Large amounts of CH4 in the form of solid hydrates are stored on continental margins and in permafrost regions. If these CH4 hydrates could be converted into CO 2 hydrates, they would serve double duty as CH4 sources and CO2 storage sites. We explore here the swapping phenomenon occurring in structure I (sI) and structure II (sII) CH 4 hydrate deposits through spectroscopic analyses and its potential application to CO2 sequestration at the preliminary phase. The present 85% CH4 recovery rate in sI CH4 hydrate achieved by the direct use of binary N 2 ؉ CO2 guests is surprising when compared with the rate of 64% for a pure CO 2 guest attained in the previous approach. The direct use of a mixture of N2 ؉ CO2 eliminates the requirement of a CO2 separation͞purification process. In addition, the simultaneously occurring dual mechanism of CO 2 sequestration and CH4 recovery is expected to provide the physicochemical background required for developing a promising large-scale approach with economic feasibility. In the case of sII CH 4 hydrates, we observe a spontaneous structure transition of sII to sI during the replacement and a cage-specific distribution of guest molecules. A significant change of the lattice dimension caused by structure transformation induces a relative number of small cage sites to reduce, resulting in the considerable increase of CH 4 recovery rate. The mutually interactive pattern of targeted guestcage conjugates possesses important implications for the diverse hydrate-based inclusion phenomena as illustrated in the swapping process between CO2 stream and complex CH4 hydrate structure.clathrate ͉ CO2 sequestration ͉ methane ͉ swapping phenomenon ͉ NMR B ecause the total amount of natural gas hydrate was estimated to be about twice as much as the energy contained in fossil fuel reserves (1, ʈ), many researchers have tried to find a way to exploit CH 4 hydrates deposited worldwide as a new energy source. For recovering them at various conditions in an efficient way, several strategies such as thermal treatment, depressurization, and inhibitor addition into the hydrate layer have been proposed (2). However, all of these methods are based on the decomposition of CH 4 hydrate by external stimulation, which can trigger catastrophic slope failures (3). Furthermore, if CH 4 hydrate decomposes rapidly, it is also possible that the CH 4 released from the hydrate could transfer to the air and significantly accelerate the greenhouse effect (4).Recently, the replacement of CH 4 hydrate with CO 2 has been suggested as an alternative option for recovering CH 4 gas. When CO 2 itself is put under certain pressure, a solid CO 2 hydrate can be formed according to the stability regime (5). In addition, the formation condition of CO 2 hydrate is known to be more stable than that of CH 4 hydrate. Therefore, the swapping process between two gaseous guests is considered to be a favorable approach toward long-term storage of CO 2 . It not only enables the ocean floor to remain stabilized even after recovering the CH 4 ga...

KIF1A is a neuron-specific motor protein that plays important roles in cargo transport along neurites. Recessive mutations in KIF1A were previously described in families with spastic paraparesis or sensory and autonomic neuropathy type-2. Here, we report 11 heterozygous de novo missense mutations (p.S58L, p.T99M, p.G102D, p.V144F, p.R167C, p.A202P, p.S215R, p.R216P, p.L249Q, p.E253K, and p.R316W) in KIF1A in 14 individuals, including two monozygotic twins. Two mutations (p.T99M and p.E253K) were recurrent, each being found in unrelated cases. All these de novo mutations are located in the motor domain (MD) of KIF1A. Structural modeling revealed that they alter conserved residues that are critical for the structure and function of the MD. Transfection studies suggested that at least five of these mutations affect the transport of the MD along axons. Individuals with de novo mutations in KIF1A display a phenotype characterized by cognitive impairment and variable presence of cerebellar atrophy, spastic paraparesis, optic nerve atrophy, peripheral neuropathy, and epilepsy. Our findings thus indicate that de novo missense mutations in the MD of KIF1A cause a phenotype that overlaps with, while being more severe, than that associated with recessive mutations in the same gene.

