Advances in cryo-electron microscopy (cryoEM) for structure-based drug discovery.

Introduction: Macromolecular X-ray crystallography (XRC), nuclear magnetic resonance (NMR), and cryo-electron microscopy (cryoEM) are the primary techniques for determining atomic-level, three-dimensional structures of macromolecules essential for drug discovery. With advancements in artificial intelligence (AI) and cryoEM, the Protein Data Bank (PDB) is solidifying its role as a key resource for 3D macromolecular structures. These developments underscore the growing need for enhanced quality metrics and robust validation standards for experimental structures.

Waterless structures in the Protein Data Bank.

The absence of solvent molecules in high-resolution protein crystal structure models deposited in the Protein Data Bank (PDB) contradicts the fact that, for proteins crystallized from aqueous media, water molecules are always expected to bind to the protein surface, as well as to some sites in the protein interior. An analysis of the contents of the PDB indicated that the expected ratio of the number of water molecules to the number of amino-acid residues exceeds 1.5 in atomic resolution structures, decreasing to 0.

Metal ions in biomedically relevant macromolecular structures.

Understanding the functions of metal ions in biological systems is crucial for many aspects of research, including deciphering their roles in diseases and potential therapeutic use. Structural information about the molecular or atomic details of these interactions, generated by methods like X-ray crystallography, cryo-electron microscopy, or nucleic magnetic resonance, frequently provides details that no other method can. As with any experimental method, they have inherent limitations that sometimes lead to an erroneous interpretation.

CheckMyMetal (CMM): validating metal-binding sites in X-ray and cryo-EM data.

Identifying and characterizing metal-binding sites (MBS) within macromolecular structures is imperative for elucidating their biological functions. CheckMyMetal (CMM) is a web based tool that facilitates the interactive validation of MBS in structures determined through X-ray crystallography and cryo-electron microscopy (cryo-EM). Recent updates to CMM have significantly enhanced its capability to efficiently handle large datasets generated from cryo-EM structural analyses.

A structural role for tryptophan in proteins, and the ubiquitous Trp C-H...O=C (backbone) hydrogen bond.

Tryptophan is the most prominent amino acid found in proteins, with multiple functional roles. Its side chain is made up of the hydrophobic indole moiety, with two groups that act as donors in hydrogen bonds: the N-H group, which is a potent donor in canonical hydrogen bonds, and a polarized C-H group, which is capable of forming weaker, noncanonical hydrogen bonds. Due to adjacent electron-withdrawing moieties, C-H.

Targeted removal of the FA2 site on human albumin prevents fatty acid-mediated inhibition of Zn binding.

Zinc is required for virtually all biological processes. In plasma, Zn is predominantly transported by human serum albumin (HSA), which possesses two Zn-binding sites of differing affinities (sites A and B). Fatty acids (FAs) are also transported by HSA, with seven structurally characterized FA-binding sites (named FA1-FA7) known.

PinMyMetal: A hybrid learning system to accurately model metal binding sites in macromolecules.

Metal ions are vital components in many proteins for the inference and engineering of protein function, with coordination complexity linked to structural (4-residue predominate), catalytic (3-residue predominate), or regulatory (2-residue predominate) roles. Computational tools for modeling metal ions in protein structures, especially for transient, reversible, and concentration-dependent regulatory sites, remain immature. We present PinMyMetal (PMM), a sophisticated hybrid machine learning system for predicting zinc ion localization and environment in macromolecular structures.

A high-throughput structural system biology approach to increase structure representation of proteins from .

causes life-threatening gastrointestinal infections. It is a high-risk pathogen due to a lack of effective treatments, antimicrobial resistance, and a poorly conserved genomic core. Herein, we report 30 X-ray structures from a structure genomics pipeline spanning 13 years, representing 10.

The current role and evolution of X-ray crystallography in drug discovery and development.

Introduction: Macromolecular X-ray crystallography and cryo-EM are currently the primary techniques used to determine the three-dimensional structures of proteins, nucleic acids, and viruses. Structural information has been critical to drug discovery and structural bioinformatics. The integration of artificial intelligence (AI) into X-ray crystallography has shown great promise in automating and accelerating the analysis of complex structural data, further improving the efficiency and accuracy of structure determination.

Continuous Validation Across Macromolecular Structure Determination Process.

The overall quality of the experimentally determined structures contained in the PDB is exceptionally high, mainly due to the continuous improvement of model building and structural validation programs. Improving reproducibility on a large scale requires expanding the concept of validation in structural biology and all other disciplines to include a broader framework that encompasses the entire project. A successful approach to science requires diligent attention to detail and a focus on the future.

Structural biology and public health response to biomedical threats.

Over the course of the pandemic caused by SARS-CoV-2, structural biologists have worked hand in hand with groups developing vaccines and treatments. However, relying solely on and clinical studies may be insufficient to guide vaccination and treatment developments, and other healthcare policies during virus mutations or peaks in infections and fatalities. Therefore, it is crucial to track statistical data related to the number of infections, deaths, and vaccinations in specific regions and present it in an easy-to-understand way.

Structural and biochemical characterisation of Co-binding sites on serum albumins and their interplay with fatty acids.

Serum albumin-Co interactions are of clinical importance. They play a role in mediating the physiological effects associated with cobalt toxicity and are central to the albumin cobalt binding (ACB) assay for diagnosis of myocardial ischemia. To further understand these processes, a deeper understanding of albumin-Co interactions is required.

Structure, Mutagenesis, and QM:MM Modeling of 3-Ketosteroid Δ-Dehydrogenase from ─The Role of a New Putative Membrane-Associated Domain and Proton-Relay System in Catalysis.

