The LH – DH module of bacterial replicative helicases is the common binding site for DciA and other helicase loaders
During the initiation step of bacterial genome replication, replicative helicases depend on specialized proteins for their loading onto oriC. DnaC and DnaI were the first loaders to be characterized. However, most bacteria do not contain any of these genes, which are domesticated phage elements that have replaced the ancestral and unrelated loader gene dciA several times during evolution. To understand how DciA assists the loading of DnaB, the crystal structure of the complex from Vibrio cholerae was determined, in which two VcDciA molecules interact with a dimer of VcDnaB without changing its canonical structure. The data...
Source: Acta Crystallographica Section D - February 6, 2023 Category: Biochemistry Authors: Cargemel, C. Marsin, S. Noiray, M. Legrand, P. Bounoua, H. Li de la Sierra-Gallay, I. Walbott, H. Quevillon-Cheruel, S. Tags: DnaB · DciA complex crystal structure helicase loaders bacterial replicative helicases interaction modules replicative helicase hijacking Vibrio cholerae research papers Source Type: research
Crystal structure of a polyglycine hydrolase determined using a RoseTTAFold model
The objective of this research was to investigate the proteolytic mechanism and other characteristics by structural and biochemical means. Here, the first atomic structure of a polyglycine hydrolase was identified. It was solved by X-ray crystallography using a RoseTTAFold model, taking advantage of recent technical advances in structure prediction. PGHs are composed of two domains: the N- and C-domains. The N-domain is a novel tertiary fold with an as-yet unknown function that is found across all kingdoms of life. The C-domain shares structural similarities with class C β -lactamases, including a common catalytic nucleop...
Source: Acta Crystallographica Section D - February 6, 2023 Category: Biochemistry Authors: Dowling, N.V. Naumann, T.A. Price, N.P.J. Rose, D.R. Tags: RoseTTAFold fungi chitinase-modifying proteins polyglycine hydrolases β -lactamases research papers Source Type: research
30 years of Acta D
(Source: Acta Crystallographica Section D)
Source: Acta Crystallographica Section D - February 1, 2023 Category: Biochemistry Authors: Garman, E.F. Read, R.J. Bond, C.S. Tags: editorial anniversaries structural biology Source Type: research
Towards the standardized presentation and publication of small-angle scattering data from biomolecules in solution
(Source: Acta Crystallographica Section D)
Source: Acta Crystallographica Section D - February 1, 2023 Category: Biochemistry Authors: Czjzek, M. Tags: commentary small-angle scattering data presentation standardized descriptions templates scientific commentaries Source Type: research
Structural insight into the hydrolase and synthase activities of an alkaline α -galactosidase from Arabidopsis from complexes with substrate/product
The alkaline α -galactosidase AtAk α Gal3 from Arabidopsis thaliana catalyzes the hydrolysis of α -d-galactose from galacto-oligosaccharides under alkaline conditions. A phylogenetic analysis based on sequence alignment classifies AtAk α Gal3 as more closely related to the raffinose family of oligosaccharide (RFO) synthases than to the acidic α -galactosidases. Here, thin-layer chromatography is used to demonstrate that AtAk α Gal3 exhibits a dual function and is capable of synthesizing stachyose using raffinose, instead of galactinol, as the galactose donor. Crystal structures of complexes of AtAk α Gal3 and its D3...
Source: Acta Crystallographica Section D - January 20, 2023 Category: Biochemistry Authors: Chuankhayan, P. Lee, R.-H. Guan, H.-H. Lin, C.-C. Chen, N.-C. Huang, Y.-C. Yoshimura, M. Nakagawa, A. Chen, C.-J. Tags: Arabidopsis thaliana alkaline α -galactosidases raffinose RFO synthases transferase mechanism research papers Source Type: research
Cryo-EM structure of adeno-associated virus 4 at 2.2 Å resolution
Adeno-associated virus (AAV) is the vector of choice for several approved gene-therapy treatments and is the basis for many ongoing clinical trials. Various strains of AAV exist (referred to as serotypes), each with their own transfection characteristics. Here, a high-resolution cryo-electron microscopy structure (2.2 Å ) of AAV serotype 4 (AAV4) is presented. The receptor responsible for transduction of the AAV4 clade of AAV viruses (including AAV11, AAV12 and AAVrh32.33) is unknown. Other AAVs interact with the same cell receptor, adeno-associated virus receptor (AAVR), in one of two different ways. AAV5-like viruse...
