Molecular and hydrodynamic properties of human epidermal growth factor receptor HER2 extracellular domain and its homodimer: Experiments and multi-scale simulations

BACKGROUND

In a broad range of human carcinomas gene amplification leads to HER2 overexpression, which has been proposed to cause spontaneous dimerization and activation in the absence of ligand. This makes HER2 attractive as a therapeutic target. However, the HER2 homodimerization mechanism remains unexplored. It has been suggested that the "back-to-back" homodimer does not form in solution. Notwithstanding, very recently the crystal structure of the HER2 extracellular domain homodimer formed with a "back-to-head" interaction has been resolved. We intend to explore the existence of such interactions.

METHODS

A combination of experiments, molecular dynamics and hydrodynamic modeling were used to monitor the transport properties of HER2 in solution.

RESULTS & CONCLUSIONS

We have detected the HER2 extracellular domain homodimer in solution. The results show a high degree of molecular flexibility, which ultimately leads to quite higher values of the intrinsic viscosity and lower values of diffusion coefficient than those corresponding to globular proteins. This flexibility obeys to the open conformation of the receptor and to the large fluctuations of the different domains. We also report that for obtaining the correct hydrodynamic constants from the modeling one must consider the glycosylation of the systems.

GENERAL SIGNIFICANCE

Conformational features of epidermal growth factor receptors regulate their hydrodynamic properties and control their activity. It is essential to understand the dynamics of these systems and the role of the specific domains involved. To find biophysical correlations between dynamics and macroscopic transport properties is of general interest for researches working in this area. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.

Mapping the Mechanical Properties of Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) Banded Spherulites by Nanoindentation

Nanoindentation provides clear evidence that spherulite banding can be associated with a continuous modulation of mechanical properties from the more compliant peaks to the stiffer valleys. The structural arrangement in polymer-banded spherulites has intrigued scientists for many decades, and the debate has been recently intensified with the advent of new experimental evidence. The present paper approaches this issue by exploring the local mechanical properties of poly(3-hydroxybutyrate-co-3-hydroxyvalerate)-ringed spherulites via nanoindentation and discussing the confidence of the results. It was found that storage modulus and hardness across the banding morphology can be described as a sequence of regular oscillations with a periodicity that exactly matches the one observed using optical and atomic force microscopy. Results are consistent with the model of regular twisting of the lamellae, with flat-on arrangement in the low regions and edge-on lamellae in the crests.

A new insight into the conformation and melt dynamics of hydrogenated polybutadiene as revealed by computer simulations

Extensive molecular dynamics simulations of the macromolecular conformation and the melt dynamics for model polymers of different molecular weights have been carried out. The selected models are hydrogenated polybutadienes with a 2% content of ethyl branches and linear polyethylene. It will be shown that the density and chain stiffness are clearly affected by both the molecular weight and the presence of ethyl branches. Furthermore, the results obtained from the simulations on the molecular size and, more remarkably, chain dynamics, perfectly match the neutron scattering experiments performed by Zamponi et al. in hydrogenated polybutadienes. We observe a clear chain contraction and a slow dynamics for the hydrogenated polybutadiene with respect to the linear chain of the same molecular length. Using the Likhtman-McLeish definitions, the obtained values of the entanglement relaxation time (τe) and the tube diameter (a) are found to be in agreement with the available experimental data (by rheology and neutron spin echo) as well as with those obtained by the simulations. Finally, a very good agreement of diffusion coefficients as a function of the molecular weight between simulations and experiments is observed. Therefore, there exists a clear difference between the results obtained for branched and linear polyethylene, accounting for a definitive effect of the short chain branching on the conformational properties and the melt dynamics of polyolefins.

