Functional Significance of Calcium Binding to Tissue-Nonspecific Alkaline Phosphatase

The conserved active site of alkaline phosphatases (AP) contains catalytically important Zn²⁺ (M1 and M2) and Mg²⁺-sites (M3) and a fourth peripheral Ca²⁺ site (M4) of unknown significance. We have studied Ca²⁺ binding to M1-4 of tissue-nonspecific AP (TNAP), an enzyme crucial for skeletal mineralization, using recombinant TNAP and a series of M4 mutants. Ca²⁺ could substitute for Mg²⁺ at M3, with maximal activity for Ca²⁺/Zn²⁺-TNAP around 40% that of Mg²⁺/Zn²⁺-TNAP at pH 9.8 and 7.4. At pH 7.4, allosteric TNAP-activation at M3 by Ca²⁺ occurred faster than by Mg²⁺. Several TNAP M4 mutations eradicated TNAP activity, while others mildly influenced the affinity of Ca²⁺ and Mg²⁺ for M3 similarly, excluding a catalytic role for Ca²⁺ in the TNAP M4 site. At pH 9.8, Ca²⁺ competed with soluble Zn²⁺ for binding to M1 and M2 up to 1 mM and at higher concentrations, it even displaced M1- and M2-bound Zn²⁺, forming Ca²⁺/Ca²⁺-TNAP with a catalytic activity only 4–6% that of Mg²⁺/Zn²⁺-TNAP. At pH 7.4, competition with Zn²⁺ and its displacement from M1 and M2 required >10-fold higher Ca²⁺ concentrations, to generate weakly active Ca²⁺/Ca²⁺-TNAP. Thus, in a Ca²⁺-rich environment, such as during skeletal mineralization at pH 7.4, Ca²⁺ adequately activates Zn²⁺-TNAP at M3, but very high Ca²⁺ concentrations compete with available Zn²⁺ for binding to M1 and M2 and ultimately displace Zn²⁺ from the active site, virtually inactivating TNAP. Those ALPL mutations that substitute critical TNAP amino acids involved in coordinating Ca²⁺ to M4 cause hypophosphatasia because of their 3D-structural impact, but M4-bound Ca²⁺ is catalytically inactive. In conclusion, during skeletal mineralization, the building Ca²⁺ gradient first activates TNAP, but gradually inactivates it at high Ca²⁺ concentrations, toward completion of mineralization.     

