Structure In Trifluoroethanol Research Articles

Unusual structural transition of antimicrobial VP1 peptide

VP1 peptide, an active domain of m-calpain enzyme with antimicrobial activity is found to undergo an unusual conformational transition in trifluoroethanol (TFE) solvent. The nature of, and time dependent variations in, circular dichroism associated with the amide I vibrations, suggest that VP1 undergoes self-aggregation forming anti-parallel β-sheet structure in TFE. Transmission electron micrograph (TEM) images revealed that β-sheet aggregates formed by VP1 possess fibril-like assemblies.

Evaluation of lipid‐binding properties of the N‐terminal helical segments in human apolipoprotein A‐I using fragment peptides

Although the N-terminal region in human apolipoprotein (apo) A-I is thought to stabilize the lipid-free structure of the protein, its role in lipid binding is unknown. Using synthetic fragment peptides, we examined the lipid-binding properties of the first 43 residues (1-43) of apoA-I in comparison with residues 44-65 and 220-241, which have strong lipid affinity in the molecule. Circular dichroism measurements demonstrated that peptides corresponding to each segment have potential propensity to form alpha-helical structure in trifluoroethanol. Spectroscopic and thermodynamic measurements revealed that apoA-I (1-43) peptide has the strong ability to bind to lipid vesicles and to form alpha-helical structure comparable to apoA-I (220-241) peptide. Substitution of Tyr-18 located at the center of the most hydrophobic region in residues 1-43 with a helix-breaking proline resulted in the impaired lipid binding, indicating that the alpha-helical structure in this region is required to trigger the lipid binding. In contrast, apoA-I (44-65) peptide exhibited a lower propensity to form alpha-helical structure upon binding to lipid, and apoA-I (44-65/S55P) peptide exhibited diminished, but not completely impaired, lipid binding, suggesting that the central region of residues 44-65 is not pivotally involved in the formation of the alpha-helical structure and lipid binding. These results indicate that the most N-terminal region of apoA-I molecule, residues 1-43, contributes to the lipid interaction of apoA-I through the hydrophobic helical residues.

Elastic Protein-Based Polymers a Step Towards Plasticity: Thermal Stability of Glu-Containing Co-Polypeptides as Analyzed by Differential Scanning Calorimetry

Plastic protein-based polymers with the same conformational potential, but with different degree of thermal stability have been synthesized and thermally characterized by differential scanning calorimetry to provide the conception of behavior of thermoplasticity. Dramatic increase in the temperature between melting and decomposition transitions has been observed, upon inclusion of glutamic acid residue into the hydrophobic sequence of FVGVP. Glu-containing co-polymers of IVGVP showed a markedly different behavior by exhibiting exothermic crystallization transition before melting shows the typical thermoplasticity. Secondary structure in trifluoroethanol for all the polymers show, a well behaved alpha-helix as evident from the circular dichroism studies, in association with a significant amount of random structure contributes to extended stability.

Binding of copper (II) ion to an Alzheimer's tau peptide as revealed by MALDI‐TOF MS, CD, and NMR

