Secret of Life: Rosalind Franklin, James Watson, Francis Crick, and the discovery of DNA's Double Helix. By Howard Markel. W. W. Norton & Co., 2021. Hardback, pp. 608. ISBN 978-1324002239. Price USD 30.00.
(Source: Acta Crystallographica Section D)
Source: Acta Crystallographica Section D - November 29, 2022 Category: Biochemistry Authors: Derewenda, Z.S. Tags: book review DNA double helix Rosalind Franklin James Watson Francis Crick book reviews Source Type: research
Structure of a hydrophobic leucinostatin derivative determined by host lattice display
Peptides comprising many hydrophobic amino acids are almost insoluble under physiological buffer conditions, which complicates their structural analysis. To investigate the three-dimensional structure of the hydrophobic leucinostatin derivative ZHAWOC6027, the previously developed host lattice display technology was applied. Two designed ankyrin-repeat proteins (DARPins) recognizing a biotinylated ZHAWOC6027 derivative were selected from a diverse library by ribosome display under aqueous buffer conditions. ZHAWOC6027 was immobilized by means of the DARPin in the host lattice and the structure of the complex was determined...
Source: Acta Crystallographica Section D - November 29, 2022 Category: Biochemistry Authors: Kiss, C. Gall, F.M. Dreier, B. Adams, M. Riedl, R. Pl ü ckthun, A. Mittl, P.R.E. Tags: crystal engineering host lattice display leucinostatins research papers Source Type: research
Direct calculation of cryo-EM and crystallographic model maps for real-space refinement
This work addresses the problem of the calculation of limited-resolution maps from an atomic model in cryo-electron microscopy and in X-ray and neutron crystallography, including cases where the resolution varies from one molecular region to another. Such maps are necessary in real-space refinement for comparison with the experimental maps. For an appropriate numeric comparison, the calculated maps should reproduce not only the structural features contained in the experimental maps but also the principal map distortions. These model maps can be obtained with no use of Fourier transforms but, similar to density distribution...
Source: Acta Crystallographica Section D - November 25, 2022 Category: Biochemistry Authors: Urzhumtsev, A.G. Urzhumtseva, L.M. Lunin, V.Y. Tags: real-space refinement map calculation atomic images Fourier ripples truncation distances resolution atomic displacement parameters shell decomposition interference functions research papers Source Type: research
Serial femtosecond X-ray crystallography of an anaerobically formed catalytic intermediate of copper amine oxidase
In this study, SFX measurements using a liquid-jet system were performed on microcrystals of bacterial copper amine oxidase anaerobically premixed with a substrate amine solution. The structure determined at 1.94 Å resolution indicated that the peptidyl quinone cofactor is in equilibrium between the aminoresorcinol and semiquinone radical intermediates, which accumulate only under anaerobic single-turnover conditions. These results show that anaerobic conditions were well maintained throughout the liquid-jet SFX measurements, preventing the catalytic intermediates from reacting with dioxygen. These results also provid...
Source: Acta Crystallographica Section D - November 25, 2022 Category: Biochemistry Authors: Murakawa, T. Suzuki, M. Fukui, K. Masuda, T. Sugahara, M. Tono, K. Tanaka, T. Iwata, S. Nango, E. Yano, T. Tanizawa, K. Okajima, T. Tags: serial femtosecond X-ray crystallography copper amine oxidases catalytic intermediates mix-and-inject method peptidyl quinone cofactor research papers Source Type: research
Using deep-learning predictions of inter-residue distances for model validation
Determination of protein structures typically entails building a model that satisfies the collected experimental observations and its deposition in the Protein Data Bank. Experimental limitations can lead to unavoidable uncertainties during the process of model building, which result in the introduction of errors into the deposited model. Many metrics are available for model validation, but most are limited to consideration of the physico-chemical aspects of the model or its match to the experimental data. The latest advances in the field of deep learning have enabled the increasingly accurate prediction of inter-residue d...
Source: Acta Crystallographica Section D - November 25, 2022 Category: Biochemistry Authors: S á nchez Rodr í guez, F. Chojnowski, G. Keegan, R.M. Rigden, D.J. Tags: model validation inter-residue distances AlphaFold2 ConKit conkit-validate research papers Source Type: research
Unravelling the regulation pathway of photosynthetic AB-GAPDH
Oxygenic phototrophs perform carbon fixation through the Calvin – Benson cycle. Different mechanisms adjust the cycle and the light-harvesting reactions to rapid environmental changes. Photosynthetic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a key enzyme in the cycle. In land plants, different photosynthetic GAPDHs exist: the most abundant isoform is formed by A2B2 heterotetramers and the least abundant by A4 homotetramers. Regardless of the subunit composition, GAPDH is the major consumer of photosynthetic NADPH and its activity is strictly regulated. While A4-GAPDH is regulated by CP12, AB-GAPDH is auto...
