PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins

Information on structures of protein-ligand complexes, including comparisons of known and putative protein-ligand-binding pockets, is valuable for protein annotation and drug discovery and development. To facilitate biomedical and pharmaceutical research, we developed PoSSuM (https://possum.cbrc.pj.aist.go.jp/PoSSuM/), a database for identifying similar binding pockets in proteins. The current PoSSuM database includes 191 million similar pairs among almost 10 million identified pockets. PoSSuM drug search (PoSSuMds) is a resource for investigating ligand and receptor diversity among a set of pockets that can bind to an approved drug compound. The enhanced PoSSuMds covers pockets associated with both approved drugs and drug candidates in clinical trials from the latest release of ChEMBL. Additionally, we developed two new databases: PoSSuMAg for investigating antibody-antigen interactions and PoSSuMAF to simplify exploring putative pockets in AlphaFold human protein models.

A multipoint guidance mechanism for β-barrel folding on the SAM complex

Mitochondrial β-barrel proteins are essential for the transport of metabolites, ions and proteins. The sorting and assembly machinery (SAM) mediates their folding and membrane insertion. We report the cryo-electron microscopy structure of the yeast SAM complex carrying an early eukaryotic β-barrel folding intermediate. The lateral gate of Sam50 is wide open and pairs with the last β-strand (β-signal) of the substrate-the 19-β-stranded Tom40 precursor-to form a hybrid barrel in the membrane plane. The Tom40 barrel grows and curves, guided by an extended bridge with Sam50. Tom40's first β-segment (β1) penetrates into the nascent barrel, interacting with its inner wall. The Tom40 amino-terminal segment then displaces β1 to promote its pairing with Tom40's last β-strand to complete barrel formation with the assistance of Sam37's dynamic α-protrusion. Our study thus reveals a multipoint guidance mechanism for mitochondrial β-barrel folding.

Protein-protein interaction prediction methods: from docking-based to AI-based approaches

Protein-protein interactions (PPIs), such as protein-protein inhibitor, antibody-antigen complex, and supercomplexes play diverse and important roles in cells. Recent advances in structural analysis methods, including cryo-EM, for the determination of protein complex structures are remarkable. Nevertheless, much room remains for improvement and utilization of computational methods to predict PPIs because of the large number and great diversity of unresolved complex structures. This review introduces a wide array of computational methods, including our own, for estimating PPIs including antibody-antigen interactions, offering both historical and forward-looking perspectives.

Application of Homology Modeling by Enhanced Profile-Profile Alignment and Flexible-Fitting Simulation to Cryo-EM Based Structure Determination

Application of cryo-electron microscopy (cryo-EM) is crucially important for ascertaining the atomic structure of large biomolecules such as ribosomes and protein complexes in membranes. Advances in cryo-EM technology and software have made it possible to obtain data with near-atomic resolution, but the method is still often capable of producing only a density map with up to medium resolution, either partially or entirely. Therefore, bridging the gap separating the density map and the atomic model is necessary. Herein, we propose a methodology for constructing atomic structure models based on cryo-EM maps with low-to-medium resolution. The method is a combination of sensitive and accurate homology modeling using our profile–profile alignment method with a flexible-fitting method using molecular dynamics simulation. As described herein, this study used benchmark applications to evaluate the model constructions of human two-pore channel 2 (one target protein in CASP13 with its structure determined using cryo-EM data) and the overall structure of Enterococcus hirae V-ATPase complex.

Crystal structure of Tam41 cytidine diphosphate diacylglycerol synthase from a Firmicutes bacterium

Translocator assembly and maintenance 41 (Tam41) catalyzes the synthesis of cytidine diphosphate diacylglycerol (CDP-DAG), which is a high-energy intermediate phospholipid critical for generating cardiolipin in mitochondria. Although Tam41 is present almost exclusively in eukaryotic cells, a Firmicutes bacterium contains the gene encoding Tam41-type CDP-DAG synthase (FbTam41). FbTam41 converted phosphatidic acid (PA) to CDP-DAG using a ternary complex mechanism in vitro. Additionally, FbTam41 functionally substituted yeast Tam41 in vivo. These results demonstrate that Tam41-type CDP-DAG synthase functions in some prokaryotic cells. We determined the crystal structure of FbTam41 lacking the C-terminal 18 residues in the cytidine triphosphate (CTP)-Mg2+ bound form at a resolution of 2.6 Å. The crystal structure showed that FbTam41 contained a positively charged pocket that specifically accommodated CTP-Mg2+ and PA in close proximity. By using this structure, we constructed a model for the full-length structure of FbTam41 containing the last α-helix, which was missing in the crystal structure. Based on this model, we propose a molecular mechanism for CDP-DAG synthesis in bacterial cells and mitochondria.

