Hydrophobic basis of packing in globular proteins

Hydrophobicity of amino acid residues in globular proteins

During biosynthesis, a globular protein folds into a tight particle with an interior core that is shielded from the surrounding solvent. The hydrophobic effect is thought to play a key role in mediating this process: nonpolar residues expelled from water engender a molecular interior where they can be buried. Paradoxically, results of earlier quantitative analyses have suggested that the tendency for nonpolar residues to be buried within proteins is weak. However, such analyses merely classify residues as either "exposed" or "buried." In the experiment reported in this article proteins of known structure were used to measure the average area that each residue buries upon folding. This characteristic quantity, the average area buried, is correlated with residue hydrophobicity.

Similarity between the vaccinia virus 19K early protein and epidermal growth factor

An analysis of the 1,217-amino acid residue sequence of the precursor of mouse epidermal growth factor (mEGF) revealed regions of considerable similarity with bovine factor X, a blood coagulation factor. Similarities of mEGF itself with factor X, pancreatic secretory trypsin inhibitor and, most strikingly, transforming growth factor I (TGF-I) have been observed. On the basis of the comparisons described here, it seems that the presumptive 140-residue 19K early protein (relative molecular mass (Mr) 19,000) of vaccinia virus from residues 40-91 shows an overall identity of 36% (19/53 residues) with both mEGF and urogastrone (human epidermal growth factor, hEGF); a single deletion is assumed for vaccinia virus 19K protein which allows the six Cys residues (positions 45-80) to be aligned with those of mEGF or hEGF. This protein is encoded in the 10.3-kilobase (kb) inverted terminal repeat. Because it is an early protein with an EGF-like central portion, the 19K vaccinia virus protein may have an autocrine function and may be required for DNA synthesis.

Antibodies to peptides corresponding to a conserved sequence of gonococcal pilins block bacterial adhesion

Antisera generated against each of seven synthetic peptides corresponding to constant and variable sequences of the pilin from gonococcal strain MS11 were assayed for their ability to crossreact with intact pili from both homologous and heterologous strains. The peptides elicited roughly equal antipeptide responses but varied substantially in their ability to elicit antisera that crossreacted with intact pili. Of the antisera to peptides corresponding to regions of conserved sequence, antisera directed against residues 69-84 were the most efficient in binding pili from all strains tested in both solid-phase assays and immunoblots. Anti-69-84 also efficiently precipitated a tryptic fragment of pilin known to bind human endocervical cells. Sera against the two peptides (121-134 and 135-151) previously shown to contain strain-specific epitopes crossreacted with MS11 pili equally well, but differed in their ability to bind pili from heterologous strains. Anti-121-134 was strain-specific whereas anti-135-151 bound all pilin tested. Each of the sera was examined for its ability to inhibit bacterial adhesion to a human endometrial carcinoma cell line. Sera generated against residues 41-50 and 69-84 successfully inhibited a heterologous gonococcal strain from binding. These peptides could be important components of an effective vaccine for the prevention of gonorrhea.

Amino acid side-chain partition energies and distribution of residues in soluble proteins

Energies required to transfer amino acid side chains from water to less polar environments were calculated from results of several studies and compared with several statistical analyses of residue distributions in soluble proteins. An analysis that divides proteins into layers parallel with their surfaces is more informative than those that simply classify residues as exposed or buried. Most residues appear to be distributed as a function of the distance from the protein-water interface in a manner consistent with partition energies calculated from partitioning of amino acids between water and octanol phases and from solubilities of amino acids in water, ethanol, and methanol. Lys, Arg, Tyr, and Trp residues tend to concentrate near the water-protein interface where their apolar side-chain components are more buried than their polar side-chain components. Residue distributions calculated in this manner do not correlate well with side-chain solvation energies calculated from vapor pressures of side-chain analogs over a water phase. Results of statistical studies that classify residues as exposed to solvent or buried inside the protein interior appear to depend on the method used to classify residues. Data from some of these studies correlate better with solvation energies, but other data correlate better with partition energies. Most other statistical methods that have been used to evaluate effects of water on residue distributions yield results that correlate better with partition energies than with solvation energies.

