Villin-type headpiece domains show a wide range of F-actin-binding affinities.

The villin-type "headpiece" domain is a modular motif found at the extreme C-terminus of larger "core" domains in over 25 cytoskeletal proteins in plants and animals. Although headpiece is classified as an F-actin-binding domain, it has been suggested that some expressed fusion-proteins containing headpiece may lack F-actin-binding in vivo. To determine the intrinsic F-actin affinity of headpiece domains, we quantified the F-actin affinity of seven headpiece domains and three N-terminal truncations, under identical in vitro conditions. The constructs are folded and adopt the native headpiece structure. However, they show a wide range of affinities that can be grouped into high, low, and nonspecific-binding categories. Computer models of the structure and charged surface potential of these headpiece domains suggest features important for high F-actin affinity. We conclude that not all headpiece domains are intrinsically F-actin-binding motifs, and suggest that the surface charge distribution may be an important element for F-actin recognition.

Zinc and copper bind to unique sites of histatin 5.

Metal binding has been suggested to be relevant in the antifungal and antibacterial mechanism of histatin 5, a human salivary protein. Proton nuclear magnetic resonance (NMR) spectra were obtained to investigate the specificity of metal binding to the seven histidyl, one aspartyl and one glutamyl amino acid side-chains of histatin 5 in aqueous solutions. Three C(epsilon1)-H histidyl and the C(gamma)-H glutamyl resonances of histatin 5 were selectively altered in spectra of solutions containing three equivalents of zinc. Copper binding to histatin 5 resulted in a reduced intensity of C(beta)-H aspartyl resonances, while no evidence for calcium binding was found. These results indicate that zinc binding to histatin 5 involves His-15 present within the -H-E-X-X-H- zinc binding motif, and copper binding occurs within the N-terminal D-S-H-, ATCUN motif.

The N-terminal 17% of apoB binds tightly and irreversibly to emulsions modeling nascent very low density lipoproteins.

The N-terminal 17% of apolipoprotein B (apoB-17) readily associates with dimyristoylphosphatidylcholine (DMPC) multilamellar vesicles (MLV) to form large (240-A diameter) discoidal particles. Because apoB is normally secreted with triacylglycerol (TAG)-rich lipoproteins, we studied the binding of apoB-17 to triolein-rich emulsions modeling nascent TAG-rich very low density-like lipoproteins. Emulsions with the following composition (by weight) were prepared: 85--89% triolein, 1.1--1.4% cholesterol, and 10--14% phosphatidylcholines (PC) including either egg yolk (EY)-, dimyristoyl (DM)-, or dipalmitoyl (DP)-PC representing (at 25 degrees C), respectively, a fluid surface, a surface at transition, and a mainly solid surface. The respective sizes were 1,260 +/- 500, 1,070 +/- 450, and 830 +/- 300 A mean diameter. The emulsions were incubated with conditioned medium containing apoB-17, and then reisolated by ultracentrifugation. Analysis of the emulsion-bound proteins by gel electrophoresis showed that all three emulsions bound primarily apoB-17. The DPPC emulsions bound more apoB-17 than EYPC or DMPC emulsions. Immunoaffinity-purified apoB-17 exhibited saturable, high affinity binding to EYPC and DPPC emulsions. The respective K(d) values were 32 +/- 23 and 85 +/- 27 nM and capacities (N) were 10 and 58 molecules of apoB-17 per particle. When apoB-17 bound to emulsions was incubated with DMPC MLV at 26 degrees C for 18 h, it remained bound to the emulsions, indicating that once bound to these emulsions it is unable to exchange off and solubilize DMPC into discs. In contrast, apoE-3 bound to emulsions dissociated from the emulsions when incubated with DMPC MLV and formed discs.Thus, apoB-17 binds strongly and irreversibly to emulsions modeling nascent lipoproteins. It therefore may play an important role in the stabilization of nascent VLDL and chylomicrons.- Herscovitz, H., A. Derksen, M. T. Walsh, C. J. McKnight, D. L. Gantz, M. Hadzopoulou-Cladaras, V. Zannis, C. Curry, and D. M. Small. The N-terminal 17% of apoB binds tightly and irreversibly to emulsions modeling nascent very low density lipoproteins. J. Lipid Res. 2001. 42: 51;-59.

An evolutionary bridge to a new protein fold.

