Evidence for a major conformational change of coat protein in assembly of fl bacteriophage

Membrane partitioning of the pore-forming domain of colicin A. Role of the hydrophobic helical hairpin

The colicins are bacteriocins that target Escherichia coli and kill bacterial cells through different mechanisms. Colicin A forms ion channels in the inner membranes of nonimmune bacteria. This activity resides exclusively in its C-terminal fragment (residues 387-592). The soluble free form of this domain is a 10 α-helix bundle. The hydrophobic helical hairpin, H8-H9, is buried inside the structure and shielded by eight amphipathic surface helices. The interaction of the C-terminal colicin A domain and several chimeric variants with lipidic vesicles was examined here by isothermal titration calorimetry. In the mutant constructions, natural sequences of the hydrophobic helices H8 and H9 were either removed or substituted by polyalanine or polyleucine. All the constructions fully associated with DOPG liposomes including the mutant that lacked helices H8 and H9, indicating that amphipathic rather than hydrophobic helices were the major determinants of the exothermic binding reactions. Alanine is not specially favored in the lipid-bound form; the chimeric construct with polyalanine produced lower enthalpy gain. On the other hand, the large negative heat capacities associated with partitioning, a characteristic feature of the hydrophobic effect, were found to be dependent on the sequence hydrophobicity of helices H8 and H9.

Filamentous bacteriophage stability in non-aqueous media

BACKGROUND

Filamentous bacteriophage are used as general cloning vectors as well as phage display vectors in order to study ligand-receptor interactions. Exposure to biphasic chloroform-water interface leads to specific contraction of phage, to non-infective I- or S-forms.

RESULTS

Upon exposure, phage were inactivated (non-infective) at methanol, ethanol and 1-propanol concentrations inversely dependent upon alcohol hydrophobicity. Infectivity loss of phage at certain concentrations of 1-propanol or ethanol coincided with changes in the spectral properties of the f1 virion in ultraviolet fluorescence and circular dichroism studies.

CONCLUSIONS

The alcohols inactivate filamentous phage by a general mechanism--solvation of coat protein--thereby disrupting the capsid in a manner quite different from the previously reported I- and S-forms. The infectivity retention of phagemid pG8H6 in 99% acetonitrile and the relatively high general solvent resistance of the phage strains studied here open up the possibility of employing phage display in non-aqueous media.

Peptide mimics of the M13 coat protein transmembrane segment. Retention of helix-helix interaction motifs

Sequence-specific noncovalent helix-helix interactions between transmembrane (TM) segments in proteins are investigated by incorporating selected TM sequences into synthetic peptides using the construct CKKK-TM-KKK. The peptides are of suitable hydrophobicity for spontaneous membrane insertion, whereas formation of an N-terminal S-S bond can bring pairs of TM helices into proximity and promote their parallel orientation. Using the propensity of the protein to undergo thermally induced alpha-helix --> beta-sheet transitions as a parameter for helix stability, we compared the wild type and mutant (V29A and V31A) bacteriophage M13 coat proteins with their corresponding TM peptide constructs (M13 residues 24-42). Our results demonstrated that the relevant helix-helix tertiary contacts found in the intact proteins persist in the peptide mimics. Molecular dynamics simulations support the tight "two in-two out" dimerization motif for V31A consistent with mutagenesis data. The overall results reinforce the notion of TM segments as autonomous folding domains and suggest that the generic peptide construct provides a viable reductionist system for membrane protein structural and computational analysis.

The use of sodium dodecyl sulfate to model the apolipoprotein environment. Evidence for peptide-SDS complexes using pulsed-field-gradient NMR spectroscopy

Pulsed-field-gradient NMR spectroscopy was used to measure translational diffusion coefficients (Ds) for a peptide corresponding to a proposed lipid-binding domain of human apolipoprotein C-I, residues 7-24 (apoC-I(7-24)). Diffusion coefficients for apoC-I(7-24) were determined directly by following the decay of the resonance intensity of selected peptide protons at various concentrations of sodium dodecyl sulfate (SDS), a detergent increasingly being used to model the apolipoprotein environment. Previously, diffusion coefficients of peptides in the presence of SDS have been determined indirectly by monitoring the SDS diffusion coefficient. The direct measurement of the diffusion coefficient of the peptide enables one to distinguish whether SDS simply coats the peptide's surface to produce a uniformly charged 'rod' or if the peptide associates with a micelle. Using the direct method, at SDS concentrations above 5 mM (which is below the SDS critical micelle concentration (8.1 mM)), apoC-I(7-24) exhibited diffusion coefficients consistent with the formation of a large-molecular-weight complex. Based on the ratio of the diffusion coefficients for free- and SDS-associated peptide, the molecular weight of the peptide-SDS complex was much larger than a factor of 1. 4, the increase in molecular weight of the free peptide predicted if apoC-I(7-24) was uniformly surface coated with SDS.

