Conformational Changes and Unfolding of ß-Amyloid Substrates in the Active Site of γ-Secretase.

Alzheimer's disease (AD) is the leading cause of dementia and is characterized by a presence of amyloid plaques, composed mostly of the amyloid-ß (Aß) peptides, in the brains of AD patients. The peptides are generated from the amyloid precursor protein (APP), which undergoes a sequence of cleavages, referred as trimming, performed by γ-secretase. Here, we investigated conformational changes in a series of ß-amyloid substrates (from less and more amyloidogenic pathways) in the active site of presenilin-1, the catalytic subunit of γ-secretase. The substrates are trimmed every three residues, finally leading to Aß40 and Aß42, which are the major components of amyloid plaques. To study conformational changes, we employed all-atom molecular dynamics simulations, while for unfolding, we used steered molecular dynamics simulations in an implicit membrane-water environment to accelerate changes. We have found substantial differences in the flexibility of extended C-terminal parts between more and less amyloidogenic pathway substrates. We also propose that the positively charged residues of presenilin-1 may facilitate the stretching and unfolding of substrates. The calculated forces and work/energy of pulling were exceptionally high for Aß40, indicating why trimming of this substrate is so infrequent.

The Role of Electrostatic Interactions in IFIT5-RNA Complexes Predicted by the UBDB+EPMM Method.

Electrostatic energy has a significant contribution to intermolecular interaction energy, especially in biological systems. Unfortunately, precise quantum mechanics calculations are not feasible for large biological systems; hence, simpler calculation methods are required. We propose a method called UBDB+EPMM (University at Buffalo Pseudoatom DataBank + Exact Potential Multipole Moments), which shortens computational time without losing accuracy. Here, we characterize electrostatic interactions in selected complexes of IFIT proteins with RNA. IFIT proteins are effectors of the innate immune system, and by binding foreign RNA, they prevent the synthesis of viral proteins in human host cells; hence, they block the propagation of viruses. We show that by using the UBDB+EPMM method it is possible to describe protein-RNA interactions not only qualitatively but also quantitatively. Looking at the charge penetration contribution to electrostatic interactions, we find all amino acid residues with strong local interactions. Moreover, we confirm that electrostatic interaction of IFIT5 with pppRNA does not depend on the sequence of the RNA.

COGRIMEN: Coarse-Grained Method for Modeling of Membrane Proteins in Implicit Environments.

The presented methodology is based on coarse-grained representation of biomolecules in implicit environments and is designed for the molecular dynamics simulations of membrane proteins and their complexes. The membrane proteins are not only found in the cell membrane but also in all membranous compartments of the cell: Golgi apparatus, mitochondria, endosomes and lysosomes, and they usually form large complexes. To investigate such systems the methodology is proposed based on two independent approaches combining the coarse-grained MARTINI model for proteins and the effective energy function to mimic the water/membrane environments. The latter is based on the implicit environment developed for all-atom simulations in the IMM1 method. The force field solvation parameters for COGRIMEN were initially calculated from IMM1 all-atom parameters and then optimized using Genetic Algorithms. The new methodology was tested on membrane proteins, their complexes and oligomers. COGRIMEN method is implemented as a patch for NAMD program and can be useful for fast and brief studies of large membrane protein complexes.

The Role of Cholesterol in Amyloidogenic Substrate Binding to the γ-Secretase Complex.

Alzheimer's disease is the most common progressive neurodegenerative disorder and is characterized by the presence of amyloid ß (Aß) plaques in the brain. The γ-secretase complex, which produces Aß, is an intramembrane-cleaving protease consisting of four membrane proteins. In this paper we investigated the amyloidogenic fragments of amyloid precursor protein (substrates Aß43 and Aß45, leading to less amyloidogenic Aß40 and more amyloidogenic Aß42, respectively) docked to the binding site of presenilin, the catalytic subunit of γ-secretase. In total, we performed 9 µs of all-atom molecular dynamics simulations of the whole γ-secretase complex with both substrates in low (10%) and high (50%) concentrations of cholesterol in the membrane. We found that, at the high cholesterol level, the Aß45 helix was statistically more flexible in the binding site of presenilin than Aß43. An increase in the cholesterol concentration was also correlated with a higher flexibility of the Aß45 helix, which suggests incompatibility between Aß45 and the binding site of presenilin potentiated by a high cholesterol level. However, at the C-terminal part of Aß45, the active site of presenilin was more compact in the case of a high cholesterol level, which could promote processing of this substrate. We also performed detailed mapping of the cholesterol binding sites at low and high cholesterol concentrations, which were independent of the typical cholesterol binding motifs.

