Molecular Dynamics Simulations of Ion Transport through Protein Nanochannels in Peritoneal Dialysis.

In recent decades, the development of dialysis techniques has greatly improved the survival rate of renal failure patients, and peritoneal dialysis is gradually showing dominance over hemodialysis. This method relies on the abundant membrane proteins in the peritoneum, avoiding the use of artificial semipermeable membranes, and the ion fluid transport is partly controlled by the protein nanochannels. Hence, this study investigated ion transport in these nanochannels by using molecular dynamics (MD) simulations and an MD Monte Carlo (MDMC) algorithm for a generalized protein nanochannel model and a saline fluid environment. The spatial distribution of ions was determined via MD simulations, and it agreed with that modeled via the MDMC method; the effects of simulation duration and external electronic fields were also explored to validate the MDMC algorithm. The specific atomic sequence within a nanochannel was visualized, which was the rare transport state during the ion transport process. The residence time was assessed through both methods to represent the involved dynamic process, and its values showed the temporal sequential order of different components in the nanochannel as follows: H2O > Na+ > Cl-. The accurate prediction using the MDMC method of the spatial and temporal properties proves its suitability to handle ion transport problems in protein nanochannels.

TRPC1 regulates brown adipose tissue activity in a PPARγ-dependent manner.

Brown adipose tissue (BAT) has the unique ability to convert energy stored in the form of triglycerides into heat. This property makes BAT a target tissue to increase energy expenditure and improve systemic metabolic control. TRPC1 is a founding member of the TRP protein family that also includes several temperature sensitive channels. We show that TRPC1 is highly expressed in all adipocyte depots including BAT and that Trpc1-deficient mice are prone to weight gain and manifest reduced metabolic control. We also demonstrate that knockdown of TRPC1 in cultured brown adipocytes leads to a downregulation of several metabolic genes, including UCP1 and PPARγ, as well as upregulation of a BAT-specific thermosensitive channel TRPV2, ultimately resulting in impaired respiratory function. We also show that TRPC1 is a possible target of PPARγ, suggesting that TRPC1 is a downstream component of a mechanism that translates metabolic or environmental stimuli into output in the form of BAT activity. Better understanding of the possible role of TRPC1 and other TRP channels in body temperature regulation and BAT function may help us to develop obesity therapies based on BAT activation.

Selective molecular transport through the protein shell of a bacterial microcompartment organelle.

Bacterial microcompartments are widespread prokaryotic organelles that have important and diverse roles ranging from carbon fixation to enteric pathogenesis. Current models for microcompartment function propose that their outer protein shell is selectively permeable to small molecules, but whether a protein shell can mediate selective permeability and how this occurs are unresolved questions. Here, biochemical and physiological studies of structure-guided mutants are used to show that the hexameric PduA shell protein of the 1,2-propanediol utilization (Pdu) microcompartment forms a selectively permeable pore tailored for the influx of 1,2-propanediol (the substrate of the Pdu microcompartment) while restricting the efflux of propionaldehyde, a toxic intermediate of 1,2-propanediol catabolism. Crystal structures of various PduA mutants provide a foundation for interpreting the observed biochemical and phenotypic data in terms of molecular diffusion across the shell. Overall, these studies provide a basis for understanding a class of selectively permeable channels formed by nonmembrane proteins.

Correlated trapping of sugar molecules by the trimeric protein channel chitoporin.

The protein channel chitoporin (ChiP), which is used by marine bacteria to translocate selected sugar molecules through the outer cell membrane, is studied via single channel current measurements in water and heavy water sugar solutions. The dynamic trapping and escape probabilities of sugar molecules from different monomers in the trimeric channel are characterized, including their dependence on channel orientation and sensitivity to a deuterium isotope effect. A detailed analysis of stochastic current fluctuations reveals that the trapping properties of chitoporin exhibit memory effects: the rate of trapping transitions depends on the previous sequence of transitions; and intermonomer correlations: the average trapping rate of an unblocked monomer is larger when its neighboring monomers are blocked. The latter, likely resulting from rapid re-trapping of recently escaped sugar molecules, is considered as a possible design strategy to enhance sugar transport.

F1099L-CFTR (c.3297C>G) has Impaired Channel Function and Associates with Mild Disease Phenotypes in Two Pediatric Patients.

