Small Globular Domains Research Articles

Structure of the Borrelia Bacteriophage φBB1 Procapsid

Bacteriophages of Borrelia burgdorferi are a biologically important but under-investigated feature of the Lyme disease-causing spirochete. No virulent borrelial viruses have been identified, but all B. burgdorferi isolates carry a prophage φBB1 as resident circular plasmids. Like its host, the φBB1 phage is quite distinctive and shares little sequence similarity with other known bacteriophages. We expressed φBB1 head morphogenesis proteins in Escherichia coli which resulted in assembly of homogeneous prolate procapsid structures and used cryo-electron microscopy to determine the three-dimensional structure of these particles.The φBB1 procapsids consist of 415 copies of the major capsid protein and an equal combined number of three homologous capsid decoration proteins that form trimeric knobs on the outside of the particle. One of the end vertices of the particle is occupied by a portal assembled from twelve copies of the portal protein. The φBB1 scaffolding protein is entirely α-helical and has an elongated shape with a small globular domain in the middle. Within the tubular section of the procapsid, the internal scaffold is built of stacked rings, each composed of 32 scaffolding protein molecules, which run in opposite directions from both caps with a heterogeneous part in the middle. Inside the portal-containing cap, the scaffold is organized asymmetrically with ten scaffolding protein molecules bound to the portal. The φBB1 procapsid structure provides better insight into the vast structural diversity of bacteriophages and presents clues of how elongated bacteriophage particles might be assembled.

Membrane Interactions of the Peroxisomal Proteins PEX5 and PEX14.

Human PEX5 and PEX14 are essential components of the peroxisomal translocon, which mediates import of cargo enzymes into peroxisomes. PEX5 is a soluble receptor for cargo enzymes comprised of an N-terminal intrinsically disordered domain (NTD) and a C-terminal tetratricopeptide (TPR) domain, which recognizes peroxisomal targeting signal 1 (PTS1) peptide motif in cargo proteins. The PEX5 NTD harbors multiple WF peptide motifs (WxxxF/Y or related motifs) that are recognized by a small globular domain in the NTD of the membrane-associated protein PEX14. How the PEX5 or PEX14 NTDs bind to the peroxisomal membrane and how the interaction between the two proteins is modulated at the membrane is unknown. Here, we characterize the membrane interactions of the PEX5 NTD and PEX14 NTD in vitro by membrane mimicking bicelles and nanodiscs using NMR spectroscopy and isothermal titration calorimetry. The PEX14 NTD weakly interacts with membrane mimicking bicelles with a surface that partially overlaps with the WxxxF/Y binding site. The PEX5 NTD harbors multiple interaction sites with the membrane that involve a number of amphipathic α-helical regions, which include some of the WxxxF/Y-motifs. The partially formed α-helical conformation of these regions is stabilized in the presence of bicelles. Notably, ITC data show that the interaction between the PEX5 and PEX14 NTDs is largely unaffected by the presence of the membrane. The PEX5/PEX14 interaction exhibits similar free binding enthalpies, where reduced binding enthalpy in the presence of bicelles is compensated by a reduced entropy loss. This demonstrates that docking of PEX5 to PEX14 at the membrane does not reduce the overall binding affinity between the two proteins, providing insights into the initial phase of PEX5-PEX14 docking in the assembly of the peroxisome translocon.

Thermodynamic stability of hnRNP A1 low complexity domain revealed by high-pressure NMR.

We have investigated the pressure- and temperature-induced conformational changes associated with the low complexity domain of hnRNP A1, an RNA-binding protein able to phase separate in response to cellular stress. Solution NMR spectra of the hnRNP A1 low-complexity domain fused with protein-G B1 domain were collected from 1 to 2500 bar and from 268 to 290 K. While the GB1 domain shows the typical pressure-induced and cold temperature-induced unfolding expected for small globular domains, the low-complexity domain of hnRNP A1 exhibits unusual pressure and temperature dependences. We observed that the low-complexity domain is pressure sensitive, undergoing a major conformational transition within the prescribed pressure range. Remarkably, this transition has the inverse temperature dependence of a typical folding-unfolding transition. Our results suggest the presence of a low-lying extended and fully solvated state(s) of the low-complexity domain that may play a role in phase separation. This study highlights the exquisite sensitivity of solution NMR spectroscopy to observe subtle conformational changes and illustrates how pressure perturbation can be used to determine the properties of metastable conformational ensembles.