Mitochondrial sorting and assembly machinery operates by β-barrel switching

The mitochondrial outer membrane contains so-called β-barrel proteins, which allow communication between the cytosol and the mitochondrial interior^1-3. Insertion of β-barrel proteins into the outer membrane is mediated by the multisubunit mitochondrial sorting and assembly machinery (SAM, also known as TOB)^4-6. Here we use cryo-electron microscopy to determine the structures of two different forms of the yeast SAM complex at a resolution of 2.8-3.2 Å. The dimeric complex contains two copies of the β-barrel channel protein Sam50-Sam50a and Sam50b-with partially open lateral gates. The peripheral membrane proteins Sam35 and Sam37 cap the Sam50 channels from the cytosolic side, and are crucial for the structural and functional integrity of the dimeric complex. In the second complex, Sam50b is replaced by the β-barrel protein Mdm10. In cooperation with Sam50a, Sam37 recruits and traps Mdm10 by penetrating the interior of its laterally closed β-barrel from the cytosolic side. The substrate-loaded SAM complex contains one each of Sam50, Sam35 and Sam37, but neither Mdm10 nor a second Sam50, suggesting that Mdm10 and Sam50b function as placeholders for a β-barrel substrate released from Sam50a. Our proposed mechanism for dynamic switching of β-barrel subunits and substrate explains how entire precursor proteins can fold in association with the mitochondrial machinery for β-barrel assembly.

Fatal case of ST8/SCCmecIVl community-associated methicillin-resistant Staphylococcus aureus infection in Japan

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) with ST8/SCCmecIV threatens human health. However, its pathogenesis remains unclear. ST8 CA-MRSA (CA-MRSA/J) with SCCmecIVl, which carries the large LPXTG-motif-containing putative adhesin gene, spj, has emerged in Japan. We present the first reported case of death from CA-MRSA/J. The patient was a 64-year-old woman with iliopsoas abscesses complicated by septic pulmonary embolism and multiorgan abscesses. Vancomycin, arbekacin, daptomycin and rifampicin were ineffective. CA-MRSA/J was resistant to erythromycin, clindamycin and antiseptics and was invasive in a HEp-2 cell assay, in contrast to skin-derived villous-adherent CA-MRSA/J. This suggests the strongly invasive pathotype of CA-MRSA/J.

Probabilistic analysis for identifying the driving force of protein folding

Toward identifying the driving force of protein folding, energetics was analyzed in water for Trp-cage (20 residues), protein G (56 residues), and ubiquitin (76 residues) at their native (folded) and heat-denatured (unfolded) states. All-atom molecular dynamics simulation was conducted, and the hydration effect was quantified by the solvation free energy. The free-energy calculation was done by employing the solution theory in the energy representation, and it was seen that the sum of the protein intramolecular (structural) energy and the solvation free energy is more favorable for a folded structure than for an unfolded one generated by heat. Probabilistic arguments were then developed to determine which of the electrostatic, van der Waals, and excluded-volume components of the interactions in the protein-water system governs the relative stabilities between the folded and unfolded structures. It was found that the electrostatic interaction does not correspond to the preference order of the two structures. The van der Waals and excluded-volume components were shown, on the other hand, to provide the right order of preference at probabilities of almost unity, and it is argued that a useful modeling of protein folding is possible on the basis of the excluded-volume effect.

