Intrinsic motions in the N-terminal domain of an ionotropic glutamate receptor detected by fluorescence correlation spectroscopy

Ionotropic glutamate receptors (iGluRs) mediate excitatory neurotransmission in the central nervous system and play key roles in brain development and disease. iGluRs have two distinct extracellular domains, but the functional role of the distal N-terminal domain (NTD) is poorly understood. Crystal structures of the NTD from some non-N-methyl-d-aspartate (NMDA) iGluRs are consistent with a rigid body that facilitates receptor assembly but suggest an additional dynamic role that could modulate signaling. Here, we moved beyond spatial and temporal limitations of conventional protein single-molecule spectroscopy by employing correlation analysis of extrinsic oxazine fluorescence fluctuations. We observed nanosecond (ns)-to-microsecond (μs) motions of loop segments and helices within a region of an AMPA-type iGluR NTD, which has been identified previously to be structurally variable. Our data reveal that the AMPA receptor NTD undergoes rapid conformational fluctuations, suggesting an inherent allosteric capacity for this domain in addition to its established assembly function.     

Exploring protein domain structure

The protein databank contains coordinates of over 10,000 protein structures, which constitute more than 25,000 structural domains in total. The investigation of protein structural, functional and evolutionary relationships is fundamental to many important fields in bioinformatics research, and will be crucial in determining the function of the human and other genomes.This review describes the SCOP and CATH databases of protein structure classification, which define, classify and annotate each domain in the protein databank. The hierarchical structure, use and annotation of the databases are explained. Other tools for exploring protein structure relationships are also described.     

Exploring the interaction of the surfactant N-terminal domain of gamma-Zein with soybean phosphatidylcholine liposomes

Zeins are maize storage proteins that accumulate inside large vesicles called protein bodies. gamma-Zein lines the inner surface of the protein body membrane, and its N-terminal, proline-rich, repetitive domain with the sequence (VHLPPP)(8) appears to be necessary for the accumulation of the protein within the organelle. Synthetic (VHLPPP)(8) adopts an amphipathic polyproline II conformation and forms cylindrical micelles in aqueous solution. Here we explore the interaction of (VHLPPP)(8) with soybean phosphatidylcholine unilamellar lipid vesicles and examine its effect on the stability and permeability of the liposome membrane. The amphipathic N-terminal domain of gamma-zein interacts with the membrane and assembles to form extended domains over the phospholipid membrane. The interaction between the peptide and the membrane increases the stability and permeability of the liposome membrane. The spontaneous amphipathic aggregation of (VHLPPP)(8) on the membrane suggests a mechanism of gamma-zein deposition inside maize protein bodies.     

Solution structure of the COMMD1 N-terminal domain

COMMD1 is the prototype of a new protein family that plays a role in several important cellular processes, including NF-kappaB signaling, sodium transport, and copper metabolism. The COMMD proteins interact with one another via a conserved C-terminal domain, whereas distinct functions are predicted to result from a variable N-terminal domain. The COMMD proteins have not been characterized biochemically or structurally. Here, we present the solution structure of the N-terminal domain of COMMD1 (N-COMMD1, residues 1-108). This domain adopts an alpha-helical structure that bears little resemblance to any other helical protein. The compact nature of N-COMMD1 suggests that full-length COMMD proteins are modular, consistent with specific functional properties for each domain. Interactions between N-COMMD1 and partner proteins may occur via complementary electrostatic surfaces. These data provide a new foundation for biochemical characterization of COMMD proteins and for probing COMMD1 protein-protein interactions at the molecular level.     

