 is enthalpy driven and binding with TMD2 is guided by entropic conditions.</p

Weak Selectivity Predicted for Modeled Bundles of Viral Channel-Forming Protein E5 of Human Papillomavirus-16

Protein E5 is a polytopic 83 amino acid membrane protein with three transmembrane domains (TMDs), encoded by high-risk human papillomavirus-16 (HPV-16). HPV-16 is found to be the causative agent for cervical cancer. Protein E5, among other proteins (e.g., E6, E7), is expressed at an “early” (E) stage when the cell turns malignant. It has been experimentally found that E5 forms hexameric assemblies, which show the characteristics of the class of so-called channel-forming proteins by rendering lipid membranes permeable to ions and small molecules. Protein E5 is used to achieve structural models of the protein in assembled bundles using a force field-based docking approach. Extended molecular dynamics simulations of selected bundles in fully hydrated lipid bilayers suggest the second TMD to be pore-lining, allowing for water columns to exist within the lumen of the pore. Full correlation analysis indicates asymmetric dynamics within the monomers of the bundle. Potential of mean force calculations of a snapshot structure of the putative open pore of the protein bundle propose low selectivity

Estimating binding free energy of a putative growth factors EGF–VEGF complex – a computational bioanalytical study

<p>Epidermal growth factor (EGF) and homodimeric vascular endothelial growth factor (VEGF) bind to cell surface receptors. They are responsible for cell growth and angiogenesis, respectively. Docking of the individual proteins as monomeric units using ZDOCK 2.3.2 reveals a partial blocking of the receptor binding site of VEGF by EGF. The receptor binding site of EGF is not affected by VEGF. The calculated binding energy is found to be intermediate between the binding energies calculated for Alzheimer’s Aß42 and the barnase/barstar complex.</p

Membrane undulation induced by NS4A of Dengue virus: a molecular dynamics simulation study

<div><p>Nonstructural protein 4A (NS4A) of Dengue virus (DENV) is a membrane protein involved in rearrangements of the endoplasmic reticulum membrane that are required for formation of replication vesicles. NS4A is composed most likely of three membrane domains. The N- and C-terminal domains are supposed to traverse the lipid membrane whereas the central one is thought to reside on the membrane surface, thus forming a <i>u</i>-shaped protein. All three membrane domains are proposed to be helical by secondary structure prediction programs. After performing multi nanosecond molecular dynamics (MD) simulations at various temperatures (300, 310, and 315.15 K) with each of the individual domains, they are used in a docking approach to define putative association motifs of the transmembrane domains (TMDs). Two structures of the <i>u</i>-shaped protein are generated by separating two assembled TMDs linking them with the membrane-attached domain. Lipid undulation is monitored with the structures embedded in a fully hydrated lipid bilayer applying multiple 200 ns MD simulations at 310 K. An intact structure of the protein supports membrane undulation. The strong unwinding of the helices in the domain-linking section of one of the structures lowers its capability to induce membrane curvature. Unwinding of the link region is due to interactions of two tryptophan residues, Trp-96 and 104. These results provide first insights into the membrane-altering properties of DENV NS4A.</p></div

<i>In Silico</i> Analysis Reveals Sequential Interactions and Protein Conformational Changes during the Binding of Chemokine CXCL-8 to Its Receptor CXCR1

<div><p>Chemokine CXCL-8 plays a central role in human immune response by binding to and activate its cognate receptor CXCR1, a member of the G-protein coupled receptor (GPCR) family. The full-length structure of CXCR1 is modeled by combining the structures of previous NMR experiments with those from homology modeling. Molecular docking is performed to search favorable binding sites of monomeric and dimeric CXCL-8 with CXCR1 and a mutated form of it. The receptor-ligand complex is embedded into a lipid bilayer and used in multi ns molecular dynamics (MD) simulations. A multi-steps binding mode is proposed: (i) the N-loop of CXCL-8 initially binds to the N-terminal domain of receptor CXCR1 driven predominantly by electrostatic interactions; (ii) hydrophobic interactions allow the N-terminal Glu-Leu-Arg (ELR) motif of CXCL-8 to move closer to the extracellular loops of CXCR1; (iii) electrostatic interactions finally dominate the interaction between the N-terminal ELR motif of CXCL-8 and the EC-loops of CXCR1. Mutation of CXCR1 abrogates this mode of binding. The detailed binding process may help to facilitate the discovery of agonists and antagonists for rational drug design.</p></div

The surface lipophilicity distribution for ligand binding with receptor.