Arc repressor bearing the N11L substitution (Arc-N11L) is an evolutionary intermediate between the wild type protein, in which the region surrounding position 11 forms a beta-sheet, and a double mutant 'switch Arc', in which this region is helical. Here, Arc-N11L is shown to be able to adopt either the wild type or mutant conformations. Exchange between these structures occurs on the millisecond time scale in a dynamic equilibrium in which the relative populations of each fold depend on temperature, solvent conditions and ligand binding. The N11L mutation serves as an evolutionary bridge from the beta-sheet to the helical fold because in the mutant, Leu is an integral part of the hydrophobic core of the new structure but can also occupy a surface position in the wild type structure. Conversely, the polar Asn 11 side chain serves as a negative design element in wild type Arc because it cannot be incorporated into the core of the mutant fold.

NMR structure of an F-actin-binding "headpiece" motif from villin.

A growing family of F-actin-bundling proteins harbors a modular F-actin-binding headpiece domain at the C terminus. Headpiece provides one of the two F-actin-binding sites essential for filament bundling. Here, we report the first structure of a functional headpiece domain. The NMR structure of chicken villin headpiece (HP67) reveals two subdomains that share a tightly packed hydrophobic core. The N-terminal subdomain contains bends, turns, and a four-residue alpha-helix as well as a buried histidine residue that imparts a pH-dependent folding. The C-terminal subdomain is composed of three alpha-helices and its folding is pH-independent. Two residues previously implicated in F-actin-binding form a buried salt-bridge between the N and C-terminal subdomains. The rest of the identified actin-binding residues are solvent-exposed and map onto a unique F-actin-binding surface.

Evolution of a protein fold in vitro.

A "switch" mutant of the Arc repressor homodimer was constructed by interchanging the sequence positions of a hydrophobic core residue, leucine 12, and an adjacent surface polar residue, asparagine 11, in each strand of an intersubunit beta sheet. The mutant protein adopts a fold in which each beta strand is replaced by a right-handed helix and side chains in this region undergo significant repacking. The observed structural changes allow the protein to maintain solvent exposure of polar side chains and optimal burial of hydrophobic side chains. These results suggest that new protein folds can evolve from existing folds without drastic or large-scale mutagenesis.

NMR structure of the 35-residue villin headpiece subdomain.

The NMR structure of an autonomously folding subdomain from villin headpiece is reported. It forms a novel three helix structure with the actin-binding residues arrayed on the C-terminal helix.

A thermostable 35-residue subdomain within villin headpiece.

The actin-bundling protein villin contains, at its extreme C terminus, a compact f-actin binding domain called "headpiece". This 76-amino acid domain from chicken is highly thermostable. Here, we show that the stable folded structure in headpiece is localized to a subdomain formed by the C-terminal 35 residues. The subdomain, denoted HP-35, is monomeric and retains high thermostability, with a Tm of 70( +/- 1) degree C at PH 7.0. There are no cysteine residues in HP-35 and its folding is not dependent on the binding of metals or other ligands. HP-35 is not a molten globule, but instead, has properties expected for a fully folded protein with a unique structure. In particular, the slowly exchanging amide protons in HP-35 have protection factors that are slightly larger than those predicted if exchange occurred only from globally unfolded molecules. NMR studies indicate that the headpiece subdomain contains three short alpha-helices, and that these same helices are present in the corresponding regions of intact headpiece. HP-35 is the smallest monomeric polypeptide characterized consisting of only naturally occurring amino acids that autonomously folds into a unique and thermostable structure without disulfide bonds or ligand binding.

The survival of the survival lottery.

In his paper 'The Survival Lottery' John Harris suggested that there could be situations where the rational thing to do would be to kill a healthy person and harvest his organs for transplantation, thereby saving several lives at the cost of one. Anne Maclean claims that such a proposal, far from being rational, does not qualify as a moral proposal at all since what it suggests is 'plain murder'. I argue that she is correct to claim that the proposal is not uniquely rational and that doctors could quite rationally reject it, but that she overreaches herself when she holds it not to be a moral proposal at all.

Autonomy and the akratic patient.

I argue that the distinction which is current in much writing on medical ethics between autonomous and non-autonomous patients cannot cope comfortably with weak-willed (incontinent) patients. I describe a case involving a patient who refuses a blood transfusion even though he or she agrees that it would be in his or her best interests. The case is discussed in the light of the treatment of autonomy by B Brody and R Gillon. These writers appear to force us to treat an incontinent patient either as autonomous, just like a rational agent whose decisions are in accordance with his beliefs or as non-autonomous, like comatose patients or children. Though neither is entirely satisfactory I opt for describing such patients as autonomous but point out that in cases like this the principle of respect for autonomy does not give a determinate answer about how the patient ought to be treated.

Minimum length of a sequence-specific DNA binding peptide.