Effects of relative humidity and applied force on atomic force microscopy images of the filamentous phage fd

The filamentous phage fd was studied by both contact- and tapping-mode atomic force microscopy under conditions of controlled variations in relative humidity and changes in the applied tip force. By spin-coating freshly cleaved mica with phage containing solutions having very low salt content followed by rapid humidity control, stable and reliable sample preparation was achieved. The apparent height of the phage varied by about 10-fold with a quadratic dependence on the stabilized relative humidity, extrapolating to 73% of the accepted X-ray diffraction-based height at 0% relative humidity. The variation in measured height with relative humidity largely reconciles previous widely varying atomic force microscopy estimates of this dimension for the filamentous phage. Our finding that contact-mode images of phage are more difficult to analyze than those acquired in tapping mode are consistent with previously published results on other biological specimens such as DNA.

Secondary structure of M13 coat protein in phospholipids studied by circular dichroism, Raman, and Fourier transform infrared spectroscopy

There is considerable uncertainty about the precise secondary structure adopted by the M13 coat protein when embedded in a phospholipid bilayer. Circular dichroism (CD) spectroscopy suggests that a major change in the structure of the coat protein occurs upon membrane insertion. It is reported that the structure of the protein in the membrane has only about 50% alpha-helix, the rest being mainly in a beta-sheet conformation, whereas the protein is almost completely alpha-helical when intact in the phage. In this study we have undertaken a spectroscopic analysis using Fourier transform infrared, Raman, and CD spectroscopy to characterize the secondary structure of M13 coat protein when present in membranes consisting of dioleoylphosphatidylglycerol and dimyristoylphosphatidylglycerol. In sharp contrast to earlier CD studies, our results indicate that the coat protein in its membrane-embedded state has a very high alpha-helical content with virtually no beta-sheet structures present. This result indicates that the structures of the coat protein when intact in the phage or when embedded in the membrane are similar. Although our results differ from earlier CD studies, they are consistent with a recent NMR study, which showed that the M13 coat protein in sodium dodecyl sulfate micelles is primarily alpha-helical with no evidence for beta-sheet structure [Henry, G. D., & Sykes, B.D. (1992) Biochemistry 31, 5284-5297]. These results lead to the conclusion that the M13 coat protein can insert from the membrane-bound state into a virus particle with a similar secondary structure, without large energy implications.(ABSTRACT TRUNCATED AT 250 WORDS)

Evaluation of transmembrane helix prediction methods using the recently defined NMR structures of the coat proteins from bacteriophages M13 and Pf1

Currently, there are a large number of hydropathy scales available to predict the presence of transmembrane segments within integral membrane proteins. These scales and their subsequent numerical manipulations provide an aid in the determination of topology in transmembrane proteins. In order to analyse the accuracy of these procedures to correctly identify the boundaries of a transmembrane segment, 13 methods were applied to the amino-acid sequence of the coat proteins from the bacteriophages Pf1 and M13. These monotopic integral membrane proteins have been incorporated into detergent micelles and their structures have recently been solved using NMR. The predicted regions were then compared to their NMR-determined structures. All methods used were able to detect a transmembrane region within the protein sequence. However, there was considerable differences in their accuracy in determining the boundaries of the main transmembrane alpha-helix. Surprisingly, the methods which worked the best for Pf1 coat protein had poor accuracy in identifying the transmembrane region correctly in the M13 protein. It was concluded that a number of methods should be utilized in order to obtain a clear model of transmembrane protein topology, and that regardless of how closely related two proteins are, a different conclusion may be obtained from different prediction procedures.

