Small Structural Rearrangements Research Articles

Genome Sequencing for Diagnosing Rare Diseases

BackgroundGenetic variants that cause rare disorders may remain elusive even after expansive testing, such as exome sequencing. The diagnostic yield of genome sequencing, particularly after a negative evaluation, remains poorly defined.MethodsWe sequenced and analyzed the genomes of families with diverse phenotypes who were suspected to have a rare monogenic disease and for whom genetic testing had not revealed a diagnosis, as well as the genomes of a replication cohort at an independent clinical center.ResultsWe sequenced the genomes of 822 families (744 in the initial cohort and 78 in the replication cohort) and made a molecular diagnosis in 218 of 744 families (29.3%). Of the 218 families, 61 (28.0%) — 8.2% of families in the initial cohort — had variants that required genome sequencing for identification, including coding variants, intronic variants, small structural variants, copy-neutral inversions, complex rearrangements, and tandem repeat expansions. Most families in which a molecular diagnosis was made after previous nondiagnostic exome sequencing (63.5%) had variants that could be detected by reanalysis of the exome-sequence data (53.4%) or by additional analytic methods, such as copy-number variant calling, to exome-sequence data (10.8%). We obtained similar results in the replication cohort: in 33% of the families in which a molecular diagnosis was made, or 8% of the cohort, genome sequencing was required, which showed the applicability of these findings to both research and clinical environments.ConclusionsThe diagnostic yield of genome sequencing in a large, diverse research cohort and in a small clinical cohort of persons who had previously undergone genetic testing was approximately 8% and included several types of pathogenic variation that had not previously been detected by means of exome sequencing or other techniques. (Funded by the National Human Genome Research Institute and others.)

Structural relaxation dynamics of a silicate glass probed by refractive index and ionic conductivity

AbstractRelaxation occurs spontaneously in all glasses and is a fundamental step of important technological processes, such as annealing, crystal nucleation, and chemical strengthening by ion exchange. Despite extensive studies over the past decades, there are still conflicting results on whether the kinetics of structural relaxation depends on the analyzed property. Thus, in this study, we used a lithium disilicate glass as a model composition to determine the structural relaxation kinetics during physical aging experiments by measuring the time evolution of the refractive index and ionic conductivity down to 35 K below the initial fictive temperature. In all cases, variations in these properties were adequate to capture the structural changes throughout the aging experiments. At each temperature, the experimental relaxation data fit quite well with the classical stretched exponential relation. We also found that the relaxation process starts faster when probed by ionic conductivity than by refractive index; however, they show similar average relaxation times. These very small structural rearrangements are always the same, but ionic conductivity changes faster than refractive index at the beginning of the process. Our comprehensive results strongly indicate that relaxation dynamics is indeed dependent on the analyzed property.

Structure-dynamics relationships in cryogenically deformed bulk metallic glass

The atomistic mechanisms occurring during the processes of aging and rejuvenation in glassy materials involve very small structural rearrangements that are extremely difficult to capture experimentally. Here we use in-situ X-ray diffraction to investigate the structural rearrangements during annealing from 77 K up to the crystallization temperature in Cu44Zr44Al8Hf2Co2 bulk metallic glass rejuvenated by high pressure torsion performed at cryogenic temperatures and at room temperature. Using a measure of the configurational entropy calculated from the X-ray pair correlation function, the structural footprint of the deformation-induced rejuvenation in bulk metallic glass is revealed. With synchrotron radiation, temperature and time resolutions comparable to calorimetric experiments are possible. This opens hitherto unavailable experimental possibilities allowing to unambiguously correlate changes in atomic configuration and structure to calorimetrically observed signals and can attribute those to changes of the dynamic and vibrational relaxations (α-, β- and γ-transition) in glassy materials. The results suggest that the structural footprint of the β-transition is related to entropic relaxation with characteristics of a first-order transition. Dynamic mechanical analysis data shows that in the range of the β-transition, non-reversible structural rearrangements are preferentially activated. The low-temperature γ-transition is mostly triggering reversible deformations and shows a change of slope in the entropic footprint suggesting second-order characteristics.