Synaptic adhesion molecules orchestrate synaptogenesis. The presynaptic leukocyte common antigen-related receptor protein tyrosine phosphatases (LAR-RPTPs) regulate synapse development by interacting with postsynaptic Slit-and Trk-like family proteins (Slitrks), which harbour two extracellular leucine-rich repeats (LRR1 and LRR2). Here we identify the minimal regions of the LAR-RPTPs and Slitrks, LAR-RPTPs Ig1-3 and Slitrks LRR1, for their interaction and synaptogenic function. Subsequent crystallographic and structureguided functional analyses reveal that the splicing inserts in LAR-RPTPs are key molecular determinants for Slitrk binding and synapse formation. Moreover, structural comparison of the two Slitrk1 LRRs reveal that unique properties on the concave surface of Slitrk1 LRR1 render its specific binding to LAR-RPTPs. Finally, we demonstrate that lateral interactions between adjacent trans-synaptic LAR-RPTPs/Slitrks complexes observed in crystal lattices are critical for Slitrk1-induced lateral assembly and synaptogenic activity. Thus, we propose a model in which Slitrks mediate synaptogenic functions through direct binding to LAR-RPTPs and the subsequent lateral assembly of LAR-RPTPs/Slitrks complexes.

Mammalian DAI (DNA-dependent activator of IFN-regulatory factors), an activator of the innate immune response, senses cytosolic DNA by using 2 N-terminal Z-DNA binding domains (ZBDs) and a third putative DNA binding domain located next to the second ZBD. Compared with other previously known ZBDs, the second ZBD of human DAI (hZ␤DAI) shows significant variation in the sequence of the residues that are essential for DNA binding. In this article, the crystal structure of the hZ␤DAI/Z-DNA complex reveals that hZ␤DAI has a similar fold to that of other ZBDs, but adopts an unusual binding mode for recognition of Z-DNA. A residue in the first ␤-strand rather than residues in the ␤-loop contributes to DNA binding, and part of the (␣3) recognition helix adopts a 310 helix conformation. The role of each residue that makes contact with DNA was confirmed by mutational analysis. The 2 ZBDs of DAI can together bind to DNA and both are necessary for full B-to-Z conversion. It is possible that binding 2 DAIs to 1 dsDNA brings about dimerization of DAI that might facilitate DNA-mediated innate immune activation. circular dichroism ͉ hydrogen bonding ͉ interferon induction ͉ X-ray crystallography ͉ innate immunity T he innate immune response is essential for protection from foreign invasion, acting as an immediate cellular defense mechanism. Nucleic acids are known as one of the triggers for activation of the innate immune response (1-3). Recent reports have indicated the presence of a new cytosolic DNA sensor that can initiate an innate immune response independent of the endosomic Toll-like receptor 9 (4, 5). Z-DNA binding protein 1 (ZBP1), also known as DLM-1, was identified as the first innate immune activator that senses cytosolic DNAs (4). In response to foreign DNA, this protein activates type I IFN and other immune responses and was therefore named DAI (DNA-dependent activator of IFN-regulatory factors; ref 4). DAI contains 2 tandem Z-DNA binding domains (ZBDs or Z␣ and Z␤) at its N terminus and a third DNA binding region (D3) located next to the second ZBD. D3 is a novel domain and is reported to bind right-handed B-DNA (4). Upon activation, the C terminus of DAI binds to Tank binding kinase 1 (TBK1), a serine/threonine kinase, and to IFN regulatory factor 3 (IRF3), a transcription factor (4). The N-terminal region, including D3, is thought to be essential for sensing DNA, as shown by its ability to bind to Z-DNA and synthetic B-DNA (4). For the full activation of an in vivo DNA-dependent immune response, all 3 DNA-binding regions are required (5). At the molecular level, it has been suggested that dimerization of DAI results in activation of the innate immune response (5). At the cellular level, it is known that the localization of DAI and its association with stress granules is regulated by ZBDs (6,7).ZBDs that are found in DAI are also found in the editing enzyme dsRNA adenosine deaminase (ADAR1) in vertebrates and in fish PKZ protein kinase containing Z-DNA-binding domains and in the E3L of pox viruses (Fig. 1). They ...

