End-to-end protein-ligand complex structure generation with diffusion-based generative models.

BACKGROUND: Three-dimensional structures of protein-ligand complexes provide valuable insights into their interactions and are crucial for molecular biological studies and drug design. However, their high-dimensional and multimodal nature hinders end-to-end modeling, and earlier approaches depend inherently on existing protein structures. To overcome these limitations and expand the range of complexes that can be accurately modeled, it is necessary to develop efficient end-to-end methods. RESULTS: We introduce an equivariant diffusion-based generative model that learns the joint distribution of ligand and protein conformations conditioned on the molecular graph of a ligand and the sequence representation of a protein extracted from a pre-trained protein language model. Benchmark results show that this protein structure-free model is capable of generating diverse structures of protein-ligand complexes, including those with correct binding poses. Further analyses indicate that the proposed end-to-end approach is particularly effective when the ligand-bound protein structure is not available. CONCLUSION: The present results demonstrate the effectiveness and generative capability of our end-to-end complex structure modeling framework with diffusion-based generative models. We suppose that this framework will lead to better modeling of protein-ligand complexes, and we expect further improvements and wide applications.

Thermal conductivity and conductance of protein in aqueous solution: Effects of geometrical shape.

Considering the importance of elucidating the heat transfer in living cells, we evaluated the thermal conductivity κ and conductance G of hydrated protein through all-atom non-equilibrium molecular dynamics simulation. Extending the computational scheme developed in earlier studies for spherical protein to cylindrical one under the periodic boundary condition, we enabled the theoretical analysis of anisotropic thermal conduction and also discussed the effects of protein size correction on the calculated results. While the present results for myoglobin and green fluorescent protein (GFP) by the spherical model were in fair agreement with previous computational and experimental results, we found that the evaluations for κ and G by the cylindrical model, in particular, those for the longitudinal direction of GFP, were enhanced substantially, but still keeping a consistency with experimental data. We also studied the influence by salt addition of physiological concentration, finding insignificant alteration of thermal conduction of protein in the present case.

Comparison between a rotatable sphincterotome and a conventional sphincterotome for selective bile duct cannulation.

BACKGROUND: Selective biliary cannulation (SBC) is the first challenge of endoscopic retrograde cholangiopancreatography (ERCP), especially for trainees, and a rotatable sphincterotome may be useful to guide the directional axis of the scope and SBC. METHODS: We performed a prospective randomized single-center trial, enrolling 200 patients with a native papilla who required therapeutic biliary ERCP. Patients were randomly assigned to the rotatable sphincterotome group (n = 100) or the conventional sphincterotome group (n = 100). The primary endpoint was successful SBC by the trainees within 10 minutes. RESULTS: The early and late cannulation success rates did not differ significantly between the groups (P = 0.46 and P > 0.99, respectively). For the patients in whom trainees failed to achieve SBC, the rotatable sphincterotome was used as a rescue cannulation technique in four patients from the conventional group; in no patients in the rotatable group was the conventional sphincterotome used for SBC. Post-ERCP pancreatitis (PEP) occurred in 11 patients (5.5 %; 6 mild, 5 moderate); the incidence did not differ significantly between the two groups (rotatable group 3 %, conventional group 8 %; P = 0.21). The two groups were thus combined for evaluation of the factors relating to cannulation difficulty for trainees, which revealed that orientation of the papilla was a significant factor (P < 0.001). CONCLUSIONS: The type of sphincterotome used did not affect the success of SBC by trainees. However, orientation of the papilla was revealed to be a significant factor relating to cannulation difficulty for trainees overall.

Proposal of a 1-ampere-class deuteron single-cell linac for nuclear transmutation.

A 1-ampere-class high-intensity deuteron linac (ImPACT2017 model) is proposed for mitigating long-lived fission products (LLFPs) by nuclear transmutation. This accelerator consists of single-cell rf cavities with magnetic focusing elements to accelerate deuterons beyond 1 A up to 200 MeV/u.

Tumor invasion to the arteries feeding the gallbladder as a novel risk factor for cholecystitis after metallic stent placement in distal malignant biliary obstruction.