Self-analysis of repeat proteins reveals evolutionarily conserved patterns.

BACKGROUND: Protein repeats can confound sequence analyses because the repetitiveness of their amino acid sequences lead to difficulties in identifying whether similar repeats are due to convergent or divergent evolution. We noted that the patterns derived from traditional "dot plot" protein sequence self-similarity analysis tended to be conserved in sets of related repeat proteins and this conservation could be quantitated using a Jaccard metric. RESULTS: Comparison of these dot plots obviated the issues due to sequence similarity for analysis of repeat proteins. A high Jaccard similarity score was suggestive of a conserved relationship between closely related repeat proteins. The dot plot patterns decayed quickly in the absence of selective pressure with an expected loss of 50% of Jaccard similarity due to a loss of 8.2% sequence identity. To perform method testing, we assembled a standard set of 79 repeat proteins representing all the subgroups in RepeatsDB. Comparison of known repeat and non-repeat proteins from the PDB suggested that the information content in dot plots could be used to identify repeat proteins from pure sequence with no requirement for structural information. Analysis of the UniRef90 database suggested that 16.9% of all known proteins could be classified as repeat proteins. These 13.3 million putative repeat protein chains were clustered and a significant amount (82.9%) of clusters containing between 5 and 200 members were of a single functional type. CONCLUSIONS: Dot plot analysis of repeat proteins attempts to obviate issues that arise due to the sequence degeneracy of repeat proteins. These results show that this kind of analysis can efficiently be applied to analyze repeat proteins on a large scale.

WaterSpy: A High Sensitivity, Portable Photonic Device for Pervasive Water Quality Analysis.

In this paper, we present WaterSpy, a project developing an innovative, compact, cost-effective photonic device for pervasive water quality sensing, operating in the mid-IR spectral range. The approach combines the use of advanced Quantum Cascade Lasers (QCLs) employing the Vernier effect, used as light source, with novel, fibre-coupled, fast and sensitive Higher Operation Temperature (HOT) photodetectors, used as sensors. These will be complemented by optimised laser driving and detector electronics, laser modulation and signal conditioning technologies. The paper presents the WaterSpy concept, the requirements elicited, the preliminary architecture design of the device, the use cases in which it will be validated, while highlighting the innovative technologies that contribute to the advancement of the current state of the art.

Effectiveness, safety, and long-term outcomes of non-powered mechanical sheaths for transvenous lead extraction.

Aims: To analyse the effectiveness, safety and long-term outcomes of conventional non-powered mechanical systems for transvenous lead extraction (TLE) performed by experienced first operators. Outcomes were assessed according to lead location and type of operating room in which the procedure was performed. Methods and results: Data from 2049 patients (mean age: 65 years), with infectious (40%) or non-infectious (60%) indications, were analysed over a mean of 3.37 (±2.29) years. A total of 3426 leads were extracted; and, overall, 95% full procedural, 4% partial procedural, and 98% clinical success were demonstrated. Within the patient cohort, 1.8% (37/2049) experienced major complications, with cardiac tamponade being predominant (30/37). Cardiac tamponade was identified as the main cause of mortality, as well as the cause of all procedure-related deaths (6/2049; 0.3%). Cardiac tamponade occurred in 1.8% of atrial and 0.3% of right ventricular lead extractions, with fatal tamponade reported in 9% of atrial, 40% of ventricular, and 67% of coronary sinus lead extractions. No association between lead location and cardiac tamponade-related mortality was observed; however, lead location did affect the success of pericardiocentesis. The cardiac tamponade-related mortality rate was 37% when TLE was performed in an electrophysiology laboratory. No deaths were reported when the procedure was performed in a cardiac surgery or hybrid operating room. Long-term survival was improved when TLE was performed due to non-infectious indications, rather than pocket infection or lead-related endocarditis (P < 0.001). Conclusion: Using conventional non-powered mechanical sheaths, TLE was effective even in patients at high risk of complications.

Identification of Specific Effect of Chloride on the Spectral Properties and Structural Stability of Multiple Extracellular Glutamic Acid Mutants of Bacteriorhodopsin.