[Bronchospasm during crush induction with propofol under the Sellick maneuver in a patient for emergency laparotomy]

A 61-year-old man was scheduled for an emergency laparotomy due to ileus. He had a history of asthma, but it was well controlled without medication. Anesthesia was induced with propofol and ketamine under the Sellick maneuver. Following administration of vecuronium, endotracheal intubation was performed. However, he could not be ventilated. We thought that the tube had been inserted into the esophagus, and re-intubation was performed. However he could not be ventilated as in the first trial. At that time, we suspected that bronchospasm had occurred. Bronchospasm improved rapidly using hyperventilation with 100% oxygen and 3-5% sevoflurane, and intravenous aminophylline. Because he had a history of asthma, propofol was relatively indicated from the point of smooth muscle relaxant effects. However we should consider the risk of bronchospasm in a patient with a history of asthma, even if we use propofol.

[Safety of continuous epidural anesthesia during heart surgery--change of coagulation-fibrinolysis under heparinization]

To confirm the safety of continuous epidural anesthesia during extracorporeal circulation under heparinization, we investigated epidural hematoma formation following the cardiopulmonary bypass in both humans and dogs. In fifteen dogs, divided into three groups, heparin was administered at the dose of 300, 600, or 900 U.kg-1, respectively. In fourteen patients, a dose of 300 U.kg-1 haparin was administered for cardiopulmonary bypass. Although blood coagulation-fibrinolysis dropped into abnormal ranges following heparinization, no epidural hematoma was observed in dog and no patient revealed spinal complication associated with epidural hematoma. These data indicate that continuous epidural anesthesia would be a safe tool for intraoperative anesthesia even during extracorporeal circulation under heparinization.

Cutaneous responsiveness of lumbar spinal dorsal horn neurons is reduced by general anesthesia, an effect dependent in part on GABAA mechanisms

Extracellular activity was recorded from single spinal dorsal horn neurons in both chronic cat and acute rat models. This was done to define the effects of anesthesia on the processing of sensory information elicited by nonnoxious tactile stimulation of peripheral receptive fields (RFs). In the chronic cat model, baseline data were obtained in physiologically intact, awake, drug-free animals before anesthetic administration (halothane 1.0-2.0%). This made it possible to compare and contrast activity of each cell in the drug-free and anesthetized state. Halothane effects were confirmed in the acute rat model (anesthetized, spinally transected, and in some cases decerebrate). In addition, the gamma-aminobutyic acid-A (GABAA)-receptor antagonist picrotoxin (2 mg/kg) was administered intravenously to verify that the observed halothane effect on spinal dorsal horn neurons was mediated by an interaction with GABAA-receptor systems. Halothane effects on three separate measures of response to nonnoxious tactile stimuli were observed in the chronic cat model. Halothane produced a significant, dose-dependent reduction in the low-threshold RF area of the neurons studied. Halothane also caused a significant reduction in neuronal response to RF brushing (dynamic stimulus) and to maintained contact with the RF (static stimulus). A dose dependency was not observed with these latter two effects. Neurons with a predominant rapidly adapting response seemed to be less susceptible to halothane suppression than slowly adapting cells. In the acute rat model an increase in halothane caused a reduction in neuronal response similar to that seen in the cat. The intravenous administration of 2 mg/kg of picrotoxin by itself caused no significant change in RF size or response to brushing. However, the same amount of picrotoxin did cause a 50% reversal of the halothane-induced reduction in RF size without causing a significant change in the halothane effect on response to RF brushing. In contrast to work recently reported in a chronic sheep model, halothane causes a significant reduction in spinal dorsal horn neuronal response to tactile stimulation of peripheral RFs. This effect is caused by, in part, but not exclusively, to GABAA-neurotransmitter systems. However, the relative influence of GABAA systems may vary with the nature of the stimulus.

Spinal anesthesia with tetracaine in 0.75% glucose: influence of the vertebral interspace used for injection

BACKGROUND AND OBJECTIVES

The anesthetic behavior and hemodynamic consequences of spinal anesthesia with marginally hyperbaric tetracaine containing a low concentration of glucose injected at two different interspaces were examined and compared with those of conventionally hyperbaric solution.

METHODS

One-hundred twenty ASA Physical Status I or II patients scheduled for elective surgery to the lower limb were sequentially assigned to one of three equal groups to receive spinal anesthesia: Group 1 received 0.5% tetracaine in 0.75% glucose with 0.125% phenylephrine at the L2-L3 interspace; group 2 0.5% tetracaine in 0.75% glucose with 0.125% phenylephrine at the L3-L4 interspace; group 3 0.5% tetracaine in 7.5% glucose with 0.125% phenylephrine at the L3-L4 interspace. Neural block was assessed in a double-blinded manner by cold, pinprick, and touch sensation, and a modified Bromage scale after the injection of the study drug.