Sequences of the S1 genes of the three serotypes of reovirus

The S1 genes of the three serotypes of reovirus have been cloned and sequenced. The S1 genes encode protein sigma 1, the protein against which serotype-specific neutralizing antibodies are directed; it is also the reovirus hemagglutinin and cell-attachment protein and is a major determinant of host range/tissue specificity and of the nature of the interaction of reovirus with cells of the immune system. The S1 genes of serotypes 1, 2, and 3 are 1458, 1442, and 1416 nucleotides long, respectively. They possess untranslated regions 13, 13, and 12 nucleotides long at their 5' termini and 188, 229, and 36 nucleotides long at their 3' termini. They possess two open reading frames. The first starts with a "weak" initiation codon and extends for 418, 399, and 455 codons, respectively; this is the size expected for the sigma 1 proteins. The other reading frame starts at a "strong" initiation codon about 70 residues downstream from the 5' terminus but extends for only about 120 codons, being terminated by 3 in-phase termination codons in all three genes. The proteins encoded by these short open reading frames are quite basic. The serotype 1 and 2 S1 genes are much more closely related to each other (28% homology) than to the serotype 3 S1 gene (5% and 9% homology, respectively). These figures are based on direct homology calculations, adjusted for 25% random coincidence. Serologic evidence and hydrophobicity profiles agree that the sigma 1 proteins of serotypes 1 and 2 are much more closely related to each other (about 40% homology) than to that of serotype 3 (only about 20% homology). The fact that the serotype 1 and 2 S1 genes are much more closely related to each other than to the serotype 3 S1 gene is remarkable since for all other nine reovirus genes the serotype 1 and 3 genes are much more closely related to each other than to the serotype 2 gene. Mechanisms that may effect this remarkable evolutionary pattern are discussed.

Strain-specific and common epitopes of gonococcal pili

The antigenic structure of gonococcal pilin, strain MS11 (Tr), was investigated by assaying the binding of antisera engendered by intact pili from strains MS11 and R10 and their two major cyanogen bromide-generated fragments, CNBr-2 (residues 9-92) and CNBr-2 (residues 93-159), to synthetic peptides corresponding to the amino acid sequence of MS11 pilin. Four peptides were synthesized corresponding to regions of sequence variation between MS11 and R10 gonococcal pilin. Antisera against the homologous pilus filament and against its CNBr-3 fragment bind peptides equivalent to residues 121-134 and 135-151, which comprise the 30 amino acid disulfide loop near the carboxyl terminus of the protein. Heterologous pili antisera did not bind these peptides. Absorption studies proved that each peptide contained an independent, strain-specific epitope. Synthetic peptides corresponding to regions of identical sequence between MS11 and R10 pilin were used in similar binding experiments to localize a weakly immunogenic, common determinant between residues 48 and 60. less than 15% of the antibodies raised against intact pili were directed at this site. Antisera raised against MS11 or R10 CNBr-2 bind a separate peptide, residues 69-80. This region is immunogenic only as a fragment, not in the intact pilus filament.

Synthesis and physicochemical characterization of major fragments of human leucocyte interferon alpha 1

Four oligopeptides corresponding to overlapping regions of the human leucocyte interferon alpha 1 (IFN) amino acid sequence have been synthesized by the solid-phase method. The physicochemical properties of these peptides were investigated by analytical ultracentrifugation and circular dichroism, absorbance, and fluorescence spectroscopies. IFNs 24-81 and 111-166 were shown to possess considerable ordered structure in solution. IFN 111-166 appeared to adopt a beta-stranded conformation, which could be reversibly unfolded by the addition of urea. Equimolar mixtures of IFNs 24-81 and 111-166 formed a noncovalent complex that was resistant to the formation of the Cys29-Cys139 disulfide bond found in native interferon alpha 1. Predictions of the secondary structure of interferon alpha 1 were made and the results compared to the measured properties of the fragments. In general, it was found that the prediction methods favored a highly alpha-helical conformation.

A program for prediction of protein secondary structure from nucleotide sequence data: application to histocompatibility antigens

A computer program is described which, given a nucleotide or an amino acid sequence, outputs protein secondary structure prediction curves as well as hydrophobicity and charged-residue profiles. The program allows for cumulative averaging of properties (secondary structure propensities, hydrophobicity and charge profiles) from several homologous primary structures, a novel concept shown to improve the predictive accuracy. The use of the program is demonstrated on a set of nucleotide and amino acid sequences from human and murine histocompatibility antigens of class I and II. The last extracellular domains of both class I and II antigens (alpha 3 of class I, alpha 2 and beta 2 of class II) and the beta 2-microglobulin domain are predicted to consist of seven anti-parallel beta-strands, in accord with previous claims of homology between these domains and the constant domains of immunoglobulin chains. The remaining extracellular domains are all proposed to form an anti-parallel, four-stranded beta-sheet with one of its faces being covered by alpha-helices and/or structureless segments ("open face sandwiches").