3-Ketosteroid Δ-dehydrogenases (KstD) are important microbial flavin enzymes that initiate the metabolism of steroid ring A and find application in the synthesis of steroid drugs. We present a structure of the KstD from (AcmB), which contains a previously uncharacterized putative membrane-associated domain and extended proton-relay system. The experimental and theoretical studies show that the steroid Δ-dehydrogenation proceeds according to the Ping-Pong bi-bi kinetics and a two-step base-assisted elimination (E2cB) mechanism.

CMM-An enhanced platform for interactive validation of metal binding sites.

Metal ions bound to macromolecules play an integral role in many cellular processes. They can directly participate in catalytic mechanisms or be essential for the structural integrity of proteins and nucleic acids. However, their unique nature in macromolecules can make them difficult to model and refine, and a substantial portion of metal ions in the PDB are misidentified or poorly refined.

Organism-specific differences in the binding of ketoprofen to serum albumin.

Serum albumin is a circulatory transport protein that has a highly conserved sequence and structure across mammalian organisms. Its ligand-binding properties are of importance as albumin regulates the pharmacokinetics of many drugs. Due to the high degree of structural conservation between mammalian albumins, nonhuman albumins such as bovine serum albumin or animal models are often used to understand human albumin-drug interactions.

Tip60 acetylation of histone H3K4 temporally controls chromosome passenger complex localization.

The Chromosome Passenger Complex (CPC) generates chromosome autonomous signals that regulate mitotic events critical for genome stability. Tip60 is a lysine acetyltransferase that is a tumor suppressor and is targeted for proteasomal degradation by oncogenic papilloma viruses. Mitotic regulation requires the localization of the CPC to inner centromeres, which is driven by the Haspin kinase phosphorylating histone H3 on threonine 3 (H3T3ph).

New ligand-binding sites identified in the crystal structures of β-lactoglobulin complexes with desipramine.

The homodimeric β-lactoglobulin belongs to the lipocalin family of proteins that transport a wide range of hydrophobic molecules and can be modified by mutagenesis to develop specificity for novel groups of ligands. In this work, new lactoglobulin variants, FAF (I56F/L39A/M107F) and FAW (I56F/L39A/M107W), were produced and their interactions with the tricyclic drug desipramine (DSM) were studied using X-ray crystallography, calorimetry (ITC) and circular dichroism (CD). The ITC and CD data showed micromolar affinity of the mutants for DSM and interactions according to the classical one-site binding model.

Optimal structure determination from sub-optimal diffraction data.

Herein we present the newest version of the HKL-3000 system that integrates data collection, data reduction, phasing, model building, refinement, and validation. The system significantly accelerates the process of structure determination and has proven its high value for the determination of very high-quality structures. The heuristic for choosing the best approach for every step of structure determination for various quality samples and diffraction data has been optimized.

virusMED: an atlas of hotspots of viral proteins.

Metal binding sites, antigen epitopes and drug binding sites are the hotspots in viral proteins that control how viruses interact with their hosts. virusMED ( etal binding sites, pitopes and rug binding sites) is a rich internet application based on a database of atomic interactions around hotspots in 7041 experimentally determined viral protein structures. 25306 hotspots from 805 virus strains from 75 virus families were characterized, including influenza, HIV-1 and SARS-CoV-2 viruses.

Detecting anomalies in X-ray diffraction images using convolutional neural networks.

Our understanding of life is based upon the interpretation of macromolecular structures and their dynamics. Almost 90% of currently known macromolecular models originated from electron density maps constructed using X-ray diffraction images. Even though diffraction images are critical for structure determination, due to their vast amounts and noisy, non-intuitive nature, their quality is rarely inspected.

Dr. Alexander Wlodawer-celebrating five decades of service to the structural biology community.

This 75th birthday tribute to our Editorial Board member Alexander Wlodawer recounts his decades-long service to the community of structural biology researchers. His former and current colleagues tell the story of his upbringing and education, followed by an account of his dedication to quality and rigor in crystallography and structural science. The FEBS Journal Editor-in-Chief Seamus Martin further highlights Alex's outstanding contributions to the journal's success over many years.

Rapid response to emerging biomedical challenges and threats.

As part of the global mobilization to combat the present pandemic, almost 100 000 COVID-19-related papers have been published and nearly a thousand models of macromolecules encoded by SARS-CoV-2 have been deposited in the Protein Data Bank within less than a year. The avalanche of new structural data has given rise to multiple resources dedicated to assessing the correctness and quality of structural data and models. Here, an approach to evaluate the massive amounts of such data using the resource https://covid19.

Gcn5-Related Acetyltransferases (GNATs) With a Catalytic Serine Residue Can Play Ping-Pong Too.

Enzymes in the Gcn5-related acetyltransferase (GNAT) superfamily are widespread and critically involved in multiple cellular processes ranging from antibiotic resistance to histone modification. While acetyl transfer is the most widely catalyzed reaction, recent studies have revealed that these enzymes are also capable of performing succinylation, condensation, decarboxylation, and methylcarbamoylation reactions. The canonical chemical mechanism attributed to GNATs is a general acid/base mechanism; however, mounting evidence has cast doubt on the applicability of this mechanism to all GNATs.

Recognizing and validating ligands with CheckMyBlob.

Structure-guided drug design depends on the correct identification of ligands in crystal structures of protein complexes. However, the interpretation of the electron density maps is challenging and often burdened with confirmation bias. Ligand identification can be aided by automatic methods such as CheckMyBlob, a machine learning algorithm that learns to generalize ligand descriptions from sets of moieties deposited in the Protein Data Bank.