Map challenge: Analysis using a pair comparison method based on Fourier shell correlation

This document presents the analysis performed over the Map Challenge dataset using a new algorithm which we refer to as Pair Comparison Method. The new algorithm, which is described in detail in the text, is able to sort reconstructions based on a figure of merit and assigns a level of significance to the sorting. That is, it shows how likely the sorting is due to chance or if it reflects real differences.

Catalytic Adaptation of Psychrophilic Elastase

The class I pancreatic elastase from Atlantic salmon is considered to be a cold-adapted enzyme in view of the cold habitat, the reduced thermostability of the enzyme, and the fact that it is faster than its mesophilic porcine counterpart at room temperature. However, no experimental characterization of its catalytic properties at lower temperatures has actually been reported. Here we use extensive computer simulations of its catalytic reaction, at different temperatures and with different peptide substrates, to compare its characteristics with those of porcine pancreatic elastase, with which it shares 67% sequence identity. We find that both enzymes have a preference for smaller aliphatic residues at the P1 position, while the reaction rate with phenylalanine at P1 is predicted to be substantially lower. With the former class of substrates, the calculated reaction rates for salmon enzyme are consistently higher than those of the porcine ortholog at all temperatures examined, and the difference is most pronounced at the lowest temperature. As observed for other cold-adapted enzymes, this is caused by redistribution of the activation free energy in terms of enthalpy and entropy and can be linked to differences in the mobility of surface-exposed loops in the two enzymes. Such mobility changes are found to be reflected by characteristic sequence conservation patterns in psychrophilic and mesophilic species. Hence, calculations of mutations in a single surface loop show that the temperature dependence of the catalytic reaction is altered in a predictable way.

A New Approach to Survival Analysis of Head and Neck Squamous Cell Carcinoma

BACKGROUND

Squamous cell carcinoma is the most common histological subtype of head and neck cancers.

METHODS

In a retrospective longitudinal study, we assessed the risk of local or metastatic recurrence and death in 140 patients with head and neck squamous cell carcinoma (HNSCC). Multivariate and shared frailty models were used for survival analysis with sex, primary tumor site, grade and stage of the tumor, and treatment modalities as contributing factors.

RESULTS

The most frequent site for HNSCC was the oral cavity (30%), followed by the tongue (26.4%). For most primary sites, men were at nearly 2-fold higher risk of local recurrence than women, but there was no difference by sex in the risk of metastatic recurrence. Undifferentiated HNSCC was associated with a higher risk of local recurrence (nearly 4-fold) and metastasis (6-15-fold based on the primary site) than well-differentiated tumors. In early months after surgical resection alone, the risk of local recurrence was higher compared to other treatment modalities. There was a strong dependency between the risk of local and metastatic recurrence.

CONCLUSION

In conclusion, men diagnosed with HNSCC, those with higher grade or advanced state tumor, and those treated by surgery alone are at higher risk of unfavorable outcomes than others and may need more frequent follow-up visits.

Entropy and Enzyme Catalysis

The role played by entropy for the enormous rate enhancement achieved by enzymes has been debated for many decades. There are, for example, several confirmed cases where the activation free energy is reduced by around 10 kcal/mol due to entropic effects, corresponding to a rate enhancement of ∼10⁷ compared to the uncatalyzed reaction. However, despite substantial efforts from both the experimental and theoretical side, no real consensus has been reached regarding the origin of such large entropic contributions to enzyme catalysis. Another remarkable instance of entropic effects is found in enzymes that are adapted by evolution to work at low temperatures, near the freezing point of water. These cold-adapted enzymes invariably show a more negative entropy and a lower enthalpy of activation than their mesophilic orthologs, which counteracts the exponential damping of reaction rates at lower temperature. The structural origin of this universal phenomenon has, however, remained elusive. The basic problem with connecting macroscopic thermodynamic quantities, such as activation entropy and enthalpy derived from Arrhenius plots, to the 3D protein structure is that the underlying detailed (microscopic) energetics is essentially inaccessible to experiment. Moreover, attempts to calculate entropy contributions by computer simulations have mostly focused only on substrate entropies, which do not provide the full picture. We have recently devised a new approach for accessing thermodynamic activation parameters of both enzyme and solution reactions from computer simulations, which turns out to be very successful. This method is analogous to the experimental Arrhenius plots and directly evaluates the temperature dependence of calculated reaction free energy profiles. Hence, by extensive molecular dynamics simulations and calculations of up to thousands of independent free energy profiles, we are able to extract activation parameters with sufficient precision for making direct comparisons to experiment. We show here that the agreement with the measured quantities, for both enzyme catalyzed and spontaneous solution reactions, is quite remarkable. Importantly, we can now address some of the most spectacular entropy effects in enzymes and clarify their detailed microscopic origin. Herein, we discuss as examples the conversion of cytidine to uridine catalyzed by cytidine deaminase and reactions taking place on the ribosome, namely, peptide bond formation and GTP hydrolysis by elongation factor Tu. It turns out that the large entropy contributions to catalysis in these cases can now be rationalized by our computational approach. Finally, we address the problem of cold adaptation of enzyme reaction rates and prove by computational experiments that the universal activation enthalpy-entropy phenomenon originates from mechanical properties of the outer protein surface.

