Dynamics and Kinetics in Structural Biology: Unravelling Function Through Time-Resolved Structural Analysis. By Keith Moffat and Eaton E. Lattman. Wiley, New York, 2023, pp. 288. ISBN 978-1-119-69628-5. Price USD 161 (hardback), USD 128 (Kindle)
(Source: Acta Crystallographica Section D)
Source: Acta Crystallographica Section D - February 19, 2024 Category: Biochemistry Authors: Helliwell, J.R. Tags: book review dynamics kinetics structural biology time-resolved structural analysis book reviews Source Type: research
The crystal structure of mycothiol disulfide reductase (Mtr) provides mechanistic insight into the specific low-molecular-weight thiol reductase activity of Actinobacteria
Low-molecular-weight (LMW) thiols are involved in many processes in all organisms, playing a protective role against reactive species, heavy metals, toxins and antibiotics. Actinobacteria, such as Mycobacterium tuberculosis, use the LMW thiol mycothiol (MSH) to buffer the intracellular redox environment. The NADPH-dependent FAD-containing oxidoreductase mycothiol disulfide reductase (Mtr) is known to reduce oxidized mycothiol disulfide (MSSM) to MSH, which is crucial to maintain the cellular redox balance. In this work, the first crystal structures of Mtr are presented, expanding the structural knowledge and understanding ...
Source: Acta Crystallographica Section D - February 19, 2024 Category: Biochemistry Authors: Guti é rrez-Fern á ndez, J. Hersleth, H.-P. Hammerstad, M. Tags: low-molecular-weight thiols mycothiol disulfide reductase oxidoreductases redox homeostasis flavoenzymes X-ray crystallography docking protein structure Actinobacteria research papers Source Type: research
Using cryo-EM to understand the assembly pathway of respiratory complex I
Complex I (proton-pumping NADH:ubiquinone oxidoreductase) is the first component of the mitochondrial respiratory chain. In recent years, high-resolution cryo-EM studies of complex I from various species have greatly enhanced the understanding of the structure and function of this important membrane-protein complex. Less well studied is the structural basis of complex I biogenesis. The assembly of this complex of more than 40 subunits, encoded by nuclear or mitochondrial DNA, is an intricate process that requires at least 20 different assembly factors in humans. These are proteins that are transiently associated with build...
Source: Acta Crystallographica Section D - February 19, 2024 Category: Biochemistry Authors: Laube, E. Schiller, J. Zickermann, V. Vonck, J. Tags: single-particle cryo-EM respiratory complex I proton-pumping NADH ubiquinone oxidoreductase complex I assembly assembly factors research papers Source Type: research
Deciphering the crystal structure of a novel nanobody against the NEIL1 DNA glycosylase
Nanobodies (VHHs) are single-domain antibodies with three antigenic CDR regions and are used in diverse scientific applications. Here, an ∼ 14 kDa nanobody (A5) specific for the endonuclease VIII (Nei)-like 1 or NEIL1 DNA glycosylase involved in the first step of the base-excision repair pathway was crystallized and its structure was determined to 2.1 Å resolution. The crystals posed challenges due to potential twinning and anisotropic diffraction. Despite inconclusive twinning indicators, reprocessing in an orthorhombic setting and molecular replacement in space group P21212 enabled the successful modeling of 9...
Source: Acta Crystallographica Section D - January 30, 2024 Category: Biochemistry Authors: Thompson, M.K. Sharma, N. Thorn, A. Prakash, A. Tags: nanobodies X-ray crystallography pseudo-merohedral twinning orthorhombic space group NEIL1 DNA glycosylase research papers Source Type: research
Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket
To identify starting points for therapeutics targeting SARS-CoV-2, the Paul Scherrer Institute and Idorsia decided to collaboratively perform an X-ray crystallographic fragment screen against its main protease. Fragment-based screening was carried out using crystals with a pronounced open conformation of the substrate-binding pocket. Of 631 soaked fragments, a total of 29 hits bound either in the active site (24 hits), a remote binding pocket (three hits) or at crystal-packing interfaces (two hits). Notably, two fragments with a pose that was sterically incompatible with a more occluded crystal form were identified. Two is...
