The contribution of the methyl groups on thymine bases to binding specificity and affinity by alanine-rich mutants of the bZIP motif

We have used fluorescence anisotropy to measure in situ the thermodynamics of binding of alanine-rich mutants of the GCN4 basic region/leucine zipper (bZIP) to short DNA duplexes, in which thymines were replaced with uracils, in order to quantify the contributions of the C5 methyl group on thymines with alanine methyl side chains. We simplified the alpha-helical GCN4 bZIP by alanine substitution: 4A, 11A, and 18A contain four, 11, and 18 alanine mutations in their DNA-binding basic regions, respectively. Titration of fluorescein-labeled duplexes with increasing amounts of protein yielded dissociation constants in the low-to-mid nanomolar range for all bZIP mutants in complex with the AP-1 target site (5'-TGACTCA-3'); binding to the nonspecific control duplex was >1000-fold weaker. Small changes of <1 kcal/mol in binding free energies were observed for wild-type bZIP and 4A mutant to uracil-containing AP-1, whereas 11A and 18A bound almost equally well to native AP-1 and uracil-containing AP-1. These modest changes in binding affinities may reflect the multivalent nature of protein-DNA interactions, as our highly mutated proteins still exhibit native-like behavior. These protein mutations may compensate for changes in enthalpic and entropic contributions toward DNA-binding in order to maintain binding free energies similar to that of the native protein-DNA complex.

Short, hydrophobic, alanine-based proteins based on the basic region/leucine zipper protein motif: overcoming inclusion body formation and protein aggregation during overexpression, purification, and renaturation

GCN4 is a yeast transcriptional regulatory protein; its DNA-binding domain is a basic region/leucine zipper (bZIP) structure that comprises a dimer of alpha-helices capable of high-affinity, sequence-specific recognition of the DNA major groove. We are exploiting what nature has evolved by manipulating the bZIP motif as a molecular recognition scaffold; thus we reduced the elegantly minimal bZIP to an even more simplified structure by substitution with alanine residues-hence, a generic, Ala-based, helical scaffold. These Ala-based mutants are unusual proteins for expression as they are short ( approximately 100 amino acids) and hydrophobic (Ala-mutated basic regions, leucine-zipper dimerization domains). Hydrophobicity posed a major problem throughout the expression, isolation, and purification stages; inclusion body formation and protein aggregation were significant hurdles throughout protein production. We describe measures that solved these problems, including use of high concentrations of denaturant in all steps of protein isolation and purification and use of temperature-dependent renaturing techniques to obtain folded, functional protein. Despite these difficulties, we ultimately retrieved 5-10 mg/L of broth of active, correctly folded protein after the complete purification procedure. Homogeneity of the proteins was established by chromatography, electrophoresis, and mass spectrometry. Furthermore, characterization by circular dichroism and DNase footprinting analysis demonstrates that these alanine-based mutants retain the structure and function of the native GCN4 DNA-binding domain. Remarkably, the most heavily mutated protein, containing 24 alanines of 27 total amino acids in the DNA-binding basic region, still binds the AP-1 site, the target of native GCN4.

Identification of four novel mutations of the low-density lipoprotein receptor gene in Korean patients with familial hypercholesterolemia

To obtain insight into the genetic variation of the low-density lipoprotein (LDL) receptor gene in Korean patients with familial hypercholesterolemia (FH), we used single-strand conformation polymorphism to screen all 18 exons and a promotor of the LDL receptor gene in 20 unrelated Korean FH patients. Four novel point mutations were detected in 5 FH patients and were characterized by sequence analysis. Of them, one is a nonsense mutation, a Glu-->Stop (CAG-->TAG) at codon 161, and results in a large deletion. The other three, which were a Ala-->Glu (GCG-->GAG) mutation at signal peptide, Cys-->Tyr (TGC-->TAC) at codon 210, and Pro-->Leu (CTG-->CCG) at codon 584, were novel missense mutations, which modified the highly conserved region of the LDL receptor gene. All these mutations were absent in normolipidemic controls and were associated in heterozygote carriers with clinical signs of FH. Identification of these novel mutations provides another example of the molecular heterogeneity of the LDL receptor gene mutations causing FH.