The tau protein plays an important role in some neurodegenerative diseases including Alzheimer's disease (AD). Neurofibrillary tangles (NFTs), a biological marker for AD, are aggregates of bundles of paired helical filaments (PHFs). In general, the alpha-sheet structure favors aberrant protein aggregates. However, some reports have shown that the alpha-helix structure is capable of triggering the formation of aberrant tau protein aggregates and PHFs have a high alpha-helix content. In addition, the third repeat fragment in the four-repeat microtubule-binding domain of the tau protein (residues 306-336: VQIVYKPVDLSKVTSKCGSLGNIHHKPGGGQ, according to the longest tau protein) adopts a helical structure in trifluoroethanol (TFE) and may be a self-assembly model in the tau protein. In the human brain, there is a very small quantity of copper, which performs an important function. In our study, by means of matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS), circular dichroism (CD), and nuclear magnetic resonance (NMR) spectroscopy, the binding properties of copper (II) ion to the R3 peptide derived from the third repeat fragment (residues 318-335: VTSKCGSLGNIHHKPGGG) have been investigated. The results show that copper ions bind to the R3 peptide. CD spectra, ultraviolet (UV)-visible absorption spectra, and MALDI-TOF MS show pH dependence and stoichiometry of Cu2+ binding. Furthermore, CD spectra and NMR spectroscopy elucidate the copper binding sites located in the R3 peptide. Finally, CD spectra reveal that the R3 peptide adopts a mixture structure of random structures, alpha-helices, and beta-turns in aqueous solutions at physiological pH. At pH 7.5, the addition of 0.25 mol eq of Cu2+ induces the conformational change from the mixture mentioned above to a monomeric helical structure, and a beta-sheet structure forms in the presence of 1 mol eq of Cu2+. As alpha-helix and beta-sheet structures are responsible for the formation of PHFs, it is hypothesized that Cu2+ is an inducer of self-assembly of the R3 peptide and makes the R3 peptide form a structure like PHF. Hence, it is postulated that Cu2+ plays an important role in the aggregation of the R3 peptide and tau protein and that copper (II) binding may be another possible involvement in AD.

Conformational analysis by NMR and distance geometry techniques of a peptide mimetic of the third helix of the Antennapedia homeodomain*

The Antennapedia homeodomain structure consists of four helices. The helices II and III are connected by a tripeptide that forms a turn, and constitute the well-known helix-turn-helix motif. The recognition helix penetrates the DNA major groove, gives specific protein-DNA contacts and forms direct, or water-mediated, intermolecular hydrogen bonds. It was suggested that helix III (and perhaps also helix IV) might represent the recognition helix of Antennapedia homeodomain, which makes contact with the surface of the major groove of the DNA. In an attempt to clarify the helix III capabilities of assuming an helical conformation when separated from the rest of the protein, we carried out the structural determination of the recognition helix III in different solvent media. The conformational study of fragments 42-53, where residues W48 and F49, not involved in the protein-DNA interaction, were substituted by two alanines, was conducted in sodium dodecyl sulfate (SDS), trifluoroethanol (TFE) and TFE/water, using circular dichroism, nuclear magnetic resonance (NMR) and distance geometry (DG) techniques. The fragment assumes a well-defined secondary structure in TFE and in TFE/water (90/10, v/v) with an alpha-helix encompassing residues 4-9, while in TFE/water (70/30, v/v) a less regular structure was found. The DG results in the micellar system evidence the presence of a distorted alpha-helical conformation involving residues 4-8. Our results reveal that the isolated Antennapedia recognition helix III tend to preserve in solution the alpha-helical conformation even if separated from the rest of the molecule.

Membrane-inserted conformation of transmembrane domain 4 of divalent-metal transporter.

