Statistical Theory of Protein Combinatorial Libraries

Combinatorial experiments provide new ways to probe the determinants of protein folding and to identify novel folding amino acid sequences. These types of experiments, however, are complicated both by enormous conformational complexity and by large numbers of possible sequences. Therefore, a quantitative computational theory would be helpful in designing and interpreting these types of experiment. Here, we present and apply a statistically based, computational approach for identifying the properties of sequences compatible with a given main-chain structure. Protein side-chain conformations are included in an atom-based fashion. Calculations are performed for a variety of similar backbone structures to identify sequence properties that are robust with respect to minor changes in main-chain structure. Rather than specific sequences, the method yields the likelihood of each of the amino acids at preselected positions in a given protein structure. The theory may be used to quantify the characteristics of sequence space for a chosen structure without explicitly tabulating sequences. To account for hydrophobic effects, we introduce an environmental energy that it is consistent with other simple hydrophobicity scales and show that it is effective for side-chain modeling. We apply the method to calculate the identity probabilities of selected positions of the immunoglobulin light chain-binding domain of protein L, for which many variant folding sequences are available. The calculations compare favorably with the experimentally observed identity probabilities

Analysis of forensic autopsy cases associated with epilepsy: Comparison between sudden unexpected death in epilepsy (SUDEP) and not-SUDEP groups

Background and aimsEpilepsy is a common and chronic neurological disorder characterized by seizures that increase the risk of mortality. SUDEP is the most common seizure-related category of death. The study aimed to evaluate the key characteristics between SUDEP and not-SUDEP death cases.MethodsA retrospective study of forensic autopsy cases from 2002 to 2021, performed by the Academy of Forensic Science (Ministry of Justice, China), identified a total of 31 deaths associated with epilepsy. We compared the different characteristics between individuals who died of SUDEP (SUDEP group) and individuals with epilepsy died suddenly due to unrelated causes (not-SUDEP group).Results and conclusions13 cases met the general accepted definition of SUDEP; and 18 cases were classified as not-SUDEP. The mean age of the not-SUDEP group was significantly higher than that of the SUDEP groups (p < 0.05) and there were more cases without a clear cause of epilepsy in the SUDEP group than in the not-SUDEP group (p < 0.05). Death position differed significantly between the two groups, with more cases dying in the prone position in the SUDEP group (p < 0.05). Complete autopsies were performed in 24 of the 31 cases. There were no significant differences in heart, lungs and brain weights, or in ventricular thickness (p > 0.05) between the SUDEP and not-SUDEP groups. In addition, compared to the not-SUDEP group, the SUDEP group featured a significantly more cases with coronary lesions (grades 1-3, p < 0.05). Neuropathological lesions were identified in 12 of the 13 SUDEP cases (92.3%), cardiac lesions were present in 10 cases (76.9%) and pulmonary edema and pulmonary congestion were present in all cases. The primary cause of death in 13 of the 31 cases was seizure disorder or epilepsy. The primary mechanism of death in SUDEP group was mainly asphyxia while that in the not-SUDEP group was cardiopulmonary failure (p < 0.05). Patients in the prone position had a significantly higher risk of asphyxia than those who were not. Here, we investigated the key characteristics between SUDEP and not-SUDEP death cases, which may help to facilitate forensic diagnosis in presumed SUDEP cases

Atomically dispersed quintuple nitrogen and oxygen co-coordinated zirconium on graphene-type substrate for highly efficient oxygen reduction reaction.

A cost-effective and long stability catalyst with decent electrochemical activity would play a crucial role in accelerating applications of metal-air batteries. Here, we report quintuple nitrogen and oxygen co-coordinated Zr sites on graphene (Zr-N/O-C) by using a ball-milling, solid-solution-assisted pyrolysis method. The as-prepared Zr-N/O-C catalyst with 2.93 wt % Zr shows a half-wave potential of 0.910 V, an onset potential of 1.000 V in 0.1 M KOH, impressive durability (95.1% remains after 16,000 s), and long-term stability (5 mV loss over 10,000 cycles). Zn-air batteries with the Zr-N/O-C electrode exhibit a maximum power density of 217.9 mW cm−2 and a high cycling life of over 1,000 h, exceeding the counterpart equipped with a Pt/C benchmark. Theoretical simulations demonstrate that nitrogen and oxygen dual-ligand confinement effectively tunes the d-band center and balances key intermediates binding energy of intrinsic quintuple coordination Zr sites

Multiobjective optimization algorithm for accurate MADYMO reconstruction of vehicle-pedestrian accidents

In vehicle–pedestrian accidents, the preimpact conditions of pedestrians and vehicles are frequently uncertain. The incident data for a crash, such as vehicle deformation, injury of the victim, distance of initial position and rest position of accident participants, are useful for verification in MAthematical DYnamic MOdels (MADYMO) simulations. The purpose of this study is to explore the use of an improved optimization algorithm combined with MADYMO multibody simulations and crash data to conduct accurate reconstructions of vehicle–pedestrian accidents. The objective function of the optimization problem was defined as the Euclidean distance between the known vehicle, human and ground contact points, and multiobjective optimization algorithms were employed to obtain the local minima of the objective function. Three common multiobjective optimization algorithms—nondominated sorting genetic algorithm-II (NSGA-II), neighbourhood cultivation genetic algorithm (NCGA), and multiobjective particle swarm optimization (MOPSO)—were compared. The effect of the number of objective functions, the choice of different objective functions and the optimal number of iterations were also considered. The final reconstructed results were compared with the process of a real accident. Based on the results of the reconstruction of a real-world accident, the present study indicated that NSGA-II had better convergence and generated more noninferior solutions and better final solutions than NCGA and MOPSO. In addition, when all vehicle-pedestrian-ground contacts were considered, the results showed a better match in terms of kinematic response. NSGA-II converged within 100 generations. This study indicated that multibody simulations coupled with optimization algorithms can be used to accurately reconstruct vehicle-pedestrian collisions