Discordance for keratoconus in two pairs of monozygotic twins

PURPOSE

We present two pairs of monozygotic twins discordant for keratoconus.

METHODS

Two pairs of twins, each with one twin with keratoconus, and available family members were examined clinically and with computer-assisted videokeratography. Polymerase chain reaction-based zygosity assays using between nine and 11 unique, anonymous DNA markers were performed on blood obtained from the twins and surviving parents to assess the probability of genetic monozygosity.

RESULTS

DNA probes showed a >99% probability that each of the two sets of twins was monozygotic. One twin from each pair had clinically diagnosed keratoconus. The remaining twins were normal by clinical examination and corneal topography. Clinical results for all family members examined were normal except that five of 13 from one family and one of six from the other family demonstrated "suspicious" corneal topography.

CONCLUSION

Recent advances in knowledge and understanding of the twinning process suggest that monozygotic twins discordant for keratoconus does not preclude the possibility of a significant genetic component.

Short-term repeatability of hand-held keratometry measurements

PURPOSE

The Collaborative Longitudinal Evaluation of Ethnicity and Refractive Error (CLEERE) Study is a multi-center, observational investigation of ocular component and refractive error development in schoolchildren. Anterior corneal curvature is one of several ocular components which influence refractive status of the eye, and the CLEERE Study uses the Alcon Auto-Keratometer to measure corneal curvature. This report assesses the repeatability of this hand-held instrument. Previous studies have demonstrated the validity of the Alcon Auto-Keratometer; however, none have assessed its repeatability.

METHODS

Sixty children were recruited from clinics affiliated with the Southern California College of Optometry and the University of Houston College of Optometry. Two sets of five hand-held keratometry measurements were obtained on the right eye of each child by one investigator at each site using the Alcon Auto-Keratometer. The two sets of measurements were performed at least 10 minutes apart.

RESULTS

The mean differences between the two occasions were not significantly different from zero for either the flat or steep corneal curvature measurements regardless of the number of readings taken. The largest improvement in repeatability, primarily for the steep meridian, occurred when the first two readings were averaged. The addition of readings 3, 4, and 5 to the average did not substantially improve repeatability for either meridian. The 95% limits of agreement between the average of two readings on two occasions for the flat and steep meridians were +/-0.28 and +/-0.39 D, respectively. The 95% limits of agreement after two readings were +/-0.28, +/-0.20, and +/-0.24 D for the M, J0, and J45 vectors, respectively.

CONCLUSION

The Alcon hand-held keratometer provides a repeatable measure of corneal curvature as demonstrated by short-term repeat agreement within +/-0.50 D. This level of repeatability can be achieved only by manually averaging two consecutive measurements.

Cycloplegia in African-American children

PURPOSE

The selection of a cycloplegic agent depends on the desired outcome, the characteristics of the patient receiving the drug, and the associated risks. The Orinda Longitudinal Study of Myopia (OLSM) has used 1% tropicamide to assess the ocular components and cycloplegic refractions in a large cohort of predominantly Caucasian children. Although tropicamide has provided adequate cycloplegia and mydriasis for the OLSM cohort, conventional clinical wisdom and scientific investigations have suggested that tropicamide might not produce adequate cycloplegia and mydriasis for subjects with darker iris pigmentation. In this study one drop of 1% tropicamide followed by one drop of 1% cyclopentolate was used to determine their effectiveness in producing adequate cycloplegia and mydriasis for cycloplegic refraction and ocular component measurements in a group of African-American children.

