Prediction of the tertiary structure of the alpha-subunit of tryptophan synthase

The tertiary structure of the alpha-subunit of tryptophan synthase was proposed using a combination of experimental data and computational methods. The vacuum-ultraviolet circular dichroism spectrum was used to assign the protein to the alpha/beta-class of supersecondary structures. The two-domain structure of the alpha-subunit (Miles et al.: Biochemistry 21:2586, 1982; Beasty and Matthews: Biochemistry 24:3547, 1985) eliminated consideration of a barrel structure and focused attention on a beta-sheet structure. An algorithm (Cohen et al.: Biochemistry 22:4894, 1983) was used to generate a secondary structure prediction that was consistent with the sequence data of the alpha-subunit from five species. Three potential secondary structures were then packed into tertiary structures using other algorithms. The assumption of nearest neighbors from second-site revertant data eliminated 97% of the possible tertiary structures; consideration of conserved hydrophobic packing regions on the beta-sheet eliminated all but one structure. The native structure is predicted to have a parallel beta-sheet flanked on both sides by alpha-helices, and is consistent with the available data on chemical cross-linking, chemical modification, and limited proteolysis. In addition, an active site region containing appropriate residues could be identified as well as an interface for beta 2-subunit association. The ability of experimental data to facilitate the prediction of protein structure is discussed.     

Characterization of the mechanism of interaction between α1-acid glycoprotein and lipid membranes by vacuum-ultraviolet circular-dichroism spectroscopy

α₁-Acid glycoprotein (AGP) interacts with lipid membranes as a peripheral membrane protein so as to decrease the drug-binding capacity accompanying the β→α conformational change that is considered a protein-mediated uptake mechanism for releasing drugs into membranes or cells. This study characterized the mechanism of interaction between AGP and lipid membranes by measuring the vacuum-ultraviolet circular-dichroism (VUVCD) spectra of AGP down to 170 nm using synchrotron radiation in the presence of five types of liposomes whose constituent phospholipid molecules have different molecular characteristics in the head groups (e.g., different net charges). The VUVCD analysis showed that the α-helix and β-strand contents and the numbers of segments of AGP varied with the constituent phospholipid molecules of liposomes, while combining VUVCD data with a neural-network method predicted that these membrane-bound conformations comprised several common long helix and small strand segments. The amino-acid composition of each helical segment of the conformations indicated that amphiphilic and positively charged helices formed at the N- and C-terminal regions of AGP, respectively, were candidate sites for the membrane interaction. The addition of 1 M sodium chloride shortened the C-terminal helix while having no effect on the length of the N-terminal one. These results suggest that the N- and C-terminal helices can interact with the membrane via hydrophobic and electrostatic interactions, respectively, demonstrating that the liposome-dependent conformations of AGP analyzed using VUVCD spectroscopy provide useful information for characterizing the mechanism of interaction between AGP and lipid membranes.     

Effect of lysine modification on the secondary structure of ovalbumin

In order to determine the effect of chemical modification of the -amino groups on the secondary structure of ovalbumin, we prepared six acetylated (17, 36, 54, 70, 82, and 98%) and four succinylated derivatives (25, 50, 72, and 97%) of the protein. Native ovalbumin and the acylated derivatives were homogeneous as revealed by the electrophoretic pattern. The UV-absorption and fluorescence spectra changed progressively with the extent of modification. However, circular dichroic (CD) studies indicated that acylation of 15 of the 20 lysine residues had little effect on the secondary structure of ovalbumin. Acylation of the remaining five lysine residues resulted in a fairly severe change in the secondary structure. The -helical content decreased from about 31% in the native state to 16.5% in the 97% succinylated ovalbumin and to 21.5% in the 98% acetylated derivative. A comparison of these data with the spectral and hydrodynamic data of Qasim and Salahuddin (1978) suggested that the secondary structure of ovalbumin is more resistant to acylation than is the tertiary structure and, thus, the tertiary and the secondary structures are, to some extent, mutually independent. Raising thepH to 11.2 did not alter the secondary structure of ovalbumin and increasing the ionic strength by more than 20-fold did not reverse the loss of helical structure in 97% succinylated protein. These two observations suggest that the change in secondary structure upon maximal acylation may not only involve electrostatic effects, but also certain other factors, such as steric hindrance due to the entering bulky groups.     

Solution conformations of peptides representing the sequence of the toxin pardaxin and analogues in trifluoroethanol-water mixtures: Analysis of CD spectra

The cytolytic activities and conformational properties of pardaxin (GFFALIPKIISSPLFKTLLSAVGSALSSSGEQE), a 33-residue linear peptide that exhibits unusual shark repellent and cytolytic activities, and its analogues have been examined in aqueous environment and trifluoroethanol (TFE) using CD spectroscopy. A peptide corresponding to the 1–26 segment and an analogue where P7 has been changed to A show greater hemolytic activity than pardaxin. While the peptide corresponding to the N-terminal 18-residue segment does not exhibit hemolytic activity, its analogue where P7 is replaced by A is hemolytic. The secondary structural propensities of the peptides were inferred by deconvolution of the experimental spectra into pure components. Pardaxin, its variant where proline at position 7 was replaced by alanine, and shorter peptides corresponding to N-terminal segments exist in multiple conformations in aqueous medium that are comprised of β-turn, β-sheet, and distorted helical structures. With increasing proportions of TFE, while helical conformation predominates in all the peptides, both distorted and the regular α-helices appear to be populated. Analysis of CD spectra by deconvolution methods appears to be a powerful tool for delineating multiple conformations in peptides, especially membrane-active peptides that encounter media of different polarity ranging from aqueous environment to one of low dielectric constant in the hydrophobic interior of membranes. Our study provides further insights into the structural requirements for the biological activity of pardaxin and related peptides. © 1997 John Wiley & Sons, Inc. Biopoly 41: 635–645, 1997     

