Computational design of new proteins is often performed by optimizing the amino acid sequence. This sequence is characterized by an energy (lower energy means better propensity to form the desired 3D structure) that is sampled and minimized. Here, we use the parallel tempering algorithm to accelerate this task. ESMfold was used to predict the structures of the sampled proteins and calculate energy. Starting from random amino acid sequences, each sequence was sampled using the Monte Carlo method at one of a series of temperatures, and these replicas were being exchanged by the parallel tempering method. A series of 100 or 200 residue proteins was designed to maximize confidence in structure prediction and globularity and minimize surface hydrophobic residues. We show that parallel tempering is a viable alternative to Monte Carlo sampling without replica exchanges and simulated annealing or related energy-based protein design methods, especially in the situation where a continuous flow of designed sequences is desired.

• Klíčová slova
• ESMfold, Monte Carlo, machine learning, parallel tempering, protein design, replica exchange,
• MeSH
• algoritmy * MeSH
• hydrofobní a hydrofilní interakce MeSH
• konformace proteinů MeSH
• metoda Monte Carlo MeSH
• molekulární modely MeSH
• proteinové inženýrství * metody   MeSH
• proteiny * chemie   genetika   MeSH
• sekvence aminokyselin MeSH
• termodynamika MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• proteiny * MeSH

We have investigated different approaches to handling parallel-tempering Monte Carlo (PTMC) simulations in the isothermal-isobaric ensemble of molecular cluster/nanoparticle systems for predicting structural phase diagram transitions. We have implemented various methodologies that consist of treating pressure implicitly through its effect on the volume. Thus, the main problem in the simulations under nonzero pressure becomes the volume definition of the finite nonperiodic system, and we considered approaches based on the particles' coordinates. Various volume models, namely container-volume, particle-volume, average-volume, ellipsoids-volume, and convex hull-volume, were employed, and the required corrections for each of them in the Monte Carlo computations were introduced. Finally, we explored the effects of volume/pressure changes for all models on structural phase transitions of a test system, such as the small "icelike" (H2O)12 water cluster. The temperature and pressure dependence of the cluster's heat capacity and energy-volume Pearson correlation coefficient were studied, phase diagrams were constructed using a multiple-histogram method, and attempts were made to identify phase transitions to particular cluster structures. Our results show significant differences between the employed volume models, and we discuss all pressure-induced, such as solid-solid-, solid-liquid-, and liquid-gas-like, phase transformations in the present study.

• Publikační typ
• časopisecké články MeSH

Keystone mutualisms, such as corals, lichens or mycorrhizae, sustain fundamental ecosystem functions. Range dynamics of these symbioses are, however, inherently difficult to predict because host species may switch between different symbiont partners in different environments, thereby altering the range of the mutualism as a functional unit. Biogeographic models of mutualisms thus have to consider both the ecological amplitudes of various symbiont partners and the abiotic conditions that trigger symbiont replacement. To address this challenge, we here investigate 'symbiont turnover zones'--defined as demarcated regions where symbiont replacement is most likely to occur, as indicated by overlapping abundances of symbiont ecotypes. Mapping the distribution of algal symbionts from two species of lichen-forming fungi along four independent altitudinal gradients, we detected an abrupt and consistent β-diversity turnover suggesting parallel niche partitioning. Modelling contrasting environmental response functions obtained from latitudinal distributions of algal ecotypes consistently predicted a confined altitudinal turnover zone. In all gradients this symbiont turnover zone is characterized by approximately 12°C average annual temperature and approximately 5°C mean temperature of the coldest quarter, marking the transition from Mediterranean to cool temperate bioregions. Integrating the conditions of symbiont turnover into biogeographic models of mutualisms is an important step towards a comprehensive understanding of biodiversity dynamics under ongoing environmental change.

• Klíčová slova
• altitude-for-latitude, beta-diversity turnover, facilitation, lichen symbiosis, mutualist-mediated effects, range predictions,
• MeSH
• ekosystém * MeSH
• podnebí * MeSH
• symbióza * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Biomolecular simulations are routinely used in biochemistry and molecular biology research; however, they often fail to match expectations of their impact on pharmaceutical and biotech industry. This is caused by the fact that a vast amount of computer time is required to simulate short episodes from the life of biomolecules. Several approaches have been developed to overcome this obstacle, including application of massively parallel and special purpose computers or non-conventional hardware. Methodological approaches are represented by coarse-grained models and enhanced sampling techniques. These techniques can show how the studied system behaves in long time-scales on the basis of relatively short simulations. This review presents an overview of new simulation approaches, the theory behind enhanced sampling methods and success stories of their applications with a direct impact on biotechnology or drug design.

