Spin-labeled Peptides Research Articles

The Dynamic Interactions of a Multitargeting Domain in Ameloblastin Protein with Amelogenin and Membrane.

The enamel matrix protein Ameloblastin (Ambn) has critical physiological functions, including regulation of mineral formation, cell differentiation, and cell-matrix adhesion. We investigated localized structural changes in Ambn during its interactions with its targets. We performed biophysical assays and used liposomes as a cell membrane model. The xAB2N and AB2 peptides were rationally designed to encompass regions of Ambn that contained self-assembly and helix-containing membrane-binding motifs. Electron paramagnetic resonance (EPR) on spin-labeled peptides showed localized structural gains in the presence of liposomes, amelogenin (Amel), and Ambn. Vesicle clearance and leakage assays indicated that peptide-membrane interactions were independent from peptide self-association. Tryptophan fluorescence and EPR showed competition between Ambn-Amel and Ambn-membrane interactions. We demonstrate localized structural changes in Ambn upon interaction with different targets via a multitargeting domain, spanning residues 57 to 90 of mouse Ambn. Structural changes of Ambn following its interaction with different targets have relevant implications for the multifunctionality of Ambn in enamel formation.

Probing P(T/S)XP peptides for novel structural interactions with Tsg101 UEV.

To complete their lifecycle, enveloped viruses such as human immunodeficiency virus type-1 (HIV-1) recruit host machinery to facilitate budding and egress. For HIV-1, this involves an interaction between a PTAP motif in the HIV-1 Gag polyprotein and the ubiquitin E2 variant (UEV) domain of tumor susceptibility gene 101 (Tsg101). The latter is part of the native endosomal sorting complex required for transport (ESCRT) machinery, which functions in endosomal cargo sorting but is hijacked by HIV-1 for plasma membrane budding. The interaction between the PTAP signal of HIV-1 Gag and the UEV domain of Tsg101 is well characterized biochemically and structurally, with the PTAP motif binding into a groove in the UEV domain. The HIV-1 PTAP sequence emulates similar P(T/S)XP signals that drive host protein interactions involved with ESCRT, where some host proteins may contain several potential P(T/S)XP motifs. This suggested potential competitive or cooperative action on the UEV surface, and so we screened two additional P(T/S)XP motifs from the ESCRT-0 protein Hrs and several motifs identified in other viruses for interaction with the Tsg101 UEV domain using solution nuclear magnetic resonance. In the process, we identified an additional interaction mode for P(T/S)XP peptides with the Tsg101 UEV, involving both a charged surface and a cluster of aromatic residues, neither of which are implicated in the previously characterized PTAP interaction. We identified several binding determinants of this P(T/S)XP interaction using alanine mutant peptides and combined chemical shift perturbations with distance data from paramagnetic relaxation enhancement experiments using spin-labeled peptides to build a structural model of the interaction on the UEV surface. This additional P(T/S)XP interaction may reflect a novel viral strategy to recruit Tsg101 and by extension ESCRT for egress, or hijacking of a different endogenous role of Tsg101 altogether.

Ulf Diederichsen (1963–2021)

