nils-herrmann/clean_scirepeval huggingface dataset:
A conserved two-step binding for the UAF1 regulator to the USP12 deubiquitinating enzyme
Venue: Journal of structural biology

Regulation of deubiquitinating enzyme (DUB) activity is an essential step for proper function of cellular ubiquitin signals. UAF1 is a WD40 repeat protein, which binds and activates three important DUBs, USP1, USP12 and USP46. Here, we report the crystal structure of the USP12-Ub/UAF1 complex at a resolution of 2.8 Å and of UAF1 at 2.3 Å. In the complex we find two potential sites for UAF1 binding, analogous to what was seen in a USP46/UAF1 complex. In line with these observed dual binding states, we show here that USP12/UAF1 complex has 1:2 stoichiometry in solution, with a two-step binding at 4 nM and 325 nM respectively. Mutagenesis studies show that the fingers sub-domain of USP12 interacts with UAF1 to form the high affinity interface. Our activation studies confirm that the high affinity binding is important for activation while the second UAF1 binding does not affect activation. Nevertheless, we show that this two step binding is conserved in the well-studied USP12 paralog, USP1. Our results highlight the interfaces essential for regulation of USP12 activity and show a conserved second binding of UAF1 which could be important for regulatory functions independent of USP12 activity.
Lattice distortions in coccolith calcite crystals originate from occlusion of biomacromolecules.
Venue: Journal of structural biology

During biomineralization, organisms control the formation and morphology of a mineral using biomacromolecules. The biomacromolecules that most strongly interact with the growing crystals frequently get occluded within. Such an observation has been recently obtained for the calcium carbonate producing coccolithophore species Pleurochrysis carterae. Coccolithophores are unicellular algae that produce calcified scales built from complex-shaped calcite crystals, termed coccoliths. It is unclear how widespread the phenomenon of biomacromolecular occlusion within calcite crystals is in calcifying haptophytes such as coccolithophores. Here, the coccoliths of biological replicates of the bloom forming Emiliania huxleyi are compared with that of Pleurochrysis carterae, two species with different coccolith morphologies and crystal growth mechanisms. From high-resolution synchrotron X-ray diffraction, changes in the lattice parameters of coccolith calcite, after heating to 450°C, are observed and associated with macrostrain originating from occluded biomacromolecules. We propose a mechanism governing the biomacromolecules' interaction with the growing coccolith crystals and their likely origin.
Structures of PspAG97A α-glucoside hydrolase reveal a novel mechanism for chloride induced activation.
Venue: Journal of structural biology

Here we report the first crystal structure of a secretory α-glucoside hydrolase isolated from Pseudoalteromonas sp. K8, PspAG97A, which belongs to glycoside hydrolase family 97 and exhibits halophilic property. PspAG97A lacks an acidic surface, that is considered essential for protein stability at high salinity. Interestingly, PspAG97A unusually contains a chloride ion coordinated by the guanidinium group of Arg171 and the main chain amide groups of Tyr172 and Glu173 at the active site. The structures of PspAG97A complexed with acarbose and panose demonstrate that residues Glu173, Arg171 and Asn170 for subsite +1 decide the substrate specificity of the enzyme for the α-1,6-glucosidic linkage. Structural alterations observed in the R171K variant and enzyme kinetic experiments focusing on chloride assisted activation suggest that the active site chloride serves to properly orient Glu173, Arg171 and Asn170 to facilitate substrate recognition. Furthermore, the chloride assists the binding of Glu173 to the conserved calcium ion and plays an essential role in properly positioning the base catalyst Glu456. In sum, our results provide valuable insight into the structural basis of protein halophilicity.
The nanostructure of murine alveolar bone and its changes due to type 2 diabetes.
Venue: Journal of structural biology

