Biomedical subjects

Ralf Langen

Publications and source records attributed to Ralf Langen.

At least 19 recordsLinked to original sources

PubMed2006

Side chain-dependent stacking modulates tau filament structure.

The misfolding of proteins into highly ordered fibrils with similar physical properties is a hallmark of many degenerative diseases. Here, we use the microtubule associated protein tau as a model system to investigate the role of amino acid side chains in the formation of such fibrils. We identify a region (positions 272-289) in the tau protein that, in the fibrillar state, either forms part of a core of parallel, in-register, beta-strands, or remains unfolded. Single point mutations are sufficient to control this conformational switch with disease mutants G272V and DeltaK280 (found in familial forms of dementia) inducing a folded state. Through systematic mutagenesis we derive a propensity scale for individual amino acids to form fibrils with parallel, in-register, beta-strands. This scale should not only apply to tau fibrils but generally to all fibrils with same strand arrangement.

Amino Acid Sequence↗

PubMed2006

Inhibition of human IAPP fibril formation does not prevent beta-cell death: evidence for distinct actions of oligomers and fibrils of human IAPP.

Type 2 diabetes mellitus (T2DM) is characterized by an approximately 60% deficit in beta-cell mass, increased beta-cell apoptosis, and islet amyloid derived from islet amyloid polypeptide (IAPP). Human IAPP (hIAPP) forms oligomers, leading to either amyloid fibrils or toxic oligomers in an aqueous solution in vitro. Either application of hIAPP on or overexpression of hIAPP in cells induces apoptosis. It remains controversial whether the fibrils or smaller toxic oligomers induce beta-cell apoptosis. Rifampicin prevents hIAPP amyloid fibril formation and has been proposed as a potential target for prevention of T2DM. We examined the actions of rifampicin on hIAPP amyloid fibril and toxic oligomer formation as well as its ability to protect beta-cells from either application of hIAPP or endogenous overexpression of hIAPP (transgenic rats and adenovirus-transduced beta-cells). We report that rifampicin (Acocella G. Clin Pharmacokinet 3: 108-127, 1978) prevents hIAPP fibril formation, but not formation of toxic hIAPP oligomers (Bates G. Lancet 361: 1642-1644, 2003), and does not protect beta-cells from apoptosis induced by either overexpression or application of hIAPP. These data emphasize that toxic hIAPP oligomers, rather than hIAPP fibrils, initiate beta-cell apoptosis and that screening tools to identify inhibitors of amyloid fibril formation are likely to be less useful than those that identify inhibitors of toxic oligomer formation. Finally, rifampicin and related molecules do not appear to be useful as candidates for prevention of T2DM.

Adenoviridae↗

PubMed2006

Mechanism of endophilin N-BAR domain-mediated membrane curvature.

Endophilin-A1 is a BAR domain-containing protein enriched at synapses and is implicated in synaptic vesicle endocytosis. It binds to dynamin and synaptojanin via a C-terminal SH3 domain. We examine the mechanism by which the BAR domain and an N-terminal amphipathic helix, which folds upon membrane binding, work as a functional unit (the N-BAR domain) to promote dimerisation and membrane curvature generation. By electron paramagnetic resonance spectroscopy, we show that this amphipathic helix is peripherally bound in the plane of the membrane, with the midpoint of insertion aligned with the phosphate level of headgroups. This places the helix in an optimal position to effect membrane curvature generation. We solved the crystal structure of rat endophilin-A1 BAR domain and examined a distinctive insert protruding from the membrane interaction face. This insert is predicted to form an additional amphipathic helix and is important for curvature generation. Its presence defines an endophilin/nadrin subclass of BAR domains. We propose that N-BAR domains function as low-affinity dimers regulating binding partner recruitment to areas of high membrane curvature.

Acyltransferases↗

PubMed2006

A novel calcium-independent peripheral membrane-bound form of annexin B12.