RESULTS

Injection at the L2-L3 interspace produced significantly higher spread of analgesia [median T7 (10th, 90th percentiles T10, T4)] than injection at L3-L4 interspace [T10 (L1, T5)] when using the solution in 0.75% glucose. There were no significant differences in peak dermatomal levels between groups 1 and 3, but the number of patients who required ephedrine for the treatment of hypotension was larger in group 3.

CONCLUSIONS

A marginally hyperbaric tetracaine solution injected at the L2-L3 interspace with the patient in the lateral position produced greater extent of cephalad spread than that at the L3-L4 interspace. When compared to a conventionally hyperbaric tetracaine solution injected at the L3-L4 interspace, the marginally hyperbaric solution injected at the L2-L3 interspace caused less hemodynamic variability despite similar levels of maximum sensory block.

[Postoperative brain infarction in a patient with the previous asymptomatic brain infarction]

We report a case of a postoperative brain infarction, in which an asymptomatic preoperative brain infarction was also revealed postoperatively. A 63-year-old man with bladder carcinoma was scheduled for the cystoplasty. The patient had no prominent preoperative abnormality. Anesthesia was maintained with isoflurane in N2O/oxygen combined with a spinal block and a continuous epidural block. Anesthesia lasted uneventfully for 16.5 hours. However, emergence from anesthesia was delayed. On the first postoperative day, motor aphasia and right hemiparalysis was confirmed. The computed tomography (CT) of the brain demonstrated a low density area in the frontoparietal region. The magnetic resonance imaging (MRI) indicated the corresponding lesion as the CT had demonstrated, and an old brain infarction in the parietal region. This meant that the patient had a history of asymptomatic brain infarction (ABI). Patients with ABI are considered to be a high-risk group for a brain infarction. It is important to evaluate the risk factors of brain infarction preoperatively and to minimize those risks during the operation. Maintenance of the cerebral perfusion pressure is imperative.

Antinociceptive effects of ONO-9902, an enkephalinase inhibitor, after visceral stress condition in rats

PURPOSE

The present study was designed to examine the antinociceptive effects of orally administered ONO-9902, an enkephalinase inhibitor, on both somatic and visceral pain after visceral stress conditions.

METHODS

Twenty six male rats were examined. Tail-flick (TF) and colorectal distension (CD) tests were used to determine somatic and visceral antinociceptive effects, respectively. Measurements were performed in rats under immediate post-stress conditions (group ST; n = 14) and in rats nor under stress conditions (group NST; n = 12). In the stressed group, the same device, CD, for visceral antinociceptive effects was used for visceral stress and was applied with an intracolonic pressure of 60 mmHg for 20 min after drug administration. The TF latency and CD threshold were measured before and at 30, 40, 50, 60 and 90 min after administration of ONO-9902 300 mg.kg-1 or distilled water.

RESULTS

Orally administered ONO-9902 did not produce any changes in the % maximum possible effect (%MPE) in either TF or CD tests in the unstressed group. In the stressed group, %MPE in the CD test increased 18% and 31% at 30 and 40 min, respectively, after oral administration of ONO-9902 compared with the control group (P < 0.05). However, %MPE to TF test did not alter even after the CD-induced stress condition.

CONCLUSION

These results suggest that ONO-9902 may have analgesic effects on visceral pain but not on somatic pain under immediate post-stress conditions.

Halothane effects on low-threshold receptive field size of rat spinal dorsal horn neurons appear to be independent of supraspinal modulatory systems