Source: Acta Crystallographica Section D - January 30, 2024 Category: Biochemistry Authors: Huang, C.-Y. Metz, A. Lange, R. Artico, N. Potot, C. Hazemann, J. M ü ller, M. Dos Santos, M. Chambovey, A. Ritz, D. Eris, D. Meyer, S. Bourquin, G. Sharpe, M. Mac Sweeney, A. Tags: 3CLpro SARS-CoV-2 fragment screening covalent binders surface plasmon resonance X-ray crystallography research papers Source Type: research
Structural flexibility of Toscana virus nucleoprotein in the presence of a single-chain camelid antibody
Phenuiviridae nucleoprotein is the main structural and functional component of the viral cycle, protecting the viral RNA and mediating the essential replication/transcription processes. The nucleoprotein (N) binds the RNA using its globular core and polymerizes through the N-terminus, which is presented as a highly flexible arm, as demonstrated in this article. The nucleoprotein exists in an `open' or a `closed' conformation. In the case of the closed conformation the flexible N-terminal arm folds over the RNA-binding cleft, preventing RNA adsorption. In the open conformation the arm is extended in such a way that both RNA...
Source: Acta Crystallographica Section D - January 24, 2024 Category: Biochemistry Authors: Papageorgiou, N. Baklouti, A. Lichi è re, J. Desmyter, A. Canard, B. Coutard, B. Ferron, F. Tags: Bunyavirales Toscana virus nucleoprotein flexibility research papers Source Type: research
Investigation of how gate residues in the main channel affect the catalytic activity of Scytalidium thermophilum catalase
Catalase is an antioxidant enzyme that breaks down hydrogen peroxide (H2O2) into molecular oxygen and water. In all monofunctional catalases the pathway that H2O2 takes to the catalytic centre is via the `main channel'. However, the structure of this channel differs in large-subunit and small-subunit catalases. In large-subunit catalases the channel is 15 Å longer and consists of two distinct parts, including a hydrophobic lower region near the heme and a hydrophilic upper region where multiple H2O2 routes are possible. Conserved glutamic acid and threonine residues are located near the intersection of these two regio...
Source: Acta Crystallographica Section D - January 24, 2024 Category: Biochemistry Authors: Yuzugullu Karakus, Y. Goc, G. Zengin Karatas, M. Balci Unver, S. Yorke, B.A. Pearson, A.R. Tags: catalases phenol oxidases main channel gate residues oxidoreductases Scytalidium thermophilum catalase variants research papers Source Type: research
A web-based dashboard for RELION metadata visualization
Cryo-electron microscopy (cryo-EM) has witnessed radical progress in the past decade, driven by developments in hardware and software. While current software packages include processing pipelines that simplify the image-processing workflow, they do not prioritize the in-depth analysis of crucial metadata, limiting troubleshooting for challenging data sets. The widely used RELION software package lacks a graphical native representation of the underlying metadata. Here, two web-based tools are introduced: relion_live.py, which offers real-time feedback on data collection, aiding swift decision-making during data acquisition,...
Source: Acta Crystallographica Section D - January 24, 2024 Category: Biochemistry Authors: Gonz á lez-Rodr í guez, N. Are á n-Ulloa, E. Fern á ndez-Leiro, R. Tags: cryo-electron microscopy RELION ice thickness estimation graphical user interface web-based cryo-EM tools research papers Source Type: research
The High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX), an ancillary tool for the macromolecular crystallography beamlines at the ESRF
This article describes the High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX) at the ESRF, and highlights new and complementary research opportunities that can be explored using this facility. The laboratory is dedicated to investigating interactions between macromolecules and gases in crystallo, and finds applications in many fields of research, including fundamental biology, biochemistry, and environmental and medical science. At present, the HPMX laboratory offers the use of different high-pressure cells adapted for helium, argon, krypton, xenon, nitrogen, oxygen, carbon dioxide and methane. Imp...
Source: Acta Crystallographica Section D - January 24, 2024 Category: Biochemistry Authors: Carpentier, P. van der Linden, P. Mueller-Dieckmann, C. Tags: high pressure macromolecular crystals gas derivatives protein channels HPMX High-Pressure Freezing Laboratory for Macromolecular Crystallography ESRF research papers Source Type: research
From femtoseconds to minutes: time-resolved macromolecular crystallography at XFELs and synchrotrons
Over the last decade, the development of time-resolved serial crystallography (TR-SX) at X-ray free-electron lasers (XFELs) and synchrotrons has allowed researchers to study phenomena occurring in proteins on the femtosecond-to-minute timescale, taking advantage of many technical and methodological breakthroughs. Protein crystals of various sizes are presented to the X-ray beam in either a static or a moving medium. Photoactive proteins were naturally the initial systems to be studied in TR-SX experiments using pump – probe schemes, where the pump is a pulse of visible light. Other reaction initiations through small-mole...
