Biophysical studies and anti-growth activities of a peptide, a certain analog and a fragment peptide derived from alpha-fetoprotein

A chemically synthesized 34-amino acid peptide, an analog, and a fragment of the peptide have been purified and studied. Biophysical studies were carried out to determine some of the metal ion binding properties of the original peptide and an analog of this parent peptide, in which the two histidine residues were replaced by alanines. As shown by visible absorption spectroscopy, Co (II) forms a complex with the parent peptide, but not with the analog peptide, and one or two histidines in the parent peptide are ligands for Co (II) ion binding. The effects on disulfide bond formation in the peptide by Zn (II) and Co (II) ions were also examined for this analog. Anti-growth assays were performed using the original cysteine-containing peptide with Zn (II) ion complexed to the peptide through the two cysteine residues. These rat uterine growth assays showed that the complexing of Zn (II) ion to the peptide maintained the anti-growth activity of the peptide, while gel-filtration experiments showed the zinc ions maintained the peptide in its anti-growth form indefinitely in solution. A saliently important part of this research was the discovery that a fragment of the peptide consisting of a middle sequence of 14 amino acids was found to have significant anti-growth activity in the rat uterine assay. Its activity suggested that this fragment might be considered a viable candidate for testing in anti-cancer protocols.

Biliproteins and phycobilisomes from cyanobacteria and red algae at the extremes of habitat

This review considers the properties of biliproteins from cyanobacteria and red algae that grow in extreme habitats. Three situations are presented: cyanobacteria that grow at high temperatures; a red alga that grows in acidic conditions at high temperature; and an Antarctic red alga that grows in the cold in dim light conditions. In particular, the properties of their biliproteins are compared to those from organisms from more usual environments. C-phycocyanins from two cyanobacteria able to grow at high temperatures are found to differ in their stabilities when compared to C-phycocyanin from mesophilic algae. They differ in opposite ways, however. One is more stable to dissociation than the mesophilic protein, and the other is more easily dissociated at low temperatures. The thermophilic proteins resist thermal denaturation much better than the mesophilic proteins. The most thermophilic cyanobacterium has a C-phycocyanin with a unique blue-shifted absorption maximum which does not appear to be part of the adaptation of the cyanobacterium to high temperature. The C-phycocyanin from the high-temperature red alga is able to resist dissociation better than mesophilic C-phycocyanins. Electron micrographs show the phycobilisomes of these algae. The Antarctic alga grows under ice at some distance down the water column. Its R-phycoerythrin has a novel absorption spectrum that gives the alga an improved ability to harvest blue light. This may enhance its survival in its light-deprived habitat.

Interrelationships among biological activity, disulfide bonds, secondary structure, and metal ion binding for a chemically synthesized 34-amino-acid peptide derived from alpha-fetoprotein

A 34-amino-acid peptide has been chemically synthesized based on a sequence from human alpha-fetoprotein. The purified peptide is active in anti-growth assays when freshly prepared in pH 7.4 buffer at 0.20 g/l, but this peptide slowly becomes inactive. This functional change is proven by mass spectrometry to be triggered by the formation of an intrapeptide disulfide bond between the two cysteine residues on the peptide. Interpeptide cross-linking does not occur. The active and inactive forms of the peptide have almost identical secondary structures as shown by circular dichroism (CD). Zinc ions bind to the active peptide and completely prevents formation of the inactive form. Cobalt(II) ions also bind to the peptide, and the UV-Vis absorption spectrum of the cobalt-peptide complex shows that: (1) a near-UV sulfur-to-metal-ion charge-transfer band had a molar extinction coefficient consistent with two thiolate bonds to Co(II); (2) the lowest-energy visible d-d transition maximum at 659 nm, also, demonstrated that the two cysteine residues are ligands for the metal ion; (3) the d-d molar extinction coefficient showed that the metal ion-ligand complex was in a distorted tetrahedral symmetry. The peptide has two cysteines, and it is speculated that the other two metal ion ligands might be the two histidines. The Zn(II)- and Co(II)-peptide complexes had similar peptide conformations as indicated by their ultraviolet CD spectra, which differed very slightly from that of the free peptide. Surprisingly, the cobalt ions acted in the reverse of the zinc ions in that, instead of stabilizing anti-growth form of the peptide, they catalyzed its loss. Metal ion control of peptide function is a saliently interesting concept. Calcium ions, in the conditions studied, apparently do not bind to the peptide. Trifluoroethanol and temperature (60 degrees C) affected the secondary structure of the peptide, and the peptide was found capable of assuming various conformations in solution. This conformational flexibility may possibly be related to the biological activity of the peptide.

Hormone-induced conformational change of the purified soluble hormone binding domain of follitropin receptor complexed with single chain follitropin

Human follicle-stimulating hormone receptor (hFSHR) belongs to family I of G protein-coupled receptors. FSHR extracellular domain (ECD) is predicted to have 8-9 alphabeta or leucine-rich repeat motif elements. The objective of this study was to identify elements of the FSHR ECD involved in ligand binding. Preincubation of recombinant hFSHR ECD with rabbit antisera raised against synthetic peptides of hFSHR ECD primary sequence abolished follitropin binding primarily in the region of amino acids 150-254. Accessibility of hFSHR ECD after hormone binding, captured by monoclonal antibodies against either ECD or FSH, was decreased for the region of amino acids 150-220 but additionally for amino acids 15-100. Thus, when hFSH bound first, accessibility of antibody binding was decreased to a much larger extent than if antibody was bound first. This suggestion of a conformational change upon binding was examined further. Circular dichroism spectra were recorded for purified single chain hFSH, hFSHR ECD, and hFSHR ECD-single chain hFSH complex. A spectral change indicated a small but consistent conformational change in the ECD.FSH complex after hormone binding. Taken together, these data demonstrate that FSH binding requires elements within the leucine-rich repeat motifs that form a central region of hFSHR ECD, and a conformational change occurs upon hormone binding.

