Comprehensive computational analysis of Hmd enzymes and paralogs in methanogenic Archaea

<p>Abstract</p> <p>Background</p> <p>Methanogenesis is the sole means of energy production in methanogenic Archaea. H₂-forming methylenetetrahydromethanopterin dehydrogenase (Hmd) catalyzes a step in the hydrogenotrophic methanogenesis pathway in class I methanogens. At least one <it>hmd </it>paralog has been identified in nine of the eleven complete genome sequences of class I hydrogenotrophic methanogens. The products of these paralog genes have thus far eluded any detailed functional characterization.</p> <p>Results</p> <p>Here we present a thorough computational analysis of Hmd enzymes and paralogs that includes state of the art phylogenetic inference, structure prediction, and functional site prediction techniques. We determine that the Hmd enzymes are phylogenetically distinct from Hmd paralogs but share a common overall structure. We predict that the active site of the Hmd enzyme is conserved as a functional site in Hmd paralogs and use this observation to propose possible molecular functions of the paralog that are consistent with previous experimental evidence. We also identify an uncharacterized site in the N-terminal domains of both proteins that is predicted by our methods to directly impart function.</p> <p>Conclusion</p> <p>This study contributes to our understanding of the evolutionary history, structural conservation, and functional roles, of the Hmd enzymes and paralogs. The results of our phylogenetic and structural analysis constitute datasets that will aid in the future study of the Hmd protein family. Our functional site predictions generate several testable hypotheses that will guide further experimental characterization of the Hmd paralog. This work also represents a novel approach to protein function prediction in which multiple computational methods are integrated to achieve a detailed characterization of proteins that are not well understood.</p

The evolution and functional repertoire of translation proteins following the origin of life

<p>Abstract</p> <p>Background</p> <p>The RNA world hypothesis posits that the earliest genetic system consisted of informational RNA molecules that directed the synthesis of modestly functional RNA molecules. Further evidence suggests that it was within this RNA-based genetic system that life developed the ability to synthesize proteins by translating genetic code. Here we investigate the early development of the translation system through an evolutionary survey of protein architectures associated with modern translation.</p> <p>Results</p> <p>Our analysis reveals a structural expansion of translation proteins immediately following the RNA world and well before the establishment of the DNA genome. Subsequent functional annotation shows that representatives of the ten most ancestral protein architectures are responsible for all of the core protein functions found in modern translation.</p> <p>Conclusions</p> <p>We propose that this early robust translation system evolved by virtue of a positive feedback cycle in which the system was able to create increasingly complex proteins to further enhance its own function.</p> <p>Reviewers</p> <p>This article was reviewed by Janet Siefert, George Fox, and Antonio Lazcano (nominated by Laura Landweber)</p

Measurements of the ClO radical vibrational band intensity and the ClO + ClO + M reaction product

There is considerable interest in the kinetics and concentrations of free radicals in the stratosphere. Chlorine monoxide is a critically important radical because of its role in catalytic cycles for ozone depletion. Depletion occurs under a wide variety of conditions including the Antarctic spring when unusual mechanisms such as the BrO sub x/ClO sub x, ClO dimer (Cl sub 2 O sub 2), and ClO sub x/HO sub x cycles are suggested to operate. Infrared spectroscopy is one of the methods used to measure ClO in the stratosphere (Menzies 1979 and 1983; Mumma et al., 1983). To aid the quantification of such infrared measurements, researchers measured the ClO ground state fundamental band intensity

Valence Quark Distribution in A=3 Nuclei

We calculate the quark distribution function for 3He/3H in a relativistic quark model of nuclear structure which adequately reproduces the nucleon approximation, nuclear binding energies, and nuclear sizes for small nuclei. The results show a clear distortion from the quark distribution function for individual nucleons (EMC effect) arising dominantly from a combination of recoil and quark tunneling effects. Antisymmetrization (Pauli) effects are found to be small due to limited spatial overlaps. We compare our predictions with a published parameterization of the nuclear valence quark distributions and find significant agreement.Comment: 18pp., revtex4, 4 fig

Effects of resonant tunneling in electromagnetic wave propagation through a polariton gap

We consider tunneling of electromagnetic waves through a polariton band gap of a 1-D chain of atoms. We analytically show that a defect embedded in the structure gives rise to the resonance transmission at the frequency of a local polariton state associated with the defect. Numerical Monte-Carlo simulations are used to examine properties of the electromagnetic band arising inside the polariton gap due to finite concentration of defects.Comment: 12 pages, 6 figures, RevTe