Structural Model for Dihydropyridine Binding to L-type Calcium Channels

1,4-Dihydropyridines (DHPs) constitute a major class of ligands for L-type Ca²⁺ channels (LTCC). The DHPs have a boat-like, six-membered ring with an NH group at the stern, an aromatic moiety at the bow, and substituents at the port and starboard sides. Various DHPs exhibit antagonistic or agonistic activities, which were previously explained as stabilization or destabilization, respectively, of the closed activation gate by the portside substituents. Here we report a novel structural model in which agonist and antagonist activities are determined by different parts of the DHP molecule and have different mechanisms. In our model, which is based on Monte Carlo minimizations of DHP-LTCC complexes, the DHP moieties at the stern, bow, and starboard form H-bonds with side chains of the key DHP-sensing residues Tyr_IIIS6, Tyr_IVS6, and Gln_IIIS5, respectively. We propose that these H-bonds, which are common for agonists and antagonists, stabilize the LTCC conformation with the open activation gate. This explains why both agonists and antagonists increase probability of the long lasting channel openings and why even partial disruption of the contacts eliminates the agonistic action. In our model, the portside approaches the selectivity filter. Hydrophobic portside of antagonists may induce long lasting channel closings by destabilizing Ca²⁺ binding to the selectivity filter glutamates. Agonists have either hydrophilic substituents or a hydrogen atom at their portside, and thus lack this destabilizing effect. The predicted orientation of the DHP core allows accommodation of long substituents in the domain interface or in the inner pore. Our model may be useful for developing novel clinically relevant LTCC blockers.1,4-Dihydropyridines (DHPs)² form a major class of L-type Ca²⁺ channel (LTCC) ligands. DHPs can operate as agonists or antagonists depending on their chemical structure. Importantly, activity of some DHP derivatives may shift from agonism to antagonism (and vice versa) upon site-specific mutation of the channel or modified experimental conditions (for reviews, see Refs. 1 and 2). It has been the dual nature of DHP activity (agonism and antagonism), which has made it challenging for interpretation in structural terms. The other major classes of LTCC ligands, the phenylalkylamines and benzothiazepines, are strictly antagonists.Despite a number of studies, the molecular mechanism for the activity of DHPs on LTCC remains unclear. In the present work we have addressed this problem by combining a molecular modeling approach with analyses of relevant published data. We employed a method of multiple Monte Carlo energy minimizations for docking various DHPs in our earlier reported homology model of LTCC (3), which is based on the crystal structure of the KvAP K⁺ channel (4). We constrained our analyses to potential ligand-binding modes that would be consistent with the features of the ligand-channel activity relationship described in published experiments. These include the structure-activity relationship of the many derivatives of DHPs and the results of mutational analyses of the DHP binding site. These experiments were mostly patch clamp electrophysiology and in vitro binding studies with LTCC heterologously expressed in Xenopus oocytes or human cell lines.The biophysical features of Ca²⁺ channels are important for understanding the action of DHPs. Ca²⁺ channels operate in three gating modes: (i) an inactivated mode from which channels do not open upon depolarization, (ii) a depolarization-elicited mode with multiple short openings, and (iii) a naturally occurring, but usually infrequent, long openings mode. Hess and coauthors (5) reported that DHP agonists stabilized long openings, whereas DHP antagonists promoted inactivated modes. In many respects, the separation of DHP agonists and antagonists is not so clear. DHP antagonists can exhibit agonist-like features, by increasing the percentage of available channels in the long opening mode (5). DHPs can also act as either agonists or antagonists under different experimental conditions (6–8). The effect of DHPs is Ca²⁺-dependent. It has been proposed that DHP antagonists bind to and stabilize a non-conducting channel state in which the selectivity filter is occupied by a single Ca²⁺ ion. Binding of a second Ca²⁺ ion is considered to destabilize DHP binding (9–11).The structure of DHPs can be described as a flattened-boat six-membered ring with the NH group at the stern, an aromatic moiety at the bow, and various substituents at the port and starboard sides (Fig. 1). Experimental data reveals that the agonistic or antagonistic action is primarily determined by