Genetically Encoded Quinone Methides Enabling Rapid, Site-Specific, and Photocontrolled Protein Modification with Amine Reagents

Site-specific modification of proteins with functional molecules provides powerful tools for researching and engineering proteins. Here we report a new chemical conjugation method which photocages highly reactive but chemically selective moieties, enabling the use of protein-inert amines for selective protein modification. New amino acids FnbY and FmnbY, bearing photocaged quinone methides (QMs), were genetically incorporated into proteins. Upon light activation, they generated highly reactive QM, which rapidly reacted with amine derivatives. This method features a rare combination of desired properties including fast kinetics, small and stable linkage, compatibility with low temperature, photocontrollability, and widely available reagents. Moreover, labeling via FnbY occurs on the β-carbon, affording the shortest linkage to protein backbone which is essential for advanced studies involving orientation and distance. We installed various functionalities onto proteins and attached a spin label as close as possible to the protein backbone, achieving high resolution in double electron-electron paramagnetic resonance distance measurements.

The crystal structures of a chloride-pumping microbial rhodopsin and its proton-pumping mutant illuminate proton transfer determinants

Microbial rhodopsins are versatile and ubiquitous retinal-binding proteins that function as light-driven ion pumps, light-gated ion channels, and photosensors, with potential utility as optogenetic tools for altering membrane potential in target cells. Insights from crystal structures have been central for understanding proton, sodium, and chloride transport mechanisms of microbial rhodopsins. Two of three known groups of anion pumps, the archaeal halorhodopsins (HRs) and bacterial chloride-pumping rhodopsins, have been structurally characterized. Here we report the structure of a representative of a recently discovered third group consisting of cyanobacterial chloride and sulfate ion-pumping rhodopsins, the Mastigocladopsis repens rhodopsin (MastR). Chloride-pumping MastR contains in its ion transport pathway a unique Thr-Ser-Asp (TSD) motif, which is involved in the binding of a chloride ion. The structure reveals that the chloride-binding mode is more similar to HRs than chloride-pumping rhodopsins, but the overall structure most closely resembles bacteriorhodopsin (BR), an archaeal proton pump. The MastR structure shows a trimer arrangement reminiscent of BR-like proton pumps and shows features at the extracellular side more similar to BR than the other chloride pumps. We further solved the structure of the MastR-T74D mutant, which contains a single amino acid replacement in the TSD motif. We provide insights into why this point mutation can convert the MastR chloride pump into a proton pump but cannot in HRs. Our study points at the importance of precise coordination and exact location of the water molecule in the active center of proton pumps, which serves as a bridge for the key proton transfer.

X-ray Crystallographic Structure and Oligomerization of Gloeobacter Rhodopsin

Gloeobacter rhodopsin (GR) is a cyanobacterial proton pump which can be potentially applied to optogenetics. We solved the crystal structure of GR and found that it has overall similarity to the homologous proton pump from Salinibacter ruber, xanthorhodopsin (XR). We identified distinct structural characteristics of GR’s hydrogen bonding network in the transmembrane domain as well as the displacement of extracellular sides of the transmembrane helices relative to those of XR. Employing Raman spectroscopy and flash-photolysis, we found that GR in the crystals exists in a state which displays retinal conformation and photochemical cycle similar to the functional form observed in lipids. Based on the crystal structure of GR, we selected a site for spin labeling to determine GR’s oligomerization state using double electron–electron resonance (DEER) spectroscopy and demonstrated the pH-dependent pentamer formation of GR. Determination of the structure of GR as well as its pentamerizing propensity enabled us to reveal the role of structural motifs (extended helices, 3-omega motif and flipped B-C loop) commonly found among light-driven bacterial pumps in oligomer formation. Here we propose a new concept to classify these pumps based on the relationship between their oligomerization propensities and these structural determinants.

Light-independent phospholipid scramblase activity of bacteriorhodopsin from Halobacterium salinarum

The retinylidene protein bacteriorhodopsin (BR) is a heptahelical light-dependent proton pump found in the purple membrane of the archaeon Halobacterium salinarum. We now show that when reconstituted into large unilamellar vesicles, purified BR trimers exhibit light-independent lipid scramblase activity, thereby facilitating transbilayer exchange of phospholipids between the leaflets of the vesicle membrane at a rate >10,000 per trimer per second. This activity is comparable to that of recently described scramblases including bovine rhodopsin and fungal TMEM16 proteins. Specificity tests reveal that BR scrambles fluorescent analogues of common phospholipids but does not transport a glycosylated diphosphate isoprenoid lipid. In silico analyses suggest that membrane-exposed polar residues in transmembrane helices 1 and 2 of BR may provide the molecular basis for lipid translocation by coordinating the polar head-groups of transiting phospholipids. Consistent with this possibility, extensive coarse-grained molecular dynamics simulations of a BR trimer in an explicit phospholipid membrane revealed water penetration along transmembrane helix 1 with the cooperation of a polar residue (Y147 in transmembrane helix 5) in the adjacent protomer. These results suggest that the lipid translocation pathway may lie at or near the interface of the protomers of a BR trimer.

