Xplor ‐NIH: Better parameters and protocols for NMR protein structure determination
AbstractThe present work describes an update to the protein covalent geometry and atomic radii parameters in the Xplor-NIH biomolecular structure determination package. In combination with an improved treatment of selected non-bonded interactions between atoms three bonds apart, such as those involving methyl hydrogens, and a previously developed term that affects the system's gyration volume, the new parameters are tested using structure calculations on 30 proteins with restraints derived from nuclear magnetic resonance data. Using modern structure validation criteria, including several formally adopted by the Protein Dat...
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Guillermo A. Bermejo,
Nico Tjandra,
G. Marius Clore,
Charles D. Schwieters Tags: TOOLS FOR PROTEIN SCIENCE Source Type: research
The dynamics of the flavin, NADPH, and active site loops determine the mechanism of activation of class B flavin ‐dependent monooxygenases
AbstractFlavin-dependent monooxygenases (FMOs) constitute a diverse enzyme family that catalyzes crucial hydroxylation, epoxidation, and Baeyer –Villiger reactions across various metabolic pathways in all domains of life. Due to the intricate nature of this enzyme family's mechanisms, some aspects of their functioning remain unknown. Here, we present the results of molecular dynamics computations, supplemented by a bioinformatics analysis , that clarify the early stages of their catalytic cycle. We have elucidated the intricate binding mechanism of NADPH and L-Orn to a class B monooxygenase, the ornithine hydroxylase fro...
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Gustavo Pierdominici ‐Sottile,
Juliana Palma,
María Leticia Ferrelli,
Pablo Sobrado Tags: RESEARCH ARTICLE Source Type: research
Transmembrane conformation of the envelope protein of an alpha coronavirus, NL63
AbstractThe envelope (E) proteins of coronaviruses (CoVs) form cation-conducting channels that are associated with the pathogenicity of these viruses. To date, high-resolution structural information about these viroporins is limited to the SARS-CoV E protein. To broaden our structural knowledge of other members of this family of viroporins, we now investigate the conformation of the E protein of the human coronavirus (hCoV), NL63. Using two- and three-dimensional magic-angle-spinning NMR, we have measured13C and15N chemical shifts of the transmembrane domain of E (ETM), which yielded backbone ( ϕ, ψ) torsion angles. We f...
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Iva Su čec,
Yanina Pankratova,
Mriganka Parasar,
Mei Hong Tags: RESEARCH ARTICLE Source Type: research
Dual ‐wield NTPases: A novel protein family mined from AlphaFold DB
AbstractAlphaFold protein structure database (AlphaFold DB) archives a vast number of predicted models. We conducted systematic data mining against AlphaFold DB and discovered an uncharacterized P-loop NTPase family. The structure of the protein family was surprisingly novel, showing an atypical topology for P-loop NTPases, noticeable twofold symmetry, and two pairs of independent putative active sites. Our findings show that structural data mining is a powerful approach to identifying undiscovered protein families. (Source: Protein Science)
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Koya Sakuma,
Ryotaro Koike,
Motonori Ota Tags: RESEARCH ARTICLE Source Type: research
RrA, an enzyme from Rhodospirillum rubrum, is a prototype of a new family of short ‐chain L‐asparaginases
In this study, we demonstrate that RrA belongs to a unique family of cytoplasmic, short-chain ASNases (scASNases). These proteins occupy a distinct region in the sequence space, separate from the regions typically assigned to class 1 ASNases. The scASNases are present in approximately 7% of eubacterial species, spanning diverse bacterial lineages. They seem to be significantly enriched in species that encode for more than one class 1 ASNase. Here, we report biochemical, biophysical, and structural properties of RrA, a member of scASNases family. Crystal structures of the wild-type RrA, both with and without bound L-Asp, as...
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Di Zhang,
Honorata Czapinska,
Matthias Bochtler,
Alexander Wlodawer,
Jacek Lubkowski Tags: RESEARCH ARTICLE Source Type: research
Design of AsLOV2 domain as a carrier of light ‐induced dissociable FMN photosensitizer
AbstractFlavin mononucleotide (FMN) is a highly efficient photosensitizer (PS) yielding singlet oxygen (1O2). However, its1O2 production efficiency significantly decreases upon isoalloxazine ring encapsulation into the protein matrix in genetically encoded photosensitizers (GEPS). Reducing isoalloxazine ring interactions with surrounding amino acids by protein engineering may increase1O2 production efficiency GEPS, but at the same time weakened native FMN –protein interactions may cause undesirable FMN dissociation. Here, in contrast, we intentionally induce the FMN release by light-triggered sulfur oxidation of strategi...
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Krist ína Felčíková,
Andrej Hovan,
Marek Polák,
Dmitry S. Loginov,
Veronika Holotová,
Carlos Díaz,
Tibor Kožár,
One‐Sun Lee,
Rastislav Varhač,
Petr Novák,
Gregor Bánó,
Erik Sedlák Tags: RESEARCH ARTICLE Source Type: research
Classifying protein kinase conformations with machine learning
AbstractProtein kinases are key actors of signaling networks and important drug targets. They cycle between active and inactive conformations, distinguished by a few elements within the catalytic domain. One is the activation loop, whose conserved DFG motif can occupy DFG-in, DFG-out, and some rarer conformations. Annotation and classification of the structural kinome are important, as different conformations can be targeted by different inhibitors and activators. Valuable resources exist; however, large-scale applications will benefit from increased automation and interpretability of structural annotation. Interpretable m...