the nature of the portside group in the ortho position of the DHP ring relative to the bowsprit. Hydrophobic groups such as COOMe promote an antagonistic effect, whereas hydrophilic groups like NO₂ promote an agonistic effect (12). Intriguingly, enantiomers of some DHPs, e.g. (R)- and (S)-Bay k 8644 demonstrate opposite, antagonistic and agonistic effects on LTCC (13, 14).Open in a separate windowFIGURE 1.Chemical structures of DHPs. Some compounds are named with the prefix GS that stands for Goldmann and Stoltefuss, the authors of a fundamental review on structure-activity of DHPs (12), and the compound number as it appears in the review. Abbreviation BK-10 includes initials of the first and last authors of Ref. 18, and the length of an oligomethylene linker between the DHP core and trimethylammonium group.The access of DHPs to LTCCs has been studied by several groups (15–17) and the consensus is that DHPs reach their binding site within the pore-forming α₁-subunit from the extracellular side. A series of DHP derivatives with a permanently charged ammonium group was used to estimate the distance of the DHP binding site from the extracellular surface of the membrane (18). The optimal potency was found with an ammonium group linked to the dihydropyridine ring via a decamethylene chain.The DHP binding site has been outlined to the interface between repeats III and IV of the pore-forming α₁-subunit of LTCC using antibody mapping of proteolytically labeled channel fragments and a series of subsequent studies with chimeras and site-specific mutations (19–29). Key DHP-sensing residues were defined in transmembrane segments IIIS5, IIIS6, and IVS6 and in the pore helix IIIP. Using the x-ray structure of K⁺ channels as a guide, the corresponding DHP residues appear tightly spaced at the interface of the III/IV domain in the expected three-dimensional structure of LTCC.The available experimental data are insufficient to elaborate structural models of DHP-LTCC complexes. An experimental structure of such a complex would be of great importance, but x-ray structures of voltage-gated Ca²⁺ channels are unavailable. Crystallographic studies of DHP-LTCC complexes are even more challenging. Indeed, many small-molecule ligands of K⁺ channels are known, but only a few ligands have so far been co-crystallized with KcsA. In these circumstances, molecular modeling remains the only feasible approach to provide insights into atomic details of ligand-channel interactions such as positions and orientations of DHP ligands and determinants for their agonistic and antagonistic actions. Predictions from a modeling study remain hypothetical until they are experimentally confirmed, but hypotheses that explain numerous experimental observations stimulate further experimental studies.To date three models of DHP-bound LTCC have been published (30–32). Despite differences in the proposed location of ligands and patterns of the ligand-receptor interactions, all three models suggest a similar molecular mechanism for DHP action. The portside group in these models is oriented toward the ring of hydrophobic residues in the C-terminal halves of S6 helices, close to the proposed activation gate in LTCC. Hydrophobic groups at the portside of the DHP antagonists are proposed to stabilize the closed state of the activation gate, whereas hydrophilic groups of agonists are considered to destabilize the closed state (or stabilize the open state). A primary weakness of these models is that agonistic and antagonistic activities of DHPs are considered to be caused by opposite (stabilizing and destabilizing) effects on the same molecular target (near the activation gate). This “single target” model does not adequately account for the wide variety of observed behaviors of DHP derivatives in published experiments.We have elaborated an alternative model in our present work that suggests different molecular targets and different mechanisms for agonistic and antagonistic activities of DHPs. As published experiments have revealed, the agonistic or antagonistic activity of a DHP ligand not only depends on its chemical structure, but also is sensitive to the experimental conditions and the structure of the drug target. Small changes to the structure of LTCC (as revealed by the behaviors of DHPs in chimeric and mutagenized LTCC) can shift a DHP agonist into an antagonist. The model that explains these behaviors is one where atomic determinants for both agonist and antagonist capacities are present within a single DHP molecule. Manifestation of these capacities depends on structural peculiarities of the DHP ligand and the DHP receptor, as well as on the ligand-receptor orientation that can be sensitive to experimental conditions.     