A Versatile System for High-Throughput In Situ X-ray Screening and Data Collection of Soluble and Membrane-Protein Crystals

In recent years, in situ data collection has been a major focus of progress in protein crystallography. Here, we introduce the Mylar in situ method using Mylar-based sandwich plates that are inexpensive, easy to make and handle, and show significantly less background scattering than other setups. A variety of cognate holders for patches of Mylar in situ sandwich films corresponding to one or more wells makes the method robust and versatile, allows for storage and shipping of entire wells, and enables automated crystal imaging, screening, and goniometer-based X-ray diffraction data-collection at room temperature and under cryogenic conditions for soluble and membrane-protein crystals grown in or transferred to these plates. We validated the Mylar in situ method using crystals of the water-soluble proteins hen egg-white lysozyme and sperm whale myoglobin as well as the 7-transmembrane protein bacteriorhodopsin from Haloquadratum walsbyi. In conjunction with current developments at synchrotrons, this approach promises high-resolution structural studies of membrane proteins to become faster and more routine.

Pancreatic Stenting Reduces Post-ERCP Pancreatitis and Biliary Sepsis in High-Risk Patients: A Randomized, Controlled Study

Background. Endoscopic retrograde cholangiopancreatography (ERCP) is an established treatment modality for bile duct disorders, but patients have a risk of post-ERCP pancreatitis (PEP) and biliary sepsis. Aim. To evaluate the effectiveness and safety of pancreatic stent for prophylaxis of PEP and biliary sepsis in high-risk patients with complicating common bile duct (CBD) disorders. Methods. Two hundred and six patients with complicating confirmed or suspected CBD disorders were randomly assigned to receive ERCP with pancreatic stenting (experimental group) or without stenting (control group). Primary outcome measure was frequency of PEP, and secondary outcome measures included operative time, blood loss, postoperative recovery times, and other ERCP-associated morbidities. Results. Baseline age, sex, CBD etiology, concomitant medical/surgical conditions, cannulation difficulty, and ERCP success were comparable between the two groups (all P > 0.05). Compared to the control group, the experimental group had a significantly lower frequency of PEP (7.7% versus 17.7%, P < 0.05) and positive bile microbial culture (40.4% versus 62.7%, P < 0.05). However, the two groups were similar in operative time, blood loss, postoperative recovery times, and other ERCP-associated morbidities (all P > 0.05). Conclusions. Pancreatic stenting can reduce the occurrence of PEP and biliary sepsis in high-risk patients with complicating CBD disorders but does not increase other ERCP-associated morbidities. This trial is registered with the Chinese Clinical Trial Registry (registration identifier ChiCTR-OCH-14005134).

The effect of phosphorylation on arrestin-rhodopsin interaction in the squid visual system

Invertebrate visual opsins are G protein-coupled receptors coupled to retinoid chromophores that isomerize reversibly between inactive rhodopsin and active metarhodopsin upon absorption of photons of light. The squid visual system has an arrestin protein that binds to metarhodopsin to block signaling to Gq and activation of phospholipase C. Squid rhodopsin kinase (SQRK) can phosphorylate both metarhodopsin and arrestin, a dual role that is unique among the G protein-coupled receptor kinases. The sites and role of arrestin phosphorylation by SQRK were investigated here using recombinant proteins. Arrestin was phosphorylated on serine 392 and serine 397 in the C-terminus. Unphosphorylated arrestin bound to metarhodopsin and phosphorylated metarhodopsin with similar high affinities (Kd 33 and 21 nM respectively), while phosphorylation of arrestin reduced the affinity 3- to 5-fold (Kd 104 nM). Phosphorylation of metarhodopsin slightly increased the dissociation of arrestin observed during a 1 hour incubation. Together these studies suggest a unique role for SQRK in phosphorylating both receptor and arrestin and inhibiting the binding of these two proteins in the squid visual system. Invertebrate visual systems are inactivated by arrestin binding to metarhodopsin that does not require receptor phosphorylation. Here we show that squid rhodopsin kinase phosphorylates arrestin on two serines (S392,S397) in the C-terminus and phosphorylation decreases the affinity of arrestin for squid metarhodopsin. Metarhodopsin phosphorylation has very little effect on arrestin binding but does increase arrestin dissociation.

[Expression and significance of toll-like receptors 7 and 8 in brain and lung tissues of death cases caused by EV71 infection]

OBJECTIVE

To study the significance of toll-like receptors (TLR) -7 and -8 in the pathogenesis of infection caused by Enterovirus type 71 (EV71) through measuring the expression of TLR7 and TLR8 in brain and lung tissues from the death cases caused by EV71 infection.

