Molecular
Vision 2008
; 14:666-674
<http://www.molvis.org/molvis/v14/a80>
Received 31 January 2008 | Accepted 21 March 2008 | Published 26 March
2008
Guruprasad Rao,1 Puttur Santhoshkumar,1 K. Krishna Sharma1,2
1Department of Ophthalmology, University of Missouri-Columbia, Columbia, MO; 2Department of Biochemistry, University of Missouri-Columbia, Columbia, MO
Correspondence to: K. Krishna Sharma, Ph.D., Department of Ophthalmology, University of Missouri-Columbia, 1 Hospital Drive, Columbia, MO, 65212; Phone: (573) 882-8478; FAX: (573) 884-4100; email: sharmak@health.missouri.edu
Purpose: Our previous work identified 23 low molecular weight (<3.5 kDa) crystallin peptides in the urea-soluble fractions of normal young, normal aged, and aged cataract human lenses. We found that one of these crystallin fragments, βA3/A1102–117 peptide (SDAYHIERLMSFRPIC), that are present in aged and cataract lens, increased the scattering of light by β- and γ-crystallins and alcohol dehydrogenase (ADH) and also reduced the chaperone-like activity of αB-crystallin. The present study was performed to identify the interacting sites of the βA3/A1102–117 peptide in αB-crystallin.
Methods: βA3/A1102–117 peptide was first derivatized with sulfo-succinimidyl-2-[6-(biotinamido)-2-{p-azidobenzamido}-hexanoamido] ethyl-1–3 dithio propionate (sulfo-SBED), a photoactivable, heterotrifunctional biotin-containing cross-linker. The biotin-derivatized peptide was then incubated with αB-crystallin at 37 °C for 2 h to allow complex formation followed by photolysis to facilitate the transfer of the biotin label from the peptide to αB-crystallin. Label transfer was confirmed by western blot, and the labeled αB-crystallin was digested with trypsin. Tryptic peptides from αB-crystallin carrying the biotin label were purified by avidin affinity chromatography, and βA3/A1102–117 peptide interacting sites in αB-crystallin were identified by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and nanospray quadrupole time-of-flight mass spectrometry (QqTOF MS/MS).
Results: We found that the βA3/A1102–117 peptide interacted with αB-crystallin regions 70LEKDR74, 83HFSPEELKVK92, 91VKVLGDVIEVHGK103, 93VLGDVIEVHGKHEER107, and 121KYR123, which are part of the α-crystallin domain, and were previously shown to be part of the functional chaperone site in αB-crystallin. The βA3/A1102–117 peptide also interacted with regions at the COOH-terminal extension of αB-crystallin, 150KQVSGPER157, 164EEKPAVTAAPK174, and 164EEKPAVTAAPKK175. When two of the hydrophobic residues of βA3/A1102–117 peptide were replaced with hydrophilic residues, the resulting substituted peptide, SDADHGERLMSFRPIC, did not show the anti-chaperone property.
Conclusions: This study confirmed the interactions between a low molecular weight peptide derived from βA3/A1-crystallin found in aged and cataract lenses and αB-crystallin. The binding of βA3/A1102–117 peptide to the chaperone site and the COOH-terminal extension of αB-crystallin may explain its anti-chaperone property.
Human lens crystallins are organized into three classes, α-, β-, and γ-crystallins, based on sequence homology and the size of aggregates isolated under physiologic conditions. Since lens crystallins undergo little or no turnover, there is opportunity for numerous post-translational modifications as the lens ages [1-4]. Some modifications of lens crystallins identified in young clear lenses may reflect normal development and maturation of the lens [5,6] whereas other modifications associated with aged lenses- such as deamidation, phosphorylation, truncation, glycation, oxidation, and cross-linking could negatively impact crystallin conformation, aggregation state, or solubility, resulting in increased light scattering and eventual loss of transparency in aged lenses [7-10].
In comparison to normal lenses, cataract lenses show greater fragmentation of crystallins due to proteolysis [1,11-13]. Increased crystallin fragmentation has also been reported in aged and cataract lenses of non-human species [6,14-17]. It has been reported that proteolysis may be a contributing factor in the insolubilization of crystallins occurring during normal maturation of lens or during cataract formation in human and bovine lenses [18]. It has been shown that the fragments of βA3/A1- and βB1-crystallins are selectively insolubilized during cataract development compared to normal aging [13]. These authors also reported increased crystallin truncation, the deamidation of Asn to Asp residues, and the oxidation of a Trp residue in cataract lenses.