Annexins are soluble proteins that can interact with membranes in a Ca2+-dependent manner. Recent studies have shown that they can also undergo Ca2+-independent membrane interactions that are modulated by pH and phospholipid composition. Here, we investigated the structural changes that occurred during Ca2+-independent interaction of annexin B12 with phospholipid vesicles as a function of pH. Electron paramagnetic resonance analysis of a helical hairpin encompassing the D and E helices in the second repeat of the protein showed that this region refolded and formed a continuous amphipathic alpha helix following Ca2+-independent binding to membranes at mildly acidic pH. At pH 4.0, this helix assumed a transmembrane topography, but at pH approximately 5.0-5.5, it was peripheral and approximately parallel to the membrane. The peripheral form was reversibly converted into the transmembrane form by lowering the pH and vice versa. Furthermore, analysis of vesicles incubated with annexin B12 using freeze-fracture electron microscopy methods showed classical intramembrane particles at pH 4.0 but none at pH 5.3. Together, these data raise the possibility that the peripheral-bound form of annexin B12 could act as a kinetic intermediate in the formation of the transmembrane form of the protein.

Annexins↗

PubMed2006

Spin labeling analysis of amyloids and other protein aggregates.

Because of the enormous size of amyloid fibrils and their low tendency to form crystal lattices, it has been difficult to obtain high-resolution structural information on these aggregates. Magnetic resonance methods, such as solid-state nuclear magnetic resonance spectroscopy and electron paramagnetic resonance (EPR) spectroscopy, are promising new technologies by which to obtain molecular models. This chapter will focus on the application of EPR spectroscopy to amyloids and other protein aggregates. Site-directed spin labeling (SDSL), in combination with EPR spectroscopy, has been successfully used to study protein structure and the dynamics of soluble as well as membrane proteins. Recent studies indicate that this strategy is also well suited for studying amyloid fibrils. For example, an important outcome of the SDSL studies performed in our laboratory is that fibrils of amyloid beta, islet amyloid polypeptide, alpha-synuclein, and tau have their beta-strands aligned in an in-register, parallel fashion. Future studies promise to yield molecular information about fibril topography and protofilament arrangement and can be extended to include oligomeric structures.

Amyloid↗

PubMed2006

Drusen deposits associated with aging and age-related macular degeneration contain nonfibrillar amyloid oligomers.

Protein misfolding and aggregation are thought to underlie the pathogenesis of many amyloid diseases, such as Alzheimer and Parkinson diseases, whereby a stepwise protein misfolding process begins with the conversion of soluble protein monomers to prefibrillar oligomers and progresses to the formation of insoluble amyloid fibrils. Drusen are extracellular deposits found in aging eyes and in eyes afflicted with age-related macular degeneration (AMD). Recent characterizations of drusen have revealed protein components that are shared with amyloid deposits. However, characteristic amyloid fibrils have thus far not been identified in drusen. In this study, we tested the hypothesis that nonfibrillar oligomers may be a common link in amyloid diseases. Oligomers consisting of distinct amyloidogenic proteins and peptides can be detected by a recently developed antibody that is thought to recognize a common structure. Notably, oligomers exhibit cellular toxicity, which suggests that they play a role in the pathogenesis of neurodegenerative diseases. Through use of the anti-oligomer antibody, we came to observe the presence of nonfibrillar, toxic oligomers in drusen. Conversely, no reactivity was observed in age-matched control eyes without drusen. These results suggest that amyloid oligomers may be involved in drusen biogenesis and that similar protein misfolding processes may occur in AMD and amyloid diseases.

Adult↗

PubMed2005

Calcium- and membrane-induced changes in the structure and dynamics of three helical hairpins in annexin B12.

