Proton-decoupled deuterium NMR study of an asymmetric liquid crystal dimer having two nematic phases.

Proton-decoupled deuterium NMR spectra were obtained for an asymmetric liquid crystal dimer 1-(4-cyanobiphenyl-4'-yloxy)-6-(4-cyanobiphenyl-4'-yl)hexane (CB6OCB) containing a single -CD_{2}- group. The sample has two nematic liquid crystal phases: a twist-bend nematic, N_{TB}, at the lowest temperature followed by a uniaxial nematic, N_{U}, on increasing the temperature. Proton decoupling reduces the linewidths of the peaks in the deuterium spectrum from kHz to ∼100Hz, enabling quadrupolar splittings, Δν, to be obtained with enhanced precision as well as the dipolar coupling between deuterium nuclei within the CD_{2} group, hence enhancing the information content.

Crystal structure of ADAMTS13 CUB domains reveals their role in global latency.

ADAMTS13 is a plasma metalloprotease that is essential for the regulation of von Willebrand factor (VWF) function, mediator of platelet recruitment to sites of blood vessel damage. ADAMTS13 function is dynamically regulated by structural changes induced by VWF binding that convert it from a latent to active conformation. ADAMTS13 global latency is manifest by the interaction of its C-terminal CUB1-2 domains with its central Spacer domain. We resolved the crystal structure of the ADAMTS13 CUB1-2 domains revealing a previously unreported configuration for the tandem CUB domains. Docking simulations between the CUB1-2 domains with the Spacer domain in combination with enzyme kinetic functional characterization of ADAMTS13 CUB domain mutants enabled the mapping of the CUB1-2 domain site that binds the Spacer domain. Together, these data reveal the molecular basis of the ADAMTS13 Spacer-CUB interaction and the control of ADAMTS13 global latency.

Thrombin in the Activation of the Fluid Contact Phase in Patients with Hereditary Angioedema Carrying the F12 P.Thr309Lys Variant.

Hereditary angioedema due to pathogenic FXII variants (HAE-FXII) is a rare dominant disease caused by increased activation of the plasma contact system. The most prevalent HAE-FXII variant, c.1032C > A p.Thr309Lys (FXII309Lys), results in a smaller FXII protein with increased sensitivity to fluid-phase activation by poorly understood mechanisms. We aimed to investigate the functionality of the FXII309Lys variant in 33 HAE-FXII patients, 25 healthy controls and 46 patients with congenital disorders of glycosylation (CDG). Activation of the plasma contact system was assessed by western blot and amidolytic assay in basal conditions or after treatment with either artificial or physiological activators. Recombinant wild-type and FXII309Lys variants were expressed in S2 insect (Drosophila) cells. Amidolytic and fibrin generation assays were performed in fresh plasma samples. FXII309Lys samples exhibited an increased electrophoretic mobility comparable with N-glycan-deficient FXII from CDG patients and asialo-FXII generated by neuraminidase treatment. They presented increased sensitivity to activation by dextran sulphate and silica which resulted in the generation of an aberrant 37-kDa heavy chain. We did not observe increased susceptibility of FXII309Lys to proteolysis by exogenous or tPA-generated plasmin. However, both exogenous and endogenous thrombin cleaved the FXII309Lys variant, releasing a 37-kDa fragment and resulting in enhanced proteolytic activation on the fluid phase. This model supports a sequential proteolytic activation process involving thrombin priming of FXII309Lys, followed by kallikrein cleavage and generation of active ßFXIIa. The present results and the observation that angioedema episodes in HAE-FXII patients occur predominantly during hypercoagulable situations suggest a key role for thrombin.

Phase transitions in a high magnetic field of an odd, symmetric liquid crystal dimer having two nematic phases, N_{U} and N_{TB}, studied by NMR spectroscopy.