BACKGROUND AND AIM: Cholecystitis is a major complication after self-expandable metallic stent (SEMS) placement for malignant biliary obstruction. Ischemia is one of the risk factors for cholecystitis, but little is known about the influence of tumor invasion to the feeding artery of the gallbladder on the onset of cholecystitis after SEMS placement. The aim of the present study was to identify risk factors for cholecystitis after SEMS placement. METHODS: Incidence and nine predictive factors of cholecystitis were retrospectively evaluated in 107 patients who underwent SEMS placement for unresectable distal malignant biliary obstruction at Kyoto University Hospital and Otsu Red Cross Hospital between January 2012 and June 2016. RESULTS: Cholecystitis occurred in 13 of 107 patients (12.1%) after SEMS placement during the median follow-up period of 262 days. Univariate analyses showed that tumor invasion to the feeding artery of the gallbladder and tumor involvement to the orifice of the cystic duct were significant predictors of cholecystitis (P = 0.001 and P < 0.001). Multivariate analysis confirmed that these two factors were significant and independent risks for cholecystitis with odds ratios of 22.13 (95% CI, 3.57-137.18; P = 0.001) and 25.26 (95% CI, 4.12-154.98; P < 0.001), respectively. CONCLUSIONS: This study showed for the first time that tumor invasion to the feeding artery of the gallbladder as well as tumor involvement to the orifice of the cystic duct are independent risk factors for cholecystitis after SEMS placement.

Conformational changes of ubiquitin under high pressure conditions: A pressure simulated tempering molecular dynamics study.

Molecular dynamics simulations for the system of ubiquitin were performed with pressure simulated tempering to study pressure-induced conformational changes of ubiquitin. The pressure dependence of ubiquitin was analyzed in a wide range of pressure from atmospheric pressure (0.1 MPa) to 1.0 GPa. The fluctuation of the distance between amino-acid residues and the distribution of a largely fluctuating distance were calculated. The large fluctuation of the L8-E34 distance induced by pressure means that the conformation of ubiquitin changes under high pressure conditions. There were more water molecules near the largely fluctuating region at high pressure than at low pressure. The pressure dependence of interaction energies among ubiquitin and water was also calculated to investigate the role of water for the pressure-induced conformational changes of ubiquitin. The protein-water interaction is important when the conformation of ubiquitin changes at high pressure. © 2017 Wiley Periodicals, Inc.

Modeling (15)N NMR chemical shift changes in protein backbone with pressure.

Nitrogen chemical shift is a useful parameter for determining the backbone three-dimensional structure of proteins. Empirical models for fast calculation of N chemical shift are improving their reliability, but there are subtle effects that cannot be easily interpreted. Among these, the effects of slight changes in hydrogen bonds, both intramolecular and with water molecules in the solvent, are particularly difficult to predict. On the other hand, these hydrogen bonds are sensitive to changes in protein environment. In this work, the change of N chemical shift with pressure for backbone segments in the protein ubiquitin is correlated with the change in the population of hydrogen bonds involving the backbone amide group. The different extent of interaction of protein backbone with the water molecules in the solvent is put in evidence.

Simulated tempering based on global balance or detailed balance conditions: Suwa-Todo, heat bath, and Metropolis algorithms.

Simulated tempering (ST) is a useful method to enhance sampling of molecular simulations. When ST is used, the Metropolis algorithm, which satisfies the detailed balance condition, is usually applied to calculate the transition probability. Recently, an alternative method that satisfies the global balance condition instead of the detailed balance condition has been proposed by Suwa and Todo. In this study, ST method with the Suwa-Todo algorithm is proposed. Molecular dynamics simulations with ST are performed with three algorithms (the Metropolis, heat bath, and Suwa-Todo algorithms) to calculate the transition probability. Among the three algorithms, the Suwa-Todo algorithm yields the highest acceptance ratio and the shortest autocorrelation time. These suggest that sampling by a ST simulation with the Suwa-Todo algorithm is most efficient. In addition, because the acceptance ratio of the Suwa-Todo algorithm is higher than that of the Metropolis algorithm, the number of temperature states can be reduced by 25% for the Suwa-Todo algorithm when compared with the Metropolis algorithm.

Further evidence that a new type of Japanese pickles reduce the blood pressure of spontaneously hypertensive rats.