Several proteolytic enzymes have been shown to play a role in aging of the lens and cataract formation [19-25]. Activities of several peptidases were reported to be highest in the outer cortical fibers and decreased to one half or below in the inner cortical fibers and nucleus. An inverse correlation between peptidase activities and the amount of crystallin fragments was observed in different regions of the lens. The amount of crystallin fragments and the amount of water-insoluble proteins were greater in the lens nucleus than in the outer cortical fibers [21]. An age-dependent decline in proteasome activity and a concomitant accumulation of modified proteins in human lens has been reported earlier [26]. Increased opacification of the lens nucleus in cataract was significantly correlated with decreased peptidase activities of the proteasome [27]. Although a protein oxidation reaction may render the protein susceptible to proteolysis, heavily oxidized proteins appear to first aggregate (via new hydrophobic and ionic bonds) and then to form covalent cross-links that make them highly resistant to proteolysis by 20S proteasome [28]. In fact, these aggregated, cross-linked oxidized proteins actually bind to the 20S proteasome and inhibit its ability to degrade the oxidized forms of other proteins [29].
Low molecular weight crystallin fragments have been isolated and characterized from both the water-soluble and water-insoluble fractions of the lens with greater prevalence in the water-insoluble fractions [11,21,30-32]. As many as 13 crystallin fragments with molecular masses between 3 and 17 kDa and originating from α-, β-, and γ-crystallins have been isolated from the water-soluble, high molecular weight aggregates of 60-80-year-old human lenses [31]. Accumulation of such crystallin fragments may be a cause for age-related lens opacity. It has been hypothesized that the interaction of short peptides derived from crystallins with lens proteins may increase the formation of high molecular weight aggregates and the scattering of light [33]. Though it is hypothesized that cataract develops as a result of improper interaction of crystallin fragments generated by proteolysis [25], the underlying mechanism is not clear. Earlier work by our group has shown that in vitro-oxidized crystallin peptides enhance the aggregation of βL-crystallin and γ-crystallin and also exhibit anti-chaperone-like properties [33-35]. Interaction of peptide fragments with lens proteins and their aggregation-enhancing nature may have some implications for age-related cataract formation.
Recent studies in our laboratory have revealed the presence of 23 low molecular weight (<3.5 kDa) peptides in the urea-soluble fractions of normal young, normal aged, and aged cataract human lenses, and the amount of crystallin fragments was found to increase with age [36]. Out of these 23 peptides, 15 were derived from αA- and αB-crystallin. Most of the 15 came from the NH2-terminal region, a few from the α-crystallin domain, and none from the COOH-terminal extension. Two crystallin peptides predominant in the nucleus of aged lens and cataract lens but not in young lens, αB1–18 (MDIAIHHPWIRRPFFPFH, GenBank NP_001876) and βA3/A1102–117 (SD(N)AYHIERLMSFRPIC, GenBank NP_005199), increased the molecular mass, polydispersity, and hydrodynamic radius of αA- and αB-crystallins [36]. Our study also showed that the peptides, αB1–18 and βA3/A1102–117, increased the scattering of light by β- and γ-crystallins and alcohol dehydrogenase (ADH) and also reduced the chaperone-like activity of α-crystallin.
The present study was undertaken to identify the binding sites for the βA3/A1102–117 peptide in αB-crystallin. We used the photoactive cross-linker sulfo-SBED (sulfo-succinimidyl-2-[6-(biotinamido)-2-{p-azidobenzamido}-hexanoamido] ethyl-1–3 dithio propionate) [37] to confirm the interaction between αB-crystallin and the βA3/A1102–117 peptide. The βA3/A1102–117 peptide interacting sites in αB-crystallin are reported here.