Structural Model for Phenylalkylamine Binding to L-type Calcium Channels

Phenylalkylamines (PAAs), a major class of L-type calcium channel (LTCC) blockers, have two aromatic rings connected by a flexible chain with a nitrile substituent. Structural aspects of ligand-channel interactions remain unclear. We have built a KvAP-based model of LTCC and used Monte Carlo energy minimizations to dock devapamil, verapamil, gallopamil, and other PAAs. The PAA-LTCC models have the following common features: (i) the meta-methoxy group in ring A, which is proximal to the nitrile group, accepts an H-bond from a PAA-sensing Tyr_IIIS6; (ii) the meta-methoxy group in ring B accepts an H-bond from a PAA-sensing Tyr_IVS6; (iii) the ammonium group is stabilized at the focus of P-helices; and (iv) the nitrile group binds to a Ca²⁺ ion coordinated by the selectivity filter glutamates in repeats III and IV. The latter feature can explain Ca²⁺ potentiation of PAA action and the presence of an electronegative atom at a similar position of potent PAA analogs. Tyr substitution of a Thr in IIIS5 is known to enhance action of devapamil and verapamil. Our models predict that the para-methoxy group in ring A of devapamil and verapamil accepts an H-bond from this engineered Tyr. The model explains structure-activity relationships of PAAs, effects of LTCC mutations on PAA potency, data on PAA access to LTCC, and Ca²⁺ potentiation of PAA action. Common and class-specific aspects of action of PAAs, dihydropyridines, and benzothiazepines are discussed in view of the repeat interface concept.L-type calcium channels (LTCCs)² are targets for different drugs. Benzo(thi)azepines (BTZs), dihydropyridines (DHPs), and phenylalkylamines (PAAs) constitute the three major classes of the LTCC ligands (for reviews, see Refs. 1 and 2). All of these ligands bind to overlapping binding sites in the pore-forming domain of the α₁ subunit, but each class demonstrates unique characteristics of action. Depending on their chemical structure, DHPs act as agonists or antagonists (3). All known PAAs and BTZs are antagonists, but they have different access pathways to their binding sites: external for BTZs (4, 5) and predominantly internal for PAAs (6). Clinical use of verapamil in treatments of hypertension and arrhythmias (7) had stimulated intensive electrophysiological, mutational, and pharmacological studies involving PAAs.The pore-forming domain of LTCC includes the pore-lining inner helices S6, the outer helices S5, and the P-loops from all four repeats of the α₁ subunit. According to mutational analyses, the PAA-binding site is located in the interface between repeats III and IV. In particular, residues in transmembrane helices IIIS5, IIIS6, and IVS6 and P-loops of repeats III and IV contribute to binding of PAAs (8–14).Structure-activity relationships of PAAs were intensively studied (15–17). A common feature of potent PAAs is the presence of two methoxylated aromatic rings (named A and B). The rings are connected by a flexible alkylamine chain with a nitrile and an isopropyl group at the chiral tetrasubstituted carbon atom, which is proximal to ring A. Ring B is proximal to the amino group (see Fig. 1).Open in a separate windowFIGURE 1.Structural formulae of PAAs.Despite the fact that some specific contacts between functional groups of PAAs and PAA-sensing residues (residues that, when mutated, affect action of PAAs) have been proposed (10, 14), the flexibility of the ligands did not allow the characterization of the binding mode and the general pattern of ligand-channel interactions. In the absence of such knowledge, it is hardly possible to provide a molecular basis for structure-activity relationships. The problem is further complicated by the dependence of PAA action on the functional state of the channel, the ionic environment, the transmembrane voltage, and other factors. For example, it is generally believed that PAAs bind to the open/inactivated channels with higher affinities than to the closed state (for review, see Ref 1). However, the molecular basis for this state dependence is unclear.Lipkind and Fozzard (18) docked devapamil in a KcsA-based homology model of the L-type Ca²⁺ channel. They suggested an angular conformation of the drug, with ring B extended into the III/IV repeat interface and ring A in the central cavity. They also suggested that the protonated amino group of devapamil interacts directly with the selectivity filter glutamates. This model explains the effect of some mutations, particularly those in the P-loops and IVS6. However, other important aspects of PAA action such as the role of the nitrile group, the Ca²⁺ potentiation effect, and the effects of mutations in IIIS6 and IIIS5 remain unexplained.The gap between the amount of experimental data on PAA action and the level of understanding of the atomic level mechanisms necessitates further studies. In the absence of x-ray structures of Ca²⁺ channels, molecular modeling is the only available approach to address the structural aspects of PAA-LTCC interactions. Recently, we proposed molecular models for the action of other classes of L-type channel ligands. In the BTZ-LTCC models (19), the main body of the ligands binds in the repeat interface, whereas the amino group protrudes into the inner pore, where it is stabilized by nucleophilic C-terminal ends of the pore helices. In the DHP-LTCC models (20), the ligands also bind in the interface between repeats III and IV, whereas the moieties that differ between agonist and antagonists extend to the pore. Both models suggest direct interactions between the ligands and a Ca²⁺ ion bound to the selectivity filter glutamates in repeats III and IV.In this work, we elaborate molecular models for PAA·LTCC complexes that agree with a large body of experimental data. We further discuss common and different aspects of action of different ligands on LTCC and propose that certain aspects of the ligand action may be relevant to other P-loop channels.     

Membrane Modulates Affinity for Calcium Ion to Create an Apparent Cooperative Binding Response by Annexin a5

Isothermal titration calorimetry was used to characterize the binding of calcium ion (Ca²⁺) and phospholipid to the peripheral membrane-binding protein annexin a5. The phospholipid was a binary mixture of a neutral and an acidic phospholipid, specifically phosphatidylcholine and phosphatidylserine in the form of large unilamellar vesicles. To stringently define the mode of binding, a global fit of data collected in the presence and absence of membrane concentrations exceeding protein saturation was performed. A partition function defined the contribution of all heat-evolving or heat-absorbing binding states. We find that annexin a5 binds Ca²⁺ in solution according to a simple independent-site model (solution-state affinity). In the presence of phosphatidylserine-containing liposomes, binding of Ca²⁺ differentiates into two classes of sites, both of which have higher affinity compared with the solution-state affinity. As in the solution-state scenario, the sites within each class were described with an independent-site model. Transitioning from a solution state with lower Ca²⁺ affinity to a membrane-associated, higher Ca²⁺ affinity state, results in cooperative binding. We discuss how weak membrane association of annexin a5 prior to Ca²⁺ influx is the basis for the cooperative response of annexin a5 toward Ca²⁺, and the role of membrane organization in this response.     

