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Actin is essential for key processes in all eukaryotic cells. Cellpermeable optojasps provide spatiotemporal control of the actin cytoskeleton, confining toxicity and potentially rendering F‐actin druggable by photopharmacology. Here, we report cryo electron microscopy (cryo‐EM) structures of both isomeric states of one optojasp bound to actin filaments. The high‐resolution structures reveal for the first time the pronounced effects of photoswitching a functionalized azobenzene. By characterizing the optojasp binding site and identifying conformational changes within F‐actin that depend on the optojasp isomeric state, we refine determinants for the design of functional F‐actin photoswitches. [ABSTRACT FROM AUTHOR]

The tumor necrosis factor (TNF)‐like core domain of receptor activator of nuclear factor‐κB ligand (RANKL) is a functional domain critical for osteoclast differentiation. One of the missense mutations identified in patients with osteoclast‐poor autosomal recessive osteopetrosis (ARO) is located in residue methionine 199 that is replaced with lysine (M199K) amid the TNF‐like core domain. However, the structure–function relationship of this mutation is not clear. Sequence‐based alignment revealed that the fragment containing human M199 is highly conserved and equivalent to M200 in rat. Using site‐directed mutagenesis, we generated three recombinant RANKL mutants M200K/A/E (M200s) by replacing the methionine 200 with lysine (M200K), alanine (M200A), and glutamic acid (M200E), representative of distinct physical properties. TRAcP staining and bone pit assay showed that M200s failed to support osteoclast formation and bone resorption, accompanied by impaired osteoclast‐related signal transduction. However, no antagonistic effect was found in M200s against wild‐type rat RANKL. Analysis of the crystal structure of RANKL predicted that this methionine residue is located within the hydrophobic core of the protein, thus, likely to be crucial for protein folding and stability. Consistently, differential scanning fluorimetry analysis suggested that M200s were less stable. Western blot analysis analyses further revealed impaired RANKL trimerization by M200s. Furthermore, receptor–ligand binding assay displayed interrupted interaction of M200s to its intrinsic receptors. Collectively, our studies revealed the molecular basis of human M199‐induced ARO and elucidated the indispensable role of rodent residue M200 (equivalent to human M199) for the RANKL function. [ABSTRACT FROM AUTHOR]

Silk fibroin (SF) solution is characterized by its structural instability. Despite many efforts to uncover the structural features of SF, the time‐dependent conformation transition behaviors of SF solutions prepared under different conditions have not yet been investigated in detail. Therefore, in this study, the conformation transition changes of SF were dynamically monitored in an aqueous state using circular dichroism (CD) spectroscopic analysis. CD spectra of SF continuously change during ethanol treatment and storage, showing growth with a positive peak at 197 nm and a negative peak at 218 nm, consistent with β‐sheet development. Additionally, the time points for SF to begin and complete changing structures, including its changing rates, were confirmed. In particular, the transition kinetics follow the one‐phase exponential decay function, quantitatively showing a longer dissolution time and lower storage temperature delay for the development of β‐sheets with lower rate constants. In conclusion, our investigation provides useful information on the intrinsic properties of SF and environmental factors that can affect the structural stability of SF. [ABSTRACT FROM AUTHOR]

The successful design of a hydrogel for tissue engineering requires a profound understanding of its constituents’ structural and molecular properties, as well as the proper selection of components. If the engineered processes are in line with the procedures that natural materials undergo to achieve the best network structure necessary for the formation of the hydrogel with desired properties, the failure rate of tissue engineering projects will be significantly reduced. In this review, we examine the behavior of proteins as an essential and effective component of hydrogels, and describe the factors that can enhance the protein-based hydrogels’ structure. Furthermore, we outline the fabrication route of protein-based hydrogels from protein microstructure and the selection of appropriate materials according to recent research to growth factors, crucial members of the protein family, and their delivery approaches. Finally, the unmet needs and current challenges in developing the ideal biomaterials for protein-based hydrogels are discussed, and emerging strategies in this area are highlighted.

NMR spectroscopy is a particularly informative method for studying protein structures and dynamics in solution; however, it is also one of the most time‐consuming. Modern approaches to biomolecular NMR spectroscopy are based on lengthy multidimensional experiments, the duration of which grows exponentially with the number of dimensions. The experimental time may even be several days in the case of 3D and 4D spectra. Moreover, the experiment often has to be repeated under several different conditions, for example, to measure the temperature‐dependent effects in a spectrum (temperature coefficients (TCs)). Herein, a new approach that involves joint sampling of indirect evolution times and temperature is proposed. This allows TCs to be measured through 3D spectra in even less time than that needed to acquire a single spectrum by using the conventional approach. Two signal processing methods that are complementary, in terms of sensitivity and resolution, 1) dividing data into overlapping subsets followed by compressed sensing reconstruction, and 2) treating the complete data set with a variant of the Radon transform, are proposed. The temperature‐swept 3D HNCO spectra of two intrinsically disordered proteins, osteopontin and CD44 cytoplasmic tail, show that this new approach makes it possible to determine TCs and their non‐linearities effectively. Non‐linearities, which indicate the presence of a compact state, are particularly interesting. The complete package of data acquisition and processing software for this new approach are provided. [ABSTRACT FROM AUTHOR]