Divalent-metal transporter 1 (DMT1) is involved in the intestinal iron absorption and in iron transport in the transferrin cycle. It transports metal ions at low pH ( approximately 5.5), but not at high pH (7.4), and the transport is a proton-coupled process. Previously it has been shown that transmembrane domain 4 (TM4) is crucial for the function of this protein. Here we provide the first direct experimental evidence for secondary-structural features and membrane insertions of a 24-residue peptide, corresponding to TM4 of DMT1 (DMTI-TM4), in various membrane-mimicking environments by the combined use of CD and NMR spectroscopies. The peptide mainly adopts an alpha-helical structure in trifluoroethanol, SDS and dodecylphosphocholine micelles, and dimyristoyl phosphatidylcholine and dimyristoyl phosphatidylglycerol small unilamellar vesicles. It has been demonstrated from both Halpha secondary shifts and nuclear-Overhauser-enhancement (NOE) connectivities that the peptide is well folded into an alpha-helix from Val(8) to Lys(23) in SDS micelles at pH 4.0, whereas the N-terminus is highly flexible. The alpha-helical content estimated from NMR data is in agreement with that extracted from CD simulations. The highest helicity was observed in the anionic phospholipids [1,2-dimyristoyl- sn -glycero-3-[phospho-rac -(1-glycerol)]], indicating that electrostatic attraction is important for peptide binding and insertion into the membranes. The secondary-structural transition of the peptide occurred at pH 4.3 in the 2,2,2-trifluoroethanol (TFE) water mixed solvent, whereas at a higher pH value (5.6) in SDS micelles, DMT1-TM4 exhibited a more stable structure in SDS micelles than that in TFE in terms of changing the pH and temperature. PAGE did not show high-molecular-mass aggregates in SDS micelles. The position of the peptide relative to SDS micelles was probed by the effects of 5- and 16-doxylstearic acids on the intensities of the peptide proton resonances. The results showed that the majority of the peptide is inserted into the hydrophobic interior of SDS micelles, whereas the C-terminal residues are surface-exposed. The ability of DMT1-TM4 to assume transmembrane features may be crucial for its biological function in vivo.

Dissecting the effect of trifluoroethanol on ribonuclease A. Subtle structural changes detected by nonspecific proteases.

With the aim to distinguish between local and global conformational changes induced by trifluoroethanol in RNase A, spectroscopic and activity measurements in combination with proteolysis by unspecific proteases have been exploited for probing structural transitions of RNase A as a function of trifluoroethanol concentration. At > 30% (v/v) trifluoroethanol (pH 8.0; 25 degrees C), circular dichroism and fluorescence spectroscopy indicate a cooperative collapse of the tertiary structure of RNase A coinciding with the loss of its enzymatic activity. In contrast to the denaturation by guanidine hydrochloride, urea or temperature, the breakdown of the tertiary structure in trifluoroethanol is accompanied by an induction of secondary structure as detected by far-UV circular dichroism spectroscopy. Proteolysis with the nonspecific proteases subtilisin Carlsberg or proteinase K, both of which attack native RNase A at the Ala20-Ser21 peptide bond, yields refined information on conformational changes, particularly in the pretransition region. While trifluoroethanol at concentrations > 40% results in a strong increase of the rate of proteolysis and new primary cleavage sites (Tyr76-Ser77, Met79-Ser80) were identified, the rate of proteolysis at trifluoroethanol concentrations < 40% (v/v) is much smaller (up to two orders of magnitude) than that of the native RNase A. The proteolysis data point to a decreased flexibility in the surrounding of the Ala20-Ser21 peptide bond, which we attribute to subtle conformational changes of the ribonuclease A molecule. These changes, however, are too marginal to alter the overall catalytic and spectroscopic properties of ribonuclease A.

Structural study of novel antimicrobial peptides, nigrocins, isolated from Rana nigromaculata

Novel cationic antimicrobial peptides, named nigrocin 1 and 2, were isolated from the skin of Rana nigromaculata and their amino acid sequences were determined. These peptides manifested a broad spectrum of antimicrobial activity against various microorganisms with different specificity. By primary structural analysis, it was revealed that nigrocin 1 has high sequence homology with brevinin 2 but nigrocin 2 has low sequence homology with any other known antimicrobial peptides. To investigate the structure–activity relationship of nigrocin 2, which has a unique primary structure, circular dichroism (CD) and homonuclear nuclear magnetic resonance spectroscopy (NMR) studies were performed. CD investigation revealed that nigrocin 2 adopts mainly an α-helical structure in trifluoroethanol (TFE)/H 2O solution, sodium dodecyl sulfate (SDS) micelles, and dodecylphosphocholine micelles. The solution structures of nigrocin 2 in TFE/H 2O (1:1, v/v) solution and in SDS micelles were determined by homonuclear NMR. Nigrocin 2 consists of a typical amphipathic α-helix spanning residues 3–18 in both 50% TFE solution and SDS micelles. From the structural comparison of nigrocin 2 with other known antimicrobial peptides, nigrocin 2 could be classified into the family of antimicrobial peptides containing a single linear amphipathic α-helix that potentially disrupts membrane integrity, which would result in cell death.

