Beta Domain Research Articles

NMR-detected conformational exchange observed in a computationally designed variant of protein G 1

Detailed biophysical characterization of computationally designed proteins has become increasingly important in order to thoroughly understand the properties of these variants compared with wild-type and to apply this knowledge to future designs. The protein dynamics and structural properties of a computationally designed variant (Delta1.5) of the beta1 domain of streptococcal protein G (Gbeta1) were measured using multinuclear NMR methods. Results from relaxation, diffusion and hydrogen exchange experiments indicate that the variant weakly self-associates at NMR concentrations, with evidence for multiple binding sites. Although comparison of fast (ps-ns) timescale motions shows only small differences in dynamics between Delta1.5 and wild-type, results from the measurement of intermediate (mus-ms) timescale motions are very different. Significant backbone conformational exchange has been observed in the variant at positions all along the sequence, whereas the wild-type Gbeta1 shows little evidence for this type of motion. This increased conformational exchange in Delta1.5 has been attributed to core overpacking resulting from the incorporation of two large hydrophobic side chains and the loss of an aromatic T-stacking interaction. These data highlight, in detail, the potential consequences of incorporating major perturbations in the core of a protein and the need to carry out more detailed analyses of the biophysical properties of designed proteins in order to better understand and predict the effects of mutations.

Structural evidence for lack of inhibition of fish goose-type lysozymes by a bacterial inhibitor of lysozyme

It is known that bacteria contain inhibitors of lysozyme activity. The recently discovered Escherichia coli inhibitor of vertebrate lysozyme (Ivy) and its potential interactions with several goose-type (g-type) lysozymes from fish were studied using functional enzyme assays, comparative homology modelling, protein-protein docking, and molecular dynamics simulations. Enzyme assays carried out on salmon g-type lysozyme revealed a lack of inhibition by Ivy. Detailed analysis of the complexes formed between Ivy and both hen egg white lysozyme (HEWL) and goose egg white lysozyme (GEWL) suggests that electrostatic interactions make a dominant contribution to inhibition. Comparison of three dimensional models of aquatic g-type lysozymes revealed important insertions in the beta domain, and specific sequence substitutions yielding altered electrostatic surface properties and surface curvature at the protein-protein interface. Thus, based on structural homology models, we propose that Ivy is not effective against any of the known fish g-type lysozymes. Docking studies suggest a weaker binding mode between Ivy and GEWL compared to that with HEWL, and our models explain the mechanistic necessity for conservation of a set of residues in g-type lysozymes as a prerequisite for inhibition by Ivy.

Determination of disulfide bond patterns in laminin β1 chain N‐terminal domains by nano‐high‐performance liquid chromatography/matrix‐assisted laser desorption/ionization time‐of‐flight/time‐of‐flight mass spectrometry

The disulfide bonding patterns in the N-terminal (LN) domains of the basement membrane protein laminin beta1 have not been investigated so far. We report an in-depth mass spectrometric analysis using offline nano-high-performance liquid chromatography/matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry (nano-HPLC/MALDI-TOF/TOF-MS) for determining the disulfide bond patterns in the LN-domain of recombinant mouse laminin beta1 chain for the first time. Mass spectra were recorded and the putatively disulfide-linked peptides were subjected to LIFT-TOF/TOF-MS to confirm the disulfide bond. Screening the fragment ion mass spectra of disulfide-linked peptides for characteristic 66-amu patterns (34 u +32 u), arising from symmetric and asymmetric cleavage of disulfide bonds, facilitated their identification. Using various enzymes for proteolytic digestion of a recombinant laminin beta1 chain N-terminal protein fragment, a linear bonding pattern of the eight cysteine residues in the LN-domain of the laminin beta1 chain was observed with a (1-2, 3-4, 5-6, 7-8) connectivity of cysteines. The identical disulfide-bonding pattern was found in E4, the N-terminal laminin beta1 chain fragment derived by elastase digestion of mouse tumor laminin-111, confirming that this pattern also occurs in native laminin.