The discovery of lytic polysaccharide monooxygenases (LPMOs), a family of copper-dependent enzymes that play a major role in polysaccharide degradation, has revealed the importance of oxidoreductases in the biological utilization of biomass. In fungi, a range of redox proteins have been implicated as working in harness with LPMOs to bring about polysaccharide oxidation. In bacteria, less is known about the interplay between redox proteins and LPMOs, or how the interaction between the two contributes to polysaccharide degradation. We therefore set out to characterize two previously unstudied proteins from the shipworm symbiont Teredinibacter turnerae that were initially identified by the presence of carbohydrate binding domains appended to uncharacterized domains with probable redox functions. Here, X-ray crystal structures of several domains from these proteins are presented together with initial efforts to characterize their functions. The analysis suggests that the target proteins are unlikely to function as LPMO electron donors, raising new questions as to the potential redox functions that these large extracellular multi-haem-containing c-type cytochromes may perform in these bacteria., (open access.)

Highly accurate protein structure prediction can generate accurate models of protein and protein-protein complexes in X-ray crystallography. However, the question of how to make more effective use of predicted models for completing structure analysis, and which strategies should be employed for the more challenging cases such as multi-helical structures, multimeric structures and extremely large structures, both in the model preparation and in the completion steps, remains open for discussion. In this paper, a new strategy is proposed based on the framework of direct methods and dual-space iteration, which can greatly simplify the pre-processing steps of predicted models both in normal and in challenging cases. Following this strategy, full-length models or the conservative structural domains could be used directly as the starting model, and the phase error and the model bias between the starting model and the real structure would be modified in the direct-methods-based dual-space iteration. Many challenging cases (from CASP14) have been tested for the general applicability of this constructive strategy, and almost complete models have been generated with reasonable statistics. The hybrid strategy therefore provides a meaningful scheme for X-ray structure determination using a predicted model as the starting point., (open access.)

The application of double electron‐electron resonance (DEER) with site‐directed spin labeling (SDSL) to measure distances in proteins and protein complexes in living cells puts rigorous restraints on the spin‐label. The linkage and paramagnetic centers need to resist the reducing conditions of the cell. Rigid attachment of the probe to the protein improves precision of the measured distances. Here, three two‐armed GdIII complexes, GdIII‐CLaNP13a/b/c were synthesized. Rather than the disulfide linkage of most other CLaNP molecules, a thioether linkage was used to avoid reductive dissociation of the linker. The doubly GdIII labeled N55C/V57C/K147C/T151C variants of T4Lysozyme were measured by 95 GHz DEER. The constructs were measured in vitro, in cell lysate and in Dictyostelium discoideum cells. Measured distances were 4.5 nm, consistent with results from paramagnetic NMR. A narrow distance distribution and typical modulation depth, also in cell, indicate complete and durable labeling and probe rigidity due to the dual attachment sites. [ABSTRACT FROM AUTHOR]

The hexameric p97 enzyme plays an integral role in cellular homeostasis. Large changes to the orientation of its N‐terminal domains (NTDs), corresponding to NTD‐down (p97‐ADP) or NTD‐up (p97‐ATP), accompany ATP hydrolysis. The NTDs in a series of p97 disease mutants interconvert rapidly between up and down conformations when p97 is in the ADP‐bound state. While the populations of up and down NTDs can be determined from bulk measurements, information about the cooperativity of the transition between conformations is lacking. Here we use cryo‐EM to determine populations of the 14 unique up/down NTD states of the homo‐hexameric R95G disease‐causing p97 ring, showing that NTD orientations do not depend on those of neighboring subunits. In contrast, NMR studies establish that inter‐protomer cooperativity is important for regulating the orientation of NTDs in p97 particles comprising mixtures of different subunits, such as wild‐type and R95G, emphasizing the synergy between cryo‐EM and NMR in establishing how the components of p97 function. [ABSTRACT FROM AUTHOR]

Summary of main observation and conclusion: The active Ras subfamily GTPases, Rap1 and Ras, can be specifically recognized by the SPN domain of SHANK3, mutations of which are associated with many neuropsychiatric diseases such as autism spectrum disorder (ASD). However, the mechanistic bases underlying the interactions of SHANK3 SPN and those Ras subfamily proteins are still elusive. Here, we reported the crystal structures of SHANK3 SPN in complex with the GTP‐bound Rap1b and the Ras‐mimetic Rap1b E30D/K31E double mutant. In addition to uncovering the detailed molecular mechanism governing the specific interactions of SHANK3 SPN with those Ras subfamily proteins, the determined structures also reveal a general binding mode between SHANK3 SPN and its associated Ras subfamily proteins. Finally, our study also provides mechanistic insights into two ASD‐causing R12C and L68P mutations found in the SPN domain of SHANK3, and expands our understanding of the etiology of neuropsychiatric diseases caused by defective SHANK3. [ABSTRACT FROM AUTHOR]