Source: Acta Crystallographica Section D - October 27, 2022 Category: Biochemistry Authors: Marotta, R. Del Giudice, A. Gurrieri, L. Fanti, S. Swuec, P. Galantini, L. Falini, G. Trost, P. Fermani, S. Sparla, F. Tags: photosynthesis redox regulation cryo-electron microscopy small-angle X-ray scattering photosynthetic glyceraldehyde 3-phosphate dehydrogenase AB-GAPDH research papers Source Type: research
Crystal structure of DNA polymerase I from Thermus phage G20c
This study describes the structure of DNA polymerase I from Thermus phage G20c, termed PolI_G20c. This is the first structure of a DNA polymerase originating from a group of related thermophilic bacteriophages infecting Thermus thermophilus, including phages G20c, TSP4, P74-26, P23-45 and phiFA and the novel phage Tth15-6. Sequence and structural analysis of PolI_G20c revealed a 3 ′ – 5 ′ exonuclease domain and a DNA polymerase domain, and activity screening confirmed that both domains were functional. No functional 5 ′ – 3 ′ exonuclease domain was present. Structural analysis also revealed a novel specific str...
Source: Acta Crystallographica Section D - October 27, 2022 Category: Biochemistry Authors: Ahlqvist, J. Linares-Past é n, J.A. Jasilionis, A. Welin, M. H å kansson, M. Svensson, L.A. Wang, L. Watzlawick, H. Æ varsson, A. Fri ð j ó nsson, Ó .H. Hreggvi ð sson, G. Ó . Ketelsen Striberny, B. Glomsaker, E. Lanes, O. Al-Karadaghi, S. Nordber Tags: DNA polymerase I Thermus phage G20c Thermus thermophilus thermophilic bacteriophages structural motifs PolI_G20c research papers Source Type: research
Structural and functional investigation of the human snRNP assembly factor AAR2 in complex with the RNase H-like domain of PRPF8
Small nuclear ribonucleoprotein complexes (snRNPs) represent the main subunits of the spliceosome. While the assembly of the snRNP core particles has been well characterized, comparably little is known of the incorporation of snRNP-specific proteins and the mechanisms of snRNP recycling. U5 snRNP assembly in yeast requires binding of the the Aar2 protein to Prp8p as a placeholder to preclude premature assembly of the SNRNP200 helicase, but the role of the human AAR2 homolog has not yet been investigated in detail. Here, a crystal structure of human AAR2 in complex with the RNase H-like domain of the U5-specific PRPF8 (P...
Source: Acta Crystallographica Section D - October 27, 2022 Category: Biochemistry Authors: Preussner, M. Santos, K.F. Alles, J. Heroven, C. Heyd, F. Wahl, M.C. Weber, G. Tags: spliceosomal assembly U5 snRNP AAR2 PRPF8 research papers Source Type: research
Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE
AlphaFold has recently become an important tool in providing models for experimental structure determination by X-ray crystallography and cryo-EM. Large parts of the predicted models typically approach the accuracy of experimentally determined structures, although there are frequently local errors and errors in the relative orientations of domains. Importantly, residues in the model of a protein predicted by AlphaFold are tagged with a predicted local distance difference test score, informing users about which regions of the structure are predicted with less confidence. AlphaFold also produces a predicted aligned error mat...
Source: Acta Crystallographica Section D - October 27, 2022 Category: Biochemistry Authors: Oeffner, R.D. Croll, T.I. Mill á n, C. Poon, B.K. Schlicksup, C.J. Read, R.J. Terwilliger, T.C. Tags: AlphaFold Phenix ISOLDE process_predicted_model confidence measures research papers Source Type: research
Exiting the tunnel of uncertainty: crystal soak to validated hit
Crystallographic fragment screens provide an efficient and effective way to identify small-molecule ligands of a crystallized protein. Due to their low molecular weight, such hits tend to have low, often unquantifiable, affinity for their target, complicating the twin challenges of validating the hits as authentic solution-phase ligands of the target and identifying the `best' hit(s) for further elaboration. In this article, approaches that address these challenges are assessed. Using retrospective analysis of a recent ATAD2 hit-identification campaign, alongside other examples of successful fragment-screening campaigns, i...
Source: Acta Crystallographica Section D - October 27, 2022 Category: Biochemistry Authors: Martin, M.P. Noble, M.E.M. Tags: orthogonal assays qualitative structure – activity relationships fragment screening hit validation drug discovery biophysical techniques research papers Source Type: research
Glycoside hydrolase subfamily GH5_57 features a highly redesigned catalytic interface to process complex hetero- β -mannans
Glycoside hydrolase family 5 (GH5) harbors diverse substrate specificities and modes of action, exhibiting notable molecular adaptations to cope with the stereochemical complexity imposed by glycosides and carbohydrates such as cellulose, xyloglucan, mixed-linkage β -glucan, laminarin, (hetero)xylan, (hetero)mannan, galactan, chitosan, N-glycan, rutin and hesperidin. GH5 has been divided into subfamilies, many with higher functional specificity, several of which have not been characterized to date and some that have yet to be discovered with the exploration of sequence/taxonomic diversity. In this work, the current GH5 su...