Ca2+ as activator of pseudoperoxidase activity of pigeon, Eurasian woodcock and chicken myoglobins: New features for meat preservation studies

Myoglobin (Mb), hemeprotein that binds dioxygen in muscle, affects meat colour. Moreover, in presence of peroxides, metMb is a potent oxidant involved in oxidative rancidity in meat. Here, following pigeon Mb purification and primary structure mass spectroscopy characterization, we determined its autoxidation rate and pseudoperoxidase activity with respect to chicken and E. woodcock Mbs. The three Mbs exhibit different autoxidation rates (0.153-h−1 pigeon, 0.194-h−1 chicken and 0.220-h−1 E. woodcock Mbs) and similar specificity constant (9.86x103 M−1s−1 pigeon, 8.81x103 M−1s−1 chicken and 9.90x103 M−1s−1 E. woodcock Mbs), considering their pseudoperoxidase activity. Moreover, for the first time, we detected an increase in pseudoperoxidase activity in presence of Ca2+, particularly at pH 5.8. NMR and CD data indicate that the nonspecific Ca2+ binding induces small local structural rearrangements that in turn slightly reduce pigeon Mb thermal stability. However, considering Ca2+ concentration variations before and post-mortem, this finding must be considered for meat preservation.

On the Molecular Mechanism of a Photo‐Responsive Phase Change Memory

AbstractInducing well‐defined transitions by external stimuli between different states of matter is at the core of responsive functional materials. Using light to interconvert between states with distinct and externally readable features such as optical properties, these photo‐responsive phase change materials (PCMs) are ideal candidates for photonic applications. In this context, correlating macroscopic phenomena with properties at the atomistic level is crucial to systematically tailor the performance of PCMs. In particular, to establish a bottom‐up strategy to engineer PCMs based on molecular building units, a detailed understanding of the dynamic properties is needed. Therefore, an atomistic study is reported capturing the structural evolution during the light‐induced phase transition of a tetra‐(azobenzene)‐methane based PCM. This out‐of‐equilibrium dynamics is accurately represented by an atomistic potential, developed using a population swapping genetic algorithm. The molecular mechanism of the phase transition is deciphered and the refractive index of the periodic matrix is investigated. Due to an interplay of structural rigidity and flexibility, already small structural rearrangements lead to alteration of the optical properties, which is fundamental to ensure high data‐transfer rates. By correlating molecular properties with the resulting functionality, the reported work provides an important step towards in silico engineering of photo‐responsive PCMs.

Protein loops with multiple meta‐stable conformations: A challenge for sampling and scoring methods

Flexible regions in proteins, such as loops, cannot be represented by a single conformation. Instead, conformational ensembles are needed to provide a more global picture. In this context, identifying statistically meaningful conformations within an ensemble generated by loop sampling techniques remains an open problem. The difficulty is primarily related to the lack of structural data about these flexible regions. With the majority of structural data coming from x-ray crystallography and ignoring plasticity, the conception and evaluation of loop scoring methods is challenging. In this work, we compare the performance of various scoring methods on a set of eight protein loops that are known to be flexible. The ability of each method to identify and select all of the known conformations is assessed, and the underlying energy landscapes are produced and projected to visualize the qualitative differences obtained when using the methods. Statistical potentials are found to provide considerable reliability despite their being designed to tradeoff accuracy for lower computational cost. On a large pool of loop models, they are capable of filtering out statistically improbable states while retaining those that resemble known (and thus likely) conformations. However, computationally expensive methods are still required for more precise assessment and structural refinement. The results also highlight the importance of employing several scaffolds for the protein, due to the high influence of small structural rearrangements in the rest of the protein over the modeled energy landscape for the loop.