Protein 3D structures support their biological functions. As the number of protein structures is negligible in regards to the number of available protein sequences, prediction methodologies relying only on protein sequences are essential tools. In this field, protein secondary structure prediction (PSSPs) is a mature area, and is considered to have reached a plateau. Nonetheless, proteins are highly dynamical macromolecules, a property that could impact the PSSP methods. Indeed, in a previous study, the stability of local protein conformations was evaluated demonstrating that some regions easily changed to another type of secondary structure. The protein sequences of this dataset were used by PSSPs and their results compared to molecular dynamics to investigate their potential impact on the quality of the secondary structure prediction. Interestingly, a direct link is observed between the quality of the prediction and the stability of the assignment to the secondary structure state. The more stable a local protein conformation is, the better the prediction will be. The secondary structure assignment not taken from the crystallized structures but from the conformations observed during the dynamics slightly increase the quality of the secondary structure prediction. These results show that evaluation of PSSPs can be done differently, but also that the notion of dynamics can be included in development of PSSPs and other approaches such as de novo approaches. Image 1 • Assessment of protein secondary structure prediction was done in the light of protein dynamics. • A direct link was observed between the quality of the prediction and the stability of the assignment to the secondary structure state. • More a local protein conformation was stable, better was the prediction. • The notion of dynamics can be included in development of protein secondary structure prediction and other approaches. [ABSTRACT FROM AUTHOR]

Summary of main observation and conclusion: The active Ras subfamily GTPases, Rap1 and Ras, can be specifically recognized by the SPN domain of SHANK3, mutations of which are associated with many neuropsychiatric diseases such as autism spectrum disorder (ASD). However, the mechanistic bases underlying the interactions of SHANK3 SPN and those Ras subfamily proteins are still elusive. Here, we reported the crystal structures of SHANK3 SPN in complex with the GTP‐bound Rap1b and the Ras‐mimetic Rap1b E30D/K31E double mutant. In addition to uncovering the detailed molecular mechanism governing the specific interactions of SHANK3 SPN with those Ras subfamily proteins, the determined structures also reveal a general binding mode between SHANK3 SPN and its associated Ras subfamily proteins. Finally, our study also provides mechanistic insights into two ASD‐causing R12C and L68P mutations found in the SPN domain of SHANK3, and expands our understanding of the etiology of neuropsychiatric diseases caused by defective SHANK3. [ABSTRACT FROM AUTHOR]

Human diseases are attributed in part to the ability of pathogens to evade the eukaryotic immune systems. A subset of these pathogens has developed mechanisms to survive in human macrophages. Yersinia pestis, the causative agent of the bubonic plague, is a predominately extracellular pathogen with the ability to survive and replicate intracellularly. A previous study has shown that a novel rip (required for intracellular proliferation) operon (ripA, ripB and ripC) is essential for replication and survival of Y. pestis in postactivated macrophages, by playing a role in lowering macrophage-produced nitric oxide (NO) levels. A bioinformatics analysis indicates that the rip operon is conserved among a distally related subset of macrophage-residing pathogens, including Burkholderia and Salmonella species, and suggests that this previously uncharacterized pathway is also required for intracellular survival of these pathogens. The focus of this study is ripA, which encodes for a protein highly homologous to 4-hydroxybutyrate-CoA transferase; however, biochemical analysis suggests that RipA functions as a butyryl-CoA transferase. The 1.9 Å X-ray crystal structure reveals that RipA belongs to the class of Family I CoA transferases and exhibits a unique tetrameric state. Molecular dynamics simulations are consistent with RipA tetramer formation and suggest a possible gating mechanism for CoA binding mediated by Val227. Together, our structural characterization and molecular dynamic simulations offer insights into acyl-CoA specificity within the active site binding pocket, and support biochemical results that RipA is a butyryl-CoA transferase. We hypothesize that the end product of the rip operon is butyrate, a known anti-inflammatory, which has been shown to lower NO levels in macrophages. Thus, the results of this molecular study of Y. pestis RipA provide a structural platform for rational inhibitor design, which may lead to a greater understanding of the role of RipA in this unique virulence pathway.

