How clustered protocadherin binding specificity is tuned for neuronal self-/nonself-recognition

The stochastic expression of fewer than 60 clustered protocadherin (cPcdh) isoforms provides diverse identities to individual vertebrate neurons and a molecular basis for self-/nonself-discrimination. cPcdhs form chains mediated by alternating cis and trans interactions between apposed membranes, which has been suggested to signal self-recognition. Such a mechanism requires that cPcdh cis dimers form promiscuously to generate diverse recognition units, and that trans interactions have precise specificity so that isoform mismatches terminate chain growth. However, the extent to which cPcdh interactions fulfill these requirements has not been definitively demonstrated. Here, we report biophysical experiments showing that cPcdh cis interactions are promiscuous, but with preferences favoring formation of heterologous cis dimers. Trans homophilic interactions are remarkably precise, with no evidence for heterophilic interactions between different isoforms. A new C-type cPcdh crystal structure and mutagenesis data help to explain these observations. Overall, the interaction characteristics we report for cPcdhs help explain their function in neuronal self-/nonself-discrimination.

Effects of ALS-associated TANK binding kinase 1 mutations on protein-protein interactions and kinase activity

Exonic DNA sequence variants in the Tbk1 gene associate with both sporadic and familial amyotrophic lateral sclerosis (ALS). Here, we examine functional defects in 25 missense TBK1 mutations, focusing on kinase activity and protein-protein interactions. We identified kinase domain (KD) mutations that abolish kinase activity or display substrate-specific defects in specific pathways, such as innate immunity and autophagy. By contrast, mutations in the scaffold dimerization domain (SDD) of TBK1 can cause the loss of kinase activity due to structural disruption, despite an intact KD. Familial ALS mutations in ubiquitin-like domain (ULD) or SDD display defects in dimerization; however, a subset retains kinase activity. These observations indicate that TBK1 dimerization is not required for kinase activation. Rather, dimerization seems to increase protein stability and enables efficient kinase-substrate interactions. Our study revealed many aspects of TBK1 activities affected by ALS mutations, highlighting the complexity of disease pathogenicity and providing insights into TBK1 activation mechanism.

γ-Protocadherin structural diversity and functional implications

Stochastic cell-surface expression of α-, β-, and γ-clustered protocadherins (Pcdhs) provides vertebrate neurons with single-cell identities that underlie neuronal self-recognition. Here we report crystal structures of ectodomain fragments comprising cell-cell recognition regions of mouse γ-Pcdhs γA1, γA8, γB2, and γB7 revealing trans-homodimers, and of C-terminal ectodomain fragments from γ-Pcdhs γA4 and γB2, which depict cis-interacting regions in monomeric form. Together these structures span the entire γ-Pcdh ectodomain. The trans-dimer structures reveal determinants of γ-Pcdh isoform-specific homophilic recognition. We identified and structurally mapped cis-dimerization mutations to the C-terminal ectodomain structures. Biophysical studies showed that Pcdh ectodomains from γB-subfamily isoforms formed cis dimers, whereas γA isoforms did not, but both γA and γB isoforms could interact in cis with α-Pcdhs. Together, these data show how interaction specificity is distributed over all domains of the γ-Pcdh trans interface, and suggest that subfamily- or isoform-specific cis-interactions may play a role in the Pcdh-mediated neuronal self-recognition code.

Molecular basis of sidekick-mediated cell-cell adhesion and specificity

Sidekick (Sdk) 1 and 2 are related immunoglobulin superfamily cell adhesion proteins required for appropriate synaptic connections between specific subtypes of retinal neurons. Sdks mediate cell-cell adhesion with homophilic specificity that underlies their neuronal targeting function. Here we report crystal structures of Sdk1 and Sdk2 ectodomain regions, revealing similar homodimers mediated by the four N-terminal immunoglobulin domains (Ig1-4), arranged in a horseshoe conformation. These Ig1-4 horseshoes interact in a novel back-to-back orientation in both homodimers through Ig1:Ig2, Ig1:Ig1 and Ig3:Ig4 interactions. Structure-guided mutagenesis results show that this canonical dimer is required for both Sdk-mediated cell aggregation (via trans interactions) and Sdk clustering in isolated cells (via cis interactions). Sdk1/Sdk2 recognition specificity is encoded across Ig1-4, with Ig1-2 conferring the majority of binding affinity and differential specificity. We suggest that competition between cis and trans interactions provides a novel mechanism to sharpen the specificity of cell-cell interactions.