A new type of pickles (nukazuke) that contain GABA and angiotensin converting enzyme-inhibitory peptides and that reduce blood pressure of rats was studied further. Seven kinds of nukazuke forcefully administrated orally for one day reduced temporarily the blood pressure of spontaneously hypertensive rats. In addition, a fermented shougoin daikon administrated freely for 4 weeks did not increase the blood pressure of the rats, but suppressed it throughout the experiment. Taken together with previous data (Oda et al., Biosci. Biotechnol. Biochem., 2014) it was concluded that the nukazuke could reduce the blood pressure of spontaneously hypertensive rats. Thus, the newly developed functional pickles appear to be beneficial for pickles business.

Molecular dynamics of the structural changes of helical peptides induced by pressure.

An AK16 peptide and a C-peptide analog are experimentally known to form more helical structures under high-pressure conditions than those at atmospheric pressure, even though most proteins usually unfold at high pressure. To understand the pressure-induced structural changes of the two peptides, molecular dynamics simulations with the simulated tempering method for the isobaric-isothermal ensemble were performed in a wide pressure range from 0.1 MPa to 1.4 GPa. We found that the fraction of the folded state decreases once and then increases with increasing pressure for both peptides. The partial molar volume change of both peptides from the folded state to the unfolded state increases monotonically from a negative value to a positive value as pressure increases. By calculating the radius of gyration and interatomic distances of the AK16 peptide and the C-peptide analog, we found that these peptides are compressed under high-pressure conditions, which causes the folded state to be more stable at high pressure. Furthermore, we found that the salt bridge of the C-peptide analog is broken under high pressure.

Bio-functional pickles that reduce blood pressure of rats.

Addition of γ-aminobutyric acid (GABA) and angiotensin converting enzyme (ACE)-inhibitory peptides to the pickles was studied in order to develop a new type of pickles that reduce blood pressure. Based on the outcome of these studies, a new type of fermentation bed composed of rice bran and white miso has been successfully developed. The advantage of such pickles is that they not only contain both GABA and ACE-inhibitory peptides, but also that their taste and flavor are excellent, with colors close to the original ones. The new type of pickles could temporarily reduce blood pressure in two types of rats, spontaneously hypertensive rats and NaCl-sensitive model rats. Thus, the newly developed pickles appear to be beneficial for pickle business.

Anesthetic Binding Induced Motion of GABAA Receptors Revealed by Coarse-Grained Molecular Dynamics Simulations.

General anesthetics are indispensable in modern medicine because they induce a reversible loss of consciousness and sensation in humans. On the other hand, their molecular mechanisms of action have not yet been elucidated. Several studies have identified the main targets of some general anesthetics. The structures of γ-aminobutyric acid A (GABAA) receptors with the intravenous anesthetics such as propofol and etomidate have recently been determined. Although these anesthetic binding structures provide essential insights into the mechanism of action of anesthetics, the detailed molecular mechanism of how the anesthetic binding affects the Cl- permeability of GABAA receptors remains to be elucidated. In this study, we performed coarse-grained molecular dynamics simulations for GABAA receptors and analyzed the resulting simulation trajectories to investigate the effects of anesthetic binding on the motion of GABAA receptors. The results showed large structural fluctuations in GABAA receptors, correlations of motion between the amino acid residues, large amplitude motion, and autocorrelated slow motion, which were obtained by advanced statistical analyses. In addition, a comparison of the resulting trajectories in the presence or absence of the anesthetic molecules revealed a characteristic pore motion related to the gate-opening motion of GABAA receptors.

Propensity score analysis comparing off-pump versus on-pump coronary artery bypass grafting in older adults.