Membrane proteins require lipid bilayers for function. While lipid compositions reach enormous complexities, high‐resolution structures are usually obtained in artificial detergents. To understand whether and how lipids guide membrane protein function, we use single‐molecule FRET to probe the dynamics of DtpA, a member of the proton‐coupled oligopeptide transporter (POT) family, in various lipid environments. We show that detergents trap DtpA in a dynamic ensemble with cytoplasmic opening. Only reconstitutions in more native environments restore cooperativity, allowing an opening to the extracellular side and a sampling of all relevant states. Bilayer compositions tune the abundance of these states. A novel state with an extreme cytoplasmic opening is accessible in bilayers with anionic head groups. Hence, chemical diversity of membranes translates into structural diversity, with the current POT structures only sampling a portion of the full structural space. [ABSTRACT FROM AUTHOR]

[FeFe] hydrogenases are the most active H2 converting catalysts in nature, but their extreme oxygen sensitivity limits their use in technological applications. The [FeFe] hydrogenases from sulfate reducing bacteria can be purified in an O2‐stable state called Hinact. To date, the structure and mechanism of formation of Hinact remain unknown. Our 1.65 Å crystal structure of this state reveals a sulfur ligand bound to the open coordination site. Furthermore, in‐depth spectroscopic characterization by X‐ray absorption spectroscopy (XAS), nuclear resonance vibrational spectroscopy (NRVS), resonance Raman (RR) spectroscopy and infrared (IR) spectroscopy, together with hybrid quantum mechanical and molecular mechanical (QM/MM) calculations, provide detailed chemical insight into the Hinact state and its mechanism of formation. This may facilitate the design of O2‐stable hydrogenases and molecular catalysts. [ABSTRACT FROM AUTHOR]

Herein, we report the biosynthesis of protein heterocatenanes using a programmed sequence of multiple post‐translational processing events including intramolecular chain entanglement, in situ backbone cleavage, and spontaneous cyclization. The approach is general, autonomous, and can obviate the need for any additional enzymes. The catenane topology was convincingly proven using a combination of SDS‐PAGE, LC‐MS, size exclusion chromatography, controlled proteolytic digestion, and protein crystallography. The X‐ray crystal structure clearly shows two mechanically interlocked protein rings with intact folded domains. It opens new avenues in the nascent field of protein‐topology engineering. [ABSTRACT FROM AUTHOR]

Summary of main observation and conclusion: Collismycins (COLs) are antibiotics characterized by a 2,2′‐bipyridine (2,2′‐BP) core composed of a trisubstituted ring A and an unmodified ring B. The 2,2′‐BP core, which possesses metal‐chelating ability and plays key roles in various biological activities of COLs, is biosynthesized by a nonribosomal peptide synthetase (NRPS)‐polyketide synthase (PKS) hybrid machinery. The starter module of the NRPS‐PKS hybrid machinery consists of a type II peptidyl carrier protein (PCP) ColA1a and an adenylation protein ColA1b. We here report the functional characterization of ColA1a and ColA1b in vitro, confirming their functions in selection and loading of picolinic acid (PA), instead of normal amino acid substrates, as the origin of ring B in COLs. The 2.1 Å crystal structure of ColA1a was solved, revealing structural features including the additional helices α1a, α1b and missing helix α3, which may reflect unique interactions of ColA1a with other NRPS‐PKS proteins/domains or substrate. Primary and tertiary structural comparison of ColA1a with other PCPs revealed the structural basis for their typical α‐helical bundle, providing a better understanding of the structural flexibility of PCPs. These results facilitate the starter module engineering for the generation of COL derivatives with ring B modifications in the future. [ABSTRACT FROM AUTHOR]

Summary of main observation and conclusion: Collismycins (COLs) are antibiotics characterized by a 2,2′‐bipyridine (2,2′‐BP) core composed of a trisubstituted ring A and an unmodified ring B. The 2,2′‐BP core, which possesses metal‐chelating ability and plays key roles in various biological activities of COLs, is biosynthesized by a nonribosomal peptide synthetase (NRPS)‐polyketide synthase (PKS) hybrid machinery. The starter module of the NRPS‐PKS hybrid machinery consists of a type II peptidyl carrier protein (PCP) ColA1a and an adenylation protein ColA1b. We here report the functional characterization of ColA1a and ColA1b in vitro, confirming their functions in selection and loading of picolinic acid (PA), instead of normal amino acid substrates, as the origin of ring B in COLs. The 2.1 Å crystal structure of ColA1a was solved, revealing structural features including the additional helices α1a, α1b and missing helix α3, which may reflect unique interactions of ColA1a with other NRPS‐PKS proteins/domains or substrate. Primary and tertiary structural comparison of ColA1a with other PCPs revealed the structural basis for their typical α‐helical bundle, providing a better understanding of the structural flexibility of PCPs. These results facilitate the starter module engineering for the generation of COL derivatives with ring B modifications in the future. [ABSTRACT FROM AUTHOR]

