Macromolecular ab initio phasing enforcing secondary and tertiary structure.

Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors' approach relies on the combination of locating model fragments such as polyalanine α-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a 'still-life', but some are correct enough for density modification and main-chain tracing to reveal the protein's true portrait. Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases

Grotta dell\u2019Acqua Mintina a peculiar geosite with the smell of sulfur

Riassunto La grotta dell\u2019Acqua Mintina (comune di Butera, Caltanissetta, Sicilia) si estende per una lunghezza totale di 140 m nel Calcare di Base di et\ue0 messiniana (Miocene superiore) ed \ue8 caratterizzata dalla spettacolare presenza di concrezioni e cristalli di zolfo nativo e gesso secondario. Lo zolfo si \ue8 formato sulle pareti e sul soffitto della grotto in cristalli fino a 1 cm di lunghezza e in concrezioni microcristalline di forma botroidale, a nuvola, a popcorn e a \u201cmensola\u201d. Il gesso \ue8 presente in aggregati cristallini aciculari, prismatici e fibrosi con cristalli fino a 3 cm di lunghezza. La grotta mostra morfologie non compatibili con i consueti fenomeni carsici ma legate ad attacco acido su calcare. L\u2019acido solforico \ue8 stato generato in corrispondenza della falda acquifera per miscelazione di acque ricche di H2S risalite dai sedimenti sottostanti con acque ricche in ossigeno infiltrate dalla superficie. Il gesso si \ue8 formato attraverso il fenomeno della condensazione-corrosione di acido solforico sulle pareti calcaree della grotta, mentre lo zolfo si \ue8 formato per degassamento di H2S e CO2 al di sotto della superficie dell\u2019acqua, con parziale ossidazione dell\u2019acido solfidrico. L\u2019acido solfidrico \ue8 stato a sua volta generato dalla degradazione dei sedimenti ricchi in materia organica del Tripoli che si trovano immediatamente al di sotto del Calcare di Base e/o per riduzione batterica del gesso primario della Formazione di Pasquasia affiorante al di sopra. La grotta, per la presenza di spettacolari concrezioni di zolfo e gesso, rappresenta un geosito di interesse nazionale da tutelare e conservare attivamente.The Acqua Mintina cave (Butera, Caltanissetta, Sicily) cuts for a total length of 140 m the Messinian Calcare di base unit and is characterized by the spectacular, and fortunately still poorly degraded, presence of native sulfur and secondary gypsum. The sulfur occurs on the walls and ceiling in crystals up to 1 cm in length and centimeter-thick microcrystalline botroydal, cloud, popcorn, and folia concretions. Gypsum is present in acicular, prismatic and fibrous crystal aggregates consisting of crystals of up to 3 cm in length. The cave shows karst morphologies due to acid attack on limestone and not the usual dissolution by water flow. The organic-rich Tripoli sediments below the Calcare di Base unit and/or the bacterial reduction of gypsum from the Upper Gypsum unit probably provided the original H2S. Sulfuric acid was generated when H2S-rich water encountered oxygen-rich water at or near the water table. Gypsum formed by condensation-corrosion of sulfuric acid on the cave walls, while the sulfur concretion probably formed where H2S and CO2 were outgassing below the water surface, with the H2S partially oxidizing to sulfur. The cave for its widespread presence of spectacular crusts of sulfur and gypsum crystals represents a rare and valuable geosite to be actively protected and preserved

Castello dei Tre Cantoni in Scicli in the light of new excavations. First observations