The basal transcription factors TBP and TFB from the mesophilic archaeon Methanosarcina mazeii: structure and conformational changes upon interaction with stress-gene promoters

Transcription of archaeal non-stress genes involves the basal factors TBP and TFB, homologs of the eucaryal TATA-binding protein and transcription factor IIB, respectively. No comparable information exists for the archaeal molecular-chaperone, stress genes hsp70(dnaK), hsp40(dnaJ), and grpE. These do not occur in some archaeal species, but are present in others possibly due to lateral transfer from bacteria, which provides a unique opportunity to study regulation of stress-inducible bacterial genes in organisms with eukaryotic-like transcription machinery. Among the Archaea with the genes, those from the mesophilic methanogen Methanosarcina mazeii are the only ones whose basal (constitutive) and stress-induced transcription patterns have been determined. To continue this work, tbp and tfb were cloned from M. mazeii, sequenced, and the encoded recombinant proteins characterized in solution, separately and in complex with each other and with DNA. M. mazeii TBP ranks among the shortest within Archaea and, contrary to other archaeal TBPs, it lacks tryptophan or an acidic tail at the C terminus and has a basic N-terminal third. M. mazeii TFB is similar in length to archaeal and eucaryal homologs and all have a zinc finger and HTH motifs. Phylogenetically, the archaeal and eucaryal proteins form separate clusters and the M. mazeii molecules are closer to the homologs from Archaeoglobus fulgidus than to any other. Antigenically, M. mazeii TBP and TFB are close to archaeal homologs within each factor family, but the two families are unrelated. The purified recombinant factors were functionally active in a cell-free in vitro transcription system, and were interchangeable with the homologs from Methanococcus thermolithotrophicus. The M. mazeii factors have a similar secondary structure by circular dichroism (CD). The CD spectra changed upon binding to the promoters of the stress genes grpE, dnaK, and dnaJ, with the changes being distinctive for each promoter; in contrast, no effect was produced by the promoter of a non-stress-gene. Factor(s)-DNA modeling predicted that modifications of H bonds are caused by TBP binding, and that these modifications are distinctive for each promoter. It also showed which amino acid residues would contact an extended TATA box with a B recognition element, and evolutionary conservation of the TBP-TFB-DNA complex orientation between two archaeal organisms with widely different optimal temperature for growth (37 and 100 degrees C).

Studies on analogs of a peptide derived from alpha-fetoprotein having antigrowth properties

A 34-amino acid portion of the third domain of alpha-fetoprotein possesses antigrowth and anticancer activities. Three analogs of this sequence were chemically synthesized, in which the two cysteines of the original sequence were replaced by alanines, glycines or serines. The original cysteine and alanine peptides formed trimers at 0.20 g/L in pH 7.4 phosphate buffer, and the glycine and serine peptides formed dimers. Trimer preparations were more potent in inhibiting estrogen-induced growth in the mouse uterine assays than the two dimeric oligomers. Of salient importance is that the alanine peptide retained its trimeric form in solution much longer than the cysteine peptide. Antigrowth assays were performed starting with stock solutions at a peptide concentration of 0.20 g/L, because at very high peptide concentration (8.0 g/L) the peptides aggregated extensively. All the peptides, although differing in biological activity, had almost identical secondary structures. Unlike alpha-fetoprotein, the three peptides have low amounts of alpha-helix. Trifluoroethanol has the ability to convert peptides into a helical conformation when they have a propensity for that structure. At trifluoroethanol concentrations of 20% and higher, the alanine and glycine peptides were changed into highly helical structures.

Autologous biological response modification of the gonadotropin receptor

It is generally held with respect to heterotrimeric guanine nucleotide binding protein-coupled receptors that binding of ligand stabilizes a conformation of receptor that activates adenylyl cyclase. It is not formally appreciated if, in the case of G-protein-coupled receptors with large extracellular domains (ECDs), ECDs directly participate in the activation process. The large ECD of the glycoprotein hormone receptors (GPHRs) is 350 amino acids in length, composed of seven leucine-rich repeat domains, and necessary and sufficient for high affinity binding of the glycoprotein hormones. Peptide challenge experiments to identify regions in the follicle-stimulating hormone (FSH) receptor (FSHR) ECD that could bind its cognate ligand identified only a single synthetic peptide corresponding to residues 221-252, which replicated a leucine-rich repeat domain of the FSHR ECD and which had intrinsic activity. This peptide inhibited human FSH binding to the human FSHR (hFSHR) and also inhibited human FSH-induced signal transduction in Y-1 cells expressing recombinant hFSHR. The hFSHR-(221-252) domain was not accessible to anti-peptide antibody probes, suggesting that this domain resides at an interface between the hFSHR ECD and transmembrane domains. CD spectroscopy of the peptide in dodecyl phosphocholine micelles showed an increase in the ordered structure of the peptide. CD and NMR spectroscopies of the peptide in trifluoroethanol confirmed that hFSHR-(221-252) has the propensity to form ordered secondary structure. Importantly and consistent with the foregoing results, dodecyl phosphocholine induced a significant increase in the ordered secondary structure of the purified hFSHR ECD as well. These data provide biophysical evidence of the influence of environment on GPHR ECD subdomain secondary structure and identify a specific activation domain that can autologously modify GPHR activity.

Studies on a growth-inhibitory peptide derived from alpha-fetoprotein and some analogs

A 34-amino acid synthetic peptide was derived from the third domain of human alpha-fetoprotein, and the peptide was shown to inhibit estrogen-stimulated growth. Under certain conditions, however, the peptide lost growth-inhibitory activity. A biophysical study of the peptide was undertaken with a goal of obtaining completely reliable preparations. The peptide was studied using gel-filtration column chromatography as a function of peptide concentration and age of solution, and was found to exhibit complex aggregation behaviors. During the early period (0-3 h) after dissolving lyophilized peptide into pH 7.4 buffer, solutions were composed mostly of trimers. At higher peptide concentrations (> or = 3.0 g/L), the trimers aggregated extensively to a large aggregate (minimum size approximately 102 peptides). At 5.0-8.0 g/L, these large aggregates increased in size (up to approximately 146 peptides) until trimers were largely exhausted from solution. During the later times (>3 h) after sample preparation, the trimeric oligomer of the peptide dissociated slowly to form dimers for samples at 0.10-3.0 g/L. After their build-up, a very small number of dimers associated to form hexamers. Disulfide bonds stabilized the dimers as indicated by the conversion of dimers to trimers upon the addition of a reducing agent, and the failure of dimers to form in the presence of reducing agent. Reducing agent did not affect trimer or large aggregate formation. Trimers were found to be active in an assay monitoring inhibition of estrogen-stimulated growth, whereas dimers and large aggregates were inactive. The two cysteines in the peptide were modified to either S-methylcysteine or S-(2-aminoethyl)cysteine, and both derivatives showed significant growth-inhibition activity. A serine analog in which both cysteines were replaced had very different aggregation behavior than the cysteine peptide and lacked its growth inhibitory ability. Peptide aggregation is critically important in establishing the ability of the peptide to inhibit growth and have anticancer activity, but the state of its two cysteines is of little influence.