Z-DNA, a left-handed isoform of Watson and Crick’s B-DNA, is rarely formed without the help of high salt concentrations or negative supercoiling. However, Z-DNA-binding proteins can efficiently convert specific sequences of the B conformation into the Z conformation in relaxed DNA under physiological salt conditions. As in the case of many other specific interactions coupled with structural rearrangements in biology, it has been an intriguing question whether the proteins actively induce Z-DNAs or passively trap transiently preformed Z-DNAs. In this study, we used single-molecule fluorescence assays to observe intrinsic B-to-Z transitions, protein association/dissociation events, and accompanying B-to-Z transitions. The results reveal that intrinsic Z-DNAs are dynamically formed and effectively stabilized by Z-DNA-binding proteins through efficient trapping of the Z conformation rather than being actively induced by them. Our study provides, for the first time, detailed pictures of the intrinsic B-to-Z transition dynamics and protein-induced B-to-Z conversion mechanism at the single-molecule level.

In this contribution, we first found the novel clathrate hydrate containing two gaseous guests of hydrogen and carbon dioxide by spectroscopic analysis. X-ray powder diffraction and NMR spectroscopy were used to identify structure and guest distribution of the mixed H2 + CO2 hydrate. X-ray diffraction result confirmed that the unit cell parameter was 11.8602 +/- 0.0010 A, and the formed hydrate was identified as structure I hydrate. 1H magic angle spinning (MAS) NMR and 13C cross-polarization (CP) NMR spectroscopy were used to examine the distribution of hydrogen and carbon dioxide molecules in the cages of structure I, respectively. These NMR spectra showed that carbon dioxide molecules occupied both small 512 cages and large 51262 cages, and hydrogen molecules only were occluded in small 512 cages of structure I. The new finding of the mixed hydrogen hydrate is expected to contribute toward the development of hydrogen production technology and, particularly, inclusion chemistry.

Synaptogenic adhesion molecules play critical roles in synapse formation. SALM5/Lrfn5, a SALM/Lrfn family adhesion molecule implicated in autism spectrum disorders (ASDs) and schizophrenia, induces presynaptic differentiation in contacting axons, but its presynaptic ligand remains unknown. We found that SALM5 interacts with the Ig domains of LAR family receptor protein tyrosine phosphatases (LAR-RPTPs; LAR, PTPδ, and PTPσ). These interactions are strongly inhibited by the splice insert B in the Ig domain region of LAR-RPTPs, and mediate SALM5-dependent presynaptic differentiation in contacting axons. In addition, SALM5 regulates AMPA receptor-mediated synaptic transmission through mechanisms involving the interaction of postsynaptic SALM5 with presynaptic LAR-RPTPs. These results suggest that postsynaptic SALM5 promotes synapse development by trans-synaptically interacting with presynaptic LAR-RPTPs and is important for the regulation of excitatory synaptic strength.

SummarySynaptic adhesion molecules regulate synapse development and plasticity through mechanisms including trans-synaptic adhesion and recruitment of diverse synaptic proteins. We report here that the immunoglobulin superfamily member 11 (IgSF11), a homophilic adhesion molecule preferentially expressed in the brain, is a novel and dual-binding partner of the postsynaptic scaffolding protein PSD-95 and AMPAR glutamate receptors (AMPARs). IgSF11 requires PSD-95 binding for its excitatory synaptic localization. In addition, IgSF11 stabilizes synaptic AMPARs, as shown by IgSF11 knockdown-induced suppression of AMPAR-mediated synaptic transmission and increased surface mobility of AMPARs, measured by high-throughput, single-molecule tracking. IgSF11 deletion in mice leads to suppression of AMPAR-mediated synaptic transmission in the dentate gyrus and long-term potentiation in the CA1 region of the hippocampus. IgSF11 does not regulate the functional characteristics of AMPARs, including desensitization, deactivation, or recovery. These results suggest that IgSF11 regulates excitatory synaptic transmission and plasticity through its tripartite interactions with PSD-95 and AMPARs.