Both ^{1}H and ^{13}C NMR spectra have been obtained in a static magnetic field of 23.5 T on a bent-shaped dimer molecule, 1^{''},7^{''}-bis(4-cyanobiphenyl-4'-yl) nonane (CB9CB), which shows the sequence of liquid crystal phases twist-bend nematic, N_{TB}, and uniaxial nematic, N_{U}, before entering the isotropic phase. The ^{1}H spectra are used to locate the temperature at which the sample melts to form a twist-bend nematic, T_{CrN_{TB}}, and then T_{N_{U}I} when the isotropic phase is entered, both in a magnetic field of 23.5 T, and to compare these with those measured at the Earth's field. The differences between these transition temperatures are found to be zero within the error in their measurement, in stark contrast to previous measurements by Salili et al. [Phys. Rev. Lett. 116, 217801 (2016)10.1103/PhysRevLett.116.217801]. In the isotropic phase in the presence of the field the sample exists in a paranematic phase in which the molecules of CB9CB are partially ordered. The ^{1}H and ^{13}C NMR spectra in the paranematic phase are used to measure the critical temperature T* below which this phase is unstable. The spectra are also used to study the structure, molecular orientational order, and distribution of molecular conformations in the paranematic phase.

Publisher's Note:

This corrects the article DOI: 10.1103/PhysRevE.96.062702.

Assessment of the protein interaction between coagulation factor XII and corn trypsin inhibitor by molecular docking and biochemical validation.

Essentials Corn Trypsin Inhibitor (CTI) is a selective inhibitor of coagulation Factor XII (FXII). Molecular modelling of the CTI-FXIIa complex suggested a canonical inhibitor binding mode. Mutagenesis revealed the CTI inhibitory loop and helices α1 and α2 mediate the interaction. This confirms that CTI inhibits FXII in canonical fashion and validates the molecular model. SUMMARY: Background Corn trypsin inhibitor (CTI) has selectivity for the serine proteases coagulation factor XII and trypsin. CTI is in widespread use as a reagent that specifically inhibits the intrinsic pathway of blood coagulation but not the extrinsic pathway. Objectives To investigate the molecular basis of FXII inhibition by CTI. Methods We performed molecular docking of CTI, using its known crystal structure, with a model of the activated FXII (FXIIa) protease domain. The interaction model was verified by use of a panel of recombinant CTI variants tested for their ability to inhibit FXIIa enzymatic activity in a substrate cleavage assay. Results The docking predicted that: (i) the CTI central inhibitory loop P1 Arg34 side chain forms a salt bridge with the FXIIa S1 pocket Asp189 side chain; (ii) Trp22 from CTI helix α1 interacts with the FXIIa S3 pocket; and (iii) Arg43 from CTI helix α2 forms a salt bridge with FXIIa H1 pocket Asp60A. CTI amino acid substitution R34A negated all inhibitory activity, whereas the G32W, L35A, W22A and R42A/R43A substitutions reduced activity by large degrees of 108-fold, 41-fold, 158-fold, and 100-fold, respectively; the R27A, W37A, W39A and R42A substitutions had no effect. Synthetic peptides spanning CTI residues 20-44 had inhibitory activity that was three-fold to 4000-fold less than that of full-length CTI. Conclusions The data confirm the validity of a canonical model of the FXIIa-CTI interaction, with helix α1 (Trp22), central inhibitory loop (Arg34) and helix α2 (Arg43) of CTI being required for effective binding by contacting the S1, S3 and H1 pockets of FXIIa, respectively.

Similarities and differences between molecular order in the nematic and twist-bend nematic phases of a symmetric liquid crystal dimer.