Source: Acta Crystallographica Section D - October 20, 2022 Category: Biochemistry Authors: Martins, M.P. Morais, M.A.B. Persinoti, G.F. Galinari, R.H. Yu, L. Yoshimi, Y. Passos Nunes, F.B. Lima, T.B. Barbieri, S.F. Silveira, J.L.M. Lombard, V. Terrapon, N. Dupree, P. Henrissat, B. Murakami, M.T. Tags: glycoside hydrolase GH5 family capybara gut microbiome heteromannans crystal structure endo- β -mannanases research papers Source Type: research
Zymogenic latency in an ∼ 250-million-year-old astacin metallopeptidase
The horseshoe crab Limulus polyphemus is one of few extant Limulus species, which date back to ∼ 250 million years ago under the conservation of a common Bauplan documented by fossil records. It possesses the only proteolytic blood-coagulation and innate immunity system outside vertebrates and is a model organism for the study of the evolution and function of peptidases. The astacins are a family of metallopeptidases that share a central ∼ 200-residue catalytic domain (CD), which is found in>1000 species across holozoans and, sporadically, bacteria. Here, the zymogen of an astacin from L. polyphemus was crystallized an...
Source: Acta Crystallographica Section D - October 20, 2022 Category: Biochemistry Authors: Guevara, T. Rodr í guez-Banqueri, A. St ö cker, W. Becker-Pauly, C. Gomis-R ü th, F.X. Tags: metallopeptidase zymogenic latency astacin metallopeptidase Limulus polyphemus horseshoe crab aspartate-switch mechanism catalytic domain pro-peptide research papers Source Type: research
Polyelectrolyte coating of cryo-EM grids improves lateral distribution and prevents aggregation of macromolecules
Cryo-electron microscopy (cryo-EM) is one of the primary methods used to determine the structures of macromolecules and their complexes. With the increased availability of cryo-electron microscopes, the preparation of high-quality samples has become a bottleneck in the cryo-EM structure-determination pipeline. Macromolecules can be damaged during the purification or preparation of vitrified samples for cryo-EM, making them prone to binding to the grid support, to aggregation or to the adoption of preferential orientations at the air – water interface. Here, it is shown that coating cryo-EM grids with a negatively charged...
Source: Acta Crystallographica Section D - October 20, 2022 Category: Biochemistry Authors: Hreb í k, D. Gondov á , M. Valentov á , L. F ü zik, T. P ř idal, A. Nov á č ek, J. Plevka, P. Tags: cryo-EM sample preparation ssDNA coating cryo-EM grids aggregation research papers Source Type: research
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking
Through an expansive international effort that involved data collection on 12 small-angle X-ray scattering (SAXS) and four small-angle neutron scattering (SANS) instruments, 171 SAXS and 76 SANS measurements for five proteins (ribonuclease A, lysozyme, xylanase, urate oxidase and xylose isomerase) were acquired. From these data, the solvent-subtracted protein scattering profiles were shown to be reproducible, with the caveat that an additive constant adjustment was required to account for small errors in solvent subtraction. Further, the major features of the obtained consensus SAXS data over the q measurement range 0 – ...
Source: Acta Crystallographica Section D - October 20, 2022 Category: Biochemistry Authors: Trewhella, J. Vachette, P. Bierma, J. Blanchet, C. Brookes, E. Chakravarthy, S. Chatzimagas, L. Cleveland, T.E. Cowieson, N. Crossett, B. Duff, A.P. Franke, D. Gabel, F. Gillilan, R.E. Graewert, M. Grishaev, A. Guss, J.M. Hammel, M. Hopkins, J. Huang, Q. Tags: biomolecular small-angle scattering X-ray scattering neutron scattering standards benchmarking standards scattering-profile calculation research papers Source Type: research
Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER
Structure predictions have matched the accuracy of experimental structures from close homologues, providing suitable models for molecular replacement phasing. Even in predictions that present large differences due to the relative movement of domains or poorly predicted areas, very accurate regions tend to be present. These are suitable for successful fragment-based phasing as implemented in ARCIMBOLDO. The particularities of predicted models are inherently addressed in the new predicted_model mode, rendering preliminary treatment superfluous but also harmless. B-value conversion from predicted LDDT or error estimates, the ...
Source: Acta Crystallographica Section D - October 20, 2022 Category: Biochemistry Authors: Medina, A. Jim é nez, E. Caballero, I. Castellv í , A. Trivi ñ o Valls, J. Alcorlo, M. Molina, R. Hermoso, J.A. Sammito, M.D. Borges, R. Us ó n, I. Tags: phasing ARCIMBOLDO ARCIMBOLDO_SHREDDER fragment-based molecular replacement verification model bias predictions AlphaFold RoseTTAFold research papers Source Type: research