METHODS

Nineteen children [age range 5.5 to 15.6 years, mean 8.4 years +/- (SD) 2.5 years] were tested at Family HealthCare of Alabama, Eutaw, AL. Their accommodative responses were measured using a Canon R-1 autorefractor prior to and at 30, 45, and 60 min after instillation of one drop of 0.5% proparacaine, 1% tropicamide (Mydriacyl), and 1% cyclopentolate (Cyclogyl) in both eyes. A target of 20/155 letters in a 4x4 grid positioned behind a +6.50 diopter (D) Badal lens provided accommodative stimuli of 1.00 D, 2.00 D, and 4.00 D.

RESULTS

All results are presented as mean +/-1 SD. Pupils, measured from video frames, dilated rapidly and maximally at 30 min after instillation of eye drops (7.3+/-0.5 mm) Predilation, the mean accommodative responses were 0.17+/-0.29 D for the 1.00 D stimulus, 1.01+/-0.40 D for the 2.00 D stimulus, and 2.77+/-0.74 for the 4.00 D stimulus. At 30 min after drop instillation, the responses were 0.07+/-0.14 D for the 1.00 D stimulus, 0.36+/-0.35 D for the 2.00 D stimulus, and 0.77+/-0.61 for the 4.00 D stimulus. Results were very similar at 45 and 60 min after drop instillation.

CONCLUSIONS

Combining 1% tropicamide and 1% cyclopentolate was very effective in providing both cycloplegia and mydriasis adequate for ocular biometry and cycloplegic refractions 30 min after drop instillation in African-American children.

Baseline findings in the Collaborative Longitudinal Evaluation of Keratoconus (CLEK) Study

PURPOSE

To describe the baseline findings in patients enrolled in the Collaborative Longitudinal Evaluation of Keratoconus (CLEK) Study.

METHODS

This is a longitudinal observational study of 1209 patients with keratoconus enrolled at 16 clinical centers. Its main outcome measures are corneal scarring, visual acuity, keratometry, and quality of life.

RESULTS

The CLEK Study patients had a mean age of 39.29+/-10.90 years with moderate to severe disease, assessed by a keratometric-based criterion (95.4% of patients had steep keratometric readings of at least 45 D) and relatively good visual acuity (77.9% had best corrected visual acuity of at least 20/40 in both eyes). Sixty-five percent of the patients wore rigid gas-permeable contact lens, and most of those (73%) reported that their lenses were comfortable. Only 13.5% of patients reported a family history of keratoconus. None reported serious systemic diseases that had been previously reported to be associated with keratoconus. Many (53%) reported a history of atopy. Fifty-three percent had corneal scarring in one or both eyes.

CONCLUSIONS

Baseline findings suggest that keratoconus is not associated with increased risk of connective tissue disease and that most patients in the CLEK Study sample represent mild to moderate keratoconus. Additional follow-up of at least 3 years will provide new information about the progression of keratoconus, identify factors associated with progression, and assess its impact on quality of life.

Repeatability of refraction and corrected visual acuity in keratoconus. The CLEK Study Group. Collaborative Longitudinal Evaluation of Keratoconus

PURPOSE

The purpose of the test-retest phase of the Collaborative Longitudinal Evaluation of Keratoconus (CLEK) Study was to determine the repeatability of the various parts of the CLEK Study protocol. This paper presents the test-retest parameters of the refraction protocol.

METHODS

We examined 138 CLEK Study-eligible patients on two occasions (median, 90 days; range, 22 to 268 days). All patients underwent subjective refraction on two occasions, and contact lens over-refractions were performed either over the patient's habitual rigid contact lenses or over a trial rigid contact lens equal in base curve to the steep keratometric reading in nonrigid contact lens wearers.