Evidences of Changes in Surface Electrostatic Charge Distribution during Stabilization of HPV16 Virus-Like Particles

The stabilization of human papillomavirus type 16 virus-like particles has been examined by means of different techniques including dynamic and static light scattering, transmission electron microscopy and electrophoretic mobility. All these techniques provide different and often complementary perspectives about the aggregation process and generation of stabilized virus-like particles after a period of time of 48 hours at a temperature of 298 K. Interestingly, static light scattering results point towards a clear colloidal instability in the initial systems, as suggested by a negative value of the second virial coefficient. This is likely related to small repulsive electrostatic interactions among the particles, and in agreement with relatively small absolute values of the electrophoretic mobility and, hence, of the net surface charges. At this initial stage the small repulsive interactions are not able to compensate binding interactions, which tend to aggregate the particles. As time proceeds, an increase of the size of the particles is accompanied by strong increases, in absolute values, of the electrophoretic mobility and net surface charge, suggesting enhanced repulsive electrostatic interactions and, consequently, a stabilized colloidal system. These results show that electrophoretic mobility is a useful methodology that can be applied to screen the stabilization factors for virus-like particles during vaccine development.

Willingness to pay and conjoint analysis to determine women's preferences for ovarian stimulating hormones in the treatment of infertility in Spain

BACKGROUND

Despite many advances in assisted reproductive techniques (ART), little is known about preferences for technological developments of women undergoing fertility treatments. The aims of this study were to investigate the preferences of infertile women undergoing ART for controlled ovarian stimulation (COS) treatments; to determine the utility values ascribed to different attributes of COS treatments; and to estimate women's willingness to pay (WTP) for COS.

METHODS

A representative sample of ambulatory patients ready to receive, or receiving, COS therapies for infertility were recruited from seven specialized private centres in six autonomous communities in Spain. Descriptive, inferential and conjoint analyses (CA) were used to elicit preferences and WTP. Attributes and levels of COS treatments were identified by literature review and two focus groups with experts and patients. WTP valuations were derived by a combination of double-bounded (closed-ended) and open questions and contingent ranking methods.

RESULTS

In total, 160 patients [mean (standard deviation; SD) age: 35.8 (4.2) years] were interviewed. Over half of the participants (55.0%) had a high level of education (university degree), most (78.8%) were married and half (50.0%) had an estimated net income of >€1502 per month and had paid a mean (SD) €1194.17 (€778.29) for their most recent hormonal treatment. The most frequent causes of infertility were related to sperm abnormalities (50.3%). In 30.6% of cases, there were two causes of infertility. The maximum WTP for COS treatment was €800 (median) per cycle; 35.5% were willing to pay an additional €101-€300 for a 1-2% effectiveness gain in the treatment. Utility values (CA) showed that effectiveness was the most valued attribute (39.82), followed by costs (18.74), safety (17.75) and information sharing with physicians (14.93).

CONCLUSIONS

WTP for COS therapies exceeds current cost. Additional WTP exists for 1-2% effectiveness improvement. Effectiveness and costs were the most important determinants of preferences, followed by safety and information sharing with physicians.

Size and conformational features of ErbB2 and ErbB3 receptors: a TEM and DLS comparative study

ErbB2 and ErbB3 receptors belong to the epidermal growth factor receptor family. The members of this family are able to form homo- and heterodimers that trigger diverse downstream signalling concerned to multiple cellular events. In the absence of a ligand, ErbB3 adopts a characteristic tethered conformation, which differs from ErbB2 extended conformation. In this work, transmission electron microscopy (TEM) and dynamic light scattering (DLS) have been used to characterize the conformational features and the size of ErBb2 and ErbB3 receptors. Two main objectives are presented. The first one is to evaluate the use of TEM as a tool for structural studies for this family of receptors. The low molecular weight of these proteins represents a challenging purpose for TEM studies. The other one is to search for a relationship between the results obtained by TEM and those obtained for the hydrodynamic size measured by DLS. This comparison has allowed us to identify the conformational differences of the receptors and to anticipate the use of these experimental techniques for the study of the ligand activated heterodimerization, a process related to a significant number of human malignancies.

Ethylene-styrene copolymerization with constrained geometry catalysts: A density functional study

A density functional theory (DFT) study of the ethylene-styrene copolymerization process with titanium-based constrained geometry catalyst (CGC) is presented. To establish the difference between simplified CGC or real CGC models, i.e., considering all ligands of the catalyst, we have performed calculations for ethylene and styrene insertions in both models. Thus, we have used two different DFT functional, BP86 and B3L YP along with two basis set, LANL 2DZ (without polarization functions) and DZVP (including polarization functions). We have noted certain differences between theoretical results published by other authors and our theoretical and experimental data.