Recent evidence strongly supports the importance of spinal sites of action for the ability of general anesthetic agents to block response to noxious stimuli. This study was designed to examine possible spinal anesthetic effects on non-noxiously evoked activity. Three groups of rats were prepared for acute experiments in which the response of spinal dorsal horn neurons to low threshold receptive field (RF) stimulation was evaluated. In each animal in each group extracellular activity was recorded from a single spinal dorsal horn neuron. A low-threshold RF of each neuron and, at times, the sensitivity to low-threshold stimulation of multiple sites in the RF were determined under baseline conditions (light anesthesia or decerebrate). In Group 1, reversible cooling of the thoracic spinal cord in the presence of either 0.5% or 1% halothane anesthesia caused no change in RF size. However, an increase from 0.5% to 1% halothane caused a 53% decrease in RF size both in the presence and absence of a reversible cold block of the spinal cord. In Group 2, animals with spinal cords transected at the thoracic level had a similar change in low-threshold receptive field size (52%) when halothane concentrations were increased from 0.5% to 1%. Testing sensitivity within the RF areas indicated that the silenced areas at the fringe of the receptive field could still elicit activation of spinal dorsal horn neurons but at a higher threshold. In the final group of animals, decerebration and spinal cord transection allowed us to compare effects of 0.5% and 1% halothane with an anesthetic free baseline. Here, again, a dose-dependent reduction in RF area was observed although the baseline RFs were significantly smaller than those in Groups 1 and 2. These results demonstrate that the reduction in low-threshold receptive field size due to the administration of the inhalation anesthetic halothane occurs in the absence of descending modulation from supraspinal sites. This implicates the spinal dorsal horn as a potentially important site of action for general anesthetics. These results also support the spinal cord as an important tool to study the pharmacology responsible for anesthetic effects on sensory processing.

Low-threshold neuronal activity of spinal dorsal horn neurons increases during REM sleep in cats: comparison with effects of anesthesia

1. Cats were prepared for chronic recordings from the lumbar enlargement of the spinal dorsal horn. At the beginning of each recording session, a tungsten microelectrode was advanced through the dura in a physiologically intact, awake, drug-free animal, until amplitude discrimination provided a single neuron with a receptive field on the hindquarters. 2. Extracellular recordings of activity of each neuron were made during receptive field stimulation with tactile and thermal nonnoxious and noxious stimuli. 3. Baseline responses obtained in the awake state were compared with responses of the same neurons during slow-wave or rapid-eye-movement (REM) sleep. In a subpopulation of neurons, the effects of anesthesia (propofol, 7.5 mg/kg iv) were observed after the completion of sleep studies. 4. The low-threshold receptive fields of the seven neurons studied during REM sleep were all increased in size when compared with the baseline value. The average increase was 52.6% (range 26.2-96.7%). 5. The low-threshold receptive fields of the seven neurons studied during REM sleep were reduced by propofol anesthesia by an average of 49.1% (range 29-74%). 6. Neuronal response to receptive field brushing was observed in 15 neurons during REM sleep. The effect of propofol on receptive field brushing was observed in 8 of those neurons. In only one of those eight neurons were the effects of REM sleep and anesthesia in the same direction. 7. Changes in neuronal responses were less consistent during slow-wave sleep but still differed from changes induced by propofol.(ABSTRACT TRUNCATED AT 250 WORDS)

Utilization of a glucose/fructose/xylitol carbohydrate solution during surgery

The utilization of a 4:2:1 mixture of glucose, fructose, and xylitol (GFX) was studied by indirect calorimetry in patients undergoing abdominal surgery. Sixteen patients undergoing gastrectomy under general anesthesia received GFX intravenously at 0.25 g/kg h-1 during surgery. VO2, VCO2, and RQ were measured continuously for 150 min using an Engström metabolic computer, and urea nitrogen excretion was determined at 30-min intervals during surgery. Blood levels of glucose, fructose, and xylitol plateaued after 1 h. The RQ decreased over the first 90 min from 0.84 +/- 0.06 to 0.75 +/- 0.05 and then gradually increased to 0.79 +/- 0.04 at 150 min. VO2 did not change significantly over the 150-min period. From the RQ, VO2, and nitrogen excretion data, carbohydrate oxidation was estimated. The amount of carbohydrate oxidized was 9.7 +/- 6.9 g during the first 30-min period, 3.5 +/- 5.2 g during the 60 to 90-min period, and 7.5 +/- 4.5 g in the 120 to 150-min study period. Simultaneously, lipid oxidation increased. These observations suggest that the GFX solution is adequately metabolized during surgery and therefore may be a suitable energy source for patients.