RESULTS

Mean interoccasion differences +/- SD were -0.32 +/- 2.91 D and -0.17 +/- 1.39 D for subjective refraction sphere and cylinder power, respectively, and the mean absolute difference for subjective refraction cylinder axis was 18.1 +/- 20.2 degrees. The mean interoccasion difference +/- SD for high-contrast visual acuity with subjective refraction was 0.38 +/- 10.9 letters correct. Mean interoccasion differences +/- SD were -0.11 +/- 0.81 D and 0.02 +/- 0.67 D for contact lens over-refraction sphere and cylinder power, respectively, and the mean absolute difference for contact lens over-refraction cylinder axis was 11.6 +/- 9.9 degrees. The mean interoccasion difference +/- SD for visual acuity with contact lens over-refraction was 0.50 +/- 5.2 letters correct and 0.71 +/- 6.9 letters correct for high- and low-contrast visual acuity, respectively.

CONCLUSIONS

The repeatability of subjective refraction in keratoconus patients is good but somewhat lower than that found in nondiseased eyes. Only 36% of our repeat measures of sphere power from subjective refraction fell within 0.50 D of each other, compared with more than 90% in studies of normal eyes.

Capsular opening contraction after continuous curvilinear capsulorhexis and intraocular lens implantation

PURPOSE

To evaluate the progressive constriction of the anterior capsule opening that can occur after continuous curvilinear capsulorhexis (CCC).

SETTING

Kangnam St. Mary's Hospital, Seoul, Korea.

METHODS

Changes in the anterior capsule opening after CCC were evaluated in 166 pseudophakic eyes at 1 week and 1 and 3 months postoperatively. The capsular opening diameter was measured with an image analysis system.

RESULTS

The capsular opening diameter was reduced by an average of 13.87% 3 months after CCC. There was more dense opacity in the anterior than in the posterior capsule. Lens epithelial cells (LECs) were the main cause of capsule contraction; sex, age, intraocular lens haptic length and haptic material, and CCC size did not have a statistically significant effect on capsule shrinkage (P > .05). Three months after surgery, most eyes with an initial capsular opening diameter of less than 5.5 mm had an opening diameter smaller than 5.0 mm. In most eyes with an initial capsular opening larger than 5.5 mm, the opening remained larger than 5.0 mm.

CONCLUSION

Our results suggest that the ideal CCC size is 5.5 to 6.0 mm or larger and that LEC removal is necessary to preserve the pupillary zone and thus prevent progressive capsular opening shrinkage.

Orientation of the Lac repressor DNA binding domain in complex with the left lac operator half site characterized by affinity cleaving

Lac repressor (LacR) is a helix-turn-helix motif sequence-specific DNA binding protein. Based on proton NMR spectroscopic investigations, Kaptein and co-workers have proposed that the helix-turn-helix motif of LacR binds to DNA in an orientation opposite to that of the helix-turn-helix motifs of lambda repressor, lambda cro, 434 repressor, 434 cro, and CAP [Boelens, R., Scheek, R., van Boom, J. and Kaptein, R., J. Mol. Biol. 193, 1987, 213-216]. In the present work, we have determined the orientation of the helix-turn-helix motif of LacR in the LacR-DNA complex by the affinity cleaving method. The DNA cleaving moiety EDTA.Fe was attached to the N-terminus of a 56-residue synthetic protein corresponding to the DNA binding domain of LacR. We have formed the complex between the modified protein and the left DNA half site for LacR. The locations of the resulting DNA cleavage positions relative to the left DNA half site provide strong support for the proposal of Kaptein and co-workers.

Orientation of the putative recognition helix in the DNA-binding domain of Hin recombinase complexed with the hix site

On the basis of sequence similarity with other known DNA-binding proteins, the DNA-binding domain of Hin recombinase, residues 139-190, is thought to bind DNA by a helix-turn-helix motif. Two models can be considered that differ in the orientation of the recognition helix in the major groove of DNA. One is based on the orientation of the recognition helix found in the 434 repressor (1-69) and lambda repressor-DNA cocrystals, and the other is based on the NMR studies of lac repressor headpiece. Cleavage by EDTA.Fe attached to a lysine side chain (Ser183----Lys183) near the COOH terminus of Hin(139-184) reveals that the putative recognition helix is oriented toward the center of the inverted repeats in a manner similar to that seen in the 434 and lambda repressor-DNA cocrystals.