Subtilisin removes the surface layer of the phage fd coat

The major coat protein of native filamentous phage fd is vulnerable to digestion by subtilisin, but not by any of a number of other proteolytic enzymes. Degradation by the non-specific protease subtilisin occurs at specific sites in the N-terminal portion of g8p. The N-terminal part of the protein is considered to be the outer layer of a two-layered coat. Thus, subtilisin treatment results in a monolayered phage particle. These particles possess the morphology and stability of native phage fd. Furthermore, subtilisin proteolysis proved to be an efficient instrument in detecting variations in the topology of the g8p of related filamentous phages.

Influence of glycine residues on peptide conformation in membrane environments

Transmembrane (TM) segments of integral membrane proteins are putatively alpha-helical in conformation, yet their primary sequences are rich in residues known in globular proteins as helix-breakers (Gly) and beta-sheet promoters (Ile, Val, Thr). To examine the specific 2 degrees structure propensities of such residues in membrane environments, we have now designed and synthesized a series of model 20-residue peptides with "guest" hydrophobia segments embedded in "host" N- and C-terminal hydrophilic matrices. Molecular design was based on the prototypical sequence NH2-(Ser-Lys)2-Ala5-Leu6-x7-Ala8-Leu9-y10-Trp 11-Ala12-Leu13-z14-(Lys-Ser)3-OH. The 10-residue hydrophobic mid-segment 5-14 is expected to act as ca. three turns of an alpha-helix. In the present work, we compare the 20-residue peptide having three "helix-forming" Ala residues [x = y = z = Ala (peptide 3A)] to the corresponding peptide 3G (x = y = z = Gly) which contains three "helix-breaking" Gly residues. Trp was inserted to provide a measure of aromatic character typical of TM segments; Ser and Lys enhanced solubility in aqueous media. Circular dichroism studies in water, in a membrane-mimetic [sodium dodecylsulfate (SDS)], medium, and in methanol solutions, demonstrated the exquisite sensitivity of the conformations of these peptides to environment, and proved that despite its backbone flexibility, Gly can be accommodated as readily as Ala into a hydrophobic alpha-helix in a membrane. Nevertheless, the relative stability of Ala- vs. Gly-containing helices emerged in methanol solvent titration and temperature dependence experiments in SDS.(ABSTRACT TRUNCATED AT 250 WORDS)

Stoichiometry, selectivity, and exchange dynamics of lipid-protein interaction with bacteriophage M13 coat protein studied by spin label electron spin resonance. Effects of protein secondary structure

Bacteriophage M13 major coat protein has been isolated with cholate and reconstituted in dimyristoyl- and dioleoylphosphatidylcholine (DMPC and DOPC, respectively) bilayers by dialysis. Fourier transform infrared spectra of DMPC/coat protein recombinants confirmed that, whereas the protein isolated by phenol extraction was predominantly in a beta-sheet conformation, the cholate-isolated coat protein contained a higher proportion of the alpha-helical conformation [cf. Spruijt, R. B., Wolfs, C. J. A. M., & Hemminga, M. A. (1989) Biochemistry 28, 9158-9165]. The cholate-isolated coat protein/lipid recombinants gave different electron spin resonance (ESR) spectral line shapes of incorporated lipid spin labels, as compared with those from recombinants with the phenol-extracted protein that were studied previously [Wolfs, C. J. A. M., Horváth, L. I., Marsh, D., Watts, A., & Hemminga, M. A. (1989) Biochemistry 28, 9995-10001]. Plots of the ratio of the fluid/motionally restricted components in the ESR spectra of spin-labeled phosphatidylglycerol were linear with respect to the lipid/protein ratio in the recombinants up to 20 mol/mol. The corresponding values of the relative association constants, Kr, and number of association sites, N1, on the protein were Kr approximately 1 and N1 approximately 4 for DMPC recombinants and Kr approximately 1 and N1 approximately 5 for DOPC recombinants. Simulation of the two-component lipid spin label ESR spectra with the exchange-coupled Bloch equations gave values for the off-rate of the lipids leaving the protein surface of 2.0 x 10(7) s-1 at 27 degrees C in DMPC recombinants and 3.0 x 10(7) s-1 at 24 degrees C in DOPC recombinants.(ABSTRACT TRUNCATED AT 250 WORDS)

A model for fd phage penetration and assembly

Below 15 degrees C, chloroform causes fd phage to contract to I-forms, which are compact structures about 1/3 as long as the original phage. Above 15 degrees C, chloroform causes I-forms to contract to even more compact spheroidal S-forms. Here we show that the coat protein structure in I-forms is the same as the protein structure in the phage and the protein structure in S-forms is the same as the protein structure in bilayers. The conversions from fd----I-forms----S-forms are therefore suggested to mimic steps in fd penetration. The same conversions, in reverse order, are suggested to mimic steps in fd assembly.