Structural analysis of a natural apolipoprotein A-I variant (L60R) associated with amyloidosis

The reason that determines the pathological deposition of human apolipoprotein A-I variants inducing organ failure has been under research since the early description of natural mutations in patients. To shed light into the events associated with protein aggregation, we studied the structural perturbations that may occur in the natural variant that shows a substitution of a Leucine by an Arginine in position 60 (L60R). Circular dichroism, intrinsic fluorescence measurements, and proteolysis analysis indicated that L60R was more unstable, more sensitive to cleavage and the N-terminus was more disorganized than the protein with the native sequence (Wt). A higher tendency to aggregate was also detected when L60R was incubated at physiological pH. In addition, the small structural rearrangement observed for the freshly folded variant led to the release of tumor necrosis factor-α and interleukin-1β from a model of macrophages. However, the mutant preserved both its dimeric conformation and its lipid-binding capacity. Our results strongly suggest that the chronic disease may be a consequence of the native conformation loss which elicits the release of protein conformations that could be either cytotoxic or precursors of amyloid conformations.

Dynamics of the PAS and CNBHD Domain Interaction Probed with a Fluorescent Noncanonical Amino Acid (L-ANAP) in hERG Potassium Channels

The voltage-gated potassium channel hERG plays a critical role in cardiac repolarization and is characterized by unusually slow deactivation kinetics. Slow deactivation in hERG channels is regulated by a direct interaction between the N-terminal PAS domain and the C-terminal CNBHD. The PAS-CNBHD interaction is sensitive to point mutations at the domain interface in hERG but less is known about potential dynamic rearrangements of the PAS domain relative to the CNBHD and the rest of the channel. Here, we report that hERG channels showed FRET that is sensitive to voltage and potassium-induced cell depolarization, consistent with a PAS-CNBHD rearrangement. We took advantage of a fluorescent noncanonical amino acid (L-ANAP) and a metal ion bound to a dihistidine motif that can be used to monitor small structural rearrangements within ion channels using patch-clamp fluorometry (PCF) and transition metal FRET (tmFRET). Using amber stop codon suppression technology, we show that amber stop codon-containing mutants in the PAS domain incorporate L-ANAPs as shown by robust currents measured with two-electrode voltage-clamp. Likewise, the addition of dihistidine mutations in the CNBHD also result in functional channels. We performed PCF recordings of excised patches containing L-ANAP-incorporated channels and show that hERG channels are stable in excised patches with robust L-ANAP and Citrine fluorescence that is linearly correlated, suggesting that L-ANAP has been site-specifically incorporated into the channel. We then exposed the internal face of the excised patch to transition metal ions, which bind to the dihistidine motif to quench nearby L-ANAP in a distance- dependent matter. We report a voltage-dependent change in L-ANAP fluorescence in the presence of metal ions, demonstrating a rearrangement of the PAS and CNBHD during slow deactivation of the channel.

High-throughput long paired-end sequencing of a Fosmid library by PacBio

BackgroundLarge insert paired-end sequencing technologies are important tools for assembling genomes, delineating associated breakpoints and detecting structural rearrangements. To facilitate the comprehensive detection of inter- and intra-chromosomal structural rearrangements or variants (SVs) and complex genome assembly with long repeats and segmental duplications, we developed a new method based on single-molecule real-time synthesis sequencing technology for generating long paired-end sequences of large insert DNA libraries.ResultsA Fosmid vector, pHZAUFOS3, was developed with the following new features: (1) two 18-bp non-palindromic I-SceI sites flank the cloning site, and another two sites are present in the skeleton of the vector, allowing long DNA inserts (and the long paired-ends in this paper) to be recovered as single fragments and the vector (~ 8 kb) to be fragmented into 2–3 kb fragments by I-SceI digestion and therefore was effectively removed from the long paired-ends (5–10 kb); (2) the chloramphenicol (Cm) resistance gene and replicon (oriV), necessary for colony growth, are located near the two sides of the cloning site, helping to increase the proportion of the paired-end fragments to single-end fragments in the paired-end libraries. Paired-end libraries were constructed by ligating the size-selected, mechanically sheared pooled Fosmid DNA fragments to the Ampicillin (Amp) resistance gene fragment and screening the colonies with Cm and Amp. We tested this method on yeast and Setaria italica Yugu1. Fosmid-size paired-ends with an average length longer than 2 kb for each end were generated. The N50 scaffold lengths of the de novo assemblies of the yeast and S. italica Yugu1 genomes were significantly improved. Five large and five small structural rearrangements or assembly errors spanning tens of bp to tens of kb were identified in S. italica Yugu1 including deletions, inversions, duplications and translocations.ConclusionsWe developed a new method for long paired-end sequencing of large insert libraries, which can efficiently improve the quality of de novo genome assembly and identify large and small structural rearrangements or assembly errors.