Trypsin gold (mass spectrometry grade) was purchased from Promega Corporation (Madison, WI). Sulfo-SBED, immobilized monomeric avidin kit, and micro-bicinchoninic acid (BCA) protein assay kit were procured from Pierce (Rockford, IL). Trypsin inhibitor, TLCK (N α-p-tosyl-L-lysine chloromethyl ketone), was obtained from Sigma Chemical Company (St. Louis, MO). The βA3/A1102–117 peptide, SDAYHIERLMSFRPIC, and the substituted peptide, SDADHGERLMSFRPIC (in which the tyrosine and isoleucine corresponding to 105 and 107 in βA3/A1-crystallin are replaced by aspartate and by glycine, respectively), were synthesized at the University of Missouri core facility and purified by HPLC. Their masses (1936.9 Da and 1833 Da, respectively) were ascertained by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). Blotting grade avidin-horseradish peroxidase conjugate was obtained from Bio-Rad Laboratories (Hercules, CA). Bovine βL-crystallin was isolated from lens extract using the procedure described earlier [35]. All other chemicals were of analytical grade.
Human αB-crystallin cDNA (obtained from J.M. Petrash, Washington University, St. Louis, MO) was cloned into the pET-23d (+) vector (Novagen, Madison, WI), and the recombinant protein was expressed in Escherichia coli BL21(DE3) pLysS cells (Invitrogen, Carlsbad, CA) as described earlier [38]. The protein was purified by size exclusion chromatography followed by ion-exchange chromatography as described previously [39].
The βA3/A1102–117 peptide (SDAYHIERLMSFRPIC) as well as the substituted peptide (SDADHGERLMSFRPIC) were dissolved in 50 μl of DMSO and diluted to 0.5 ml with 0.05 M phosphate buffer containing 0.15 M NaCl (pH 7.4), hereafter referred to as phosphate buffered saline (PBS). The peptide concentration was measured using the micro-BCA assay method. Thermal aggregation assay of bovine βL-crystallin and chaperone assay of αB-crystallin were performed according to the method previously described [35]. Briefly, substrate protein, βL-crystallin (100 μg), was heat-denatured at 55 °C in 1 ml of PBS for 60 min in the presence or absence of αB-crystallin (5 μg) and the βA3/A1102–117 peptide or the substituted peptide (60 μg). Aggregation was monitored by recording the light scattering at 360 nm as a function of time at 55 °C in a Shimadzu spectrophotometer equipped with a temperature-controlled multicell transporter.
To determine whether prior binding of the βA3/A1102–117 peptide alters the chaperone-like activity of αB-crystallin toward denaturing proteins, 50 μg of αB-crystallin was incubated with 100 μg of βA3/A1102–117 in a total volume of 0.2 ml of PBS at 37 °C for 12 h. A sample containing αB-crystallin alone served as a control. After the incubation, samples were briefly centrifuged to separate any visible precipitate. The supernatant was injected into a TSK G5000PWXL (Tosoh Bioscience, Montgomeryville, PA) size exclusion column fitted to an HPLC system with an ultraviolet (UV) detector and equilibrated with PBS. The peak containing the αB-crystallin-peptide complex was pooled (free of unbound peptide) and used in the chaperone assay as described in the previous section.
To identify the βA3/A1102–117 peptide binding sites in αB-crystallin, the purified peptide was derivatized with sulfo-SBED, a biotin-containing and photoactivable as well as heterotrifunctional and amine-group specific reagent [37]. The procedure described by the supplier (Pierce) was used. In brief, 1.78 mg of βA3/A1 peptide was dissolved in 10 μl DMSO and the volume was made up to 50 μl with PBS. Then, 2.5 mg of sulfo-SBED dissolved in 10 μl DMSO and made up to 50 μl with PBS was added to the peptide, and the final volume of the reaction mixture was made up to 0.3 ml with phosphate buffer. This achieved a threefold molar excess of the sulfo-SBED over the peptide. The mixture was incubated in the dark at room temperature for 45 min. The unreacted sulfo-SBED was removed by dialyzing extensively against PBS using a 1000 Da cut-off membrane. Similarly, the substituted peptide, SDADHGERLMSFRPIC, was derivatized with sulfo-SBED for use in the interaction studies.