Affinity labeling fatty acyl-CoA synthetase with 9-p-azidophenoxy nonanoic acid and the identification of the fatty acid-binding site

Fatty acyl-CoA synthetase (FACS, fatty acid:CoA ligase, AMP-forming, EC ) catalyzes the esterification of fatty acids to CoA thioesters for further metabolism and is hypothesized to play a pivotal role in the coupled transport and activation of exogenous long-chain fatty acids in Escherichia coli. Previous work on the bacterial enzyme identified a highly conserved region (FACS signature motif) common to long- and medium-chain acyl-CoA synthetases, which appears to contribute to the fatty acid binding pocket. In an effort to further define the fatty acid-binding domain within this enzyme, we employed the affinity labeled long-chain fatty acid [(3)H]9-p-azidophenoxy nonanoic acid (APNA) to specifically modify the E. coli FACS. [(3)H]APNA labeling of the purified enzyme was saturable and specific for long-chain fatty acids as shown by the inhibition of modification with increasing concentrations of palmitate. The site of APNA modification was identified by digestion of [(3)H]APNA cross-linked FACS with trypsin and separation and purification of the resultant peptides using reverse phase high performance liquid chromatography. One specific (3)H-labeled peptide, T33, was identified and following purification subjected to NH(2)-terminal sequence analysis. This approach yielded the peptide sequence PDATDEIIK, which corresponded to residues 422 to 430 of FACS. This peptide is immediately adjacent to the region of the enzyme that contains the FACS signature motif (residues 431-455). This work represents the first direct identification of the carboxyl-containing substrate-binding domain within the adenylate-forming family of enzymes. The structural model for the E. coli FACS predicts this motif lies within a cleft separating two distinct domains of the enzyme and is adjacent to a region that contains the AMP/ATP signature motif, which together are likely to represent the catalytic core of the enzyme.

Studies on C-phycocyanin from Cyanidium caldarium, a eukaryote at the extremes of habitat

C-Phycocyanin, a biliprotein, was purified from the red alga, Cyanidium caldarium. This alga grows at temperatures up to 57 degrees C, a very high temperature for a eukaryote, and at pH values down to 0.05. Using the chromophores on C-phycocyanin as naturally occurring reporter groups, the effects of temperature on the stability of the protein were studied by circular dichroism and absorption spectroscopy. The protein was unchanged from 10 to 50 degrees C, which indicates that higher temperatures are not required to cause the protein to be photosynthetically active. At 60 and 65 degrees C, which are above the temperatures at which the alga can survive, the protein undergoes irreversible denaturation. Gel-filtration column chromatography demonstrated that the irreversibility is caused by the dissociation of the trimeric protein to its constitutive polypeptides. Upon cooling, the alpha and beta polypeptides did not reassemble to the trimer. Unlike phycocyanins 645 and 612, the C-phycocyanin does not show a reversible conformational change at moderately high temperatures. At constant temperature, the C-phycocyanin was more stable than a mesophilic counterpart. It is designated a temperature-resistant protein.

Fluorescence polarization studies on four biliproteins and a bilin model for phycoerythrin 545

Fluorescence (excitation) polarization spectroscopy in the wavelength region of the bilin chromophores was applied to phycoerythrocyanin (CV-phycocyanin), phycocyanins 645 and 612, and phycoerythrin 545. The cryptomonad biliproteins - phycoerythrin 545 and phycocyanins 612 and 645 - were studied as both protein dimers having an alpha(2)beta(2) polypeptide structure and as alphabeta monomers. The cyanobacterial phycoerythrocyanin (CV-phycocyanin) was a trimeric oligomer. The changes in polarization across the spectrum were attributed to transfers of energy between bilins. Cryptomonad biliproteins are isolated as dimers. The similarities between their steady-state fluorescence polarization spectra and those of the corresponding monomers suggested that the monomers' conformations were analogous to the dimers. This supports the use of monomers in the study of dimer bilin organization. The unusual polarization spectrum of phycoerythrin 545 was explained using a model for the topography of its bilins. Obtaining the emission spectra of phycoerythrin 545 at several temperatures and a deconvolution of the dimer circular dichroism spectrum also successfully tested the bilin model. Circular dichroism spectroscopy was used to determine which polarization changes are formed by Förster resonance energy transfers and which may be produced by internal conversions between high- and low-energy states of pairs of exciton-coupled bilins. Attempts were made to assign energy transfer events to the corresponding changes in fluorescence polarization for each of the four biliproteins.

Bilin organization in cryptomonad biliproteins

The bilin organization of three cryptomonad biliproteins (phycocyanins 612 and 645 and phycoerythrin 545) was examined in detail. Two others (phycocyanin 630 and phycoerythrin 566) were studied less extensively. Phycocyanin 645 and phycoerythrin 545 were suggested to have one bilin in each monomeric (alphabeta) unit of the dimer (alpha2beta2) isolated from the others, and the remaining six bilins may be in pairs. One pair was found across the monomer-monomer interface of the protein dimer, and two identical pairs were proposed to be within the monomer protein units. For phycocyanin 612, a major surprise was that a pair of bilins was apparently not found across the monomer-monomer interface, but the remaining bilins were distributed as in the other two cryptomonad proteins. The effect of temperature on the CD spectra of phycocyainin 612 demonstrated that two of the bands (one positive and one negative) behaved identically, which is required if they are coupled. The two lowest-energy CD bands of phycocyanin 612 originated from paired bilins, and the two higher-energy bands were from more isolated bilins. The paired bilins within the protein monomers contained the lowest-energy transition for these biliproteins. Using the bilins as naturally occurring reporter groups, phycocyanin 612 was shown to undergo a reversible change in tertiary structure at 40 degrees C. Protein monomers were shown to be functioning biliproteins. A hypothesis is that the coupled pair of bilins within the monomeric units offers important advantages for efficient energy migration, and other bilins transfer energy to this pair, extending the wavelength range or efficiency of light absorption.