Locked nucleic acid anti-miR-21 inhibits cell growth and invasive behaviors of a colorectal adenocarcinoma cell line: LNA-anti-miR as a novel approach

Colorectal cancer (CRC) is the third leading cause of cancer-related death and has an extremely poor prognosis. Dysregulation of microRNAs (miRNAs) has been shown to be involved in the pathogenesis and progression of many malignancies. Recent data suggest that microRNA-21 (miR-21) is significantly elevated in different types of cancer, especially colon adenocarcinoma. Against this background, locked nucleic acid (LNA)-modified oligonucleotides have recently been suggested as a novel approach for targeting miRNAs as antisense-based gene silencing. The aim of the current study was to explore the functional role of LNA-anti-miR-21 in a colon adenocarcinoma LS174T cell line. LS174T cells were transfected with LNA-anti-miR-21 for 24, 48 and 72 h. Quantitative real-time reverse transcriptase-PCR (qRT-PCR) was performed to assess miR-21 expression by LNA-anti-miR-21. The viability of the cells was evaluated by MTT (3-[4, 5-dimethylthiazol-2-yl]-2, 5-diphenyl tetrazolium bromide) assay and Annexin V/propidium iodide staining assay was used to detect apoptosis. Moreover, invasive behavior of the cells was evaluated before and after therapy by transwell assay. LNA-anti-miR-21 was successfully transfected in human LS174T cells and suppressed the endogenous miR-21. LNA-anti-miR-21 inhibited the cells' growth followed by induction of apoptosis. LNA-anti-miR-21 (50 pmol/μl) reduced the invasive behaviors of LS174T cells after 24 h, compared with untreated cells and scrambled LNA-transfected cells. However, this effect was more pronounced after 72 h. Our findings suggest the therapeutic potential of LNA-anti-miR-21 in a colon adenocarcinoma for targeting miR-21 expression. Further studies are warranted to investigate the molecular mechanisms underlying this novel inhibitor in colorectal cancer to establish its potential value for treatment of CRC patients with high miR-21 expression.

Origin of the Enigmatic Stepwise Tight-Binding Inhibition of Cyclooxygenase-1

Nonsteroidal anti-inflammatory drugs (NSAIDs) are widely used for the treatment of pain, fever, inflammation, and some types of cancers. Their mechanism of action is the inhibition of isoforms 1 and 2 of the enzyme cyclooxygenase (COX-1 and COX-2, respectively). However, both nonselective and selective NSAIDs may have side effects that include gastric intestinal bleeding, peptic ulcer formation, kidney problems, and occurrences of myocardial infarction. The search for selective high-affinity COX inhibitors resulted in a number of compounds characterized by a slow, tight-binding inhibition that occurs in a two-step manner. It has been suggested that the final, only very slowly reversible, tight-binding event is the result of conformational changes in the enzyme. However, the nature of these conformational changes has remained elusive. Here we explore the structural determinants of the tight-binding phenomenon in COX-1 with molecular dynamics and free energy simulations. The calculations reveal how different classes of inhibitors affect the equilibrium between two conformational substates of the enzyme in distinctly different ways. The class of tight-binding inhibitors is found to exclusively stabilize an otherwise unfavorable enzyme conformation and bind significantly stronger to this state than to that normally observed in crystal structures. By also computing free energies of binding to the two enzyme conformations for 16 different NSAIDs, we identify an induced-fit mechanism and the key structural features associated with high-affinity tight binding. These results may facilitate the rational development of new COX inhibitors with improved selectivity profiles.