Homotetrameric structure of the SNAP-23 N-terminal coiled-coil domain

SNARE proteins mediate intracellular membrane fusion by forming a coiled-coil complex to merge opposing membranes. A "fusion-active" neuronal SNARE complex is a parallel four-helix bundle containing two coiled-coil domains from SNAP-25 and one coiled-coil domain each from syntaxin-1a and VAMP-2. "Prefusion" assembly intermediate complexes can also form from these SNAREs. We studied the N-terminal coiled-coil domain of SNAP-23 (SNAP-23N), a non-neuronal homologue of SNAP-25, and its interaction with other coiled-coil domains. SNAP-23N can assemble spontaneously with the coiled-coil domains from SNAP-23C, syntaxin-4, and VAMP-3 to form a heterotetrameric complex. Unexpectedly, pure SNAP-23N crystallizes as a coiled-coil homotetrameric complex. The four helices have a parallel orientation and are symmetrical about the long axis. The complex is stabilized through the interaction of conserved hydrophobic residues comprising the a and d positions of the coiled-coil heptad repeats. In addition, a central, highly conserved glutamine residue (Gln-48) is buried within the interface by hydrogen bonding between glutamine side chains derived from adjacent subunits and to solvent molecules. A comparison of the SNAP-23N structure to other SNARE complex structures reveals how a simple coiled-coil motif can form diverse SNARE complexes.     

Exploring the conformational equilibrium of E. coli thioredoxin reductase: characterization of two catalytically important states by ultrafast flavin fluorescence spectroscopy

The conformational dynamics of wild-type Escherichia coli thioredoxin reductase (TrxR) and the mutant enzyme C138S were studied by ultrafast time-resolved fluorescence of the flavin cofactor in combination with circular dichroism (both in the flavin fingerprint and far-UV regions) and steady-state fluorescence and absorption spectroscopy. The spectroscopic data show two conformational states of the enzyme (named FO and FR), of which the physical characteristics differ considerably. Ultrafast fluorescence lifetime measurements make it possible to distinguish between the two different populations: Dominant picosecond lifetimes of approximately 1 ps (contribution 75%) and 7 ps (8%) are associated with the FO species in TrxR C138S. Long-lived fluorescence with two time constants in the range of 0.2-1 ns (total contribution 17%) originates from enzyme molecules in the FR conformation. The near absence of fast lifetime components in oxidized wild-type TrxR supports the idea of this enzyme being predominantly in the FR conformation. The emission spectrum of the FO conformation is blue-shifted with respect to that of the FR conformation. Because of the large difference in fluorescence characteristics, fluorescence measurements on time scales longer than 100 ps are fully determined by the fraction of enzyme molecules in the FR conformation. Binding of the thiol reagent phenyl mercuric acetate to wild-type enzyme and TrxR C138S stabilizes the enzymes in the FR conformation. Specific binding of the NADPH-analog, AADP(+), to the FR conformation resulted in dynamic fluorescence quenching in support of the multiple quenching sites model. Raising the temperature from 277K-323K resulted in a moderate shift to the FR conformation for TrxR C138S. High concentrations of the cosolvent glycerol triggered the domain rotation from the FO to the FR conformation.     

Reconstituted CP29: multicomponent fluorescence decay from an optically homogeneous sample

The multiexponential fluorescence decay of the CP29 complex in which the apoprotein and pigments were reconstituted in vitro was examined. Of the three decay components observed only the two dominant ones, with about 3 and 5?ns lifetimes, were studied. The main question addressed was whether the multicomponent decay was associated with sample optical heterogeneity. To this end, we examined the optical absorption and fluorescence of the CP29 sample by means of two different and independent experimental strategies. This approach was used as the wavelength positions of the absorption/fluorescence spectral forms has recently been shown to be a sensitive indicator of the binding site-induced porphyrin ring deformation (Zucchelli et al. Biophys J 93:2240-2254, 2007) and hence of apoprotein conformational changes. The data indicate that this CP29 sample is optically homogeneous. It is hypothesised that the different lifetimes are explained in terms of multiple detergent/CP29 interactions leading to different quenching states, a suggestion that allows for optical homogeneity.     

