John I. Clark

Shotgun identification of protein modifications from protein complexes and lens tissue

Large-scale genomics has enabled proteomics by creating sequence infrastructures that can be used with mass spectrometry data to identify proteins. Although protein sequences can be deduced from nucleotide sequences, posttranslational modifications to proteins, in general, cannot. We describe a process for the analysis of posttranslational modifications that is simple, robust, general, and can be applied to complicated protein mixtures. A protein or protein mixture is digested by using three different enzymes: one that cleaves in a site-specific manner and two others that cleave nonspecifically. The mixture of peptides is separated by multidimensional liquid chromatography and analyzed by a tandem mass spectrometer. This approach has been applied to modification analyses of proteins in a simple protein mixture, Cdc2p protein complexes isolated through the use of an affinity tag, and lens tissue from a patient with congenital cataracts. Phosphorylation sites have been detected with known stoichiometry of as low as 10%. Eighteen sites of four different types of modification have been detected on three of the five proteins in a simple mixture, three of which were previously unreported. Three proteins from Cdc2p isolated complexes yielded eight sites containing three different types of modifications. In the lens tissue, 270 proteins were identified, and 11 different crystallins were found to contain a total of 73 sites of modification. Modifications identified in the crystallin proteins included Ser, Thr, and Tyr phosphorylation, Arg and Lys methylation, Lys acetylation, and Met, Tyr, and Trp oxidations. The method presented will be useful in discovering co- and posttranslational modifications of proteins.

Small heat-shock proteins and their potential role in human disease.

The elevated expression of stress proteins is considered to be a universal response to adverse conditions, representing a potential mechanism of cellular defense against disease and a potential target for novel therapeutics, including gene therapy and chaperone-modulating reagents. Recently, a single mutation in the small heat-shock protein human alphaB-crystallin was linked to desmin-related myopathy, which is characterized by abnormal intracellular aggregates of intermediate filaments in human muscle. New findings demonstrate that the high level of expression of stress proteins can contribute to an autoimmune response and can protect proteins that contribute to disease processes.

Mice deficient in Six5 develop cataracts : implications for myotonic dystrophy

Expansion of a CTG trinucleotide repeat in the 3′ UTR of the gene DMPK at the DM1 locus on chromosome 19 causes myotonic dystrophy, a dominantly inherited disease characterized by skeletal muscle dystrophy and myotonia, cataracts and cardiac conduction defects. Targeted deletion of Dm15, the mouse orthologue of human DMPK, produced mice with a mild myopathy and cardiac conduction abnormalities, but without other features of myotonic dystrophy, such as myotonia and cataracts. We, and others, have demonstrated that repeat expansion decreases expression of the adjacent gene SIX5 (refs 7,8), which encodes a homeodomain transcription factor. To determine whether SIX5 deficiency contributes to the myotonic dystrophy phenotype, we disrupted mouse Six5 by replacing the first exon with a β-galactosidase reporter. Six5-mutant mice showed reporter expression in multiple tissues, including the developing lens. Homozygous mutant mice had no apparent abnormalities of skeletal muscle function, but developed lenticular opacities at a higher rate than controls. Our results suggest that SIX5 deficiency contributes to the cataract phenotype in myotonic dystrophy, and that myotonic dystrophy represents a multigenic disorder.

The Cardiomyopathy and Lens Cataract Mutation in αB-crystallin Alters Its Protein Structure, Chaperone Activity, and Interaction with Intermediate Filaments in Vitro

Desmin-related myopathy and cataract are both caused by the R120G mutation in αB-crystallin. Desmin-related myopathy is one of several diseases characterized by the coaggregation of intermediate filaments with αB-crystallin, and it identifies intermediate filaments as important physiological substrates for αB-crystallin. Using recombinant human αB-crystallin, the effects of the disease-causing mutation R120G upon the structure and the chaperone activities of αB-crystallin are reported. The secondary, tertiary, and quaternary structural features of αB-crystallin are all altered by the mutation as deduced by near- and far-UV circular dichroism spectroscopy, size exclusion chromatography, and chymotryptic digestion assays. The R120G αB-crystallin is also less stable than wild type αB-crystallin to heat-induced denaturation. These structural changes coincide with a significant reduction in thein vitro chaperone activity of the mutant αB-crystallin protein, as assessed by temperature-induced protein aggregation assays. The mutation also significantly altered the interaction of αB-crystallin with intermediate filaments. It abolished the ability of αB-crystallin to prevent those filament-filament interactions required to induce gel formation while increasing αB-crystallin binding to assembled intermediate filaments. These activities are closely correlated to the observed disease pathologies characterized by filament aggregation accompanied by αB-crystallin binding. These studies provide important insight into the mechanism of αB-crystallin-induced aggregation of intermediate filaments that causes disease.