(1) Background: many rare cystic fibrosistransmembrane conductance regulator (CFTR) mutations remain poorly characterized with regard to functional consequences of the mutation. We present the clinical features of two pediatric cystic fibrosis (CF) subjects who are heterozygous for F1099L (c.3297C>G), one with G551D (a class III mutation) and one with 3849 + 10kbC->T (a class V mutation). We also identified the molecular defect(s) that are associated with F1099L mutation to correlate with the clinical features that we observed; (2) Methods: clinical findings and history were extracted from the electronic medical record and de-identified. F1099L-CFTR protein expression level and maturation status, channel function, and the effects of CFTR modulation on these characteristics were investigated using western blotting and iodide efflux assay; (3) Results: these two subjects have mild CF phenotypes when F1099L is combined with two known disease-causing mutations. F1099L-CFTR has a moderate defect in processing and maturation, causing fewer CFTR channels at the cell surface and, therefore, impaired channel activities. These defects could be effectively corrected using VX-809 (lumacaftor); and, (4) Conclusions: our biochemical data correlate with the disease manifestations and suggest that F1099L is potentially a CF-causing mutation. The study expands our knowledge of rare CFTR mutations and may help in developing effective therapies for subjects with F1099L mutation.

Oxygen-oxygen distances in protein-bound crystallographic water suggest the presence of protonated clusters.

BACKGROUND: The availability of high-resolution X-ray structures has shown that proteins contain numerous water molecules, but their role is still not fully understood. Protonated and deprotonated water species are often involved in biochemical reactions. However protons are exceedingly difficult to detect directly because they are electron-poor species. METHODS: The oxygen­oxygen distance of the crystallographic water molecules was analyzed in a large high-resolution data set. Moreover, a detailed analysis was carried out on the protein-bound water in the available structures of carbonic anhydrase II and cytochrome c oxidase, chosen as protein models in which protonated and deprotonated water species play a significant role. RESULTS: The analysis shows an excess of water-water distances below the expected value for hydrogen bond. In the cavities and on the surface of the considered model proteins, clusters of water molecules are found, whose structure suggests the presence of chemical species deriving from self-ionization of water. CONCLUSIONS: The presence of a small maximum below the hydrogen bond threshold in the oxygen­oxygen distance distribution of crystallographic water molecules, along with the location of many of these water clusters, suggest the presence of Zundel-like structures in, or near, the proteins. Particularly significant is the presence of such structures in protein regions which have been identified as proton antennae or channels. GENERAL SIGNIFICANCE: This work shows the possibilities, still unexplored, offered by this type of analysis in detecting in structures obtained by X-ray diffraction the presence of aqueous protons or hydroxide ions, which are chemical species as important as elusive.

Structural components involved in plastid protein import.

Import of preproteins into chloroplasts is an essential process, requiring two major multisubunit protein complexes that are embedded in the outer and inner chloroplast envelope membrane. Both the translocon of the outer chloroplast membrane (Toc), as well as the translocon of the inner chloroplast membrane (Tic) have been studied intensively with respect to their individual subunit compositions, functions and regulations. Recent advances in crystallography have increased our understanding of the operation of these proteins in terms of their interactions and regulation by conformational switching. Several subdomains of components of the Toc translocon have been studied at the structural level, among them the polypeptide transport-associated (POTRA) domain of the channel protein Toc75 and the GTPase domain of Toc34. In this review, we summarize and discuss the insight that has been gained from these structural analyses. In addition, we present the crystal structure of the Toc64 tetratrico-peptide repeat (TPR) domain in complex with the C-terminal domains of the heat-shock proteins (Hsp) Hsp90 and Hsp70.

Channel directed rutin nano-encapsulation in phytoferritin induced by guanidine hydrochloride.

Phytoferritin cage has a nano-sized cavity to encapsulate bioactive molecules. In this work, a novel approach is presented that guanidine hydrochloride (GuHCl) (2mM) can expand the channel of apo-soybean seed ferritin (apoSSF) and promote the encapsulation of rutin molecules in apoSSF at pH 7.0 without the disassembly of the protein cage. Upon removal of GuHCl from SSF, a rutin encapsulation ratio of 10.1% was obtained; and the prepared rutin-loaded ferritin nanoparticles were homogeneously distributed, showing a shell-like morphology with a size of 12nm. By virtue of this interesting method, core molecules can be encapsulated within the ferritin cage in a benign condition without extreme pH changes, which is beneficial for the stability and bioactivity of the pH-sensitive molecules in food encapsulation and delivery of functional molecules.

An Ultrasensitive, Visco-Poroelastic Artificial Mechanotransducer Skin Inspired by Piezo2 Protein in Mammalian Merkel Cells.

An artificial ionic mechanotransducer skin with an unprecedented sensitivity over a wide spectrum of pressure by fabricating visco-poroelastic nanochannels and microstructured features, directly mimicking the physiological tactile sensing mechanism of Piezo2 protein is demonstrated. This capability enables voice identification, health monitoring, daily pressure measurements, and even measurements of a heavy weight beyond capabilities of human skin.