Affinity of nonhomologous amphiphilic peptides toward a monoclonal antibody raised against apolipoprotein A-I

Monoclonal antibodies against human apolipoprotein A-I (apoA-I) were generated by the hybridoma technique. Clone G-10 was selected on the basis of its highest titer. The affinity of this antibody toward a series of synthetic peptides differing in length, amino acid composition, and amphiphilicity was tested by using both the indirect and the competitive enzyme-linked immunosorbent techniques (ELISA). From these measurements we calculated dissociation constants of the complexes of the antibody with apoA-I bound to the surface of the microtiter plate, apoA-I in solution, and any of the several peptides in solution. The dissociation constant (Kd) of the immobilized apoA-I/anti-apoA-I-complex, Kd = 2 x 10(-9) M, was significantly lower than that of the complex resulting from the interaction between anti-apoA-I and either apoA-I in solution or any of the several amphiphilic helical peptides in solution. Peptides devoid of amphiphilic secondary structure were inert. These data are consistent with the proposal that monoclonal G-10 recognizes in antigenic peptides an alpha-helical secondary structure of defined hydrophilic-lipophilic balance and comparatively less the specific amino acid side chains. We propose that the highest contribution to the free energy of binding (8 Kcal/mole) is derived from the docking of the helix to the antibody. It follows that in probing the specificity of a monoclonal antibody the conformation and the physical environment of the interacting antigen must be taken into account.     

Secondary structures of peptides: 5 · 15N n.m.r. CP/MAS spectroscopy of solid polypeptides and gramicidin-S

30.5 MHz ¹⁵N m.m.r. (CP/MAS) spectra of various solid polypeptides were measured using the cross-polarization/magic angle spinning technique. In order to obtain optimum signal-to-noise ratios, relatively short contact times (1 ± 0.5 ms) are required, because the cross-polarization times (T_NH) are short and because the proton rotating-frame relaxation times (T_1p) are in the order of 20 ms. The ¹⁵N n.m.r. signals of copolypeptides may be sensitive to sequence effects; yet they are in most cases more sensitive to the nature of the secondary structure. The signals of α-helices absorb ca. 8–10 ppm upfield of β-sheet structures, whereas the polyglycine II helix absorbs downfield. The natural abundance spectrum of crystalline gramicidin-S exhibits a signal at ?247 ppm, a characteristic chemical shift of the antiparallel pleated sheet structure.     

Orientations of amphipathic helical peptides in membrane bilayers determined by solid-state NMR spectroscopy

Summary Solid-state NMR spectroscopy was used to determine the orientations of two amphipathic helical peptides associated with lipid bilayers. A single spectral parameter provides sufficient orientational information for these peptides, which are known, from other methods, to be helical. The orientations of the peptides were determined using the¹⁵N chemical shift observed for specifically labeled peptide sites. Magainin, an antibiotic peptide from frog skin, was found to lie in the plane of the bilayer. M2, a helical segment of the nicotinic acetylcholine receptor, was found to span the membrane, perpendicular to the plane of the bilayer. These findings have important implications for the mechanisms of biological functions of these peptides.     

Conformational studies on poly(N-δ-trimethyl-l-ornithine)

$\text{Poly}\text{(N-δ-}\text{trimethyl-}\text{l}\text{-ornithine}$), (Me₃Orn)_n, is usually not able to attain the α-helical conformation in aqueous solution independent of its pH value; however, it becomes α-helical at low concentrations of sodium perchlorate over a wide pH range according to the circular dichorism (c.d.) spectra. Cl^?, SO₄^2? and H₂PO₄^? do not induce α-helix formation. One can conclude that a distinct topology of the anions bound by the side chains is responsible for the α-helix-inducing effect of some water-structure-breaking anions such as perchlorate. This means that the anions are inserted between the ?N⁺ of the side groups shielding the positive charges repelling one another. The insertion of the anions requires that the water molecules surrounding the ions can be stripped off, which is easily possible if they are water-structure-breaking ones. At higher perchlorate concentrations, the c.d. spectrum changes. It is characterized by a negative shoulder near 208 nm and a pronounced minimum at ≈ 226 nm. With increasing temperature, the c.d. spectrum of the α-helix occurs. Finally the α-helix undergoes a conformational change to the random coil. The apparent transition enthalpy ΔH_vH is remarkably lower than that of the homologue (Me₃Lys)_n, obviously due to a lower cooperativity of the transition. In contrast to poly(l-ornithine), (Orn)_n, the c.d. spectrum of (Me₃Orn)_n remains almost unchanged after adding anionic surfactants such as sodium octyl sulphate (SOS) or sodium dodecyl sulphate (SDS). In organic solvents like methanol or isopropanol, in contrast to (Orn)_a and (Lys)_n, no α-helix formation occurs. However, in mixtures of these alcohols or dioxane with water, α-helix formation is induced by perchlorate, as in pure water. The thermal stability of the α-helix in these systems is increased.     

Human endothelial cells contain one type of plasminogen activator

RNA-binding protein kinase from amphibian oocytes modifies serine and threonine residues in the molecules of substrates and utilizes both ATP and GTP. Low concentrations of heparin inhibit protein kinase. The foregoing suggests that this enzyme is casein kinase II. It is shown that RNA-binding proteins lack active forms of phosphatases and proteases which may affect the results of phosphorylation of both endogenous and exogenous substrates.     