Fractal analysis of region-based vascular change in the normal and non-proliferative diabetic retina

Purpose. Evaluation of normal and abnormal vascular pattern in the human retina using a novel method: quantitative region-based fractal analysis. Methods. Binary (black/white) vascular patterns of the human retina originating at the optic disc were obtained by semi-automatic computer processing of digital images from 60-degree fundus fluorescein angiography of 5 normal eyes and 5 eyes with non-proliferative diabetic retinopathy (NPDR). As determined by image resolution, vascular patterns included vessels with diameters =50 µm and excluded small vessels and capillaries. The density of linearized (i.e., skeletonized) vascular patterns in the macular region versus paramacular region (termed “region-based” linearized vascular pattern) was quantified with the fractal dimension (D f) and confirmed by grid intersection (? v) . Results. By region-based quantification, D f and ? v were significantly higher in the normal macular region than in the NPDR macular region (p = 0.008 and p = 0.019, respectively). However, differences in D f and ? v between the normal and NPDR paramacular regions were not strongly signficant (p = 0.168 and p = 0.337, respectively). Conclusions. Results from the retrospective analytical study demonstrate the feasibility of using quantitative region-based fractal analysis of early-stage vascular disease in the human retina. The results are encouraging for a broader study of diverse patient populations.

Human alpha B-crystallin - Small heat shock protein and molecular chaperone

The polymerase chain reaction was used to amplify a cDNA sequence encoding the human αB-crystallin. The amplified cDNA fragment was cloned into the bacterial expression vector pMAL-c2 and expressed as a soluble fusion protein coupled to maltose-binding protein (MBP). After maltose affinity chromatography and cleavage from MBP by Factor Xa, the recombinant human αB-crystallin was separated from MBP and Factor Xa by anion exchange chromatography. Recombinant αB-crystallin was characterized by SDS-polyacrylamide electrophoresis (PAGE), Western immunoblot analysis, Edman degradation, circular dichroism spectroscopy, and size exclusion chromatography. The purified crystallin migrated on SDS-PAGE to an apparent molecular weight (Mr ∼22,000) that corresponded to total native human α-crystallin and was recognized on Western immunoblots by antiserum raised against human αB-crystallin purified from lens homogenates. Chemical sequencing, circular dichroism spectroscopy, and size exclusion chromatography demonstrated that the recombinant crystallin had properties similar or identical to its native counterpart. Both recombinant αB-crystallin and MBP-αB fusion protein associated to form high molecular weight complexes that displayed chaperone-like function by inhibiting the aggregation of alcohol dehydrogenase at 37°C and demonstrated the importance of the C-terminal domain of αB-crystallin for chaperone-like activity.

