How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM

The atomic coordinates derived from cryo-electron microscopy (cryo-EM) maps can be inaccurate when the voxel scaling factors are not properly calibrated. Here, we describe a method for correcting relative voxel scaling factors between pairs of cryo-EM maps for the same or similar structures that are expanded or contracted relative to each other. We find that the correction of scaling factors reduces the amplitude differences of Fourier-inverted structure factors from voxel-rescaled maps by up to 20–30%, as shown by two cryo-EM maps of the SARS-CoV-2 spike protein measured at pH 4.0 and pH 8.0. This allows for the calculation of the difference map after properly scaling, revealing differences between the two structures for individual amino acid residues. Unexpectedly, the analysis uncovers two previously overlooked differences of amino acid residues in structures and their local structural changes. Furthermore, we demonstrate the method as applied to two cryo-EM maps of monomeric apo-photosystem II from the cyanobacteria Synechocystis sp. PCC 6803 and Thermosynechococcus elongatus. The resulting difference maps reveal many changes in the peripheral transmembrane PsbX subunit between the two species.     

Crystal structures of arginine sensor CASTOR1 in arginine-bound and ligand free states

The mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) is a master regulator of metabolism and cell growth. Among the numerous extracellular and intracellular signals, certain amino acids activate mTORC1 in a Rag-dependent manner. Arginine can stimulate mTORC1 activity by releasing the inhibitor CASTOR1 (Cellular Arginine Sensor of mTORC1) from GATOR2, a positive regulator of mTORC1 which interacts with GATOR1, the GAP for RagA/B. Three groups have resolved the structures of arginine-CASTOR1 complex, shedding a new light on molecular basis of the regulation of mTORC1 activity by arginine. However, lacking the apo structure of CASTOR1 prelimited the molecular understanding of mechanism underlying mTORC1 regulation. Here, we report crystal structures of arginine sensor CASTOR1 in arginine-bound and ligand free states at 2.05?Å and 2.8?Å, respectively. Structural comparison of CASTOR1 between two states reveals near identical conformations, except in two loop regions. It indicates CASTOR1 does not undergo large conformational change during arginine binding. Therefore, we conclude a detailed structural interpretation of arginine sensing by CASTOR1 in mTORC1 pathway.     

A Model of the Membrane-bound Cytochrome b5-Cytochrome P450 Complex from NMR and Mutagenesis Data

Microsomal cytochrome b₅ (cytb₅) is a membrane-bound protein that modulates the catalytic activity of its redox partner, cytochrome P4502B4 (cytP450). Here, we report the first structure of full-length rabbit ferric microsomal cytb₅ (16 kDa), incorporated in two different membrane mimetics (detergent micelles and lipid bicelles). Differential line broadening of the cytb₅ NMR resonances and site-directed mutagenesis data were used to characterize the cytb₅ interaction epitope recognized by ferric microsomal cytP450 (56 kDa). Subsequently, a data-driven docking algorithm, HADDOCK (high ambiguity driven biomolecular docking), was used to generate the structure of the complex between cytP4502B4 and cytb₅ using experimentally derived restraints from NMR, mutagenesis, and the double mutant cycle data obtained on the full-length proteins. Our docking and experimental results point to the formation of a dynamic electron transfer complex between the acidic convex surface of cytb₅ and the concave basic proximal surface of cytP4502B4. The majority of the binding energy for the complex is provided by interactions between residues on the C-helix and β-bulge of cytP450 and residues at the end of helix α4 of cytb₅. The structure of the complex allows us to propose an interprotein electron transfer pathway involving the highly conserved Arg-125 on cytP450 serving as a salt bridge between the heme propionates of cytP450 and cytb₅. We have also shown that the addition of a substrate to cytP450 likely strengthens the cytb₅-cytP450 interaction. This study paves the way to obtaining valuable structural, functional, and dynamic information on membrane-bound complexes.     

Mango ripening--chemical and structural characterization of pectic and hemicellulosic polysaccharides

Ripening of mango is characterized by a gradual, but natural softening of the fruit, which is due to progressive depolymerization of pectic and hemicellulosic polysaccharides with significant loss of galactose, arabinose and mannose residues at the ripe stage. Structural characterization employing permethylation followed by GC-MS analysis, IR and ¹³C NMR measurements revealed the major CWS fractions of both unripe and ripe mangoes to be of variable molecular weights and having a 1,4-linked galactan/galacturonan backbone, which is occasionally involved in side chain branches consisting of single residues of galactose and arabinose or oligomeric 1,5-linked arabinofuranose residues linked through 1,3-linkages; whereas the major hemicellulosic fractions of unripe mango to be of xyloglucan-type having 1,4-linked glucan backbone with branching by non-reducing terminal arabinose and xylose residues.     