To study the interaction between the sulfo-SBED-derivatized βA3/A1102–117 peptide (or the substituted peptide) and αB-crystallin, 0.25 mg of the derivatized peptide was incubated with 0.25 mg of human recombinant αB-crystallin at 37 °C for 2 h. Subsequently, the mixture was filtered in a 10,000 Da cut-off centrifugal filter to remove unbound peptide (all steps were performed in the dark). Following this, the sample was photolyzed on an ice bath for 15 min using a UV lamp (365 nm) held at a distance of 2 cm from the sample. Transfer of the biotin label from the sulfo-SBED-derivatized peptide to αB-crystallin was confirmed by SDS–PAGE followed by western blot. The intensities of labeled bands in blots were quantified using Kodak 1D image analysis software (Eastman Kodak Company, Rochester, NY). The labeled αB-crystallin was then reduced by DTT and alkylated with iodoacetamide. Following this, the sample was dialyzed extensively for 24 h against 50 mM Tris (pH 7.6) containing 1 mM CaCl2 using a 15,000 Da cut-off membrane and digested by mass spectrometry grade trypsin (1:25 w/w) at 37 °C for 12 h. Trypsin digestion was terminated by the addition of the trypsin inhibitor, TLCK (1 mM); the sample was filtered through a microcon 10 kDa filter (Millipore, Bedford, MA), and the filtrate was collected. Trypsin-digested αB-crystallin peptides having the biotin group derived from the sulfo-SBED cross-linker were isolated by Pierce immobilized monomeric avidin affinity gel chromatography [37]. The biotin-labeled peptides were concentrated by Speed Vac, desalted by C-18 spin columns, and analyzed in an Applied Biosystems 4700 MALDI TOF/TOF mass spectrometer. The sequences of the labeled peptides were determined by nanospray quadrupole time-of-flight mass spectrometry (QqTOF MS/MS).
The βA3/A1102–117 peptide found in aged lenses is present in both deamidated (at Asn103) and non-deamidated forms in vivo. Both the native peptide and the deamidated form of the same peptide displayed similar anti-chaperone activity (data not shown here). In this study, we used the deamidated form of the peptide. Thermal denaturation of βL-crystallin at 55 °C resulted in aggregation and light scattering. The addition of the βA3/A1102–117 peptide to the incubation mixture resulted in increased light scattering by βL-crystallin by 58% whereas the substituted peptide increased the light scattering only by 4% at 60 min. The βA3/A1102–117 peptide by itself did not scatter light (Figure 1A). When the βL-crystallin was heat-denatured in the presence of αB-crystallin, the light scattering was decreased by 41% at 60 min due to the chaperone-like action of αB-crystallin. However, when βL-crystallin was denatured in the presence of αB-crystallin and βA3/A1102–117 peptide, the light scattering increased by 20% showing the decreased chaperone action of αB-crystallin. The substituted peptide, on the other hand, caused a slight improvement in the chaperone action of αB-crystallin. The light scattering by denatured βL-crystallin was decreased by 53% in the presence of αB-crystallin and substituted peptide (Figure 1B). The αB-crystallin-βA3/A1102–117 peptide complex showed a lowered ability to prevent thermal aggregation of βL-crystallin. This complex (5 μg) decreased the light scattering by heat-denatured βL-crystallin at 60 min by only 3% (Figure 2, curve D) as opposed to a 51% decrease caused by an equivalent amount of the control, αB-crystallin (Figure 2, curve B). When a higher concentration of αB-crystallin-βA3/A1102–117 peptide complex (10 μg) was used in the assay, it caused only a 24% decrease in light scattering (Figure 2, curve E) compared to the 81% decrease caused by an equivalent amount of the control, αB-crystallin (Figure 2, curve C).
Photoinsertion of the biotin label from the derivatized βA3/A1102–117 peptide to αB-crystallin was confirmed by SDS–PAGE and western blot analysis (Figure 3, lane 1). The derivatized substituted peptide incorporated the biotin label into αB-crystallin to a significantly lesser extent than the native peptide (about 1.2% of the band intensity in western blot as compared to βA3/A1102–117 peptide) as seen in Figure 3, lane 2.