Structural Basis of Diverse Homophilic Recognition by Clustered α- and β-Protocadherins

Clustered protocadherin proteins (α-, β-, and γ-Pcdhs) provide a high level of cell-surface diversity to individual vertebrate neurons, engaging in highly specific homophilic interactions to mediate important roles in mammalian neural circuit development. How Pcdhs bind homophilically through their extracellular cadherin (EC) domains among dozens of highly similar isoforms has not been determined. Here, we report crystal structures for extracellular regions from four mouse Pcdh isoforms (α4, α7, β6, and β8), revealing a canonical head-to-tail interaction mode for homophilic trans dimers comprising primary intermolecular EC1:EC4 and EC2:EC3 interactions. A subset of trans interface residues exhibit isoform-specific conservation, suggesting roles in recognition specificity. Mutation of these residues, along with trans-interacting partner residues, altered the specificities of Pcdh interactions. Together, these data show how sequence variation among Pcdh isoforms encodes their diverse strict homophilic recognition specificities, which are required for their key roles in neural circuit assembly.

Sequence variability, gene structure, and expression of full-length human endogenous retrovirus H

Recently, we identified and classified 926 human endogenous retrovirus H (HERV-H)-like proviruses in the human genome. In this paper, we used the information to, in silico, reconstruct a putative ancestral HERV-H. A calculated consensus sequence was nearly open in all genes. A few manual adjustments resulted in a putative 9-kb HERV-H provirus with open reading frames (ORFs) in gag, pro, pol, and env. Long terminal repeats (LTRs) differed by 1.1%, indicating proximity to an integration event. The gag ORF was extended upstream of the normal myristylation start site. There was a long leader (including a "pre-gag" ORF) region positioned like the N terminus of murine leukemia virus (MLV) "glyco-Gag," potentially encoding a proline- and serine-rich domain remotely similar to MLV pp12. Another ORF, starting inside the 5' LTR, had no obvious similarity to known protein domains. Unlike other hitherto described gammaretroviruses, the reconstructed Gag had two zinc finger motifs. Alternative splicing of sequences related to the HERV-H consensus was confirmed using dbEST data. env transcripts were most prevalent in colon tumors, but also in normal testis. We found no evidence for full length env transcripts in the dbEST. HERV-H had a markedly skewed nucleotide composition, disfavoring guanine and favoring cytidine. We conclude that the HERV-H consensus shared a gene arrangement common to gammaretroviruses with gag separated by stop codon from pro-pol in the same reading frame, while env resides in another reading frame. There was also alternative splicing. HERV-H consensus yielded new insights in gammaretroviral evolution and will be useful as a model in studies on expression and function.

Optimization of P1-P3 groups in symmetric and asymmetric HIV-1 protease inhibitors

HIV-1 protease is an important target for treatment of AIDS, and efficient drugs have been developed. However, the resistance and negative side effects of the current drugs has necessitated the development of new compounds with different binding patterns. In this study, nine C-terminally duplicated HIV-1 protease inhibitors were cocrystallised with the enzyme, the crystal structures analysed at 1.8-2.3 A resolution, and the inhibitory activity of the compounds characterized in order to evaluate the effects of the individual modifications. These compounds comprise two central hydroxy groups that mimic the geminal hydroxy groups of a cleavage-reaction intermediate. One of the hydroxy groups is located between the delta-oxygen atoms of the two catalytic aspartic acid residues, and the other in the gauche position relative to the first. The asymmetric binding of the two central inhibitory hydroxyls induced a small deviation from exact C2 symmetry in the whole enzyme-inhibitor complex. The study shows that the protease molecule could accommodate its structure to different sizes of the P2/P2' groups. The structural alterations were, however, relatively conservative and limited. The binding capacity of the S3/S3' sites was exploited by elongation of the compounds with groups in the P3/P3' positions or by extension of the P1/P1' groups. Furthermore, water molecules were shown to be important binding links between the protease and the inhibitors. This study produced a number of inhibitors with Ki values in the 100 picomolar range.