• Klíčová slova
• Alchemistic simulations, Drug design, Free energy surface, Metadynamics, Molecular dynamics simulation, Parallel tempering,
• MeSH
• metody pro přípravu analytických vzorků metody   MeSH
• simulace molekulární dynamiky * MeSH
• termodynamika MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

Tardigrada is an invertebrate phylum that often constitutes a dominant micrometazoan group on glaciers worldwide. We investigated tardigrades residing in surface ice above the equilibrium line altitude (ELA) on three temperate glaciers of New Zealand's Southern Alps. Morphological, morphometric and multilocus DNA analyses (CO1, 18S rRNA, 28S rRNA, ITS-2) revealed two new genera comprising four species, of which two are formally described here: Kopakaius gen. nov. nicolae sp. nov. and Kararehius gen. nov. gregorii sp. nov. The former is represented by three genetically distinct phyletic lineages akin to species. According to CO1, Kopakaius gen. nov. nicolae sp. nov. inhabits Whataroa Glacier only while the remaining two Kopakaius species occur on Fox and Franz Joseph Glaciers, suggesting low dispersal capabilities. Although morphological characteristics of the new genera could indicate affinity with the subfamily Itaquasconinae, phylogenetic analysis placed them confidently in the subfamily Diphasconinae. Kopakaius gen. nov. lack placoids in the pharynx similar with some Itaquasconinae, whereas dark pigmentation and claw shape aligns them with the glacier-obligate genus, Cryobiotus (subfamily Hypsibiinae), which is an example of parallel evolution. The second genus, Kararehius gen nov. could be classified as Adropion-like (subfamily Itaquasconinae), but differs greatly by genetics (placed in the subfamily Diphasconinae) as well as morphology (e.g., lack of septulum), exemplify deep stasis in Hypsibiidae. Our results suggest that glacier fragmentation during the Pleistocene triggered tardigrade speciation, making it a suitable model for studies on allopatric divergence in glacier meiofauna.

• Klíčová slova
• Accumulation zone, Biodiversity, Convergence, Cryophiles, Fox Glacier, Hypsibiidae, New species, Whataroa Glacier,
• MeSH
• fylogeneze MeSH
• ledový příkrov MeSH
• RNA ribozomální 28S genetika   MeSH
• Tardigrada * genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Nový Zéland MeSH
• Názvy látek
• RNA ribozomální 28S MeSH

OBJECTIVES: Determine community needs and perspectives as part of planning health service incorporation into Wanang Conservation Area, in support of locally driven sustainable development. DESIGN: Clinical and rapid anthropological assessment (individual primary care assessments, key informant (KI) interviews, focus groups (FGs), ethnography) with treatment of urgent cases. SETTING: Wanang (pop. c189), a rainforest community in Madang province, Papua New Guinea. PARTICIPANTS: 129 villagers provided medical histories (54 females (f), 75 males (m); median 19 years, range 1 month to 73 years), 113 had clinical assessments (51f, 62m; median 18 years, range 1 month to 73 years). 26 ≥18 years participated in sex-stratified and age-stratified FGs (f<40 years; m<40 years; f>40 years; m>40 years). Five KIs were interviewed (1f, 4m). Daily ethnographic fieldnotes were recorded. RESULTS: Of 113 examined, 11 were 'well' (a clinical impression based on declarations of no current illness, medical histories, conversation, no observed disease signs), 62 (30f, 32m) were treated urgently, 31 referred (15f, 16m), indicating considerable unmet need. FGs top-4 ranked health issues concorded with KI views, medical histories and clinical examinations. For example, ethnoclassifications of three ((A) 'malaria', (B) 'sotwin', (C) 'grile') translated to the five biomedical conditions diagnosed most ((A) malaria, 9 villagers; (B) upper respiratory infection, 25; lower respiratory infection, 10; tuberculosis, 9; (C) tinea imbricata, 15) and were highly represented in declared medical histories ((A) 75 participants, (B) 23, (C) 35). However, 29.2% of diagnoses (49/168) were limited to one or two people. Treatment approaches included plant medicines, stored pharmaceuticals, occasionally rituals. Travel to hospital/pharmacy was sometimes undertaken for severe/refractory disease. Service barriers included: no health patrols/accessible aid post, remote hospital, unfamiliarity with institutions and medicine costs. Service introduction priorities were: aid post, vaccinations, transport, perinatal/birth care and family planning. CONCLUSIONS: This study enabled service planning and demonstrated a need sufficient to acquire funding to establish primary care. In doing so, it aided Wanang's community to develop sustainably, without sacrificing their forest home.

