Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study

Reliably scoring and ranking candidate models of protein complexes and assigning their oligomeric state from the structure of the crystal lattice represent outstanding challenges. A community-wide effort was launched to tackle these challenges. The latest resources on protein complexes and interfaces were exploited to derive a benchmark dataset consisting of 1677 homodimer protein crystal structures, including a balanced mix of physiological and non-physiological complexes. The non-physiological complexes in the benchmark were selected to bury a similar or larger interface area than their physiological counterparts, making it more difficult for scoring functions to differentiate between them. Next, 252 functions for scoring protein-protein interfaces previously developed by 13 groups were collected and evaluated for their ability to discriminate between physiological and non-physiological complexes. A simple consensus score generated using the best performing score of each of the 13 groups, and a cross-validated Random Forest (RF) classifier were created. Both approaches showed excellent performance, with an area under the Receiver Operating Characteristic (ROC) curve of 0.93 and 0.94, respectively, outperforming individual scores developed by different groups. Additionally, AlphaFold2 engines recalled the physiological dimers with significantly higher accuracy than the non-physiological set, lending support to the reliability of our benchmark dataset annotations. Optimizing the combined power of interface scoring functions and evaluating it on challenging benchmark datasets appears to be a promising strategy.

Molecular Understanding and Practical In Silico Catalyst Design in Computational Organocatalysis and Phase Transfer Catalysis-Challenges and Opportunities

Through the lens of organocatalysis and phase transfer catalysis, we will examine the key components to calculate or predict catalysis-performance metrics, such as turnover frequency and measurement of stereoselectivity, via computational chemistry. The state-of-the-art tools available to calculate potential energy and, consequently, free energy, together with their caveats, will be discussed via examples from the literature. Through various examples from organocatalysis and phase transfer catalysis, we will highlight the challenges related to the mechanism, transition state theory, and solvation involved in translating calculated barriers to the turnover frequency or a metric of stereoselectivity. Examples in the literature that validated their theoretical models will be showcased. Lastly, the relevance and opportunity afforded by machine learning will be discussed.

Thigh and Shank, Kinetic and Potential Energies during Gait Swing Phase in Healthy Adults and Stroke Survivors

Background/Problem. Given the treatment-resistant gait deficits after stroke and known elevated energy cost of gait after stroke, it is important to study the patterns of mechanical energies of the lower limb segments. There is a dearth of information regarding mechanical energies specifically for the thigh and shank across the gait cycle. Therefore, the purpose of the current work was to characterize the following: (1) relative patterns of oscillation kinetic energy (KE) and potential energy (PE) within lower limb segments and across lower limb segments in healthy adults during the swing phase at chosen and slow gait speeds; (2) KE and PE swing phase patterns and values for stroke survivors versus healthy adults walking at slow speed; and (3) KE and PE patterns during the swing phase for two different compensatory gait strategies after stroke,. Methods. This was a gait characterization study, a two-group, parallel-cohort study of fourteen stroke survivors with gait deficits, walking at <0.4 m/s and eight adults with no gait deficits. For testing, the eight healthy adults walked at their chosen speed, and then at the imposed slow speed of <0.04 m/s. We used a standard motion capture system and calculation methods to acquire, calculate, and characterize oscillation patterns of KE and PE of the limb segments (thigh and shank) across the gait cycle. Results. In healthy adults, we identified key energy conservation mechanisms inherent in the interactions of KE and PE, both within the thigh and shank segments and across those limb segments, partially explaining the low cost of energy of the normal adult chosen speed gait pattern, and the underlying mechanism affording the known minimal set of activated muscles during walking, especially during the early swing phase. In contrast, KE was effectively absent for both healthy adults at imposed slow walking speed and stroke survivors at their very slow chosen speed, eliminating the normal conservation of energy between KE and PE within the thigh and across the thigh and shank. Moreover, and in comparison to healthy adult slow speed, stroke survivors exhibited greater abnormalities in mechanical energies patterns, reflected in either a compensatory stepping strategy (over-flexing the hip) or circumducting strategy (stiff-legged gait, with knee extended throughout the swing phase). Conclusions and contribution to the field. Taken together, these findings support targeted training to restore normal balance control and normal activation and de-activation coordination of hip, knee, and ankle muscles, respectively (agonist/antagonist at each joint), so as to eliminate the known post-stroke abnormal co-contractions; this motor training is critical in order to release the limb to swing normally in response to mechanical energies and afford the use of conservation of KE and PE energies within the thigh and across thigh and shank.