Resistance profiles of cyclic and linear inhibitors of HIV-1 protease

Resistance to anti-HIV protease drugs is a major problem in the design of AIDS drugs with long-term efficacy. To identify structural features associated with a certain resistance profile, the inhibitory properties of a series of symmetric and asymmetric cyclic sulfamide, cyclic urea and linear transition-state analogue inhibitors of HIV-1 protease were investigated using wild-type and mutant enzyme. To allow a detailed structure-inhibition analysis, enzyme with single, double, triple and quadruple combinations of G48V, V82A, 184V and L90M substitutions was used. Kinetic analysis of the mutants revealed that catalytic efficiency was 1-30% of that for the wild-type enzyme, a consequence of reduced kcat in all cases and an increased KM for all mutants except for the G48V enzyme. The overall structure-inhibitory profiles of the cyclic compounds were similar, and the inhibition of the V82A, 184V and G48V/L90M mutants were less efficient than of the wild-type enzyme. The greatest increase in Ki was generally observed for the 184V mutant and least for the G48V/L90M mutant, and additional combinations of mutations did not result in improved inhibition profiles for the cyclic compounds. An extended analysis of additional mutants, and including a set of linear compounds, showed that the profile was unique for each compound, and did not reveal any general structural features associated with a certain inhibition profile. The effects of structural modifications in the inhibitors, or of mutations, were not additive and they differed depending on their context. The results demonstrate the difficulties in predicting resistance, even for closely related compounds, and designing compounds with improved resistance profiles.

Synthesis and comparative molecular field analysis (CoMFA) of symmetric and nonsymmetric cyclic sulfamide HIV-1 protease inhibitors

We have previously reported on the unexpected flipped conformation in the cyclic sulfamide class of inhibitors. An attempt to induce a symmetric binding conformation by introducing P2/P2' substituents foreseen to bind preferentially in the S2/S2' subsite was unsuccessful. On the basis of the flipped conformation we anticipated that nonsymmetric sulfamide inhibitors, with P2/P2' side chains modified individually for the S1' and S2 subsites, should be more potent than the corresponding symmetric analogues. To test this hypothesis, a set of 18 cyclic sulfamide inhibitors (11 nonsymmetric and 7 symmetric) with different P2/P2' substituents was prepared and evaluated in an enzyme assay. To rationalize the structure-activity relationship (SAR) and enable the alignment of the nonsymmetric inhibitors, i.e., which of the P2/P2' substituents of the nonsymmetric inhibitors interact with which subsite, a CoMFA study was performed. The CoMFA model, constructed from the 18 inhibitors in this study along with seven inhibitors from previous work by our group, has successfully been used to rationalize the SAR of the cyclic sulfamide inhibitors. Furthermore, from the information presented herein, the SAR of the cyclic sulfamide class of inhibitors seems to differ from the SAR of the related cyclic urea inhibitors reported by DuPont and DuPont-Merck.

Autism and hearing loss

A group of 199 children and adolescents (153 boys, 46 girls) with autistic disorder was audiologically evaluated. Mild to moderate hearing loss was diagnosed in 7.9% and unilateral hearing loss in 1.6% of those who could be tested appropriately. Pronounced to profound bilateral hearing loss or deafness was diagnosed in 3.5% of all cases, representing a prevalence considerably above that in the general population and comparable to the prevalence found in populations with mental retardation. Hearing deficits in autism occurred at similar rates at all levels of intellectual functioning, so it does not appear that the covariation with intellectual impairment per se can account for all of the variance of hearing deficit in autism. Hyperacusis was common, affecting 18.0% of the autism group and 0% in an age-matched nonautism comparison group. In addition, the rate of serous otitis media (23.5%) and related conductive hearing loss (18.3%) appeared to be increased in autistic disorder. The study emphasizes the need for auditory evaluation of individuals with autism in order to refer those with pronounced to profound hearing loss for aural habilitation and to follow those with mild to moderate hearing loss because of the risk of deterioration.