Alzheimer's Disease Amyloid-β Links Lens and Brain Pathology in Down Syndrome

Down syndrome (DS, trisomy 21) is the most common chromosomal disorder and the leading genetic cause of intellectual disability in humans. In DS, triplication of chromosome 21 invariably includes the APP gene (21q21) encoding the Alzheimers disease (AD) amyloid precursor protein (APP). Triplication of the APP gene accelerates APP expression leading to cerebral accumulation of APP-derived amyloid-β peptides (Aβ), early-onset AD neuropathology, and age-dependent cognitive sequelae. The DS phenotype complex also includes distinctive early-onset cerulean cataracts of unknown etiology. Previously, we reported increased Aβ accumulation, co-localizing amyloid pathology, and disease-linked supranuclear cataracts in the ocular lenses of subjects with AD. Here, we investigate the hypothesis that related AD-linked Aβ pathology underlies the distinctive lens phenotype associated with DS. Ophthalmological examinations of DS subjects were correlated with phenotypic, histochemical, and biochemical analyses of lenses obtained from DS, AD, and normal control subjects. Evaluation of DS lenses revealed a characteristic pattern of supranuclear opacification accompanied by accelerated supranuclear Aβ accumulation, co-localizing amyloid pathology, and fiber cell cytoplasmic Aβ aggregates (∼5 to 50 nm) identical to the lens pathology identified in AD. Peptide sequencing, immunoblot analysis, and ELISA confirmed the identity and increased accumulation of Aβ in DS lenses. Incubation of synthetic Aβ with human lens protein promoted protein aggregation, amyloid formation, and light scattering that recapitulated the molecular pathology and clinical features observed in DS lenses. These results establish the genetic etiology of the distinctive lens phenotype in DS and identify the molecular origin and pathogenic mechanism by which lens pathology is expressed in this common chromosomal disorder. Moreover, these findings confirm increased Aβ accumulation as a key pathogenic determinant linking lens and brain pathology in both DS and AD.

THEORETICAL AND EXPERIMENTAL BASIS FOR THE INHIBITION OF CATARACT

Aggregation of the lens proteins to form high molecular weight clusters is a major contributing factor in age-onset nuclear cataract [Benedek, G. B. (1971) Theory of transparency of the eye. Appl. Optics, 10, 459-473]. This aggregation occurs continually throughout life and contributes to an exponential increase, as a function of age, in the intensity of the light backscattered out of the lens. The time constant deltaT for this exponential increase in human populations is a valuable index, helpful for conducting clinical trials. In-vitro studies have identified reagents capable of inhibiting high molecular weight aggregate formation, as well as the non-covalent interprotein interactions responsible for phase separation. These reagents are also found experimentally to be effective cataract inhibitors in animal model systems in vivo. We believe that the stage is now set for human clinical trials of putative cataract inhibitors. We present rough quantitative estimates of the trial parameters needed to assure an unambiguous determination of efficacy in a trial population. Such a trial simply requires a measurement of the time constant deltaT in the treated population relative to the untreated population. A successful outcome of the trial is indicated if deltaT increases by 20% over that found for the untreated population. Our estimates suggest efficacy could be determined in a two year trial involving about 300 subjects in the treated group.

Cortical opacity, calcium concentration and fiber membrane structure in the calf lens

We studied the dependence of calf lens transparency on the concentration of calcium in bathing solutions using turbidimetric methods and scanning electron microscopy. The calf lens is transparent in concentrations of calcium between 0·5 and 1·3 m m which correspond to the levels of calcium found inside the normal transparent lens. The calf lens cortex opacifies in concentrations of calcium which are either above or below the levels of calcium found in the normal lens. Scanning electron microscope studies show that lens fiber membranes are disrupted at both high and low calcium concentrations but normal membrane structure is maintained in calcium concentrations between 0·5 and 1·3 m m . These results quantitatively demonstrate the relationship between cortical opacity, fiber membrane structure and calcium concentrations.

Light scattering and reversible cataracts in the calf and human lens

By using measurements of the intensity of light scattered from intact calf lenses, we have determined a number of reagents that induce nuclear and cortical opacification at body temperature. Diffusion of buffered saline solutions of glycerol, other glycols, urea, guanidine hydrochloride or glycine into the lens reverses the opacity of all the reagent-induced cataracts. Similar findings are obtained with lens homogenates, which have gel-like properties as determined from viscosity measurements. A 50 % (by volume) glycerol or 5 M urea solution clarifies human pathologic cataractous lenses by reducing the opacification due to light scattering. These findings suggest that it may be possible, in principle, to reverse human lens cataracts chemically in situ. The scattering of laser light from quasi-periodic lattice of normal lens cells produces a regular diffraction pattern containing many Bragg spots whose positions are those predicted from the basis vectors of the cellular lattice. The intensity of the Bragg reflexions increases greatly when cataracts are formed in the calf and human lens, and falls greatly when the lenses are clarified. The spatial variation in the scattered light intensity of the Bragg spots and between these spots contains detailed information on the structure of the scattering elements associated with opacification.