Hydrogen exchange kinetics in a membrane protein determined by 15N NMR spectroscopy: use of the INEPT experiment to follow individual amides in detergent-solubilized M13 coat protein

The coat protein of the filamentous coliphage M13 is a 50-residue polypeptide which spans the inner membrane of the Escherichia coli host upon infection. Amide hydrogen exchange kinetics have been used to probe the structure and dynamics of M13 coat protein which has been solubilized in sodium dodecyl sulfate (SDS) micelles. In a previous 1H nuclear magnetic resonance (NMR) study [O'Neil, J. D. J., & Sykes, B. D. (1988) Biochemistry 27, 2753-2762], multiple exponential analysis of the unresolved amide proton envelope revealed the existence of two slow "kinetic sets" containing a total of about 30 protons. The slower set (15-20 amides) originates from the hydrophobic membrane-spanning region and exchanges at least 10(5)-fold slower than the unstructured, non-H-bonded model polypeptide poly(DL-alanine). Herein we use 15N NMR spectroscopy of biosynthetically labeled coat protein to follow individual, assigned, slowly exchanging amides in or near the hydrophobic segment. The INEPT (insensitive nucleus enhancement by polarization transfer) experiment [Morris, G. A., & Freeman, R. (1979) J. Am. Chem. Soc. 101, 760-762] can be used to transfer magnetization to the 15N nucleus from a coupled proton; when 15N-labeled protonated protein is dissolved in 2H2O, the INEPT signal disappears with time as the amide protons are replaced by solvent deuterons. Amide hydrogen exchange is catalyzed by both H+ and OH- ions. Base catalysis is significantly more effective, resulting in a characteristic minimum rate in model peptides at pH approximately equal to 3. Rate versus pH profiles have been obtained by using the INEPT experiment for the amides of leucine-14, leucine-41, tyrosine-21, tyrosine-24, and valines-29, -30, -31, and -33 in M13 coat protein. The valine residues exchange most slowly and at very similar rates, showing an apparent 10(6)-fold retardation over poly(DL-alanine). A substantial basic shift in the pH of the minimum rate (up to 1.5 pH units) was also observed for some residues. Possible reasons for the shift include accumulation of catalytic H+ ions at the negatively charged micelle surface or destabilization of the negatively charged transition state of the base-catalyzed reaction by either charge or hydrophobic effects within the micelle. The time-dependent exchange-out experiment is suitable for slow exchange rates (kex), i.e., less than (1-2) x 10(-4) s-1.(ABSTRACT TRUNCATED AT 400 WORDS)

Analysis of time-resolved fluorescence anisotropy in lipid-protein systems. II. Application to tryptophan fluorescence of bacteriophage M13 coat protein incorporated in phospholipid bilayers

The subnanosecond fluorescence and motional dynamics of the tryptophan residue in the bacteriophage M13 coat protein incorporated within pure dioleoylphosphatidylcholine (DOPC) as well as dioleoylphosphatidylcholine/dioleoylphosphatidylglycerol (DOPC/DOPG) and dimyristoylphosphatidylcholine/dimyristoylphosphatidylglycerol (DMPC/DMPG) bilayers (80/20 w/w) with various L/P ratio have been investigated. The fluorescence decay is decomposed into four components with lifetimes of about 0.5, 2.0, 4.5 and 10.0 ns, respectively. In pure DOPC and DOPC/DOPG lipid bilayers, above the phase transition temperature, the rotational diffusion of the protein molecules contributes to the depolarization and the anisotropy of tryptophan is fitted to a dual exponential function. The longer correlation time, describing the rotational diffusion of the whole protein, shortens with increasing temperature and decreasing protein aggregation number. In DMPC/DMPG lipid bilayers, below the phase transition, the rotational diffusion of the protein is slowed down such that the subnanosecond anisotropy decay of tryptophan in this system reflects only the segmental motion of the tryptophan residue. Because of a heterogeneous microenvironment, the anisotropy decay must be described by three exponentials with a constant term, containing a negative coefficient and a negative decay time constant. From such a decay, the tryptophan residue within the aggregate undergoes a more restricted motion than the one exposed to the lipids. At 20 degrees C, the order parameter of the transition moment of the isolated tryptophan is about 0.9 and that for the exposed one is about 0.5.