“For he was our own! … Fruitful both in counsel and deed; this we experienced and appreciated.” With the death of Ulf Diederichsen on November 11, 2021, after a short but severe illness, we lost a great scientist in chemical biology and good friend. He was a generous and extremely gifted man whose strength was to tackle essential biological problems at a molecular level with simple model systems and to draw insightful conclusions realizing a hallmark of chemical biology by addressing biological challenges with chemical approaches derived from simple principles. Ulf Diederichsen was born on October 7, 1963, in Munich and grew up in Göttingen, enjoying excellent scholar education at the Max-Planck Gymnasium. He moved to Freiburg im Breisgau in 1983 to study Chemistry at the Albert-Ludwigs-University. For his doctorate he moved to Zurich in 1988 to work with Prof. Eschenmoser at the ETH on the question why Nature chose pentose—but not hexose nucleic acids. He received the Dr. rer. nat. in 1993 on the Base pairing of hypoxanthine in HOMO DNA oligonucleotides and the question of the pairing behavior of glucopyranosyl oligonucleotides. He then joined the group of Prof. Dennis P. Curran at the University of Pennsylvania (Pittsburgh/USA) as postdoctoral researcher (1993–1994) investigating radical chemistry. Back to Europe he started his habilitation on “Linear nucleic acid analogues with peptidic backbones” under the mentorship of Prof. Horst Kessler at the Technical University of Munich, which was finished in 1999. He then joined the University of Würzburg as Professor of Organic Chemistry, and finally, in 2001, the University of Göttingen. He served as Dean (2005 to 2007) and Vice President for Research (2015 to 2021). In addition, he was Guest Professor at the Ludwig-Maximilians-University in Munich (1998–1999) and Goering Visiting Professor at the University of Wisconsin, USA (2000). He was elected member of the Academy of Sciences in Göttingen in 2012 and became its president in 2020. His scientific interest was mainly centered on the non-covalent interaction of peptide helices with respect to the incorporation, organization, and dynamics in lipid membranes. He successfully employed spin-labeled peptides for distance measurements. Similarly, he addressed the membrane attachment and fusion processes of SNARE proteins with model systems (conjugates of transmembrane peptides with coiled coil peptides or peptide nucleic acids). He was interested in functionalized β-peptides as artificial matrices for aggregation and modification of model membranes. The excellent results of this outstanding research were summarized in largely over 100 publications in highly renowned international journals. Besides his exceptional scientific achievements and admirable mentorship for a large number of doctoral students and postdocs, he deserves high recognition for his excellent research management particularly as Vice President of the University of Göttingen. He also served as a highly esteemed reviewer in various panels, including the German Research Foundation. The large experience collected in this important activity, particularly also for the German peptide community, he adapted in a very successful manner also in his editorial engagement as Deputy Editor of the Journal of Peptide Science since 2012, where he was supposed to take over the full responsibility as the Editor-in-Chief from 2022. Those of us who knew him are saddened by his sudden passing away and mourn the great loss of a dear friend and colleague. He will always be remembered as an inspiring teacher and mentor, as an enthusiastic scientist, but first and foremost as a warm and sincere human being, as a “feiner Kerl.”

TOAC spin-labeled peptides tailored for DNP-NMR studies in lipid membrane environments

The benefit of combining in-cell solid-state dynamic nuclear polarization (DNP) NMR and cryogenic temperatures is providing sufficient signal/noise and preservation of bacterial integrity via cryoprotection to enable in situ biophysical studies of antimicrobial peptides. The radical source required for DNP was delivered into cells by adding a nitroxide-tagged peptide based on the antimicrobial peptide maculatin 1.1 (Mac1). In this study, the structure, localization, and signal enhancement properties of a single (T-MacW) and double (T-T-MacW) TOAC (2,2,6,6-tetramethylpiperidine-N-oxyl-4-amino-4-carboxylic acid) spin-labeled Mac1 analogs were determined within micelles or lipid vesicles. The solution NMR and circular dichroism results showed that the spin-labeled peptides adopted helical structures in contact with micelles. The peptides behaved as an isolated radical source in the presence of multilamellar vesicles, and the electron paramagnetic resonance (EPR) electron-electron distance for the doubly spin-labeled peptide was ∼1 nm. The strongest paramagnetic relaxation enhancement (PRE) was observed for the lipid NMR signals near the glycerol-carbonyl backbone and was stronger for the doubly spin-labeled peptide. Molecular dynamics simulation of the T-T-MacW radical source in phospholipid bilayers supported the EPR and PRE observations while providing further structural insights. Overall, the T-T-MacW peptide achieved better 13C and 15N signal NMR enhancements and 1H spin-lattice T1 relaxation than T-MacW.

Electron spin echo detection of stochastic molecular librations: Non-cooperative motions on solid surface.