Calcium Ion Binding Properties of Medicago truncatula Calcium/Calmodulin-Dependent Protein Kinase

A calcium/calmodulin-dependent protein kinase (CCaMK) is essential in the interpretation of calcium oscillations in plant root cells for the establishment of symbiotic relationships with rhizobia and mycorrhizal fungi. Some of its properties have been studied in detail, but its calcium ion binding properties and subsequent conformational change have not. A biophysical approach was taken with constructs comprising either the visinin-like domain of Medicago truncatula CCaMK, which contains EF-hand motifs, or this domain together with the autoinhibitory domain. The visinin-like domain binds three calcium ions, leading to a conformational change involving the exposure of hydrophobic surfaces and a change in tertiary but not net secondary or quaternary structure. The affinity for calcium ions of visinin-like domain EF-hands 1 and 2 (K(d) = 200 ± 50 nM) was appropriate for the interpretation of calcium oscillations (～125-850 nM), while that of EF-hand 3 (K(d) ≤ 20 nM) implied occupancy at basal calcium ion levels. Calcium dissociation rate constants were determined for the visinin-like domain of CCaMK, M. truncatula calmodulin 1, and the complex between these two proteins (the slowest of which was 0.123 ± 0.002 s(-1)), suggesting the corresponding calcium association rate constants were at or near the diffusion-limited rate. In addition, the dissociation of calmodulin from the protein complex was shown to be on the same time scale as the dissociation of calcium ions. These observations suggest that the formation and dissociation of the complex between calmodulin and CCaMK would substantially mirror calcium oscillations, which typically have a 90 s periodicity.     

Solvation Effects on the Conformational Behaviour of Gellan and Calcium Ion Binding to Gellan Double Helices

The contribution of the presence of solvent to the conformations adopted by disaccharide fragments within the repeat unit of gellan have been studied by molecular modelling techniques. Initial conformational energy searches, using a dielectric continuum to represent the solvent, provided starting geometries for a series of molecular dynamics simulations. The solution behaviour from these simulations was subsequently compared to fibre diffraction data of the potassium gellan salt. The present calculations indicate considerable flexibility of the glycosidic linkages, and this is discussed in relation to its effect on gel formation. One of the fragments was solvated with explicit water molecules. These calculations showed the same conformational behaviour as those simulations conducted in implicit solvent.Finally, a series of molecular dynamics (MD) simulations were performed to study the calcium binding to gellan. The results from this clearly showed a well defined binding site for this ion.Abbreviations MM molecular mechanics - MD molecular dynamics     

Molecular Modeling of Mechanosensory Ion Channel Structural and Functional Features

The DEG/ENaC (Degenerin/Epithelial Sodium Channel) protein family comprises related ion channel subunits from all metazoans, including humans. Members of this protein family play roles in several important biological processes such as transduction of mechanical stimuli, sodium re-absorption and blood pressure regulation. Several blocks of amino acid sequence are conserved in DEG/ENaC proteins, but structure/function relations in this channel class are poorly understood. Given the considerable experimental limitations associated with the crystallization of integral membrane proteins, knowledge-based modeling is often the only route towards obtaining reliable structural information. To gain insight into the structural characteristics of DEG/ENaC ion channels, we derived three-dimensional models of MEC-4 and UNC-8, based on the available crystal structures of ASIC1 (Acid Sensing Ion Channel 1). MEC-4 and UNC-8 are two DEG/ENaC family members involved in mechanosensation and proprioception respectively, in the nematode Caenorhabditis elegans. We used these models to examine the structural effects of specific mutations that alter channel function in vivo. The trimeric MEC-4 model provides insight into the mechanism by which gain-of-function mutations cause structural alterations that result in increased channel permeability, which trigger cell degeneration. Our analysis provides an introductory framework to further investigate the multimeric organization of the DEG/ENaC ion channel complex.     

