RESUMEN
The amyloid ß (A ß) peptide is important in the context of Alzheimer's disease, since it is one of the major components of the fibrils that constitute amyloid plaques. Agents that can influence fibril formation are important, and of those, membrane mimics are particularly relevant, because the hydrophobic part of A ß suggests a possible membrane activity of the peptide. We employed spin-label EPR to investigate the aggregation process of A ß1-40 in the presence of the sodium dodecyl sulfate (SDS) detergent as a membrane-mimicking agent. In this work, the effect of SDS on A ß is studied using two positions of spin label, the N-terminus and position 26. By comparing the two label positions, the effect of local mobility of the spin label is eliminated, revealing A ß aggregation in the SDS concentration regime below the critical micelle concentration (CMC). We demonstrate that, at low SDS concentrations, the N-terminus of A ß participates in the solubilization, most likely by being located at the particle-water interface. At higher SDS concentrations, an SDS-solubilized state that is a precursor to the one A ß/micelle state above the CMC of SDS prevails. We propose that A ß is membrane active and that aggregates include SDS. This study reveals the unique potential of EPR in studying A ß aggregation in the presence of detergent.
Asunto(s)
Péptidos beta-Amiloides/metabolismo , Detergentes/metabolismo , Membranas Artificiales , Fragmentos de Péptidos/metabolismo , Dodecil Sulfato de Sodio/metabolismo , Secuencia de Aminoácidos , Péptidos beta-Amiloides/química , Detergentes/farmacología , Relación Dosis-Respuesta a Droga , Fragmentos de Péptidos/química , Unión Proteica , Rotación , Dodecil Sulfato de Sodio/farmacología , Marcadores de SpinRESUMEN
The structure of the unusually long (â¼100 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.
Asunto(s)
Proteínas de Arabidopsis/química , Proteínas de Cloroplastos/química , Simulación de Dinámica Molecular , Ribonucleoproteínas/química , Secuencia de Aminoácidos , Arabidopsis/química , Proteínas de Arabidopsis/genética , Proteínas de Cloroplastos/genética , Datos de Secuencia Molecular , Mutación , Estructura Terciaria de Proteína , Ribonucleoproteínas/genéticaRESUMEN
For 3D-structure determination in biophysical systems EPR is rapidly gaining ground. Proteins labeled specifically with two nitroxide spin labels can be prepared, and several EPR methods are available for distance determination, which makes it possible to determine distance constraints. However, such methods require frozen solutions, potentially causing non-physiological states of the sample. Here, we target spin- spin interaction in liquid solution at room temperature using rigid model compounds. A series of 310 -helical peptides, based on α-aminoisobutyric acid (Aib), is synthesized with pairs of spin labels separated by three, four, and five amino acids. To avoid flexibility, the noncoded nitroxyl-containing α-amino acid TOAC that is rigidly connected with the peptide backbone, is used. The EPR spectra of the peptides show a decreasing amount of coupling between the two spin labels within this series. We suggest through-bond interaction as the dominating mechanism for exchange interaction (J) and find a stronger J-coupling than in the corresponding Ala-based TOAC-peptides investigated previously (Hanson, et al., J Am Chem Soc 1996, 118, 7618-7625). We speculate that stronger coupling in Aib- vs Ala- peptides is due to intrinsically stronger through-bond interaction in the Aib-based peptides.
Asunto(s)
Óxidos N-Cíclicos/química , Espectroscopía de Resonancia por Spin del Electrón , Modelos Moleculares , Péptidos/química , Marcadores de Spin , Simulación por Computador , Estructura Secundaria de ProteínaRESUMEN
Cytochrome f (Cyt f) and plastocyanin (Pc) form a highly transient complex as part of the photosynthetic redox chain. The complex from Nostoc sp. PCC 7119 was studied by NMR relaxation spectroscopy with the aim of determining the orientation of Pc relative to Cyt f. Chemical-shift-perturbation analysis showed that the presence of spin labels on the surface of Cyt f does not significantly affect the binding of Pc. The paramagnetic relaxation enhancement results are not consistent with a single orientation of Pc, thus indicating that multiple orientations must occur and suggesting that an encounter state represents a large fraction of the complex.