Alveolar bone - the bony ridge containing the tooth sockets - stands out by its remodeling activity where bone is being formed and resorbed at a much higher rate than in any other bony tissue. Teeth that are anchored in the jaw through the periodontal ligament exert very large localized loads during mastication that could lead to a unique adaptation of the collagen/mineral structure in the bone. Our aim was to characterize the nanostructure of alveolar bone and to determine the influence of diabetes on structural characteristics of the mineralized matrix. Using small- and wide-angle X-ray scattering (SAXS/WAXS), we studied a spontaneous diabetic mouse model (KK+) and its corresponding healthy controls (KK-) (n=6) to determine the size and mutual alignment of the mineral nanoparticles embedded in the collagen matrix. On cross-sections (buccal-lingual) of the first molar multiple line scans with a spatial resolution of 30μm were performed on each sample, from the lingual to the buccal side of the mandible. Mineral particle thickness and length are decreasing towards the tooth in both buccal and lingual sides of alveolar bone. While mineral particles are well aligned with the long axis of the tooth on the buccal side, they are in a quarter of the measurements oriented along two preferred directions on the lingual side. These nanostructural differences can be interpreted as the result of an asymmetric loading during mastication, leading to a tilting of the tooth in its socket. In diabetic mice particle thicknesses are smaller compared to control animals.
Structural and functional analyses of PolyProline-II helices in globular proteins.
Venue: Journal of structural biology

PolyProline-II (PPII) helices are defined as a continuous stretch of a protein chain in which the constituent residues have backbone torsion angle (φ, ψ) values of (-75°, 145°) and take up an extended left handed helical conformation, without any intra-chain hydrogen bonds. They are found to occur quite frequently in protein structures, with their number exceeding that of π-helices, though it is considerably less than that of α-helices and β-strands. A relatively new procedure, ASSP, for the identification of regular secondary structures using Cα trace identifies 3597 PPII-helices in 3582 protein chains, solved at resolution ⩽2.0Å. Taking advantage of this significantly expanded database of PPII-helices, we have analyzed their structural and functional roles as well as determined the amino acid propensity within and around them. Though Pro residues are highly preferred, their presence is not a mandatory requirement for the formation of PPII-helices, since ∼40% PPII-helices were found to contain no Pro residues. Aromatic amino acids are avoided within this helix, while Gly, Asn and Asp residues are preferred in the proximal flanking regions. The PPII-helices range from 3 to 13 residues in length with the average twist and rise being -121.2°±9.2° and 3.0Å±0.1Å respectively. A majority (∼72%) of PPII-helices were found to occur in conjunction with α-helices and β-strands, and serve as linkers as well. The analysis of various intra-helical non-bonded interactions revealed frequent presence of CH⋯O H-bonds. PPII-helices participate in maintaining the three-dimensional structure of proteins and are important constituents of binding motifs involved in various biological functions.
Studying the role of cooperative hydration in stabilizing folded protein states
Venue: Journal of structural biology

Understanding and modelling protein folding remains a key scientific and engineering challenge. Two key questions in protein folding are (1) why many proteins adopt a folded state and (2) how these proteins transition from the random coil ensemble to a folded state. In this paper we employ molecular dynamics simulations to address the first of these questions. Computational methods are well-placed to address this issue due to their ability to analyze systems at atomic-level resolution. Traditionally, the stability of folded proteins has been ascribed to the balance of two types of intermolecular interactions: hydrogen-bonding interactions and hydrophobic contacts. In this study, we explore a third type of intermolecular interaction: cooperative hydration of protein surface residues. To achieve this, we consider multiple independent simulations of the villin headpiece domain to quantify the contributions of different interactions to the energy of the native and fully extended states. In addition, we consider whether these findings are robust with respect to the protein forcefield, the water model, and the presence of salt. In all cases, we identify many cooperatively hydrated interactions that are transient but energetically favor the native state. Whilst further work on additional protein structures, forcefields, and water models is necessary, these results suggest a role for cooperative hydration in protein folding that should be explored further. Rational design of cooperative hydration on the protein surface could be a viable strategy for increasing protein stability.
Iterative projection algorithms for ab initio phasing in virus crystallography.
Venue: Journal of structural biology