Annexins are a family of soluble proteins that can undergo reversible Ca(2+)-dependent interaction with the interfacial region of phospholipid membranes. The helical hairpins on the convex face of the crystal structure of soluble annexins are proposed to mediate binding to membranes, but the mechanism is not defined. For this study, we used a site-directed spin labeling (SDSL) experimental approach to investigate Ca(2+) and membrane-induced structural and dynamic changes that occurred in the helical hairpins encompassing three of the four D and E helices of annexin B12. Electron paramagnetic resonance (EPR) parameters were analyzed for the soluble and Ca(2+)-dependent membrane-bound states of the following nitroxide scans of annexin B12: a continuous 24-residue scan of the D and E helices in the third repeat (residues 219-242) and short scans encompassing the D-E loop regions of the first repeat (residues 68-74) and the fourth repeat (300-305). EPR mobility and accessibility parameters of most sites were similar when the protein was in solution or in the membrane-bound state, and both sets of data were consistent with the crystal structure of the protein. However, membrane-induced changes in mobility and accessibility were observed in all three loop regions, with the most dramatic changes noted at sites corresponding to the highly conserved serine and glycine residues in the loops. EPR accessibility parameters clearly established that nitroxide side chains placed at these sites made direct contact with the bilayer. EPR mobility parameters showed that these sites were very mobile in solution, but immobilized on the EPR time scale in the membrane-bound state. Since the headgroup regions of bilayer phospholipids are relatively mobile in the absence of annexins, Ca(2+)-dependent binding of annexin B12 appears to form a complex in which the mobility of the D-E loop region of the protein and the headgroup region of the phospholipid are highly constrained. Possible biological consequences of annexin-induced restriction of membrane mobility are discussed.

Amino Acid Sequence↗

PubMed2005

Light causes phosphorylation of nonactivated visual pigments in intact mouse rod photoreceptor cells.

Phosphorylation of G-protein-coupled receptors (GPCRs) is a required step in signal deactivation. Rhodopsin, a prototypical GPCR, exhibits high gain phosphorylation in vitro whereby a hundred-fold molar excess of phosphates are incorporated into the rhodopsin pool per molecule of activated rhodopsin. The extent by which high gain phosphorylation occurs in the intact mammalian photoreceptor cell, and the molecular mechanism underlying this reaction in vivo, is not known. Trans-phosphorylation is a mechanism proposed for high gain phosphorylation, whereby rhodopsin kinase, upon phosphorylating the activated receptor, continues to phosphorylate nearby nonactivated rhodopsin. We used two different transgenic mouse models to test whether trans-phosphorylation occurs in the intact photoreceptor cell. The first transgenic model expressed a murine cone pigment, S-opsin, together with the endogenous rhodopsin in the rod cell. We showed that selective stimulation of rhodopsin also led to phosphorylation of S-opsin. The second mouse model expressed the constitutively active human opsin mutant K296E. K296E, in the arrestin-/- background, also led to phosphorylation of endogenous mouse rhodopsin in the dark-adapted retina. Both mouse models provide strong support of trans-phosphorylation as an underlying mechanism of high gain phosphorylation, and provide evidence that a substantial fraction of nonactivated visual pigments becomes phosphorylated through this mechanism. Because activated, phosphorylated receptors exhibit decreased catalytic activity, our results suggest that dephosphorylation would be an important step in the full recovery of visual sensitivity during dark adaptation. These results may also have implications for other GPCR signaling pathways.

Animals↗

PubMed2005

Lipid membranes modulate the structure of islet amyloid polypeptide.

The 37-residue islet amyloid polypeptide (IAPP) is thought to play an important role in the pathogenesis of type II diabetes. Despite a growing body of evidence implicating membrane interaction in IAPP toxicity, the membrane-bound form has not yet been well characterized. Here we used circular dichroism (CD) and fluorescence spectroscopy to investigate the molecular details of the interaction of IAPP with lipid membranes of varying composition. In the presence of membranes containing negatively charged phosphatidylserine (PS), we observed significant acceleration in the formation of IAPP aggregates. This acceleration is strongly modulated by the PS concentration and ionic strength, and is also observed at physiologically relevant PS concentrations. CD spectra of IAPP obtained immediately after the addition of membranes containing PS revealed features characteristic of an alpha-helical conformation approximately approximately 15-19 residues in length. After a longer incubation with membranes, IAPP gave rise to CD spectra characteristic of a beta-sheet conformation. Taken together, our CD and fluorescence data indicate that conditions that promote weakly stable alpha-helical conformations may promote IAPP aggregation. The potential roles of IAPP-membrane interaction and the novel membrane-bound alpha-helical conformation in IAPP aggregation are discussed.

