European Biophysics Journal

The aim of this study is to investigate if the packing motifs of native transmembrane helices can be produced by simulations with simple potentials and to develop a method for the rapid generation of initial candidate models for integral membrane proteins composed of bundles of transmembrane helices. Constituent residues are mapped along the helix axis in order to maintain the amino acid sequence-dependent properties of the helix. Helix packing is optimized according to a semi-empirical potential mainly composed of four components: a bilayer potential, a crossing angle potential, a helix dipole potential and a helix-helix distance potential. A Monte Carlo simulated annealing protocol is employed to optimize the helix bundle system. Necessary parameters are derived from theoretical studies and statistical analysis of experimentally determined protein structures. Preliminary testing of the method has been conducted with idealized seven Ala20 helix bundles. The structures generated show a high degree of compactness. It was observed that both bacteriorhodopsin-like and δ-endotoxin-like structures are generated in seven-helix bundle simulations, within which the composition varies dependent upon the cooling rate. The simulation method has also been employed to explore the packing of N = 4 and N = 12 transmembrane helix bundles. The results suggest that seven and 12 transmembrane helix bundles resembling those observed experimentally (e.g., bacteriorhodopsin, rhodopsin and cytochrome c oxidase subunit I) may be generated by simulations using simple potentials.

The effects of binding calcium ions to the double helical forms of gramicidin present in methanol solution were examined using circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopies. It was found that calcium ions principally alter the relative composition of the equilibrium mixture of gramicidin conformers present in the solvent. In the absence of calcium, both parallel and antiparallel double helices are present. However, the addition of small amounts of Ca2+ shifts the equilibrium towards the left-handed parallel double helical form. This conformational change prevents monovalent cations (caesiums) from binding to the gramicidin double helix, and even converts the shorter, wider anti-parallel double helical form normally produced in the presence of caesium into the longer, narrower parallel double helical form. Furthermore, a temperature study showed that calcium ions tend to stabilize this form relative to the ion-free forms. The conformation of gramicidin is further changed, becoming a disordered structure, when the concentration of Ca2+ is raised. Thus, the binding of divalent calcium ions has a number of dramatic effects on the conformations of gramicidin present in solution.

Familial hypertrophic cardiomyopathy is an autosomal dominant genetic disorder caused by mutations in cardiac sarcomeric proteins. One such mutation is a six amino acid duplication of residues 1248–1253 in the C-terminal immunoglobulin domain of cardiac myosin binding protein-C, referred to as Motif X. Motif X binds the myosin rod and titin. Here we investigate the structural and functional alteration in the mutant Motif X protein to understand how sarcomeric dysfunction may occur. The cDNA encoding Motif X was cloned, mutated and expressed as wild-type and mutant proteins in a bacterial expression system. Circular dichroism spectroscopy confirmed that the normal and mutant Motif X exhibited a high β-content, as predicted for immunoglobulin domains. Thermal denaturation curves showed that Motif X unfolded with at least two structural transitions, with the first transition occurring at 63 °C in the wild-type but at 40 °C in the mutant, consistent with the mutant being structurally less stable. Sedimentation binding studies with synthetic myosin filaments revealed no significant difference in binding to myosin between the wild-type and the mutant Motif X. Molecular modeling of this duplication mutation onto an homologous IgI structure (telokin) revealed that the duplicated residues lie within the F strand of the immunoglobulin fold, on a surface of Motif X distant from residues previously implicated in myosin binding. Taken together, these data suggest that the Motif X mutation may interfere with other, as yet unidentified, functional interactions.

Recently, the scanning force microscope (SFM) has been widely used for direct monitoring of specific interactions between biologically active molecules. Such studies have employed the SFM liquid-cell setup, which allows measurements to be made in the native environment with force resolution down to a tenth of a picoNewton. In this study, the ligand–receptor strength of monoclonal anti-human prostatic acid phosphatase and prostatic acid phosphatase, representing an antigen–antibody system with a single type of interaction, was determined. Then, the interaction force occurring between concanavalin A and the carbohydrate component of the glycoproteins arylsulfatase A and carboxypeptidase Y was measured. High mannose-type glycans were sought on the human prostate carcinoma cell surface. Application of an analysis based on the Poisson distribution of the number of bonds formed in all these measured systems allowed the strength of the molecular interaction to be calculated. The values of the force acting between two single molecules were 530±25, 790±32, and 940±39 pN between prostatic acid phosphatase and monoclonal anti-human prostatic acid phosphatase, between concanavalin A and arylsulfatase A, and between concanavalin A and carboxypeptidase Y, respectively. The value calculated from data collected for the force between concanavalin A and mannose-containing ligands present on the surface of human prostate carcinoma cells was smaller, 116±17 pN. The different values of the binding force between concanavalin A and mannose-containing ligands were attributed to the structural changes of the carbohydrate components.

The immobilization of gold nanoparticles (AuNPs) with antimicrobial peptides (AMPs) is a new and promising way to enhance both the activity and targeting capabilities of AMPs. However, a full understanding of the adsorption process underlying these materials is still lacking. Cecropin-melittin is a peptide with a broad antimicrobial activity while displaying low hemolytic properties, whose conjugation with AuNPs has not been studied before. In this context, we report the investigation of the adsorption process of the cecropin-melittin peptide, with (CM-SH) and without (CM) cysteine at its C-terminus, onto a gold surface based on all-atom MD simulations. Our results show that the way the peptides approach the surface dictates the final conformation and the time required to achieve it in both CM-SH and CM cases. Most important, it is demonstrated that the presence of cysteine promotes a faster conformational stabilization during the lockdown regime of the CM-SH peptide, noticeably affecting this by acting as a preferential anchoring point. This investigation represents a first step in rationalizing, with atomistic detail, some experimentally observed features of CM-SH and CM immobilized gold nanoparticles.

Two new methods for preparing phospholipid coated microbubble suspensions are elucidated. Firstly, co-axial electrohydrodynamic atomisation was utilized to generate 3–7 µm diameter microbubbles. Secondly, a specially designed and constructed T-junction device was used to prepare monodisperse microbubbles. Characteristics of microbubbles prepared by these two methods are compared with those obtained by sonication of the phospholipid suspension.