Structural homology of corticotropin-releasing factor, sauvagine, and urotensin I: circular dichroism and prediction studies

Three recently isolated peptides, whose sequences have been determined--the corticotropin (adrenocorticotropic hormone)-releasing factor of ovine origin, sauvagine, from the skin of the frog Phyllomedusa sauvagei, and urotensin I from the teleost fish, Catostomus commersoni--show high (greater than 50%) sequence homology. CD spectra of the three peptides in trifluoroethanol indicate predominantly helical character for these peptides. Analysis of the secondary structures by the Chou-Fasman method predicts that the overall structural organization of the peptides is the same. All three possess a long internal helix, spanning about 25 residues, connected by a turn region to a COOH-terminal structural element that is an alpha-helix in corticotropin-releasing factor and urotensin I and a beta-sheet in sauvagine. The values for helical content estimated from the prediction method agree reasonably well with those computed from the CD spectra. This agreement as well as the CD spectra of corticotropin-releasing factor fragment 5-33 support the specific assignments of helical regions derived from the Chou-Fasman analysis. The three peptides exhibit significantly less helical structure in water than in trifluoroethanol as indicated by CD spectra. Hydrophilicity profiles provided comparison of the three peptides in terms of their overall hydrophilicity and the location of the regions of maximal hydrophilicity. A unique distribution of hydrophilic and hydrophobic residues within the internal helices is revealed by helical wheel analysis. Patches of both types of residues are formed following a heptad (four/three) rule. Since the two patches are shifted by one residue relative to one another, together they occupy only one face of the helical surface, a feature distinct from other amphiphilic structures.

Interior turns in globular proteins

Reverse turns are specific sites in proteins at which the polypeptide chain changes its overall direction. This category of secondary structure enables the chain to turn a corner, and its frequent occurrence is the geometric basis for the ultimate globular shape of the protein. beta-Turns in particular are comprised of four consecutive residues with a stereochemistry that constrains the turn to be polar. In consequence, turns are almost always situated at the surface of the protein, in contact with solvent water. We have searched proteins of known structure and find that, on occasion, a turn may be buried within the hydrophobic interior of the molecule. In every instance of a buried turn, one or more solvent molecules were also found in a hydrogen-bonded complex with main-chain atoms of the turn residues. These bound water molecules appear to function as an integral part of the protein structure.

Hierarchic organization of globular proteins. A control study

In previous work, globular proteins of known structure were shown to be iteratively subdivisible into a hierarchy of disjunct, contiguous-chain regions, ranging in size from whole protein monomers down to individual helices and strands (1, 2). We now report the results of a similar analysis performed on a set of 1000 simulated chain folds that were generated by a method due to Schulz (3). The organization of these simulated proteins was found to be similar to that of authentic molecules. This control study strengthens earlier evidence suggesting that hierarchic architecture is a ubiquitous attribute of protein chain folds.

A general model of the P2 protein of peripheral nervous system myelin based on secondary structure predictions, tertiary folding principles, and experimental observations

The amino acid sequence of the P2 protein of peripheral myelin was analyzed with regard to regions of probable alpha-helix, beta-structure, beta-turn, and unordered conformation by means of several algorithms commonly used to predict secondary structure in proteins. Because of the high beta-sheet content and virtual absence of alpha-helix shown by the circular dichroic spectra of the protein, a bias was introduced into the algorithms to favor the beta-structure over the alpha-helical conformation. In order to define those beta-sheet residues that could lie on the external hydrophilic surface of the protein and those that could lie in its hydrophobic interior, the predicted beta-strands were examined for charged and uncharged amino acids located at alternating positions in the sequence. The sequential beta-strands in the predicted secondary structure were then ordered into beta-sheets and aligned according to generally accepted tertiary folding principles and certain chemical properties peculiar to the P2 protein. The general model of the P2 protein that emerged was a "Greek key" beta-barrel, consisting of eight antiparallel beta-strands with a two-stranded ribbon of antiparallel beta-structure emerging from one end. The model has an uncharged, hydrophobic core and a highly hydrophilic surface. The two Cys residues, which form a disulfide, occur in a loop connecting two adjacent antiparallel strands. Two hydrophilic loops, each containing a cluster of acidic residues and a single Phe, protrude from one end of the molecule. The general model is consistent with many of the properties of the actual protein, including the relatively weak nature of its association with myelin lipids and the positions of amino acid substitutions. Alternative beta-strand orderings yield three specific models having different interstrand connections across the barrel ends.

Structural homology of lens crystallins. A method to detect protein structural homology from primary sequences

The X-ray crystallographic structure of bovine gamma-crystallin shows four similar folding motifs each composed of about 42 residues arranged as four topologically sequential, anti-parallel beta-strands. Since the beta and gamma-crystallin sequences show good homology, proposals for a four-motif beta-crystallin model have been made. The other bovine eye-lens protein species, alpha-crystallins, are not homologous to beta or gamma-crystallin in primary structure. In the present work, smoothed plots of amino acid sequence number versus a residue characteristic (e.g. hydrophobicity) were calculated for the various crystallins. Cross-correlation coefficients were then determined between pairs of crystallin plots for various registers of the curves. The correlation plots were then combined for several characteristics and for pairwise comparisons between beta or gamma-crystallin and the alpha-crystallins. The resulting plots showed four peaks separated by about 42 residues for the alpha-crystallins, suggesting that they also possess a four-motif beta-barrel structure. The physical parameter comparison technique appears generally applicable in suggesting a structural and functional relationship amongst proteins that show no primary sequence homology.