NMR experiments show that a stable complex can be formed between a 14-base-pair oligonucleotide and a disulfide-bonded dimer of a peptide containing 27 residues of the basic region of the yeast transcriptional activator GCN4; the complex is in slow exchange on the NMR time scale. In contrast, a nonspecific complex is in fast exchange on the NMR time scale. DNase I footprinting experiments show that dimers of peptides containing as few as 20 residues of GCN4 bind DNA with sequence specificity similar to that of the intact protein. Circular dichroism experiments suggest that specific binding involves only 15 residues, corresponding to residues 231-245 of GCN4, in an alpha-helical conformation. These results limit substantially the region of GCN4 involved in sequence-specific DNA contacts and provide a uniquely simple model for studying protein-DNA interactions in detail.

Conformational and membrane-binding properties of a signal sequence are largely unaltered by its adjacent mature region.

We have synthesized a peptide corresponding to the 25-residue signal sequence plus the first 28 residues of the Escherichia coli outer membrane protein LamB in order to explore the properties of a signal sequence in the presence of the N-terminal region of its passenger. In the last few years, there have been several observations of differing efficiencies of export when signal sequences are attached to different passenger proteins or when the first part of a passenger protein undergoes mutation. In the LamB case, gene fusions with lacZ have shown that the signal sequence plus the first 28 residues of mature LamB are necessary to direct beta-galactosidase into the export pathway [Rasmussen, B. A. & Silhavy, T. J. (1987) Genes Dev. 1, 185-196]. The origin of these observations and whether there is an influence of the mature region on the properties of the signal sequence have not been known. We find that the conformational and membrane-binding properties of the LamB signal sequence manifest in a 25-residue peptide are essentially unaltered in the context of the 53-residue peptide corresponding to this signal sequence plus the first 28 residues of the mature LamB protein. CD spectra show that the signal peptide and passenger domains are conformationally independent of each other in micelle or bilayer environments. Furthermore, the signal sequence leads to the spontaneous association of the 53-residue peptide with a lipid bilayer; alone, the mature domain does not interact with lipid bilayers. Fluorescence results show that the mode of interaction of the signal peptide with a bilayer is essentially unaltered by the presence of its mature region. This lack of influence of the mature domain on the behavior of the signal sequence is unexpected for juxtaposed polypeptides of comparable length and may be of physiological importance: N-terminal regions of secreted proteins may be selected to be passive, by comparison with their cognate signal sequences, which themselves must engage the export apparatus and actively interact with its components.

Fluorescence analysis of tryptophan-containing variants of the LamB signal sequence upon insertion into a lipid bilayer.

To investigate the interaction of the LamB signal sequence with lipid bilayers, we have synthesized three tryptophan-containing analogues of the wild-type signal peptide. The tryptophan residues were used as intrinsic fluorescent probes of the N-terminal (position 5), central (position 18), and C-terminal (position 24) regions of the 25-residue peptide. The tryptophan substitutions did not significantly alter the physical properties of the wild-type signal peptide. In the presence of lipid vesicles which mimic the composition of the Escherichia coli inner membrane, the peptides adopt alpha-helical structure, and the tryptophan fluorescence emission maximum is shifted to shorter wavelength, indicating that the peptides insert into the acyl chain region of the lipid bilayer. Fluorescence quenching by soluble, aqueous-phase (I-), and membrane-resident (nitroxide-labeled lipids) quenchers was used to locate the tryptophans in each peptide within the bilayer. The C-terminus was interfacial while the central region of the signal sequence was deeply buried within the acyl chain region of the bilayer. The tryptophan at position 5 was buried but less deeply than the tryptophan at position 18. This topology is consistent with either a looped or a transmembrane orientation of signal peptide. However, either structure must accommodate the high helical content of the peptides in vesicles. These results indicate that the LamB signal sequence spontaneously inserts into the acyl chain region of lipid membranes in the absence of any of the proteins involved in protein secretion.

Sequence-specific DNA binding by a short peptide dimer.

A recently described class of DNA binding proteins is characterized by the "bZIP" motif, which consists of a basic region that contacts DNA and an adjacent "leucine zipper" that mediates protein dimerization. A peptide model for the basic region of the yeast transcriptional activator GCN4 has been developed in which the leucine zipper has been replaced by a disulfide bond. The 34-residue peptide dimer, but not the reduced monomer, binds DNA with nanomolar affinity at 4 degrees C. DNA binding is sequence-specific as judged by deoxyribonuclease I footprinting. Circular dichroism spectroscopy suggests that the peptide adopts a helical structure when bound to DNA. These results demonstrate directly that the GCN4 basic region is sufficient for sequence-specific DNA binding and suggest that a major function of the GCN4 leucine zipper is simply to mediate protein dimerization. Our approach provides a strategy for the design of short sequence-specific DNA binding peptides.

Biophysical studies of signal peptides: implications for signal sequence functions and the involvement of lipid in protein export.