Dynamics of the EAG Domain and Cyclic Nucleotide-Binding Homology Domain Interaction Probed with a Fluorescent Noncanonical Amino Acid (L-ANAP) in hERG Potassium Channels

The voltage-gated potassium channel hERG (KCNH2, Kv11.1) plays a critical role in cardiac repolarization and is characterized by unusually slow deactivation kinetics. Slow deactivation in hERG channels is regulated by a direct interaction between the N-terminal eag domain and the C-terminal CNBHD. The eag-CNBHD interaction is sensitive to point mutations at the domain interface in hERG but less is known about potential dynamic rearrangements of the eag domain relative to the CNBHD and the rest of the channel. Here, we report that hERG channels formed from eag-CFP domains and Δeag-Citrine channels showed FRET (Förster resonance energy transfer) that is sensitive to potassium-induced cell depolarization, consistent with an eag-CNBHD rearrangement. To examine this in more detail, we took advantage of a fluorescent noncanonical amino acid (L-ANAP) and a metal ion bound to a dishistidine motif that can be used to monitor small structural rearrangements within ion channels using patch-clamp fluorometry (PCF) and transition metal FRET. We found that amber stop codon-containing mutants N33X, E50X, and C64X in the eag domain incorporate L-ANAPs as shown by robust currents measured with two-electrode voltage-clamp. Likewise, the addition of dihistidine mutations in the CNBHD (N33X_E788H,L790H, E50X_S855H,H851 and C64X_V796H,I798H) also result in functional channels. The voltage dependence of these channels was comparable to control, indicating incorporation of L-ANAP and introduction of histidines did not measurably alter channel gating. We then performed PCF recordings of excised patches with L-ANAP incorporated hERG channels and found that hERG channels are stable in excised patches and that hERG E50X_S855H channels showed robust L-ANAP and Citrine fluorescence. The above techniques will determine how the eag-CNBHD interaction dynamically regulates conformational changes and ionic current in hERG.

Structural and dynamic characterization of a freestanding acyl carrier protein involved in the biosynthesis of cyclic lipopeptide antibiotics.

Friulimicin is a cyclic lipodecapeptide antibiotic that is produced by Actinoplanes friuliensis. Similar to the related lipopeptide drug daptomycin, the peptide skeleton of friulimicin is synthesized by a large multienzyme nonribosomal peptide synthetase (NRPS) system. The LipD protein plays a major role in the acylation reaction of friulimicin. The attachment of the fatty acid group promotes its antibiotic activity. Phylogenetic analysis reveals that LipD is most closely related to other freestanding acyl carrier proteins (ACPs), for which the genes are located near to NRPS gene clusters. Here, we report that the solution NMR structure of apo-LipD is very similar to other four-helix bundle forming ACPs from fatty acid synthase (FAS), polyketide synthase, and NRPS systems. By recording NMR dynamics data, we found that the backbone motions in holo-LipD are more restricted than in apo-LipD due to the attachment of phosphopantetheine moiety. This enhanced stability of holo-LipD was also observed in differential scanning calorimetry experiments. Furthermore, we demonstrate that, unlike several other ACPs, the folding of LipD does not depend on the presence of divalent cations, although the presence of Mg2+ or Ca2+ can increase the protein stability. We propose that small structural rearrangements in the tertiary structure of holo-LipD which lead to the enhanced stability are important for the cognate enzyme recognition for the acylation reaction. Our results also highlight the different surface charges of LipD and FAS-ACP from A. friuliensis that would allow the acyl-CoA ligase to interact preferentially with the LipD instead of binding to the FAS-ACP.