The order parameter, Szz, where z is the para axis of the difluoroterphenyl groups in DTC5C9, has been obtained from chemical shift anisotropies measured by (13)C - {(1)H} NMR experiments at temperatures throughout the nematic, NU, and twist-bend nematic, NTB, phases shown by this compound. The order parameter temperature profiles are unusual in having a maximum value in the NU phase and then decreasing until the NTB phase is reached. There is a small discontinuity (∼2%) in Szz at TNNTB and then a gradual decrease until a new phase appears. This behaviour is interpreted as revealing a temperature-dependent tilting of local directors in both phases away from the applied magnetic field direction. In the enantiomorphic twist-bend phase this tilt is consistent with the structure of the phase as a helical arrangement of local directors, whilst in the high-temperature non-chiral nematic the tilt must involve a non-chiral arrangement. It is proposed that in both phases the tilting of directors has a common origin in the bent shape of the molecules.

Benzene at 1GHz. Magnetic field-induced fine structure.

The deuterium NMR spectrum of benzene-d6 in a high field spectrometer (1GHz protons) exhibits a magnetic field-induced deuterium quadrupolar splitting Δν. The magnitude of Δν observed for the central resonance is smaller than that observed for the (13)C satellite doublets Δν'. This difference, Δ(Δν)=Δν'-Δν, is due to unresolved fine structure contributions to the respective resonances. We determine the origins of and simulate this difference, and report pulse sequences that exploit the connectivity of the peaks in the (13)C and (2)H spectra to determine the relative signs of the indirect coupling, JCD, and Δν. The positive sign found for Δν is consonant with the magnetic field biasing of an isolated benzene molecule-the magnetic energy of the aromatic ring is lowest for configurations where the C6 axis is normal to the field. In the neat liquid the magnitude of Δν is decreased by the pair correlations in this prototypical molecular liquid.

Coagulation factor XII protease domain crystal structure.

BACKGROUND: Coagulation factor XII is a serine protease that is important for kinin generation and blood coagulation, cleaving the substrates plasma kallikrein and FXI. OBJECTIVE: To investigate FXII zymogen activation and substrate recognition by determining the crystal structure of the FXII protease domain. METHODS AND RESULTS: A series of recombinant FXII protease constructs were characterized by measurement of cleavage of chromogenic peptide and plasma kallikrein protein substrates. This revealed that the FXII protease construct spanning the light chain has unexpectedly weak proteolytic activity compared to ß-FXIIa, which has an additional nine amino acid remnant of the heavy chain present. Consistent with these data, the crystal structure of the light chain protease reveals a zymogen conformation for active site residues Gly193 and Ser195, where the oxyanion hole is absent. The Asp194 side chain salt bridge to Arg73 constitutes an atypical conformation of the 70-loop. In one crystal form, the S1 pocket loops are partially flexible, which is typical of a zymogen. In a second crystal form of the deglycosylated light chain, the S1 pocket loops are ordered, and a short α-helix in the 180-loop of the structure results in an enlarged and distorted S1 pocket with a buried conformation of Asp189, which is critical for P1 Arg substrate recognition. The FXII structures define patches of negative charge surrounding the active site cleft that may be critical for interactions with inhibitors and substrates. CONCLUSIONS: These data provide the first structural basis for understanding FXII substrate recognition and zymogen activation.

Analysis of the factor XI variant Arg184Gly suggests a structural basis for factor IX binding to factor XIa.

BACKGROUND: A patient with factor XI (FXI) deficiency was reported with an Arg184Gly substitution in the FXI A3 domain. The A3 domain contains an exosite required for binding of FIX to activated FXI (FXIa). OBJECTIVE: To test the effects of the Arg184Gly substitution on FIX activation, and to characterize the FIX-binding site on FXIa. METHODS: Recombinant FXIa and FIX variants were used to identify residues involved in FIX activation by FXIa. Analysis of the FXI structure was used to identify potential FIX-binding sites. RESULTS: The Km for FIX activation by FXIa-Gly184 was approximately three-fold higher than for FXIa, suggesting that Arg184 is part of the exosite. Arg184 and the adjacent residues, Ile183 and Asp185, contribute to charged and hydrophobic areas that are not present in the FXI homolog prekallikrein (PK). Replacing residues 183-185 with alanine abolished exosite activity, similarly to replacement of the entire A3 domain with the A3 domain from PK (FXIa/PKA3). Reintroducing FXI residues 183-185 into FXIa/PKA3 partially restored the exosite, and replacing residues 183-185 and 260-264 completely restored exosite function. FIX in which the Ω-loop (residues 4-11) was replaced with the FVII Ω-loop was activated poorly by FXIa, suggesting that the FIX Ω-loop binds to FXIa. CONCLUSIONS: The results support a model in which the Ω-loop of FIX binds to an area on FXIa composed of residues from the N-terminus and C-terminus of the A3 domain. These residues are buried in zymogen FXI, and must be exposed upon conversion to FXIa to permit FIX binding.