METHODS

Nine children who died of EV71 infection (EV71 group) were selected as study subjects, and 7 children who died of accidents or non-infectious diseases were used as the control group. Brain and lung tissues from the death cases in both groups at autopsy were collected, and immunohistochemistry was applied to detect the expression of TLR7 and TLR8 in lung and brain tissues in both groups. Integrated optical density (IOD) was applied for semi-quantitative analysis of the expression of TLR7 and TLR8.

RESULTS

Immunohistochemical results showed that the expression of TLR7 and TLR8 in lung and brain tissues was strongly positive in the EV71 group, and the IOD values in the EV71 group were also significantly higher than those in the control group (P<0.05). There was no significant difference in the expression of TLR7 and TLR8 between lung and brain tissues in the EV71 group (P>0.05).

CONCLUSIONS

TLR7 and TLR8 are highly expressed in lung and brain tissues from the patients who die of severe EV71 infection, suggesting that TLR7 and TLR8 may be involved in the pathogenesis of brain and lung damages caused by severe EV71 infection.

[Chest X-ray findings in children with enterovirus 71 infection]

OBJECTIVE

To study the characteristics of the chest X-ray images in children infected with enterovirus 71.

METHODS

A total of 120 children with enterovirus 71 infection between April, 2010 and July, 2011 were classified into three groups according to the disease condition: mild (31 cases), severe (43 cases) and life-threatening (46 cases). The period from the onset of clinical symptoms to the first chest X-ray imaging examination and the results of the first chest X-ray findings were compared among the three groups.

RESULTS

The period from the onset of clinical symptoms to the first chest X-ray imaging examination in the mild, severe and life-threatening groups was 26-48 hrs (median 37 hrs), 10-36 h (median 23 hrs) and 2-36 hrs (median 19 hrs) respectively. Chest X-ray abnormalities were initially observed at 30 hrs after the onset of clinical symptoms in the mild group, at 23 hrs in the severe group and at 2 hrs in the life-threatening group (P<0.01). The mild group presented an initial imaging abnormality rate of 5.8%, the severe group 81.3% and the life-threatening group 100%. The life-threatening group showed a significantly higher initial X-ray abnormality rate than the other two groups (P<0.01). In terms of chest X-ray performance, the mild group usually presented lung marking thickening or vagueness. Most children in the severe group presented lung effusion and consolidation. Signs of pulmonary edema were found in the life-threatening group, and lesions in the life-threatening group were characterized by wide distribution and many lung lobe involvements.

CONCLUSIONS

The interval between the onset of clinical symptoms and the initial chest X-ray examination, the period of time of, and the onset of clinical symptoms, at which chest X-ray abnormalities, the abnormality rate and the severity of chest X-ray findings may be paralleled to the clinical situation in children with enterovirus 71 infection.

[Hematologic parameters and genotype analysis in 166 children with HbH disease in the North Guangxi region]

OBJECTIVE

To study the characteristics of genotype spectrum and hematologic parameters in children with HbH disease in the North Guangxi region.

METHODS

HbH disease was identified by clinical manifestations, routine blood tests and hemoglobin electrophoresis in 166 children who came form the North Guangxi region. Genotypes were determined by Multi-PCR combined with PCR reverse dot blot. DNA sequencing was used when the genotype could not be identified by regular methods.

RESULTS

Of the 166 children with HbH disease, 8 genotypes were identified: --SEA/-α3.7 (82 cases), --SEA/-α4.2 (40 cases), --SEA/αCSα (38 cases), --SEA/αQSα (1 case), --SEA/αWSα (1 case), --SEA/αCD43/44 (-C) α (1 case), --SEA/-α3.7 plus CD17 (A→T) (1 case) and --SEA/-α4.2 plus CD41-42(-TTCT) (1 case). One case was confirmed as the heterozygote of --SEA and an unknown mutation. In the 134 cases with complete medical data, 2 had normal hemoglobin levels, 36 manifested mild anemia, 90 manifested moderate anemia, and 6 (genotype: --SEA/αCSα) showed severe anemia because of the coexistence of infection. Children with the genotype of --SEA/-α3.7 (69 cases), --SEA/-α4.2 (31 cases) and --SEA/αCSα (34 cases) had hemoglobin levels of 62-120, 69-127 and 34-110 g/L respectively. The hemoglobin level in the --SEA/αCSα group was significantly lower than in the deletional HbH disease group (genotypes: --SEA/-α3.7 and --SEA/-α4.2 ) (P<0.05). In contrast, MCV levels in the --SEA/αCSα group were significantly higher than in the deletional HbH disease group (P<0.05).

CONCLUSIONS

The genotype spectrum of HbH disease is diverse in the North Guangxi region. Deletional genotype is prevalent. The disease is heterogeneous. The children with --SEA/αCSα HbH disease have severer anemia and higher MCV levels than those with deletional HbH disease.