Integrin β1 is involved in the signaling of glial cell line‐derived neurotrophic factor

Glial cell line-derived neurotrophic factor (GDNF) is a potent neurotrophic factor for the substantia nigra (SN) dopamine (DA) neurons. The transmembrane signaling of GDNF is mediated by a unique receptor system, including the ligand binding receptor GDNF family receptor alpha (GFRalpha) and the transmembrane signaling receptor Ret or neural cell adhesion molecule-140 (NCAM-140). Here, we found that another transmembrane cell adhesion molecule, integrin, a heterodimer consisting of alpha and beta subunits, also mediates the transmembrane signaling of GDNF. The results showed that the level of phosphorylated Src homology 2 domain containing (Shc), which was associated with the cytoplasmic domain of integrin beta1, increased after GDNF administration. Coimmunoprecipitation analysis demonstrated that integrin beta1 could form a complex with GFRalphal. The simulation of molecular modeling showed that four H-bonds were formed between integrin beta1 and GFRalpha. These data indicate that integrin beta1 is involved in the transmembrane signaling of GDNF and suggest that integrin beta1 may be an alternative signaling receptor for GDNF.

Structural insights on the pamoic acid and the 8 kDa domain of DNA polymerase beta complex: towards the design of higher-affinity inhibitors.

BackgroundDNA polymerase beta (pol beta), the error-prone DNA polymerase of single-stranded DNA break repair as well as base excision repair pathways, is overexpressed in several tumors and takes part in chemotherapeutic agent resistance, like that of cisplatin, through translesion synthesis. For this reason pol beta has become a therapeutic target. Several inhibitors have been identified, but none of them presents a sufficient affinity and specificity to become a drug. The fragment-based inhibitor design allows an important improvement in affinity of small molecules. The initial and critical step for setting up the fragment-based strategy consists in the identification and structural characterization of the first fragment bound to the target.ResultsWe have performed docking studies of pamoic acid, a 9 micromolar pol beta inhibitor, and found that it binds in a single pocket at the surface of the 8 kDa domain of pol beta. However, docking studies provided five possible conformations for pamoic acid in this site. NMR experiments were performed on the complex to select a single conformation among the five retained. Chemical Shift Mapping data confirmed pamoic acid binding site found by docking while NOESY and saturation transfer experiments provided distances between pairs of protons from the pamoic acid and those of the 8 kDa domain that allowed the identification of the correct conformation.ConclusionCombining NMR experiments on the complex with docking results allowed us to build a three-dimensional structural model. This model serves as the starting point for further structural studies aimed at improving the affinity of pamoic acid for binding to DNA polymerase beta.

Characterization of the Interaction of Phorbol Esters with the C1 Domain of MRCK (Myotonic Dystrophy Kinase-related Cdc42 Binding Kinase) α/β

C1 domains mediate the recognition and subsequent signaling response to diacylglycerol and phorbol esters by protein kinase C (PKC) and by several other families of signal-transducing proteins such as the chimerins or RasGRP. MRCK (myotonic dystrophy kinase-related Cdc42 binding kinase), a member of the dystrophia myotonica protein kinase family that functions downstream of Cdc42, contains a C1 domain with substantial homology to that of the diacylglycerol/phorbol ester-responsive C1 domains and has been reported to bind phorbol ester. We have characterized here the interaction of the C1 domains of the two MRCK isoforms alpha and beta with phorbol ester. The MRCK C1 domains bind [20-(3)H]phorbol 12,13-dibutyrate with K(d) values of 10 and 17 nm, respectively, reflecting 60-90-fold weaker affinity compared with the protein kinase C delta C1b domain. In contrast to binding by the C1b domain of PKCdelta, the binding by the C1 domains of MRCK alpha and beta was fully dependent on the presence of phosphatidylserine. Comparison of ligand binding selectivity showed resemblance to that by the C1b domain of PKCalpha and marked contrast to that of the C1b domain of PKCdelta. In intact cells, as in the binding assays, the MRCK C1 domains required 50-100-fold higher concentrations of phorbol ester for induction of membrane translocation. We conclude that additional structural elements within the MRCK structure are necessary if the C1 domains of MRCK are to respond to phorbol ester at concentrations comparable with those that modulate PKC.

Calcineurin B‐like domains in the large regulatory α/β subunits of phosphorylase kinase

Phosphorylase kinase (PhK) is a large hexadecameric complex that catalyzes the phosphorylation and activation of glycogen phosphorylase (GP). It consists in four copies each of a catalytic subunit (gamma) and three regulatory subunits (alpha beta delta). Delta corresponds to endogenous calmodulin, whereas little is known on the molecular architecture of the large alpha and beta subunits, which probably arose from gene duplication. Here, using sensitive methods of sequence analysis, we show that the C-terminal domain (named domain D) of these alpha and beta subunits can be significantly related to calcineurin B-like (CBL) proteins. CBL are members of the EF-hand family that are involved in the regulation of plant-specific kinases of the CIPK/PKS family, and relieve autoinhibition of their target kinases by binding to their regulatory region. The relationship highlighted here suggests that PhK alpha and/or beta domain D may be involved in a similar regulation mechanism, a hypothesis which is supported by the experimental observation of a direct interaction between domain D of PhKalpha and the regulatory region of the Gamma subunit. This finding, together the identification of significant similarities of domain D with the preceding domain C, may help to understand the molecular mechanism by which PhK alpha and/or beta domain D might regulate PhK activity.