Cyanobacterial phycobilisomes

Cyanobacterial phycobilisomes harvest light and cause energy migration usually toward photosystem II reaction centers. Energy transfer from phycobilisomes directly to photosystem I may occur under certain light conditions. The phycobilisomes are highly organized complexes of various biliproteins and linker polypeptides. Phycobilisomes are composed of rods and a core. The biliproteins have their bilins (chromophores) arranged to produce rapid and directional energy migration through the phycobilisomes and to chlorophyll a in the thylakoid membrane. The modulation of the energy levels of the four chemically different bilins by a variety of influences produces more efficient light harvesting and energy migration. Acclimation of cyanobacterial phycobilisomes to growth light by complementary chromatic adaptation is a complex process that changes the ratio of phycocyanin to phycoerythrin in rods of certain phycobilisomes to improve light harvesting in changing habitats. The linkers govern the assembly of the biliproteins into phycobilisomes, and, even if colorless, in certain cases they have been shown to improve the energy migration process. The Lcm polypeptide has several functions, including the linker function of determining the organization of the phycobilisome cores. Details of how linkers perform their tasks are still topics of interest. The transfer of excitation energy from bilin to bilin is considered, particularly for monomers and trimers of C-phycocyanin, phycoerythrocyanin, and allophycocyanin. Phycobilisomes are one of the ways cyanobacteria thrive in varying and sometimes extreme habitats. Various biliprotein properties perhaps not related to photosynthesis are considered: the photoreversibility of phycoviolobilin, biophysical studies, and biliproteins in evolution. Copyright 1998 Academic Press.

Circular dichroism analysis of the glucan binding domain of Streptococcus mutans glucan binding protein-A

The glucan binding domain (GBD) of the glucan binding protein-A (GBP-A) from the cariogenic bacterium Streptococcus mutans was studied using circular dichroism (CD) analysis, Chou-Fasman-Rose secondary structure prediction, and absorption and fluorescence spectroscopy. Our data show that the binding domain undergoes a conformational shift upon binding to the ligand dextran. The CD spectrum shows two positive bands at 280 nm and 230 nm which were assigned to aromatic residues. The 230-nm band was seen at 20 degrees C and 30 degrees C, lost intensity at 40 degrees C, and was eliminated at 45 degrees C coinciding with complete denaturation. The protein was stable at physiological pH, but precipitated at pH 5. A pH of 10 changed the secondary structure but had no effect on the 230-nm band. Analysis of the CD data in the far UV using the SELCON computer program revealed a high content of beta-sheets and a lack of alpha-helical structures. Secondary structure prediction based on the amino acid sequence of GBD agreed with the CD analysis. The fluorescence emission maximum at 339 nm suggested that the majority of the tryptophans were located in the interior of the protein. This maximum shifted to higher energy upon binding to the ligand dextran.

Phycoerythrin 545: monomers, energy migration, bilin topography, and monomer/dimer equilibrium

Phycoerythrin 545 was isolated having an alpha2beta2 (dimer) protein structure at pH 6.0 and 2 g/L protein concentration with eight bilin chromophores. Monomers (alphabeta) were produced by lowering the protein concentration to 0.15 g/L and the pH to 4.5. Dimer dissociation was monitored by dynamic light scattering and gel-filtration column chromatography. Monomers were stable and had bilin optical spectra different from the alpha2beta2 dimers, although they have very similar protein secondary structures. The optical spectra of phycoerythrin 545 showed four types of behavior with temperature: 10-20 degrees C, dimers; 40-50 degrees C, dimers/monomers; 60 degrees C, nearly fully disordered; 70 degrees C, disordered alpha and beta polypeptides. At 40 degrees C, the protein dissociated partially to monomer, which could be totally reversed to dimers at 20-25 degrees C. The visible circular dichroism difference spectrum for the protein dimers minus monomers exhibited positive and negative bands--such spectra may indicate exciton splitting between closely-spaced bilins. Circular dichroism also revealed a spectrum suggesting exciton coupling for the second excited state of the bilins. Ultrafast fluorescence using a two-photon method showed the fastest time for protein dimers to be 2. 4 ps and monomers had a 39-ps lifetime. Phycocyanin 645 was found to have a 550-fs lifetime.

Bilin chromophores as reporters of unique protein conformations of phycocyanin 645

At 45 degrees C, phycocyanin 645 maximally undergoes a reversible and stable conformational change. The change is observed in the visible (chromophore) region of the absorption and circular dichroism (CD) spectra. In the absorption spectrum, the absorbance is lower at 45 degrees C but remains much closer to the normal spectrum than to a strongly denatured spectrum. In the CD, a similar situation exists except that a negative band on the blue edge of the spectrum is much more strongly affected at 45 degrees C than the other bands. On returning to 20 degrees C, all these changes are restored to the original states. The protein is an alpha 2 beta 2 dimer at both 20 and 45 degrees C, and CD in the far-UV shows the identical protein secondary structures at both 20 and 45 degrees C. Fluorescence studies show that energy transfer occurs at both temperatures. At 50 degrees C the results are saliently different as the secondary structure changes and the spectral changes are mostly irreversible. At 50 degrees C, some monomers (alpha beta) are produced, and these monomers are very unstable at that temperature, resulting in the formation of some fully denatured polypeptides. Stable monomers can be produced at 20 degrees C and have visible absorption and CD spectra identical to the dimer at 45 degrees C. Therefore, the chromophores are reporting a tertiary conformational change at 45 degrees C, in which the two halves of the dimer each assume a monomer-like conformation prior to dissociating. These results are compared with a hypothesis for the chromophore topography, and the CD change at the blue edge of the spectra may result from the separation at 45 degrees C of a chromophore pair.

R-phycoerythrins having two conformations for the same aggregate

The visible circular dichroism (CD) spectrum of an R-phycoerythrin (Porphyra tenera) is composed of several positive bands. The protein in aqueous buffer very slowly exhibits changes in the CD spectrum of its chromophores, a band at 489 nm undergoes an increase in intensity and a red shift. When the band reached a 493 nm maximum, the spectrum became very stable. The aggregation state of the protein did not change during this spectral conversion. The chromophore CD spectrum was also obtained in the presence of a low concentration of urea or sodium thiocyanate, and the identical change in the CD was noted, but the change was much faster. The visible absorption and CD in the far UV spectra were unaffected by urea. Unchanged visible absorption and protein secondary structure (61% alpha helix) contradicted by comparatively salient alterations in the visible CD spectra suggested very subtle structural changes are influencing some of the chromophores. For a second R-phycoerythrin (Gastroclonium coulteri), the CD of the chromophores had a negative band on the blue edge of the spectrum. This is the first negative CD band observed for any R-phycoerythrin. Treatment of this protein with low concentrations of urea produced a change in the visible CD with the negative band being completely converted to a positive band. Fluorescence studies showed that the treatment by urea did not affect energy migration. Deconvolution of the CD spectra were used to monitor the chromophores. The results demonstrated that the same aggregate of each R-phycoerythrin could exist in two conformations, and this is a novel finding for any red algal or cyanobacterial biliprotein. The two forms of each protein would differ in tertiary structure, but retain the same secondary structures.

