Effect of Direct and Water-Mediated Interactions on the Identification of Hotspots in Biomolecular Complexes with Multiple Subsystems.

Identification of important residues in biochemical complexes is often a crucial step for many problems in molecular biology and biochemistry. A method is proposed to identify hotspots in biomolecular complexes based on a new metric, derived from networks representing molecular subunits (residues, bridging solvent molecules, ligands etc.) connected by interactions. A singular value decomposition of the weighted adjacency matrix is used to construct a scalar rank for each subunit that reflects its importance in the residue interaction network. This metric is called the singular value centrality. In addition, a new formalism is proposed to account for water-mediated interactions in the ranking of residues. Interactions for a residue network can be provided by various computational methods. In this work interactions are obtained from full quantum-mechanical calculations of protein-protein complexes using the fragment molecular orbital method. The ranking results are shown to be in good agreement with earlier computational and experimental studies. The developed method can be used to gain a deeper insight into the role of subunits in complex biomolecular systems.

How E-, L-, and P-Selectins Bind to sLex and PSGL-1: A Quantification of Critical Residue Interactions.

Selectins and their ability to interact with specific ligands are a cornerstone in cell communication. Over the last three decades, a considerable wealth of experimental and molecular modeling insights into their structure and modus operandi were gathered. Nonetheless, explaining the role of individual selectin residues on a quantitative level remained elusive, despite its importance in understanding the structure-function relationship in these molecules and designing their inhibitors. This work explores essential interactions of selectin-ligand binding, employing a multiscale approach that combines molecular dynamics, quantum-chemical calculations, and residue interaction network models. Such an approach successfully reproduces most of the experimental findings. It proves to be helpful, with the potential for becoming an established tool for quantitative predictions of residue contribution to the binding of biomolecular complexes. The results empower us to quantify the importance of particular residues and functional groups in the protein-ligand interface and to pinpoint differences in molecular recognition by the three selectins. We show that mutations in the E-, L-, and P-selectins, e.g., different residues in positions 46, 85, 97, and 107, present a crucial difference in how the ligand is engaged. We assess the role of sulfation of tyrosine residues in PSGL-1 and suggest that TyrSO3- in position 51 interacting with Arg85 in P-selectin is a significant factor in the increased affinity of P-selectin to PSGL-1 compared to E- and L-selectins. We propose an original pharmacophore targeting five essential PSGL-binding sites based on the analysis of the selectin···PSGL-1 interactions.

Comparing walking and running in persistence hunting.

It has been proposed that humans' exceptional locomotor endurance evolved partly with foraging in hot open habitats and subsequently about 2 million years ago with persistence hunting, for which endurance running was instrumental. However, persistence hunting by walking, if successful, could select for locomotor endurance even before the emergence of any running-related traits in human evolution. Using a heat exchange model validated here in 73 humans and 55 ungulates, we simulated persistence hunts for prey of three sizes (100, 250, and 400 kg) and three sweating capacities (nonsweating, low, high) at 6237 combinations of hunter's velocity (1-5 m s-1, intermittent), air temperature (25-45 °C), relative humidity (30-90%), and start time (8:00-16:00). Our simulations predicted that walking would be successful in persistence hunting of low- and nonsweating prey, especially under hot and humid conditions. However, simulated persistence hunts by walking yielded a 30-74% lower success rate than hunts by running or intermittent running. In addition, despite requiring 10-30% less energy, successful simulated persistence hunts by walking were twice as long and resulted in greater exhaustion of the hunter than hunts by running and intermittent running. These shortcomings of pursuit by walking compared to running identified in our simulations could explain why there is only a single direct description of persistence hunting by walking among modern hunter-gatherers. Nevertheless, walking down prey could be a viable option for hominins who did not possess the endurance-running phenotype of the proposed first persistence hunter, Homo erectus. Our simulation results suggest that persistence hunting could select for both long-distance walking and endurance running and contribute to the evolution of locomotor endurance seen in modern humans.

The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides.

Quantum mechanical (QM) calculations at the level of density-functional tight-binding are applied to a protein-DNA complex (PDB: 2o8b) consisting of 3763 atoms, averaging 100 snapshots from molecular dynamics simulations. A detailed comparison of QM and force field (Amber) results is presented. It is shown that, when solvent screening is taken into account, the contributions of the backbones are small, and the binding of nucleotides in the double helix is governed by the base-base interactions. On the other hand, the backbones can make a substantial contribution to the binding of amino acid residues to nucleotides and other residues. The effect of charge transfer on the interactions is also analyzed, revealing that the actual charge of nucleotides and amino acid residues can differ by as much as 6 and 8% from the formal integer charge, respectively. The effect of interactions on topological models (protein -residue networks) is elucidated.