Maternal cardiovascular potential and kinetic energy indices in pre-eclamptic and small-for-gestational-age pregnancies

OBJECTIVE

Non-invasive assessment of maternal cardiovascular potential and kinetic energy can be used to derive potential-to-kinetic-energy ratio (PKR) and Smith-Madigan inotropic index (SMII), which reflect the balance between blood pressure and blood flow. The aim of this study was to evaluate PKR and SMII in pregnancies complicated by hypertensive disorders of pregnancy (HDP) and/or small-for-gestational-age (SGA) birth.

METHODS

This was a prospective study that enrolled women with a singleton pregnancy between 5 and 41 weeks' gestation. Women who developed HDP and/or SGA underwent cardiovascular profiling from 20 weeks. To establish reference ranges for PKR and SMII, women without any pre-existing medical problems at the time of booking who did not develop HDP, SGA or other complications during pregnancy were also recruited for cardiovascular profiling. Measurements of cardiovascular parameters were obtained using a non-imaging ultrasound cardiac output monitor.

RESULTS

A total of 688 women completed the study, including 626 controls, 21 cases with HDP, 19 cases with SGA and 22 cases with HDP and SGA. PKR was significantly elevated in pregnancies with placental dysfunction compared with controls (HDP only, 29.81 ± 9.5; HDP and SGA, 44.33 ± 24.27; SGA only, 31.05 ± 13.14; vs controls, 22.30 ± 7.93; all P < 0.05). SMII values were significantly lower only in cases affected by SGA alone when compared with controls (1.47 ± 0.23 W/m² vs 1.75 ± 0.40 W/m² ; P < 0.005). These differences remained statistically significant when the analysis was undertaken using multiples of the median values corrected for gestational age.

CONCLUSIONS

The findings of this study suggest that point-of-care non-invasive cardiovascular profiling using PKR and SMII may help distinguish between pregnancies affected by specific placental disorders and those exhibiting healthy cardiovascular adaptation to pregnancy. Women with HDP and/or SGA appear to have distinctive PKR and SMII profiles that reflect low kinetic energy in pregnancies with SGA and high potential energy in pregnancies affected by HDP. Finally, non-invasive assessment of potential and kinetic cardiovascular energy demonstrates physiological high-flow and low-resistance adaptation in uncomplicated pregnancies. © 2022 International Society of Ultrasound in Obstetrics and Gynecology.

Ab initio characterization of the aluminum dimer in its X 3 Π u $$ {}^3{\Pi}_u $$ and A 3 Σ g - $$ {}^3{\Sigma}_g^{-} $$ electronic states

The potential energy functions of the aluminum dimer, Al₂ , in its lowest-energy electronic states, X 3 Π u $$ {}^3{\Pi}_u $$ and A 3 Σ g - , $$ {}^3{\Sigma}_g^{-}, $$ have been determined from ab initio calculations using the multi-reference averaged coupled-pair functional method in conjunction with the correlation-consistent basis sets up to septuple-zeta quality. The core-electron correlation, scalar relativistic, and spin-orbit effects were taken into account. The vibration-rotation energy levels for both the states of Al₂ were calculated to near the "spectroscopic" accuracy. The 3 Π u $$ {}^3{\Pi}_u $$ state was unequivocally confirmed to be the electronic ground state of Al₂ , and the electronic term value T 0 $$ {T}_0 $$ of the 3 Σ g - $$ {}^3{\Sigma}_g^{-} $$ state was predicted to be 247 cm^-1 . The energies and intensities of direct electronic-vibration transitions X 3 Π u $$ {}^3{\Pi}_u $$  ↔ A 3 Σ g - $$ {}^3{\Sigma}_g^{-} $$ were predicted.