5-脂氧化酶转基因小鼠模型的制备

目的建立5-脂氧化酶(5-LO)转基因小鼠进行动脉粥样硬化的发病分子机制的研究。方法通过显微注射的方法,将5-脂氧化酶基因片段(6.8 kb)导入BDF1受精卵雄原核并移植到同期受孕的假孕母鼠输卵管中,对产出仔鼠的鼠尾组织DNA进行PCR、Southern blot检测,对9、20、24号转基因小鼠分别提取腹腔细胞、骨髓细胞及脾、肾组织总RNA和蛋白,并采用RT-PCR、Western blot方法进行转录水平检测和蛋白表达检测。结果共产生25只子代小鼠,经PCR和Southern检测获得7只阳性小鼠,经RT-PCR和Western blot检测结果表明,9、20、24号转基因小鼠腹腔细胞、骨髓细胞、脾、肾5-LO和5-脂氧化酶激活蛋白(FLAP)在RNA和蛋白水平表达均高于正常BDF1对照小鼠,且统计学分析腹腔细胞、骨髓细胞表达均具有显著差异(P0.05)。结论成功建立5-LO转基因小鼠模型。     

Equilibrium Analysis of Calcium Binding to Cell Walls Isolated from Plant Tissue

Primary cell walls were isolated and purified from potato tubersand carrots via a Parr N₂ bomb technique. Calcium binding topurified cell walls was measured with both calcium selectiveelectrode and use of the metallochromic indicator, ArsenazoIII. The cell walls used in this study were biologically activeand presumably approached the physiological cell wall. Aliquotsof the untreated cell walls (control) were then salt-extractedor EDTA-treated and binding properties were compared to thecontrols. In addition, the binding properties of freshly preparedcell walls were compared to cell walls which were stored for1 week at 2°C. Both simple Scatchard plot analysis and anelectrostatic interaction model were used to evaluate calciumbinding parameters. The controls from the two tissue types hadinherently different calcium binding properties and these propertieswere affected by treating the cell walls with salt or EDTA.Cold storage treatment drastically changed the binding propertiesof carrot cell walls but had negligible effect on potato tubercell walls. (Received January 28, 1992; Accepted April 3, 1992)     

Structural and Functional Study of d-Glucuronyl C5-epimerase

Heparan sulfate (HS) is a glycosaminoglycan present on the cell surface and in the extracellular matrix, which interacts with diverse signal molecules and is essential for many physiological processes including embryonic development, cell growth, inflammation, and blood coagulation. d-Glucuronyl C5-epimerase (Glce) is a crucial enzyme in HS synthesis, converting d-glucuronic acid to l-iduronic acid to increase HS flexibility. This modification of HS is important for protein ligand recognition. We have determined the crystal structures of Glce in apo-form (unliganded) and in complex with heparin hexasaccharide (product of Glce following O-sulfation), both in a stable dimer conformation. A Glce dimer contains two catalytic sites, each at a positively charged cleft in C-terminal α-helical domains binding one negatively charged hexasaccharide. Based on the structural and mutagenesis studies, three tyrosine residues, Tyr⁴⁶⁸, Tyr⁵²⁸, and Tyr⁵⁴⁶, in the active site were found to be crucial for the enzymatic activity. The complex structure also reveals the mechanism of product inhibition (i.e. 2-O- and 6-O-sulfation of HS keeps the C5 carbon of l-iduronic acid away from the active-site tyrosine residues). Our structural and functional data advance understanding of the key modification in HS biosynthesis.     

Structural and Functional Insights into the HIV-1 Maturation Inhibitor Binding Pocket