In frozen biological media and molecular glasses only restricted motions exist; because of the weakness and disorder of intermolecular bonds these motions may have stochastic nature. Electron spin echo (ESE) spectroscopy of spin-labeled molecules allows detecting their restricted stochastic rotations (stochastic molecular librations). As in molecular disordered media motions may be highly cooperative, it would be desirable to investigate their spectroscopic manifestation also in the systems where cooperative effects would be certainly ruled out. In this work, ESE of spin-labeled molecules adsorbed on inorganic SiO2 surface was investigated in a wide temperature range. The rate of motion-induced spin relaxation was found to become measurable above 130 K, increasing with temperature and attaining then a saturating behavior with a well-defined maximum near 250 K. For two types of molecules differing remarkably in their size and polarity (a small highly-polar nitroxide radical and a large spin-labeled peptide), quite similar results were obtained. This saturating behavior was quantitatively reproduced in simulations within a simple model of jump between two close orientations. Comparison with experiment allowed estimate that at 250 K the correlation time of the motion τc is of the order of several tens of nanoseconds and the angle α between two orientations is around 0.02 rad. As the found saturating behavior is a property of individual motions, for any other molecular system an excess of the spin relaxation rate above the maximum found here for adsorbed molecules may be ascribed to cooperative motions. Comparison with literature data on molecular systems of different origin has shown that effects of cooperativity indeed are present and, moreover, may be very essential.

Nitroxide spin-labeled peptides for DNP-NMR in-cell studies.

Antimicrobial peptides (AMPs) that target lipid membranes show promise as alternatives to conventional antibiotics. However, the molecular mechanisms of membrane perturbation, as most studies are performed in model systems and in-cell structural studies, have yet to be achieved. Solid-state NMR spectroscopy is a valuable technique to investigate peptide-membrane interactions and to determine the structure of peptides, but the short lifespan of bacteria, especially under magic angle spinning conditions, has not permitted in-cell structural studies. Here, we present the first dynamic nuclear polarization (DNP)-NMR in-cell studies of Escherichia coli bacteria incubated with the AMP maculatin 1.1 (Mac1) in combination with novel nitroxide spin-labeled peptides 2,2,6,6-tetramethylpiperidine-N-oxyl-4-amino-4-carboxylic acid (TOAC)-[F3W]-Mac1 (MacW) and TOAC-TOAC-MacW. The in-cell 13C and 15N signal NMR enhancements, and 1H spin-lattice T1 relaxation times showed that TOAC-MacW and TOAC-TOAC-MacW performed better than the more hydrophilic biradical AMUPol used for DNP studies. Furthermore, the pores formed by the AMP increased the signal enhancements and decreased T1 values of specifically 13C- and 15N-labeled Mac1. This approach has a great potential for determining the first in situ structures of AMPs in bacteria.-Sani, M.-A., Zhu, S., Hofferek, V., Separovic, F. Nitroxide spin-labeled peptides for DNP-NMR in-cell studies.

Peptide antibiotic trichogin in model membranes: Self-association and capture of fatty acids

The antimicrobial action of peptides in bacterial membranes is commonly related to their mode of self-assembling which results in pore formation. To optimize peptide antibiotic use for therapeutic purposes, a study on the concentration dependence of self-assembling process is thus desirable. In this work, we investigate this dependence for peptaibol trichogin GA IV (Tric) in the 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) model membrane in the range of peptide concentrations between 0.5 and 3.3 mol%. Pulsed double electron-electron resonance (PELDOR) applied on spin-labeled peptide analogs highlights the onset of peptide dimerization above a critical peptide concentration value, namely ~ 2 mol%. Electron spin echo (ESE) envelope modulation (ESEEM) for D2O-hydrated bilayers shows that dimerization is accompanied by peptide re-orientation towards a trans-membrane disposition. For spin-labeled stearic acids (5-DSA) in POPC bilayers, the study of ESE decays and ESEEM in the presence of a deuterated peptide analog indicates that above the critical peptide concentration the 5-DSA molecules are attracted by peptide molecules, forming nanoclusters. As the 5-DSA molecules represent a model for the behavior of fatty acids participating in bacterial membrane homeostasis, such capturing action by Tric may represent an additional mechanism of its antibiotic activity.

