Macromolecular complexes are essential functional units in nearly all cellular processes, and their atomic-level understanding is critical for elucidating and modulating molecular mechanisms. The Protein Data Bank (PDB) serves as the global repository for experimentally determined structures of macromolecules. Structural data in the PDB offer valuable insights into the dynamics, conformation, and functional states of biological assemblies. However, the current annotation practices lack standardised naming conventions for assemblies in the PDB, complicating the identification of instances representing the same assembly. In this study, we introduce a method leveraging resources external to PDB, such as the Complex Portal, UniProt and Gene Ontology, to describe assemblies and contextualise them within their biological settings accurately. Employing the proposed approach, we assigned standard names to over 90% of unique assemblies in the PDB and provided persistent identifiers for each assembly. This standardisation of assembly data enhances the PDB, facilitating a deeper understanding of macromolecular complexes. Furthermore, the data standardisation improves the PDB's FAIR attributes, fostering more effective basic and translational research and scientific education.

• MeSH
• databáze proteinů MeSH
• konformace proteinů MeSH
• makromolekulární látky MeSH
• molekulární konformace MeSH
• translační biomedicínský výzkum * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• makromolekulární látky MeSH

Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) play a crucial role in structure-guided drug discovery and design, and also provide atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. The quality with which small-molecule ligands have been modelled in Protein Data Bank (PDB) entries has been, and continues to be, a matter of concern for many investigators. Correctly interpreting whether electron density found in a binding site is compatible with the soaked or co-crystallized ligand or represents water or buffer molecules is often far from trivial. The Worldwide PDB validation report (VR) provides a mechanism to highlight any major issues concerning the quality of the data and the model at the time of deposition and annotation, so the depositors can fix issues, resulting in improved data quality. The ligand-validation methods used in the generation of the current VRs are described in detail, including an examination of the metrics to assess both geometry and electron-density fit. It is found that the LLDF score currently used to identify ligand electron-density fit outliers can give misleading results and that better ligand-validation metrics are required.

• Klíčová slova
• PDB, Protein Data Bank, ligands, three-dimensional macromolecular structure, validation,
• MeSH
• databáze proteinů * MeSH
• konformace proteinů * MeSH
• krystalografie rentgenová MeSH
• lidé MeSH
• ligandy MeSH
• makromolekulární látky chemie   MeSH
• molekulární modely MeSH
• molekulární struktura MeSH
• proteiny analýza   chemie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• validační studie MeSH
• Názvy látek
• ligandy MeSH
• makromolekulární látky MeSH
• proteiny MeSH

With the ever-expanding toolkit of molecular viewers, the ability to visualize macromolecular structures has never been more accessible. Yet, the idiosyncratic technical intricacies across tools and the integration complexities associated with handling structure annotation data present significant barriers to seamless interoperability and steep learning curves for many users. The necessity for reproducible data visualizations is at the forefront of the current challenges. Recently, we introduced MolViewSpec (homepage: https://molstar.org/mol-view-spec/, GitHub project: https://github.com/molstar/mol-view-spec), a specification approach that defines molecular visualizations, decoupling them from the varying implementation details of different molecular viewers. Through the protocols presented herein, we demonstrate how to use MolViewSpec and its 3D view-building Python library for creating sophisticated, customized 3D views covering all standard molecular visualizations. MolViewSpec supports representations like cartoon and ball-and-stick with coloring, labeling, and applying complex transformations such as superposition to any macromolecular structure file in mmCIF, BinaryCIF, and PDB formats. These examples showcase progress towards reusability and interoperability of molecular 3D visualization in an era when handling molecular structures at scale is a timely and pressing matter in structural bioinformatics as well as research and education across the life sciences. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Creating a MolViewSpec view using the MolViewSpec Python package Basic Protocol 2: Creating a MolViewSpec view with reference to MolViewSpec annotation files Basic Protocol 3: Creating a MolViewSpec view with labels and other advanced features Support Protocol 1: Computing rotation and translation vectors Support Protocol 2: Creating a MolViewSpec annotation file.

• Klíčová slova
• 3D visualization, Protein Data Bank, interoperability, macromolecular structure, mmCIF,
• MeSH
• makromolekulární látky chemie   MeSH
• molekulární modely MeSH
• software * MeSH
• zobrazování trojrozměrné MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• makromolekulární látky MeSH

We report a rigorous investigation into the detailed structure of nanoparticles already shown to be successful drug delivery nanocarriers. The basic structure of the drug conjugates consists of an N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer bearing the anticancer drug doxorubicin (Dox) bound via a pH-sensitive hydrazone bond and a defined amount of cholesterol moieties that vary in hydrophobicity. The results show that size, anisotropy, and aggregation number N(aggr) of the nanoparticles grows with increasing cholesterol content. From ab initio calculations, we conclude that the most probable structure of HPMA copolymer-cholesterol nanoparticles is a pearl necklace structure, where ellipsoidal pearls mainly composed of cholesterol are covered by a HPMA shell; pearls are connected by bridges composed of hydrophilic HPMA copolymer chains. Using a combination of techniques, we unambiguously show that the Dox moieties are not impregnated inside a cholesterol core but are instead uniformly distributed across the whole nanoparticle, including the hydrophilic HPMA shell surface.