Source: Acta Crystallographica Section D - January 20, 2023 Category: Biochemistry Authors: Zane, G. Silveria, M. Meyer, N. White, T. Duan, R. Zou, X. Chapman, M. Tags: AAV4 cryo-electron microscopy adeno-associated virus receptor gene therapy research papers Source Type: research
Right-handed Z-DNA at ultrahigh resolution: a tale of two hands and the power of the crystallographic method
The self-complementary l-d(CGCGCG)2 purine/pyrimidine hexanucleotide was crystallized in complex with the polyamine cadaverine and potassium cations. Since the oligonucleotide contained the enantiomeric 2 ′ -deoxy-l-ribose, the Z-DNA duplex is right-handed, as confirmed by the ultrahigh-resolution crystal structure determined at 0.69 Å resolution. Although the X-ray diffraction data were collected at a very short wavelength (0.7085 Å ), where the anomalous signal of the P and K atoms is very weak, the signal was sufficiently outstanding to clearly indicate the wrong hand when the structure was mistakenly solved...
Source: Acta Crystallographica Section D - January 20, 2023 Category: Biochemistry Authors: Drozdzal, P. Manszewski, T. Gilski, M. Brzezinski, K. Jaskolski, M. Tags: Z-DNA handedness anomalous signal 2 ′ -deoxy-l-ribose dual-conformation backbone cadaverinium cation biogenic polyamines biological potassium complex research papers Source Type: research
Cryo-EM reveals binding of linoleic acid to SARS-CoV-2 spike glycoprotein, suggesting an antiviral treatment strategy
The COVID-19 pandemic and concomitant lockdowns presented a global health challenge and triggered unprecedented research efforts to elucidate the molecular mechanisms and pathogenicity of SARS-CoV-2. The spike glycoprotein decorating the surface of SARS-CoV-2 virions is a prime target for vaccine development, antibody therapy and serology as it binds the host cell receptor and is central for viral cell entry. The electron cryo-microscopy structure of the spike protein revealed a hydrophobic pocket in the receptor-binding domain that is occupied by an essential fatty acid, linoleic acid (LA). The LA-bound spike protein adop...
Source: Acta Crystallographica Section D - January 20, 2023 Category: Biochemistry Authors: Toelzer, C. Gupta, K. Berger, I. Schaffitzel, C. Tags: cryogenic electron microscopy betacoronaviruses SARS-CoV-2 spike protein free fatty acids linoleic acid phospholipase A2 drug design research papers Source Type: research
In situ ligand restraints from quantum-mechanical methods
In macromolecular crystallographic structure refinement, ligands present challenges for the generation of geometric restraints due to their large chemical variability, their possible novel nature and their specific interaction with the binding pocket of the protein. Quantum-mechanical approaches are useful for providing accurate ligand geometries, but can be plagued by the number of minima in flexible molecules. In an effort to avoid these issues, the Quantum Mechanical Restraints (QMR) procedure optimizes the ligand geometry in situ, thus accounting for the influence of the macromolecule on the local energy minima of the ...
Source: Acta Crystallographica Section D - January 20, 2023 Category: Biochemistry Authors: Liebschner, D. Moriarty, N.W. Poon, B.K. Adams, P.D. Tags: macromolecular crystallography ligand restraints refinement quantum mechanics Quantum Mechanical Restraints research papers Source Type: research
Determining biomolecular structures near room temperature using X-ray crystallography: concepts, methods and future optimization
For roughly two decades, cryocrystallography has been the overwhelmingly dominant method for determining high-resolution biomolecular structures. Competition from single-particle cryo-electron microscopy and micro-electron diffraction, increased interest in functionally relevant information that may be missing or corrupted in structures determined at cryogenic temperature, and interest in time-resolved studies of the biomolecular response to chemical and optical stimuli have driven renewed interest in data collection at room temperature and, more generally, at temperatures from the protein – solvent glass transition near...
Source: Acta Crystallographica Section D - January 1, 2023 Category: Biochemistry Authors: Thorne, R.E. Tags: room-temperature crystallography multi-temperature crystallography radiation damage serial crystallography conformational heterogeneity research papers Source Type: research
Structural insights into the effects of glycerol on ligand binding to cytochrome P450
New antitubercular drugs are vital due to the spread of resistant strains. Carbethoxyhexyl imidazole (CHImi) inhibits cytochrome P450 CYP124, which is a steroid-metabolizing enzyme that is important for the survival of Mycobacterium tuberculosis in macrophages. The available crystal structure of the CYP124 – CHImi complex reveals two glycerol molecules in the active site. A 1.15 Å resolution crystal structure of the glycerol-free CYP124 – CHimi complex reported here shows multiple conformations of CHImi and the CYP124 active site which were previously restricted by glycerol. Complementary molecular dynamics simula...