Amino Acid Sequence↗

PubMed2005

A helical hairpin region of soluble annexin B12 refolds and forms a continuous transmembrane helix at mildly acidic pH.

Annexins are soluble proteins that are best known for their ability to undergo reversible Ca(2+)-dependent binding to the surface of phospholipid bilayers. Recent studies, however, have shown that annexins also reversibly bind to membranes in a Ca(2+)-independent manner at mildly acidic pH. We investigated the structural changes that occur upon pH-dependent membrane binding by performing a nitroxide scan on the helical hairpin encompassing helices A and B in the fourth repeat of annexin B12. Residues 251-273 of annexin B12 were replaced, one at a time, with cysteine and then labeled with a nitroxide spin label. Electron paramagnetic resonance (EPR) mobility and accessibility analyses of soluble annexin B12 derivatives were in excellent agreement with the known crystal structure of annexin B12. However, EPR studies of annexin B12 derivatives bound to membranes at pH 4.0 indicated major structural changes in the scanned region. The helix-loop-helix structure present in the soluble protein was converted into a continuous transmembrane alpha-helix that was exposed to the hydrophobic core of the bilayer on one side and exposed to an aqueous pore on the other side. Asp-264 was on the hydrophobic membrane-exposed face of the amphipathic transmembrane helix, thereby suggesting that protonation of its carboxylate group stabilized the transmembrane form. Inspection of the amino acid sequence of annexin B12 revealed several other helical hairpin regions that might refold and form continuous amphipathic transmembrane helices in response to protonation of Asp or Glu switch residues on or near the hydrophobic face of the helix.

Annexins↗

PubMed2005

Evidence for a triplex DNA conformation at the bcl-2 major breakpoint region of the t(14;18) translocation.

The most common chromosomal translocation in cancer, t(14;18), occurs at the bcl-2 major breakpoint region (Mbr) in follicular lymphomas. The 150-bp bcl-2 Mbr, which contains three breakage hotspots (peaks), has a single-stranded character and, hence, a non-B DNA conformation both in vivo and in vitro. Here, we use gel assays and electron microscopy to show that a triplex-specific antibody binds to the bcl-2 Mbr in vitro. Bisulfite reactivity shows that the non-B DNA structure is favored by, but not dependent upon, supercoiling and suggests a possible triplex conformation at one portion of the Mbr (peak I). We have used circular dichroism to test whether the predicted third strand of that suggested structure can indeed form a triplex with the duplex at peak I, and it does so with 1:1 stoichiometry. Using an intracellular minichromosomal assay, we show that the non-B DNA structure formation is critical for the breakage at the bcl-2 Mbr, because a 3-bp mutation that disrupts the putative peak I triplex also markedly reduces the recombination of the Mbr. A three-dimensional model of such a triplex is consistent with bond length, bond angle, and energetic restrictions (stacking and hydrogen bonding). We infer that an imperfect purine/purine/pyrimidine (R.R.Y) triplex likely forms at the bcl-2 Mbr in vitro, and in vivo recombination data favor this as the major DNA conformation in vivo as well.

Antibodies, Monoclonal↗

PubMed2005

The conserved core domains of annexins A1, A2, A5, and B12 can be divided into two groups with different Ca2+-dependent membrane-binding properties.

The hallmark of the annexin super family of proteins is Ca(2+)-dependent binding to phospholipid bilayers, a property that resides in the conserved core domain of these proteins. Despite the structural similarity between the core domains, studies reported herein showed that annexins A1, A2, A5, and B12 could be divided into two groups with distinctively different Ca(2+)-dependent membrane-binding properties. The division correlates with the ability of the annexins to form Ca(2+)-dependent membrane-bound trimers. Site-directed spin-labeling and Forster resonance energy transfer experimental approaches confirmed the well-known ability of annexins A5 and B12 to form trimers, but neither method detected self-association of annexin A1 or A2 on bilayers. Studies of chimeras in which the N-terminal and core domains of annexins A2 and A5 were swapped showed that trimer formation was mediated by the core domain. The trimer-forming annexin A5 and B12 group had the following Ca(2+)-dependent membrane-binding properties: (1) high Ca(2+) stoichiometry for membrane binding ( approximately 12 mol of Ca(2+)/mol of protein); (2) binding to membranes was very exothermic (> -60 kcal/ mol of protein); and (3) binding to bilayers that were in the liquid-crystal phase but not to bilayers in the gel phase. In contrast, the nontrimer-forming annexin A1 and A2 group had the following Ca(2+)-dependent membrane-binding properties: (1) lower Ca(2+) stoichiometry for membrane binding (<or=4 mol of Ca(2+)/mol of protein); (2) binding to membranes was relatively less exothermic (< -33 kcal/ mol of protein); and (3) binding to bilayers that were in either the liquid-crystal phase or gel phase. The biological implications of this subdivision are discussed.

