Efficient algorithms to explore conformation spaces of flexible protein loops

Several applications in biology - e.g., incorporation of protein flexibility in ligand docking algorithms, interpretation of fuzzy X-ray crystallographic data, and homology modeling - require computing the internal parameters of a flexible fragment (usually, a loop) of a protein in order to connect its termini to the rest of the protein without causing any steric clash. One must often sample many such conformations in order to explore and adequately represent the conformational range of the studied loop. While sampling must be fast, it is made difficult by the fact that two conflicting constraints - kinematic closure and clash avoidance - must be satisfied concurrently. This paper describes two efficient and complementary sampling algorithms to explore the space of closed clash-free conformations of a flexible protein loop. The "seed sampling" algorithm samples broadly from this space, while the "deformation sampling" algorithm uses seed conformations as starting points to explore the conformation space around them at a finer grain. Computational results are presented for various loops ranging from 5 to 25 residues. More specific results also show that the combination of the sampling algorithms with a functional site prediction software (FEATURE) makes it possible to compute and recognize calcium-binding loop conformations. The sampling algorithms are implemented in a toolkit (LoopTK), which is available at https://simtk.org/home/looptk.     

Nucleic acid sensor for insecticide detection

Nucleic acid sensor based on polyaniline (PANI) has been fabricated by covalently immobilizing double stranded calf thymus (dsCT) DNA onto perchlorate (ClO(-) (4))-doped PANI film deposited onto indium-tin-oxide (ITO) glass plate using 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (EDC)/N-hydroxysuccinimide (NHS) chemistry. These dsCT-DNA-PANI-ClO(4)/ITO and PANI-ClO(4)/ITO electrodes have been characterized using square wave voltammetry, electrochemical impedance, scanning electron microscopy (SEM) and Fourier-transform-infrared (FTIR) measurements. This disposable dsCT-DNA-PANI-ClO(4)/ITO bioelectrode, stable for about 4 months, can be used to detect cypermethrin (0.005 ppm) and trichlorfon (0.01 ppm) in 30 and 60 s, respectively.     

Electrical detection of the temperature induced melting transition of a DNA hairpin covalently attached to gold interdigitated microelectrodes

The temperature induced melting transition of a self-complementary DNA strand covalently attached at the 5′ end to the surface of a gold interdigitated microelectrode (GIME) was monitored in a novel, label-free, manner. The structural state of the hairpin was assessed by measuring four different electronic properties of the GIME (capacitance, impedance, dissipation factor and phase angle) as a function of temperature from 25°C to 80°C. Consistent changes in all four electronic properties of the GIME were observed over this temperature range, and attributed to the transition of the attached single-stranded DNA (ssDNA) from an intramolecular, folded hairpin structure to a melted ssDNA. The melting curve of the self-complementary single strand was also measured in solution using differential scanning calorimetry (DSC) and UV absorbance spectroscopy. Temperature dependent electronic measurements on the surface and absorbance versus temperature values measured in solution experiments were analyzed assuming a two-state process. The model analysis provided estimates of the thermodynamic transition parameters of the hairpin on the surface. Two-state analyses of optical melting data and DSC measurements provided evaluations of the thermodynamic transition parameters of the hairpin in solution. Comparison of surface and solution measurements provided quantitative evaluation of the effect of the surface on the thermodynamics of the melting transition of the DNA hairpin.     

Bioactive compounds from marine actinomycetes

Actinomycetes are one of the most efficient groups of secondary metabolite producers and are very important from an industrial point of view. Among its various genera, Streptomyces, Saccharopolyspora, Amycolatopsis, Micromonospora and Actinoplanes are the major producers of commercially important biomolecules. Several species have been isolated and screened from the soil in the past decades. Consequently the chance of isolating a novel actinomycete strain from a terrestrial habitat, which would produce new biologically active metabolites, has reduced. The most relevant reason for discovering novel secondary metabolites is to circumvent the problem of resistant pathogens, which are no longer susceptible to the currently used drugs. Existence of actinomycetes has been reported in the hitherto untapped marine ecosystem. Marine actinomycetes are efficient producers of new secondary metabolites that show a range of biological activities including antibacterial, antifungal, anticancer, insecticidal and enzyme inhibition. Bioactive compounds from marine actinomycetes possess distinct chemical structures that may form the basis for synthesis of new drugs that could be used to combat resistant pathogens.     

Oxazolidinone: search for highly potent antibacterial

A number of substituted piperazinyl oxazolidinone derivatives have been synthesized and their antibacterial activities were evaluated by MIC determination. A systematic SAR was carried out to get highly potent oxazolidinone derivatives.     

