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Paul H Axelsen

Publications and source records attributed to Paul H Axelsen.

15 recordsLinked to original sources
PubMed2006

Two-dimensional infrared spectroscopy displays signatures of structural ordering in peptide aggregates.

In the presence of lipid bilayers, the hexapeptide AcWL(5) forms membrane-bound aggregates dominated by beta-secondary structure and is thus a useful model for the onset of peptide aggregation in membrane environments. Two-dimensional infrared (2D IR) spectra in the amide I region for aggregates of AcWL(5) peptides with single isotopic labels provide new insight into the residue-level structural ordering of the aggregated peptides. Separation of spectral information along two axes provides clear indications of the band frequencies and relative intensities, which together are an indication of extended amide coupling networks across structural regions of a particular size. The lowered anharmonicities, relative to free peptide, and the narrow, homogeneous lineshapes of the 2D IR peaks indicate the delocalization of vibrational modes through an ordered structure whose flexibility varies with relative peptide concentration. Crosspeaks between delocalized transitions can be used to estimate the strength of the coupling interactions between neighboring residues. The sensitivity of 2D IR spectra to residue-level structural ordering shows that 2D IR spectroscopy is a powerful technique for probing structures formed during the onset of peptide aggregation.

Algorithms↗
PubMed2006

Conformational and quantitative characterization of oritavancin-peptidoglycan complexes in whole cells of Staphylococcus aureus by in vivo 13C and 15N labeling.

Solid-state NMR has been used to examine the cell walls of intact whole cells of Staphyloccus aureus grown on media containing D-[1-(13)C]alanine, [(15)N]glycine, and the alanine racemase inhibitor, alaphosphin. The results of in situ site-selective, four-frequency NMR experiments show directly for the first time that (i) 54% of the cell-wall peptidoglycan stems have D-alanine termini and 46%, D-alanine-D-alanine termini; (ii) the molar ratio of stems ending in D-alanine to esterified alditol repeats of cell-wall teichoic and lipoteichoic acids is 3:2; and (iii) 50% of the mature cell-wall binding sites for a fluorinated oritavancin analogue consist of two nearest-neighbor peptide stems of different glycan strands. The drug is bound to the D-Ala-D-Ala terminus of one stem and is proximate to the bridging pentaglycyl segment that cross-links the two stems. Structural details of the binding site are revealed in a model of the glycopeptide-peptidoglycan interaction produced by molecular dynamics simulations with internuclear distance restraints determined by NMR.

Anti-Bacterial Agents↗
PubMed2005

Properties and structures of the influenza and HIV fusion peptides on lipid membranes: implications for a role in fusion.

The fusion peptides of HIV and influenza virus are crucial for viral entry into a host cell. We report the membrane-perturbing and structural properties of fusion peptides from the HA fusion protein of influenza virus and the gp41 fusion protein of HIV. Our goals were to determine: 1), how fusion peptides alter structure within the bilayers of fusogenic and nonfusogenic lipid vesicles and 2), how fusion peptide structure is related to the ability to promote fusion. Fluorescent probes revealed that neither peptide had a significant effect on bilayer packing at the water-membrane interface, but both increased acyl chain order in both fusogenic and nonfusogenic vesicles. Both also reduced free volume within the bilayer as indicated by partitioning of a lipophilic fluorophore into membranes. These membrane ordering effects were smaller for the gp41 peptide than for the HA peptide at low peptide/lipid ratio, suggesting that the two peptides assume different structures on membranes. The influenza peptide was predominantly helical, and the gp41 peptide was predominantly antiparallel beta-sheet when membrane bound, however, the depths of penetration of Trps of both peptides into neutral membranes were similar and independent of membrane composition. We previously demonstrated: 1), the abilities of both peptides to promote fusion but not initial intermediate formation during PEG-mediated fusion and 2), the ability of hexadecane to compete with this effect of the fusion peptides. Taken together, our current and past results suggest a hypothesis for a common mechanism by which these two viral fusion peptides promote fusion.

Amino Acid Sequence↗
PubMed2005

Structural analysis of lipoprotein E particles.