In recent years, three‐dimensional density maps reconstructed from single particle images obtained by electron cryo‐microscopy (cryo‐EM) have reached unprecedented resolution. However, map interpretation can be challenging, in particular if the constituting structures require de‐novo model building or are very mobile. Herein, we demonstrate the potential of convolutional neural networks for the annotation of cryo‐EM maps: our network Haruspex has been trained on a carefully curated set of 293 experimentally derived reconstruction maps to automatically annotate RNA/DNA as well as protein secondary structure elements. It can be straightforwardly applied to newly reconstructed maps in order to support domain placement or as a starting point for main‐chain placement. Due to its high recall and precision rates of 95.1 % and 80.3 %, respectively, on an independent test set of 122 maps, it can also be used for validation during model building. The trained network will be available as part of the CCP‐EM suite. [ABSTRACT FROM AUTHOR]

Using prediction and experimental determination, we compared the RNA‐editing sites in chloroplast protein‐coding genes in an early‐maturity mutant (KFJT‐1) induced by carbon‐ion beam irradiation in sweet sorghum and its wild type (KFJT‐CK). Twenty‐two and 20 editing sites were identified in the KFJT‐CK and KFJT‐1 chloroplast, respectively, and the differential editing sites between KFJT‐CK and KFJT‐1 were mainly in mat, ndh and rpo genes. Furthermore, mutations in RNA‐editing sites in KFJT‐1 affected the structure of the encoded protein, which implying that RNA‐editing events might influence the function of essential genes. Finally, a comparative analysis of the RNA‐editing events between KFJT‐1 and other 10 Poaceae species revealed that the RNA‐editing sites in matK‐1002, rpoC1‐1163 and rpoC2‐242 were unique to KFJT‐1. This suggested that RNA‐editing events due to carbon‐ion beam irradiation affected the structure of the encode proteins, thereby influenced their biological functions. This study is the first to report on the variation in chloroplast RNA‐editing patterns induced by carbon‐ion beams irradiation, and its effect on the chloroplast in KFJT‐1 at the post‐transcriptional level. [ABSTRACT FROM AUTHOR]

We studied and compared in detail an elusive matrix open (m‐state) and cytoplasmic open (c‐state) state of ADP/ATP carrier (AAC) protein embedded in the DOPC bilayer by microsecond molecular dynamics (MD) simulations. We analyzed both states with and without cardiolipin (CDL) molecules, with a special emphasis on the recently obtained crystallographic structure of the AAC m‐state. The obtained results show that both states of the protein are stable in the DOPC bilayer and impermeable to water. In comparison with the c‐state of AAC, the m‐state is more dynamic, but at the same time possesses a larger occluded area in the protein cavity. Both states of the protein are less flexible in simulations when CDL molecules are present, which is especially visible for the m‐state. Finally, the analysis of the protein conformational changes during MD simulations shows that protein parts at the protein/lipid boundaries are prone to larger conformational changes in contrast to central region of the protein embedded in the bilayer core, thus further supporting the cycling mechanism suggested for ADP/ATP exchange by AAC. [ABSTRACT FROM AUTHOR]

The hydrogen evolution reaction (HER), catalysed by proteins at mercury electrodes and reflected in chronopotentiometric stripping peak H, provides a label-free and reagentless analytical technique that is sensitive to protein structure. Here we show how the kinetic isotope effect affected the HER catalysed by the protein bovine serum albumin (BSA). We found that the deuteron bond, which is stronger than that of a proton, contributed to less effective transport of deuterons mediated by BSA at the HgjD2O interface, and enhanced structural stability of the surface-attached native BSA in D2O solution. A structural transition was also observed in the surface-attached urea-denatured BSA, and is probably due to the destabilisation of some secondary structural remnants retained by the 17 SSbonds. Because the catalytically active groups involved in proton or deuteron transfer in native proteins are often exposed towards solutions and their protons exchange almost instantly, no signs of H/D exchange were observed in native BSA using peak H under the given conditions. [ABSTRACT FROM AUTHOR]

The enoyl‐acyl carrier protein reductase enzyme FabI is essential for fatty acid biosynthesis in Staphylococcus aureus and represents a promising target for the development of novel, urgently needed anti‐staphylococcal agents. Here, we elucidate the mode of action of the kalimantacin antibiotics, a novel class of FabI inhibitors with clinically‐relevant activity against multidrug‐resistant S. aureus. By combining X‐ray crystallography with molecular dynamics simulations, in vitro kinetic studies and chemical derivatization experiments, we characterize the interaction between the antibiotics and their target, and we demonstrate that the kalimantacins bind in a unique conformation that differs significantly from the binding mode of other known FabI inhibitors. We also investigate mechanisms of acquired resistance in S. aureus and identify key residues in FabI that stabilize the binding of the antibiotics. Our findings provide intriguing insights into the mode of action of a novel class of FabI inhibitors that will inspire future anti‐staphylococcal drug development. [ABSTRACT FROM AUTHOR]