PDZ Sample Quality Assessment by Biochemical and Biophysical Characterizations.

PDZ domains are small globular domains involved in protein-protein interactions. They participate in a wide range of critical cellular processes. These domains, very abundant in the human proteome, are widely studied by high-throughput interactomics approaches and by biophysical and structural methods. However, the quality of the results is strongly related to the optimal folding and solubility of the domains. We provide here a detailed description of protocols for a strict quality assessment of the PDZ constructs. We describe appropriate experimental approaches that have been selected to overcome the small size of such domains to check the purity, identity, homogeneity, stability, and folding of samples.

Globular domain structure and function of restriction-like-endonuclease LINEs: similarities to eukaryotic splicing factor Prp8

BackgroundR2 elements are a clade of early branching Long Interspersed Elements (LINEs). LINEs are retrotransposable elements whose replication can have profound effects on the genomes in which they reside. No crystal or EM structures exist for the reverse transcriptase (RT) and linker regions of LINEs.ResultsUsing limited proteolysis as a probe for globular domain structure, we show that the protein encoded by the Bombyx mori R2 element has two major globular domains: (1) a small globular domain consisting of the N-terminal zinc finger and Myb motifs, and (2) a large globular domain consisting of the RT, linker, and type II restriction-like endonuclease (RLE). Further digestion of the large globular domain occurred within the RT. Mapping these RT cleavages onto an updated model of the R2Bm RT indicated that the thumb of the RT was largely protected from proteolytic cleavage. The crystal structure of the large globular domain of Prp8, a eukaryotic splicing factor, was a major template used in building the R2Bm RT model, particularly the thumb region. The large fragment of Prp8 consists not only of a RT similar to R2Bm, but also an RLE and a linker connecting the two regions. The linker sequences adjacent to the RLE in LINEs and Prp8 share a set of two important α-helices and a (presumptive) knuckle/ββα structural motif that are closely associated with the thumb. The RLEs of LINEs and Prp8 share a unique catalytic core residue spacing as well as other key residues.ConclusionsThe protein encoded by RLE LINEs consists of two major globular domains. The larger of the two globular domain contains the RT, linker, and RLE and is similar to the large fragment of the spliceosomal protein Prp8. The similarities are suggestive of possible common ancestry.

Unusual Reversible Oligomerization of Unfolded Dengue Envelope Protein Domain 3 at High Temperatures and Its Abolition by a Point Mutation.

We report differential scanning calorimetry (DSC) experiments between 10 and 120 °C of Dengue 4 envelope protein domain 3 (DEN4 ED3), a small 107-residue monomeric globular protein domain. The thermal unfolding of DEN4 ED3 was fully reversible and exhibited two peculiar endothermic peaks. AUC (analytical ultracentrifugation) experiments at 25 °C indicated that DEN4 ED3 was monomeric. Detailed thermodynamic analysis indicated that the two endothermic peaks separated with an increasing protein concentration, and global fitting of the DSC curves strongly suggested the presence of unfolded tetramers at temperatures around 80-90 °C, which dissociated to unfolded monomers at even higher temperatures. To further characterize this rare thermal unfolding process, we designed and constructed a DEN4 ED3 variant that would unfold according to a two-state model, typical of globular proteins. We thus substituted Val 380, the most buried residue at the dimeric interface in the protein crystal, with less hydrophobic amino acids (Ala, Ser, Thr, Asn, and Lys). All variants showed a single heat absorption peak, typical of small globular proteins. In particular, the DSC thermogram of DEN4 V380K indicated a two-state reversible thermal unfolding independent of protein concentration, indicating that the high-temperature oligomeric state was successfully abolished by a single mutation. These observations confirmed the standard view that small monomeric globular proteins undergo a two-state unfolding. However, the reversible formation of unfolded oligomers at high temperatures is a truly new phenomenon, which was fully inhibited by an accurately designed single mutation.

Revealing the Mechanisms of Protein Disorder and N-Glycosylation in CD44-Hyaluronan Binding Using Molecular Simulation.