Characterization of proline-containing α-helix (helix F model of bacteriorhodopsin) by molecular dynamics studies

Many of the bilayer spanning segments of membrane transport proteins contain proline residues, and most of them are believed to occur in α-helical form. A proline residue in the middle of an α-helix is known to produce a bend in the helix, and recent studies have focused on characterizing such a bend at atomic level. In the present case, molecular dynamics (MD) studies are carried out on helix F model of bacteriorhodopsin (BR) Ace-(Ala)₇-Trp-(Ala)₂-Tyr-Pro-(Ala)₂-Trp-(Ala)₈-NHMe and compared with Ace-(Ala)₇-Trp-(Ala)₂-Tyr-(Ala)₃-Trp-(Ala)₈-NHMe in which the proline is replaced by alanine. The bend in the helix is characterized by structural parameters such as kink angle (α), wobble angle (θ), virtual torsion angle (ρ), and the hydrogen bond distance d (O_p?3 … N_p+1). The average values and the flexibility involved in these parameters are evaluated. The correlation among the bend related parameters are estimated. The equilibrium side chain orientations of tryptophan and tyrosine residues are discussed and compared with those found in the recently proposed model of bacteriorhodopsin. Finally, a detailed characterization of the bend in terms of secondary structures such as α_I, α_II and goniometric helices are discussed, which can be useful in the interpretation of the experimental results on the secondary structures of membrane proteins involving the proline residue. © 1993 Wiley-Liss, Inc.     

Crystal Structure of the Multidrug Exporter MexB from Pseudomonas aeruginosa

We report here the crystal structure of the Pseudomonas aeruginosa multidrug exporter MexB, an intensively studied member of the resistance-nodulation-cell division family of secondary active transporters, at 3.0 Å. MexB forms an asymmetric homotrimer where each subunit adopts a different conformation representing three snapshots of the transport cycle similar to the recently determined structures of its close homologue AcrB from Escherichia coli, so far the sole structurally characterized member of the superfamily. As for AcrB, the conformations of two subunits can be clearly assigned to either the binding step or the extrusion step in the transport process. Unexpectedly, a remarkable conformational shift in the third subunit is observed in MexB, which has potential implications for the assembly of the tripartite MexAB-OprM drug efflux system. Furthermore, an n-dodecyl-d-maltoside molecule was found bound to the internal multidrug-binding cavity, which might indicate that MexB binds and transports detergent molecules as substrates. As the only missing piece of the puzzle in the MexAB-OprM system, the X-ray structure of MexB completes the molecular picture of the major pump mediating intrinsic and acquired multidrug resistance in P. aeruginosa.     

The Ferritin-like superfamily: Evolution of the biological iron storeman from a rubrerythrin-like ancestor

Background

The Ferritins are part of the extensive ‘Ferritin-like superfamily’ which have diverse functions but are linked by the presence of a common four-helical bundle domain. The role performed by Ferritins as the cellular repository of excess iron is unique. In many ways Ferritins act as tiny organelles in their ability to secrete iron away from the delicate machinery of the cell, and then to release it again in a controlled fashion avoiding toxicity. The Ferritins are ancient proteins, being common in all three domains of life. This ubiquity reflects the key contribution that Ferritins provide in achieving iron homeostasis.

Scope of the review

This review compares the features of the different Ferritins and considers how they, and other members of the Ferritin-like superfamily, have evolved. It also considers relevant features of the eleven other known families within the Ferritin-like superfamily, particularly the highly diverse rubrerythrins.

Major conclusions

The Ferritins have travelled a considerable evolutionary journey, being derived from far more simplistic rubrerythrin-like molecules which play roles in defence against toxic oxygen species. The forces of evolution have moulded such molecules into three distinct types of iron storing (or detoxifying) protein: the classical and universal 24-meric ferritins; the haem-containing 24-meric bacterioferritins of prokaryotes; and the prokaryotic 12-meric Dps proteins. These three Ferritin types are similar, but also possess unique properties that distinguish them and enable then to achieve their specific physiological purposes.

General significance

A wide range of biological functions have evolved from a relatively simple structural unit.     

Evolutionary origin of a secondary structure: π-helices as cryptic but widespread insertional variations of α-helices that enhance protein functionality

Formally annotated π-helices are rare in protein structures but have been correlated with functional sites. Here, we analyze protein structures to show that π-helices are the same as structures known as α-bulges, α-aneurisms, π-bulges, and looping outs, and are evolutionarily derived by the insertion of a single residue into an α-helix. This newly discovered evolutionary origin explains both why π-helices are cryptic, being rarely annotated despite occurring in 15% of known proteins, and why they tend to be associated with function. An analysis of π-helices in the diverse ferritin-like superfamily illustrates their tendency to be conserved in protein families and identifies a putative π-helix-containing primordial precursor, a “missing link” intermediary form of the ribonucleotide reductase family, vestigial π-helices, and a novel function for π-helices that we term a “peristaltic-like shift.” This new understanding of π-helices paves the way for this generally overlooked motif to become a noteworthy feature that will aid in tracing the evolution of many protein families, guide investigations of protein and π-helix functionality, and contribute additional tools to the protein engineering toolkit.