Metalloproteinases in plasma of the spontaneously hypertensive rats cleave the extracellular domain of beta 2‐adrenergic receptor.

We recently observed enhanced metalloproteinase (MMP) activity in spontaneously hypertensive rats (SHR) compared to its normotensive Wistar Kyoto (WKY) rats and lyses of membrane receptors in the SHR by MMPs. The beta2‐adrenergic receptor (B2AR) is susceptible to the action of endogenous MMPs (Biochim Biophys Acta, 802:390, 1984). Thus we hypothesize that MMPs in plasma of SHR are able to lyse B2AR. Aorta of control Wistar rats was exposed for 24h (37°C) to fresh plasma of male Wistar and WKY rats and SHR with and without doxycycline (Doxy 30 μM) or EDTA (10 mM), to reduce MMP activity. The density of extracellular and intracellular domains of B2AR was determined by quantitative immunohistochemistry. The density of the extracellular, but not intracellular, domains of B2AR is reduced in aortic endothelial cells of the SHR compared with WKY or Wistar rats. Treatment of the aorta from Wistars with plasma from SHR, but not from WKY rats, reduced the number of extracellular domain, but not intracellular domain, of B2AR in aortic endothelial cells. Both Doxy and EDTA are able to prevent the cleavage of the extracellular domain. MMPs in plasma of SHR, but not WKY rats, cause cleavage of the extracellular domain of B2AR in endothelial cells of the aorta of Wistars. Thus MMPs may be responsible for the reduced density of the extracellular domain of B2AR in aortic endothelial cells of SHR compared to WKY rats.

The Vps4 C‐terminal helix is a critical determinant for assembly and ATPase activity and has elements conserved in other members of the meiotic clade of AAA ATPases

Sorting of membrane proteins into intralumenal endosomal vesicles, multivesicular body (MVB) sorting, is critical for receptor down regulation, antigen presentation and enveloped virus budding. Vps4 is an AAA ATPase that functions in MVB sorting. Although AAA ATPases are oligomeric, mechanisms that govern Vps4 oligomerization and activity remain elusive. Vps4 has an N-terminal microtubule interacting and trafficking domain required for endosome recruitment, an AAA domain containing the ATPase catalytic site and a beta domain, and a C-terminal alpha helix positioned close to the catalytic site in the 3D structure. Previous attempts to identify the role of the C-terminal helix have been unsuccessful. Here, we show that the C-terminal helix is important for Vps4 assembly and ATPase activity in vitro and function in vivo, but not endosome recruitment or interactions with Vta1 or ESCRT-III. Unlike the beta domain, which is also important for Vps4 assembly, the C-terminal helix is not required in vivo for Vps4 homotypic interaction or dominant-negative effects of Vps4-E233Q, carrying a mutation in the ATP hydrolysis site. Vta1 promotes assembly of hybrid complexes comprising Vps4-E233Q and Vps4 lacking an intact C-terminal helix in vitro. Formation of catalytically active hybrid complexes demonstrates an intersubunit catalytic mechanism for Vps4. One end of the C-terminal helix lies in close proximity to the second region of homology (SRH), which is important for assembly and intersubunit catalysis in AAA ATPases. We propose that Vps4 SRH function requires an intact C-terminal helix. Co-evolution of a distinct Vps4 SRH and C-terminal helix in meiotic clade AAA ATPases supports this possibility.