Iterative projection algorithms are proposed as a tool for ab initio phasing in virus crystallography. The good global convergence properties of these algorithms, coupled with the spherical shape and high structural redundancy of icosahedral viruses, allows high resolution phases to be determined with no initial phase information. This approach is demonstrated by determining the electron density of a virus crystal with 5-fold non-crystallographic symmetry, starting with only a spherical shell envelope. The electron density obtained is sufficiently accurate for model building. The results indicate that iterative projection algorithms should be routinely applicable in virus crystallography, without the need for ancillary phase information.
Nonclassical crystallization in vivo et in vitro (II): Nanogranular features in biomimetic minerals disclose a general colloid-mediated crystal growth mechanism.
Venue: Journal of structural biology

Recent research has shown that biominerals and their biomimetics (i) typically form via an amorphous precursor phase, and (ii) commonly display a nanogranular texture. Apparently, these two key features are closely related, underlining the fact that the formation of biominerals and their biomimetics does not necessarily follow classical crystallization routes, and leaves a characteristic nanotextural imprint which may help to disclose their origins and formation mechanisms. Here we present a general overview of the current theories and models of nonclassical crystallization and their applicability for the advance of our current understanding of biomineralization and biomimetic mineralization. We pay particular attention to the link between nonclassical crystallization routes and the resulting nanogranular textures of biomimetic CaCO3 mineral structures. After a general introductory section, we present an overview of classical nucleation and crystal growth theories and their limitations. Then, we introduce the Ostwald's step rule as a general framework to explain nonclassical crystallization. Subsequently, we describe nonclassical crystallization routes involving stable prenucleation clusters, dense liquid and solid amorphous precursor phases, as well as current nonclassical crystal growth models. The latter include oriented attachment, mesocrystallization and the new model based on the colloidal growth of crystals via attachment of amorphous nanoparticles. Biomimetic examples of nanostructured CaCO3 minerals formed via these nonclassical routes are presented which help us to show that colloid-mediated crystal growth can be regarded as a wide-spread growth mechanism. Implications of these observations for the advance in the current understanding on the formation of biomimetic materials and biominerals are finally outlined.
High-resolution structural and elemental analyses of calcium storage structures synthesized by the noble crayfish Astacus astacus.
Venue: Journal of structural biology

During premolt, crayfish develop deposits of calcium ions, called gastroliths, in their stomach wall. The stored calcium is used for the calcification of parts of the skeleton regularly renewed for allowing growth. Structural and molecular analyses of gastroliths have been primarily performed on three crayfish species, Orconectes virilis, Procambarus clarkii, and more recently, Cherax quadricarinatus. We have performed high-resolution analyses of gastroliths from the native noble crayfish, Astacus astacus, focusing on the microstructure, the mineralogical and elemental composition and distribution in a comparative perspective. Field emission scanning electron microscopy (FESEM) and atomic force microscopy (AFM) observations showed a classical layered microstructure composed of 200-nm diameter granules aligned along fibers. These granules are themselves composed of agglomerated nanogranules of 50nm-mean diameters. Denser regions of bigger fused granules are also present. Micro-Raman spectroscopy show that if A. astacus gastroliths, similarly to the other analyzed gastroliths, are mainly composed of amorphous calcium carbonate (ACC), they are also rich in amorphous calcium phosphate (ACP). The presence of a carotenoid pigment is also observed in A. astacus gastrolith contrary to C. quadricarinatus. Energy-dispersive X-ray spectroscopy (EDX) analyses demonstrate the presence of minor elements such as Mg, Sr, Si and P. The distribution of this last element is particularly heterogeneous. X-ray absorption near edge structure spectroscopy (XANES) reveals an alternation of layers more or less rich in phosphorus evidenced in the mineral phase as well as in the organic matrix in different molecular forms. Putative functions of the different P-comprising molecules are discussed.
Structures of type IV pilins from Thermus thermophilus demonstrate similarities with type II secretion system pseudopilins
Venue: Journal of structural biology