The most common denominator of many of the neurodegenerative diseases is badly folded protein accumulation, which results in the formation of insoluble protein deposits located in different parts of the organism, causing cell death and tissue degeneration. Dendritic systems have turned out to be a promising new therapeutic approach for the treatment of these diseases due to their ability to modulate the folding of these proteins. With this perspective, and focused on type 2 diabetes (T2D), characterized by the presence of deposits containing the amyloidogenic islet amyloid polypeptide (IAPP), we demonstrate how different topologies of cationic carbosilane dendrimers inhibit the formation of insoluble protein deposits in pancreatic islets isolated from transgenic Tg‐hIAPP mice. Also, the results obtained by the modification of dendritic carbosilane wedges with the chemical chaperone 4‐phenylbutyric acid (4‐PBA) at the focal point confirmed their potential as anti‐amyloid agents with a concentration efficiency in their therapeutic action five orders of magnitude lower than that observed for free 4‐PBA. Computational studies, which determined the main interaction between IAPP and dendrimers at the atomic level, support the experimental work. [ABSTRACT FROM AUTHOR]

To investigate the structural impact of phosphorylation on the human histone H1.0 C‐terminal domain, we performed NMR structural studies of model peptides containing a single phosphorylation site: T118‐H1.0 (T118PKK motif) and T140‐H1.0 (T140PVK motif). Both model peptides are mainly disordered in aqueous solution in their non‐phosphorylated and phosphorylated forms, but become structured in the presence of trifluoroethanol. The peptides T118‐H1.0 and pT118‐H1.0 contain two helical regions, a long amphipathic α helix spanning residues 104–115 and a short α/310 helix (residues 119–123), that are almost perpendicular in T118‐H1.0 but have a poorly defined orientation in pT118‐H1.0. Peptides T140‐H1.0 and pT140‐H1.0 form very similar α helices between residues 141–147. The TPKK and TPVK motifs show the same backbone conformation, but differ in their side‐chain contacts; the Thr and pThr side chains interact with the i+2 Lys side chain in the TPKK motif, and with the i+3 Lys side chain in the TPVK motif. The pT phosphate group in pT118‐H1.0 and pT140‐H1.0 has pKa values below the intrinsic values, which can be explained by non‐specific charge–charge interactions with nearby Lys. The non‐polar Val in the TPVK motif accounts for the pT140 pKa being closer to the intrinsic pKa value than the pT118 pKa. Altogether, these results validate that minimalist strategies using model peptides can provide structural details difficult to obtain in short‐lived intrinsically disordered proteins and domains. [ABSTRACT FROM AUTHOR]

Despite CYP102A1 (P450BM3) representing one of the most extensively researched metalloenzymes, crystallisation of its haem domain upon modification can be a challenge. Crystal structures are indispensable for the efficient structure‐based design of P450BM3 as a biocatalyst. The abietane diterpenoid derivative N‐abietoyl‐l‐tryptophan (AbiATrp) is an outstanding crystallisation accelerator for the wild‐type P450BM3 haem domain, with visible crystals forming within 2 hours and diffracting to a near‐atomic resolution of 1.22 Å. Using these crystals as seeds in a cross‐microseeding approach, an assortment of P450BM3 haem domain crystal structures, containing previously uncrystallisable decoy molecules and diverse artificial metalloporphyrins binding various ligand molecules, as well as heavily tagged haem‐domain variants, could be determined. Some of the structures reported herein could be used as models of different stages of the P450BM3 catalytic cycle. [ABSTRACT FROM AUTHOR]

Vibralactone is isolated from the basidiomycete fungus Boreostereum vibrans as one of the strongest lipase inhibitors. Its unusual β‐lactone‐fused bicycle is derived from an aryl ring moiety by an oxidative ring‐expansion prior to an intramolecular cyclization. Herein, we report the discovery of the cyclase VibC which belongs to the α/β‐hydrolase superfamily and is involved in the vibralactone biosynthesis. Biochemical and crystal studies suggest that VibC may catalyze an aldol or an electrocyclic reaction initiated by the Ser‐His‐Asp catalytic triad. For the aldol and pericyclic chemistry in living cells, VibC is a unique hydrolase performing the carbocycle formation of an oxepinone to a fused bicyclic β‐lactone. This presents a naturally occurring, new enzymatic reaction in both aldol and hydrolase (bio)chemistry that will guide future exploitation of these enzymes in synthetic biology for chemical‐diversity expansion of natural products. [ABSTRACT FROM AUTHOR]