Residue Folding Degree-Relationship to Secondary Structure Categories and Use as Collective Variable.

Recently, we have shown that the residue folding degree, a network-based measure of folded content in proteins, is able to capture backbone conformational transitions related to the formation of secondary structures in molecular dynamics (MD) simulations. In this work, we focus primarily on developing a collective variable (CV) for MD based on this residue-bound parameter to be able to trace the evolution of secondary structure in segments of the protein. We show that this CV can do just that and that the related energy profiles (potentials of mean force, PMF) and transition barriers are comparable to those found by others for particular events in the folding process of the model mini protein Trp-cage. Hence, we conclude that the relative segment folding degree (the newly proposed CV) is a computationally viable option to gain insight into the formation of secondary structures in protein dynamics. We also show that this CV can be directly used as a measure of the amount of α-helical content in a selected segment.

Dehydration and persistence hunting in Homo erectus.

Persistence hunting has been suggested to be a key strategy for meat acquisition in Homo erectus. However, prolonged locomotion in hot conditions is associated with considerable water losses due to sweating. Consequently, dehydration has been proposed to be a critical limiting factor, effectively curtailing the usefulness of persistence hunting prior to the invention of water containers. In this study, we aimed to determine the extent to which dehydration limited persistence hunting in H. erectus. We simulated ambient conditions and spatiotemporal characteristics of nine previously reported persistence hunts in the Kalahari. We used a newly developed and validated heat exchange model to estimate the water loss in H. erectus and a recent Kalahari hunter. Water loss equivalent to 10% of the hunter's body mass was considered the physiological limit of a hunt with no drinking. Our criterion for ruling dehydration out of being a limit for persistence hunting was the ability to hunt without drinking for at least 5 h, as this was the longest duration reported for a successful persistence hunt of large prey. Our results showed that H. erectus would reach the dehydration limit in 5.5-5.7 h of persistence hunting at the reported Kalahari conditions, which we argue represent a conservative model also for Early Pleistocene East Africa. Maximum hunt duration without drinking was negatively related to the relative body surface area of the hunter. Moreover, H. erectus would be able to persistence hunt over 5 h without drinking despite possible deviations from modern-like heat dissipation capacity, aerobic capacity, and locomotor economy. We conclude that H. erectus could persistence hunt large prey without the need to carry water.

Protein Dynamics and the Folding Degree.

The analysis of folding trajectories for proteins is an open challenge. One of the problems is how to describe the amount of folded secondary structure in a protein. We extend the use of Estradas' folding degree (Bioinformatics 2002, 18, 697) for the analysis of the evolution of the folding stage during molecular dynamics (MD) simulation. It is shown that residue contribution to the total folding degree is a predominantly local property, well-defined by the backbone dihedral angles at the given residue, without significant contribution from the backbone conformation of other residues. Moreover, the magnitude of this residue contribution can be quite easily associated with characteristic motifs of secondary protein structures such as the α-helix, ß-sheet (hairpin), and so on by means of a Ramachandran-like plot as a function of backbone dihedral angles φ,ψ. Additionally, the understanding of the free energy profile associated with the folding process becomes much simpler. Often a 1D profile is sufficient to locate global minima and the corresponding structure for short peptides.

Ab initio relativistic potential energy surfaces of benzene-Xe complex with application to intermolecular vibrations.

The benzene-Xe (BXe) complex in its electronic ground state is studied using ab initio methods. Since this complex contains the heavy Xe atom, the relativistic effects cannot be neglected. We test two different approaches that describe the scalar relativistic effects in the framework of the coupled-cluster level of theory with single, double, and perturbative triple excitations, used for the interaction energy calculations. The first one is based on the small core pseudopotential (PP), and the second one is based on the explicit treatment of scalar relativistic effects using the Douglas-Kroll-Hess (DKH) Hamiltonian. A few basis sets are tested with the PP and DKH, and for each one, the analytical potential energy surface (PES) is constructed. It is shown that the difference between PESs determined with PP and DKH methods is small, if the orbitals of the 4d subshell in Xe are correlated. We select the most appropriate approach for the calculation of the potential energy surface of BXe, with respect to accuracy and computational cost. The optimal level of theory includes a small Dunning's basis set for the benzene monomer and a larger PP basis set for Xe supplemented by midbond functions. The PES obtained using such an approach provides a reasonable accuracy when compared to the empirical one derived from the microwave spectra of BXe. The empirical and the theoretical values of intermolecular vibrational energies agree within 0.5 cm-1 up to second overtones. The vibrational energy level pattern of BXe is characterized by a distinct polyad structure.

Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins.

Nontargeted parallel cascade selection molecular dynamics (nt-PaCS-MD) is a method for enhanced conformational sampling of proteins. To search a broad conformational subspace, nt-PaCS-MD repeats cycles of conformational resampling from relevant initial structures. Generally, the conformational sampling efficiency of nt-PaCS-MD depends on a selection rule for the initial structures. In the original nt-PaCS-MD, the initial structures were selected by referring to structural distributions of protein configurations generated by conformational resampling (multiple short-time MD simulations). However, their structural redundancy among the initial structures was neglected for the cycles of conformational resampling, indicating that similar protein configurations might be frequently specified and resampled in every cycle in the original nt-PaCS-MD. To reduce the possibility of resampling from redundant initial structures, we propose an alternative selection rule that accounts for structural similarity among the initial structures. Specifically, a pairwise root-mean-square deviation (RMSD) is defined for all of the initial structures selected for all of the past cycles. Then a set of protein configurations with a larger pairwise RMSD is sequentially specified and resampled in the next cycle, which is regarded to as a history-dependent selection of initial structures by considering a profile of the past specified initial structures. The present scheme, termed extended nt-PaCS-MD, prevents us from resampling a set of redundant protein configurations. To check the conformational sampling efficiency of the extended nt-PaCS-MD, we used a middle-sized protein, T4 lysozyme, in explicit water. Through the assessment, this extended nt-PaCS-MD identified the open-closed transitions of T4 lysozyme more efficiently than the original nt-PaCS-MD.

Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations.

In modern praxis, a knowledge-driven design of pharmaceutical compounds relies heavily on protein structure data. Nonetheless, quantification of the interaction between protein and ligand is of great importance in the theoretical evaluation of the ability of a pharmaceutical compound to comply with certain expectations. The FMO (fragment molecular orbital) method is handy in this regard. However, the physical complexity and the number of the interactions within a protein-ligand complex renders analysis of the results somewhat complicated. This situation prompted us to develop the 3D-visualization of interaction energies in protein (3D-VIEP) method; the toolkit AnalysisFMO, which should enable a more efficient and convenient workflow with FMO data generated by quantum-chemical packages such as GAMESS, PAICS, and ABINIT-MP. AnalysisFMO consists of two separate units, RbAnalysisFMO, and the PyMOL plugins. The former can extract interfragment interaction energies (IFIEs) or pair interaction energies (PIEs) from the FMO output files generated by the aforementioned quantum-chemical packages. The PyMOL plugins enable visualization of IFIEs or PIEs in the protein structure in PyMOL. We demonstrate the use of this tool on a lectin protein from Burkholderia cenocepacia in which FMO analysis revealed the existence of a new interaction between Gly84 and fucose. Moreover, we found that second-shell interactions are crucial in forming the sugar binding site. In the case of bilirubin oxidase from Myrothecium verrucaria (MvBO), we predict that interactions between Asp105 and three His residues (His401, His403, and His136) are essential for optimally positioning the His residues to coordinate Cu atoms to form one Type 2 and two Type 3 Cu ions.

Error in the estimation of periosteal and endosteal contours from micro-CT scans for nonadult tibiae and humeri.

OBJECTIVES: This article summarized errors obtained by diverse techniques used for the derivation of cross-sectional contours in nonadult humeri and tibiae. MATERIALS AND METHODS: We analyzed cross-sectional contours in a total sample of 62 humeral and 75 tibial diaphyses in the age between birth and 12 years divided into three age groups. Long bone 35% (humeri) and midshaft (tibiae) cross-sections were taken on micro-CT images and analyzed by EPJMacro in FIJI. Properties were extracted from contours derived by manual, automatic, spline, and ellipse techniques. Agreement between techniques was assessed using manually extracted properties such as the true value using percent prediction error (%PE), reduced major axis regression, and ±95% limits of agreement. RESULTS: The lowest measurement errors were obtained for total areas, moderate errors for cortical areas and section moduli, and the highest errors for medullary areas for both bones. Derivation of humeral nonadult cross-sectional properties is less sensitive to the technique used for derivation of periosteal and endosteal contours, reaching mean %PEs below 5%. In contrast, tibial nonadult cross-sectional properties are more sensitive to the technique used and exceed 5% for some combinations. DISCUSSION: Automatic techniques provide reasonably high agreement with manually extracted contours for nonadult humeri but low agreement for tibiae. Semiautomatic approaches-spline and ellipse techniques-may reduce the error for all studied properties in tibiae, especially when combined with manually traced periosteal contours. The positive effect of the semiautomatic technique on measurement error is low for humeri.