Karyotype variation in 11 species of the Vernonieae Cass. tribe (Asteraceae Bercht. & J. Presl)

The Vernonieae tribe presents strong taxonomic delimitation problems as it is considered one of the most complex groups of the Asteraceae family, comprising approximately 1100 species distributed across 129 genera. In this study, a comparative analysis of the Vernonieae species was performed to understand the events involved in the chromosome evolution of these species and to further deduce their taxonomy. The representatives were cytogenetically characterized via analyses of morphology, karyotype asymmetry and differential staining with fluorochromes CMA and DAPI as well as FISH. According to morphometric data, all species showed symmetrical karyotypes with prevailing metacentric chromosomes, even in species belonging to different genera. Variability in diploid chromosome number was detected (2n = 18 to 2n = 60), and chromosome sizes were observed to be between 1.00 and 4.09 μm. Additionally, variation in the pattern of heterochromatin was observed mainly in relation to CMA+ bands, in which the number varied from 4 to 16 heterochromatic regions. Only one species, Vernonia scorpioides, presented positive DAPI bands, which were located in the terminal position in most of the chromosomes. The differences in the sizes and quantities of heterochromatic bands may be related to small structural rearrangements during karyotype evolution of the Vernonieae tribe.

Crystal structures of two monomeric triosephosphate isomerase variants identified via a directed-evolution protocol selecting for L-arabinose isomerase activity.

The crystal structures are described of two variants of A-TIM: Ma18 (2.7 Å resolution) and Ma21 (1.55 Å resolution). A-TIM is a monomeric loop-deletion variant of triosephosphate isomerase (TIM) which has lost the TIM catalytic properties. Ma18 and Ma21 were identified after extensive directed-evolution selection experiments using an Escherichia coli L-arabinose isomerase knockout strain expressing a randomly mutated A-TIM gene. These variants facilitate better growth of the Escherichia coli selection strain in medium supplemented with 40 mM L-arabinose. Ma18 and Ma21 differ from A-TIM by four and one point mutations, respectively. Ma18 and Ma21 are more stable proteins than A-TIM, as judged from CD melting experiments. Like A-TIM, both proteins are monomeric in solution. In the Ma18 crystal structure loop 6 is open and in the Ma21 crystal structure loop 6 is closed, being stabilized by a bound glycolate molecule. The crystal structures show only small differences in the active site compared with A-TIM. In the case of Ma21 it is observed that the point mutation (Q65L) contributes to small structural rearrangements near Asn11 of loop 1, which correlate with different ligand-binding properties such as a loss of citrate binding in the active site. The Ma21 structure also shows that its Leu65 side chain is involved in van der Waals interactions with neighbouring hydrophobic side-chain moieties, correlating with its increased stability. The experimental data suggest that the increased stability and solubility properties of Ma21 and Ma18 compared with A-TIM cause better growth of the selection strain when coexpressing Ma21 and Ma18 instead of A-TIM.

Acceleration of protein folding by four orders of magnitude through a single amino acid substitution.

Cis prolyl peptide bonds are conserved structural elements in numerous protein families, although their formation is energetically unfavorable, intrinsically slow and often rate-limiting for folding. Here we investigate the reasons underlying the conservation of the cis proline that is diagnostic for the fold of thioredoxin-like thiol-disulfide oxidoreductases. We show that replacement of the conserved cis proline in thioredoxin by alanine can accelerate spontaneous folding to the native, thermodynamically most stable state by more than four orders of magnitude. However, the resulting trans alanine bond leads to small structural rearrangements around the active site that impair the function of thioredoxin as catalyst of electron transfer reactions by more than 100-fold. Our data provide evidence for the absence of a strong evolutionary pressure to achieve intrinsically fast folding rates, which is most likely a consequence of proline isomerases and molecular chaperones that guarantee high in vivo folding rates and yields.