Design of analogues of parathyroid hormone: A conformational approach

An approach to the design of peptide-hormone analogues in which amino acid substitutions are based on predicted effects on secondary structure was investigated. The structural requirements for parathyroid-hormone (PTH) action are distinct from the determinants necessary for receptor binding alone without subsequent activation of adenylate cyclase. Two analogues of PTH containing substitutions in the principal binding domain of PTH, the region 25–34, were synthesized by the solid-phase method and evaluated for bioactivity. The sequence 25–34 was predicted to have nearly equal conformational potential for both -helix and -sheet using Chou and Fasman parameters. A previously studied analogue, [Tyr³⁴]bPTH(1–34) amide, containing substitutions in this region, was more active than was bPTH-(1–34). The substitution of tyrosine for phenylalanine at position 34 in this analogue is predicted to promote -sheet conformation. The analogues [Ile²⁸, Tyr³⁰, Tyr³⁴]bPTH-(1–34) amide and [Arg³², Tyr³⁴]bPTH-(1–34) amide each contain substitutions predicted to further enhance or stabilize -sheet formation. The solution conformation of these analogues, determined by circular dichroism studies in an aqueous buffer and an organic solvent, indicated promotion of -sheet secondary structural content in both analogues in a hydrophobic environment chosen to simulate that of the interaction of the peptide and the membrane receptor. In contrast, the native sequence lacks -structure. Biological activity of these analogues in the rat renal adenylate cyclase assay in vitro and binding affinity in a radioreceptor assay were threefold those of unsubstituted PTH-(1–34). Peptide analogue design based on conformational prediction, rather than substitution of primary structure alone, offers an attractive alternative approach to the development of hormone analogues and antagonists.     

Conformation of the abortifacient protein pinellin: A circular dichroic study

The conformation of pinellin was studied by circular dichroism, which showed a minimum at 223 nm and a double maximum at 198–200 nm. The protein was rich in -sheet (about 40%) with little -helix, based on current CD analyses. It was stable betweenpH 4 and 10 beyond which it unfolded reversibly, but in alkaline solution, prolongly stored at, say,pH 12, it became irreversibly denatured. Thermal denaturation indicated a transition between 55° and 68°C; the solution at 80°C was partially renatured upon air-cooling back to room temperature. Addition of sodium dodecyl sulfate caused a sharp increase in -helix, which leveled off at 0.25 mM surfactant.     

Circular dichroism study of ribonuclease A mutants containing the minimal structural requirements for dimerization and swapping

Four residues Pro19, Leu28, Cys31 and Cys32 proved to be the minimal structural requirements in determining the dimeric structure and the N-terminal segment swapping of bovine seminal ribonuclease, BS-RNase. We analyzed the content of secondary and tertiary structures in RNase A, P-RNase A, PL-RNase A, MCAM-PLCC-RNase A and MCAM-BS-RNase, performing near and far-UV CD spectra. It results that the five proteins have very similar native conformations. Thermal denaturation at pH 5.0 of the proteins, studied by means of CD measurements, proved reversible and well represented by the two-state ND transition model. Thermodynamic data are discussed in the light of the structural information available for RNase A and BS-RNase.     

Circular dichroism studies on conformational changes in protein molecules upon adsorption on ultrafine polystyrene particles

The conformational changes in well-characterized model proteins [bovine ribonuclease A (RNase A), horseradish peroxidase, sperm-whole myoglobin, human hemoglobin, and bovine serum albumin (BSA)] upon adsorption on ultrafine polystyrene (PS) particles have been studied using circular dichroism (CD) spectroscopy. These proteins were chosen with special attention to molecular flexibility. The ultrafine PS particles were negatively charged and have average diameters of 20 or 30 nm. Utilization of these ultrafine PS particles makes it possible to apply the CD technique to determine the secondary structure of proteins adsorbed on the PS surface. Effects of protein properties and adsorption conditions on the extent of the changes in the secondary structure of protein molecules upon adsorption on ultrafine PS particles were studied. The CD spectrum changes upon adsorption were significant in the "soft" protein molecules (myoglobin, hemoglobin, and BSA), while they were insingnificant in the "rigid" proteins (RNase A and peroxidase). The soft proteins sustained a marked decrease in alpha-helix content upon adsorption. Moreover, the native alpha-helix content, which is given as the percentage of the alpha-helix content in the free proteins, of adsorbed BSA was found to decrease with decreasing pH and increase with increasing adsorbed amount. These observations confirm some well-known hypotheses for the confirmational chages in protein molecules upon adsorption. (c) 1992 John Wiley & Sons, Inc.     

The stabilisation of insect cuticles

The possible means by which insect cuticle is stabilised are examined: evidence is presented that secondary interactions between the components are very important in stabilisation. Cuticular proteins are shown to be able to adopt stable secondary structures. It is concluded that cuticle may well be stabilised by changes in the conformation of the proteins, changes in the secondary bonding between the proteins and the inclusion of a polymer filler. Crosslinking of the cuticular components may be of little consequence: the stabilisation would be a result of cuticular dehydration.