Detergent-solubilized M13 coat protein exists as an asymmetric dimer. Observation of individual monomers by 15N, 13C and 1H nuclear magnetic resonance spectroscopy

M13 coat protein is a simple integral membrane protein isolated from the filamentous coliphage M13. Isotopic labels (13C and 15N) may be incorporated biosynthetically into the protein backbone. 13C nuclear magnetic resonance spectroscopy of carbonyl carbon atoms and two-dimensional 1H-detected 15N-1H heteronuclear shift correlation of coat protein in dodecylsulphate micelles have shown many residues throughout the protein to give rise to two distinct resonances of equal intensity. Chemical shift differences between the two forms are small, indicating the existence of two slightly different but equally populated conformational states. We suggest that the two conformers correspond to the inequivalent monomers of an asymmetric coat protein dimer and propose a mechanism for the generation of such a dimer.

Deuterium nuclear magnetic resonance investigation of bacteriophage M13 coat protein in dimyristoylphosphatidylcholine liposomes using palmitic acid as a probe

The effect of incorporation of various amounts of M13 bacteriophage coat protein on the bilayer order and acyl chain motion in dimyristoylphosphatidylcholine (DMPC) liposomes has been investigated using deuterium NMR of specifically deuterated palmitic acid as a bilayer probe, phosphorus NMR and additional spin-label electron spin resonance (ESR). The secondary structure of the M13 coat protein in these bilayers was determined from circular dichroism spectra. Phosphorus NMR spectra of the mixed liposomes are characteristic for DMPC organized in bilayers, also after incorporation of various levels of M13 protein. Circular dichroism spectra of the coat protein indicate that the protein conformation is predominantly a beta-structure (more than 75%). Various incorporation levels of M13 coat protein do not affect the order of the deuterium-labelled positions along the acyl chain at the carbon-2, 9 and 16 positions. In contrast, the spin-spin relaxation times decrease at higher protein levels, especially at the carbon-16 position. The spin-label ESR spectra of the same system using 14-doxylstearic acid as a label show a second, motionally restricted component, that is not observed by deuterium NMR. The NMR and ESR results are consistent with a model in which the fatty acid molecules are in a fast two-site exchange (at a rate of approx. 10(7) Hz) between the sites in the bulk of the lipid bilayer and the motionally restricted sites on the coat protein.

Comparison of the dynamics of the membrane-bound form of fd coat protein in micelles and in bilayers by solution and solid-state nitrogen-15 nuclear magnetic resonance spectroscopy

Solid-state and solution 15N nuclear magnetic resonance experiments on uniformly and specifically 15N labeled coat protein in phospholipid bilayers and in detergent micelles are used to describe the dynamics of the membrane-bound form of the protein. The residues in the N- and C-terminal portions of the coat protein in both phospholipid bilayers and in detergent micelles are mobile, while those in the hydrophobic midsection are immobile. There is evidence for a gradient of mobility in the C-terminal region of the coat protein in micelles; at 25 degrees C only the last two residues are mobile on the 10(9)-Hz timescale, while the last six to eight residues appear to be mobile on slower timescales and highly mobile at higher temperatures. Since all of the C-terminal residues are immobile in the virus particles, the mobility of these residues in the membrane-bound form of the protein may be important for the formation of protein-DNA interactions in the assembly process.