X-ray crystal structure of the trimeric N-terminal domain of gephyrin

Gephyrin is a ubiquitously expressed protein that, in the central nervous system, forms a submembraneous scaffold for anchoring inhibitory neurotransmitter receptors in the postsynaptic membrane. The N- and C-terminal domains of gephyrin are homologous to the Escherichia coli enzymes MogA and MoeA, respectively, both of which are involved in molybdenum cofactor biosynthesis. This enzymatic pathway is highly conserved from bacteria to mammals, as underlined by the ability of gephyrin to rescue molybdenum cofactor deficiencies in different organisms. Here we report the x-ray crystal structure of the N-terminal domain (amino acids 2-188) of rat gephyrin at 1.9-A resolution. Gephyrin-(2-188) forms trimers in solution, and a sequence motif thought to be involved in molybdopterin binding is highly conserved between gephyrin and the E. coli protein. The atomic structure of gephyrin-(2-188) resembles MogA, albeit with two major differences. The path of the C-terminal ends of gephyrin-(2-188) indicates that the central and C-terminal domains, absent in this structure, should follow a similar 3-fold arrangement as the N-terminal region. In addition, a central beta-hairpin loop found in MogA is lacking in gephyrin-(2-188). Despite these differences, both structures show a high degree of surface charge conservation, which is consistent with their common catalytic function.     

The solution structure of the N-terminal domain of riboflavin synthase

The structure of the amino-terminal domain of Escherichia coli riboflavin synthase (RiSy) has been determined by NMR spectroscopy with riboflavin as a bound ligand. RiSy is functional as a 75 kDa homotrimer, each subunit of which consists of two domains which share very similar sequences and structures. The N-terminal domain (RiSy-N; 97 residues) forms a 20 kDa homodimer in solution which binds riboflavin with high affinity. The structure features a six-stranded antiparallel beta-barrel with a Greek-key fold, both ends of which are closed by an alpha-helix. One riboflavin molecule is bound per monomer in a site at one end of the barrel which is comprised of elements of both monomers. The structure and ligand binding are similar to that of the FAD binding domains of ferrodoxin reductase family proteins. The structure provides insights into the structure of the whole enzyme, the organisation of the functional trimer and the mechanism of riboflavin synthesis. C48 from the N-terminal domain is identified as the free cysteine implicated in a nucleophilic role in the synthesis mechanism, while H102 from the C-terminal domains is also likely to play a key role. Both are invariant in all known riboflavin synthase sequences.     

The structure of photosystem II in Arabidopsis: localization of the CP26 and CP29 antenna complexes

A genetic approach has been adopted to investigate the organization of the light-harvesting proteins in the photosystem II (PSII) complex in plants. PSII membrane fragments were prepared from wild-type Arabidopis thaliana and plants expressing antisense constructs to Lhcb4 and Lhcb5 genes, lacking CP29 and CP26, respectively (Andersson et al. (2001) Plant Cell 13, 1193-1204). Ordered PS II arrays and PS II supercomplexes were isolated from the membranes of plants lacking CP26 but could not be prepared from those lacking CP29. Membranes and supercomplexes lacking CP26 were less stable than those prepared from the wild type. Transmission electron microscopy aided by single-particle image analysis was applied to the ordered arrays and the isolated PSII complexes. The difference between the images obtained from wild type and antisense plants showed the location of CP26 to be near CP43 and one of the light-harvesting complex trimers. Therefore, the location of the CP26 within PSII was directly established for the first time, and the location of the CP29 complex was determined by elimination. Alterations in the packing of the PSII complexes in the thylakoid membrane also resulted from the absence of CP26. The minor light-harvesting complexes each have a unique location and important roles in the stabilization of the oligomeric PSII structure.     

A study of molecular interactions in light-harvesting complexes LHCIIb, CP29, CP26 and CP24 by Stark effect spectroscopy

Electric field-induced absorption changes (electrochromism or Stark effect) of the light-harvesting PSII pigment-protein complexes LHCIIb, CP29, CP26 and CP24 were investigated. The results indicate the lack of strong intermolecular interactions in the chlorophyll a (Chl a) pools of all complexes. Characteristic features occur in the electronic spectrum of Chl b, which reflect the increased values of dipole moment and polarizability differences between the ground and excited states of interacting pigment systems. The strong Stark signal recorded for LHCIIb at 650-655 nm is much weaker in CP29, where it is replaced by a unique Stark band at 639 nm. Electrochromism of Chl b in CP26 and CP24 is significantly weaker but increased electrochromic parameters were also noticed for the Chl b transition at 650 nm. The spectra in the blue region are dominated by xanthophylls. The differences in Stark spectra of Chl b are linked to differences in pigment content and organization in individual complexes and point to the possibility of electron exchange interactions between energetically similar and closely spaced Chl b molecules.     