Type IV pilins are proteins which form polymers that extend from the surface of the bacterial cell; they are involved in mediating a wide variety of functions, including adhesion, motility and natural competence. Here we describe the determination of the crystal structures of three type IVa pilins proteins from the thermophile Thermus thermophilus. They form part of a cluster of pilus-like proteins within the genome; our results show that one, Tt1222, is very closely related to the main structural type IV pilin, PilA4. The other two, Tt1218 and Tt1219, also adopt canonical pilin-like folds but, interestingly, are most closely related to the structures of the type II secretion system pseudopilins, EpsI/GspI and XcpW/GspJ. GspI and GspJ have been shown to form a complex with another pseudopilin, GspK, and this heterotrimeric complex is known to play a key role in initiating assembly of a pseudopilus which is thought to drive the secretion process. The structural similarity of Tt1218 and Tt1219 to GspI and GspJ suggests that they might work in a similar way, to deliver functions associated with type IV pili in T. thermophilus, such as natural competence.
Nitrogen depletion in Arthrospira sp. PCC 8005, an ultrastructural point of view.
Venue: Journal of structural biology

In cyanobacteria, the nitrogen and carbon metabolisms are functionally bridged and consequently respond to the carbon-to-nitrogen ratio. Consequently, a nitrogen deficiency results in carbon excess. For the first time, the biological adaptation of Arthrospira sp. PCC 8005 to nitrogen starvation has been deeply characterized at the cellular structure scale. The results indicated that the carbon excess is rerouted into carbon storage granules, such as the polyhydroxyalkanoate and glycogen granules corroborating existing data. Additionally, this photosynthetic organism hugely secreted exopolysaccharides, which could constitute another biological carbon reservoir. It has been reported that few cells in trichomes of Arthrospira sp. PCC 8005 still display a high level of fluorescence after a long-term nitrogen starvation. The transmission electron microscopy showed that some cells still contained thylakoids and phycobilisomes after this long-term nitrogen starvation, which could explain the remaining fluorescence.
Crystal structure of pentapeptide-independent chemotaxis receptor methyltransferase (CheR) reveals idiosyncratic structural determinants for receptor recognition.
Venue: Journal of structural biology

Chemotactic methyltransferase, CheR catalyse methylation of specific glutamate residues in the cytoplasmic domain of methyl-accepting chemotactic protein receptors (MCPRs). The methylation of MCPRs is essential for the chemical sensing and chemotactic bacterial mobility towards favorable chemicals or away from unfavorable ones. In this study, crystal structure of B. subtilis CheR (BsCheR) in complex with S-adenosyl-l-homocysteine (SAH) has been determined to 1.8Å resolution. This is the first report of crystal structure belonging to the pentapeptide-independent CheR (PICheR) class. Till date, only one crystal structure of CheR from S. typhimurium (StCheR) belonging to pentapeptide-dependent CheR (PDCheR) class is available. Structural analysis of BsCheR reveals a helix-X-helix motif (HXH) with Asp53 as the linker residue in the N-terminal domain. The key structural features of the PDCheR β-subdomain involved in the formation of a tight complex with the pentapeptide binding motif in MCPRs were found to be absent in the structure of BsCheR. Additionally, isothermal titration calorimetry (ITC) experiments were performed to investigate S-adenosyl-(l)-methionine (SAM) binding affinity and KD was determined to be 0.32mM. The structure of BsCheR reveals that mostly residues of the large C-terminal domain contribute to SAH binding, with contributions of few residues from the linker region and the N-terminal domain. Structural investigations and sequence analysis carried out in this study provide critical insights into the distinct receptor recognition mechanism of the PDCheR and PICheR methyltransferase classes.
An atypical segment swap in the DN and DC domains of the Acr_tran family resistance-nodulation-cell division pump.
Venue: Journal of structural biology