Structure and dynamics of the Pf1 filamentous bacteriophage coat protein in micelles

The major coat protein of filamentous bacteriophage adopts its membrane-bound conformation in detergent micelles. High-resolution 1H and 15N NMR experiments are used to characterize the structure and dynamics of residues 30-40 in the hydrophobic midsection of Pf1 coat protein in sodium dodecyl sulfate micelles. Uniform and specific-site 15N labels enable the immobile backbone sites to be identified by their 1H/15N heteronuclear nuclear Overhauser effect and allow the assignment of 1H and 15N resonances. About one-third of the amide N-H protons in the protein undergo very slow exchange with solvent deuterons, which is indicative of sites in highly structured environments. The combination of results from 1H/15N heteronuclear correlation, 1H homonuclear correlation, and 1H homonuclear Overhauser effect experiments assigns the resonances to specific residues and demonstrates that residues 30-40 of the coat protein have a helical secondary structure.

Hydrogen exchange in the hydrophilic regions of detergent-solubilized M13 coat protein detected by 13C nuclear magnetic resonance isotope shifts

Images

Reconstitution of M13 bacteriophage coat protein. A new strategy to analyze configuration of the protein in the membrane

The configuration of M13 bacteriophage coat protein in a model membrane was analyzed using protease digestion followed by gel permeation chromatography on Fractogel TSK in formic acid/ethanol. Important information is contained in the chromatographic patterns of the membrane-bound fragments, as well as of the fragments released by the digestion. A new reconstitution was thereby developed which involves adding a small volume of a concentrated solution of cholate-solubilized coat protein to preformed vesicles (with the amount of detergent added being less than that required to solubilize the vesicles), freezing in liquid nitrogen, thawing, followed by dialysis to remove excess detergent. The coat protein is incorporated with high efficiency (95 percent) making subsequent fractionation unnecessary. In addition, the incorporated protein is not aggregated, and is incorporated with most molecules spanning the membrane, oriented in the same manner as in vivo (N-terminus outwards). Two previously described reconstitutions, using sonication or cholate dialysis, are analyzed and found to be less satisfactory.

One- and two- dimensional 15N/1H NMR of filamentous phage coat proteins in solution

High resolution 15N NMR studies of proteins in solution can be performed efficiently by combining the use of isotopically enriched proteins and pulse sequences that generate polarization transfer from protons and result in two-dimensional heteronuclear chemical shift correlation spectra. The coat proteins of the filamentous bacteriophages fd and Pf1 solubilized in detergent micelles give one- and two- dimensional NMR spectra with resolved resonances for nearly all of the nitrogen sites in the proteins. The resonances from the amide sites with slowly exchanging protons can be obtained as a subset of the resonances of all amide sites by comparing the spectra of proteins in D2O and H2O solutions at pH = 4.0.

Association of M13 I-forms and spheroids with lipid vesicles

Electron microscopy and density gradient centrifugation were used to demonstrate that the coat protein of M13 I-forms and spheroids, but not of filaments, can form some type of association with lipid vesicles in vitro. The association was detected only when the phage particles were incubated with dilauroylphosphatidylcholine (DLPC) or dimyristoylphosphatidylcholine (DMPC) small unilamellar vesicles (SUV) above the phase transition temperature of the lipid. Under these conditions the I-form coat protein was resistant to proteolytic digestion, and the viral DNA was also associated with the vesicles.

Raman spectroscopy and deuterium exchange of the filamentous phage fd

The filamentous phage fd has been investigated using the techniques of Raman spectroscopy and deuterium exchange. Despite the rather uniform secondary structure of the fd phage coat protein, which is predominantly alpha-helix, the deuterium exchange is complex. A substantial fraction of the helical peptides exchange deuterium by 8 h at room temperature, yet another substantial fraction does not exchange following an additional 5 months at 4 degrees C. Heating the phage to 70 degrees C for several hours leads to additional deuterium exchange compared to samples soaked for 5 months in heavy water. We suggest that the wide variation in peptide exchange rates may be related to the phage protein quaternary structure, which has been shown to be a double layer of tightly packed helices. The accomplishment of enhanced exchange by reaction at high temperature combined with digital difference spectroscopic methods has enabled us to define the structure of the amide III and III' bands. The complexity of these bands is unexpected for a simple helical protein, but we suggest that the complexity arises at least in part from end-effects that become important in short alpha-helices.

Coat protein conformation in M13 filaments, I-forms and spheroids

Circular dichroism studies of the filamentous coliphage M13 were carried out to determine conformational changes in the major capsid protein (the B protein) that occur during contraction of the filaments to I-forms and spheroids. The alpha-helicity of the B protein is somewhat lower in the I-forms than in filaments and much lower in spheroids. This conformational change may explain the increased detergent and lipid solubility of both I forms and spheroids relative to filaments.