Structural prediction of membrane-bound proteins

A prediction algorithm based on physical characteristics of the twenty amino acids and refined by comparison to the proposed bacteriorhodopsin structure was devised to delineate likely membrane-buried regions in the primary sequences of proteins known to interact with the lipid bilayer. Application of the method to the sequence of the carboxyl terminal one-third of bovine rhodopsin predicted a membrane-buried helical hairpin structure. With the use of lipid-buried segments in bacteriorhodopsin as well as regions predicted by the algorithm in other membrane-bound proteins, a hierarchical ranking of the twenty amino acids in their preferences to be in lipid contact was calculated. A helical wheel analysis of the predicted regions suggests which helical faces are within the protein interior and which are in contact with the lipid bilayer.

Nucleotide sequence of the 3' half of AKV

We report the nucleotide sequence of the 3' half of the ecotropic murine leukemia virus AKV genome. To obtain a preliminary sequence, we developed a sequencing strategy whereby a nested set of restriction fragments is chemically modified prior to gel purification and strand scission. The sequence defines the genetic map of the 3' half of AKV and locates recombinant regions previously identified in structural analyses of MCF viruses.

Antibodies against a synthetic peptide of the poliovirus replicase protein: reaction with native, virus-encoded proteins and inhibition of virus-specific polymerase activities in vitro

A carboxy-terminal peptide of the poliovirus replicase protein (p63) was chemically synthesized, coupled to bovine serum albumin carrier, and injected into rabbits. The resulting antisera reacted with six virus-specific proteins from HeLa cells infected with poliovirus: NCVP 0b, NCVP 1b, NCVP 2, a protein of about 60,000 daltons, p63, and NCVP 6b. The identity of the 60,000-dalton protein is not known, but the other results were consistent with previous experimental approaches which demonstrated that p63 and the other four polypeptides have common coding sequences. An amino-terminal peptide of p63 failed to elicit an immune response in rabbits. Antibodies raised against the p63 carboxy-terminal peptide inhibited poliovirus replicase and polyuridylic acid polymerase activities in vitro, providing strong support for earlier suggestions that these activities are a property of a single virus-specific polypeptide.

Prediction of secondary structural elements in the phosphatidylcholine-transfer protein from bovine liver

Secondary structural elements of the phosphatidylcholine-transfer protein from bovine liver have been predicted from its primary structure with the aid of two computerized methods. The predicted alpha-helix and beta-strand content have been compared with the values derived from circular dichroism spectra. The hydrophobicity profile (Rose plot) of the protein indicated that the supposed lipid-binding site occurs in the most hydrophobic region. The predicted secondary structural elements have been folded in a tentative model of the protein molecule according to its hydrophobicity profile.

Folding units in globular proteins

We present a method to identify all compact, contiguous-chain, structural units in a globular protein from x-ray coordinates. These units are then used to describe a complete set of hierarchic folding pathways for the molecule. Our analysis shows that the larger units are combinations of smaller units, giving rise to a structural hierarchy ranging from the whole protein monomer through supersecondary structures down to individual helices and strands. It turns out that there is more than one way to assemble the protein by self-association of its compact units. However, the number of possible pathways is small--small enough to be exhaustively explored by a computer program. The hierarchic organization of compact units in protein molecules is consistent with a model for folding by hierarchic condensation. In this model, neighboring hydrophobic chain sites interact to form folding clusters, with further stepwise cluster association giving rise to a population of folding intermediates.

Prediction of protein antigenic determinants from amino acid sequences

A method is presented for locating protein antigenic determinants by analyzing amino acid sequences in order to find the point of greatest local hydrophilicity. This is accomplished by assigning each amino acid a numerical value (hydrophilicity value) and then repetitively averaging these values along the peptide chain. The point of highest local average hydrophilicity is invariably located in, or immediately adjacent to, an antigenic determinant. It was found that the prediction success rate depended on averaging group length, with hexapeptide averages yielding optimal results. The method was developed using 12 proteins for which extensive immunochemical analysis has been carried out and subsequently was used to predict antigenic determinants for the following proteins: hepatitis B surface antigen, influenza hemagglutinins, fowl plague virus hemagglutinin, human histocompatibility antigen HLA-B7, human interferons, Escherichia coli and cholera enterotoxins, ragweed allergens Ra3 and Ra5, and streptococcal M protein. The hepatitis B surface antigen sequence was synthesized by chemical means and was shown to have antigenic activity by radioimmunoassay.