Apolipoprotein E (apoE) is a key regulator of cholesterol homeostasis. Human apoE has three common isoforms, each with different risk implications for cardiovascular and neurodegenerative disease. Neither the structure of lipoprotein E particles nor the structural consequences of the isoform differences are known. In this investigation, synthetic lipoprotein particles were prepared by complexing phospholipids with full-length apoE isoforms, or with truncated N-terminal and C-terminal domains of apoE. These particles were examined with calorimetry, electron microscopy, circular dichroism spectroscopy, and internal reflection infrared spectroscopy. Results indicate that particles made with the three full-length apoE isoforms are discoidal in shape, and structurally indistinguishable. Thus, differences in their pathological consequences are not due to gross differences in particle structure. Although apoE is predominantly helical, and the axes of the helices are parallel to the flat surfaces of the particles, the orientational order of lipid acyl chains is low and inconsistent with the belt model of lipoprotein A-I structure. Instead, the data suggest that there are at least two different types of apoE-lipid interactions within lipoprotein E particles. One type occurs between apoE helices and the edge of the lipid bilayer as in the belt model, while a second type involves apoE helices that situate in the plane of the membrane and disturb acyl chain order. These interactions allow LpE particles to form with different protein/lipid ratios, and they account for the structure of LpE particles made with only the truncated domains.

Apolipoproteins E↗
PubMed2005

Promotion of oxidative lipid membrane damage by amyloid beta proteins.

Senile plaques in the cerebral parenchyma are a pathognomonic feature of Alzheimer's disease (AD) and are mainly composed of aggregated fibrillar amyloid beta (Abeta) proteins. The plaques are associated with neuronal degeneration, lipid membrane abnormalities, and chemical evidence of oxidative stress. The view that Abeta proteins cause these pathological changes has been challenged by suggestions that they have a protective function or that they are merely byproducts of the pathological process. This investigation was conducted to determine whether Abeta proteins promote or inhibit oxidative damage to lipid membranes. Using a mass spectrometric assay of oxidative lipid damage, the 42-residue form of Abeta (Abeta42) was found to accelerate the oxidative lipid damage caused by physiological concentrations of ascorbate and submicromolar concentrations of copper(II) ion. Under these conditions, Abeta42 was aggregated, but nonfibrillar. Ascorbate and copper produced H(2)O(2), but Abeta42 reduced H(2)O(2) concentrations, and its ability to accelerate oxidative damage was not affected by catalase. Lipids could be oxidized by H(2)O(2) and copper(II) in the absence of ascorbate, but only at significantly higher concentrations, and Abeta42 inhibited this reaction. These results indicate that the ability of Abeta42 to promote oxidative damage is more potent and more likely to be manifest in vivo than its ability to inhibit oxidative damage. In conjunction with prior results demonstrating that oxidatively damaged membranes cause Abeta42 to misfold and form fibrils, these results suggest a specific chemical mechanism linking Abeta42-promoted oxidative lipid damage to amyloid fibril formation.

Amyloid beta-Peptides↗
PubMed2005

beta Sheet structure in amyloid beta fibrils and vibrational dipolar coupling.

Fibrils formed by amyloid beta proteins were labeled with 13C at various positions and examined by infrared spectroscopy to detect vibrational dipolar coupling, implying close physical proximity. The results support key features of several recently proposed models for amyloid fibril structure, but they also add some important caveats. For instance, they support the conclusion that the beta structure is parallel; however, the coupling is not as strong as expected when residues are in register. This may be explained by out-of-register alignment of adjacent strands, or nonstandard parallel sheet structure that yields suboptimal alignment of labeled dipole moments. The data also point to a significant structural difference between fibrils formed by the 40-residue amyloid beta protein and fibrils formed by residues 10-35.

Amyloid beta-Peptides↗
PubMed2005

The E46K mutation in alpha-synuclein increases amyloid fibril formation.

The identification of a novel mutation (E46K) in one of the KTKEGV-type repeats in the amino-terminal region of alpha-synuclein suggests that this region and, more specifically, Glu residues in the repeats may be important in regulating the ability of alpha-synuclein to polymerize into amyloid fibrils. It was demonstrated that the E46K mutation increased the propensity of alpha-synuclein to fibrillize, but this effect was less than that of the A53T mutation. The substitution of Glu(46) for an Ala also increased the assembly of alpha-synuclein, but the polymers formed can have different ultrastructures, further indicating that this amino acid position has a significant effect on the assembly process. The effect of residue Glu(83) in the sixth repeat of alpha-synuclein, which lies closest to the amino acid stretch critical for filament assembly, was also studied. Mutation of Glu(83) to a Lys or Ala increased polymerization but perturbed some of the properties of mature amyloid. These results demonstrated that some of the Glu residues within the repeats can have significant effects on modulating the assembly of alpha-synuclein to form amyloid fibrils. The greater effect of the A53T mutation, even when compared with what may be predicted to be a more dramatic mutation such as E46K, underscores the importance of protein microenvironment in affecting protein structure. Moreover, the relative effects of the A53T and E46K mutations are consistent with the age of onset of disease. These findings support the notion that aberrant alpha-synuclein polymerization resulting in the formation of pathological inclusions can lead to disease.