Deep sequencing with intronic capture enables identification of an APC exon 10 inversion in a patient with polyposis

Single-exon inversions have rarely been described in clinical syndromes and are challenging to detect using Sanger sequencing. We report the case of a 40-year-old woman with adenomatous colon polyps too numerous to count and who had a complex inversion spanning the entire exon 10 in APC (the gene encoding for adenomatous polyposis coli), causing exon skipping and resulting in a frameshift and premature protein truncation. In this study, we employed complete APC gene sequencing using high-coverage next-generation sequencing by ColoSeq, analysis with BreakDancer and SLOPE software, and confirmatory transcript analysis. ColoSeq identified a complex small genomic rearrangement consisting of an inversion that results in translational skipping of exon 10 in the APC gene. This mutation would not have been detected by traditional sequencing or gene-dosage methods. We report a case of adenomatous polyposis resulting from a complex single-exon inversion. Our report highlights the benefits of large-scale sequencing methods that capture intronic sequences with high enough depth of coverage-as well as the use of informatics tools-to enable detection of small pathogenic structural rearrangements.

Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase

Nitric oxide reductases (NORs) are membrane proteins that catalyze the reduction of nitric oxide (NO) to nitrous oxide (N2O), which is a critical step of the nitrate respiration process in denitrifying bacteria. Using the recently determined first crystal structure of the cytochrome c-dependent NOR (cNOR) [Hino T, Matsumoto Y, Nagano S, Sugimoto H, Fukumori Y, et al. (2010) Structural basis of biological N2O generation by bacterial nitric oxide reductase. Science 330: 1666–70.], we performed extensive all-atom molecular dynamics (MD) simulations of cNOR within an explicit membrane/solvent environment to fully characterize water distribution and dynamics as well as hydrogen-bonded networks inside the protein, yielding the atomic details of functionally important proton channels. Simulations reveal two possible proton transfer pathways leading from the periplasm to the active site, while no pathways from the cytoplasmic side were found, consistently with the experimental observations that cNOR is not a proton pump. One of the pathways, which was newly identified in the MD simulation, is blocked in the crystal structure and requires small structural rearrangements to allow for water channel formation. That pathway is equivalent to the functional periplasmic cavity postulated in cbb 3 oxidase, which illustrates that the two enzymes share some elements of the proton transfer mechanisms and confirms a close evolutionary relation between NORs and C-type oxidases. Several mechanisms of the critical proton transfer steps near the catalytic center are proposed.

The Overall Architecture and Receptor Binding of Pneumococcal Carbohydrate-Antigen-Hydrolyzing Enzymes

The TIGR4 and SP3-BS71 strains of Streptococcus pneumoniae each produce family 98 glycoside hydrolases, called Sp4GH98 and Sp3GH98, respectively, which have different modular architectures and substrate specificities. Sp4GH98 degrades the Lewis Y antigen and possesses three C-terminal family 47 carbohydrate-binding modules (CBMs) that bind to this substrate. Sp3GH98 degrades the blood group A/B antigens and has two N-terminal family 51 CBMs that are of unknown function. Here, we examine the complex carbohydrate-binding specificity of the family 51 CBMs from Sp3GH98 (referred to as CBM51-1 and CBM51-2), the structural basis of this interaction, and the overall solution conformations of both Sp3GH98 and Sp4GH98, which are shown to be fully secreted proteins. Through glycan microarray binding analysis and isothermal titration calorimetry, CBM51-1 is found to bind specifically to the blood group A/B antigens. However, due to a series of relatively small structural rearrangements that were revealed in structures determined by X-ray crystallography, CBM51-2 appears to be incapable of binding carbohydrates. Analysis of small-angle X-ray scattering data in combination with the available high-resolution X-ray crystal structures of the Sp3GH98 and Sp4GH98 catalytic modules and their CBMs yielded models of the biological solution structures of the full-length enzymes. These studies reveal the complex architectures of the two enzymes and suggest that carbohydrate recognition by the CBMs and the activity of the catalytic modules are not directly coupled.