The Ginger-shaped Asteroid 4179 Toutatis: New Observations from a Successful Flyby of Chang'e-2

On 13 December 2012, Chang'e-2 conducted a successful flyby of the near-Earth asteroid 4179 Toutatis at a closest distance of 770 $\pm$ 120 meters from the asteroid's surface. The highest-resolution image, with a resolution of better than 3 meters, reveals new discoveries on the asteroid, e.g., a giant basin at the big end, a sharply perpendicular silhouette near the neck region, and direct evidence of boulders and regolith, which suggests that Toutatis may bear a rubble-pile structure. Toutatis' maximum physical length and width are (4.75 $\times$ 1.95 km) $\pm$10$\%$, respectively, and the direction of the +$z$ axis is estimated to be (250$\pm$5$^\circ$, 63$\pm$5$^\circ$) with respect to the J2000 ecliptic coordinate system. The bifurcated configuration is indicative of a contact binary origin for Toutatis, which is composed of two lobes (head and body). Chang'e-2 observations have significantly improved our understanding of the characteristics, formation, and evolution of asteroids in general.Comment: 21 pages, 3 figures, 1 tabl

Postoperative ctDNA detection predicts relapse but has limited effects in guiding adjuvant therapy in resectable stage I NSCLC

BackgroundTo date, identifying resectable stage I non-small cell lung cancer (NSCLC) patients likely to benefit from adjuvant therapy (ADT) remains a major challenge. Previous studies suggest that circulating tumor DNA (ctDNA) is emerging as a promising biomarker for NSCLC. However, the effectiveness of ctDNA detection in guiding ADT for resectable stage I NSCLC patients remains elusive. This study aimed to elucidate the role of ctDNA detection in estimating prognosis and guiding ADT for resectable stage I NSCLC patients.MethodsIndividual patient data and ctDNA results data were collected from 270 patients across four independent cohorts. The detection of ctDNA was conducted at 3 days to 1 month after surgery. The endpoint for this study was relapse-free survival (RFS) and overall survival (OS).ResultsOf the 270 resectable stage I NSCLC patients, 9 patients with ctDNA-positive and 261 patients with ctDNA-negative. We found that the risk of recurrence was significantly lower in the ctDNA-negative group compared to the ctDNA-positive group(HR=0.11, p<0.0001). However, there is no difference in the risk of death between the two groups (p =0.39). In the ctDNA-positive group, there were no significant differences in RFS between patients who received ADT and patients who did not receive ADT (p =0.58). In the ctDNA-negative group, those who received ADT had a worse RFS in comparison with those who did not receive ADT (HR=2.36, p =0.029). No difference in OS was seen between patients who received ADT and patients who did not receive ADT in both the ctDNA-positive group and the ctDNA-negative group (All p values>0.05). Furthermore, there was no difference in RFS and OS between patients who received chemotherapy-based or tyrosine kinase inhibitor-based ADT and patients who did not receive ADT in both the ctDNA-positive group and the ctDNA-negative group (All p values>0.05).ConclusionsPostoperative ctDNA detection can be a prognostic marker to predict recurrence but has limited effects in guiding ADT for resectable stage I NSCLC. Future prospective investigations are needed to verify these results

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Statistical theory of combinatorial library of proteins with negative design and biased Monte Carlo method for protein sequence optimization and sampling

Combinatorial experiments provide a way to study a large number (10 4–1012) of protein sequences at the same time. Sequences are created with a desired degree of diversity and screened for the evidence of folding to a predetermined structure or specific functional properties. The exponentially huge number (10130 for a 100-residue protein) of possible sequences, however, complicates combinatorial experiments. A statistical theory for combinatorial library design of folding proteins is developed. The theory addresses the whole space of available compositions, not just the small fraction that is accessible to experiment and to computational enumeration and sampling. The theory takes as input a target backbone structure and a scoring or energy function for quantifying sequence-structure compatibility and yields the site-specific amino acid probabilities. The theory is formulated to include not only the energy of the target structure but also elements of negative design. The theory is tested using a simple lattice model, and excellent agreement with exact enumeration results is observed. The theory is applied to an all-atom protein. Atomistic and simplified potentials for protein design are examined. A Mean Field bias Monte Carlo (MFBMC) method is developed that utilizes the identity probabilities from the statistical theory for protein sequence optimization and sampling. Comparing with the classic Monte Carlo and configurational bias Monte Carlo methods, the MFBMC is more efficient for sequence design and sampling in most cases. Using a cluster variational method, the statistical theory is also formulated to directly address correlations among residue sites. In an application using a higher order foldability criterion, superposition approximations for three-body and four-body probabilities give excellent results