Source: Acta Crystallographica Section D - January 1, 2023 Category: Biochemistry Authors: Bukhdruker, S. Varaksa, T. Orekhov, P. Grabovec, I. Marin, E. Kapranov, I. Kovalev, K. Astashkin, R. Kaluzhskiy, L. Ivanov, A. Mishin, A. Rogachev, A. Gordeliy, V. Gilep, A. Strushkevich, N. Borshchevskiy, V. Tags: cytochrome P450 carbethoxyhexyl imidazole glycerol protein crystallography Mycobacterium tuberculosis research papers Source Type: research
Molecular-dynamics simulation methods for macromolecular crystallography
It is investigated whether molecular-dynamics (MD) simulations can be used to enhance macromolecular crystallography (MX) studies. Historically, protein crystal structures have been described using a single set of atomic coordinates. Because conformational variation is important for protein function, researchers now often build models that contain multiple structures. Methods for building such models can fail, however, in regions where the crystallographic density is difficult to interpret, for example at the protein – solvent interface. To address this limitation, a set of MD – MX methods that combine MD simulations o...
Source: Acta Crystallographica Section D - December 31, 2022 Category: Biochemistry Authors: Wych, D.C. Aoto, P.C. Vu, L. Wolff, A.M. Mobley, D.L. Fraser, J.S. Taylor, S.S. Wall, M.E. Tags: molecular-dynamics simulations water structure conformational ensembles protein kinases research papers Source Type: research
Structures of permuted halves of a modern ribose-binding protein
Periplasmic binding proteins (PBPs) are a class of proteins that participate in the cellular transport of various ligands. They have been used as model systems to study mechanisms in protein evolution, such as duplication, recombination and domain swapping. It has been suggested that PBPs evolved from precursors half their size. Here, the crystal structures of two permuted halves of a modern ribose-binding protein (RBP) from Thermotoga maritima are reported. The overexpressed proteins are well folded and show a monomer – dimer equilibrium in solution. Their crystal structures show partially noncanonical PBP-like fold typ...
Source: Acta Crystallographica Section D - December 31, 2022 Category: Biochemistry Authors: Michel, F. Shanmugaratnam, S. Romero-Romero, S. H ö cker, B. Tags: periplasmic binding proteins ribose binding protein Thermotoga maritima flavodoxin-like fold circular permutation domain swapping protein evolution research papers Source Type: research
A scoring function for the prediction of protein complex interfaces based on the neighborhood preferences of amino acids
Proteins often assemble into functional complexes, the structures of which are more difficult to obtain than those of the individual protein molecules. Given the structures of the subunits, it is possible to predict plausible complex models via computational methods such as molecular docking. Assessing the quality of the predicted models is crucial to obtain correct complex structures. Here, an energy-scoring function was developed based on the interfacial residues of structures in the Protein Data Bank. The statistically derived energy function (Nepre) imitates the neighborhood preferences of amino acids, including the...
Source: Acta Crystallographica Section D - December 20, 2022 Category: Biochemistry Authors: Nagaraju, M. Liu, H. Tags: protein – protein interactions interface residues iNepre scoring functions neighborhood preference of amino acids research papers Source Type: research
Drosophila melanogaster frataxin: protein crystal and predicted solution structure with identification of the iron-binding regions
Friedreich's ataxia (FRDA) is a hereditary cardiodegenerative and neurodegenerative disease that affects 1 in 50 000 Americans. FRDA arises from either a cellular inability to produce sufficient quantities or the production of a nonfunctional form of the protein frataxin, a key molecule associated with mitochondrial iron – sulfur cluster biosynthesis. Within the mitochondrial iron – sulfur cluster (ISC) assembly pathway, frataxin serves as an allosteric regulator for cysteine desulfurase, the enzyme that provides sulfur for [2Fe – 2S] cluster assembly. Frataxin is a known iron-binding protein and is also linked t...
Source: Acta Crystallographica Section D - December 20, 2022 Category: Biochemistry Authors: Rodrigues, A.V. Batelu, S. Hinton, T.V. Rotondo, J. Thompson, L. Brunzelle, J.S. Stemmler, T.L. Tags: Friedreich's ataxia frataxin iron – sulfur clusters Drosophila melanogaster ISC pathway research papers Source Type: research