Biological activities of retro and diastereo analogs of a 13‐residue peptide with antimicrobial and hemolytic activities

The biological activities of synthetic retro and diastereo analogs of PKLLKTFLSKWIG (SPFK), a 13-residue peptide with antimicrobial and hemolytic activities, have been investigated. Retro peptides with C-terminal acid and amide exhibited antibacterial activities comparable with those of SPFK. Their hemolytic activities were, however, only marginally lower. The diastereo analog with C-terminal acid was not antibacterial and was weakly hemolytic. Amidation of this analog could restore antibacterial activity. Both retro analogs were unordered in aqueous medium but had a propensity for a helical structure in trifluoroethanol. However, diastereo analogs were unordered in both aqueous medium and trifluoroethanol. Thus, reversing the sequence in a short amphiphilic peptide may not always result in the selective loss of biological activity such as hemolytic activity. Also, introduction of enantiomeric amino acids in a short peptide to generate a diastereomer may result in loss of structure as well as antimicrobial and hemolytic activities, unless compensated by an increase in positive charges.

End-to-end distance distribution in bradykinin observed by Förster resonance energy transfer

Förster resonance energy transfer (FRET) was used to study the conformational dynamics of bradykinin related peptides. The fluorescent probe aminobenzoic acid (Abz) bound to the amino terminal of bradykinin maintained its fluorescence characteristics, like high quantum yield and excited state decay dominated by a lifetime of 8.3 ns. The binding of the acceptor group N-[2,4-dinitrophenyl]-ethylenediamine (EDDnp) to the carboxy terminal of Abz labeled bradykinin resulted in a drastic decrease of the fluorescence intensity and in a fastening of the excited state decay. The change of the decay kinetics to an heterogeneous process, precludes the use of energy transfer models based on a single fixed distance between donor and acceptor. The computational package CONTIN was employed to the analysis of time-resolved fluorescence data, allowing the recovery of a distance distribution between donor and acceptor corresponding to the end-to-end distance of the labeled peptide. The distance distribution reflects the occurrence of distinct conformations for the peptide, that coexist in equilibrium during the fluorescence lifetime. We observed three distance populations for bradykinin in water, that merged to two populations when the solvent was trifluoroethanol (TFE). The results were consistent with those obtained from circular dichroism spectroscopy, that showed structural flexibility in water and the presence of more defined secondary structure in TFE. We also studied several peptides related to bradykinin, and the results emphasized the formation of turns involving the proline residues and the decrease of conformational flexibility induced by using TFE as the solvent.

Conformational Studies of a Synthetic Peptide from the Putative Lipid-binding Domain of Bovine Milk Component PP3

In bovine milk, a glycosylated phosphoprotein, component PP3, is known for its remarkable emulsifying properties and its capability to inhibit lipolytic activities. The determination of its primary structure is not sufficient to explain these properties. Secondary structure predictions of component PP3 and of its homologous proteins were achieved using a combination of multiple predictive methods. Based on this study, the f 119–135 region of component PP3 was proposed to be likely to adopt an amphipathic helical conformation, which is a lipid-binding motif. The conformation of the synthetic peptide corresponding to the C-terminal f 119–135 part of bovine component PP3 was analyzed by circular dichroism experiments using various media. The circular dichroism data indicated that the peptide was able to form an amphipathic α-helix structure in trifluoroethanol as well as in the presence of sodium dodecyl sulfate or acidic and neutral lipids, but not in water. Moreover, the conformation of this peptide is solvent dependent because it was found to adopt a β-sheet structure for low concentrations of sodium dodecyl sulfate or a low molar ratio of acidic lipid to peptide. Tensiometric measurements showed that the amphipathic C-terminal region of component PP3 is highly tensioactive and, thus, must be responsible for the particular behavior of the protein in emulsions.