In the present work we combine spectroscopic, DSC and computational approaches to examine the multiple extracellular Glu mutants E204Q/E194Q, E204Q/E194Q/E9Q and E204Q/E194Q/E9Q/E74Q of bacteriorhodopsin by varying solvent ionic strength and composition. Absorption spectroscopy data reveal that the absorption maxima of multiple EC Glu mutants can be tuned by the chloride concentration in the solution. Visible Circular dichroism spectra imply that the specific binding of Cl- can modulate weakened exciton chromophore coupling and reestablish wild type-like bilobe spectral features of the mutants. The DSC data display reappearance of the reversible thermal transition, higher Tm of denaturation and an increase in the enthalpy of unfolding of the mutants in 1 M KCl solutions. Molecular dynamics simulations indicate high affinity binding of Cl- to Arg82 and to Gln204 and Gln194 residues in the mutants. Analysis of the experimental data suggests that simultaneous elimination of the negatively charged side chain of Glu194 and Glu204 is the major cause for mutants' alterations. Specific Cl- binding efficiently coordinates distorted hydrogen bonding interactions of the EC region and reconstitutes the conformation and structure stability of mutated bR in WT-like fashion.

Feasibility of implementation of a "simplified, No-X-Ray, no-lead apron, two-catheter approach" for ablation of supraventricular arrhythmias in children and adults.

INTRODUCTION: Although the "near-zero-X-Ray" or "No-X-Ray" catheter ablation (CA) approach has been reported for treatment of various arrhythmias, few prospective studies have strictly used "No-X-Ray," simplified 2-catheter approaches for CA in patients with supraventricular tachycardia (SVT). We assessed the feasibility of a minimally invasive, nonfluoroscopic (MINI) CA approach in such patients. METHODS: Data were obtained from a prospective multicenter CA registry of patients with regular SVTs. After femoral access, 2 catheters were used to create simple, 3D electroanatomic maps and to perform electrophysiologic studies. Medical staff did not use lead aprons after the first 10 MINI CA cases. RESULTS: A total of 188 patients (age, 45 ± 21 years; 17% <19 years; 55% women) referred for the No-X-Ray approach were included. They were compared to 714 consecutive patients referred for a simplified approach using X-rays (age, 52 ± 18 years; 7% <19 years; 55% women). There were 9 protocol exceptions that necessitated the use of X-rays. Ultimately, 179/188 patients underwent the procedure without fluoroscopy, with an acute success rate of 98%. The procedure times (63 ± 26 vs. 63 ± 29 minutes, P > 0.05), major complications (0% vs. 0%, P > 0.05) and acute (98% vs. 98%, P > 0.05) and long-term (93% vs. 94%, P > 0.05) success rates were similar in the "No-X-Ray" and control groups. CONCLUSIONS: Implementation of a strict "No-X-Ray, simplified 2-catheter" CA approach is safe and effective in majority of the patients with SVT. This modified approach for SVTs should be prospectively validated in a multicenter study.

The effect of triple glutamic mutations E9Q/E194Q/E204Q on the structural stability of bacteriorhodopsin.

In the present study, we report on the structural features of the bacteriorhodopsin triple mutant E9Q/E194Q/E204Q (3Glu) of bacteriorhodopsin by combining experimental and molecular dynamics (MD) approaches. In 3Glu mutant, Glu9, Glu194 and Glu204 residues located at the extracellular side of the protein were mutated altogether to glutamines. UV-visible and differential scanning calorimetry experiments served as diagnostic tools for monitoring the resistance against thermal stress of the active site and the tertiary structures of the 3Glu. The analyses of the UV-visible thermal difference spectra demonstrate that the spectral forms at room temperature and the thermal unfolding path differ in the wild-type bacteriorhodopsin and the 3Glu. Even with these spectral differences, the thermal unfolding of the active site occurs at rather similar melting temperatures in both proteins. A noteworthy consequence of the mutations is the altered two-dimensional packing revealed by the lack of the pre-transition peak in differential scanning calorimetry traces of 3Glu mutant, as previously detected in wild-type and the corresponding single mutants. The infrared spectroscopy data agree with the loss of paracrystalinity, illustrating a substantial conversion of αII to αI helical conformation in the 3Glu mutant. Molecular dynamics simulations show higher dynamics flexibility of most of the extracellular regions of 3Glu, which may account for the somewhat lower tertiary structural stability of the mutated protein. Finally, hydrogen bond analysis reveals that the mutated Glu194 and Glu204 residues create ~ 50% less hydrogen bonds with water molecules compared to wild-type bacteriorhodopsin. These results exemplify the role of the water hydrogen-bonding network for structural integrity and conformational flexibility of bacteriorhodopsin.