The extracellular N-terminal hyaluronan binding domain (HABD) of CD44 is a small globular domain that confers hyaluronan (HA) binding functionality to this large transmembrane glycoprotein. When recombinantly expressed by itself, HABD exists as a globular water-soluble protein that retains the capacity to bind HA. This has enabled atomic-resolution structural biology experiments that have revealed the structure of HABD and its binding mode with oligomeric HA. Such experiments have also pointed to an order-to-disorder transition in HABD that is associated with HA binding. However, it had remained unclear how this structural transition was involved in binding since it occurs in a region of HABD distant from the HA-binding site. Furthermore, HABD is known to be N-glycosylated, and such glycosylation can diminish HA binding when the associated N-glycans are capped with sialic acid residues. The intrinsic flexibility of disordered proteins and of N-glycans makes it difficult to apply experimental structural biology approaches to probe the molecular mechanisms of how the order-to-disorder transition and N-glycosylation can modulate HA binding by HABD. We review recent results from molecular dynamics simulations that provide atomic-resolution mechanistic understanding of such modulation to help bridge gaps between existing experimental binding and structural biology data. Findings from these simulations include: Tyr42 may function as a molecular switch that converts the HA-binding site from a low affinity to a high affinity state; in the partially disordered form of HABD, basic amino acids in the C-terminal region can gain sufficient mobility to form direct contacts with bound HA to further stabilize binding; and terminal sialic acids on covalently attached N-glycans can form charge-paired hydrogen bonding interactions with basic amino acids that could otherwise bind to HA, thereby blocking HA binding to glycosylated CD44 HABD.

Role of the U2AF Homology Motif in Human Tat‐SF1 as a Cofactor for HIV‐1 Splicing

The HIV‐1 life cycle relies on controlled ratios of unspliced and alternatively spliced mRNAs. Human Tat‐SF1 is a requisite host factor for the regulation of HIV‐1 RNA splicing. It is known that Tat‐SF1 associates with the U2 small nuclear ribonucloprotein particle (snRNP) of the spliceosome. However, the underlying mechanisms by which Tat‐SF1 affects HIV‐1 RNA splicing remain elusive.The core U2 snRNP protein subunit SF3b155 comprises five tryptophan‐containing motifs, termed U2AF ligand motifs (ULM) interspersed with regulated phosphorylation sites. Our lab has shown previously that the SF3b155 ULMs are recognized by splicing factors containing a small globular domain named U2AF homology motif (UHM). Based on sequence homology, we identified a putative UHM in Tat‐SF1. We hypothesize that this UHM provides a phosphorylation‐sensitive link between this alternative splicing factor and the splicing machinery via SF3b155.To investigate the Tat‐SF1 UHM interactions with SF3b155 and the role of phosphorylation, we determined the crystal structures of the Tat‐SF1 UHM in complex with a minimal phosphorylated SF3b155 ULM and for comparison the unphosphorylated and apo‐forms at 1.7 Å, 1.9 Å, and 1.1 Å, respectively. The apo‐Tat‐SF1 UHM displays a canonical UHM‐fold. The complex with the phosphorylated ULM reveals that the phosphorylation site is located closely above the plane of an aromatic residue. This suggests a reduced affinity of phosphorylated SF3b155 for the UHM due to electrostatic repulsion between the phosphate‐anion and the π‐cloud of the aromatic side chain. We are currently testing the phosphorylation‐sensitivity and significance of these Tat‐SF1 UHM/SF3b155 ULM‐interactions for HIV‐1 infectivity in vivo.