• Klíčová slova
• anthropology, epidemiology, health services administration & management, neglected diseases, primary care, qualitative research,
• MeSH
• deštný prales * MeSH
• dospělí MeSH
• lidé MeSH
• zdravotnické služby * MeSH
• Check Tag
• dospělí MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Papua Nová Guinea MeSH

Metadynamics method has been widely used to enhance sampling in molecular simulations. Its original form suffers two major drawbacks, poor convergence in complex (especially biomolecular) systems and its serial nature. The first drawback has been addressed by introduction of a convergent variant known as well-tempered metadynamics. The second was addressed by introduction of a parallel multisystem metadynamics referred to as altruistic metadynamics. Here, we combine both approaches into well-tempered altruistic metadynamics. We provide mathematical arguments and trial simulations to show that it accurately predicts free energy surfaces.

• Publikační typ
• časopisecké články MeSH

AlphaFold is a neural network-based tool for the prediction of 3D structures of proteins. In CASP14, a blind structure prediction challenge, it performed significantly better than other competitors, making it the best available structure prediction tool. One of the outputs of AlphaFold is the probability profile of residue-residue distances. This makes it possible to score any conformation of the studied protein to express its compliance with the AlphaFold model. Here, we show how this score can be used to drive protein folding simulation by metadynamics and parallel tempering metadynamics. Using parallel tempering metadynamics, we simulated the folding of a mini-protein Trp-cage and β hairpin and predicted their folding equilibria. We observe the potential of the AlphaFold-based collective variable in applications beyond structure prediction, such as in structure refinement or prediction of the outcome of a mutation.

• Klíčová slova
• AlphaFold, collective variable, deep learning, free-energy simulation, metadynamics, protein folding, protein structure prediction,
• Publikační typ
• časopisecké články MeSH

In spite of the growth of molecular ecology, systematics and next-generation sequencing, the discovery and analysis of diversity is not currently integrated with building the tree-of-life. Tropical arthropod ecologists are well placed to accelerate this process if all specimens obtained through mass-trapping, many of which will be new species, could be incorporated routinely into phylogeny reconstruction. Here we test a shotgun sequencing approach, whereby mitochondrial genomes are assembled from complex ecological mixtures through mitochondrial metagenomics, and demonstrate how the approach overcomes many of the taxonomic impediments to the study of biodiversity. DNA from approximately 500 beetle specimens, originating from a single rainforest canopy fogging sample from Borneo, was pooled and shotgun sequenced, followed by de novo assembly of complete and partial mitogenomes for 175 species. The phylogenetic tree obtained from this local sample was highly similar to that from existing mitogenomes selected for global coverage of major lineages of Coleoptera. When all sequences were combined only minor topological changes were induced against this reference set, indicating an increasingly stable estimate of coleopteran phylogeny, while the ecological sample expanded the tip-level representation of several lineages. Robust trees generated from ecological samples now enable an evolutionary framework for ecology. Meanwhile, the inclusion of uncharacterized samples in the tree-of-life rapidly expands taxon and biogeographic representation of lineages without morphological identification. Mitogenomes from shotgun sequencing of unsorted environmental samples and their associated metadata, placed robustly into the phylogenetic tree, constitute novel DNA "superbarcodes" for testing hypotheses regarding global patterns of diversity.

• Klíčová slova
• Coleoptera, Illumina MiSeq, biodiversity, bulk samples, community ecology, metagenome skimming, mitochondrial genomes, mitochondrial metagenomics, phylogeny, tree-of-life,
• MeSH
• brouci genetika   MeSH
• deštný prales MeSH
• frekvence genu MeSH
• fylogeneze MeSH
• genetická variace MeSH
• genom mitochondriální MeSH
• hmyzí geny MeSH
• kontigové mapování MeSH
• metagenom MeSH
• mitochondrie genetika   MeSH
• sekvenční analýza DNA MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Borneo MeSH

Thermal properties and structures of the water cluster containing fifteen molecules, either pure or doped with methane, are studied via classical parallel tempering Monte Carlo calculations in the isothermal-isobaric ensemble. The main emphasis is on structural transformations the cluster undergoes with increasing temperature and pressure. A simple TIP4P interaction model is employed for water and the unified-atom approximation with a Lennard-Jones potential is used to model the methane-water interaction. The results are compared with the data obtained recently for zero temperature via evolutionary algorithm calculations [Hartke, J. Chem. Phys., 2009, 130 art. no. 024905].

• MeSH
• methan chemie   MeSH
• metoda Monte Carlo MeSH
• termodynamika * MeSH
• tlak MeSH
• voda chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• methan MeSH
• voda MeSH