Epr Spectroscopy of Adsorbed Spin-Labeled Peptides: Immobilization of Trichogin on the Titanium Oxide

The TOAC-spin-labeled peptide Trichogin GA IV adsorbed on the TiO2 surface is studied. It is shown that the continuous wave (CW) electron paramagnetic resonance (EPR) spectrum does not depend on temperature in a wide range of 77–300 K. A pulsed EPR method of electron spin echo (ESE) utilizing a two-pulse sequence (π/2-τ-π) is used to study temperature dependence of the phase relaxation time, TF. The TF values are found to change from 750 ns to 100 ns in the interval of 77–300 K. The pulsed electronelectron double resonance (PELDOR) measurements utilizing the pulse sequence((π/2)A,-T-πB,-(τ-T)-πA) show that the space distribution of spin labels on the surface remains uniform irrespective of the temperature, and provide the fractal dimension of the surface of 2.7±0.1. The obtained results testify that EPR pulse experiments can be used to study adsorbed spin-labeled molecules at room temperatures, i.e. not only at cryogenic temperatures.

Probing Membrane Hydration at the Interface of Self-Assembled Peptide Amphiphiles Using Electron Paramagnetic Resonance.

The relative hydrophilicity at the interface of a nanoparticle was measured utilizing electron paramagnetic resonance (EPR) spectroscopy. The supramolecular structure was assembled from spin-labeled peptide amphiphiles (PA) derived from N-carboxy anhydrides (NCA). Cyanuric chloride, or 2,4,6-trichloro-1,3,5-triazine (TCT), was used as a modular platform to synthesize the spin-labeled, lipid-mimetic macroinitiator used for the ring-opening polymerization of γ-benzyl-l-glutamic acid NCA to produce polyglutamate-b-dodecanethiol2. Through static and dynamic light scattering, as well as transmission electron microscopy, PAs with DP of 50 and 17 were shown to assemble into stable nanoparticles with an average hydrodynamic radius of 117 and 84 nm, respectively. Continuous wave EPR spectroscopy revealed that the mobility parameter (h-1/h0) and 2Aiso of the nitroxide radical increased with increasing pH, in concert with the deprotonation of the PE side chains and associated helix-coil transition. These results are consistent with an increase in the relative hydration and polarity at the nanoparticle interface, which would be dependent on the secondary structure of the polypeptide. This research suggests that a pH stimulus could be used to facilitate water diffusion through the membrane.

ЭПР спектроскопия адсорбированных спин-меченых пептидов: иммобилизация трихогина на диоксиде титана

ЭПР спектроскопия адсорбированных спин-меченых пептидов: иммобилизация трихогина на диоксиде титана

Calcium-Dependent Structural Dynamics of a Spin-Labeled RyR Peptide Bound to Calmodulin

We have used chemical synthesis, electron paramagnetic resonance (EPR), and circular dichroism to detect and analyze the structural dynamics of a ryanodine receptor (RyR) peptide bound to calmodulin (CaM). The skeletal muscle calcium release channel RyR1 is activated by Ca2+-free CaM and inhibited by Ca2+-bound CaM. To probe the structural mechanism for this regulation, wild-type RyRp and four spin-labeled derivatives were synthesized, each containing the nitroxide probe 2,2,6,6-tetramethyl-piperidine-1-oxyl-4-amino-4-carboxylic acid substituted for a single amino acid. In 2,2,6,6-tetramethyl-piperidine-1-oxyl-4-amino-4-carboxylic acid, the probe is rigidly and stereospecifically coupled to the α-carbon, enabling direct detection by EPR of peptide backbone structural dynamics. In the absence of CaM, circular dichroism indicates a complete lack of secondary structure, while 40% trifluoroethanol (TFE) induces >90% helicity and is unperturbed by the spin label. The EPR spectrum of each spin-labeled peptide indicates nanosecond dynamic disorder that is substantially reduced by TFE, but a significant gradient in dynamics is observed, decreasing from N- to C-terminus, both in the presence and absence of TFE. When bound to CaM, the probe nearest RyRp’s N-terminus shows rapid rotational motion consistent with peptide backbone dynamics of a locally unfolded peptide, while the other three sites show substantial restriction of dynamics, consistent with helical folding. The two N-terminal sites, which bind to the C-lobe of CaM, do not show a significant Ca2+-dependence in mobility, while both C-terminal sites, which bind to the N-lobe of CaM, are significantly less mobile in the presence of bound Ca2+. These results support a model in which the interaction of RyR with CaM is nonuniform along the peptide, and the primary effect of Ca2+ is to increase the interaction of the C-terminal portion of the peptide with the N-terminal lobe of CaM. These results provide, to our knowledge, new insight into the Ca2+-dependent regulation of RyR by CaM.