Role of the tertiary structure in the diphenol oxidase activity of Octopus vulgaris hemocyanin

The functional differences between the oxygen transport protein Hemocyanin and the enzymes Tyrosinase and Catechol oxidase are believed to be governed, at least in part, by the tertiary structure, which differs in these molecules and controls the accessibility of their copper containing active site for substrate(s). Accordingly, Octopus vulgaris Hemocyanin catalyses the o-diphenol oxidation to o-quinone at a very low rate. The crystallographic structure of one of the functional units (called Odg) of O. dofleini Hemocyanin shows two domains, a mainly α-helical domain that directly binds the copper ions of the reaction center and a β-strand domain that precludes access to the active site to ligands bigger than molecular oxygen. In this work, we have first cleaved the whole protein and then purified different oxygen binding functional units from O. vulgaris Hemocyanin. These functional units were used in activity assays with l-DOPA, the paradigmatic substrate for Catechol oxidase. All functional units show a negligible enzymatic activity. The procedure to generate the functional units induces in only one of them a proteolytic cleavage. Amino terminal sequencing and mass spectroscopy of the fragments allow to place the cleavage site between the alpha and beta domains of the functional unit homologous to Odd, in the O. dofleini sequence. An increase, up to three orders of magnitude, of Tyrosinase-like activity was observed when the cleaved Odd-like was incubated with the substrate in the presence of trifluoroethanol or hexafluoroisopropanol.

On the Inhibitory Affect of Some Dementia Drugs on DNA Polymerase β Activity

Some drugs are routinely prescribed for dementia that sets in either due to normal ageing or due to neurodegenerative disorders. We have studied the effect of three of these drugs, Donepezil hydrochloride, Rivastigmine tartrate and Nootropyl, on the activity of DNA polymerases beta, a crucial enzyme in the base excision repair pathway, the most important mode of DNA repair in brain. All the three drugs inhibited DNA polymerase beta activity to varying degrees although the affects of Donepezil being the least and inconsistent. The drugs preferentially bind to and inhibit the activities of 8 kDa domain of DNA polymerase beta that is known to possess the dRP lyase activity. The function of 31 kDa domain dealing with template driven addition of nucleotides at 3' end of the primer is not adversely affected. The inhibitory action of most widely used dementia drugs on DNA repair potential signifies that pharma sector needs to consider this aspect especially while designing drugs targeted towards brain.

Homology Modeling of Hemagglutinin/Protease [HA/P (vibriolysin)] from Vibrio Cholerae: Sequence Comparision, Residue Interactions and Molecular Mechanism

Vibrio cholerae produces a zinc-containing and calcium-stabilized soluble hemagglutinin/protease, which has been earlier shown to have the ability to cleave several physiologically important substrates including mucin, fibronectin and lactoferin. This study presents homology modeling of hemagglutinin/protease (vibriolysin) from Vibrio cholerae in the presence of inhibitor HPI [N-(1-carboxy-3-phenylpropyl)-phenylalanyl-alpha-aspargine]. The 3D structure was predicted based on its sequence homology with Pseudomonas aeruginosa elastase (PAE). Comparison of the 3D structures of PAE and HA/P reveals a remarkable similarity having a conserved alpha + beta domain. The inhibitor shows similar binding features as seen in other metalloproteases of M4 peptidase family. The study also highlights the key catalytic residues as well as the residues at the S1 and S1' binding sub-sites. The similarities between the two proteins provide support for the hypothesis that the two enzymes have similar three-dimensional structures and a common mechanism of action. The fact that both enzymes are secreted as zinc-containing proteases, led us to further hypothesize that they may play similar role in pathogenesis.

Spin selective multiple quantum NMR for spectral simplification, determination of relative signs, and magnitudes of scalar couplings by spin state selection

In the present work we demonstrate a novel method for spectral simplification and determination of the relative signs of the scalar couplings using a spin selective multiple quantum NMR experiment. A spin selective excitation of double quantum coherence of A and M spins in a weakly coupled three spin system of the type AMX, results in a doublet in the double quantum dimension whose separation corresponds to the sum of couplings of the active spins to the passive spin X. One component of the doublet has the passive spin X in mid R:alpha state while the other component has the passive spin X in mid R:beta state. The spin selective conversion of double quantum coherence to single quantum coherence does not disturb the spin states of the passive spin thereby providing the spin state selection. There will be two domains of single quantum transitions in single quantum dimension at the chemical shift positions of A and M spins. The mid R:alpha domain of A spin is a doublet because of mid R:alpha and mid R:beta states of M spin only, while that of mid R:beta domain is another doublet in a different cross section of the spectra. The scalar coupling J(AM) can be extracted from any of the mid R:alpha and mid R:beta domain transitions while the relative displacements of the two doublets between the two domains at the two chemical shifts provides the magnitude and sign of the scalar coupling J(AX) relative to the coupling J(MX). Similar result is obtained for zero quantum studies on AMX spin system. The proposed technique is discussed theoretically using product operator approach. The new spin state selective double quantum J-resolved sequence has also been developed. The methodology is confirmed experimentally on a homonuclear weakly coupled three spin system and applied to two different heteronuclear five spin systems.