<p>The complex structure is represented as ribbon structure with the N-loop of the ligand colored green, the N-terminus of receptor colored pink, and the EC-loops colored yellow. Blue color represents the hydrophilic part while green color represents hydrophobic part. Residues around the binding interface are labeled and shown as sticks; black font is for receptor, while red font is for ligand. (A): Monomeric CXCL-8 binding with CXCR1 at the initial time. Hydrophobic pocket of ligand CXCL-8 is also marked. (B): Monomeric CXCL-8 binding with CXCR1 at the final simulation time. (C): CXCL-8 binding with CXCR1_mut at the initial time. (D): CXCL-8 binding with CXCR1_mut after the 300 ns runs.</p

The surface charge distribution of the complex structure based on Poisson-Boltzmann equation.

<p>The complex structure is represented as ribbon structure with the N-loop of the ligand colored green, the N-terminus of receptor colored pink, and the EC-loops colored yellow. Blue color corresponds to positive and red color to negative electrostatic potential. Residues around the binding interface are labeled and shown as sticks, black is for receptor, while red is for ligand. (A): Monomeric CXCL-8 binding with CXCR1 at the initial time. Binding groove of CXCR1 is also marked. (B): Monomeric CXCL-8 binding with CXCR1 at the final simulation time. (C): CXCL-8 binding with CXCR1_mut at the initial time. (D): CXCL-8 binding with CXCR1_mut after the 300 ns runs.</p

The distances between the charged groups of ligand and receptor forming electrostatic interactions.

<p>(A) Some positively charged residues of the N-loop of CXCL-8 gradually approach to the negatively charged residues of the N-terminus of CXCR1 by electrostatic interactions (K3^CXCL-8-D194^CXCR1 (black), K11^CXCL-8-D14^CXCR1 (red), K15^CXCL-8-D13^CXCR1 (green)) during 300 ns MD simulations. (B) Other positively charged residues of CXCL-8 interact with the negatively charged residues of CXCR1 by electrostatic interactions (R47^CXCL-8-D14^CXCR1 (pink), K64^CXCL-8-E35^CXCR1 (blue), R60^CXCL-8-E275^CXCR1 (yellow)) during 300 ns MD simulations. Distances are the average values with the function of time for three replicates of the system monomeric CXCL-8 binding to CXCR1. Error bars of the curves are omitted for figure clarity.</p

Modeled full-length CXCR1 structure and RMSD values during MD simulations.

<p>(A) Ribbon representations of the modeled full-length receptor CXCR1 (residues 2∼347) after embedded into a POPC lipid bilayer for 50 ns MD simulations. The CXCR1 is composed of the structure from the NMR experiment (residues 29∼324, red color), the N-terminal (residues 2∼28) and C-terminal (residues 325∼347) domains from homology modeling results (green color). (B) Plot of the RMSD for the backbone atoms of CXCR1 embedded into POPC lipid bilayers throughout 50 ns MD trajectory.</p

The binding orientation of ligand for various systems at different MD simulation time.

<p>Due to the similar final binding orientations of the three replicates of each system and the figure clarity, only one representative simulation run of each system is shown herein. (A) and (B): For monomeric CXCL-8 system at initial and final simulation time; (C) and (D): For mutated receptor CXCR1_mut system at initial and final simulation time. In all figures, ligands are colored with green, receptors are colored with red, and phosphorous and nitrogen atoms are colored with pink and blue, respectively. The direction of dipole moment of ligand is represented as blue arrow. The distance between the two layers is represented as the thickness of the membrane.</p