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Ivan Reveguk,
Thomas Simonson Tags: RESEARCH ARTICLE Source Type: research
Biochemical and structural characterization reveals Rv3400 codes for β‐phosphoglucomutase in Mycobacterium tuberculosis
This study further helps in understanding the role of β-PGM in the physiology of Mtb. (Source: Protein Science)
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Latika Singh,
Subramanian Karthikeyan,
Krishan Gopal Thakur Tags: RESEARCH ARTICLE Source Type: research
Cell surface β‐lactamase recruitment: A facile selection to identify protein–protein interactions
AbstractProtein –protein interactions (PPIs) are central to many cellular processes, and the identification of novel PPIs is a critical step in the discovery of protein therapeutics. Simple methods to identify naturally existing or laboratory evolved PPIs are therefore valuable research tools. We have developed a facile selection that links PPI-dependent β-lactamase recruitment on the surface ofEscherichia coli with resistance to ampicillin. Bacteria displaying a protein that forms a complex with a specific protein- β-lactamase fusion are protected from ampicillin-dependent cell death. In contrast, bacteria that do not...
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Jordan A. Hinmon,
Jade M. King,
Latrina J. Mayo,
Cierra R. Faries,
Ya'hnis T. Lockett,
David W. Crawford,
Patrick C. Beardslee,
Alexander Hendricks,
Brian R. McNaughton Tags: RESEARCH NOTE Source Type: research
Issue information
(Source: Protein Science)
Source: Protein Science - March 19, 2024 Category: Biochemistry Tags: Issue Information Source Type: research
Cover Image
Superposed ccGFP E6 (orange) and ccGFP 8 (blue) in cartoon representation centered at R70 showing the side-chain rotamer differences of R70 between ccGFP E6 and the other variants (represented by ccGFP 8). For details, see: Li-Wei Hung et al., Protein Science, 2023.https://doi.org/10.1002/pro.4886 (Source: Protein Science)
Source: Protein Science - March 18, 2024 Category: Biochemistry Tags: Cover Image Source Type: research
Direct evidence of lipid transport by the Drs2 –Cdc50 flippase upon truncation of its terminal regions
AbstractP4-ATPases in complex with Cdc50 subunits are lipid flippases that couple ATP hydrolysis with lipid transport to the cytoplasmic leaflet of membranes to create lipid asymmetry. Such vectorial transport has been shown to contribute to vesicle formation in the late secretory pathway. Some flippases are regulated by autoinhibitory regions that can be destabilized by protein kinase-mediated phosphorylation and possibly by binding of cytosolic proteins. In addition, the binding of lipids to flippases may also induce conformational changes required for the activity of these transporters. Here, we address the role of phos...
Source: Protein Science - February 27, 2024 Category: Biochemistry Authors: Sara Abad Herrera,
Bo H øjen Justesen,
Thibaud Dieudonné,
Cédric Montigny,
Poul Nissen,
Guillaume Lenoir,
Thomas Günther Pomorski Tags: RESEARCH ARTICLE Source Type: research
Molecular mechanisms of chaperone ‐directed protein folding: Insights from atomistic simulations
AbstractMolecular chaperones, a family of proteins of which Hsp90 and Hsp70 are integral members, form an essential machinery to maintain healthy proteomes by controlling the folding and activation of a plethora of substrate client proteins. This is achieved through cycles in which Hsp90 and Hsp70, regulated by task-specific co-chaperones, process ATP and become part of a complex network that undergoes extensive compositional and conformational variations. Despite impressive advances in structural knowledge, the mechanisms that regulate the dynamics of functional assemblies, their response to nucleotides, and their relevan...
Source: Protein Science - February 26, 2024 Category: Biochemistry Authors: Matteo Castelli,
Andrea Magni,
Giorgio Bonollo,
Silvia Pavoni,
Francesco Frigerio,
A. Sofia F. Oliveira,
Fabrizio Cinquini,
Stefano A. Serapian,
Giorgio Colombo Tags: RESEARCH ARTICLE Source Type: research
The ratio of fibroin to sericin in the middle silk gland of Bombyx mori and its correlation with the extensional behavior of the silk dope
AbstractUnderstanding how native silk spinning occurs is crucial for designing artificial spinning systems. One often overlooked factor inBombyx mori is the secretion of sericin proteins. Herein, we investigate the variation in amino acid content at different locations in the middle silk gland (MSG) ofB. mori. This variation corresponds to an increase in sericin content when moving towards the anterior region of the MSG, while the posterior region predominantly contains fibroin. We estimate the mass ratio of sericin to fibroin to be ~25/75 wt% in the anterior MSG, depending on the fitting method. Then, we demonstrate th...
Source: Protein Science - February 22, 2024 Category: Biochemistry Authors: Teemu V älisalmi,
Markus B. Linder Tags: RESEARCH ARTICLE Source Type: research
Degradation versus fibrillogenesis, two alternative pathways modulated by seeds and glycosaminoglycans
AbstractThe mechanism that converts native human transthyretin into amyloid fibrilsin vivo is still a debated and controversial issue. Commonly, non-physiological conditions of pH, temperature, or organic solvents are used inin vitro models of fibrillogenesis of globular proteins. Transthyretin amyloid formation can be achieved under physiological conditions through a mechano-enzymatic mechanism involving specific serine proteases such as trypsin or plasmin. Here, we investigate S52P and L111M transthyretin variants, both causing a severe form of systemic amyloidosis mostly targeting the heart at a relatively young age wit...
Source: Protein Science - February 21, 2024 Category: Biochemistry Authors: Guglielmo Verona,
Sara Raimondi,
Diana Canetti,
P. Patrizia Mangione,
Loredana Marchese,
Alessandra Corazza,
Francesca Lavatelli,
Julian D. Gillmore,
Graham W. Taylor,
Vittorio Bellotti,
Sofia Giorgetti Tags: RESEARCH ARTICLE Source Type: research