To identify the βA3/A1102–117 peptide interacting sites in αB-crystallin, the tryptic digest of αB-crystallin containing the biotin-labeled peptides was enriched by immobilized monomeric avidin affinity gel chromatography. The masses of the labeled peptides were determined by MALDI TOF/TOF MS. Since sulfo-SBED contains a cleavable disulfide bond, reduction and alkylation of the labeled αB-crystallin with iodoacetamide will add a net mass of 603.22 Da to the mass of the αB-crystallin-derived peptide containing the biotin label. Before assigning the amino acid sequence for each biotin-labeled αB-crystallin peptide, the presence of biotin label in those peptides was confirmed by detection of the fragment ions generating specifically from sulfo-SBED during MS/MS analysis [34]. MALDI-TOF MS spectra of biotin-labeled αB-crystallin peptides obtained from monomeric avidin affinity column is shown in Figure 4. The peptide peaks labeled in Figure 4 were analyzed further by nanospray QqTOF MS/MS. The amino acid sequence of those peptides is indicated in the αB-crystallin sequence in Figure 5. The amino acid sequences of tryptic digest peptides of αB-crystallin carrying the biotin label and their masses (in parentheses) were 70LEKDR74 (1263.64 Da), 83HFSPEELKVK92 (1816.93 Da), 91VKVLGDVIEVHGK103 (1996.06 Da), 93VLGDVIEVHGKHEER107 (2320.26 Da), 121KYR123 (1069.51 Da), 150KQVSGPER157 (1503.75 Da), 164EEKPAVTAAPK174 (1743.86 Da), and 164EEKPAVTAAPKK175 (1871.99 Da). A peptide with a mass of 1388.77 Da without any modifications, corresponding to residues 1–11 in αB-crystallin, was also found among the purified peptides.
The presence of crystallin fragments in water-soluble and water-insoluble fractions of lens proteins has been known for some years [11,40]. We first suggested that anti-chaperone peptides accumulating in vivo may be contributing to lens opacification during aging [33]. Recent studies in our laboratory have revealed the presence of 23 low molecular weight (<3.5 kDa) peptides in the urea-soluble fractions of normal young, normal aged, and aged cataract human lenses, and the amount of crystallin fragments was found to increase with age [36]. Our study also showed that βA3/A1102–117 peptide, found in aged and cataract lens, increased the scattering of light by β- and γ-crystallins and alcohol dehydrogenase (ADH). βA3/A1102–117 peptide also exhibited an anti-chaperone property by decreasing the ability of α-crystallin to prevent aggregation of β- and γ-crystallins and non-crystallin protein substrates, a process believed to be essential for maintenance of lens transparency [36].
The present study has confirmed the aggregation-enhancing property of the βA3/A1-crystallin-derived peptide, 102SDAYHIERLMSFRPIC117, since it promoted the aggregation of βL-crystallin during thermal denaturation (Figure 1A). The presence of this peptide in the assay mixture reduced the ability of αB-crystallin to protect βL-crystallin against thermal aggregation (Figure 1B). Since the βA3/A1102–117 peptide interacts with both βL-crystallin and αB-crystallin, the enhanced light scattering observed in its presence may be due to a combination of its interaction with the substrate as well as the chaperone protein. To confirm the anti-chaperone nature of the peptide, we pretreated αB-crystallin with βA3/A1102–117 peptide and separated the complex from the free peptide. The αB-crystallin-βA3/A1102–117 peptide complex showed a considerable loss of chaperone-like activity against heat-denatured βL-crystallin (Figure 2). Since free peptide was removed before the assay, we believe that the decreased chaperoning ability of αB-crystallin was specifically due to the binding of the peptide to αB-crystallin. When the βA3/A1102–117 peptide was derivatized with sulfo-SBED, incubated with αB-crystallin, and photolyzed, the biotin label transferred to αB-crystallin (Figure 3, lane 1). The MALDI-TOF MS of the peptides derived from the αB-crystallin by trypsin digestion showed the presence of biotin from sulfo-SBED in several peptides (Figure 4). The identity of those peptides was obtained by sequencing in a nanospray QqTOF mass spectrometer. The sites on αB-crystallin where the label was observed (Figure 5) included the sequences, 70LEKDR74 and 83HFSPEELKVK92. Earlier, we showed that 73DRFSVNLDVKHFSPEELKVK92 is one of the well characterized functional chaperone sites in αB-crystallin [41]. Therefore, we can conclude that the anti-chaperone peptide βA3/A1102–117 binds to αB-crystallin at the chaperone site. The binding of the βA3/A1102–117 peptide to this substrate-binding site in αB-crystallin may have diminished the ability of the protein to effectively chaperone the denaturing βL-crystallin.