Cerebellins meet neurexins (Commentary on Matsuda & Yuzaki)

How synapses are formed and maintained is a fundamental question in neuroscience that is assuming increasing importance for our understanding of numerous neurological disorders. Recently, proteins containing complement factor C1Q-related domains (C1q-domains) have been attracting interest because of their potential role in synapse formation and/or maintenance. C1q-domains are small globular domains found in the eponymous complement factor C1Q and in a multitude of other proteins, including both small secreted proteins such as cerebellins and C1ql proteins, and large multidomain proteins such as emilins and multimerins (Ghai et al., 2007). Accumulating evidence is now implicating several C1q-domain proteins in synapse formation and/or elimination: cerebellin-1 was revealed to function in synapse maturation (Yuzaki, 2009) (Hirai et al., 2005), complement factor C1Q was implicated in synapse elimination (Stevens et al., 2007), and members of a third C1q-domain protein family, C1qls (for C1q-like), were demonstrated to reduce synapse numbers in cultured neurons (Bolliger et al., 2011). New data now published in this issue of EJN (Matsuda and Yuzaki, 2011), complementing earlier reports published in Cell and Science (Matsuda et al., 2010; Uemura et al., 2010), reveal that cerebellin-1 functions in synapse formation by binding to the presynaptic cell-adhesion neurexin molecules, and that other cerebellin isoforms may also do so. Cerebellin-1 is secreted from cerebellar granule cells, and acts as a ligand for the postsynaptic glutamate receptor (GluR)δ2 on Purkinje cells (Matsuda et al., 2010). Cerebellin-1 additionally binds to presynaptic neurexin-1β, resulting in a trimeric trans-synaptic complex composed of cerebellin-1, GluRδ2, and neurexin-1β (Uemura et al., 2010). In the present EJN article, Matsuda and Yuzaki use cell-based binding assays to demonstrate that cerebellin-1 also binds to neurexin-1α, as well as to all three β-neurexins. This binding interaction requires the inclusion of an alternatively spliced exon known as ‘splice site #4’ (Ushkaryov et al., 1992), and appears to be Ca2+-independent. The cerebellin-1 binding properties for neurexins are thus distinct from those of neuroligins (Ichtchenko et al., 1995) or LRRTMs (Ko et al., 2009; de Wit et al., 2009). This result suggests that alternative splicing of neurexins at splice site #4 influences whether they bind to either cerebellin-1 or to neuroligins and LRRTM2. Matsuda and Yuzaki further demonstrate that cerebellin-2 (but, interestingly, not cerebellin-4) also binds to neurexin-1β. The authors provide evidence that cerebellin-1 and cerebellin-2 have similar synaptogenic activities in cultured hippocampal and cortical neurons, not just in cerebellar neurons. Thus, the new article provides further evidence that cerebellin-1 acts as a bi-directional synapse organizer, initiating the recruitment of both presynaptic and postsynaptic proteins to the points of contact with both neurexin-1β and GluRδ2. The picture of cerebellins emerging from these studies suggests that they function as ‘connectors’, linking presynaptic neurexins to postsynaptic GluRδ-type receptors, and that, in doing so, they activate synapse formation. This attractive hypothesis raises a slew of new questions. For example, what is the mechanism by which such binding activates synapse formation – possibly by multimerization of the binding partners – and does this binding initiate synapse formation, or stabilize transient synapses established by other mechanisms? On a higher level, these results raise the questions of whether cerebellin binding is the primary function of neurexin proteins containing splice site #4, how important such binding is for the formation of brain circuits, and whether other postsynaptic cerebellin receptors exist. Answers to these questions will yield a greater understanding of how synapses are formed and maintained in the cerebellum and the numerous other brain regions where cerebellin family members are expressed.

LOTUS, a new domain associated with small RNA pathways in the germline

We describe here LOTUS, a hitherto uncharacterized small globular domain, which was identified using sensitive sequence profile analysis. The LOTUS domain is found in germline-specific proteins that are present in the nuage/polar granules of germ cells. TDRD5 and TDRD7, two mammalian members of the germline Tudor group, possess three copies of the LOTUS domain in their extreme N-termini. The Tudor domains of these proteins bind symmetric dimethyl arginines present on the germ cell-specific Piwi proteins, which form a particular clade of Argonaute proteins. Piwi proteins interact with a specific class of non-coding RNAs [piwi-interacting RNAs (piRNAs)] and play a key role in the repression (silencing) of transposons and possibly other germline-specific functions. A LOTUS domain is also present in the Oskar protein, a critical component of the pole plasm in the Drosophila oocyte, which is required for germ cell formation. LOTUS domains are found in various proteins from metazoans and plants, are often associated with RNA-specific modules and are likely to adopt a winged helix fold. This suggests a germline-specific role in the mRNA localization and/or translation or a specific function toward piRNAs.

