Hinge sequences as signaling agents?

AbstractWe report an unexpected finding of common structural principles in two unrelated signaling systems: the FAS death domain transformation that initializes the extrinsic apoptotic pathway and signaling by calmodulin bending. The location and design of the hinge is postulated to be a general principle for creating potential signaling event. We suggest that already existing tool can predict the existence of such a hinge and formulate the hypothesis that the internal instabilities designed into the hinge sequences are necessary devices in effective signaling events

Between Order and Disorder in Protein Structures: Analysis of “Dual Personality” Fragments in Proteins

SummaryIn their natural environment, three-dimensional structures of proteins undergo significant fluctuations and are often partially or completely disordered. This phenomenon recently became the focus of much attention, as many proteins, especially from higher organisms, were shown to contain large intrinsically disordered regions. Such disordered regions may become ordered only under very specific circumstances, if at all, and can be recognized by specific amino acid composition and sequence signatures. Here, we suggest that the balance between order and disorder is much more subtle in that many regions are very close to the order/disorder boundary. Specifically, analysis of redundant sets of experimental models of protein structures, where emphasis is put on comparison of structures of identical proteins solved in different conditions and functional states, shows hundreds of fragments captured in two states: ordered and disordered. We show that such fragments, which we call here “dual personality” (DP) fragments, have distinctive features that differentiate them from both regularly folded and intrinsically disordered fragments. We hypothesize, and show on several examples, that such fragments are often targets of regulation, either by allostery or posttranslational modifications

Conformational Communication Mediates the Reset Step in t6A Biosynthesis

The universally conserved N 6-threonylcarbamoylade nosine (t 6 A) modification of tRNA is essential for translational fidelity. In bacteria, t 6 A biosynthesis starts with the TsaC/TsaC2-catalyzed synthesis of the intermediate threonylcarbamoyl adenylate (TC-AMP), followed by transfer of the threonylcarbamoyl (TC) moiety to adenine-37 of tRNA by the TC-transfer complex comprised of TsaB, TsaD and TsaE sub-units and possessing an ATPase activity required for multi-turnover of the t 6 A cycle. We report a 2.5-˚ A crystal structure of the T. maritima TC-transfer complex (TmTsaB 2 D 2 E 2) bound to Mg 2+-ATP in the AT-Pase site, and substrate analog carboxy-AMP in the TC-transfer site. Site directed mutagenesis results show that residues in the conserved Switch I and Switch II motifs of TsaE mediate the ATP hydrolysis-driven reactivation/reset step of the t 6 A cycle. Further , SAXS analysis of the TmTsaB 2 D 2-tRNA complex in solution reveals bound tRNA lodged in the TsaE binding cavity, confirming our previous biochemical data. Based on the crystal structure and molecular docking of TC-AMP and adenine-37 in the TC-transfer site, we propose a model for the mechanism of TC transfer by this universal biosynthetic system

Crystal Structure of a Nonsymbiotic Plant Hemoglobin

Background: Nonsymbiotic hemoglobins (nsHbs) form a new class of plant proteins that is distinct genetically and structurally from leghemoglobins. They are found ubiquitously in plants and are expressed in low concentrations in a variety of tissues including roots and leaves. Their function involves a biochemical response to growth under limited O2 conditions. Results: The first X-ray crystal structure of a member of this class of proteins, riceHb1, has been determined to 2.4 Å resolution using a combination of phasing techniques. The active site of ferric riceHb1 differs significantly from those of traditional hemoglobins and myoglobins. The proximal and distal histidine sidechains coordinate directly to the heme iron, forming a hemichrome with spectral properties similar to those of cytochrome b5. The crystal structure also shows that riceHb1 is a dimer with a novel interface formed by close contacts between the G helix and the region between the B and C helices of the partner subunit. Conclusions: The bis-histidyl heme coordination found in riceHb1 is unusual for a protein that binds O2 reversibly. However, the distal His73 is rapidly displaced by ferrous ligands, and the overall O2 affinity is ultra-high (KD ≈ 1 nM). Our crystallographic model suggests that ligand binding occurs by an upward and outward movement of the E helix, concomitant dissociation of the distal histidine, possible repacking of the CD corner and folding of the D helix. Although the functional relevance of quaternary structure in nsHbs is unclear, the role of two conserved residues in stabilizing the dimer interface has been identified

Autocatalytic Activation of the Furin Zymogen Requires Removal of the Emerging Enzyme's N-Terminus from the Active Site

Before furin can act on protein substrates, it must go through an ordered process of activation. Similar to many other proteinases, furin is synthesized as a zymogen (profurin) which becomes active only after the autocatalytic removal of its auto-inhibitory prodomain. We hypothesized that to activate profurin its prodomain had to be removed and, in addition, the emerging enzyme's N-terminus had to be ejected from the catalytic cleft.We constructed and analyzed the profurin mutants in which the egress of the emerging enzyme's N-terminus from the catalytic cleft was restricted. Mutants were autocatalytically processed at only the primary cleavage site Arg-Thr-Lys-Arg(107) downward arrowAsp(108), but not at both the primary and the secondary (Arg-Gly-Val-Thr-Lys-Arg(75) downward arrowSer(76)) cleavage sites, yielding, as a result, the full-length prodomain and mature furins commencing from the N-terminal Asp108. These correctly processed furin mutants, however, remained self-inhibited by the constrained N-terminal sequence which continuously occupied the S' sub-sites of the catalytic cleft and interfered with the functional activity. Further, using the in vitro cleavage of the purified prodomain and the analyses of colon carcinoma LoVo cells with the reconstituted expression of the wild-type and mutant furins, we demonstrated that a three-step autocatalytic processing including the cleavage of the prodomain at the previously unidentified Arg-Leu-Gln-Arg(89) downward arrowGlu(90) site, is required for the efficient activation of furin.Collectively, our results show the restrictive role of the enzyme's N-terminal region in the autocatalytic activation mechanisms. In a conceptual form, our data apply not only to profurin alone but also to a range of self-activated proteinases