Ground-state potential energy functions and vibration-rotation energy levels of beryllium lithium and its cation

The accurate ground-state potential energy functions of the beryllium lithium dimer, BeLi, and its cation, BeLi⁺ , have been determined from ab initio calculations using the multi-reference averaged coupled-pair functional (MR-ACPF) method in conjunction with the correlation-consistent core-valence basis sets up to septuple-zeta quality. The importance of the electron correlation beyond the MR-ACPF level of approximation, scalar relativistic, and adiabatic effects was discussed. For BeLi⁺ , the similar calculation was performed using the single-reference coupled-cluster method, up to the CCSDTQ level of approximation. The vibration-rotation energy levels of the two species were predicted to near the "spectroscopic" accuracy. Strangely enough, the predicted vibrational term values do not compare well with the recent experimental data for either BeLi or BeLi⁺ , with discrepancies reaching as much as 20-60 cm^-1 for highly excited vibrational levels.

Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants

The change in the formal charge of 34 SARS-CoV-2 lineages from September 2020 to June 2021 was analyzed according to the monthly evidence of the European agency. The reported point mutations and small insertions are electrically neutral (17), positive (12), or negative (3). They had been found in the spike glycoprotein S,  in the RBD and S1/S2 regions, crucial for initiation of viral infection. The most often observed were positive mutations, especially D614G and E484K, located in the region of S1/S2 junction, and in the receptor-binding domain (RBD), respectively. They are related to G and A switching. Positive mutations are stretching equally in both areas, but in the RBD region, they are more dispersed. In the set of analyzed virus variants, the increasing tendency in the number of positively charged residues in spike protein was observed. Furthermore, the well-documented WHO classes show an increase in the COVID-19 percentage case fatality with the positive increase in the spike crucial region’s total charge. The data mining, applying classifier algorithm based on the artificial neuronal network, confirms that the value and the distribution of additional positive charge in S may be important factors enabling virus impact to immunity. This may be promoted by the stronger long-range electrostatic attraction of the virus particle to the host cell, preceding the infection. The estimation of the potential energy for the RBD approaching the angiotensin-converting enzyme (ACE2) was presented.

Verification of a Stiffness-Variable Control System with Feed-Forward Predictive Earthquake Energy Analysis

Semi-active isolation systems with controllable stiffness have been widely developed in the field of seismic mitigation. Most systems with controllable stiffness perform more robustly and effectively for far-field earthquakes than for near-fault earthquakes. Consequently, a comprehensive system that provides comparable reductions in seismic responses to both near-fault and far-field excitations is required. In this regard, a new algorithm called Feed-Forward Predictive Earthquake Energy Analysis (FPEEA) is proposed to identify the ground motion characteristics of and reduce the structural responses to earthquakes. The energy distribution of the seismic velocity spectrum is considered, and the balance between the kinetic energy and potential energy is optimized to reduce the seismic energy. To demonstrate the performance of the FPEEA algorithm, a two-degree-of-freedom structure was used as the benchmark in the numerical simulation. The peak structural responses under two near-fault and far-field earthquakes of different earthquake intensities were simulated. The isolation layer displacement was suppressed most by the FPEEA, which outperformed the other three control methods. Moreover, superior control on superstructure acceleration was also supported by the FPEEA. Experimental verification was then conducted with shaking table test, and the satisfactory performance of the FPEEA on both isolation layer displacement and superstructure acceleration was demonstrated again. In summary, the proposed FPEEA has potential for practical application to unexpected near-fault and far-field earthquakes.

Estimating Alpine Skiers' Energetics and Turn Radius Using Different Morphological Points

Alpine ski analysis has always been very challenging, mainly due to the environmental conditions, large field and rapid and dynamic skiers’ movements. Global navigation satellite system (GNSS) offers a solution adapted to outdoor testing, but the relationship between the point where the antenna is attached and the real centre of mass (CoM) position is still unknown. This article proposes to compare different points of the body used to quantify the performance of alpine skiers. 3D models of seven elite skiers performing giant slalom (GS) were built using multiple camera system and dedicated motion tracking software. CoM as well as pelvis, head and feet trajectories were deduced from the data. The potential and kinetic energies corresponding to these points were calculated, as well as the evolution of the turn radius during the turn cycle. Differences between values given by the CoM and the other morphological points were analyzed. The pelvis offered the best estimation of the CoM: No differences were found for the biomechanical parameters, except for the kinetic energy, where 2% of the turn cycle had significant different values. The head was less accurate compared to the pelvis, showing significant differences with CoM between 7 and 20% of the turn cycle depending on the parameter. Finally, the feet offered the worst results, with significant differences between 16 and 41% of the turn cycle. Energies and turn radius calculated by using pelvis in place of CoM offered similar patterns, allowing the analysis of mechanical and dissipation energy in GS. This may potentially enable easier testing methods to be proposed and tested.