The PHCCEx domain of Tiam1/2 is a novel protein- and membrane-binding module

Tiam1 and Tiam2 (Tiam1/2) are guanine nucleotide-exchange factors that possess the PH–CC–Ex (pleckstrin homology, coiled coil and extra) region that mediates binding to plasma membranes and signalling proteins in the activation of Rac GTPases. Crystal structures of the PH–CC–Ex regions revealed a single globular domain, PHCCEx domain, comprising a conventional PH subdomain associated with an antiparallel coiled coil of CC subdomain and a novel three-helical globular Ex subdomain. The PH subdomain resembles the β-spectrin PH domain, suggesting non-canonical phosphatidylinositol binding. Mutational and binding studies indicated that CC and Ex subdomains form a positively charged surface for protein binding. We identified two unique acidic sequence motifs in Tiam1/2-interacting proteins for binding to PHCCEx domain, Motif-I in CD44 and ephrinB's and the NMDA receptor, and Motif-II in Par3 and JIP2. Our results suggest the molecular basis by which the Tiam1/2 PHCCEx domain facilitates dual binding to membranes and signalling proteins.

Kinetic Analysis of the Interaction of the C1 Domain of Protein Kinase C with Lipid Membranes by Stopped-flow Spectroscopy

The diacylglycerol (DG)/phorbol ester-dependent translocation of conventional protein kinase C (PKC) isozymes is mediated by the C1 domain, a membrane-targeting module that also selectively binds phosphatidylserine (PS). Using stopped-flow spectroscopy, we dissect the contribution of DG/phorbol esters (C1 ligand) and PS in driving the association and dissociation of the C1 domain from membranes. Specifically, we examine the binding to membranes of the C1B domain of PKCbeta with a substituted Trp (Y123W) whose fluorescence is quenched upon binding to membranes. Binding of this construct (C1Bbeta-Y123W) to phospholipid vesicles is cooperative with respect to PS content and dependent on C1 ligand, as previously characterized. Stopped-flow analysis reveals that the apparent association rate (k(on)(app)), but not the apparent dissociation rate (k(off)(app)), is highly sensitive to PS content: the 60-fold increase in membrane affinity for vesicles containing no PS compared with 40 mol % PS results primarily from a robust (30-fold) increase in k(on)(app) with little effect (2-fold) on k(off)(app). Membrane affinity is also controlled by the content and structure of the C1 ligand. In contrast to PS, these ligands markedly alter k(off)(app) with smaller effects on k(on)(app). We also show that the affinity for phorbol ester-containing membranes is 2 orders of magnitude higher than that for DG-containing membranes primarily resulting from differences in k(off)(app). Our data are consistent with a model in which the C1 domain is recruited to the membrane via an initial weak electrostatic interaction with PS, followed by a rapid two-dimensional search for ligand, the binding of which retains the domain at the membrane. Thus, PS drives the initial encounter, and DG/phorbol esters retain the domain on membranes. The decreased effectiveness of DG compared with phorbol esters in retaining the C1 domain on membranes contributes to the molecular dichotomy of the rapid, transient nature of DG-dependent PKC signaling versus the chronic hyperactivity of phorbol ester-activated PKC.

Dynamics of Trigger Factor Interaction with Translating Ribosomes

In all organisms ribosome-associated chaperones assist early steps of protein folding. To elucidate the mechanism of their action, we determined the kinetics of individual steps of the ribosome binding/release cycle of bacterial trigger factor (TF), using fluorescently labeled chaperone and ribosome-nascent chain complexes. Both the association and dissociation rates of TF-ribosome complexes are modulated by nascent chains, whereby their length, sequence, and folding status are influencing parameters. However, the effect of the folding status is modest, indicating that TF can bind small globular domains and accommodate them within its substrate binding cavity. In general, the presence of a nascent chain causes an up to 9-fold increase in the rate of TF association, which provides a kinetic explanation for the observed ability of TF to efficiently compete with other cytosolic chaperones for binding to nascent chains. Furthermore, a subset of longer nascent polypeptides promotes the stabilization of TF-ribosome complexes, which increases the half-life of these complexes from 15 to 50 s. Nascent chains thus regulate their folding environment generated by ribosome-associated chaperones.