Domain/segment swapping is an exchange of equivalent secondary structure element(s) among two or more protein domains resulting in the reconstitution of the original fold while simultaneously causing oligomerization. Here we report an example of the outer membrane factor docking region of the Acr_tran family (PF00873) resistance-nodulation-cell division pump, in which a swapped, misfolded state, of the ferredoxin-like fold of the DN and DC domains, effectuates oligomerization. The atypical segment swap and the associated displacement of a region of the ferredoxin-like fold leads to a topology that is distinct from the original fold. To our knowledge, such segment swaps and associated fold change are rare. This exemplifies the role of functional constraints including oligomerization that determine the interplay between sequence and the three-dimensional structure of proteins.
Proteins of well-defined structures can be designed without backbone readjustment by a statistical model.
Venue: Journal of structural biology

We report that using mainly a statistical energy model, protein sequence design for designable backbones can be carried out with high confidence without considering backbone relaxation. A recently-developed statistical energy function for backbone-based protein sequence design has been rationally revised to improve its accuracy. As a demonstrative example, this revised model is applied to design a de novo protein for a target backbone for which the previous model had relied on after-design directed evolution to produce a well-folded protein. The actual backbone structure of the newly designed protein agrees excellently with the corresponding target. Besides presenting a new protein design protocol with experimentally verifications on different backbone types, our study implies that with an energy model of an appropriate resolution, proteins of well-defined structures instead of molten globules can be designed without the explicit consideration of backbone variations due to side chain changes, even if the side chain changes correspond to complete sequence redesigns.
A simple and fast approach for missing-wedge invariant classification of subtomograms extracted from filamentous structures.
Venue: Journal of structural biology

Unsupervised classification of subtomograms extracted from cryo-electron tomograms is often challenging due to the presence of a missing wedge in tomographic data. Here, we propose a simple new approach to classify subtomograms extracted from cryo-electron tomograms of filamentous objects. This unsupervised classification approach uses the 1D projections of the subtomograms for classification and works independently of the orientations of the missing wedge. We applied this approach to subtomograms from eukaryotic cilia and successfully detected heterogeneity including structural polymorphism of dynein molecules.
Theoretical modeling of multiprotein complexes by iSPOT: Integration of small-angle X-ray scattering, hydroxyl radical footprinting, and computational docking.
Venue: Journal of structural biology

Structural determination of protein-protein complexes such as multidomain nuclear receptors has been challenging for high-resolution structural techniques. Here, we present a combined use of multiple biophysical methods, termed iSPOT, an integration of shape information from small-angle X-ray scattering (SAXS), protection factors probed by hydroxyl radical footprinting, and a large series of computationally docked conformations from rigid-body or molecular dynamics (MD) simulations. Specifically tested on two model systems, the power of iSPOT is demonstrated to accurately predict the structures of a large protein-protein complex (TGFβ-FKBP12) and a multidomain nuclear receptor homodimer (HNF-4α), based on the structures of individual components of the complexes. Although neither SAXS nor footprinting alone can yield an unambiguous picture for each complex, the combination of both, seamlessly integrated in iSPOT, narrows down the best-fit structures that are about 3.2Å and 4.2Å in RMSD from their corresponding crystal structures, respectively. Furthermore, this proof-of-principle study based on the data synthetically derived from available crystal structures shows that the iSPOT-using either rigid-body or MD-based flexible docking-is capable of overcoming the shortcomings of standalone computational methods, especially for HNF-4α. By taking advantage of the integration of SAXS-based shape information and footprinting-based protection/accessibility as well as computational docking, this iSPOT platform is set to be a powerful approach towards accurate integrated modeling of many challenging multiprotein complexes.