The discovery of a novel R-phycoerythrin from an antarctic red alga

A novel biliprotein, named R-phycoerythrin IV, has been discovered. It absorbs blue light better than any other known red algal biliprotein. The protein was found in Phyllophora antarctica, a benthic macroalga, which grows beneath the coastal waters of McMurdo Sound, Antarctica. Fluorescence emission and fluorescence excitation polarization spectroscopy demonstrated that R-phycoerythrin IV behaved as a typical R-phycoerythrin in the functioning of energy migration and has an emission maximum at 577 nm. The circular dichroism (CD) spectrum of the chromophores was compared with visible absorption spectrum, and both were deconvoluted. This process showed the energy states of various individual chromophores. The molecular weight of the protein suggested a alpha6beta6gamma polypeptide structure, and far UV CD studies revealed polypeptides with highly alpha-helical secondary structures. Dynamic light scattering indicated that the protein had a 5.54 nm radius, and its shape was nonspherical. R-phycoerythrin was also purified from a second benthic Antarctic red alga, Iridaea cordata. Its spectroscopic properties were similar to those of some R-phycoerythrins from nonpolar regions. The unique spectroscopic properties of R-phycocerythrin IV may help enable the alga to occupy its niche deeper in the water column than the red alga that has the typical R-phycoerythrin.

Studies on the dissociation of cryptomonad biliproteins

The spectroscopic properties of two biliproteins, phycocyanin 645 and phycoerythrin 566, have been studied by treating the proteins with two different agents, NaSCN at pH 6.0, or pH 4.0 without NaSCN. For phycoerythrin 566, treatment with NaSCN revealed that the visible CD spectrum of its chromophores was separated into a pair of different spectra, and each of these spectra was observed as a negative and one or more positive bands. For phycocyanin 645, two negative CD bands have been observed previously, together with two or more positive bands, in the dimer (alpha 2 beta 2) state, and NaSCN treatment caused elimination of one of these negative bands. The dimer was stable at pH 6.0, but at pH 4.0 the spectra of phycocyanin 645 had one less negative band than those at pH 6.0. Chromatography demonstrated that phycocyanin 645 was a monomer (alpha beta) at pH 4.0. Monomers of cryptomonad biliproteins have never been observed before. Excitation at 514 nm, in picosecond time-resolved fluorescence studies, produced lifetimes of 11.0 and 45.2 ps for dimers and monomers, respectively. Excitation at 566 nm yielded times of 1.38 and 1.24 ps, for dimers and monomers, respectively. CD in the far UV showed that monomers and dimers had very similar secondary structures. These results have been used to test an hypothesis that proposed two types of exciton splitting among the chromophores of phycocyanin 645, and perhaps phycoerythrin 566 could also have this chromophore organization.

Spectroscopic study of the interaction of aluminum ions with human transferrin

Transferrin is the plasma protein responsible for transporting Fe3+ from the absorption to the utilization site. Interactions of apo- and holo-transferrin with Al3+ were studied by circular dichroism (CD), UV-visible, and fluorescence spectrometry. Binding of Al3+ to both metal-ion binding sites of apo-transferrin was confirmed by fluorescence studies. No interaction of Al3+ with holo-transferrin was observed, indicating that Al3+ cannot displace Fe3+ under the experimental conditions employed. An increase in tryptophan fluorescence (lambda max at 330 nm) by excitation at either 280 or 295 nm was observed after Al3+ interaction with apo-transferrin. There was no shift in wavelength of the fluorescence band of apo-transferrin after interaction with Al3+, but the intensity did increase. Since excitation at 295 nm is specific for tryptophan residues, tryptophan but not tyrosine must be responsible for the change in fluorescence intensity. Decreased fluorescence is the result of Fe3+ binding to apo-transferrin. The CD spectrum of apo-transferrin was slightly affected in the far UV by Al3+ binding, but a salient change was noted in the near UV at approximately 288 nm where tyrosine and tryptophan absorb. It is concluded that a small conformational change in the protein was induced by Al3+ binding to apo-transferrin.

Exciton splitting in phycoerythrin 545

Phycoerythrin 545 is a biliprotein having a polypeptide structure of alpha 2 beta 2, and each alpha and beta polypeptide has chromophores. Circular dichroism (CD) and absorption spectroscopy in the visible region together with various biochemical protocols have been used to study these chromophores. The CD spectrum exhibits overlapping positive and negative bands. Exciton splitting between closely-spaced pairs of chromophores produces a CD spectrum that has positive and negative bands of equal rotational strengths, a conservative spectrum. Alternatively, any positive or negative band could arise from a single chromophore. The results of this study demonstrate that exciton splitting is the likely cause of the negative and corresponding positive bands. The CD spectra of the separated alpha and beta polypeptides, under conditions where the polypeptide structure is denatured, have no negative bands. When the polypeptides are allowed to refold individually, the chromophores on the beta polypeptide regain a combination of negative and positive CD bands. The spectrum of the alpha polypeptide shows no evidence of exciton splitting under these refolding conditions. In another approach, urea is added to the protein in low concentrations, which result in changes in the conformation and perhaps association of the protein. A difference CD spectrum of native protein minus protein in 0.8 M urea shows a spectrum characteristic of exciton splitting. Moreover, the remaining CD spectra in 0.8, 1.6, or 2.4 M urea still show the possibility of further exciton splitting, but a slightly different wavelengths from the spectrum that is deleted by 0.8 M urea. This finding may suggest that there are two types of exciton splitting.