Geometry of Protein Structures. I. Why Hyperbolic Surfaces are a Good Approximation for Beta-Sheets

Protein structure is invariably connected to protein function. To analyze the structural changes of proteins, we should have a good description of basic geometry of proteins\u27 secondary structure. A beta-sheet is one of important elements of protein secondary structure that is formed by several fragments of the protein that form a surface-like feature. The actual shapes of the beta-sheets can be very complicated, so we would like to approximate them by simpler geometrical shapes from an approximating family. Which family should we choose? Traditionally, hyperbolic (second order) surfaces have been used as a reasonable approximation to the shape of beta-sheets. In this paper, we show that, under reasonable assumptions, these second order surfaces are indeed the best approximating family for beta-sheets

GEOMETRY OF PROTEIN STRUCTURES. I. WHY HYPERBOLIC SURFACES ARE A GOOD APPROXIMATION FOR BETA-SHEETS

Abstract. Protein structure is invariably connected to protein function. To analyze the structural changes of proteins, we should have a good description of basic geometry of proteins ’ secondary structure. A beta-sheet is one of important elements of protein secondary structure that is formed by several fragments of the protein that form a surface-like feature. The actual shapes of the beta-sheets can be very complicated, so we would like to approximate them by simpler geometrical shapes from an approximating family. Which family should we choose? Traditionally, hyperbolic (second order) surfaces have been used as a reasonable approximation to the shape of betasheets. In this paper, we show that, under reasonable assumptions, these second order surfaces are indeed the best approximating family for beta-sheets. Introduction. Proteins are biological polymers that perform most of the life’s function. A single chain polymer (protein) is folded i

Left ventricular diastolic dysfunction assessed by conventional echocardiography and spectral tissue Doppler imaging in adolescents with arterial hypertension

Compared to conventional echocardiography, spectral tissue Doppler imaging (s-TDI) allows more precise evaluation of diastolic cardiac function. The purpose of this study was to conduct s-TDI to analyze the slow movement of the left ventricular (LV) myocardium in adolescents with systemic arterial hypertension (HT) and to determine whether patients with HT suffer from LV diastolic dysfunction. The study group comprised 69 consecutive patients (48 boys and 21 girls aged 14–17 years [mean, 15.5 ± 1.1 years]) with primary HT, and the control group comprised 48 healthy participants (24 boys and 24 girls aged 14–17 years [mean, 15.8 ± 1.3 years]). Physical examinations, 24-hour arterial blood pressure monitoring, conventional 2-dimensional and Doppler echocardiography, and s-TDIs were performed. Analysis revealed that study group participants were significantly heavier and had greater LV mass indices than controls (P < 0.001). There were no differences between the velocities of E waves (peak early filling of mitral inflow), but the deceleration times of the mitral E waves were significantly shorter whereas the A waves survived longer in the study group than in the control group. The velocities of A waves (peak late filling of mitral inflow) were elevated (P = 0.041), and the E/A wave pattern (E/A = 1.8 ± 0.4) was normal. These results suggest pseudonormalization, a type of LV diastolic dysfunction in adolescents with HT. In the study group, when the sample volume was positioned at the septal or lateral insertion site of the mitral leaflet, the e′ wave velocity was significantly depressed whereas the a′ wave velocity was elevated, compared to those of the control group (P < 0.001). The e′/a′ ratios from the septal and lateral insertion sites were lower, whereas the E/e′ ratio from the septal insertion site was significantly higher in the study group, similar to that seen in atrial reversal velocity (P < 0.001). These findings indicate that using sTDI to find and measure diastolic LV failure is valuable when the probe is placed at the septal and lateral mitral valve annuli during examination. Changes in the myocardium appear similar to those seen in adults

Structure and Mechanism of a Bacterial t6A Biosynthesis System

The universal N(6)-threonylcarbamoyladenosine (t6A) modification at position 37 of ANN-decoding tRNAs is central to translational fidelity. In bacteria, t6A biosynthesis is catalyzed by the proteins TsaB, TsaC/TsaC2, TsaD and TsaE. Despite intense research, the molecular mechanisms underlying t6A biosynthesis are poorly understood. Here, we report biochemical and biophysical studies of the t6A biosynthesis system from Thermotoga maritima. Small angle X-ray scattering analysis reveals a symmetric 2:2 stoichiometric complex of TsaB and TsaD (TsaB2D2), as well as 2:2:2 complex (TsaB2D2E2), in which TsaB acts as a dimerization module, similar to the role of Pcc1 in the archaeal system. The TsaB2D2 complex is the minimal platform for the binding of one tRNA molecule, which can then accommodate a single TsaE subunit. Kinetic data demonstrate that TsaB2D2 alone, and a TsaB2D2E1 complex with TsaE mutants deficient in adenosine triphosphatase (ATPase) activity, can catalyze only a single cycle of t6A synthesis, while gel shift experiments provide evidence that the role of TsaE-catalyzed ATP hydrolysis occurs after the release of product tRNA. Based on these results, we propose a model for t6A biosynthesis in bacteria