Source: Acta Crystallographica Section D - January 24, 2024 Category: Biochemistry Authors: Caramello, N. Royant, A. Tags: time-resolved serial crystallography synchrotrons XFELs structural photobiology reaction-intermediate states bacteriorhodopsin cryo-trapping feature articles Source Type: research
Preparation and characterization of inactivated tick-borne encephalitis virus samples for single-particle imaging at the European XFEL
X-ray imaging of virus particles at the European XFEL could eventually allow their complete structures to be solved, potentially approaching the resolution of other structural virology methods. To achieve this ambitious goal with today's technologies, about 1 ml of purified virus suspension containing at least 1012 particles per millilitre is required. Such large amounts of concentrated suspension have never before been obtained for enveloped viruses. Tick-borne encephalitis virus (TBEV) represents an attractive model system for the development of enveloped virus purification and concentration protocols, given the avai...
Source: Acta Crystallographica Section D - January 1, 2024 Category: Biochemistry Authors: Vorovitch, M.F. Samygina, V.R. Pichkur, E. Konarev, P.V. Peters, G. Khvatov, E.V. Ivanova, A.L. Tuchynskaya, K.K. Konyushko, O.I. Fedotov, A.Y. Armeev, G. Shaytan, K.V. Kovalchuk, M.V. Osolodkin, D.I. Egorov, A.M. Ishmukhametov, A.A. Tags: tick-borne encephalitis virus virus purification virus characterization single-particle imaging research papers Source Type: research
Deep residual networks for crystallography trained on synthetic data
The use of artificial intelligence to process diffraction images is challenged by the need to assemble large and precisely designed training data sets. To address this, a codebase called Resonet was developed for synthesizing diffraction data and training residual neural networks on these data. Here, two per-pattern capabilities of Resonet are demonstrated: (i) interpretation of crystal resolution and (ii) identification of overlapping lattices. Resonet was tested across a compilation of diffraction images from synchrotron experiments and X-ray free-electron laser experiments. Crucially, these models readily execute on gra...
Source: Acta Crystallographica Section D - January 1, 2024 Category: Biochemistry Authors: Mendez, D. Holton, J.M. Lyubimov, A.Y. Hollatz, S. Mathews, I.I. Cichosz, A. Martirosyan, V. Zeng, T. Stofer, R. Liu, R. Song, J. McPhillips, S. Soltis, M. Cohen, A.E. Tags: artificial intelligence serial crystallography rotation crystallography synchrotrons XFELs research papers Source Type: research
Current trends in macromolecular model refinement and validation
(Source: Acta Crystallographica Section D)
Source: Acta Crystallographica Section D - December 21, 2023 Category: Biochemistry Authors: Vollmar, M. Nicholls, R. Antonyuk, S. Tags: CCP4 Study Weekend 2022 model refinement model validation editorial Source Type: research
The TR-icOS setup at the ESRF: time-resolved microsecond UV – Vis absorption spectroscopy on protein crystals
The technique of time-resolved macromolecular crystallography (TR-MX) has recently been rejuvenated at synchrotrons, resulting in the design of dedicated beamlines. Using pump – probe schemes, this should make the mechanistic study of photoactive proteins and other suitable systems possible with time resolutions down to microseconds. In order to identify relevant time delays, time-resolved spectroscopic experiments directly performed on protein crystals are often desirable. To this end, an instrument has been built at the icOS Lab (in crystallo Optical Spectroscopy Laboratory) at the European Synchrotron Radiation Facili...
Source: Acta Crystallographica Section D - December 13, 2023 Category: Biochemistry Authors: Engilberge, S. Caramello, N. Bukhdruker, S. Byrdin, M. Giraud, T. Jacquet, P. Scortani, D. Biv, R. Gonzalez, H. Broquet, A. van der Linden, P. Rose, S.L. Flot, D. Balandin, T. Gordeliy, V. Lahey-Rudolph, J.M. Roessle, M. de Sanctis, D. Leonard, G.A. Muell Tags: pump – probe spectroscopy photoactivable proteins in crystallo optical spectroscopy bacteriorhodopsin serial synchrotron crystallography research papers Source Type: research
Modes and model building in SHELXE
Density modification is a standard step to provide a route for routine structure solution by any experimental phasing method, with single-wavelength or multi-wavelength anomalous diffraction being the most popular methods, as well as to extend fragments or incomplete models into a full solution. The effect of density modification on the starting maps from either source is illustrated in the case of SHELXE. The different modes in which the program can run are reviewed; these include less well known uses such as reading external phase values and weights or phase distributions encoded in Hendrickson – Lattman coefficients. ...
Source: Acta Crystallographica Section D - December 13, 2023 Category: Biochemistry Authors: Us ó n, I. Sheldrick, G.M. Tags: model building phasing density modification MRSAD SHELXE research papers Source Type: research
