64 research outputs found
Designing succinct structural alphabets
Motivation: The 3D structure of a protein sequence can be assembled from the substructures corresponding to small segments of this sequence. For each small sequence segment, there are only a few more likely substructures. We call them the âstructural alphabetâ for this segment. Classical approaches such as ROSETTA used sequence profile and secondary structure information, to predict structural fragments. In contrast, we utilize more structural information, such as solvent accessibility and contact capacity, for finding structural fragments
Assigning a function to a conserved archaeal metallo-β-lactamase from Haloferax volcanii
The metallo-β-lactamase family of enzymes comprises a large group of proteins with diverse functions in the metabolism of the cell. Among others, this superfamily contains proteins which are involved in DNA and RNA metabolism, acting as nucleases in e.g. repair and maturation. Many proteins have been annotated in prokaryotic genomes as being potential metallo-β-lactamases, but very often the function has not been proven. The protein HVO_2763 from Haloferax volcanii is such a potential metallo-β-lactamase. HVO_2763 has sequence similarity to the metallo-β-lactamase tRNase Z, a tRNA 3Ⲡprocessing endonuclease. Here, we report the characterisation of this metallo-β-lactamase HVO_2763 in the halophilic archaeon Haloferax volcanii. Using different in vitro assays with the recombinant HVO_2763, we could show that the protein does not have tRNA 3Ⲡprocessing or exonuclease activity. According to transcriptome analyses of the HVO_2763 deletion strain, expression of proteins involved in membrane transport is downregulated in the mutant. Therefore, HVO_2763 might be involved directly or indirectly in membrane transport
Identification of Compounds with Nanomolar Binding Affinity for Checkpoint Kinase-1 Using Knowledge-Based Virtual Screening
Review of Wave-turbulence Interactions in the Stable Atmospheric Boundary Layer
Flow in a stably stratified environment is characterized by anisotropic and intermittent turbulence and wavelike motions of varying amplitudes and periods. Understanding turbulence intermittency and wave-turbulence interactions in a stably stratified flow remains a challenging issue in geosciences including planetary atmospheres and oceans. The stable atmospheric boundary layer (SABL) commonly occurs when the ground surface is cooled by longwave radiation emission such as at night over land surfaces, or even daytime over snow and ice surfaces, and when warm air is advected over cold surfaces. Intermittent turbulence intensification in the SABL impacts human activities and weather variability, yet it cannot be generated in state-of-the-art numerical forecast models. This failure is mainly due to a lack of understanding of the physical mechanisms for seemingly random turbulence generation in a stably stratified flow, in which wave-turbulence interaction is a potential mechanism for turbulence intermittency. A workshop on wave-turbulence interactions in the SABL addressed the current understanding and challenges of wave-turbulence interactions and the role of wavelike motions in contributing to anisotropic and intermittent turbulence from the perspectives of theory, observations, and numerical parameterization. There have been a number of reviews on waves, and a few on turbulence in stably stratified flows, but not much on wave-turbulence interactions. This review focuses on the nocturnal SABL; however, the discussions here on intermittent turbulence and wave-turbulence interactions in stably stratified flows underscore important issues in stably stratified geophysical dynamics in general
Molecular Dynamics Simulations of Sodium Dodecyl Sulfate Micelle in Water: The Behavior of Water
Proton linkage of complex formation between cytochrome c and cytochrome b5: electrostatic consequences of protein-protein interactions
Prediction of Solvation Free Energies of Small Organic Molecules:â Additive-Constitutive Models Based on Molecular Fingerprints and Atomic Constants
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