Analytical Approaches to Improve Accuracy in Solving the Protein Topology Problem

To take advantage of recent advances in genomics and proteomics it is critical that the three-dimensional physical structure of biological macromolecules be determined. Cryo-Electron Microscopy (cryo-EM) is a promising and improving method for obtaining this data, however resolution is often not sufficient to directly determine the atomic scale structure. Despite this, information for secondary structure locations is detectable. De novo modeling is a computational approach to modeling these macromolecular structures based on cryo-EM derived data. During de novo modeling a mapping between detected secondary structures and the underlying amino acid sequence must be identified. DP-TOSS (Dynamic Programming for determining the Topology Of Secondary Structures) is one tool that attempts to automate the creation of this mapping. By treating the correspondence between the detected structures and the structures predicted from sequence data as a constraint graph problem DP-TOSS achieved good accuracy in its original iteration. In this paper, we propose modifications to the scoring methodology of DP-TOSS to improve its accuracy. Three scoring schemes were applied to DP-TOSS and tested: (i) a skeleton-based scoring function; (ii) a geometry-based analytical function; and (iii) a multi-well potential energy-based function. A test of 25 proteins shows that a combination of these schemes can improve the performance of DP-TOSS to solve the topology determination problem for macromolecule proteins.

Two Perturbations for Geometry Optimization of Off-lattice Bead Protein Models

Referring to the optimization algorithm previously developed for atomic clusters, the present author develops an efficient method for geometry optimization of a coarse-grained protein model expressed with two kinds of beads (hydrophilic and hydrophobic ones). In the method, two types of geometrical perturbations, center-directed bead move and one bead rotation, are used to explore new configurations and local optimizations are performed after the perturbations. The center-directed bead move is used for hydrophobic beads and the one bead rotation is performed for both hydrophobic and hydrophilic beads. The optimization method was applied to protein models consisting of 13, 20, 21, and 34 beads. The present method produced the global minima of the 13-, 21-, and 34-bead models reported in the literature and updated the lowest energies of the protein models with 20 beads. These results indicate that the present method is efficient for searching for optimal structures of proteins.

Molecular characterization influencing metal resistance in the Cupriavidus/Ralstonia genomes

Our environment is stressed with a load of heavy and toxic metals. Microbes, abundant in our environment, are found to adapt well to this metal-stressed condition. A comparative study among five Cupriavidus/Ralstonia genomes can offer a better perception of their evolutionary mechanisms to adapt to these conditions. We have studied codon usage among 1051 genes common to all these organisms and identified 15 optimal codons frequently used in highly expressed genes present within 1051 genes. We found the core genes of Cupriavidus metallidurans CH34 have a different optimal codon choice for arginine, glycine and alanine in comparison with the other four bacteria. We also found that the synonymous codon usage bias within these 1051 core genes is highly correlated with their gene expression. This supports that translational selection drives synonymous codon usage in the core genes of these genomes. Synonymous codon usage is highly conserved in the core genes of these five genomes. The only exception among them is C. metallidurans CH34. This genomewide shift in synonymous codon choice in C. metallidurans CH34 may have taken place due to the insertion of new genes in its genomes facilitating them to survive in heavy metal containing environment and the co-evolution of the other genes in its genome to achieve a balance in gene expression. Structural studies indicated the presence of a longer N-terminal region containing a copper-binding domain in the cupC proteins of C. metallidurans CH3 that helps it to attain higher binding efficacy with copper in comparison with its orthologs.