Protein Structure Based Strategies for Antigen Discovery and Vaccine Development Against Malaria and Other Pathogens

The review surveys potential "structural antigens" which represent small protein domains that can be chemically synthesized and, isolated from the context of the whole protein, can fold in the same native structure. They include natively unfolded protein regions, small globular domains, alpha-helical coiled coils and regions with tandem repeats forming structures ranging from the collagen triple helices to solenoid-like arrangements. We also describe and compare new strategies for development of vaccine that use the concept of structural epitopes. One type of approach is based on engineering artificial mini-proteins able to mimic structural epitopes of natural proteins. The review compares the "engineering" methodologies with "bioinformatics" approaches that became possible recently, after the sequencing of the genomes of many pathogens, and involve genome-wide bioinformatics searches for "structural antigens". In particular, based on the known P. falciparum genome, we identified putative alpha-helical coiled coil regions, 30-40 amino acids long, in proteins presented in asexual malaria blood stages. Peptides of such regions frequently fold into the "native" structure. A hundred such peptides were synthesized and all of them were recognized at various degrees (5-80%) by a panel of sera from donors living in malaria-endemic areas. The results obtained demonstrate that a bioinformatics/chemical synthesis strategy can rapidly lead to the identification of new proteins that can be targets of potential vaccines and/or drugs against malaria and other infectious organisms.

Isolated ZP-N domains constitute the N-terminal extensions of Zona Pellucida proteins

Zona Pellucida (ZP) domains have been found in a wide variety of extracellular proteins, in which they play essential role for polymerization. They are shared by the ZP proteins, which constitute the extracellular coat of animal eggs. Except from ZP3, constituting the primary sperm receptor, the ZP proteins possess, in addition to their C-terminal ZP domains, N-terminal extensions, which are thought to play an important role in the species-specific gamete recognition. Here, we show that these extensions are made of single or multiple copies of a small globular domain, which can be significantly related to the N-terminal region of ZP domains (ZP-N domains). This finding brings new insights into the molecular evolution of ZP proteins, which may have evolved around a common ZP-N architecture, and more generally into the noticeable sequence diversity of ZP-N domains, which can be found as isolated subunits or tightly associated with ZP-C domains to form complete, canonical ZP domains.

Molecular Mechanism for Low pH Triggered Misfolding of the Human Prion Protein

Conformational changes in the prion protein cause transmissible spongiform encephalopathies, also referred to as prion diseases. In its native state, the prion protein is innocuous (PrPC), but it can misfold into a neurotoxic and infectious isoform (PrPSc). The full-length cellular form of the prion protein consists of residues 23-230, with over half of the sequence belonging to the unstructured N-terminal domain and the remaining residues forming a small globular domain. During misfolding and aggregation, portions of both the structured and unstructured domains are incorporated into the aggregates. After limited proteolysis by proteinase K, the most abundant fragment from brain-derived prion fibrils is a 141-residue fragment composed of residues 90-230. Here we describe simulations of this fragment of the human prion protein at low pH, which triggers misfolding, and at neutral pH as a control. The simulations, in agreement with experiment, show that this biologically and pathologically relevant prion construct is stable and native-like at neutral pH. In contrast, at low pH the prion protein is destabilized via disruption of critical long-range salt bridges. In one of the low pH simulations this destabilization resulted in a conformational transition to a PrPSc-like isoform consistent with our previous simulations of a smaller construct.

The drug designer´s guide to selectivity

Although several dual activity and so-called dirty drugs, which are active on more than one drug target or mediate more than one effect, have made it to the market the ruling paradigm in drug discovery today is to deliver selective drugs. However, it is not always a trivial task to make a priori predictions of the possibilities for achieving ligand selectivity for a given target, and compounds in late developmental phase, or even after launch, may still be found to possess activity and effects not previously foreseen. It would therefore be of great benefit if one could display any notions addressing selectivity based on database knowledge and simple calculations. In the present study, a sequence alignment-based approach will be presented and it will be applied to the PDZ class of protein domains. This protein class consists of small globular domains that easily superimpose using their 3D structure. In a recent human genomics investigation, a PDZ containing protein, i.e., DLG5, was shown to comprise a single nucleotide polymorphism related mutation in one of the DLG5 protein, which was found to be associated to an increased risk of having a Crohn's disease diagnosis. Consequently, it would be of medicinal interest to design ligands selective to the DLG5 PDZ domains and the present process aims at the possibility to achieve that using a novel chemometric approach, including a new set of amino acid property scales. Thus, in the present paper, selectivity aspects as seen from the protein target perspective will be outlined. This approach is relying on adequate multiple sequence alignments (MSA) and the PDZ protein domains provide a good example due to their firm homology in 3D structure.