OBJECTIVE: This study aimed to compare the results of off-pump and on-pump coronary artery bypass grafting in older adults and to examine early and late outcomes. METHODS: This study included 226 patients aged ≥ 75 years who underwent isolated coronary artery bypass grafting. Of these, 141 and 85 patients were included in the off-pump and on-pump groups, respectively. Propensity scores were calculated for each case, matched, and compared between the two groups (68 cases in each group), along with mid-term outcomes of survival and major adverse cardiac events. RESULTS: Operative time, red blood cell transfusion volume, and postoperative hospital stay duration were significantly higher in the on-pump group (267 vs 370 min, P < 0.001; 4.3 vs 17.2 units, P < 0.001; and 20.8 vs 35.8 days, P = 0.012, respectively). Postoperative occurrence of new atrial fibrillation was significantly higher in the on-pump group (4.4% vs 27.9%, P < 0.001), and Kaplan-Meier survival analysis showed a significantly worse prognosis in the on-pump group than in the off-pump group (3-year survival rate 90.7% vs 71.5%, log rank P = 0.007). However, there was no statistically significant difference in cardiovascular-related deaths (log rank P = 0.07). CONCLUSIONS: On-pump coronary artery bypass grafting in an older adult population resulted in increased transfusion volume and postoperative occurrence of atrial fibrillation. The mid-term postoperative outcomes were also poorer with on-pump coronary artery bypass grafting. Off-pump coronary artery bypass grafting reduced future all-cause deaths in older adults.

Time-varying overdispersion of SARS-CoV-2 transmission during the periods when different variants of concern were circulating in Japan.

Japan has implemented a cluster-based approach for coronavirus disease 2019 (COVID-19) from the pandemic's beginning based on the transmission heterogeneity (overdispersion) of severe acute respiratory coronavirus 2 (SARS-CoV-2). However, studies analyzing overdispersion of transmission among new variants of concerns (VOCs), especially for Omicron, were limited. Thus, we aimed to clarify how the transmission heterogeneity has changed with the emergence of VOCs (Alpha, Delta, and Omicron) using detailed contact tracing data in Yamagata Prefecture, Japan. We estimated the time-varying dispersion parameter ([Formula: see text]) by fitting a negative binomial distribution for each transmission generation. Our results showed that even after the emergence of VOCs, there was transmission heterogeneity of SARS-CoV-2, with changes in [Formula: see text] during each wave. Continuous monitoring of transmission dynamics is vital for implementing appropriate measures. However, a feasible and sustainable epidemiological analysis system should be established to make this possible.

High signal intensity on diffusion-weighted magnetic resonance images is a useful finding for detecting early-stage pancreatic cancer.

PURPOSE: Early detection of pancreatic ductal adenocarcinoma (PDAC) may improve the prognosis. We evaluated novel imaging findings that may contribute to early detection. METHODS: This single-center, retrospective study enrolled 37 patients with a localized main pancreatic duct (MPD) stricture and no obvious pancreatic mass. All patients underwent endoscopic retrograde cholangiopancreatography and brush sampling with cytology and serial pancreatic juice aspiration cytologic examination via endoscopic naso-pancreatic drainage. Patients with cytology-confirmed malignancy underwent surgical resection. The remaining patients were followed by contrast-enhanced computed tomography (CECT), magnetic resonance imaging (MRI), and endoscopic retrograde cholangiopancreatography. RESULTS: Twenty patients had confirmed malignancy (cancer group) and 17 did not (non-cancer group). Age, MPD stricture location, and PDAC risk factors were similar, but the sex predominance and symptom rate differed between the two groups. In the cancer group, 17 patients were diagnosed by cytology and three by clinical symptoms. CECT, MRI, and endoscopic ultrasonography (EUS) revealed no solid tumors in either group. CECT revealed no significant differences between groups. Diffusion-weighted MRI revealed significant differences in the signal intensity between groups. EUS detected indistinct and small hypoechoic areas in 70% and 41.2% of patients in the cancer and non-cancer groups, respectively. In the cancer group, 11 were diagnosed with cancer at the first indication, and nine were diagnosed at follow-up; the prognosis did not differ between these two subgroups.ss CONCLUSIONS: High signal intensity in diffusion-weighted MRI may be useful for detecting early-stage PDAC and may be an indication for surgical resection even without pathologic confirmation. CLINICAL TRIAL REGISTRATION: The study was a registered at the University Hospital Medical Information Network (UMIN000039623).

Risk factor analysis for early rebleeding after endoscopic treatment for colonic diverticular bleeding with stigmata of recent hemorrhage.