Alanine↗
PubMed2004

Synchronized conformational fluctuations and binding site desolvation during molecular recognition.

Binding site desolvation is a poorly understood prerequisite to ligand binding. Although structural fluctuations may be expected to have an important role, little is known about which fluctuations are important or the mechanism by which they promote desolvation. This investigation examines whether and how specific structural fluctuations contribute to desolvation of the ligand binding site in glycopeptide antibiotics. Backbone peptide group rotations in vancomycin, known to occur by experimental observation, were examined in this work with a two-dimensional adaptive umbrella sampling molecular dynamics simulation technique. Results indicate that energetic barriers to rotation are relatively small for two of the peptide groups intimately involved in ligand recognition. When they occur, these rotations strip water molecules away from key hydrogen bond donors and simultaneously cause significant distortions in the macrocyclic rings of the antibiotic that force water into and out of the binding site. Both events are intricately synchronized on the molecular level and have consequences that are clearly necessary to prepare the binding site for receiving a ligand. These results suggest that previously reported observations concerning structural dynamics and binding kinetics in these compounds are mechanistically linked, and they illustrate a heretofore unrecognized degree of preorganization, complexity, and synchronization that may be involved in specific molecular recognition. They also suggest that strategies for increasing antibiotic affinity through covalent dimerization may be counterproductive.

Amides↗
PubMed2004

Vibrational coupling, isotopic editing, and beta-sheet structure in a membrane-bound polypeptide.

The N-acetylated hexapeptide WLLLLL (AcWL5) partitions into lipid membranes and is believed to assemble into an antiparallel beta-sheet. As a test of this structural assignment, the peptide bonds of residues 2-6 were labeled with (13)C and allowed to adsorb onto a supported lipid membrane. Peptides bound to the membrane were examined for evidence of coupling between the labeled vibrational modes in adjacent beta-strands with internal reflection infrared spectroscopy. Experimental results indicate that the amide I absorption band in D(2)O (i.e., amide I') attributable to (13)C is selectively enhanced when the label is at any one of several positions along the peptide backbone. Simulations employing an excitonic model with through-bond and through-space interactions were performed on AcWL5 models in parallel and antiparallel beta-sheet configurations. The simulations yield spectra in good agreement with the experimental results, accounting for the enhancement of both (13)C band intensities and band frequencies. They also yield insight into the physical origin and structure selectivity of the distinctive amide I' band shapes that arise in isotopically edited spectra. It is concluded that the beta-sheet formed by membrane-bound AcWL5 is indeed antiparallel, and the enhancement of (13)C bands in the infrared spectra of these peptides is caused by both interstrand and intrastrand coupling to (12)C modes.

Amides↗
PubMed2003

Role of alpha-synuclein carboxy-terminus on fibril formation in vitro.

Alpha-synuclein (alpha-syn) is the major component of intracellular inclusions in several neurodegenerative diseases, and the conversion of soluble alpha-syn into filamentous aggregates may contribute to disease pathogenesis. Since mechanisms leading to the formation of alpha-syn inclusions are unclear, in vitro models of alpha-syn aggregation may yield insights into this process. To that end, we examined the consequences on the progressive deletion of the carboxy-terminus of alpha-syn in regulating fibril formation, and we show here that carboxy-terminal truncated alpha-syn proteins aggregate faster than the full-length molecule. Protease digestion and immunoelectron microscopy indicate that the alpha-syn amino- and carboxy-termini are more solvent exposed than the central core and that filaments formed from carboxy-terminal truncated alpha-syn are narrower in diameter than the full-length molecule. Moreover, seeding experiments under conditions where full-length alpha-syn did not readily aggregate revealed that carboxy-truncated alpha-syn extending from amino acids 1-102 and 1-110 but not 1-120 were efficient in seeding full-length alpha-syn aggregation over a range of concentrations. Using site-directed mutagenesis, the negatively charged residues 104, 105 and 114, 115 in the carboxy-terminus were implicated in this reduced aggregation and the lack of seeding of full-length alpha-syn fibrillogenesis by 1-120. Our data support the view that the middle region of alpha-syn forms the core of alpha-syn filaments and that negative charges in the carboxy-terminus counteract alpha-syn aggregation. Thus, the carboxy-terminus of alpha-syn may regulate aggregation of full-length alpha-syn and determine the diameter of alpha-syn filaments.