• MeSH
• akrylamidy chemie   MeSH
• algoritmy MeSH
• anizotropie MeSH
• cholesterol MeSH
• difrakce rentgenového záření MeSH
• doxorubicin analogy a deriváty   chemie   MeSH
• hydrofobní a hydrofilní interakce MeSH
• makromolekulární látky chemie   MeSH
• maloúhlový rozptyl MeSH
• micely MeSH
• molekulární konformace MeSH
• molekulární modely MeSH
• nanokapsle chemie   MeSH
• neutronová difrakce MeSH
• protinádorová antibiotika chemie   MeSH
• světlo MeSH
• velikost částic MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• akrylamidy MeSH
• cholesterol MeSH
• doxorubicin MeSH
• makromolekulární látky MeSH
• micely MeSH
• N-(2-hydroxypropyl)methacrylamide MeSH Prohlížeč
• nanokapsle MeSH
• protinádorová antibiotika MeSH

The new developments in Cryo-EM Single Particle Analysis are helping us to understand how the macromolecular structure and function meet to drive biological processes. By capturing many states at the particle level, it is possible to address how macromolecules explore different conformations, information that is classically extracted through 3D classification. However, the limitations of classical approaches prevent us from fully understanding the complete conformational landscape due to the reduced number of discrete states accurately reconstructed. To characterize the whole structural spectrum of a macromolecule, we propose an extension of our Zernike3D approach, able to extract per-image continuous flexibility information directly from a particle dataset. Also, our method can be seamlessly applied to images, maps or atomic models, opening integrative possibilities. Furthermore, we introduce the ZART reconstruction algorithm, which considers the Zernike3D deformation fields to revert particle conformational changes during the reconstruction process, thus minimizing the blurring induced by molecular motions.

• MeSH
• algoritmy * MeSH
• elektronová kryomikroskopie metody   MeSH
• makromolekulární látky chemie   MeSH
• molekulární konformace MeSH
• molekulární struktura MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• makromolekulární látky MeSH

Two types of clay minerals-montmorillonite and vermiculite have been chosen as a host matrix for the intercalation of methyl red (MR) in order to investigate a possible fluorescence tuning via dye-clay interactions. The effect of silicate layer charge on the structure and fluorescence of dye-clay intercalated hybrid nanostructures was investigated using combination of molecular modeling with experiment. Structure of both intercalates MR-vermiculite (MR-VER) and MR-montmorillonite (MR-MMT) exhibits high degree of structural disorder resulting in broaden emission band. The fluorescence wavelength range of MR intercalated in clays is shifted to lower wavelengths compared with the pristine MR polycrystalline sample (800 nm). Results showed the strong dependence of fluorescence band maximum on the silicate layer charge, lambda(max) = 565 nm for MR-MMT, 645 nm for MR-VER and 800 nm for the methyl red fine crystalline powder, whereas the structural disorder in the arrangement of dye molecules affects the emission band broadening.

• MeSH
• azosloučeniny chemie   MeSH
• chemické modely * MeSH
• fluorescenční barviva chemie   MeSH
• fluorescenční spektrometrie metody   MeSH
• jíl MeSH
• krystalizace metody   MeSH
• makromolekulární látky chemie   MeSH
• molekulární konformace MeSH
• molekulární modely MeSH
• nanostruktury chemie   ultrastruktura   MeSH
• nanotechnologie metody   MeSH
• počítačová simulace MeSH
• povrchové vlastnosti MeSH
• silikáty hliníku chemie   MeSH
• testování materiálů MeSH
• velikost částic MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• azosloučeniny MeSH
• fluorescenční barviva MeSH
• jíl MeSH
• makromolekulární látky MeSH
• methyl red MeSH Prohlížeč
• silikáty hliníku MeSH

Realising the importance of assessing the quality of the biomolecular structures deposited in the Protein Data Bank (PDB), the Worldwide Protein Data Bank (wwPDB) partners established Validation Task Forces to obtain advice on the methods and standards to be used to validate structures determined by X-ray crystallography, nuclear magnetic resonance spectroscopy and three-dimensional electron cryo-microscopy. The resulting wwPDB validation pipeline is an integral part of the wwPDB OneDep deposition, biocuration and validation system. The wwPDB Validation Service webserver (https://validate.wwpdb.org) can be used to perform checks prior to deposition. Here, it is shown how validation metrics can be combined to produce an overall score that allows the ranking of macromolecular structures and domains in search results. The ValTrendsDB database provides users with a convenient way to access and analyse validation information and other properties of X-ray crystal structures in the PDB, including investigating trends in and correlations between different structure properties and validation metrics.

