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Noether currents for Eulerian variational principles in non-barotropic magnetohydrodynamics and topological conservations laws
We derive a Noether current for the Eulerian variational principle of ideal non-barotropic magnetohydrodynamics (MHD). It was shown previously that ideal non-barotropic MHD is mathematically equivalent to a five function field theory with an induced geometrical structure in the case that field lines cover surfaces and this theory can be described using a variational principle. Here we use various symmetries of the flow to derive topological constants of motion through the derived Noether current and discuss their implication for non-barotropic MHD.
A moment-conserving discontinuous Galerkin representation of the relativistic Maxwellian distribution
Kinetic simulations of relativistic gases and plasmas are critical for understanding diverse astrophysical and terrestrial systems, but the accurate construction of the relativistic Maxwellian, the Maxwell–Jüttner distribution, on a discrete simulation grid is challenging. Difficulties arise from the finite velocity bounds of the domain, which may not capture the entire distribution function, as well as errors introduced by projecting the function onto a discrete grid. Here, we present a novel scheme for iteratively correcting the moments of the projected distribution applicable to all grid-based discretizations of the relativistic kinetic equation. In addition, we describe how to compute the needed nonlinear quantities, such as Lorentz boost factors, in a discontinuous Galerkin scheme through a combination of numerical quadrature and weak operations. The resulting method accurately captures the distribution function and ensures that the moments match the desired values to machine precision.
Conservation and Diversity in the Primary Reverse Photodynamics of the Canonical Red/Green Cyanobacteriochrome Family
Not provided.
Ndr/Lats Kinases Bind Specific Mob-Family Coactivators through a Conserved and Modular Interface
Abstract not provided
Catalytic Reactions and Energy Conservation in the Cytochrome bc 1 and b 6 f Complexes of Energy-Transducing Membranes
Not Available
Correction to Norm-conserving pseudopotentials and basis sets to explore Lanthanide chemistry in complex environments
Correction was made to the funding and acknowledgment: Funding V.-A.G. was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division. R.R. and M.-T.N. were supported by the Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory (PNNL) CheMSR Agile Investment. PNNL is operated by DE-AC05-76RLO01830. J.-B.L. and J.L. were supported by the National Natural Science Foundation of China (Nos. 21433005, 91645203, and 21590792). D.C.C. was supported by Research and Innovation at the University of Nevada, Reno. ACKNOWLEDGMENTS The research was performed using resources available through Research Computing at Pacific Northwest National Laboratory (PNNL), Tsinghua National Laboratory for Information Science and Technology and the Computational Chemistry Laboratory under Tsinghua Xuetang Talents Program, and University of Nevada, Reno High Performance Computing. J.- B.L. and J.L. acknowledge discussions with Dr. Yang-Gang Wang (Southern University of Science and Technology).
A Conserved Acidic Residue in Phenylalanine Hydroxylase Contributes to Cofactor Affinity and Catalysis
Abstract not provided
A Conservative Isoleucine to Leucine Mutation Causes Major Rearrangements and Cold Sensitivity in KlenTaq1 DNA Polymerase
Abstract not provided
Conservation and Functional Importance of Carbon-Oxygen Hydrogen Bonding in AdoMet-Dependent Methyltransferases
S-Adenosylmethionine (AdoMet)-based methylation is integral to metabolism and signaling. AdoMet-dependent methyltransferases belong to multiple distinct classes and share a catalytic mechanism that arose through convergent evolution; however, fundamental determinants underlying this shared methyl transfer mechanism remain undefined. A survey of high-resolution crystal structures reveals that unconventional carbon–oxygen (CH···O) hydrogen bonds coordinate the AdoMet methyl group in different methyltransferases irrespective of their class, active site structure, or cofactor binding conformation. Corroborating these observations, quantum chemistry calculations demonstrate that these charged interactions formed by the AdoMet sulfonium cation are stronger than typical CH···O hydrogen bonds. Biochemical and structural studies using a model lysine methyltransferase and an active site mutant that abolishes CH···O hydrogen bonding to AdoMet illustrate that these interactions are important for high-affinity AdoMet binding and transition-state stabilization. Further, crystallographic and NMR dynamics experiments of the wild-type enzyme demonstrate that the CH···O hydrogen bonds constrain the motion of the AdoMet methyl group, potentially facilitating its alignment during catalysis. Collectively, the experimental findings with the model methyltransferase and structural survey imply that methyl CH···O hydrogen bonding represents a convergent evolutionary feature of AdoMet-dependent methyltransferases, mediating a universal mechanism for methyl transfer.
Investigation of Indigoidine Synthetase Reveals a Conserved Active-Site Base Residue of Nonribosomal Peptide Synthetase Oxidases
Nonribosomal peptide synthetase (NRPS) oxidase (Ox) domains oxidize protein-bound intermediates to install crucial structural motifs in bioactive natural products. The mechanism of this domain remains elusive. Here, by studying indigoidine synthetase, a single-module NRPS involved in the biosynthesis of indigoidine and several other bacterial secondary metabolites, we demonstrate that its Ox domain utilizes an active-site base residue, tyrosine 665, to deprotonate a protein-bound l-glutaminyl residue. In this work, we further validate the generality of this active-site residue among NRPS Ox domains. These findings not only resolve the biosynthetic pathway mediated by indigoidine synthetase but enable mechanistic insight into NRPS Ox domains.
Sacrificial Cobalt–Carbon Bond Homolysis in Coenzyme B 12 as a Cofactor Conservation Strategy
Abstract not provided
The structure of Zika virus NS5 reveals a conserved domain conformation
The recent outbreak of Zika virus (ZIKV) has imposed a serious threat to public health. Here we report the crystal structure of the ZIKV NS5 protein in complex with S-adenosyl-L-homocysteine, in which the tandem methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRp) domains stack into one of the two alternative conformations of flavivirus NS5 proteins. In conclusion, the activity of this NS5 protein is verified through a de novo RdRp assay on a subgenomic ZIKV RNA template. Importantly, our structural analysis leads to the identification of a potential drug-binding site of ZIKV NS5, which might facilitate the development of novel antivirals for ZIKV.
The highly conserved domain of unknown function 1792 has a distinct glycosyltransferase fold
Abstract not provided
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions
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