Modified residues present in proteins are the result of post‐translational modifications (PTMs). These PTMs increase the functional diversity of the proteome and influence various biological processes and diseased conditions. Therefore, identification and understanding of PTMs in various protein structures is of great significance. In view of this, an online database, Inserted and Modified Residues in Protein Structures (IMRPS), has been developed. IMRPS is a derived database that furnishes information on the residues modified and inserted in the protein structures available in the Protein Data Bank (PDB). The database is equipped with a graphical user interface and has an option to view the data for non‐redundant protein structures (25 and 90%) as well. A quality criteria cutoff has been incorporated to assist in displaying the specific set of PDB codes. The entire protein structure along with the inserted or modified residues can be visualized in JSmol. This database will be updated regularly (presently, every three months) and can be accessed through the URL http://cluster.physics.iisc.ac.in/imrps/. [ABSTRACT FROM AUTHOR]

A non-redundant set of 231 protein crystal structures refined at a resolution better than (or equal to) 1 Å was extracted from the Protein Data Bank and the degree of conformational rigidity at the protein-water interface was examined by means of the Hirshfeld test and by comparing the orientations of the anisotropic Us for contacting protein and water atoms. Contacts between protein and water atoms are more rigid that contacts between water atoms and the degree of rigidity increases for shorter contacts and for more hydrogen-bonded atoms. Nevertheless, water and protein atoms are not rigidly held together. On the contrary, they seem to have little influence on their mobility to such an extent that hydration water, different from the protein atoms, cannot be considered to be properly in the solid state [ABSTRACT FROM AUTHOR]

A novel series of C12‐keto‐type saxitoxin (STX) derivatives bearing an unusual nonhydrated form of the ketone at C12 has been synthesized, and their NaV‐inhibitory activity has been evaluated in a cell‐based assay as well as whole‐cell patch‐clamp recording. Among these compounds, 11‐benzylidene STX (3 a) showed potent inhibitory activity against neuroblastoma Neuro 2A in both cell‐based and electrophysiological analyses, with EC50 and IC50 values of 8.5 and 30.7 nm, respectively. Interestingly, the compound showed potent inhibitory activity against tetrodotoxin‐resistant subtype of NaV1.5, with an IC50 value of 94.1 nm. Derivatives 3 a–d and 3 f showed low recovery rates from NaV1.2 subtype (ca 45–79 %) compared to natural dcSTX (2), strongly suggesting an irreversible mode of interaction. We propose an interaction model for the C12‐keto derivatives with NaV in which the enone moiety in the STX derivatives 3 works as Michael acceptor for the carboxylate of Asp1717. [ABSTRACT FROM AUTHOR]

Constraining a molecule in its bioactive conformation via macrocyclization represents an attractive strategy to rationally design functional chemical probes. While this approach has been applied to enzyme inhibitors or receptor antagonists, to date it remains unprecedented for bifunctional molecules that bring proteins together, such as PROTAC degraders. Herein, we report the design and synthesis of a macrocyclic PROTAC by adding a cyclizing linker to the BET degrader MZ1. A co‐crystal structure of macroPROTAC‐1 bound in a ternary complex with VHL and the second bromodomain of Brd4 validated the rational design. Biophysical studies revealed enhanced discrimination between the second and the first bromodomains of BET proteins. Despite a 12‐fold loss of binary binding affinity for Brd4, macroPROTAC‐1 exhibited cellular activity comparable to MZ1. Our findings support macrocyclization as an advantageous strategy to enhance PROTAC degradation potency and selectivity between homologous targets. [ABSTRACT FROM AUTHOR]

MtmOIV and MtmW catalyze the final two reactions in the mithramycin (MTM) biosynthetic pathway, the Baeyer–Villiger opening of the fourth ring of premithramycin B (PMB), creating the C3 pentyl side chain, strictly followed by reduction of the distal keto group on the new side chain. Unexpectedly this results in a C2 stereoisomer of mithramycin, iso‐mithramycin (iso‐MTM). Iso‐MTM undergoes a non‐enzymatic isomerization to MTM catalyzed by Mg2+ ions. Crystal structures of MtmW and its complexes with co‐substrate NADPH and PEG, suggest a catalytic mechanism of MtmW. The structures also show that a tetrameric assembly of this enzyme strikingly resembles the ring‐shaped β subunit of a vertebrate ion channel. We show that MtmW and MtmOIV form a complex in the presence of PMB and NADPH, presumably to hand over the unstable MtmOIV product to MtmW, yielding iso‐MTM, as a potential self‐resistance mechanism against MTM toxicity. [ABSTRACT FROM AUTHOR]

Respiratory chain complexes convert energy by coupling electron flow to transmembrane proton translocation. Owing to a lack of atomic structures of cytochrome bc1 complex (Complex III) from thermophilic bacteria, little is known about the adaptations of this macromolecular machine to hyperthermophilic environments. In this study, we purified the cytochrome bc1 complex of Aquifex aeolicus, one of the most extreme thermophilic bacteria known, and determined its structure with and without an inhibitor at 3.3 Å resolution. Several residues unique for thermophilic bacteria were detected that provide additional stabilization for the structure. An extra transmembrane helix at the N‐terminus of cyt. c1 was found to greatly enhance the interaction between cyt. b and cyt. c1, and to bind a phospholipid molecule to stabilize the complex in the membrane. These results provide the structural basis for the hyperstability of the cytochrome bc1 complex in an extreme thermal environment. [ABSTRACT FROM AUTHOR]