In connection with a research programme concerning the role of the Normans in the formation of the cultural face of medieval Europe, the Research Centre for Late Antique and Early Medieval Studies of the Institute of Archaeology and Ethnology Polish Academy of Sciences in Wrocław began excavations in Scicli based on a scientific cooperation agreement with Soprintendenza per i Beni Culturali ed Ambientali di Ragusa with the support of local volunteers. The project concerned the castle, known as Castello dei Tre Cantoni (also Castelluccio), occupying the top of the hill of S. Matteo above the town of Scicli (Fig. 1). The time of construction of both castles and their functioning period remains a subject of inquiry for archaeologists, historians, and architectural historians. The research carried out in 2018 produced the first information, documented by systematic  excavations, on the chronology of the fortification on the hill of San Matteo. Thanks to them, it was possible to discover a building workshop dating from the second half of the 14th to the first half of the 15th century and confirm the castle wall’s construction (reconstruction?) at the same time. Both the stratigraphy and the 14C dates were obtained to confirm the castle’s functioning from the 2nd half of the 14th century.In connection with a research programme concerning the role of the Normans in the formation of the cultural face of medieval Europe, the Research Centre for Late Antique and Early Medieval Studies of the Institute of Archaeology and Ethnology Polish Academy of Sciences in Wrocław began excavations in Scicli based on a scientific cooperation agreement with Soprintendenza per i Beni Culturali ed Ambientali di Ragusa with the support of local volunteers. The project concerned the castle, known as Castello dei Tre Cantoni (also Castelluccio), occupying the top of the hill of S. Matteo above the town of Scicli (Fig. 1). The time of construction of both castles and their functioning period remains a subject of inquiry for archaeologists, historians, and architectural historians. The research carried out in 2018 produced the first information, documented by systematic  excavations, on the chronology of the fortification on the hill of San Matteo. Thanks to them, it was possible to discover a building workshop dating from the second half of the 14th to the first half of the 15th century and confirm the castle wall’s construction (reconstruction?) at the same time. Both the stratigraphy and the 14C dates were obtained to confirm the castle’s functioning from the 2nd half of the 14th century

Implications of AlphaFold2 for crystallographic phasing by molecular replacement.

The AlphaFold2 results in the 14th edition of Critical Assessment of Structure Prediction (CASP14) showed that accurate (low root-mean-square deviation) in silico models of protein structure domains are on the horizon, whether or not the protein is related to known structures through high-coverage sequence similarity. As highly accurate models become available, generated by harnessing the power of correlated mutations and deep learning, one of the aspects of structural biology to be impacted will be methods of phasing in crystallography. Here, the data from CASP14 are used to explore the prospects for changes in phasing methods, and in particular to explore the prospects for molecular-replacement phasing using in silico models

Pendidikan Karakter Untuk Menyelamatkan Peserta Didik Dalam Keterpurukan Globalisasi

Perkembangan jaman sekarang mengarah ke era globalisasi membuat pendidikan menjadi terombang-ambing dalam ketidak pastian. Pendidikan yang keras tertanam sejak jaman pendidikan era terdahulu menanamkan beberapa dampak buruk bagi peserta didik. Setiap masuk jenjang sekolah lebih tinggi, selalu ada perpeloncoan. Masa orientasi peserta didik yang bertujuan menjadikan peserta didik tau dan lebih mengenal lingkungan sekolah di salah gunakan menjadi kearogansian dari senioritas. Pendidikan moral perlu di tanamkan dalam Pendidikan karakter anak sejak usia dini. Pendidikan karakter dapat mencegah terjadinya kebobrokan moral yang terjadi saat ini. Banyak sekali contoh insiden yang terjadi di lingkup Pendidikan yang seharsukanya tidak pantas terjadi. Pendidikan karakter berdasar oleh Pendidikan agama yang di tanamkan sejak dini di keluarga juga. Anak yang sudah memiliki benteng Pendidikan karakter akan lebih mudah di arahkan dan anak akan tau dengan persis mana yang baik dan mana yang benar. Kasus demi kasus membongkar tentang rendahnya moral peserta didik jaman sekarang yang jauh dari Pendidikan karakter yang sesuai. Penggalakan peningakatan kurikulum dari KTSP menjadi k13 adalah salah satu cara untuk memasukan Pendidikan karakter ke dalam Pendidikan dan keseharian anak sejak dini. Langkah pembaharuan ini untuk mencegah generasi yang semakin tidak terkendali karena era globalisasi. Dampak positif dan negative selalu beriringan dalam langkah setiap manusia, karena itulah mengapa selalu di lakukan peningkatan dalam Pendidikan. Langkah demi langkah dilakukan untuk menyokong kehidupan yang lebih bermartabat dan meninggalkan cara hidup yang tanpa moral

Fragon: rapid high-resolution structure determination from ideal protein fragments

Correctly positioning ideal protein fragments by molecular replacement presents an attractive method for obtaining preliminary phases when no template structure for molecular replacement is available. This has been exploited in several existing pipelines. This paper presents a new pipeline, named Fragon, in which fragments (ideal α-helices or β-strands) are placed using Phaser and the phases calculated from these coordinates are then improved by the density-modification methods provided by ACORN. The reliable scoring algorithm provided by ACORN identifies success. In these cases, the resulting phases are usually of sufficient quality to enable automated model building of the entire structure. Fragon was evaluated against two test sets comprising mixed α/β folds and all-β folds at resolutions between 1.0 and 1.7 Å. Success rates of 61% for the mixed α/β test set and 30% for the all-β test set were achieved. In almost 70% of successful runs, fragment placement and density modification took less than 30 min on relatively modest four-core desktop computers. In all successful runs the best set of phases enabled automated model building with ARP/wARP to complete the structure

Evaluation of model refinement in CASP13.