A study of molecular interactions in light-harvesting complexes LHCIIb, CP29, CP26 and CP24 by Stark effect spectroscopy

Electric field-induced absorption changes (electrochromism or Stark effect) of the light-harvesting PSII pigment-protein complexes LHCIIb, CP29, CP26 and CP24 were investigated. The results indicate the lack of strong intermolecular interactions in the chlorophyll a (Chl a) pools of all complexes. Characteristic features occur in the electronic spectrum of Chl b, which reflect the increased values of dipole moment and polarizability differences between the ground and excited states of interacting pigment systems. The strong Stark signal recorded for LHCIIb at 650-655 nm is much weaker in CP29, where it is replaced by a unique Stark band at 639 nm. Electrochromism of Chl b in CP26 and CP24 is significantly weaker but increased electrochromic parameters were also noticed for the Chl b transition at 650 nm. The spectra in the blue region are dominated by xanthophylls. The differences in Stark spectra of Chl b are linked to differences in pigment content and organization in individual complexes and point to the possibility of electron exchange interactions between energetically similar and closely spaced Chl b molecules.     

Crystal structure of the glutamate receptor GluA1 N-terminal domain

The AMPA (α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid) subfamily of iGluRs (ionotropic glutamate receptors) is essential for fast excitatory neurotransmission in the central nervous system. The malfunction of AMPARs (AMPA receptors) has been implicated in many neurological diseases, including Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis. The active channels of AMPARs and other iGluR subfamilies are tetramers formed exclusively by assembly of subunits within the same subfamily. It has been proposed that the assembly process is controlled mainly by the extracellular ATD (N-terminal domain) of iGluR. In addition, ATD has also been implicated in synaptogenesis, iGluR trafficking and trans-synaptic signalling, through unknown mechanisms. We report in the present study a 2.5 ? (1 ?=0.1 nm) resolution crystal structure of the ATD of GluA1. Comparative analyses of the structure of GluA1-ATD and other subunits sheds light on our understanding of how ATD drives subfamily-specific assembly of AMPARs. In addition, analysis of the crystal lattice of GluA1-ATD suggests a novel mechanism by which the ATD might participate in inter-tetramer AMPAR clustering, as well as in trans-synaptic protein-protein interactions.     

NMR assignment of the N-terminal TRAF-like RING zinc finger domain of human FLN29

Resistance of cancer cells to oncotherapeutics designed to trigger programmed cell death (a.k.a. apoptosis) greatly limits clinical efficacy. The human FLN29 protein may play a role in this process via protein-protein interactions. Here we report the NMR spectral assignment of the N-terminal TRAF2/6-RING-zinc finger-like domain of this protein.     

Exploring the Structure of the 100 Amino-Acid Residue Long N-Terminus of the Plant Antenna Protein CP29

The structure of the unusually long (∼100 amino-acid residues) N-terminal domain of the light-harvesting protein CP29 of plants is not defined in the crystal structure of this membrane protein. We studied the N-terminus using two electron paramagnetic resonance (EPR) approaches: the rotational diffusion of spin labels at 55 residues with continuous-wave EPR, and three sets of distances with a pulsed EPR method. The N-terminus is relatively structured. Five regions that differ considerably in their dynamics are identified. Two regions have low rotational diffusion, one of which shows α-helical character suggesting contact with the protein surface. This immobile part is flanked by two highly dynamic, unstructured regions (loops) that cover residues 10–22 and 82–91. These loops may be important for the interaction with other light-harvesting proteins. The region around residue 4 also has low rotational diffusion, presumably because it attaches noncovalently to the protein. This section is close to a phosphorylation site (Thr-6) in related proteins, such as those encoded by the Lhcb4.2 gene. Phosphorylation might influence the interaction with other antenna complexes, thereby regulating the supramolecular organization in the thylakoid membrane.     