Amino Acid Sequence↗

PubMed2004

Alpha-synuclein structures from fluorescence energy-transfer kinetics: implications for the role of the protein in Parkinson's disease.

Parkinson's disease is associated with the deposition and accumulation of alpha-synuclein fibrils in the brain. A30P and A53T mutations have been linked to the early-onset familial disease state. Time-resolved tryptophan fluorescence energy-transfer measurements have been used to probe the structures of pseudo-wild-type and mutant (A30P) alpha-synucleins at physiological pH (7.4), in acidic pH (4.4) solutions, and in the presence of SDS micelles, a membrane mimic. Fluorescent donor-energy acceptor (DA) distance distributions for six different tryptophan/3-nitro-tyrosine pairs reveal the presence of compact, intermediate, and extended conformations of the protein. CD spectra indicate that the protein develops substantial helical structure in the presence of SDS micelles. DA distributions show that micelles induce compaction in the N-terminal region and expansion of the acidic C terminus. In acidic solutions, there is an increased population of collapsed structures in the C-terminal region. Energy-transfer measurements demonstrate that the average DA distances for the W4-Y19 and Y19-W39 pairs are longer in one of the two disease-related mutants (A30P).

Amino Acid Sequence↗

PubMed2004

Identifying structural features of fibrillar islet amyloid polypeptide using site-directed spin labeling.

Pancreatic amyloid deposits, composed primarily of the 37-residue islet amyloid polypeptide (IAPP), are a characteristic feature found in more than 90% of patients with type II diabetes. Although IAPP amyloid deposits are associated with areas of pancreatic islet beta-cell dysfunction and depletion and are thought to play a role in disease, their structure is unknown. We used electron paramagnetic resonance spectroscopy to analyze eight spin-labeled derivatives of IAPP in an effort to determine structural features of the peptide. In solution, all eight derivatives gave rise to electron paramagnetic resonance spectra with sharp lines indicative of rapid motion on the sub-nanosecond time scale. These spectra are consistent with a rapidly tumbling and highly dynamic peptide. In contrast, spectra for the fibrillar form exhibit reduced mobility and the presence of strong intermolecular spin-spin interactions. The latter implies that the peptide subunits are ordered and that the same residues from neighboring peptides are in close proximity to one another. Our data are consistent with a parallel arrangement of IAPP peptides within the amyloid fibril. Analysis of spin label mobility indicates a high degree of order throughout the peptide, although the N-terminal region is slightly less ordered. Possible similarities with respect to the domain organization and parallelism of Alzheimer's amyloid beta peptide fibrils are discussed.

Amino Acid Sequence↗

PubMed2004

Stability and strand asymmetry in the non-B DNA structure at the bcl-2 major breakpoint region.