Water accessibility in a membrane-inserting peptide comparing Overhauser DNP and pulse EPR methods.

Water accessibility is a key parameter for the understanding of the structure of biomolecules, especially membrane proteins. Several experimental techniques based on the combination of electron paramagnetic resonance (EPR) spectroscopy with site-directed spin labeling are currently available. Among those, we compare relaxation time measurements and electron spin echo envelope modulation (ESEEM) experiments using pulse EPR with Overhauser dynamic nuclear polarization (DNP) at X-band frequency and a magnetic field of 0.33 T. Overhauser DNP transfers the electron spin polarization to nuclear spins via cross-relaxation. The change in the intensity of the (1)H NMR spectrum of H2O at a Larmor frequency of 14 MHz under a continuous-wave microwave irradiation of the nitroxide spin label contains information on the water accessibility of the labeled site. As a model system for a membrane protein, we use the hydrophobic α-helical peptide WALP23 in unilamellar liposomes of DOPC. Water accessibility measurements with all techniques are conducted for eight peptides with different spin label positions and low radical concentrations (10-20 μM). Consistently in all experiments, the water accessibility appears to be very low, even for labels positioned near the end of the helix. The best profile is obtained by Overhauser DNP, which is the only technique that succeeds in discriminating neighboring positions in WALP23. Since the concentration of the spin-labeled peptides varied, we normalized the DNP parameter ϵ, being the relative change of the NMR intensity, by the electron spin concentration, which was determined from a continuous-wave EPR spectrum.

The Interaction between Influenza HA Fusion Peptide and Transmembrane Domain Affects Membrane Structure

Viral glycoproteins, such as influenza hemagglutinin (HA) and human immunodeficiency virus gp41, are anchored by a single helical segment transmembrane domain (TMD) on the viral envelope membrane. The fusion peptides (FP) of the glycoproteins insert into the host membrane and initiate membrane fusion. Our previous study showed that the FP or TMD alone perturbs membrane structure. Interaction between the influenza HA FP and TMD has previously been shown, but its role is unclear. We used PC spin labels dipalmitoylphospatidyl-tempo-choline (on the headgroup), 5PC and 14PC (5-C and 14-C positions on the acyl chain) to detect the combined effect of FP-TMD interaction by titrating HA FP to TMD-reconstituted 1,2-dimyristoyl-sn-glycero-3-phosphocholine/1,2-dimyristoyl-sn-glycero-3-phospho-(1’-rac-glycerol)/cholesterol lipid bilayers using electron spin resonance. We found that the FP-TMD increases the lipid order at all positions, which has a greater lipid ordering effect than the sum of the FP or TMD alone, and this effect reaches deeper into the membranes. Although HA-mediated membrane fusion is pH dependent, this combined effect is observed at both pH 5 and pH 7. In addition to increasing lipid order, multiple components are found for 5PC at increased concentration of FP-TMD, indicating that distinct domains are induced. However, the mutation of Gly1 in the FP and L187 in the TMD eliminates the perturbations, consistent with their fusogenic phenotypes. Electron spin resonance on spin-labeled peptides confirms these observations. We suggest that this interaction may provide a driving force in different stages of membrane fusion: initialization, transition from hemifusion stalk to transmembrane contact, and fusion pore formation.