Exploring the Structure of the 100 Amino-Acid Residue Long N-Terminus of the Plant Antenna Protein CP29

The structure of the unusually long (∼100 amino-acid residues) N-terminal domain of the light-harvesting protein CP29 of plants is not defined in the crystal structure of this membrane protein. We studied the N-terminus using two electron paramagnetic resonance (EPR) approaches: the rotational diffusion of spin labels at 55 residues with continuous-wave EPR, and three sets of distances with a pulsed EPR method. The N-terminus is relatively structured. Five regions that differ considerably in their dynamics are identified. Two regions have low rotational diffusion, one of which shows α-helical character suggesting contact with the protein surface. This immobile part is flanked by two highly dynamic, unstructured regions (loops) that cover residues 10–22 and 82–91. These loops may be important for the interaction with other light-harvesting proteins. The region around residue 4 also has low rotational diffusion, presumably because it attaches noncovalently to the protein. This section is close to a phosphorylation site (Thr-6) in related proteins, such as those encoded by the Lhcb4.2 gene. Phosphorylation might influence the interaction with other antenna complexes, thereby regulating the supramolecular organization in the thylakoid membrane.     

Spectral substructure and excitonic interactions in the minor photosystem II antenna complex CP29 as revealed by nonlinear polarization spectroscopy in the frequency domain

CP29 (the lhcb4 gene product), a minor photosystem II antenna complex, binds six chlorophyll (Chl) a, two Chl b, and two to three xanthophyll molecules. The Chl a/b Q(y) absorption band substructure of CP29 (purified from spinach) was investigated by nonlinear polarization spectroscopy in the frequency domain (NLPF) at room temperature. A set of NLPF spectra was obtained at 11 probe wavelengths. Seven probe wavelengths were located in the Q(y) spectral region (between 630 and 690 nm) and four in the Soret band (between 450 and 485 nm). Evaluation of the experimental data within the framework of global analysis leads to the following conclusions: (i) The dominant Chl a absorption (with a maximum at 674 nm) splits into (at least) three subbands (centered at 660, 670, and 681.5 nm). (ii) In the Chl b region two subbands can be identified with maxima located at 640 and 646 nm. (iii) The lowest energy Q(y) transition (peaking at 681.5 nm) is assigned to a Chl a which only weakly interacts with other Chl aor b molecules by incoherent F?rster-type excitation energy transfer. (iv) Pronounced excitonic interaction exists between certain Chl a and Chl b molecules, which most likely form a Chl a/b heterodimer. The subbands centered at 640 and 670 nm constitute a strongly coupled Chl a/b pair. The findings of the study indicate that the currently favored view of spectral heterogeneity in CP29 being due essentially to pigment-protein interactions has to be revised.     

Topology and secondary structure of the N-terminal domain of diacylglycerol kinase

Prokaryotic diacylglycerol kinase (DAGK) functions as a homotrimer of 13 kDa subunits, each of which has three transmembrane segments. This enzyme is conditionally essential to some bacteria and serves as a model system for studies of membrane protein biocatalysis, stability, folding, and misfolding. In this work, the detailed topology and secondary structure of DAGK's N-terminus up through the loop following the first transmembrane domain were probed by NMR spectroscopy. Secondary structure was mapped by measuring 13C NMR chemical shifts. Residue-to-residue topology was probed by measuring 19F NMR relaxation rates for site-specifically labeled samples in the presence and absence of polar and hydrophobic paramagnetic probes. Most of DAGK's N-terminal cytoplasmic and first transmembrane segments are alpha-helical. The first and second transmembrane helices are separated by a short loop from residues 48 to 52. The first transmembrane segment extends from residues 32 to 48. Most of the N-terminal cytoplasmic domain lies near the interface but does not extend deeply into the membrane. Finally, catalytic activities measured for the single cysteine mutants before and after chemical labeling suggest that the N-terminal cytoplasmic domain likely contains a number of critical active site residues. The results, therefore, suggest that DAGK's active site lies very near to the water/bilayer interface.     

Exploring the domain structure of modular nonribosomal peptide synthetases

Recently, considerable insight has been gained into the modular organization of nonribosomal peptide synthetases (NRPS). The three-dimensional structures of domains associated with substrate adenylation and covalent binding have been solved as well as the structure of a priming enzyme required for the post-translational modification of NRPS. Taken together, these studies will help us to understand the architecture of these mega-enzymes.