Trifluoroethanol-induced Stabilization of the α-Helical Structure of β-Lactoglobulin: Implication for Non-hierarchical Protein Folding

Trifluoroethanol (TFE) is known to stabilize the α-helical structure in proteins and their fragments. However, the relationship between the TFE-induced structures and the native structure is not clear. Here we show that β-lactoglobulin, which consists predominantly of β-sheets, exhibited a markedly high propensity to form an α–-helical structure in the presence of TFE, as measured by far-UV circular dichroism. A cooperative transformation from the β-sheet structure to an α-helical structure occurred at a TFE concentration between 10% and 20%. These results were in contrast to a gradual β-sheet to α-helix transition of the constant fragment of the immunoglobulin light chain, which is also a β-sheet protein. To understand the significance of the high helical propensity of β-lactoglobulin we measured the LTFE-induced conformational transition of more than 20 proteins of various secondary structural types. Whereas the α-helical proteins showed a propensity to form an extensive helical structure in TFE, the helical propensity of proteins with a low helical content in the native state varied. The helical content in TFE was correlated more with the helical content predicted by a secondary structure prediction than with the helical content of the native structure, suggesting that the stability of the helical structure in TFE is determined by local interactions between nearby amino acid residues. Our results suggest that an α-helical intermediate can accumulate during the refolding process of β-lactoglobulin and that a hierarchical model of protein folding is not necessarily true for some β-sheet proteins including β-lactoglobulin.

Interactions of N-terminal fragments of groups I and II phospholipases A 2 with phospholipid bilayers and their surface recognition properties

In order to elucidate the roles of the N-terminal segments of groups I and II phospholipases A 2 (PLA 2s) which have been known to have α-helical structure and have been assumed to be involved in the water/lipid interface recognition site, the peptides corresponding to the N-terminal moieties of group I PLA 2 ( Naja naja atra) and group II PLA 2s ( Trimeresurus flavoviridis and Crotalus atrox) were synthesized and their interactions with model membranes were studied. Circular dichroism spectra showed that N-terminal peptides of both groups I and II PLA 2s took α-helical structure in trifluoroethanol but no significant secondary structure in buffer (pH 8.0). In the presence of acidic liposomes, N-terminal fragments of group II PLA 2s formed α-helical structure, while that of group I PLA 2 remained unaffected. The hydrophobic moments showed that amphipathicities of N-teriminal fragments of group II PLA 2s are evidently larger than those of N-terminal fragments of group I PLA 2s. The leakage of carboxyfluorescein from acidic liposomes was induced only with group II PLA 2 peptides. Large blue shift and increase in intensity of tryptophan fluorescence were also observed for group II PLA 2 peptides when interacting with acidic liposomes. Such difference in the modes of interactions with lipid bilayers between N-terminal peptides of groups I and II PLA 2s appears to be due in large part to the difference in intrinsic α-helix forming properties of their amino acid sequences. It is inferred that N-terminal amphipathic α-helical structures of group I PLA 2s are possibly formed by assistance of a neighboring chain bridged by Cys-11 and Cys-77.

Solution Structure of a Peptide Designed on Plastocyanin Metal Center in Trifluoroethanol and Incorporation of Cobalt(II) into the Peptide

Abstract A novel sixteen amino acid peptide which has a portion of the conserved amino acid sequence of potato plastocyanin was synthesized. Its solution structure in trifluoroethanol (TFE) was determined by 1H NMR spectroscopy. Incorporation of cobalt(II) ion into the peptide having a turn structure was examined. Cys6, His9, and Met14 of the peptide in TFE are located close to each other and suitable to bind a metal ion. Incorporation of Co(II) ion to the peptide results in formation of tetrahedral coordination site.