The t(14;18) translocation involving the Ig heavy chain locus and the BCL-2 gene is the single most common chromosomal translocation in human cancer. Recently we reported in vitro and in vivo chemical probing data indicating that the 150-bp major breakpoint region (Mbr), which contains three breakage subregions (hotspots) (known as peaks I, II, and III), has single-stranded character and hence a non-B DNA conformation. Although we could document the non-B DNA structure formation at the bcl-2 Mbr, the structural studies were limited to chemical probing. Therefore, in the present study, we used multiple methods including circular dichroism to detect the non-B DNA at the bcl-2 Mbr. We established a new gel shift method to detect the altered structure at neutral pH on shorter DNA fragments containing the bcl-2 Mbr and analyzed the fine structural features. We found that the single-stranded region in the non-B DNA structure observed is stable for days and is asymmetric with respect to the Watson and Crick strands. It could be detected by oligomer probing, a bisulfite modification assay, or a P1 nuclease assay. We provide evidence that two different non-B conformations exist at peak I in addition to the single one observed at peak III. Finally we used mutagenesis and base analogue incorporation to show that the non-B DNA structure formation requires Hoogsteen pairing. These findings place major constraints on the location and nature of the non-B conformations assumed at peaks I and III of the bcl-2 Mbr.

Base Sequence↗

PubMed2004

Template-assisted filament growth by parallel stacking of tau.

Tau filaments are found in >20 neurodegenerative diseases. Yet, because of their enormous molecular weights and poor tendency to form highly ordered 3D crystal lattices, they have evaded high-resolution structure determination. Here, we studied 25 derivatized tau mutants by using electron paramagnetic resonance and fluorescence spectroscopy to report structural details of tau filaments. Based on strong spin exchange and pyrene excimer formation of core residues, we find that individual tau proteins form single molecule layers along the fiber axis that perfectly stack on top of each other by in-register, parallel alignment of beta-strands. We suggest a model of filament growth wherein the existing filament serves as a template for the incoming, unfolded tau molecule, resulting in a new structured layer with maximized hydrogen-bonded contact surface and side-chain stacking.

Amino Acid Sequence↗

PubMed2004

Structure of membrane-bound alpha-synuclein studied by site-directed spin labeling.

Many of the proposed physiological functions of alpha-synuclein, a protein involved in the pathogenesis of Parkinson's disease, are related to its ability to interact with phospholipids. To better understand the conformational changes that occur upon membrane binding of monomeric alpha-synuclein, we performed EPR analysis of 47 singly labeled alpha-synuclein derivatives. We show that membrane interaction is mediated by major conformational changes within seven N-terminal 11-aa repeats, which reorganize from a highly dynamic structure into an elongated helical structure devoid of significant tertiary packing. Furthermore, we find that analogous positions from different repeats are in equivalent locations with respect to membrane proximity. These and other findings suggest a curved membrane-dependent alpha-helical structure, wherein each 11-aa repeat takes up three helical turns. Similar helical structures could also apply to apolipoproteins and other lipid-interacting proteins with related 11-aa repeats.

Amino Acid Sequence↗

PubMed2004

Structure and dynamics of a helical hairpin that mediates calcium-dependent membrane binding of annexin B12.

A wealth of high-resolution structural data has accumulated for soluble annexins, but only limited information is available for the biologically important membrane-bound proteins. To investigate the structural and dynamic changes that occur upon membrane binding, we analyzed the electron paramagnetic resonance (EPR) mobility and accessibility parameters of a continuous 30-residue nitroxide scan encompassing helices D and E in repeat 2 of annexin B12 (residues 134-163) while the protein was bound to phospholipid vesicles in the presence of Ca(2+). A comparison of these data to those from a previously published study of the protein in solution (Isas, J. M., Langen, R., Haigler, H. T., and Hubbell, W. L. (2002) Biochemistry 41, 1464-1473) showed that the overall backbone fold for the scanned region did not change upon membrane binding. However, side-chains in the loop between the D and E helices were highly dynamic in solution but became essentially frozen in the EPR time scale upon binding to membranes. Accessibility measurements clearly established that side-chains in this loop were exposed to the hydrophobic core of the bilayer and provide the first evidence that a D-E loop directly participates in the Ca(2+)-dependent binding of annexins to membranes. Other localized changes showed that the D-helix became much less dynamic after membrane binding and identified quaternary contact sites in the membrane-bound homo-trimer. Finally, immobilization of the D-E loop upon contact with phospholipid suggests that the bilayer, which is normally very mobile on the EPR time scale, is immobilized in the head-group region by the annexin B12. This suggests that annexin B12 alters membrane structure in a manner that may be biologically significant.

Annexins↗