Bex1, a novel interactor of the p75 neurotrophin receptor, links neurotrophin signaling to the cell cycle

A screening for intracellular interactors of the p75 neurotrophin receptor (p75NTR) identified brain-expressed X-linked 1 (Bex1), a small adaptor-like protein of unknown function. Bex1 levels oscillated during the cell cycle, and preventing the normal cycling and downregulation of Bex1 in PC12 cells sustained cell proliferation under conditions of growth arrest, and inhibited neuronal differentiation in response to nerve growth factor (NGF). Neuronal differentiation of precursors isolated from the brain subventricular zone was also reduced by ectopic Bex1. In PC12 cells, Bex1 overexpression inhibited the induction of NF-kappaB activity by NGF without affecting activation of Erk1/2 and AKT, while Bex1 knockdown accelerated neuronal differentiation and potentiated NF-kappaB activity in response to NGF. Bex1 competed with RIP2 for binding to the p75NTR intracellular domain, and elevating RIP2 levels restored the ability of cells overexpressing Bex1 to differentiate in response to NGF. Together, these data establish Bex1 as a novel link between neurotrophin signaling, the cell cycle, and neuronal differentiation, and suggest that Bex1 may function by coordinating internal cellular states with the ability of cells to respond to external signals.

Comparison of MukB homodimer versus MukBEF complex molecular architectures by electron microscopy reveals a higher-order multimerization

The complex of MukF, MukE, and MukB proteins participates in organization of sister chromosomes and partitioning into both daughter cells in Escherichia coli. We purified the MukB homodimer and the MukBEF complex and analyzed them by electron microscopy to compare both structures. A MukB homodimer shows a long rod–hinge–rod v-shape with small globular domains at both ends. The MukBEF complex shows a similar structure having larger globular domains than those of the MukB homodimer. These results suggest that MukF and MukE bind to the globular domains of a MukB homodimer. The globular domains of the MukBEF complex frequently associate with each other in an intramolecular fashion, forming a ring. In addition, MukBEF complex molecules tend to form multimers by the end-to-end joining with other MukBEF molecules in an intermolecular fashion, resulting in fibers and rosette-form structures in the absence of ATP and DNA in vitro.

Three-dimensional reconstruction of axonemal outer dynein arms in situ by electron tomography

We present here for the first time a 3D reconstruction of in situ axonemal outer dynein arms. This reconstruction has been obtained by electron tomography applied to a series of tilted images collected from metal replicas of rapidly frozen, cryofractured, and metal-replicated sperm axonemes of the cecidomid dipteran Monarthropalpus flavus. This peculiar axonemal model consists of several microtubular laminae that proved to be particularly suitable for this type of analysis. These laminae are sufficiently planar to allow the visualization of many dynein molecules within the same fracture face, allowing us to recover a significant number of equivalent objects and to improve the signal-to-noise ratio of the reconstruction by applying advanced averaging protocols. The 3D model we obtained showed the following interesting structural features: First, each dynein arm has two head domains that are almost parallel and are obliquely oriented with respect to the longitudinal axis of microtubules. The two heads are therefore positioned at different distances from the surface of the A-tubule. Second, each head domain consists of a series of globular subdomains that are positioned on the same plane. Third, a stalk domain originates as a conical region from the proximal head and ends with a small globular domain that contacts the B-tubule. Fourth, the stem region comprises several globular subdomains and presents two distinct points of anchorage to the surface of the A-tubule. Finally, and most importantly, contrary to what has been observed in isolated dynein molecules adsorbed to flat surfaces, the stalk and the stem domains are not in the same plane as the head.