Chromophore topography and exciton splitting in phycocyanin 645

The biliprotein phycocyanin 645 has been purified from a photosynthetic cryptomonad Chroomonas species. It is composed of two copies each of two polypeptides (alpha and beta); each alpha polypeptide has one chromophore, and each beta polypeptide has three. There are one cryptoviolin and two phycocyanobilins on each beta polypeptide and one 697-nm bilin on each alpha polypeptide for a total of eight chromophores on the protein. Circular dichroism (CD) spectroscopy has been used to investigate the arrangement of these chromophores. Comparisons among the intact protein (alpha 2 beta 2) and various urea-treated products have yielded a tentative model for chromophore topography. The six chromophores on the two beta polypeptides are segregated into three pairs. The chromophores of each pair are close enough to experience electronic interactions. One pair, consisting of the two cryptoviolins, produces exciton splitting on the blue edge of the visible CD spectrum, and the two pairs of phycocyanobilins cause exciton splitting on the red edge of this spectrum. Deconvolution shows that the CD spectrum of each pair has a positive and a negative band, which are nearly conservative as expected for exciton coupling. The two chromophores on the alpha polypeptides are more isolated. The pairing of cryptoviolin chromophores occurs across two beta polypeptides, but the more likely position of each of the two pairs of phycocyanobilins is probably not across a beta-beta interface but within a single beta polypeptide. The exciton splitting events both increase the range of visible light absorption for the protein and establish the routes of exciton migration through the protein.

Environmental effects on the folding of functional peptide segments from steroid hormone receptors

Recent improvements in circular dichroism (CD) instrumentation now allow investigators to obtain highly reliable and reproducible CD spectra in the far-UV range to near 180 nm. These advances, coupled with new computer software for spectral interpretation, allow accurate calculations of secondary structural content in proteins and polypeptides. CD is particularly reliable for the calculation of alpha-helical content. We have utilized these features to determine the propensity of alpha-helix formation in highly purified synthetic peptides corresponding to segments from proteins. We obtain CD spectra of the peptides in 90% 2,2,2-trifluoroethanol (90% TFE; an alpha-helix promoting solvent) and in 2 mM sodium dodecyl sulfate (2 mM SDS; a beta-sheet promoting solvent) to assess helix stability in these different chemical environments. Using this methodology, we demonstrate that a peptide corresponding to a biologically active segment of the human estrogen receptor forms a stable alpha-helix in both environments. In contrast, peptide segments of equal length from other steroid receptors are alpha-helical in TFE but not in 2 mM SDS. These results show that the conformation of a peptide is a function of both its amino acid sequence and the local chemical environment.

The binding domain structure of retinoblastoma-binding proteins

The retinoblastoma gene product (Rb), a cellular growth suppressor, complexes with viral and cellular proteins that contain a specific binding domain incorporating three invariant residues: Leu-X-Cys-X-Glu, where X denotes a nonconserved residue. Hydrophobic and electrostatic properties are strongly conserved in this segment even though the nonconserved amino acids vary considerably from one Rb-binding protein to another. In this report, we present a diagnostic computer pattern for a high-affinity Rb-binding domain featuring the three conserved residues as well as the conserved physico-chemical properties. Although the pattern encompasses only 10 residues (with only 4 of these explicitly defined), it exhibits 100% sensitivity and 99.95% specificity in database searches. This implies that a certain pattern of structural and physico-chemical properties encoded by this short sequence is sufficient to govern specific Rb binding. We also present evidence that the secondary structural conformation through this region is important for effective Rb binding.

The Chromophore and Polypeptide Composition of Aplysia Ink

The composition of the ink of the sea hare, Aplysia, was studied in regard to its tetrapyrrole and polypeptide content. The ink was separated into three pigment components by both thin-layer and gel filtration chromatography. These three pigments have distinctive visible absorption spectra, and--by comparison with known tetrapyrroles--we have demonstrated that they are derived from the three tetrapyrrole chromophores (bilins) found on the biliproteins of certain red algae, which constitute a portion of the Aplysia diet. The red component is phycourobilin; the purple is phycoerythrobilin; and the blue is phycocyanobilin. Sodium dodecyl sulfate gel electrophoresis experiments were also performed. The results of these experiments showed several polypeptides, and major bands at 78,000 and 61,000 molecular weight were noted. Biliproteins, at most, would be minor components of the ink.

Effect of oligosaccharides and chloride on the oligomeric structures of external, internal, and deglycosylated invertase

External invertase exists in an oligomeric equilibrium of dimer, tetramer, hexamer, and octamer, the concentrations of which vary with pH, time, and concentration of enzyme [Chu, F.K., Watorek, W., & Maley, F. (1983) Arch. Biochem. Biophys. 223, 543-555; Tammi, M., Ballou, L., Taylor, A., & Ballou, C.E. (1987) J. Biol. Chem. 262, 4395-4401]. To assess the influence of carbohydrate on this equilibrium, we investigated the self-association of external invertase (10 oligosaccharides per subunit), deglycosylated external invertase (2 oligosaccharides per subunit), and internal invertase (no carbohydrate) under various conditions. In addition, the effect of carbohydrate on the interaction of the subunits of these various invertases to form heterooligomers was studied. Chloride ion was found to promote subunit association in the various invertases irrespective of their glycosylation status. However, external invertase was less responsive to chloride ion relative to the internal and deglycosylated invertases. The higher oligomers of deglycosylated invertase were stable at 47 degrees C whereas those of external invertase dissociated rapidly into dimers, suggesting that the additional oligosaccharides in external invertase destabilize subunit interaction. Hybridization experiments with the various invertases showed that the dimers of internal invertase formed heterooligomers with either external or deglycosylated invertase. By contrast, the monomers of external and internal invertases formed their respective homodimers, but not heterodimers. These results suggest that the oligosaccharide content of invertase not only influences the extent of self-association but also affects heterooligomer formation.