A de novo designed protein–protein interface

As an approach to both explore the physical/chemical parameters that drive molecular self-assembly and to generate novel protein oligomers, we have developed a procedure to generate protein dimers from monomeric proteins using computational protein docking and amino acid sequence design. A fast Fourier transform-based docking algorithm was used to generate a model for a dimeric version of the 56-amino-acid beta1 domain of streptococcal protein G. Computational amino acid sequence design of 24 residues at the dimer interface resulted in a heterodimer comprised of 12-fold and eightfold variants of the wild-type protein. The designed proteins were expressed, purified, and characterized using analytical ultracentrifugation and heteronuclear NMR techniques. Although the measured dissociation constant was modest ( approximately 300 microM), 2D-[(1)H,(15)N]-HSQC NMR spectra of one of the designed proteins in the absence and presence of its binding partner showed clear evidence of specific dimer formation.

The Leu22Pro tumor-associated variant of DNA polymerase beta is dRP lyase deficient

Approximately 30% of human tumors characterized to date express DNA polymerase beta (pol β) variant proteins. Two of the polymerase beta cancer-associated variants are sequence-specific mutators, and one of them binds to DNA but has no polymerase activity. The Leu22Pro (L22P) DNA polymerase beta variant was identified in a gastric carcinoma. Leu22 resides within the 8 kDa amino terminal domain of DNA polymerase beta, which exhibits dRP lyase activity. This domain catalyzes the removal of deoxyribose phosphate during short patch base excision repair. We show that this cancer-associated variant has very little dRP lyase activity but retains its polymerase activity. Although residue 22 has no direct contact with the DNA, we report here that the L22P variant has reduced DNA-binding affinity. The L22P variant protein is deficient in base excision repair. Molecular dynamics calculations suggest that alteration of Leu22 to Pro changes the local packing, the loop connecting helices 1 and 2 and the overall juxtaposition of the helices within the N-terminal domain. This in turn affects the shape of the binding pocket that is required for efficient dRP lyase catalysis.

Enhanced Enzymatic Activity through Photoreversible Conformational Changes

The interaction of a light-responsive surfactant with lysozyme at pH 5.0 has been investigated as a means to control protein structure and enzymatic activity with light illumination. The cationic azobenzene surfactant undergoes a reversible photoisomerization upon exposure to the appropriate wavelength of light, with the visible-light (trans) form being more hydrophobic and, thus, inducing a greater degree of protein unfolding than the UV-light (cis) form. Conformational changes as a function of photoresponsive surfactant concentration and light illumination were measured through shape-reconstruction analysis of small-angle neutron scattering (SANS) data. The SANS-based in vitro structures indicate that lysozyme transitions from a nativelike structure at low surfactant concentration to a partially unfolded conformation at higher surfactant concentrations under visible light illumination, while UV-light illumination causes the protein to refold to a near-native structure. Protein swelling occurs principally away from the active site near the hinge region connecting the alpha and beta domains, leading to an increase in the observed separation distance of the alpha and beta domains in the ensemble SANS measurements, a likely result of enhanced domain motions and increased flexibility within the protein. This swelling of the hinge region is accompanied by an 8-fold increase in enzymatic activity relative to the native state. Both enzyme swelling and superactivity observed under visible light can be reversed to nativelike conditions upon exposure to UV light, leading to complete photoreversible control of the structure and function of lysozyme.

Structure of an archaeal heterotrimeric initiation factor 2 reveals a nucleotide state between the GTP and the GDP states.

Initiation of translation in eukaryotes and in archaea involves eukaryotic/archaeal initiation factor (e/aIF)1 and the heterotrimeric initiation factor e/aIF2. In its GTP-bound form, e/aIF2 provides the initiation complex with Met-tRNA(i)(Met). After recognition of the start codon by initiator tRNA, e/aIF1 leaves the complex. Finally, e/aIF2, now in a GDP-bound form, loses affinity for Met-tRNA(i)(Met) and dissociates from the ribosome. Here, we report a 3D structure of an aIF2 heterotrimer from the archeon Sulfolobus solfataricus obtained in the presence of GDP. Our report highlights how the two-switch regions involved in formation of the tRNA-binding site on subunit gamma exchange conformational information with alpha and beta. The zinc-binding domain of beta lies close to the guanine nucleotide and directly contacts the switch 1 region. As a result, switch 1 adopts a not yet described conformation. Moreover, unexpectedly for a GDP-bound state, switch 2 has the "ON" conformation. The stability of these conformations is accounted for by a ligand, most probably a phosphate ion, bound near the nucleotide binding site. The structure suggests that this GDP-inorganic phosphate (Pi) bound state of aIF2 may be proficient for tRNA binding. Recently, it has been proposed that dissociation of eIF2 from the initiation complex is closely coupled to that of Pi from eIF2gamma upon start codon recognition. The nucleotide state of aIF2 shown here is indicative of a similar mechanism in archaea. Finally, we consider the possibility that release of Pi takes place after e/aIF2gamma has been informed of e/aIF1 dissociation by e/aIF2beta.