Structure of plasma and tissue kallikreins.

The kallikrein kinin system (KKS) consists of serine proteases involved in the production of peptides called kinins, principally bradykinin and Lys-bradykinin (kallidin). The KKS contributes to a variety of physiological processes including inflammation, blood pressure control and coagulation. Here we review the protein structural data available for these serine proteases and examine the molecular mechanisms of zymogen activation and substrate recognition focusing on plasma kallikrein (PK) and tissue kallikrein (KLK1) cleavage of kininogens. PK circulates as a zymogen bound to high-molecular-weight kininogen (HK). PK is activated by coagulation factor XIIa and then cleaves HK to generate bradykinin and factor XII to generate further XIIa.A structure has been described for the activated PK protease domain in complex with the inhibitor benzamidine. Kallikrein-related peptidases (KLKs) have a distinct domain structure and exist as a family of 15 genes which are differentially expressed in many tissues and the central nervous system.They cleave a wide variety of substrates including low-molecular-weight kininogen (LK) and matrix proteins. Crystal structures are available for KLK1, 3, 4, 5, 6 and 7 activated protease domains typically in complex with S1 pocket inhibitors. A substrate mimetic complex is described for KLK3 which provides insight into substrate recognition. A zymogen crystal structure determined for KLK6 reveals a closed S1 pocket and a novel mechanism of zymogen activation. Overall these structures have proved highly informative in understanding the molecular mechanisms of the KKS and provide templates to design inhibitors for treatment of a variety of diseases.

The organizing principle of the platelet glycoprotein Ib-IX-V complex.

The glycoprotein (GP)Ib-IX-V complex is the platelet receptor for von Willebrand factor and many other molecules that are critically involved in hemostasis and thrombosis. The lack of functional GPIb-IX-V complexes on the platelet surface is the cause of Bernard-Soulier syndrome, a rare hereditary bleeding disorder that is also associated with macrothrombocytopenia. GPIb-IX-V contains GPIbα, GPIbß, GPIX and GPV subunits, all of which are type I transmembrane proteins containing leucine-rich repeat domains. Although all of the subunits were identified decades ago, not until recently did the mechanism of complex assembly begin to emerge from a systematic characterization of inter-subunit interactions. This review summarizes the forces driving the assembly of GPIb-IX-V, discusses their implications for the pathogenesis of Bernard-Soulier syndrome, and identifies questions that remain about the structure and organization of GPIb-IX-V.

Binding of platelet glycoprotein Ibbeta through the convex surface of leucine-rich repeats domain of glycoprotein IX.