Effect of long chain branching on linear-viscoelastic melt properties of polyolefins

The aim of this review is to provide evidence that rheological testing is a potent tool for characterising polymers in the melt. An effort has been made in order to gather results in conventional and model polyolefins, and correlating them with phenomena occurring at the molecular level. We have focused our interest on long chain branching (LCB). In the case of materials containing long side-chain branches, strong effects on viscosity, elastic character and activation energy of flow are general features. Literature results mostly indicate that the effect of polydispersity on these parameters could be very similar to that expected due to the presence of LCB - notwithstanding that the effects of LCB seem to be stronger than those due to polydispersity for a given molecular weight. Different relaxation processes appear as a consequence of the presence of LCB: slower terminal relaxation behaviour than of linear counterparts, and faster additional branch relaxation at higher frequencies, clearly distinguishable from polydispersity effects. To measure the amount of LCB from limited viscoelastic data and molecular properties seems to be a suitable instrument to explain the rheological features of the different polymers, but it fails when the results are compared with measured values of LCB density in model polymers. The actual framework leads us to say that the number of branches is less important than the topology itself. Therefore, the position and architecture of the branches along the polymer main chain are the main factors that control the rheology of the material.

Repeated sequences in bacterial chromosomes and plasmids: a glimpse from sequenced genomes

To gain insight into the extent of exact DNA repeats in sequenced bacterial genomes and their plasmids, we analyzed the collection of completely sequenced bacterial genomes available at GenBank using the program Miropeats. This program draws graphical representations of exact DNA repeats in whole genomes. In this work, we present maps showing the extent and type (inverted or direct) of exact DNA repeats longer than 300 bp for the whole collection. These repeats may participate in a variety of events relevant for bacterial genome plasticity, such as amplifications, deletions, inversions, and translocations (via homologous recombination), as well as transposition. Additionally, we review recent data showing that high-frequency architectural variations in genomic structure occur at both the interspecies and interstrain levels.

Evaluation of the role of recA protein in plant virulence with recA mutants of Xanthomonas campestris pv. campestris

Xanthomonas campestris pv. campestris NRRL B1459 recA mutants were isolated by recombination with an interrupted Rhizobium etli recA gene and selection of double recombinants. The mutants were impaired in homologous genetic recombination and in DNA repair as judged by their sensitivity to methyl-methane-sulfonate and to UV irradiation; these defects are complemented in trans by the R. etli recA gene. Virulence of X. campestris pv. campestris NRRL B1459 to cabbage is considerably diminished by the recA mutation. The recA mutation is not correlated with the frequency of occurrence of a genetic rearrangement that affects chemotaxis, plant virulence, and xanthan gum production.

Genetic analysis of the transcriptional arrangement of Azotobacter vinelandii alginate biosynthetic genes: identification of two independent promoters

The study of alginate biosynthesis, the exopolysaccharide produced by Azotobacter vinelandii and Pseudomonas aeruginosa, might lead to different biotechnological applications. Here we report the cloning of A. vinelandii algA, the gene coding for the bifunctional enzyme phosphomannose isomerase-guanosine diphospho-o-mannose pyrophosphorylase (PMI-GMP). This gene was selected by the complementation for xanthan gum production of Xanthomonas campestris pv. campestris xanB-mutants, which lack this enzymatic activity. The complementing cosmid clones selected, besides containing algA, presented a gene coding for an alginate lyase activity (algL), and some of them also contained algD which codes for GDP-mannose dehydrogenase. We present here the characterization of the A. vinelandii chromosomal region comprising algD and its promoter region, algA and algL, showing that, as previously reported for P. aeruginosa, A. vinelandii has a cluster of the biosynthetic alginate genes. We provide evidence for the presence of an algD-independent promoter in this region which transcribes at least algL and algA, and which is regulated in a manner that differs from that of the algD promoter.