Design and fast synthesis of C-terminal duplicated potent C(2)-symmetric P1/P1'-modified HIV-1 protease inhibitors

An analysis of the X-ray structure of a complex of HIV-1 protease with a linear C(2)-symmetric C-terminal duplicated inhibitor guided the selection of a series of diverse target compounds. These were synthesized with the objective to identify suitable P1/P1' substituents to provide inhibitors with improved antiviral activity. Groups with various physical properties were attached to the para-positions of the P1/P1' benzyloxy groups in the parent inhibitor. A p-bromobenzyloxy compound, prepared in only three steps from commercially available starting materials, was utilized as a common precursor in all reactions. The subsequent coupling reactions were completed within a few minutes and relied on palladium catalysis and flash heating with microwave irradiation. All of the compounds synthesized exhibited good inhibitory potency in the protease assay, with K(i) values ranging from 0.09 to 3.8 nM. A 30-fold improvement of the antiviral effect in cell culture, compared to the parent compound, was achieved with four of the inhibitors. The differences in K(i) values were not correlated to the differences in antiviral effect, efficiency against mutant virus, or reduced potency in the presence of human serum. The poorest enzyme inhibitors in fact belong to the group with the best antiviral effect. The binding features of two structurally related inhibitors, cocrystallized with HIV-1 protease, are discussed with special emphasis on the interaction at the enzyme/water phase.

Autistic behaviour and attention deficits in tuberous sclerosis: a population-based study

In a population-based sample of 28 individuals under the age of 20 years, autistic symptoms were present in 24 and DSM-III-R autistic disorder in 17. Many of the children and adolescents diagnosed as autistic also showed attention deficit/hyperactivity. There was no specific association between autistic behaviour and the presence of infantile spasms. Some of the children with tuberous sclerosis and autism were of near-normal intelligence. Indirectly, the results suggest that as many as 9 per cent of all children with autism may have tuberous sclerosis.

Tuberous sclerosis in Western Sweden. A population study of cases with early childhood onset

OBJECTIVE

To study the prevalence of tuberous sclerosis in children and adolescents.

DESIGN

Previously published diagnostic criteria for tuberous sclerosis were used. All physicians likely to encounter young patients with tuberous sclerosis were contacted by way of a screening questionnaire.

SETTING

The study was performed in a circumscribed geographic area (western Sweden).

PATIENTS AND OTHER PARTICIPANTS

The sample was population based. However, only patients with such severe and early symptoms that referral to a physician had been considered necessary and relatives of these patients with tuberous sclerosis could be included. This was because there is currently no diagnostic marker for tuberous sclerosis that could be used as a screening tool.

RESULTS

The peak prevalence (one in 6800 individuals) for tuberous sclerosis was found in the 11- to 15-year-old age group. For the whole age cohort, 0 to 20 years, the prevalence was one in 12,900 individuals.

CONCLUSIONS

The prevalence for the school-age group was the highest ever reported in the literature on tuberous sclerosis. However, it is likely that the true prevalence of tuberous sclerosis in the general population is even higher.

Glial fibrillary acidic protein in the cerebrospinal fluid of children with autism and other neuropsychiatric disorders

The cerebrospinal fluid (CSF) of 47 children and adolescents with autism was analyzed for the contents of two astroglial proteins, the glial fibrillary acidic protein (GFA) and S 100. The results were contrasted with those obtained in similarly aged cases with other neuropsychiatric disorders (n = 25) and in normal children (n = 10). S-100 did not discriminate the groups from each other. However, GFA in autism and autistic-like conditions was at a level almost three times that in the normal group. The results could implicate gliosis and unspecific brain damage in autism. An alternative model would be increased synapse turnover regardless of underlying cause.

A sensitive ELISA for glial fibrillary acidic protein: application in CSF of children