Molecular association model of PPARα and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARMα.

Peroxisome proliferator-activated receptor-α (PPARα) is a ligand-activated transcription factor involved in the regulation of lipid homeostasis and improves hypertriglyceridemia. Pemafibrate is a novel selective PPARα modulator (SPPARMα) that activates PPARα transcriptional activity. Here, we computationally constructed the structure of the human PPARα in a complex with pemafibrate, along with that of hPPARα complexed with the classical fenofibrate, and studied their interactions quantitatively by using the first-principles calculations-based fragment molecular orbital (FMO) method. Comprehensive structural and protein-ligand binding elucidation along with the in vitro luciferase analysis let us to identify pemafibrate as a novel SPPARMα. Unlike known fibrate ligands, which bind only with the arm I of the Y-shaped ligand binding pocket, the Y-shaped pemafibrate binds to the entire cavity region. This lock and key nature causes enhanced induced fit in pemafibrate-ligated PPARα. Importantly, this selective modulator allosterically changes PPARα conformation to form a brand-new interface, which in turn binds to PPARα co-activator, PGC-1α, resulting in the full activation of PPARα. The structural basis for the potent effects of pemafibrate on PPARα transcriptional activity predicted by the in silico FMO methods was confirmed by in vitro luciferase assay for mutants. The unique binding mode of pemafibrate reveals a new pattern of nuclear receptor ligand recognition and suggests a novel basis for ligand design, offering cues for improving the binding affinity and selectivity of ligand for better clinical consequences. The findings explain the high affinity and efficacy of pemafibrate, which is expected to be in the clinical use soon.

Effect of deriving periosteal and endosteal contours from microCT scans on computation of cross-sectional properties in non-adults: the femur.

Derivation of periosteal and endosteal contours taken from transversal long bone cross-sections limits the accuracy of calculated biomechanical properties. Although several techniques are available for deriving both contours, the effect of these techniques on accuracy of calculated cross-sectional properties in non-adults is unknown. We examine a sample of 86 non-adult femora from birth to 12 years of age to estimate the effect of error in deriving periosteal and endosteal contours on cross-sectional properties. Midshaft cross-sections were taken from microCT scans and contours were derived using manual, fully automatic, spline, and ellipse techniques. Agreement between techniques was assessed against manually traced periosteal and endosteal contours using percent prediction error (%PE), reduced major axis analysis, and limits of agreement. The %PEs were highest in the medullary area and lowest in the total area. Mean %PEs were sufficiently below the 5% level of acceptable error, except for medullary areas, but individual values can greatly exceed this 5% boundary given the high standard deviation of %PE means and wide minimum-maximum range of %PEs. Automatic processing produces greater errors than does combination with manual, spline, and ellipse processing. Although periosteal contour is estimated with stronger agreement compared with endosteal contour, error in deriving periosteal contour has a substantially greater effect on calculated section moduli than does error in deriving endosteal contours. We observed no size effect on the resulting bias. Nevertheless, cross-sectional properties in a younger age category may be estimated with greater error compared with in an older age category. We conclude that non-adult midshaft cross-sectional properties can be derived from microCT scans of femoral diaphyses with mean error of < 5% and that derivation of endosteal contour can be simplified by the ellipse technique because fully automatic derivation of endosteal contour may increase the resulting error, especially in small samples.

Can we refine body mass estimations based on femoral head breadth?

Femoral head breadth is widely used in body mass estimation in biological anthropology. Earlier research has demonstrated that reduced major axis (RMA) equations perform better than least squares (LS) equations. Although a simple RMA equation to estimate body size from femoral head breadth is sufficient in most cases, our experiments with male skeletons from European data (including late Pleistocene and Holocene skeletal samples) and the Forensic Anthropology Data Bank data (including the W. M. Bass Donated Skeletal Collection sample) show that including femoral length or anatomically estimated stature in an equation with femoral head breadth improves body mass estimation precision. More specifically, although directional bias related to body mass is not reduced within specific samples, the total estimation error range, directional bias related to stature, and temporal fluctuation in estimation error are markedly reduced. The overall body mass estimation precision of individuals representing different temporal periods and ancestry groups (e.g., African and European ancestry) is thus improved.