BACKGROUND AND AIM: Colonic diverticular bleeding is a common cause of acute lower gastrointestinal bleeding. Endoscopic hemostasis is generally selected as the first-line treatment; however, a considerable number of patients experience early rebleeding after endoscopic treatment. We investigated the risk factors for early rebleeding after endoscopic treatment. METHODS: We retrospectively evaluated the data of 142 consecutive patients who underwent endoscopic treatment (endoscopic clipping or endoscopic band ligation) for colonic diverticular bleeding with stigmata of recent hemorrhage between April 2012 and April 2020. Multivariate logistic regression analysis was conducted to evaluate the statistical relationship between patient characteristics and the incidence of early rebleeding occurring within 30 days after endoscopic treatment. RESULTS: Of 142 patients, early rebleeding was detected in 34 (23.9%) patients. According to univariate analysis, platelet count of <10 × 104/µL, bleeding from the left-sided colon, and endoscopic clipping usage were associated with early rebleeding (P < 0.05). The subsequent multivariate logistic regression analysis identified bleeding from the left-sided colon (odds ratio [OR], 4.16; 95% confidence interval [CI], 1.73-10.0; P = 0.001) and endoscopic clipping usage (OR, 2.92; 95% CI, 1.21-7.00; P = 0.017) as the independent risk factors for early rebleeding. CONCLUSIONS: Bleeding from the left-sided colon and endoscopic clipping usage were the risk factors for early rebleeding after endoscopic treatment. Using endoscopic band ligation was associated with a decreased risk for early rebleeding compared with the use of endoscopic clipping, indicating that endoscopic band ligation was a preferable endoscopic modality to prevent early recurrent bleeding.

Molecular mechanism of long-range synergetic color tuning between multiple amino acid residues in conger rhodopsin.

The synergetic effects of multiple rhodopsin mutations on color tuning need to be completely elucidated. Systematic genetic studies and spectroscopy have demonstrated an interesting example of synergetic color tuning between two amino acid residues in conger rhodopsin's ancestral pigment (p501): -a double mutation at one nearby and one distant residue led to a significant λ(max) blue shift of 13 nm, whereas neither of the single mutations at these two sites led to meaningful shifts.To analyze the molecular mechanisms of this synergetic color tuning, we performed homology modeling, molecular simulations, and electronic state calculations. For the double mutant, N195A/A292S, in silico mutation analysis demonstrated conspicuous structural changes in the retinal chromophore, whereas that of the single mutant, A292S, was almost unchanged. Using statistical ensembles of QM/MM optimized structures, the excitation energy of retinal chromophore was evaluated for the three visual pigments. As a result, the λ(max) shift of double mutant (DM) from p501 was -8 nm, while that of single mutant (SM) from p501 was +1 nm. Molecular dynamics simulation for DM demonstrated frequent isomerization between 6-s-cis and 6-s-trans conformers. Unexpectedly, however, the two conformers exhibited almost identical excitation energy, whereas principal component analysis (PCA) identified the retinal-counterion cooperative change of BLA (bond length alternation) and retinal-counterion interaction lead to the shift.

Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH.

Following the discovery of cryptochrome-DASH (CRYD) as a new type of blue-light receptor cryptochrome, theoretical and experimental findings on CRYD have been reported. Early studies identified CRYD as highly homologous to the DNA repair enzyme photolyases (PLs), suggesting the involvement of CRYD in DNA repair. However, an experimental study reported that CRYD does not exhibit DNA repair activity in vivo. Successful PL-mediated DNA repair requires: (i) the recognition of UV-induced DNA lesions and (ii) an electron transfer reaction. If either of them is inefficient, the DNA repair activity will be low. To elucidate the functional differences between CRYD and PL, we theoretically investigated the electron transfer reactivity and DNA binding affinity of CRYD and also performed supplementary experiments. The average electronic coupling matrix elements value for Arabidopsis thaliana CRYD (AtCRYD) was estimated to be 5.3 meV, comparable to that of Anacystis nidulans cyclobutane pyrimidine dimer PLs (AnPL) at 4.5 meV, indicating similar electron transfer reactivities. We also confirmed the DNA repair activity of AtCRYD for UV-damaged single-stranded DNA by the experimental analysis. In addition, we investigated the dynamic behavior of AtCRYD and AnPL in complex with double-stranded DNA using molecular dynamics simulations and observed the formation of a transient salt bridge between protein and DNA in AtCRYD, in contrast to AnPL in which it was formed stably. We suggested that the instability of the salt bridge between protein and DNA will lead to reduced DNA binding affinity for AtCRYD.