BACKGROUND: The mechanism of assembly of the platelet glycoprotein (GP) Ib-IX complex from GPIbalpha, GPIbbeta and GPIX subunits is not entirely clear. In this complex, ectodomains of both GPIbbeta and GPIX subunits contain two leucine-rich repeats (LRR) and share high sequence similarity. However, they differ noticeably in stability, hampering further analysis of their interaction. OBJECTIVES AND METHODS: Guided by analysis of the LRR structure, we report a well-folded Ibbeta/IX chimera and its usage in dissecting GPIX function. RESULTS: In this chimera, three non-contiguous sequences that may constitute the putative convex surface of the GPIbbeta ectodomain are replaced by their GPIX counterparts. Like GPIbbeta but unlike GPIX ectodomain, it can secrete from transfected Chinese hamster ovary cells and fold into a stable conformation. Furthermore, replacing the ectodomain in GPIX with the Ibbeta/IX chimera, but not the GPIbbeta ectodomain, preserved its interaction with GPIbbeta as demonstrated by its native-like GPIbbeta-induced increase in surface expression and coimmunoprecipitation. CONCLUSIONS: The putative convex surface of the LRR domain in GPIX is sufficient, in the context of full-length subunit, to mediate its association with GPIbbeta.

The indirect through-space F-F coupling in peri-difluoronaphthalene: is it anisotropic?

The (1)H, (19)F and (13)C spectra have been obtained of a sample of peri-difluoronaphthalene dissolved in the nematic liquid crystalline solvent ZLI 1695. The (13)C satellite spectra from the six, single-(13)C isotopomers at natural abundance in both the (1)H and (19)F spectra were identified and analysed to yield a set of residual total, anisotropic spin-spin couplings, T(ij). This was achieved by first obtaining residual (13)C-(19)F and (13)C-(1)H couplings from a proton-encoded, (13)C detected, local field 2D spectrum. The 45 values of T(HH), T(HF) and T(CH) were used to obtain the structure of the molecule, and then to estimate whether there is a significant contribution from the component along the magnetic field, J, of the anisotropic, electron-mediated, spin-spin coupling tensors for (13)C-(19)F and (19)F-(19)F pairs. It is found that there is strong evidence for a significant contribution of J to T(FF) but not for the (13)C-(19)F pairs.

Molecular modeling of the prekallikrein structure provides insights into high-molecular-weight kininogen binding and zymogen activation.

BACKGROUND: Prekallikrein (PK) plays a central role in the contact system that activates blood coagulation and is involved in the regulation of blood pressure. OBJECTIVES: To provide three-dimensional structural data for PK and rationalize the molecular basis of substrate recognition and zymogen activation. PATIENTS/METHODS: The PK homology model was constructed using the coagulation factor (F) XI crystal structure as a template with the program SWISS-MODEL. RESULTS: The domain organization of the PK apple domains and serine protease is conserved compared to FXI. Surface charge calculations on the PK model revealed that ligand binding to high-molecular-weight kininogen (HK) is predicted to have two key determinants: a pocket within the apple 2 domain and a basic channel formed at the interface of apple domains 1 and 4. A hereditary mutation resulting in PK deficiency (Gly104Arg) and the Lys140 alpha-kallikrein cleavage site both disrupt HK binding and are shown to map to opposite sides of the apple 2 domain pocket. The model also describes the differences in the apple 4 domain that prevents dimer formation in PK vs. FXI. A C-terminal extension in the PK serine protease domain is described as a potential substrate for prolylcarboxypeptidase. CONCLUSIONS: The interaction between PK and HK is mediated by two discrete surfaces formed by the PK A1, A2 and A4 domains with charge likely to be a critical component of the binding. A novel mode of PK activation is postulated to involve prolylcarboxypeptidase cleaving at the C-terminus rather than the activation loop.

Tetraethyl stannane: structure, conformations, and orientational order when dissolved in a nematic liquid crystalline solvent.

Quantum chemical calculations are used to investigate the structure and the distribution of conformers of tetraethyl stannane, and these are compared with those of tetraethyl methane. The calculations predict that the most abundant conformers in tetraethyl stannane are those with symmetry C1, in contrast to tetraethyl methane, in which the D2d and S4 conformers are dominant. The structural and conformational information on tetraethyl stannane are then used, together with the additive potential model, to explain the finite quadrupolar splittings observed in the deuterium NMR spectrum of tetraethyl stannane dissolved in a nematic liquid crystalline solvent. This analysis emphasizes that to understand the orientational order of a flexible molecule in a liquid crystalline phase it is essential to consider the symmetry of individual conformers rather than that of an average structure.