Fingerprinting method for phylogenetic classification and identification of microorganisms based on variation in 16S rRNA gene sequences

The paper describes a method for the classification and identification of microorganisms based on variations in 16S rRNA sequences. The 16S rRNA is one of the most conserved molecules within a cell. The nature of the variable and spacer regions has been found to be specific to a given organism. Thus, the method presented here can be very useful for the classification and identification of microorganisms for which very little information is available. To automate the method, a comprehensive computer program called FPMAP has been developed for the analysis of restriction fragment pattern data. The method involves the restriction digestion of genomic DNA, preferably using four-cutters that may recognize 6-9 sites within the 16S rDNA. The fragments are separated on a polyacrylamide gel along with a suitable marker, then transferred into a nylon membrane and hybridized with a radiolabeled 16S rDNA probe. After autoradiography, the fragment sizes are calculated, and the data are analyzed using the FPMAP software. We demonstrate that the method can be used for identification of strains of Streptomyces and mycobacteria. The software is available from our ftp site ftp:?imtech.chd.nic.in/pub/com/fpmap/unix/.     

On the accuracy of perceived parental height in a native Amazonian society

Studies of secular trends in adult height in rural pre-literate societies are likely to show no change owing to random measurement error in age. In such societies, adults lack birth certificates and guess when estimating their age. We assess the accuracy of perceived height of the same-sex parent to estimate secular trends. We tested the method among the Tsimane', a native Amazonian society of farmers and foragers in Bolivia. Subjects included 268 women and 287 men >20 years of age. Over half the sample reported inaccurately the height of their same-sex living parent, with a tendency to report no difference when, in fact, differences existed. Results highlight the pitfalls of using perceived parental height to examine secular trends in adult height among the Tsimane', though the method might yield accurate information in other societies. We discuss possible reasons for the low accuracy of Tsimane' estimates.     

Microtubules Deform the Nuclear Membrane and Disrupt Nucleocytoplasmic Transport in Tau-Mediated Frontotemporal Dementia

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Climatic variability,hydrologic anomaly,and methane emission can turn productive freshwater marshes into net carbon sources

Freshwater marshes are well‐known for their ecological functions in carbon sequestration, but complete carbon budgets that include both methane (CH₄) and lateral carbon fluxes for these ecosystems are rarely available. To the best of our knowledge, this is the first full carbon balance for a freshwater marsh where vertical gaseous [carbon dioxide (CO₂) and CH₄] and lateral hydrologic fluxes (dissolved and particulate organic carbon) have been simultaneously measured for multiple years (2011–2013). Carbon accumulation in the sediments suggested that the marsh was a long‐term carbon sink and accumulated ~96.9 ± 10.3 (±95% CI) g C m^?2 yr^?1 during the last ~50 years. However, abnormal climate conditions in the last 3 years turned the marsh to a source of carbon (42.7 ± 23.4 g C m^?2 yr^?1). Gross ecosystem production and ecosystem respiration were the two largest fluxes in the annual carbon budget. Yet, these two fluxes compensated each other to a large extent and led to the marsh being a CO₂ sink in 2011 (?78.8 ± 33.6 g C m^?2 yr^?1), near CO₂‐neutral in 2012 (29.7 ± 37.2 g C m^?2 yr^?1), and a CO₂ source in 2013 (92.9 ± 28.0 g C m^?2 yr^?1). The CH₄ emission was consistently high with a three‐year average of 50.8 ± 1.0 g C m^?2 yr^?1. Considerable hydrologic carbon flowed laterally both into and out of the marsh (108.3 ± 5.4 and 86.2 ± 10.5 g C m^?2 yr^?1, respectively). In total, hydrologic carbon fluxes contributed ~23 ± 13 g C m^?2 yr^?1 to the three‐year carbon budget. Our findings highlight the importance of lateral hydrologic inflows/outflows in wetland carbon budgets, especially in those characterized by a flow‐through hydrologic regime. In addition, different carbon fluxes responded unequally to climate variability/anomalies and, thus, the total carbon budgets may vary drastically among years.     

Exploring protein–protein intermolecular recognition between meprin-α and endogenous protease regulator cystatinC coupled with pharmacophore elucidation

Meprins are a group of zinc metalloproteases of the astacin family which play a pivotal role in several physiological and pathologocal diseases. The inhibition of the meprins by various inhibitors, macromolecular and small molecules, is crucial in the control of several diseases. Human cystatinC, an amyloidogenic protein, is reported to be an endogenous inhibitor of meprin-α. In this computational study, we elucidate a rational model for meprinα–cystatinC complex using protein–protein docking. The complex model as well as the unbound form was evaluated by molecular dynamics simulation. A simulation study revealed higher stability of the complex owing to the presence of several interactions. Virtual alanine mutagenesis helps in identifying the hotspots on both proteins. Based on the frequency of occurrence of hotspot amino acids, it was possible to enumerate the important amino acids primarily responsible for protein stability present at the amino-terminal end of cystatin. Finally, pharmacophore elucidation carried out based on the information obtained from a series of small molecular inhibitors against meprin-α can be utilized in future for rational drug design and therapy.