Performance in the model refinement category of the 13th round of Critical Assessment of Structure Prediction (CASP13) is assessed, showing that some groups consistently improve most starting models whereas the majority of participants continue to degrade the starting model on average. Using the ranking formula developed for CASP12, it is shown that only 7 of 32 groups perform better than a "naïve predictor" who just submits the starting model. Common features in their approaches include a dependence on physics-based force fields to judge alternative conformations and the use of molecular dynamics to relax models to local minima, usually with some restraints to prevent excessively large movements. In addition to the traditional CASP metrics that focus largely on the quality of the overall fold, alternative metrics are evaluated, including comparisons of the main-chain and side-chain torsion angles, and the utility of the models for solving crystal structures by the molecular replacement method. It is proposed that the introduction of these metrics, as well as consideration of the accuracy of coordinate error estimates, would improve the discrimination between good and very good models.Wellcome Trust Marie Sklowdowska-Curie grain for EU Horizon 202

ARCIMBOLDO on coiled coils.

ARCIMBOLDO solves the phase problem by combining the location of small model fragments using Phaser with density modification and autotracing using SHELXE. Mainly helical structures constitute favourable cases, which can be solved using polyalanine helical fragments as search models. Nevertheless, the solution of coiled-coil structures is often complicated by their anisotropic diffraction and apparent translational noncrystallographic symmetry. Long, straight helices have internal translational symmetry and their alignment in preferential directions gives rise to systematic overlap of Patterson vectors. This situation has to be differentiated from the translational symmetry relating different monomers. ARCIMBOLDO_LITE has been run on single workstations on a test pool of 150 coiled-coil structures with 15-635 amino acids per asymmetric unit and with diffraction data resolutions of between 0.9 and 3.0 Å. The results have been used to identify and address specific issues when solving this class of structures using ARCIMBOLDO. Features from Phaser v.2.7 onwards are essential to correct anisotropy and produce translation solutions that will pass the packing filters. As the resolution becomes worse than 2.3 Å, the helix direction may be reversed in the placed fragments. Differentiation between true solutions and pseudo-solutions, in which helix fragments were correctly positioned but in a reverse orientation, was found to be problematic at resolutions worse than 2.3 Å. Therefore, after every new fragment-placement round, complete or sparse combinations of helices in alternative directions are generated and evaluated. The final solution is once again probed by helix reversal, refinement and extension. To conclude, density modification and SHELXE autotracing incorporating helical constraints is also exploited to extend the resolution limit in the case of coiled coils and to enhance the identification of correct solutions. This study resulted in a specialized mode within ARCIMBOLDO for the solution of coiled-coil structures, which overrides the resolution limit and can be invoked from the command line (keyword coiled_coil) or ARCIMBOLDO_LITE task interface in CCP4i

Evaluation of template-based modeling in CASP13.

Performance in the template-based modeling (TBM) category of CASP13 is assessed here, using a variety of metrics. Performance of the predictor groups that participated is ranked using the primary ranking score that was developed by the assessors for CASP12. This reveals that the best results are obtained by groups that include contact predictions or inter-residue distance predictions derived from deep multiple sequence alignments. In cases where there is a good homolog in the wwPDB (TBM-easy category), the best results are obtained by modifying a template. However, for cases with poorer homologs (TBM-hard), very good results can be obtained without using an explicit template, by deep learning algorithms trained on the wwPDB. Alternative metrics are introduced, to allow testing of aspects of structural models that are not addressed by traditional CASP metrics. These include comparisons to the main-chain and side-chain torsion angles of the target, and the utility of models for solving crystal structures by the molecular replacement method. The alternative metrics are poorly correlated with the traditional metrics, and it is proposed that modeling has reached a sufficient level of maturity that the best models should be expected to satisfy this wider range of criteria