Biliprotein light-harvesting strategies, phycoerythrin 566

A series of experiments on the light-harvesting properties of the cryptomonad biliprotein phycoerythrin 566 has been carried out on purified protein isolated from Cryptomonas ovata. Although this pigment has an absorption maximum at 566 nm, a property very close to that of other phycoerythrins, it was found to have a totally unique set of chromophores. The chromophores (bilins) responsible for its absorption spectrum were analyzed by a number of approaches. Chromophore-containing peptides were produced by trypsin treatment and purified in order to isolate the individual peptide-bound bilins free of overlapping absorption. These chromopeptides, after comparison with appropriate controls, showed that three spectrally distinct bilins occurred on the purified oligomeric protein. Two of the bilins were the well-known phycoerythrobilin and cryptoviolin, but the third was previously undiscovered and had an absorption spectrum between that of cryptoviolin and phycocyanobilin. Since the spectral diversity of the three bilins was fully maintained in solvents that minimize the effects of apoprotein on the spectra of the bilins, it is likely that the three bilins are also structurally dissimilar. The alpha and beta subunits, which constitute the protein, were separated by ion-exchange chromatography, and the new bilin was found to be the sole chromophore on the alpha subunit. It was also found that at least two alpha subunits could be separated and they both had this unusual bilin (cryptobilin 596). The beta subunit, therefore, contained both phycoerythrobilin and cryptoviolin. On the basis of the spectra of the three chromopeptides, the absorption spectrum of the protein was modeled using the known absorptivities of cryptoviolin and phycoerythrobilin.

Kinetics of allophycocyanin's trimer-monomer equilibrium

Kinetic studies of the dissociation of allophycocyanin trimers to monomers have been performed by using stopped-flow techniques. The dissociation was monitored by two techniques: by light scattering to observe the molecular weight changes directly and by 650-nm absorbance to observe the linkage of quaternary structure to spectra. The light-scattering experiments showed a simple exponential decay of trimers to monomers with a dissociation constant of 0.23 s-1. The absorption changes were complex, with two processes occurring. The faster absorption change appeared to be almost simultaneous with the molecular weight change (about 0.27 s-1) and was perhaps totally coordinated with it. The slower absorption change (0.071 s-1) was possibly a result of a conformational change in the chromophore arising during the conversion from newly dissociated monomers to equilibrium monomers.

Inhibition of fibrinolytic system by liquoid (polyanetholesulfonate). A contributing factor in the liquoid-induced renal cortical necrosis

Liquoid induces microvascular thrombosis and renal cortical necrosis in experimental animals. We hypothesized that thrombosis and renal cortical necrosis may, at least in part, result from the inhibition of the fibrinolytic system by liquoid. Effects of liquoid on plasminogen activation by rat kidney, purified human tissue plasminogen activator (TPA), urokinase, streptokinase, and on the amidolytic activities of TPA, urokinase, and plasmin were studied using chromogenic substrates and clot lysis. Liquoid had a strong inhibitory effect on the fibrinolytic system in vivo and in vitro. The inhibition was most effective at the plasminogen activation level, with activation by streptokinase being most susceptible. The demonstrated stoichiometric binding between liquoid and plasminogen, and to a lesser degree the direct inactivation of plasminogen activators and plasmin, is probably responsible for the reduction of plasminogen activation in circulation and in the kidneys.

Comparative properties of amplified external and internal invertase from the yeast SUC2 gene

Saccharomyces cerevisiae external and internal invertases have been amplified by introducing the normal and modified SUC2 genes into yeast multicopy plasmids, which were then used to transform a yeast strain resistant to repression by glucose. Amino acid compositional analysis of these enzymes, in addition to end group sequencing, confirmed the DNA sequence data of Taussig and Carlson (Taussig, R., and Carlson, M. (1983) Nucleic Acids Res. 11, 1943-1954), indicating that both enzymes were encoded in the same gene. Comparison of the properties of carbohydrate-containing external invertase and its nonglycosylated internal form revealed that although the carbohydrate did not appear to influence the conformation of the peptide backbone, as determined by circular dichroism analyses, its presence considerably enhanced the ability of guanidine HCl-denatured external invertase to be renatured relative to internal invertase. The Mr of the internal enzymes was found to be greatly dependent on pH with the enzyme being a monomer at pH 9.4, a dimer at pH 8.3, and an apparent octamer at pH 4.9.

Picosecond fluorescence of cryptomonad biliproteins. Effects of excitation intensity and the fluorescence decay times of phycocyanin 612, phycocyanin 645, and phycoerythrin 545

The fluorescence of purified biliproteins (phycocyanin 645, phycocyanin 612, and phycoerythrin 545) from three cryptomonads, Chroomonas species, Hemiselmis virescens, and Rhodomonas lens, and C-phycocyanin from Anacystis nidulans has been time resolved in the picosecond region with a streak camera system having less than or equal to 2-ps jitter. The fluorescence lifetimes of phycocyanins from Chroomonas species and Hemiselmis virescens are 1.5 +/- 0.2 ns and 2.3 +/- 0.2 ns, respectively, regardless of the fluence of the 30 ps, 532-nm excitation pulse. (Fluence [or photons/cm2] = f intensity [photons/cm2s]dt.). In contrast, that of C-phycocyanin is 2.3 +/- 0.2 ns when the excitation fluence is 8.2 X 10(11) photons/cm2 and decreases to a decay approximated by an exponential decay time of 0.65 +/- 0.1 ns at 7.2 X 10(16) photons/cm2. The cryptomonad phycoerythrin fluorescence decay lifetime is also dependent on intensity, having a decay time of 1.5 +/- 0.1 ns at low fluences and becoming clearly biphasic at higher fluences (greater than 10(15) photons/cm2). We interpret the shortening of decay times for C-phycocyanin and phycoerythrin 545 in terms of exciton annihilation, and have discussed the applicability of exciton annihilation theories to the high fluence effects.

Exciton interaction in allophycocyanin

The absorption and circular dichroism (CD) spectra of allophycocyanin II in the trimer and monomer (dissociated) forms were resolved into four and two components, respectively. The short-wavelength region of the visible spectra was approximated by a chimera of Lorentzian- and Gaussian-shaped bands having a bandwidth of ca. 65 nm. The rest of the bands have a pure Gaussian form. The characteristic 652-nm band in the absorption spectrum (656 nm in the CD spectrum) is shown to arise from exciton interaction between two fluorescent phycocyanobilin chromophores.

Spectroscopic properties of tetrapyrroles on denatured biliproteins

Four biliproteins (phycoerythrin 545, phycocyanin 612, phycocyanin 645, and C-phycocyanin) were denatured by a high concentration of urea and then studied by absorption spectroscopy. Low pH and high protein concentrations conserved the tetrapyrroles' color, and mercaptoethanol and dithiothreitol promoted bleaching. One of these tetrapyrroles, cryptoviolin, appeared not to be hypochromic in the presence of depleting phycocyanobilin, but its absorbance did decay when phycocyanobilin is absent. The product from the treatment of phycocyanobilin with mercaptoethanol or dithiothreitol overlapped spectrally with cryptoviolin and gave the false appearance of maintaining a constant cryptoviolin concentration. Failure to note this effect could result in erroneous cryptoviolin/phycocyanibilin ratios.