Mechanism of coliphage M13 contraction: intermediate structures trapped at low temperatures

The filamentous coliphage M13 can be transformed into a spherical particle (termed spheroid) by exposure to an interface of water and slightly polar but hydrophobic solvent such as chloroform-water at 24 degrees C. We report here that exposure of M13 filaments to a chloroform-water interface at 2 degrees C trapped the phage particles in forms morphologically intermediate to filaments and spheroids. These structures were rods 250 nm long and 15 nm wide, and each had a closed, slightly pointed end, an open flaired end, and a hollow central channel. The final contraction of these intermediates (termed I-forms) into spheroids was dependent upon both temperature and the presence of the solvent-water interface but was apparently independent of both the minor phage coat proteins and the virion DNA. Although stable in an aqueous environment, I-forms, in contrast to filaments, were readily disrupted by detergents, suggesting that the phage structure had been altered to a form more easily solubilized by membrane lipids. These solvent-induced changes might be related to the initial steps of phage penetration in vivo.

Conformational transitions in Pf3 and their implications for the structure and assembly of filamentous bacterial viruses

Laser Raman and circular dichroism spectra of filamentous bacteriophage Pf3 show that its coat protein is predominantly alpha-helical, similar to the subunits of bacteriophages Pf1 and fd. Unlike Pf1 and fd, however, the subunits of Pf3 are converted to beta-sheet structures by raising the temperature, the transition temperature depending upon phage and NaCl concentrations. On cooling, the beta structure reverts to an alpha structure the same as or similar to the native structure. On further heating it converts irreversibly to a second alpha-helical form different from the original one. The spectra also show that aromatic amino acid residues of Pf3 undergo dramatic changes in molecular environment during the alpha leads to beta transition. Similar transitions are observed to take place in the filamentous bacteriophage Xf.

Nuclear magnetic resonance of the filamentous bacteriophage fd

The filamentous bacteriophage fd and its major coat protein are being studied by nuclear magnetic resonance (NMR) spectroscopy. 31P NMR shows that the chemical shielding tensor of the DNA phosphates of fd in solution is only slightly reduced in magnitude by motional averaging, indicating that DNA-protein interactions substantially immobilize the DNA packaged in the virus. There is no evidence of chemical interactions between the DNA backbone and the coat protein, since experiments on solid virus show the 31P resonances to have the same principle elements of its chemical shielding tensor as DNA. 1H and 13C NMR spectra of fd virus in solution indicate that the coat proteins are held rigidly in the structure except for some aliphatic side chains that undergo relatively rapid rotations. The presence of limited mobility in the viral coat proteins is substantiated by finding large quadrupole splittings in 2H NMR of deuterium labeled virions. The structure of the coat protein in a lipid environment differs significantly from that found for the assembled virus. Data from 1H and 13C NMR chemical shifts, amide proton exchange rates, and 13C relaxation measurements show that the coat protein in sodium dodecyl sulfate micelles has a native folded structure that varies from that of a typical globular protein or the coat protein in the virus by having a partially flexible backbone and some rapidly rotating aromatic rings.

Physical chemical studies of the structure and function of DNA binding (helix-destabilizing) proteins

Binding of proteins to DNA is fundamental to the mechanisms of replication, recombination and gene expression. The specific molecular features of DNA recognized by complementary features of the three-dimensional structure of the DNA binding proteins are under intensive investigation. Two large classes of DNA binding proteins have emerged. One class includes enzymes such as the RNA polymerases and restriction endonucleases and the nonenzymatic repressor proteins which recognize unique sequences present in only one or a few copies per genome. A second group is made up of non-sequence-specific DNA binding proteins which bind to DNA at high density and modulate subsequent enzymatic transformations of the DNA. Among the latter group are those proteins originally termed "unwinding proteins", which have in common a higher affinity for single-stranded than for double-stranded DNA and thus promote the melting of double-stranded DNA. They are better termed helix-destabilizing proteins to distinguish them from the enzymes which "unwind" the helix by making and breaking phosphodiester bonds. Because the helix-destabilizing proteins form complexes with all single-stranded DNA regardless of base sequence, the molecular details of complex formation have been much more accessible to direct physicochemical measurements. Structural conclusions derived with techniques which include chemical modification, ultraviolet spectroscopy, circular dichroism, NMR, and X-ray diffraction will be reviewed. The following proteins will be discussed in detail; the gene 32 protein of bacteriophage T4, the gene 5 protein from bacteriophage fd, and the helix-destabilizing protein from E. coli. The largest amount of specific structural information is available for the gene 5 protein and specific models for this protein and its complexes with DNA based on NMR and X-ray diffraction data are presented. A number of other helix-destabilizing proteins from both prokaryotes and eukaryotes have been described and a survey of these will be given. Some of the basic molecular features of DNA-protein interactions emerging from studies of the helix-destabilizing proteins are likely to be shared by the more highly specific binding proteins like the RNA polymerases and repressors. Properties of some of these more complex systems which suggest this will be discussed.