The effect of age and body composition on body mass estimation of males using the stature/bi-iliac method.

The stature/bi-iliac breadth method provides reasonably precise, skeletal frame size (SFS) based body mass (BM) estimations across adults as a whole. In this study, we examine the potential effects of age changes in anthropometric dimensions on the estimation accuracy of SFS-based body mass estimation. We use anthropometric data from the literature and our own skeletal data from two osteological collections to study effects of age on stature, bi-iliac breadth, body mass, and body composition, as they are major components behind body size and body size estimations. We focus on males, as relevant longitudinal data are based on male study samples. As a general rule, lean body mass (LBM) increases through adolescence and early adulthood until people are aged in their 30s or 40s, and starts to decline in the late 40s or early 50s. Fat mass (FM) tends to increase until the mid-50s and declines thereafter, but in more mobile traditional societies it may decline throughout adult life. Because BM is the sum of LBM and FM, it exhibits a curvilinear age-related pattern in all societies. Skeletal frame size is based on stature and bi-iliac breadth, and both of those dimensions are affected by age. Skeletal frame size based body mass estimation tends to increase throughout adult life in both skeletal and anthropometric samples because an age-related increase in bi-iliac breadth more than compensates for an age-related stature decline commencing in the 30s or 40s. Combined with the above-mentioned curvilinear BM change, this results in curvilinear estimation bias. However, for simulations involving low to moderate percent body fat, the stature/bi-iliac method works well in predicting body mass in younger and middle-aged adults. Such conditions are likely to have applied to most human paleontological and archaeological samples.

Gradual decline in mobility with the adoption of food production in Europe.

Increased sedentism during the Holocene has been proposed as a major cause of decreased skeletal robusticity (bone strength relative to body size) in modern humans. When and why declining mobility occurred has profound implications for reconstructing past population history and health, but it has proven difficult to characterize archaeologically. In this study we evaluate temporal trends in relative strength of the upper and lower limb bones in a sample of 1,842 individuals from across Europe extending from the Upper Paleolithic [11,000-33,000 calibrated years (Cal y) B.P.] through the 20th century. A large decline in anteroposterior bending strength of the femur and tibia occurs beginning in the Neolithic (∼ 4,000-7,000 Cal y B.P.) and continues through the Iron/Roman period (∼ 2,000 Cal y B.P.), with no subsequent directional change. Declines in mediolateral bending strength of the lower limb bones and strength of the humerus are much smaller and less consistent. Together these results strongly implicate declining mobility as the specific behavioral factor underlying these changes. Mobility levels first declined at the onset of food production, but the transition to a more sedentary lifestyle was gradual, extending through later agricultural intensification. This finding only partially supports models that tie increased sedentism to a relatively abrupt Neolithic Demographic Transition in Europe. The lack of subsequent change in relative bone strength indicates that increasing mechanization and urbanization had only relatively small effects on skeletal robusticity, suggesting that moderate changes in activity level are not sufficient stimuli for bone deposition or resorption.

Structural Changes of the Trinuclear Copper Center in Bilirubin Oxidase upon Reduction.

Geometric and electronic structure changes in the copper (Cu) centers in bilirubin oxidase (BOD) upon a four-electron reduction were investigated by quantum mechanics/molecular mechanics (QM/MM) calculations. For the QM region, the unrestricted density functional theory (UDFT) method was adopted for the open-shell system. We found new candidates of the native intermediate (NI, intermediate II) and the resting oxidized (RO) states, i.e., NIH+ and RO0. Elongations of the Cu-Cu atomic distances for the trinuclear Cu center (TNC) and very small structural changes around the type I Cu (T1Cu) were calculated as the results of a four-electron reduction. The QM/MM optimized structures are in good agreement with recent high-resolution X-ray structures. As the structural change in the TNC upon reduction was revealed to be the change in the size of the triangle spanned by the three Cu atoms of TNC, we introduced a new index (l) to characterize the specific structural change. Not only the wild-type, but also the M467Q, which mutates the amino acid residue coordinating T1Cu, were precisely analyzed in terms of their molecular orbital levels, and the optimized redox potential of T1Cu was theoretically reconfirmed.