Influenza Fusion Peptide and Transmembrane Domain Interaction Induces Distinct Domains in Lipid Bilayers

Viral glycoproteins, such as influenza HA2 and HIV gp41, are anchored by a single helical segment transmembrane domain (TMD) on the viral envelope membrane. The function of the TMD's is still unclear, but it is speculated to be involved in the final steps of membrane fusion. The interactions between the influenza HA fusion peptide (FP) and the TMD, as well as the HIV gp41 FP and TMD have previously been shown. We found that the FP or TMD alone perturbs membrane structure. We hypothesized that the FP-TMD interaction will further change the membrane structure which provides a driving force for the fusion between the inner membranes. We used PC spin labels DPPTC (on the head group), 5PC and 14PC (5-C and 14-C positions on the acyl chain) to detect the perturbation by titrating the FP to TMD-reconstituted POPC/POPG/Chol lipid bilayers by ESR. We found that the FP increases the lipid order in all positions. In addition to the increase of lipid order, multiple components are found for 5PC when the concentration of FP increases, indicating that distinct domains are induced. The FP or TMD alone does not induce this change. Therefore, this domain formation should be an effect of FP-TMD interaction. Although HA-mediated membrane fusion is pH dependent, the domain formation is observed at both pH5 and pH7. The mutations on TMD do not affect the domain formation. However, the deletion of G1 in the FP eliminates all perturbations. We conclude that the influenza FP-TMD interaction induces distinct domains in the lipid bilayers, which is pH independent but relies on the glycine ridge in the N-terminal helix of the FP. We are extending our research on ITC and ESR on spin-labeled peptides to further characterize this interaction.

Simulation of electron paramagnetic resonance spectra of spin-labeled molecules from replica-exchange molecular dynamics

We report a general approach for the simulation of the electron paramagnetic resonance (EPR) spectra of spin labels attached to peptides and proteins directly from replica-exchange molecular dynamics (REMD) trajectories. Conventional MD trajectories are generally inadequate for the prediction of EPR line shapes since the label can become trapped in one or more of a set of rotameric states, thus preventing both conformational sampling and accurate estimates of the exchange rates between different rotamers. The advantage of using REMD is its ability to provide both efficient conformational sampling and kinetic information for spin-label dynamics. Our approach is illustrated with spin-labeled peptide. This approach to REMD-EPR simulation paves the way for the wider application of MD modeling to the simulation and interpretation of EPR spectra of spin-labeled molecules.

Structure and Activity of the Peptidyl-Prolyl Isomerase Domain from the Histone Chaperone Fpr4 toward Histone H3 Proline Isomerization

The FK506-binding protein (FKBP) family of peptidyl-prolyl isomerases (PPIases) is characterized by a common catalytic domain that binds to the inhibitors FK506 and rapamycin. As one of four FKBPs within the yeast Saccharomyces cerevisiae, Fpr4 has been described as a histone chaperone, and is in addition implicated in epigenetic function in part due to its mediation of cis-trans conversion of proline residues within histone tails. To better understand the molecular details of this activity, we have determined the solution structure of the Fpr4 C-terminal PPIase domain by using NMR spectroscopy. This canonical FKBP domain actively increases the rate of isomerization of three decapeptides derived from the N terminus of yeast histone H3, whereas maintaining intrinsic cis and trans populations. Observation of the uncatalyzed and Fpr4-catalyzed isomerization rates at equilibrium demonstrate Pro(16) and Pro(30) of histone H3 as the major proline targets of Fpr4, with little activity shown against Pro(38). This alternate ranking of the three target prolines, as compared with affinity determination or the classical chymotrypsin-based fluorescent assay, reveals the mechanistic importance of substrate residues C-terminal to the peptidyl-prolyl bond.

Spin‐Echo Electron Paramagnetic Resonance (EPR) Spectroscopy of a Pore‐Forming (Lipo)Peptaibol in Model and Bacterial Membranes

This review compiles the unusual structural and dynamic peculiarities of trichogin GA IV and its analogs in lipid bilayers. Different electron spin echo (ESE) spectroscopic techniques were employed to study a set of spin-labeled analogs of trichogin GA IV in model and natural membranes. Pulsed electron-electron double resonance (PELDOR) method enabled the elucidation of the peptide conformation, while the ESE envelope modulation (ESEEM) technique was applied to study the insertion of the site-specifically spin-labeled peptide into the core of the membrane. The latter technique was also used to examine the water accessibility for peptide-attached spin labels at different levels of membrane depth. Finally, it will be shown that measurement of the ESE decays at different temperatures reveals molecular information on the mobility of the transmembrane lipopeptide aggregate. The experimental results are discussed in terms of the antibiotic and toxic activities of trichogin GA IV.