Phycocyanin 645. The chromophore assay of phycocyanin 645 from the cryptomonad protozoa Chroomonas species

Phycocyanin 645 was isolated and purified from the cryptomonad Chroomonas species. Its chromophore content was obtained from absorption spectra in acidic 8.0 M urea for both whole protein and the separated subunits. The principal method used to separate the alpha and beta subunits was gel filtration through a Sephacryl S-200 column in acidic urea. The subunits were shown to be completely separated during this procedure by sodium dodecyl sulfate-gel electrophoresis. Spectra were analyzed by three component Beer's law equations. The whole protein was found to consist of four phycocyanobilins (Amax at 662 nm), two cryptoviolins (Amax at 590 nm), and two unnamed bilins with an Amax at 697 nm. The separated subunits were analyzed, and the beta subunit was shown to have two phycocyanobilins for each cryptoviolin and alpha was composed of the 697-nm bilin exclusively. A comparison of the total amounts of alpha and beta from the Sephacryl columns showed that the molar ratios of phycocyanobilin on beta to the 697-nm bilin on alpha was 2:1, and the ratio of cryptoviolin on beta to 697-nm bilin on alpha was 1:1. We therefore propose that, assuming a symmetrical distribution, each beta subunit on the alpha 2 beta 2 protein has two phycocyanobilins and one cryptoviolin and each alpha subunit has one 697-nm bilin. This chromophore distribution differs from one previously reported in which the subunits were separated on a BioRex 70 cation exchange resin in 12% formic acid via a 4-10 M urea gradient.

Stability of allophycocyanin's quaternary structure

The dissociation of allophycocyanin trimers to monomers was examined under a variety of conditions. For alkyl ureas and alcohols the dissociation increased as the straight-chain alkyls increased in length. The effect of branching chains was smaller. Tetrapropylammonium chloride was found to be a very effective agent for trimer dissociation when compared to ureas and alcohols with similar or longer alkyl chains. An explanation for these observations is that the hydrocarbons have an affinity for nonpolar regions in the contact areas between monomers in a trimeric structure. A comparison among several inorganic salts demonstrated that the chaotropic salts (NaSCN greater than NaClO4 much greater than NaNO3 greater than NaBr) fostered increased trimer dissociation, while nonchaotropes (KF, (NH4)2SO4, K phosphate, and NaCl) produced no measurable amounts of monomer. Allophycocyanin dissolved in D2O was much more stable against dissociation than when dissolved in H2O. All the above observations were consistent with hydrophobic forces being the dominant source of trimer stabilization. The equilibrium constant for the dissociation of trimers to monomers was calculated to be about 6 X 10(-16) mol2 liter-2. Calculations were made of the apparent total number of amino acids (40) in the two contact regions on each monomer. An absorption change analogous but not necessarily identical to a conversion of allophycocyanin II to III was noted when (NH4)2SO4 was present. When allophycocyanin's nonexchangeable hydrogens were replaced by deuteriums, it was more readily dissociated to monomers.

Chromophore interactions in allophycocyanin

Allophycocyanin, which is normally isolated as a trimer (alpha 3 beta 3), has now been successfully dissociated into a monomer (alpha beta) with strikingly different spectroscopic properties. In particular, upon dissociation the characteristic 650-nm absorption and 661-nm fluorescence emission bands of the trimer are completely lost and its fluorescence polarization properties are sharply altered. The spectroscopic characteristics of allophycocyanin monomers are much closer to those of C-phycocyanin than to trimeric allophycocyanin. A model for trimeric allophyocyanin is presented in which the appearance of the 650-nm absorption band is induced by a particular kind of chromophore-chromophore interaction. Similar results are found for both allophycocyanin II and III.

Energy transfer among the chromophores in phycocyanins measured by picosecond kinetics

Energy-transfer processes in the algal light-harvesting proteins, the phycocyanins, have been studied by means of picosecond absorption spectroscopy. After excitation at 530 nm, the absorption at several wavelengths in the range 480--669 nm decayed with a short time constant (picosecond) and a long time constant (greater than 1 ns). For C-phycocyanin, energy transfer from the beta to the alpha subunits is interpreted as being a likely candidate for the short time constant; the long time constant probably is the excitation lifetime of the chromophore on the alpha subunits. The time constants for energy transfer in monomers, trimers, and hexamers of C-phycocyanin extracted from a blue-green alga, Phormidium luridum, were measured as approximately 85, approximately 56, and approximately 32 ps, respectively. The corresponding time constant in the cryptomonad phycocyanin 645 from Chroomonas species was found to be less than 5 ps.

Effect of aromatic molecules on the aggregation of C-phycocyanin. Quantum chemical calculations on phycocyanobilin and phycoerythrobilin

The energies of the highest occupied and lowest empty molecular orbitals were calculated for the chromophore groups of the proteins phycocyanin and phycoerythrin. These tetrapyrrole groups on the algal proteins are shown to provide them with the potential of ating as efficient electron donors and acceptors. In addition, the pi electron charges and bond orders were also computed.

Comparison of the biliproteins from two strains of the thermophilic cyanophyte Synechococcus lividus

C-Phycocyanins from two thermophilic strains of Synechococcus lividus that grow within different temperature ranges have been shown to be unalike. The aggregation ability of these two C-phycocyanins in sedimentation-velocity experiments varied dramatically. Surprisingly, the aggregation properties of mesophilic C-phycocyanins were found to lie between those of the two thermophilic proteins. Under identical conditions at pH7.0, one thermophilic protein (Sy I) was composed of 17S and larger aggregates, whereas the other (Sy III) was an almost homogeneous 6S aggregate. Mesophilic C-phycocyanins have a mixture of 6S, 11S and less stable 17S aggregates under these conditions. Amino acid analysis, absorption spectra, immunochemistry and fluorescence polarization all indicated differences in the composition and properties of the thermophilic proteins, which suggest that they have different modes of adaptation to very high temperatures. Allophycocyanins from the two strains of S. lividus were also purified and studied, but unlike the C-phycocyanins no major differences were found between them. Allophycocyanin was homogeneous at pH6.0, with a sedimentation coefficient of 5.54S and mol.wt. 1.03x10(5), as determined by sedimentation-equilibrium measurements.