Interaction Energy Decomposition in Protein–Protein Association: A Quantum Mechanical Study of Barnase–Barstar Complex

Protein–protein interactions are very important in the function of a cell. Computational studies of these interactions have been of interest, but often they have utilized classical modelling techniques. In recent years, quantum mechanical (QM) treatment of entire proteins has emerged as a powerful approach to study biomolecular systems. Herein, we apply a semi-empirical divide and conquer (DC) methodology coupled with a dielectric continuum model for the solvent, to explore the contribution of electrostatics, polarization and charge transfer to the interaction energy between barnase and barstar in their complex form. Molecular dynamic (MD) simulation was performed to account for the dynamic behavior of the complex. The results show that electrostatics, charge transfer and polarization favor the formation of the complex. Our study shows that electrostatics dominates the interaction between barnase and barstar (∼ 73%), while charge transfer and polarization are ∼ 21% and ∼ 6%, respectively. Close inspection of the polarization and charge-transfer effects on the charge distribution of the complex reveals the existence of two, well localized, regions in barstar. The first region includes the residues between P27 and Y47 and the second region is between N65 and D83. Since no such regions could be detected in barnase clearly suggests that barstar is well optimized for efficiently binding barnase. Furthermore, using our interaction energy decomposition scheme, we were able to identify all residues that have been experimentally determined to be important for the complex formation and to suggest other residues never have been investigated. This suggests that our approach will be useful as an aid in further understanding protein–protein contacts for the ultimate goal to produce successful inhibitors for protein complexes

Pervasiveness of the IQ Rise: A Cross-Temporal Meta-Analysis

Background: Generational IQ gains in the general population (termed the Flynn effect) show an erratic pattern across different nations as well as across different domains of intelligence (fluid vs crystallized). Gains of fluid intelligence in different countries have been subject to extensive research, but less attention was directed towards gains of crystallized intelligence, probably due to evidence from the Anglo-American sphere suggesting only slight gains on this measure. In the present study, development of crystallized intelligence in the German speaking general population is assessed. Methodology/Principal Findings: To investigate whether IQ gains for crystallized intelligence are in progress in Germanspeaking countries, two independent meta-analyses were performed. By means of a cited reference search in ISI Web of Science, all studies citing test manuals and review articles of two widely-used salient measures of crystallized intelligence were obtained. Additionally, the electronic database for German academic theses was searched to identify unpublished studies employing these tests. All studies reporting participants mean IQ or raw scores of at least one of the two measures were included in the present analyses, yielding over 500 studies (.1,000 samples;.45,000 individuals). We found a significant positive association between years of test performance and intelligence (1971–2007) amounting to about 3.5 IQ points per decade. Conclusions/Significance: This study clearly demonstrates that crystallized IQ gains are substantial and of comparabl

MRI in multiple myeloma : a pictorial review of diagnostic and post-treatment findings

Magnetic resonance imaging (MRI) is increasingly being used in the diagnostic work-up of patients with multiple myeloma. Since 2014, MRI findings are included in the new diagnostic criteria proposed by the International Myeloma Working Group. Patients with smouldering myeloma presenting with more than one unequivocal focal lesion in the bone marrow on MRI are considered having symptomatic myeloma requiring treatment, regardless of the presence of lytic bone lesions. However, bone marrow evaluation with MRI offers more than only morphological information regarding the detection of focal lesions in patients with MM. The overall performance of MRI is enhanced by applying dynamic contrast-enhanced MRI and diffusion weighted imaging sequences, providing additional functional information on bone marrow vascularization and cellularity. This pictorial review provides an overview of the most important imaging findings in patients with monoclonal gammopathy of undetermined significance, smouldering myeloma and multiple myeloma, by performing a 'total' MRI investigation with implications for the diagnosis, staging and response assessment. Main message aEuro cent Conventional MRI diagnoses multiple myeloma by assessing the infiltration pattern. aEuro cent Dynamic contrast-enhanced MRI diagnoses multiple myeloma by assessing vascularization and perfusion. aEuro cent Diffusion weighted imaging evaluates bone marrow composition and cellularity in multiple myeloma. aEuro cent Combined morphological and functional MRI provides optimal bone marrow assessment for staging. aEuro cent Combined morphological and functional MRI is of considerable value in treatment follow-up