Histological evidence for dissociation of lipid peroxidation and cell necrosis in bromotrichloromethane hepatotoxicity in the perfused rat liver

Bromotrichloromethane (CBrCl3)-induced hepatic lipid peroxidation and cell necrosis were studied histologically and biochemically, using isolated perfused livers from phenobarbital-pretreated rats. Lipid peroxidation was assessed by fuchsin staining of the liver slices and release of thiobarbituric acid reactive substances (TBARS) into the perfusate; necrosis was assessed by trypan blue uptake and lactate dehydrogenase (LDH) leakage. A good correlation was observed between the Schiff-positive reaction and TBARS release under various experimental conditions, supporting the validity of the fuchsin staining method for histological detection of lipid peroxidation. Lobular localization of lipid peroxidation and necrosis was as follows: Under high oxygen supply (95% O2-saturated buffer), infusion of CBrCl3 caused the Schiff-positive reaction in the pericentral to midzonal hepatocytes, irrespective of the direction of perfusion, but did not produce necrosis. Under low oxygen supply (20% O2) with retrograde perfusion, dissociation of lipid peroxidation and necrosis was observed, i.e., trypan blue uptake in the periportal zones and Schiff-positive staining in the pericentral hepatocytes. Thus, lipid peroxidation by itself may have a relatively minor role in the development of CBrCl3-induced acute hepatic cell death.

Histological detection of lipid peroxidation following infusion of tert-butyl hydroperoxide and ADP-iron complex in perfused rat livers

Lipid peroxidation was assessed histologically and biochemically in hemoglobin-free perfused rat livers using two different types of stimulators. The Schiff reaction of fuchsin with cellular aldehydes was used as a histological index for lipid peroxidation. t-Butyl hydroperoxide (BHP, 0.8 mM) infusion caused a rapid and sustained release of thiobarbituric acid reactive substances (TBARS) into the effluent perfusate for up to 60 min, which was accompanied by lactate dehydrogenase (LDH) leakage after 30 min. The Schiff positive foci were initially restricted to periportal zones and spread with time to whole areas, accompanied by periportal necrosis. Coinfusion of diphenyl-p-phenylenediamine suppressed the TBARS release, with negative fuchsin staining, but the LDH leakage was unaffected. Under retrograde perfusion, BHP produced pericentral staining and necrosis. With 2.5 mM ADP-100 microM Fe3+, little TBARS was released up to 60 min, even though the hepatic TBARS levels increased considerably by this time. By 90 min, marked TBARS release occurred, but LDH leakage remained low. Irrespective of the direction of perfusion, pericentral hepatocytes became Schiff positive after 30 min. The fuchsin staining method may be useful for detecting peroxidized zones of the liver lobules.

[Anesthetic management of caesarean section for the delivery of quadruplets]

Multiple gestation pregnancies are accompanied with risks for both mother and fetuses. Morbidity and mortality of both of them are increased compared with singleton pregnancies. We have presented a case of a 30-year-old parturient with quadruplets. The pregnancy had been complicated by premature labour, anemia, toxemia, coagulopathy, pulmonary congestion and malpresentation. On the 29th week of pregnancy, an elective Caesarean section was scheduled. There is no ideal anesthetic technique for quadruplets. In this case general anesthesia was chosen, because she had coagulopathy. The anesthesia and postoperative course were uneventful. The patient and the four babies had no complication nor sequela on their discharge. The anesthetic considerations for multiple gestation pregnancies were also discussed.

[Successful management of abdominal aortic aneurysm due to bacterial infection: report of a case]

A successful surgery of abdominal aortic aneurysm due to bacterial infection is described. The patient, 71-year-old man, had been suffering from high fever of unknown origin which had narrow escape with the several kinds of antibiotics about a month and more. During the antibiotic therapy in another hospital, he was diagnosed as an abdominal aortic aneurysm by whole body computed tomography. Immediately after the arrival to our hospital, digital subtraction angiography was done, and it showed a saccular aneurysm in the infrarenal abdominal aorta. Surgical removal of this aneurysm without opening of the aneurysmal wall was performed and the kitted dacron graft was used for aorto-biiliac anastomosis. The diagnosis of aneurysm due to bacterial infection was confirmed by bacteriological and pathological examinations. The patient in now surviving 17 months after operation. Abdominal aortic aneurysm due to bacterial infection is a serious disorder that generally carries grave prognosis. Complete removal of infected lesion without contamination and long-term follow-up with antibiotic chemotherapy are essential for this disease.