Processing of the Gag precursor protein by the viral protease during particle release triggers virion maturation, an essential step in the virus replication cycle. The first-in-class HIV-1 maturation inhibitor dimethylsuccinyl betulinic acid [PA-457 or bevirimat (BVM)] blocks HIV-1 maturation by inhibiting the cleavage of the capsid-spacer peptide 1 (CA-SP1) intermediate to mature CA. A structurally distinct molecule, PF-46396, was recently reported to have a similar mode of action to that of BVM. Because of the structural dissimilarity between BVM and PF-46396, we hypothesized that the two compounds might interact differentially with the putative maturation inhibitor-binding pocket in Gag. To test this hypothesis, PF-46396 resistance was selected for in vitro. Resistance mutations were identified in three regions of Gag: around the CA-SP1 cleavage site where BVM resistance maps, at CA amino acid 201, and in the CA major homology region (MHR). The MHR mutants are profoundly PF-46396-dependent in Gag assembly and release and virus replication. The severe defect exhibited by the inhibitor-dependent MHR mutants in the absence of the compound is also corrected by a second-site compensatory change far downstream in SP1, suggesting structural and functional cross-talk between the HIV-1 CA MHR and SP1. When PF-46396 and BVM were both present in infected cells they exhibited mutually antagonistic behavior. Together, these results identify Gag residues that line the maturation inhibitor-binding pocket and suggest that BVM and PF-46396 interact differentially with this putative pocket. These findings provide novel insights into the structure-function relationship between the CA MHR and SP1, two domains of Gag that are critical to both assembly and maturation. The highly conserved nature of the MHR across all orthoretroviridae suggests that these findings will be broadly relevant to retroviral assembly. Finally, the results presented here provide a framework for increased structural understanding of HIV-1 maturation inhibitor activity.     

Messl的结构分析和功能研究

Messl是新近鉴定的STE20家族的蛋白激酶.对Messl的基因表达和蛋白功能进行研究,发现其mRNA在鼠组织中广泛分布,但在不同细胞系中表达显著不同;结构分析表明,MeSSl蛋白N端是保守的STE20样激酶催化区,C端是高度亲水的酸性调节区,包含多个潜在的丝氨酸/苏氨酸磷酸化调节位点.哺乳动物细胞表达的MeSSl对MBP显示出激酶活性,并发生自主磷酸化.essl可被砷酸盐应激激活,但丝裂原EGF刺激无活化效应.表明Messl可能在蛋白磷酸化的早期过程中发挥作用,介导细胞对严重应激刺激引起的特异性反应.     

Structural and Functional Analysis of Viral siRNAs

A large amount of short interfering RNA (vsiRNA) is generated from plant viruses during infection, but the function, structure and biogenesis of these is not understood. We profiled vsiRNAs using two different high-throughput sequencing platforms and also developed a hybridisation based array approach. The profiles obtained through the Solexa platform and by hybridisation were very similar to each other but different from the 454 profile. Both deep sequencing techniques revealed a strong bias in vsiRNAs for the positive strand of the virus and identified regions on the viral genome that produced vsiRNA in much higher abundance than other regions. The hybridisation approach also showed that the position of highly abundant vsiRNAs was the same in different plant species and in the absence of RDR6. We used the Terminator 5′-Phosphate-Dependent Exonuclease to study the 5′ end of vsiRNAs and showed that a perfect control duplex was not digested by the enzyme without denaturation and that the efficiency of the Terminator was strongly affected by the concentration of the substrate. We found that most vsiRNAs have 5′ monophosphates, which was also confirmed by profiling short RNA libraries following either direct ligation of adapters to the 5′ end of short RNAs or after replacing any potential 5′ ends with monophosphates. The Terminator experiments also showed that vsiRNAs were not perfect duplexes. Using a sensor construct we also found that regions from the viral genome that were complementary to non-abundant vsiRNAs were targeted in planta just as efficiently as regions recognised by abundant vsiRNAs. Different high-throughput sequencing techniques have different reproducible sequence bias and generate different profiles of short RNAs. The Terminator exonuclease does not process double stranded RNA, and because short RNAs can quickly re-anneal at high concentration, this assay can be misleading if the substrate is not denatured and not analysed in a dilution series. The sequence profiles and Terminator digests suggest that CymRSV siRNAs are produced from the structured positive strand rather than from perfect double stranded RNA or by RNA dependent RNA polymerase.     

The Influence of Hydrogen Ion Concentration on Calcium Binding and Release by Skeletal Muscle Sarcoplasmic Reticulum

Calcium release and binding produced by alterations in pH were investigated in isolated sarcoplasmic reticulum (SR) from skeletal muscle. When the pH was abruptly increased from 6.46 to 7.82, after calcium loading for 30 sec, 80–90 nanomoles (nmole) of calcium/mg protein were released. When the pH was abruptly decreased from 7.56 to 6.46, after calcium loading for 30 sec, 25–30 nmole of calcium/mg protein were rebound. The calcium release process was shown to be a function of pH change: 57 nmole of calcium were released per 1 pH unit change per mg protein. The amount of adenosine triphosphate (ATP) bound to the SR was not altered by the pH changes. The release phenomenon was not due to alteration of ATP concentration by the increased pH. Native actomyosin was combined with SR in order to study the effectiveness of calcium release from the SR by pH change in inducing super-precipitation of actomyosin. It was found that SR, in an amount high enough to inhibit superprecipitation at pH 6.5, did not prevent the process when the pH was suddenly increased to 7.3, indicating that the affinity of SR for calcium depends specifically on pH. These data suggest the possible participation of hydrogen ion concentration in excitation-contraction coupling.     