First-principles design and subsequent synthesis of a material to search for the permanent electric dipole moment of the electron

We describe the first-principles design and subsequent synthesis of a new material with the specific functionalities required for a solid-state-based search for the permanent electric dipole moment of the electron. We show computationally that perovskite-structure europium barium titanate should exhibit the required large and pressure-dependent ferroelectric polarization, local magnetic moments, and absence of magnetic ordering even at liquid helium temperature. Subsequent synthesis and characterization of Eu$_{0.5}$Ba$_{0.5}$TiO$_3$ ceramics confirm the predicted desirable properties.Comment: Nature Materials, in pres

ACC/AHA/NHLBI clinical advisory on the use and safety of statins

The voluntary withdrawal of cerivastatin (Baycol) from the U.S. market on August 8, 2001, by the manufacturer, in agreement with the Food and Drug Administration (FDA), has prompted concern on the part of physicians and patients regarding the safety of the cholesterol-lowering class of drugs called HMG CoA reductase inhibitors, more commonly known as “statins.” This American College of Cardiology/American Heart Association/National Heart, Lung and Blood Institute (ACC/AHA/NHLBI) Clinical Advisory is intended to summarize for professionals the current understanding of statin use, focused on myopathy, and to provide updated recommendations for the appropriate use of statins, including cautions, contraindications, and safety monitoring for statin therapy. Its purpose is not to discourage the appropriate use of statins, which have life-saving potential in properly selected patients, particularly those with established coronary heart disease (CHD) and others at high risk for developing CHD. Included are recent myopathy information compiled by the FDA, information from clinical trials, and summaries from the recently released report of the Adult Treatment Panel III (ATP III) of the National Cholesterol Education Program (NCEP)

ACC/AHA/NHLBI clinical advisory on the use and safety of statins

The voluntary withdrawal of cerivastatin (Baycol) from the U.S. market on August 8, 2001, by the manufacturer, in agreement with the Food and Drug Administration (FDA), has prompted concern on the part of physicians and patients regarding the safety of the cholesterol-lowering class of drugs called HMG CoA reductase inhibitors, more commonly known as “statins.” This American College of Cardiology/American Heart Association/National Heart, Lung and Blood Institute (ACC/AHA/NHLBI) Clinical Advisory is intended to summarize for professionals the current understanding of statin use, focused on myopathy, and to provide updated recommendations for the appropriate use of statins, including cautions, contraindications, and safety monitoring for statin therapy. Its purpose is not to discourage the appropriate use of statins, which have life-saving potential in properly selected patients, particularly those with established coronary heart disease (CHD) and others at high risk for developing CHD. Included are recent myopathy information compiled by the FDA, information from clinical trials, and summaries from the recently released report of the Adult Treatment Panel III (ATP III) of the National Cholesterol Education Program (NCEP)

Quantum Chemistry Calculations for Metabolomics

A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials (“standards”), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for “standards-free” identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials (“standards”), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for “standards-free” identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples

Neisseria gonorrhoeae Infection Induces Altered Amphiregulin Processing and Release

Adhesion of the human pathogen Neisseria gonorrhoeae has established effects on the host cell and evokes a variety of cellular events including growth factor activation. In the present study we report that infection with N. gonorrhoeae causes altered amphiregulin processing and release in human epithelial cells. Amphiregulin is a well-studied growth factor with functions in various cell processes and is upregulated in different forms cancer and proliferative diseases. The protein is prototypically cleaved on the cell surface in response to external stimuli. We demonstrate that upon infection, a massive upregulation of amphiregulin mRNA is seen. The protein changes its subcellular distribution and is also alternatively cleaved at the plasma membrane, which results in augmented release of an infection-specific 36 kDa amphiregulin product from the surface of human cervical epithelial cells. Further, using antibodies directed against different domains of the protein we could determine the impact of infection on pro-peptide processing. In summary, we present data showing that the infection of N. gonorrhoeae causes an alternative amphiregulin processing, subcellular distribution and release in human epithelial cervical cells that likely contribute to the predisposition cellular abnormalities and anti-apoptotic features of N. gonorrhoeae infections