A patient with posterior cortical atrophy possesses a novel mutation in the presenilin 1 gene.

Posterior cortical atrophy is a dementia syndrome with symptoms of cortical visual dysfunction, associated with amyloid plaques and neurofibrillary tangles predominantly affecting visual association cortex. Most patients diagnosed with posterior cortical atrophy will finally develop a typical Alzheimer's disease. However, there are a variety of neuropathological processes, which could lead towards a clinical presentation of posterior cortical atrophy. Mutations in the presenilin 1 gene, affecting the function of γ-secretase, are the most common genetic cause of familial, early-onset Alzheimer's disease. Here we present a patient with a clinical diagnosis of posterior cortical atrophy who harbors a novel Presenilin 1 mutation (I211M). In silico analysis predicts that the mutation could influence the interaction between presenilin 1 and presenilin1 enhancer-2 protein, a protein partner within the γ-secretase complex. These findings along with published literature support the inclusion of posterior cortical atrophy on the Alzheimer's disease spectrum.

Amyloid ß-peptide 25-35 self-assembly and its inhibition: a model undecapeptide system to gain atomistic and secondary structure details of the Alzheimer's disease process and treatment.

Combined results of theoretical molecular dynamic simulations and in vitro spectroscopic (circular dichroism and fluorescence) studies are presented, providing the atomistic and secondary structure details of the process by which a selected small molecule may destabilize the ß-sheet ordered "amyloid" oligomers formed by the model undecapeptide of amyloid ß-peptide 25-35 [Aß(25-35)]. Aß(25-35) was chosen because it is the shortest fragment capable of forming large ß-sheet fibrils and retaining the toxicity of the full length Aß(1-40/42) peptides. The conformational transition, that leads to the formation of ß-sheet fibrils from soluble unordered structures, was found to depend on the environmental conditions, whereas the presence of myricetin destabilizes the self-assembly and antagonizes this conformational shift. In parallel, we analyzed several molecular dynamics trajectories describing the evolution of five monomer fragments, without inhibitor as well as in the presence of myricetin. Other well-known inhibitors (curcumin and (-)-tetracycline), found to be stronger and weaker Aß(1-42) aggregation inhibitors, respectively, were also studied. The combined in vitro and theoretical studies of the Aß(25-35) self-assembly and its inhibition contribute to understanding the mechanism of action of well-known inhibitors and the peptide amino acid residues involved in the interaction leading to a rational drug design of more potent new molecules able to antagonize the self-assembly process.

Pacemaker lead extraction and recapture of venous access: technical problems arising from extensive venous obstruction.

We report the case of the extraction of 18 year-old leads in a patient with a DDD pacemaker, and chronic obstruction of the left subclavian and innominate veins coexisting with extensive stenoses in the upper caval vein. After removal of pacing leads, angiographic guidewires were introduced via the Byrd dilatators and new pacing leads introduced with the use of long sheaths originally dedicated for transvenous left ventricular leads implantation. With this case, we discuss the problems arising during reimplantation of pacing leads in patients with chronic venous occlusion.

Structural investigation of the C-terminal catalytic fragment of presenilin 1.

The gamma-secretase complex has a decisive role in the development of Alzheimer's disease, in that it cleaves a precursor to create the amyloid beta peptide whose aggregates form the senile plaques encountered in the brains of patients. Gamma-secretase is a member of the intramembrane-cleaving proteases which process their transmembrane substrates within the bilayer. Many of the mutations encountered in early onset familial Alzheimer's disease are linked to presenilin 1, the catalytic component of gamma-secretase, whose active form requires its endoproteolytic cleavage into N-terminal and C-terminal fragments. Although there is general agreement regarding the topology of the N-terminal fragment, studies of the C-terminal fragment have yielded ambiguous and contradictory results that may be difficult to reconcile in the absence of structural information. Here we present the first structure of the C-terminal fragment of human presenilin 1, as obtained from NMR studies in SDS micelles. The structure reveals a topology where the membrane is likely traversed three times in accordance with the more generally accepted nine transmembrane domain model of presenilin 1, but contains unique structural features adapted to accommodate the unusual intramembrane catalysis. These include a putative half-membrane-spanning helix N-terminally harboring the catalytic aspartate, a severely kinked helical structure toward the C terminus as well as a soluble helix in the assumed-to-be unstructured N-terminal loop.