Other sites of interaction between the βA3/A1102–117 peptide and αB-crystallin included the sequences, 91VKVLGDVIEVHGKHEER107 and 121KYR123. These sequences are part of the α-crystallin domain. Earlier, Arg120 was shown to be important for the chaperone-like activity of αB-crystallin [42]. A recent study demonstrated that 73DRFSVNLDVKHFS85 and 101HGKHEERQDE110 sequences in αB-crystallin inhibited the fibrillation of disease-related amyloidogenic proteins including α-synuclein and amyloid-β [43]. Other binding sites of the βA3/A1peptide to αB-crystallin included the COOH-terminal region of 150KQVSGPER157 and 164EEKPAVTAAPKK175. An earlier study has shown that mutations of the two terminal lysines (174 and 175) of αB-crystallin to leucine or glycine greatly reduced its chaperone-like activity. It was postulated that mutations in these two amino acids may have resulted in the COOH-terminus folding back on itself, losing its flexibility, and sterically hindering protein binding [44]. The COOH-terminal extensions of α-crystallins are considered polar, highly flexible, and solvent-exposed. These extensions also act as solubilizing agents for the relatively hydrophobic α-crystallin molecule and the high molecular weight complex that forms during the chaperone action [45].
αB-Crystallin with five amino acids deleted from its COOH-terminus was found in lenses of hereditary cataractous iCR/f rat, and this truncated crystallin showed decreased chaperone activity [46]. Protein pin array studies have identified 157RTIPITRE164 as one of the interactive sequences for chaperone activity in human αB-crystallin [47]. Deletion of the polar COOH-terminal sequence, 155PERTIPITREE165, from human αB-crystallin resulted in poor solubility and limited or no chaperone activity against unfolding βL-crystallin, alcohol dehydrogenase, and citrate synthase. These results demonstrated the importance of the COOH-terminal residues in the recognition, selection, and maintenance of solubility of unfolding substrate proteins [48]. As identified by protein pin-array studies, the 150KQVSGPER157, 164EEKPAVTAAPK174, and 164EEKPAVTAAPKK175 sequences, which are identified as peptide interacting sites in αB-crystallin in the present study, overlap with sequences involved in dimerization and assembly of human αB-crystallin [49]. The binding of the βA3/A1102–117 peptide to the COOH-terminal extension of αB-crystallin in the present study may have interfered with substrate binding and decreased the chaperoning ability of the protein. Our recent studies showed that the βA3/A1102–117 peptide caused partial precipitation of αB-crystallin [36]. We believe that the peptide interaction at the COOH-terminal extension of αB-crystallin may have led to decreased flexibility and decreased solubilization potential of αB-crystallin. Additionally, the interactions between crystallins and low molecular weight peptides may limit the access of these peptides to peptidases, resulting in the accumulation of peptides with aging.
The substituted peptide we used in this study, SDADHGERLMSFRPIC, had two hydrophobic residues (tyrosine and isoleucine) replaced by hydrophilic (aspartate and glycine) residues. The substitution abolished the ability of the peptide to induce βL-crystallin aggregation (Figure 1A) and to act as anti-chaperone (Figure 1B). This suggests that the hydrophobic amino acids play a critical role in the interaction of the anti-chaperone peptide with αB-crystallin. The substituted peptide can also be considered a control peptide for the label transfer study. If there were any non-specific interactions between the derivatized substituted peptide and αB-crystallin, we would have seen a transfer of biotin to αB-crystallin following photolysis. The fact that the αB-crystallin incubated with derivatized substituted peptide showed only about 1.2% of the label transfer when compared to the derivatized βA3/A1102–117 peptide during the blotting experiments (Figure 3 lane 2) suggests that the non-specific interaction and label transfer was insignificant in this study.
In summary, this study confirmed the interactions between βA3/A1102–117 peptide and αB-crystallin. The binding of this peptide to regions critical for chaperone action of αB-crystallin may explain its anti-chaperone property. The modulation of structural and functional properties of crystallins by low molecular weight peptides may play an important role in protein aggregation and cataract formation.
This work was supported by National Institutes of Health Grants EY11981, EY09855, EY14795 and a grant-in-aid from Research to Prevent Blindness.