5-Lipoxygenase: regulation of expression and enzyme activity

5-Lipoxygenase (5-LO) catalyzes the first two steps in the biosynthesis of leukotrienes, a group of pro-inflammatory lipid mediators derived from arachidonic acid. Leukotriene antagonists are used in the treatment of asthma, and the potential role of leukotrienes in atherosclerosis, another chronic inflammatory disease, has recently received considerable attention. In addition, some possible effects of 5-LO metabolites in tumorigenesis have emerged. Thus, knowledge of the biochemistry of this enzyme has potential implications for the treatment of various diseases. Recent advances have expanded our understanding of the regulatory mechanisms underlying the expression and control of 5-LO activity. With regard to the control of enzyme activity, many of these findings focus on the N-terminal domain of 5-LO.     

Structural and Thermodynamic Properties of Selective Ion Binding in a K+ Channel

Thermodynamic measurements of ion binding to the Streptomyces lividans K⁺ channel were carried out using isothermal titration calorimetry, whereas atomic structures of ion-bound and ion-free conformations of the channel were characterized by x-ray crystallography. Here we use these assays to show that the ion radius dependence of selectivity stems from the channel's recognition of ion size (i.e., volume) rather than charge density. Ion size recognition is a function of the channel's ability to adopt a very specific conductive structure with larger ions (K⁺, Rb⁺, Cs⁺, and Ba²⁺) bound and not with smaller ions (Na⁺, Mg²⁺, and Ca²⁺). The formation of the conductive structure involves selectivity filter atoms that are in direct contact with bound ions as well as protein atoms surrounding the selectivity filter up to a distance of 15 Å from the ions. We conclude that ion selectivity in a K⁺ channel is a property of size-matched ion binding sites created by the protein structure.     

Structural and Functional Mimicry of the Binding Site of hYAP-WW Domain for Proline-rich Ligands

Based on the 3D structure of the WW domain of human Yes-associated protein (hYAP-WW) in complex with a proline-rich peptide ligand, we have designed and synthesized a cyclic peptide covering a fragment of hYAP-WW that contains its primary contact residues for the interaction with the ligand. This peptide was found to specifically recognize a proline-rich ligand for hYAP-WW. Its conformation was calculated using molecular dynamics simulation, based on long-range NOEs identified by NMR spectroscopy, and indicates an arrangement of primary contact residues similar to hYAP-WW.     

SIgA Binding to Mucosal Surfaces Is Mediated by Mucin-Mucin Interactions

The oral mucosal pellicle is a layer of absorbed salivary proteins, including secretory IgA (SIgA), bound onto the surface of oral epithelial cells and is a useful model for all mucosal surfaces. The mechanism by which SIgA concentrates on mucosal surfaces is examined here using a tissue culture model with real saliva. Salivary mucins may initiate the formation of the mucosal pellicle through interactions with membrane-bound mucins on cells. Further protein interactions with mucins may then trigger binding of other pellicle proteins. HT29 colon cell lines, which when treated with methotrexate (HT29-MTX) produce a gel-forming mucin, were used to determine the importance of these mucin-mucin interactions. Binding of SIgA to cells was then compared using whole mouth saliva, parotid (mucin-free) saliva and a source of purified SIgA. Greatest SIgA binding occurred when WMS was incubated with HT29-MTX expressing mucus. Since salivary MUC5B was only able to bind to cells which produced mucus and purified SIgA showed little binding to the same cells we conclude that most SIgA binding to mucosal cells occurs because SIgA forms complexes with salivary mucins which then bind to cells expressing membrane-bound mucins. This work highlights the importance of mucin interactions in the development of the mucosal pellicle.