Actin Cytoskeleton↗
PubMed2003

Early synergy between Abeta42 and oxidatively damaged membranes in promoting amyloid fibril formation by Abeta40.

Oxidative lipid membrane damage is known to promote the misfolding of Abeta42 into pathological beta structure. In fully developed senile plaques of Alzheimer's disease, however, it is the shorter and more soluble amyloid beta protein, Abeta40, that predominates. To investigate the role of oxidative membrane damage in the misfolding of Abeta40, we have examined its interaction with supported lipid monolayer membranes using internal reflection infrared spectroscopy. Oxidatively damaged lipids modestly increased Abeta40 accumulation, with adsorption kinetics and a conformation that are distinct from that of Abeta42. In stark contrast, pretreatment of oxidatively damaged monolayer membranes with Abeta42 vigorously promoted Abeta40 accumulation and misfolding. Pretreatment of saturated or undamaged membranes with Abeta42 had no such effect. Parallel studies of lipid bilayer vesicles using a dye binding assay to detect fibril formation and electron microscopy to examine morphology demonstrated that Abeta42 pretreatment of oxidatively damaged membranes promoted the formation of mature Abeta40 amyloid fibrils. We conclude that oxidative membrane damage and Abeta42 act synergistically at an early stage to promote fibril formation by Abeta40. This synergy could be detected within minutes using internal reflection spectroscopy, whereas a dye-binding assay required several days and much higher protein concentrations to demonstrate this synergy.

Amyloid↗
PubMed2003

Configurational entropy and cooperativity between ligand binding and dimerization in glycopeptide antibiotics.

Oligomerization and ligand binding are thermodynamically cooperative processes in many biochemical systems, and the mechanisms giving rise to cooperative behavior are generally attributed to changes in structure. In glycopeptide antibiotics, however, these cooperative processes are not accompanied by significant structural changes. To investigate the mechanism by which cooperativity arises in these compounds, fully solvated molecular dynamics simulations and quasiharmonic normal-mode analysis were performed on chloroeremomycin, vancomycin, and dechlorovancomycin. Configurational entropies were derived from the vibrational modes recovered from ligand-free and ligand-bound forms of the monomeric and dimeric species. Results indicate that both ligand binding and dimerization incur an entropic cost as vibrational activity in the central core of the antibiotic is shifted to higher frequencies with lower amplitudes. Nevertheless, ligand binding and dimerization are cooperative because the entropic cost of both processes occurring together is less than the cost of these processes occurring separately. These reductions in configurational entropy are more than sufficient in magnitude to account for the experimentally observed cooperativity between dimerization and ligand binding. We conclude that biochemical cooperativity can be mediated through changes in vibrational activity, irrespective of the presence or absence of concomitant structural change. This may represent a general mechanism of allostery underlying cooperative phenomena in diverse macromolecular systems.

Anti-Bacterial Agents↗
PubMed2003

Transcriptional profile of the Escherichia coli response to the antimicrobial insect peptide cecropin A.

Cationic antimicrobial peptides are believed to exert their primary activities on anionic bacterial cell membranes; however, this model does not adequately account for several important structure-activity relationships. These relationships are likely to be influenced by the bacterial response to peptide challenge. In order to characterize the genomic aspect of this response, transcription profiles were examined for Escherichia coli isolates treated with sublethal and lethal concentrations of the cationic antimicrobial peptide cecropin A. Transcript levels for 26 genes changed significantly following treatment with sublethal peptide concentrations, and half of the transcripts corresponded to protein products with unknown function. The pattern of response is distinct from that following treatment with lethal concentrations and is also distinct from the bacterial response to nutritional, thermal, osmotic, or oxidative stress. These results demonstrate that cecropin A induces a genomic response in E. coli apart from any lethal effects on the membrane and suggest that a complete understanding of its mechanism of action may require a detailed examination of this response.

Antimicrobial Cationic Peptides↗
PubMed2002

The role of configurational entropy in biochemical cooperativity.

Cooperativity is a common biochemical phenomenon in which two or more otherwise independent processes are thermodynamically coupled. Because cooperative processes are usually attended by changes in molecular conformation, thermodynamic coupling is usually attributed to an enthalpy-driven mechanism. In the family of glycopeptide antibiotics that includes vancomycin, however, cooperative phenomena occur that cannot be explained by conformational change. In this communication, we demonstrate that cooperativity in these systems can arise solely from changes in vibrational activity.

Alanine↗