Asunto(s)
Citocromos f/metabolismo , Nostoc , Plastocianina/metabolismo , Citocromos f/química , Mesilatos/metabolismo , Modelos Moleculares , Resonancia Magnética Nuclear Biomolecular , Plastocianina/química , Unión Proteica , Conformación ProteicaRESUMEN
We address the interpretation, via an integrated computational approach, of the experimental continuous-wave electron paramagnetic resonance (cw-EPR) spectra of a complete set of conformationally highly restricted, stable 310-helical peptides from hexa- to nonamers, each bis-labeled with nitroxide radical-containing TOAC (4-amino-1-oxyl-2,2,6,6-tetramethylpiperidine-4-carboxylic acid) residues. The usefulness of TOAC for this type of analysis has been shown already to be due to its cyclic piperidine side chain, which is rigidly connected to the peptide backbone α-carbon. The TOAC α-amino acids are separated by two, three, four, and five intervening residues. This set of compounds has allowed us to modulate both the radical···radical distance and the relative orientation parameters. To further validate our conclusion, a comparative analysis has been carried out on three singly TOAC-labeled peptides of similar main-chain length.
Asunto(s)
Óxidos N-Cíclicos/química , Óxidos de Nitrógeno/química , Péptidos/química , Teoría Cuántica , Espectroscopía de Resonancia por Spin del Electrón , Marcadores de SpinRESUMEN
The backbone of secreted autotransporter passenger proteins generally attains a stable ß-helical structure. The secretion of passengers across the outer membrane was proposed to be driven by sequential folding of this structure at the cell surface. This mechanism would require a relatively stable intermediate as starting point. Here, we investigated the mechanics of secreted truncated versions of the autotransporter hemoglobin protease (Hbp) of Escherichia coli using atomic force microscopy. The data obtained reveal a ß-helical structure at the C terminus that is very stable. In addition, several other distinct metastable intermediates are found which are connected during unfolding by multiroute pathways. Computational analysis indicates that these intermediates correlate to the ß-helical rungs in the Hbp structure which are clamped by stacked aromatic residues. Our results suggest a secretion mechanism that is initiated by a stable C-terminal structure and driven forward by several folding intermediates that build up the ß-helical backbone.
Asunto(s)
Proteínas de Escherichia coli , Pliegue de Proteína , Transporte de Proteínas , Sistemas de Secreción Tipo V , Escherichia coli , Estructura Terciaria de ProteínaRESUMEN
In this paper, we address the interpretation of molecular properties of selected singly and doubly spin-labeled peptides from continuous-wave electron spin resonance (cw-ESR) spectroscopy. This study is performed by means of an integrated computational approach that merges a stochastic treatment of long-term dynamics to ad hoc methodologies for the calculation of structural properties. In particular, our method is based on (i) the determination of geometric and local magnetic parameters of the peptides by quantum mechanical density functional calculations by taking into account solvent contribution; (ii) the hydrodynamic evaluation of dissipative properties; and (iii) molecular dynamics including equilibrium distribution of molecular conformations. The system is then described by a stochastic Liouville equation in which the spin Hamiltonian for the two electron spins, interacting with each other and coupled to two (14)N nuclear spins, is coupled to the diffusive operator describing the time evolution of slow coordinates. cw-ESR spectra are simulated for selected peptides built from the non-natural α-aminoacids α-aminoisobutyric acid (Aib) and 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC). In particular, we study the -Aib-TOAC-Aib- singly labeled tripeptide and the -Aib-TOAC-(Aib)(7)- singly labeled and -Aib-TOAC-(Aib)(5)-TOAC-Aib- doubly labeled nonapeptides. We show that good agreement is obtained with minimal resorting to fitting procedures, proving that the combination of sensitive ESR spectroscopy and sophisticated modeling is a powerful approach to the investigation of both molecular dynamics and 3D-structural properties.