In the present study we describe a sensitive ELISA for determination of glial fibrillary acidic protein (GFAP). To validate the method combined determinations of GFAP and S-100 protein were performed in cerebrospinal fluid (CSF) of normal children and children with autism. The GFAP ELISA is of sandwich type and uses the biotin-avidin system. Sensitivity was 16 pg/ml. Between-day precision was 0.079 (coeff. of variance). S-100 protein concentrations were measured using a commercially available ELISA kit. Normal CSF from children and young adults were analysed. The CSF levels of GFAP in normal children were low (16-163 pg/ml). Both GFAP and S-100 protein concentrations correlated with age (P < 0.01 and P < 0.05, respectively), but the GFAP increment was more pronounced, probably reflecting the age-dependent expansion of the fibrillary astrocytes in the central nervous system (CNS). GFAP levels in children with infantile autism were higher than those in normal children of the same age range. S-100 protein concentrations were similar in both groups. High levels of GFAP in combination with normal S-100 protein concentrations in CSF indicates reactive astrogliosis in the CNS. In conclusion, the sensitive ELISA described makes it possible to measure low levels of GFAP present in the CSF of children. Combined assays of GFAP and S-100 protein can be used to discriminate between acute and chronic brain disorders in children.

Interaction between inhibitory pathways to principal cells in the lateral geniculate nucleus of the cat

Inhibitory interactions between interneurones of the lateral geniculate nucleus (LGN) of the cat were studied with an indirect method based on intracellular recordings of synaptic responses in principal cells. Recurrent inhibitory postsynaptic potentials (IPSPs), evoked by antidromic activation of principal cell axons in the visual cortex, were depressed by a preceding stimulation of the optic tract or the visual cortex. Disynaptic feed-forward IPSPs, evoked by optic tract stimulation, were likewise depressed after cortex stimulation. The duration of the depression was in both cases about 100 ms. The effect was not due to conductance changes in the recorded principal cells or to activation of cortico-geniculate fibres. The observations indicate that perigeniculate neurones, the recurrent inhibitory interneurones of the LGN, have mutual inhibitory connexions and that they also project to intrageniculate interneurones, the inhibitory cells in the feed-forward pathway to principal cells. These conclusions were supported by intracellular recordings from a few interneurones. No evidence was found for interaction between feed-forward interneurones activated from separate eyes or for a projection from intrageniculate interneurones to perigeniculate cells. The results point to an unexpected similarity in the organization of the recurrent inhibitory system of principal cells in the LGN and of spinal motoneurones. It is suggested that the recurrent system of the LGN serves as a variable gain regulator in analogy with a recently proposed model for the spinal system.

Brain stem neurones with differential projection to functional subregions of the dorsal lateral geniculate complex in the cat

Neurones (n = 194) in the ponto-mesencephalic reticular formation were identified as projecting to the region of the dorsal lateral geniculate nucleus, by their antidromic activation from this region. The projection of individual neurones was investigated by mapping of thresholds at closely spaced sites in the lateral geniculate nucleus and the dorsally located perigeniculate nucleus. Low thresholds, long latencies and stepwise antidromic latency shifts, occurring together, were taken to indicate termination. Low thresholds with short antidromic latencies without stepwise latency shifts were encountered more ventrally and ascribed to stimulation of larger fibres en route to terminal fields. The conduction velocity from the stimulation site of the large fibres to the cell bodies in the reticular formation was 0.9-3.1 m/s and to regions within the terminal fields 0.06-0.2 m/s. The considerable slowing of the conduction velocity, together with the extensive regions with low thresholds and the abundance of latency shifts, 0.3-19.5 ms, suggest arborization of very thin fibres within the terminal fields. Three groups of reticular neurones with different termination were distinguished: type A neurones (n = 32) terminate exclusively in the laminae of the lateral geniculate nucleus. Type B neurones (n = 22) terminate in the perigeniculate nucleus, the overlaying part of the reticular nucleus of thalamus and in the interlaminar plexuses in the lateral geniculate nucleus. Type C neurones (n = 27) terminate both in the lateral geniculate nucleus and the perigeniculate nucleus. The projection of individual neurones of all three types extended throughout their entire target nucleus/nuclei and is thus global with respect to the visual hemifield. On the basis of previous findings that stimulation in the reticular formation inhibits interneurones in both feed-forward and recurrent inhibitory pathways to relay cells in the lateral geniculate nucleus, it is suggested that the reticular neurones are inhibitory and that the type A neurones control the feed-forward inhibition, type B neurones the recurrent inhibition and type C neurones both inhibitory mechanisms together. Findings suggesting that different reticular neurones may be related to the interneuronal circuits of the X-, Y- and W-systems are discussed. Type A, B and C neurones were found intermingled, around the brachium conjunctivum and among its fibres from the level of the decussation to the posterior end of the locus coeruleus complex.(ABSTRACT TRUNCATED AT 400 WORDS)