Protein structure reports in JIMD ‐ an important enhancement of journal scope

Protein structure reports in JIMD ‐ an important enhancement of journal scope

Folding Study of Venus Reveals a Strong Ion Dependence of Its Yellow Fluorescence under Mildly Acidic Conditions

Venus is a yellow fluorescent protein that has been developed for its fast chromophore maturation rate and bright yellow fluorescence that is relatively insensitive to changes in pH and ion concentrations. Here, we present a detailed study of the stability and folding of Venus in the pH range from 6.0 to 8.0 using chemical denaturants and a variety of spectroscopic probes. By following hydrogen-deuterium exchange of (15)N-labeled Venus using NMR spectroscopy over 13 months, residue-specific free energies of unfolding of some highly protected amide groups have been determined. Exchange rates of less than one per year are observed for some amide groups. A super-stable core is identified for Venus and compared with that previously reported for green fluorescent protein. These results are discussed in terms of the stability and folding of fluorescent proteins. Under mildly acidic conditions, we show that Venus undergoes a drastic decrease in yellow fluorescence at relatively low concentrations of guanidinium chloride. A detailed study of this effect establishes that it is due to pH-dependent, nonspecific interactions of ions with the protein. In contrast to previous studies on enhanced green fluorescence protein variant S65T/T203Y, which showed a specific halide ion-binding site, NMR chemical shift mapping shows no evidence for specific ion binding. Instead, chemical shift perturbations are observed for many residues primarily located in both lids of the beta-barrel structure, which suggests that small scale structural rearrangements occur on increasing ionic strength under mildly acidic conditions and that these are propagated to the chromophore resulting in fluorescence quenching.

Structure of the Conserved HAMP Domain in an Intact, Membrane-Bound Chemoreceptor: A Disulfide Mapping Study

The HAMP domain is a conserved motif widely distributed in prokaryotic and lower eukaryotic organisms, where it is often found in transmembrane receptors that regulate two-component signaling pathways. The motif links receptor input and output modules and is essential to receptor structure and signal transduction. Recently, a structure was determined for a HAMP domain isolated from an unusual archeal membrane protein of unknown function [Hulko, M., et al. (2006) Cell 126, 929-940]. This study uses cysteine and disulfide chemistry to test this archeal HAMP model in the full-length, membrane-bound aspartate receptor of bacterial chemotaxis. The chemical reactivities of engineered Cys residues scanned throughout the aspartate receptor HAMP region are highly correlated with the degrees of solvent exposure of corresponding positions in the archeal HAMP structure. Both domains are homodimeric, and the individual subunits of both domains share the same helix-connector-helix organization with the same helical packing faces. Moreover, disulfide mapping reveals that the four helices of the aspartate receptor HAMP domain are arranged in the same parallel, four-helix bundle architecture observed in the archeal HAMP structure. One detectable difference is the packing of the extended connector between helices, which is not conserved. Finally, activity studies of the aspartate receptor indicate that contacts between HAMP helices 1 and 2' at the subunit interface play a critical role in modulating receptor on-off switching. Disulfide bonds linking this interface trap the receptor in its kinase-activating on-state, or its kinase inactivating off-state, depending on their location. Overall, the evidence suggests that the archeal HAMP structure accurately depicts the architecture of the conserved HAMP motif in transmembrane chemoreceptors. Both the on- and off-states of the aspartate receptor HAMP domain closely resemble the archeal HAMP structure, and only a small structural rearrangement occurs upon on-off switching. A model incorporating HAMP into the full receptor structure is proposed.