Multiple roads lead to Rome: combined high-intensity aerobic and strength training vs. gross motor activities leads to equivalent improvement in executive functions in a cohort of healthy older adults

The effects of physical activity on cognition in older adults have been extensively investigated in the last decade. Different interventions such as aerobic, strength, and gross motor training programs have resulted in improvements in cognitive functions. However, the mechanisms underlying the relationship between physical activity and cognition are still poorly understood. Recently, it was shown that acute bouts of exercise resulted in reduced executive control at higher relative exercise intensities. Considering that aging is characterized by a reduction in potential energy ([Formula: see text] max - energy cost of walking), which leads to higher relative walking intensity for the same absolute speed, it could be argued that any intervention aimed at reducing the relative intensity of the locomotive task would improve executive control while walking. The objective of the present study was to determine the effects of a short-term (8 weeks) high-intensity strength and aerobic training program on executive functions (single and dual task) in a cohort of healthy older adults. Fifty-one participants were included and 47 (age, 70.7 ± 5.6) completed the study which compared the effects of three interventions: lower body strength + aerobic training (LBS-A), upper body strength + aerobic training (UBS-A), and gross motor activities (GMA). Training sessions were held 3 times every week. Both physical fitness (aerobic, neuromuscular, and body composition) and cognitive functions (RNG) during a dual task were assessed before and after the intervention. Even though the LBS-A and UBS-A interventions increased potential energy to a higher level (Effect size: LBS-A-moderate, UBS-A-small, GMA-trivial), all groups showed equivalent improvement in cognitive function, with inhibition being more sensitive to the intervention. These findings suggest that different exercise programs targeting physical fitness and/or gross motor skills may lead to equivalent improvement in cognition in healthy older adults. Such results call for further investigation of the multiple physiological pathways by which physical exercise can impact cognition in older adults.

Electrostatic interaction between dipoles and side chains in the voltage sensor domain of K(+) channel

Background:

It is well known that α-helices of protein, possessing equal and opposite charged ends, behaves like a macrodipole, but the relative importance of such macrodipoles to the aggregation of a pair of helix in the voltage sensor domain (VSD) of K+ ion channel, has not been assessed. In the VSD, importance has been given primarily to the helically arranged Arginine residues of helix, but the role of the charged residues of S3b is less focused.

Method and Objective:

Applying electrostatic theory, we have studied the interaction between the charges of S3b-S4 α-helix pair of KvAP through virtual mutagenesis.

Result and Conclusion:

We have shown that the terminal charges arising from the inherent dipolar property of α-helices play an important role in affecting the stability of the S3b-S4 pair, and in determining its spatial position at zero transmembrane potential. Moreover, the negatively charged side chain of S3b was found to be the primary stabilizing factor in holding S3b-S4 pair together as a “paddle”. Comparison of sequences of S3b helix of K+ channels from different species showed a previously unreported positional conservation of negative residues, highlighting their functional importance. These charges may contribute to the energetic of α-helix movements in an electric field.

Interparticle Interactions and Self-Assembly of Functionalized Nanodiamonds

Although unpassivated detonation nanodiamonds are known to form tightly bound (and sometimes ordered) superstructures, in most high performance applications the surface are deliberately functionalized, and this can profoundly alter the aggregation behavior. In the present study, we model the aggregation of functionalized nanodiamonds and show that functionalization greatly reduces the Coulombic interactions characteristic of unsaturated particles. Our results provide new insights into the interactions of functionalized nanoparticles.

On the Origin of the Energy Gain in Epitaxial Growth of Molecular Films

The material properties of organic thin films depend strongly on their order. The different types of epitaxy may complicate the exploration of the large variety of ordered systems and its exploitation in potential electronic devices. In this Letter, we develop a coherent description of the driving force that creates epitaxial systems. We focus on flat-lying organic adsorbates and explain the energy gain in commensurate, point-on-line, and line-on-line epitaxy. We use potential energy maps to visualize our concept and to derive a relation that allows anticipating epitaxial growth from low-energy electron diffraction (LEED) data. A unified description facilitates the identification and interpretation of experimentally observed adsorbate structures, whereas the rationalized expectation from LEED means a considerable speed gain if suitable candidates for organic-organic epitaxy are searched for in a combinatory approach.