Inhibition from the brain stem of inhibitory interneurones of the cat's dorsal lateral geniculate nucleus

Brain-stem control of inhibitory circuits in the dorsal lateral geniculate nucleus (d.l.g.n.) of the cat was studied with extracellular recordings from functionally identified interneurones and with intracellular recordings from principal cells. Perigeniculate neurones, the recurrent inhibitory interneurones of the d.l.g.n., were inhibited by low-threshold stimulation within a wide bilateral field of the brainstem reticular formation extending from the rostral mesencephalon to the caudal medulla oblongata. The inhibition had a latency of 10-12 ms for stimulation sites in the mesencephalon and a duration of about 100 ms. The brain-stem stimulation evoked large hyperpolarizing potentials in intracellularly recorded perigeniculate neurones, indicating that the effect was due to post-synaptic inhibition. Intrageniculate interneurones, the feed-forward inhibitory interneurones of the d.l.g.n., were inhibited with a similar time course from the same region of the brain stem. Both feed-forward and recurrent inhibitory post-synaptic potentials (i.p.s.p.s) in principal cells were depressed by a preceding stimulation of brain-stem sites effective for the interneurones. The depression had about the same time course as the inhibition of the interneurones and it occurred without a concomitant change in the membrane potential of the recorded principal cells. A small depolarizing potential, with a latency of 10-20 ms, was observed in some principal cells after brain-stem stimulation. The potential reversed polarity when i.p.s.p.s were reversed by current injection into the recorded cell indicating that it was due to disinhibition of the principal cells. The possible neuronal pathway for the inhibition of the d.l.g.n. in interneurones is considered and it is proposed that the effect is mediated by a group of neurones located in the caudal mesencephalon and the rostral pons close to the fibres of the brachium conjunctivum.

Projection of brain stem neurons to the perigeniculate nucleus and the lateral geniculate nucleus in the cat

Small horseradish peroxidase injections in the perigeniculate nucleus (PGN) or the lateral geniculate nucleus (LGN) gave retrograde labeling of many cells in the pontomesencephalic reticular formation (RF), the nuclei raphe dorsalis and centralis linearis, locus coeruleus, nucleus of the optic tract and nucleus parabigeminalis. Antidromic stimulation was used to identify neurons in the RF projecting to the PGN-LGN complex. Threshold mapping through the PGN and the LGN shows separate projection from the reticular formation to the PGN and the LGN.

Functional distinction of perigeniculate and thalamic reticular neurons in the cat

Two types of neurons can be recognized in the region above the lateral geniculate nucleus. One cell type is found in the caudal part of the reticular nucleus of thalamus; these cells are accordingly called reticular neurons. The other cell type is located in the perigeniculate nucleus immediately above lamina A of the lateral geniculate nucleus and in the intermediate zone between the perigeniculate nucleus and the reticular nucleus. These cells are referred to as perigeniculate neurons. Electrical stimulation of the optic tract and the visual cortex typically evokes a short burst of spikes in the perigeniculate neurons, and the excitation has a shorter latency from the cortex (range 1.2-2.5 ms) than from the optic tract (range 1.5-3.1 ms). The perigeniculate neurons are also activated by adequate visual stimuli. In contrast, the reticular neurons are unresponsive to visual stimuli and electrical stimulation of the optic tract but they may respond with a burst of spikes to cortex stimulation with rather long latency (range 2.7-5.5 ms). It is concluded that only perigeniculate neurons qualify as interneurons in the recurrent inhibitory pathway to principal cells in the lateral geniculate nucleus.

Retrograde labelling of retinogeniculate neurones in the cat by HRP uptake from the diffuse injection zone

The effective uptake region for retrograde HRP labelling was investigated in the retinogeniculate system in the cat. Contrary to previous reports, labelling of ganglion cells was found not only in the retinal area projecting to the dense central zone of the injection site, but also in areas projecting to extensive regions of its surrounding diffuse zone in the lateral geniculate nucleus. It is concluded that the widely accepted view that retrograde HRP labelling occurs only by uptake of HRP from the dense zone of the injection site is erroneous.