• Klíčová slova
• PDB, Protein Data Bank, X-ray crystallography, quality control, three-dimensional macromolecular structure, validation,
• MeSH
• databáze proteinů normy   MeSH
• datové kurátorství MeSH
• elektronová kryomikroskopie MeSH
• internet * MeSH
• konformace proteinů * MeSH
• lidé MeSH
• makromolekulární látky chemie   MeSH
• molekulární modely MeSH
• nukleární magnetická rezonance biomolekulární MeSH
• proteiny analýza   chemie   MeSH
• uživatelské rozhraní počítače * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• validační studie MeSH
• Názvy látek
• makromolekulární látky MeSH
• proteiny MeSH

One of the main purposes of CryoEM Single Particle Analysis is to reconstruct the three-dimensional structure of a macromolecule thanks to the acquisition of many particle images representing different poses of the sample. By estimating the orientation of each projected particle, it is possible to recover the underlying 3D volume by multiple 3D reconstruction methods, usually working either in Fourier or in real space. However, the reconstruction from the projected images works under the assumption that all particles in the dataset correspond to the same conformation of the macromolecule. Although this requisite holds for some macromolecules, it is not true for flexible specimens, leading to motion-induced artefacts in the reconstructed CryoEM maps. In this work, we introduce a new Algebraic Reconstruction Technique called ZART, which is able to include continuous flexibility information during the reconstruction process to improve local resolution and reduce motion blurring. The conformational changes are modelled through Zernike3D polynomials. Our implementation allows for a multiresolution description of the macromolecule adapting itself to the local resolution of the reconstructed map. In addition, ZART has also proven to be a useful algorithm in cases where flexibility is not so dominant, as it improves the overall aspect of the reconstructed maps by improving their local and global resolution.

• Klíčová slova
• Cryo-Electron Microscopy (CryoEM), Zernike polynomials, Zernike3D-based Algebraic Reconstruction Technique (ZART), map reconstruction, spherical harmonics,
• MeSH
• algoritmy MeSH
• elektronová kryomikroskopie metody   MeSH
• makromolekulární látky chemie   MeSH
• počítačové zpracování obrazu * metody   MeSH
• pohyb těles MeSH
• zobrazení jednotlivé molekuly * MeSH
• zobrazování trojrozměrné metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• makromolekulární látky MeSH

Cryo-electron microscopy has established as a mature structural biology technique to elucidate the three-dimensional structure of biological macromolecules. The Coulomb potential of the sample is imaged by an electron beam, and fast semi-conductor detectors produce movies of the sample under study. These movies have to be further processed by a whole pipeline of image-processing algorithms that produce the final structure of the macromolecule. In this chapter, we illustrate this whole processing pipeline putting in value the strength of "meta algorithms," which are the combination of several algorithms, each one with different mathematical rationale, in order to distinguish correctly from incorrectly estimated parameters. We show how this strategy leads to superior performance of the whole pipeline as well as more confident assessments about the reconstructed structures. The "meta algorithms" strategy is common to many fields and, in particular, it has provided excellent results in bioinformatics. We illustrate this combination using the workflow engine, Scipion.

• Klíčová slova
• Cryo-electron microscopy, Image processing, Scipion, Single particle,
• MeSH
• algoritmy * MeSH
• elektronová kryomikroskopie metody   MeSH
• makromolekulární látky ultrastruktura   MeSH
• molekulární biologie metody   MeSH
• počítačové zpracování obrazu metody   MeSH
• průběh práce MeSH
• výpočetní biologie MeSH
• zobrazení jednotlivé molekuly metody   MeSH
• zobrazování trojrozměrné metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• makromolekulární látky MeSH

Cryo Electron Tomography (cryoET) plays an essential role in Structural Biology, as it is the only technique that allows to study the structure of large macromolecular complexes in their close to native environment in situ. The reconstruction methods currently in use, such as Weighted Back Projection (WBP) or Simultaneous Iterative Reconstruction Technique (SIRT), deliver noisy and low-contrast reconstructions, which complicates the application of high-resolution protocols, such as Subtomogram Averaging (SA). We propose a Progressive Stochastic Reconstruction Technique (PSRT) - a novel iterative approach to tomographic reconstruction in cryoET based on Monte Carlo random walks guided by Metropolis-Hastings sampling strategy. We design a progressive reconstruction scheme to suit the conditions present in cryoET and apply it successfully to reconstructions of macromolecular complexes from both synthetic and experimental datasets. We show how to integrate PSRT into SA, where it provides an elegant solution to the region-of-interest problem and delivers high-contrast reconstructions that significantly improve template-based localization without any loss of high-resolution structural information. Furthermore, the locality of SA is exploited to design an importance sampling scheme which significantly speeds up the otherwise slow Monte Carlo approach. Finally, we design a new memory efficient solution for the specimen-level interior problem of cryoET, removing all associated artifacts.

• Klíčová slova
• 3D reconstruction, Cryo electron tomography, Metropolis–Hastings, Monte Carlo, Stochastic reconstruction, Subtomogram averaging,
• MeSH
• algoritmy MeSH
• elektronová kryomikroskopie metody   MeSH
• makromolekulární látky chemie   MeSH
• metoda Monte Carlo MeSH
• počítačové zpracování obrazu metody   MeSH
• reprodukovatelnost výsledků MeSH
• ribozomy chemie   MeSH
• stochastické procesy * MeSH
• tomografie elektronová metody   MeSH
• zobrazování trojrozměrné metody   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• makromolekulární látky MeSH