An investigation of the structure and bond rotational potential of some fluorinated ethanes by NMR spectroscopy of solutions in nematic liquid crystalline solvents.

NMR spectra of 1,2-dibromo-1,1-difluoroethane and 1-bromo-2-iodo-tetrafluoroethane dissolved in nematic liquid crystalline solvents have been analysed to yield the magnitudes and signs of the scalar couplings, J(ij), and total anisotropic couplings, T(ij), between all the (1)H, (19)F, and (13)C nuclei, except for those between two (13)C nuclei. The values obtained for T(ij) in principle contain a contribution from J(ij)(aniso), the component along the static applied magnetic field of the anisotropic part of the electron-mediated spin-spin coupling. Neglecting this contribution allows partially averaged dipolar couplings, D(ij), to be extracted from the T(ij), and these were used to determine the structure, orientational order, and the conformational distribution generated by rotation about the C-C bond. The values obtained are compared with the results of calculations by ab initio and density functional methods. The differences found are no greater than those obtained for similar compounds which do not contain fluorine, so that there is no definitive evidence for significant contributions from J(CF)(aniso) or J(FF)(aniso) in the two compounds studied.

Obtaining the structure and bond rotational potential of a substituted ethane by NMR spectroscopy of solutions in nematic liquid-crystalline solvents.

Partially averaged dipolar couplings (also referred to as residual dipolar couplings) D(ij) can be obtained from the analysis of the NMR spectra of molecules dissolved in liquid-crystalline solvents. Their values for a nonrigid molecule depend upon the bond lengths and angles, the rotational potentials, and the orientational order of the molecules. The molecule studied, 1-chloro-2-bromoethane, is one of the simplest example of a substituted alkane in which the rotational potential has three minimum-energy positions, trans and gauche+/-conformations, and the present investigation explores the problems inherent in deriving the form of the potential and the molecular geometry from the set of partially averaged couplings between the protons, and between protons and (13)C nuclei. The geometrical parameters and the rotational potential obtained are compared with the results from a density-functional theory method.

Prolonged local neurotrophin-3 infusion reduces ipsilateral collateral sprouting of spared corticospinal axons in adult rats.

The corticospinal tract is widely used to study regeneration and is essential for voluntary movements in humans. In young rats, corticospinal axons on the uninjured side sprout and grow into the denervated side. Neurotrophin-3 (NT-3) induces such crossed collateral sprouting in adults. We investigated whether local intraspinal NT-3 infusions would promote collateral sprouting of spared corticospinal terminals from within a partially denervated side, as this would be more appropriate for enhancing function of unilateral and specific movements. Adult rats received a partial bilateral transection of the pyramids, leaving approximately 40% of each tract intact. Vehicle or vehicle plus NT-3 (3 or 10 microg/day) was infused for 14 days into the left side of the cervical (C5/6) or lumbar (L2) cord. The corticospinal processes on the left side were anterogradely traced with cholera toxin B (CTB; which labeled gray matter processes more robustly than biotinylated dextran amine) injected into the front or hind limb area of the right sensorimotor cortex, respectively, 3 days before analysis. Unexpectedly, approximately 40% fewer CTB-labeled corticospinal processes were detectable in the cervical or lumbar gray matter of NT-3-treated rats than in vehicle-infused ones. Vehicle-infused injured rats had more corticospinal processes in the center of the cord than normal rats, evidence for lesion-induced collateral sprouting. NT-3 caused sprouting of local calcitonin gene-related peptide-positive fibers. These results suggest that NT-3 reduces collateral sprouting of spared corticospinal axons from within the denervated regions, possibly because of the injury environment or by increasing sprouting of local afferents. They identify an unexpected context-dependent outgrowth inhibitory effect of NT-3.