The primary structure of the coat protein of alfalfa mosaic virus strain VRU. A hypothesis on the occurrence of two conformations in the assembly of the protein shell

The complete primary structure of the coat protein of strain VRU of alfalfa mosaic virus (AMV) is reported. The strain is morphologically different from all other AMV strains as it contains large amounts of unusually long virus particles. This is caused by structural differences in the coat protein chain. The amino acid sequence has mainly been established by the characterization of peptides obtained after cleavage with cyanogen bromide and digestion with trypsin, chymotrypsin, thermolysin or Staphylococcus aureus protease. The major sequencing technique used was the dansyl-Edman procedure. The VRU coat protein consists of 219 amino acid residues corresponding to a molecular weight of 24056. Compared to the coat protein of strain 425 [Van Beynum et al. (1977) Eur. J. Biochem. 72, 63-78], 15 amino acid substitutions were localized. Most of them have a conservative character and may be explained by single-point mutations. A correction is given for the AMV 425 coat protein: Asn-216 was shown to be Asp-216. The prediction of the secondary structure for the two viral coat proteins was not significantly influenced by the various amino acid substitutions except for the region containing residues 65-100. This led us to the hypothesis that the AMV coat protein may occur in two different conformations favouring its incorporation into either a pentagonal or hexagonal quasi-equivalent position in the lattice of the protein shell. The substitutions in the above-mentioned region of the VRU coat protein may have caused a strong preference for the hexagonal lattice conformation. The model is supported by preliminary sequence data of the same coat protein region in AMV 15/64, a strain morphologically intermediate between 425 and VRU.

Laser Raman studies of lipid disordering by the B-protein of fd phage

Complexes of the B-protein of fd phage with the model lipid dipalmitoyl phosphatidylcholine (DPPC) were made by sonication of the fd phage in the presence of dipalmitoyl phosphatidylcholine. Both laser Raman spectra and circular dichroism show the protein in the membrane to be almost entirely in the beta-sheet conformation. This beta-sheet conformation is found to be independent of the temperature between 10 degrees C and 50 degrees C. On the other hand, the protein has a very dramatic effect on the organization of the lipid bilayer. An aqueous dispersion of 1 : 1 lipid/protein mixture gives a broad conformational transition of DPPC which occurs between 10 degrees C and 30 degrees C. This contrasts markedly with simple aqueous DPPC dispersions which show a sharp transition at 41 degrees C. This appears to be the first reported example of the lowering of the conformational transition of a membrane bilayer by an intrinsic membrane protein.

Association of the major coat protein of fd bacteriophage with phospholipid vesicles

The association of the major coat protein of fd bacteriophage with a phospholipid bilayer was investigated by analyzing the protein's susceptibility to proteolysis and its circular dichroism spectrum when incorporated into single-walled phospholipid vesicles. In the limits tested, this association appeared to be independent of the mass ratio of protein to lipid and of vesicle size, phospholipid composition, and method of preparation. The circular dichroism data are consistent with a similar "membrane-bound" conformation for all cases of vesicle-associated coat protein and for deoxycholate micelle-associated coat protein. Proteolysis of coat protein associated with deoxycholate micelles and with phospholipid vesicles defined the central hydrophobic core presumed to represent that portion of the protein which associates with membrane bilayers in vivo. The isolated core, which assumed a predominantly beta-type conformation in detergent solution, maintained a beta conformation when associated with a vesicle phospholipid bilayer.