Structural modeling reveals microstructure-strength relationship for human ascending thoracic aorta

High lethality of aortic dissection necessitates accurate predictive metrics for dissection risk assessment. The not infrequent incidence of dissection at aortic diameters <5.5 cm, the current threshold guideline for surgical intervention (Nishimura et al., 2014), indicates an unmet need for improved evidence-based risk stratification metrics. Meeting this need requires a fundamental understanding of the structural mechanisms responsible for dissection evolution within the vessel wall. We present a structural model of the repeating lamellar structure of the aortic media comprised of elastic lamellae and collagen fiber networks, the primary load-bearing components of the vessel wall. This model was used to assess the role of these structural features in determining in-plane tissue strength, which governs dissection initiation from an intimal tear. Ascending aortic tissue specimens from three clinically-relevant patient populations were considered: non-aneurysmal aorta from patients with morphologically normal tricuspid aortic valve (CTRL), aneurysmal aorta from patients with tricuspid aortic valve (TAV), and aneurysmal aorta from patients with bicuspid aortic valve (BAV). Multiphoton imaging derived collagen fiber organization for each patient cohort was explicitly incorporated in our model. Model parameters were calibrated using experimentally-measured uniaxial tensile strength data in the circumferential direction for each cohort, while the model was validated by contrasting simulated tissue strength against experimentally-measured strength in the longitudinal direction. Orientation distribution, controlling the fraction of loaded collagen fibers at a given stretch, was identified as a key feature governing anisotropic tissue strength for all patient cohorts.     

Five new indole derivatives from the cyanobacterium Moorea producens

Chemical analysis of the hydrophilic fraction from marine cyanobacterium Moorea producens extracts led to the isolation of five new indole derivatives (1-5). So far, 2-formyl-4,5,6,7-tetrahydroindole has been reported only for 6 from the nature, consequently compounds 1-5 were the second representatives of this class. Cytotoxicity, diatom growth inhibition, and antibacterial activity tests for compounds 1-5 showed no bioactivity at the concentration tested.     

Simulation of transcatheter aortic valve implantation through patient-specific finite element analysis: Two clinical cases

Transcatheter aortic valve implantation (TAVI) is a minimally invasive procedure introduced to treat aortic valve stenosis in elder patients. Its clinical outcomes are strictly related to patient selection, operator skills, and dedicated pre-procedural planning based on accurate medical imaging analysis. The goal of this work is to define a finite element framework to realistically reproduce TAVI and evaluate the impact of aortic root anatomy on procedure outcomes starting from two real patient datasets. Patient-specific aortic root models including native leaflets, calcific plaques extracted from medical images, and an accurate stent geometry based on micro-tomography reconstruction are key aspects included in the present study. Through the proposed simulation strategy we observe that, in both patients, stent apposition significantly induces anatomical configuration changes, while it leads to different stress distributions on the aortic wall. Moreover, for one patient, a possible risk of paravalvular leakage has been found while an asymmetric coaptation occurs in both investigated cases. Post-operative clinical data, that have been analyzed to prove reliability of the performed simulations, show a good agreement with analysis results. The proposed work thus represents a further step towards the use of realistic computer-based simulations of TAVI procedures, aiming at improving the efficacy of the operation technique and supporting device optimization.     

Exploring the role of cation-pi interactions in glycoproteins lipid-binding proteins and RNA-binding proteins

We have analyzed and compared the influence of cation-pi interactions in glycoproteins (GPs), lipid-binding proteins (LBPs) and RNA-binding proteins (RBPs) in this study. We observed that all the proteins included in the study had profound cation-pi interactions. There is an average of one energetically significant cation-pi interaction for every 71 residues in GPs, for every 58 residues in LBPs and for every 64 residues in RBPs. Long-range contacts are predominant in all the three types of proteins studied. The pair-wise cation-pi interaction energy between the positively charged and aromatic residues shows that Arg-Trp pair energy was the strongest among all six possible pairs in all the three types of proteins studied. There were considerable differences in the preference of cation-pi interacting residues to different secondary structure elements and ASA and these might contribute to differences in biochemical functions of GPs, LBPs and RBPs. It was interesting to note that all the five residues involved in cation-pi interactions were found to have stabilization centers in GPs, LBPs and RBPs. Majority of the cation-pi interacting residues investigated in the present study had a conservation score of 6, the cutoff value used to identify the stabilizing residues. A small percentage of cation-pi interacting residues were also present as stabilizing residues. The cation-pi interaction-forming residues play an important role in the structural stability of in GPs, LBPs and RBPs. The results obtained in this study will be helpful in further understanding the stability, specificity and differences in the biochemical functions of GPs, LBPs and RBPs.