Investigation of Model Membrane Disruption Mechanism by Melittin using Pulse Electron Paramagnetic Resonance Spectroscopy and Cryogenic Transmission Electron Microscopy

Studies of membrane peptide interactions at the molecular level are important for understanding essential processes such as membrane disruption or fusion by membrane active peptides. In a previous study, we combined several electron paramagnetic resonance (EPR) techniques, particularly continuous wave (CW) EPR, electron spin echo envelope modulation (ESEEM), and double electron-electron resonance (DEER) with Monte Carlo (MC) simulations to probe the conformation, insertion depth, and orientation with respect to the membrane of the membrane active peptide melittin. Here, we combined these EPR techniques with cryogenic transmission electron microscopy (cryo-TEM) to examine the effect of the peptide/phospholipid (P/PL) molar ratio, in the range of 1:400 to 1:25, on the membrane shape, lipids packing, and peptide orientation and penetration. Large unilamellar vesicles (LUVs) of DPPC/PG (7:3 dipalmitoylphosphatidylcholine/egg phosphatidylglycerol) were used as model membranes. Spin-labeled peptides were used to probe the peptide behavior whereas spin-labeled phspholipids were used to examine the membrane properties. The cryo-TEM results showed that melittin causes vesicle rupture and fusion into new vesicles with ill-defined structures. This new state was investigated by the EPR methods. In terms of the peptide, CW EPR showed decreased mobility, and ESEEM revealed increased insertion depth as the P/PL ratio was raised. DEER measurements did not reveal specific aggregates of melittin, thus excluding the presence of stable, well-defined pore structures. In terms of membrane properties, the CW EPR reported reduced mobility in both polar head and alkyl chain regions with increasing P/PL. ESEEM measurements showed that, as the P/PL ratio increased, a small increase in water content in the PL headgroup region took place and no change was observed in the alkyl chains part close to the hydrophilic region. In terms of lipid local density, opposite behavior was observed for the polar head and alkyl chain regions with increasing P/PL; while the DPPC density increased in the polar head region, it decreased in the alkyl chain region. These results are consistent with disruption of the lipid order and segregation of the PL constituents of the membrane as a consequence of the melittin binding. This work further demonstrates the applicability and potential of pulse EPR techniques for the study of peptide-membrane interactions.

In Silico Interpretation of cw-ESR at 9 and 95 GHz of Mono- and bis- TOAC-Labeled Aib-Homopeptides in Fluid and Frozen Acetonitrile

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.

Conformation of peptides bound to the transporter associated with antigen processing (TAP)

The ATP-binding cassette transporter associated with antigen processing (TAP) plays a key role in the adaptive immune defense against infected or malignantly transformed cells by translocating proteasomal degradation products into the lumen of the endoplasmic reticulum for loading onto MHC class I molecules. The broad substrate spectrum of TAP, rendering peptides from 8 to 40 residues, including even branched or modified molecules, suggests an unforeseen structural flexibility of the substrate-binding pocket. Here we used EPR spectroscopy to reveal conformational details of the bound peptides. Side-chain dynamics and environmental polarity were derived from covalently attached 2,2,5,5-tetramethylpyrrolidine-1-oxyl spin probes, whereas 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid spin-labeled peptides were used to detect backbone properties. Dependent on the spin probe's position, striking differences in affinity, dynamics, and polarity were found. The side-chains' mobility was strongly restricted at the ends of the peptide, whereas the central region was flexible, suggesting a central peptide bulge. In the end, double electron electron resonance allowed the determination of intrapeptide distances in doubly labeled peptides bound to TAP. Simulations based on a rotamer library led to the conclusion that peptides bind to TAP in an extended kinked structure, analogous to those bound to MHC class I proteins.