Benchmark CCSD-SAPT study of rare gas dimers with comparison to MP-SAPT and DFT-SAPT.

Symmetry-adapted perturbation theory (SAPT) based on coupled cluster approach with single and double excitations (CCSD) treatment of intramonomer electron correlation effects was applied to study rare gas homodimers from He2 to Kr2. The obtained benchmark CCSD-SAPT energies, including cumulant contributions to first order exchange and second-order exchange-induction terms, were then compared to their counterparts found using other methods-Møller-Plesset-SAPT based on many-body Møller-Plesset perturbation theory and DFT-SAPT based on density functional theory. The SAPT terms up to the second-order were calculated with the basis sets close to the complete basis set at the large range of interatomic distances R. It was shown that overestimation of the binding energies De found with DFT-SAPT reported in the work of Shirkov and Makarewicz [J. Chem. Phys. 142, 064102 (2015)] for Ar2 and Kr2 is mostly due to underestimation of the exchange energy Eexch(1) when comparing to the CCSD-SAPT benchmark. The CCSD-SAPT potentials were found to give the following values of the dissociation energies D0: 0.0006 cm-1 for He2, 16.71 cm-1 for Ne2, 85.03 cm-1 for Ar2, and 129.81 cm-1 for Kr2, which agree well with the values found from previously reported highly accurate ab initio supermolecular potentials and experimental data. The long-range dispersion coefficients C2n up to n = 6 that give the dispersion energy asymptotically equivalent to its SAPT counterpart were calculated from dynamic multipole polarizabilities at different levels of theory.

The impact of subsistence changes on humeral bilateral asymmetry in Terminal Pleistocene and Holocene Europe.

Analyses of upper limb bone bilateral asymmetry can shed light on manipulative behavior, sexual division of labor, and the effects of economic transitions on skeletal morphology. We compared the maximum (absolute) and directional asymmetry in humeral length, articular breadth, and cross-sectional diaphyseal geometry (CSG) in a large (n > 1200) European sample distributed among 11 archaeological periods from the Early Upper Paleolithic through the 20(th) century. Asymmetry in length and articular breadth is right-biased, but relatively small and fairly constant between temporal periods. Females show more asymmetry in length than males. This suggests a low impact of behavioral changes on asymmetry in length and breadth, but strong genetic control with probable sex linkage of asymmetry in length. Asymmetry in CSG properties is much more marked than in length and articular breadth, with sex-specific variation. In males, a major decline in asymmetry occurs between the Upper Paleolithic and Mesolithic. There is no further decline in asymmetry between the Mesolithic and Neolithic in males and only limited variation during the Holocene. In females, a major decline occurs between the Mesolithic and Neolithic, with resulting average directional asymmetry close to zero. Asymmetry among females continues to be very low in the subsequent Copper and Bronze Ages, but increases again in the Iron Age. Changes in female asymmetry result in an increase of sexual dimorphism during the early agricultural periods, followed by a decrease in the Iron Age. Sexual dimorphism again slightly declines after the Late Medieval. Our results indicate that changes in manipulative behavior were sex-specific with a probable higher impact of changes in hunting behavior on male asymmetry (e.g., shift from unimanual throwing to use of the bow-and-arrow) and food grain processing in females, specifically, use of two-handed saddle querns in the early agricultural periods and one-handed rotary querns in later agricultural periods.

Ab initio modelling of the anomeric and exo anomeric effects in 2-methoxytetrahydropyran and 2-methoxythiane corrected for intramolecular BSSE.

Accurate ab initio calculations including basis set limit (BSL) extrapolations, removal of intramolecular basis set superposition error (BSSE), solvent effect corrections, and thermal effects have been carried out to compare the structure and the anomeric and exo-anomeric effect in 2-methoxytetrahydropyran and 2-methoxythiane. The effect of intramolecular BSSE on the energetics was outlined for the first time in these types of compounds. It was found that both title compounds show comparable behaviour with respect to BSSE. The energy gap between the axial and equatorial form of 2-methoxythiane is reduced by 0.23 kcal mol(-1) due to the BSSE correction at the MP2/aug-cc-pVTZ level of theory, and in 2-methoxytetrahydropyran it is reduced by 0.21 kcal mol(-1). The intramolecular BSSE influenced also the energy differences between the gauche and trans conformers in both compounds. Energy decomposition analysis (EDA) reveals that the dominant destabilising interaction is repulsion and its primary stabilizing counterpart is the polarization interaction.