Chemical reaction mechanisms in solution from brute force computational Arrhenius plots

Decomposition of activation free energies of chemical reactions, into enthalpic and entropic components, can provide invaluable signatures of mechanistic pathways both in solution and in enzymes. Owing to the large number of degrees of freedom involved in such condensed-phase reactions, the extensive configurational sampling needed for reliable entropy estimates is still beyond the scope of quantum chemical calculations. Here we show, for the hydrolytic deamination of cytidine and dihydrocytidine in water, how direct computer simulations of the temperature dependence of free energy profiles can be used to extract very accurate thermodynamic activation parameters. The simulations are based on empirical valence bond models, and we demonstrate that the energetics obtained is insensitive to whether these are calibrated by quantum mechanical calculations or experimental data. The thermodynamic activation parameters are in remarkable agreement with experiment results and allow discrimination among alternative mechanisms, as well as rationalization of their different activation enthalpies and entropies.

Obtaining activation entropies and enthalpies of a reaction is important for distinguishing between alternative reaction mechanisms. Here the authors use computational methods to accurately obtain the enthalpic/entropic components of the activation free energy for hydrolytic deamination reactions.

Modelling bio-electrosynthesis in a reverse microbial fuel cell to produce acetate from CO2and H2O

Bio-electrosynthesis of organic compounds (citrate) in a reverse microbial fuel cell.

Phenolic profile, antioxidant capacity and anti-inflammatory activity of Anethum graveolens L. essential oil

This study reports the chemical composition, antioxidant and anti-inflammatory properties of Anethum graveolens essential oil and its main compounds. The essential oil was obtained from the aerial parts of the plant by hydrodistillation and analysed by using GC/MS. α-Phellandrene (19.12%), limonene (26.34%), dill ether (15.23%), sabinene (11.34%), α-pinene (2%), n-tetracosane (1.54%), neophytadiene (1.43%), n-docosane (1.04), n-tricosane (1%), n-nonadecane (1%), n-eicosane (0.78%), n-heneicosane (0.67%), β-myrcene (0.23%) and α-tujene (0.21%) were found to be the major constituents of the oil. A. graveolens oil exhibit a higher activity in each antioxidant system with a special attention for β-carotene bleaching test (IC50: 15.3 μg/mL) and reducing power (EC50: 11.24 μg/mL). The TLC-bioautography screening and fractionation resulted in the separation of the main antioxidant compounds, which were identified as limonene (45%) and sabinene (32%). The essential oil and its main compounds exhibited a potent NO-scavenging effect and inhibited the expression of inducible NO synthase.

A viscoelastic poromechanical model of the knee joint in large compression

The elastic response of the knee joint in various loading and pathological conditions has been investigated using anatomically accurate geometry. However, it is still challenging to predict the poromechanical response of the knee in realistic loading conditions. In the present study, a viscoelastic, poromechanical model of the knee joint was developed for soft tissues undergoing large deformation. Cartilages and menisci were modeled as fibril-reinforced porous materials and ligaments were considered as fibril-reinforced hyperelastic solids. Quasi-linear viscoelasticty was formulated for the collagen network of these tissues and nearly incompressible Neo-Hookean hyperelasticity was used for the non-fibrillar matrix. The constitutive model was coded with a user defined FORTRAN subroutine, in order to use ABAQUS for the finite element analysis. Creep and stress relaxation were investigated with large compression of the knee in full extension. The contact pressure distributions were found similar in creep and stress relaxation. However, the load transfer in the joint was completely different in these two loading scenarios. During creep, the contact pressure between cartilages decreased but the pressure between cartilage and meniscus increased with time. This led to a gradual transfer of some loading from the central part of cartilages to menisci. During stress relaxation, however, both contact pressures decreased monotonically.