Coronavirus disease 19, or COVID-19, is an infection associated with an unprecedented worldwide pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which has led to more than 215 million infected people and more than 4.5 million deaths worldwide. SARS-CoV-2 cell infection is initiated by a densely glycosylated spike (S) protein, a fusion protein, binding human angiotensin converting enzyme 2 (hACE2), that acts as the functional receptor through the receptor binding domain (RBD). In this article, the interaction of hACE2 with the RBD and how fusion is initiated after recognition are explored, as well as how mutations influence infectivity and immune response. Thus, we focused on all structures available in the Protein Data Bank for the interaction between SARS-CoV-2 S protein and hACE2. Specifically, the Delta variant carries particular mutations associated with increased viral fitness through decreased antibody binding, increased RBD affinity and altered protein dynamics. Combining both existing mutations and mutagenesis studies, new potential SARS-CoV-2 variants, harboring advantageous S protein mutations, may be predicted. These include mutations S13I and W152C, decreasing antibody binding, N460K, increasing RDB affinity, or Q498R, positively affecting both properties.

Oxygen is a key atom that maintains biomolecular structures, regulates various physiological processes, and mediates various biomolecular interactions. Oxygen-17 (17O), therefore, has been proposed as a useful probe that can provide detailed information about various physicochemical features of proteins. This is attributed to the facts that (1) 17O is an active isotope for nuclear magnetic resonance (NMR) spectroscopic approaches; (2) NMR spectroscopy is one of the most suitable tools for characterizing the structural and dynamical features of biomolecules under native-like conditions; and (3) oxygen atoms are frequently involved in essential hydrogen bonds for the structural and functional integrity of proteins or related biomolecules. Although 17O NMR spectroscopic investigations of biomolecules have been considerably hampered due to low natural abundance and the quadruple characteristics of the 17O nucleus, recent theoretical and technical developments have revolutionized this methodology to be optimally poised as a unique and widely applicable tool for determining protein structure and dynamics. In this review, we recapitulate recent developments in 17O NMR spectroscopy to characterize protein structure and folding. In addition, we discuss the highly promising advantages of this methodology over other techniques and explain why further technical and experimental advancements are highly desired.

Ice-binding proteins (IBPs) are proteins that have the remarkable ability to bind to ice, and their study has intrigued researchers for decades. This chapter explores the importance of structural biology in understanding IBPs and highlights the significant contributions of IBPs to the field of structural biology. The structures of various IBPs from different organisms have been elucidated, revealing key elements involved in ice binding. Structural biology techniques, including nuclear magnetic resonance (NMR) spectroscopy, transmission electron cryo-microscopy (cryo-EM), and X-ray crystallography, play crucial roles in solving protein structures. This article focuses on X-ray crystallography as a tool for investigating IBP structures, providing insights into its theoretical and practical aspects, experimental workflows, and common pitfalls to avoid., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Regio- and chemoselective C-H activation at multi-positions of a single molecule is fascinating but chemically challenging. The homologous cytochrome P450 enzymes IkaD and CftA catalyze multiple C-H oxidations on the same polycyclic tetramate macrolactam (PoTeM) ikarugamycin, with distinct regio- and chemoselectivity. Herein we provide mechanistic understanding of their functional differences by solving crystal structures of IkaD and CftA in complex with ikarugamycin and unnatural substrates. Distinct conformations of the F/G region in IkaD and CftA are found to differentiate the orientation of PoTeM substrates, by causing different binding patterns with polar moieties to determine site selection, oxidation order, and chemoselectivity. Fine-tuning the polar subpocket altered the regioselectivity of IkaD, indicating that substrate re-orientation by mutating residues distal to the oxidation site could serve as an important method in future engineering of P450 enzymes., (© 2023 Wiley-VCH GmbH.)

Inositol pyrophosphates (PP-IPs) are densely phosphorylated messenger molecules involved in numerous biological processes. PP-IPs contain one or two pyrophosphate group(s) attached to a phosphorylated myo-inositol ring. 5PP-IP 5 is the most abundant PP-IP in human cells. To investigate the function and regulation by PP-IPs in biological contexts, metabolically stable analogs have been developed. Here, we report the synthesis of a new fluorinated phosphoramidite reagent and its application for the synthesis of a difluoromethylene bisphosphonate analog of 5PP-IP 5 . Subsequently, the properties of all currently reported analogs were benchmarked using a number of biophysical and biochemical methods, including co-crystallization, ITC, kinase activity assays and chromatography. Together, the results showcase how small structural alterations of the analogs can have notable effects on their properties in a biochemical setting and will guide in the choice of the most suitable analog(s) for future investigations., (© 2023 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)