Modulation of hSlo BK current inactivation by fatty acid esters of CoA

Lipid metabolism influences membrane proteins, including ion channels, in health and disease. Fatty acid esters of CoA are important intermediates in fatty acid metabolism and lipid biosynthesis. In the present study, we examined the effect of acyl-CoAs on hSlo BK currents. Arachidonoyl-CoA (C(20)-CoA) induced beta2-dependent inhibition of hSlo-alpha current when applied intracellularly but not extracellularly. This action was also mimicked by other long-chain acyl-CoAs such as oleoyl-CoA (C(18)-CoA) and palmitoyl-CoA (C(16)-CoA), but not acetyl-CoA (C(2)-CoA, shorter chain), suggesting that the length of acyl chains, rather than CoA headgroups, is critical. When hSlo-alpha inactivation was induced by a free synthetic cationic beta2 NH2-terminus inactivation ball peptide, long-chain acyl-CoAs inhibited hSlo-alpha current and facilitated inactivation. The precursor fatty acids also facilitated the ball peptide-induced inactivation in a chain length-dependent manner, whereas sphingosine (positively charged) slowed this inactivation. When the beta2-induced inactivation was compared with that of the ball peptide, there was a negative shift in the steady state inactivation, slower recovery, and a reduced voltage-dependence of inactivation onset. These data suggest that electrostatic interactions with the cytosolic inactivation domain of beta2 mediate acyl-CoA modulation of BK currents. BK channel inactivation may be a specific target for lipid modulation in physiological and pathophysiological conditions.

How the regulatory protein, IF(1), inhibits F(1)-ATPase from bovine mitochondria.

The structure of bovine F(1)-ATPase inhibited by a monomeric form of the inhibitor protein, IF(1), known as I1-60His, lacking most of the dimerization region, has been determined at 2.1-A resolution. The resolved region of the inhibitor from residues 8-50 consists of an extended structure from residues 8-13, followed by two alpha-helices from residues 14-18 and residues 21-50 linked by a turn. The binding site in the beta(DP)-alpha(DP) catalytic interface is complex with contributions from five different subunits of F(1)-ATPase. The longer helix extends from the external surface of F(1) via a deep groove made from helices and loops in the C-terminal domains of subunits beta(DP), alpha(DP), beta(TP), and alpha(TP) to the internal cavity surrounding the central stalk. The linker and shorter helix interact with the gamma-subunit in the central stalk, and the N-terminal region extends across the central cavity to interact with the nucleotide binding domain of the alpha(E) subunit. To form these complex interactions and penetrate into the core of the enzyme, it is likely that the initial interaction of the inhibitor with F(1) forms via the open conformation of the beta(E) subunit. Then, as two ATP molecules are hydrolyzed, the beta(E)-alpha(E) interface converts to the beta(DP)-alpha(DP) interface via the beta(TP)-alpha(TP) interface, trapping the inhibitor progressively in its binding site and a nucleotide in the catalytic site of subunit beta(DP). The inhibition probably arises by IF(1) imposing the structure and properties of the beta(TP)-alpha(TP) interface on the beta(DP)-alpha(DP) interface, thereby preventing it from hydrolyzing the bound ATP.

Are bacterial ‘autotransporters’ really transporters?

Autotransporters are bacterial outer membrane proteins that consist of a large N-terminal extracellular domain ('passenger domain') and a C-terminal beta-barrel domain ('beta domain'). The beta domain was originally proposed to function as a channel that transports its own passenger domain across the outer membrane. Results of recent structural, biochemical and molecular genetic studies, however, have challenged this idea. Here I describe an alternative model in which translocation of the passenger domain is mediated by an exogenous factor (possibly a newly identified factor necessary for assembly of outer membrane proteins called 'Omp85/YaeT'), whereas the beta domain only targets the protein to the outer membrane and serves as a membrane anchor.