This review discusses efforts to understand the mode of action of signal sequences by biophysical study of synthetic peptides corresponding to these protein localization signals. On the basis of reports from several laboratories, it is now clear that signal peptides may adopt a variety of conformations, depending on their local environment. In membrane-mimetic systems like detergent micelles or lipid vesicles, they have a high tendency to form alpha helices. Ability to take up a helical conformation appears to be required at some point in the function of a signal sequence, since some peptides corresponding to export-defective signal sequences display reduced helical potential. By contrast, functional signal sequences share a high capacity to adopt alpha helices. High affinity for organized lipid assemblies, like monolayers or vesicles, is also a property of functional signal sequences. This correlation suggests a role for direct interaction of signal sequences with the lipids of the cytoplasmic membrane in vivo. Supporting this role are studies of the influence of signal peptides on lipid structure, which reveal an ability of these peptides to perturb lipid packing and to alter the phase state of the lipids. Insertion of the signal sequence in vivo could substantially reduce the barrier for translocation of the mature chain. Lastly, synthetic signal peptides have been added to native membranes and found to inhibit translocation of precursor proteins. This approach bridges the biophysical and the biochemical aspects of protein export and promises to shed light on the functional correlates of the properties and interactions observed in model systems.

Helix formation and stability in a signal sequence.

A detailed nuclear magnetic resonance analysis of the isolated LamB signal peptide (MMITLRKLPLAVAVAAGVMSAQAMA) under conditions defined by circular dichroism spectra to mimic the conformational distribution of this peptide in membranelike environments has provided a description of specific residue conformational preferences. This 25-residue long peptide in 20 mol % trifluoroethanol in water is in dynamic equilibrium between a helical and a more random conformation, and this equilibrium is shifted toward the more random structure as the temperature is raised. Part of the molecule, residues 10-18, exists in a stable helix at all temperatures studied (5, 25, and 50 degrees C). Propagation of the helix through the C-terminal end occurs at 25 degrees C, while the temperature must be lowered to 5 degrees C to observe any significant population of a helical conformation in the N-terminal region. These results argue that the Pro and Gly residues, which flank the helical segment, act to disfavor helix propagation on their N- or C-terminal sides, respectively. The influence of the Pro residue is stronger than that of the Gly. Furthermore, the most stable part of the helix in this signal peptide under the conditions studied is the hydrophobic core, which is the hallmark of functional signal sequences.

Functional and nonfunctional LamB signal sequences can be distinguished by their biophysical properties.

The role of the signal sequence in the secretion of proteins remain unclear despite extensive research. We have examined properties of synthetic peptides corresponding to a family of signal sequences derived from the lamB gene of Escherichia coli, including five examples of known phenotype that contain mutations in the signal sequence. By circular dichroism spectroscopy, the wild type and export-component mutant signal peptides show a high alpha-helix content in membrane mimetic environments (sodium dodecyl sulfate micelles and phospholipid vesicles). Tendency to adopt helical conformations is clearly not sufficient to define a functional signal sequence, however, as some nonfunctional mutant signal peptides also contain a relatively high proportion of alpha-helix. The affinity of these peptides for phospholipid monolayers as assessed by surface tensiometry reveals further distinguishing properties. Export-competent peptides show an increased affinity for and greater perturbation of phospholipid monolayers and bilayers than to export-defective peptides. These results suggest a lipid binding role for the signal sequence during protein export in addition to its recognition by proteins of the export pathway.

Conformations and orientations of a signal peptide interacting with phospholipid monolayers.

The interaction of a chemically synthesized 25-residue signal peptide of LamB protein from Escherichia coli with phospholipids has been studied with a film balance technique. The conformation, orientation, and concentration of the peptides in lipid monolayers have been determined from polarized infrared spectroscopy, ultraviolet spectroscopy, and assay of 14C-labeled peptide in transferred films. When the LamB signal peptide is injected into the subphase under a phosphatidylethanolamine-phosphatidylglycerol monolayer at low initial pressure, insertion of a portion of the peptide into the lipid film is evidenced by a rapid rise in film pressure. Spectroscopic results obtained on films transferred to quartz plates and Ge crystals show that the peptide is a mixture of alpha-helix and beta-conformation where the long axis of the alpha-helix penetrates the monolayer plane and the beta-structure is coplanar with the film. By contrast, when peptide is injected under lipid at high initial pressure, no pressure rise is observed, and the spectroscopic results show the presence of only beta-structure which is coplanar with the monolayer. The spectroscopic and radioassay results are all consistent with the picture of a peptide anchored to the monolayer through electrostatic binding with a helical portion inserted into the lipid region of the monolayer and a beta-structure portion resident in the aqueous phase. The negative charges on the lipid molecules are roughly neutralized by the positive charges of the peptide.