Evaluating the accuracy of a three-term pencil beam algorithm in heterogeneous media.

The goal of this work was to evaluate the accuracy of our in-house analytical dose calculation code against MCNPX data in heterogeneous phantoms. The analytical model utilizes a pencil beam model based on Fermi-Eyges theory to account for multiple Coulomb scattering and a least-squares fit to Monte Carlo data to account for nonelastic nuclear interactions as well as any remaining, uncharacterized scatter (the 'nuclear halo'). The model characterized dose accurately (up to 1% of maximum dose in broad fields (4 × 4 cm2 and 10 × 10 cm2) and up to 0.01% in a narrow field (0.1 × 0.1 cm2) fit to MCNPX data). The accuracy of the model was benchmarked in three types of stylized phantoms: (1) homogeneous, (2) laterally infinite slab heterogeneities, and (3) laterally finite slab heterogeneities. Results from homogeneous phantoms and laterally infinite slab heterogeneities showed high levels of accuracy (>98% of points within 2% or 0.1 cm distance-to-agreement (DTA)). However, because range straggling and secondary particle production were not included in our model, central-axis dose differences of 2-4% were observed in laterally infinite slab heterogeneities when compared to Monte Carlo dose. In the presence of laterally finite slab heterogeneities, the analytical model resulted in lower pass rates (>96% of points within 2% or 0.1 cm DTA), which was attributed to the use of the central-axis approximation.

Biophysical characterization of one-, two-, and three-tandem repeats of human mucin (muc-1) protein core.

Until recently mucin tandem repeat protein cores were believed to exist in random-coil conformations and to attain structure solely by the addition of carbohydrates to serine and threonine residues. Matsushima et al. (Proteins Struct. Funct. Genet., 7: 125-155, 1990) recently proposed a model of the secondary structure of proline rich tandem repeat proteins that has challenged this idea, especially for the case of the human polymorphic epithelial mucin encoded by the muc-1 gene. We report here results of structural analyses of the muc-1 protein core by using synthetic peptide analogues. Synthetic peptides were prepared to correspond to one-, two-, and three-tandem repeats of muc-1. Results of one- and two-dimensional 1H NMR correlation spectroscopy on these peptides confirm that the muc-1 protein core is not a random-coil secondary structure. Long-lived amide protons are protected in D2O, and increasing spectral complexity in the region of the beta-protons of Asp2 and His 15 reveals that structural changes are occurring as the number of repeats increases. The greatest changes occur when the number of repeats increases from one to two. These results are supported by the reactivity of a panel of monoclonal antibodies raised against tumor associated muc-1 with these synthetic peptides in enzyme-linked immunosorbent assay. The primary immunodominant mucin epitope, PDTRP, does not appear to attain a native conformation in the single repeat peptide (20 amino acids, starting with P), but is expressed on peptides with multiple repeats. Intrinsic viscosity measurements of the peptide containing three repeats indicate that an ordered structure present in solution is rod shaped. The circular dichroism spectrum of the same peptide is dominated by proline in the trans conformation. These results are all consistent with the prediction that the muc-1 tandem repeat polypeptide core forms a polyproline beta-turn helix.

Humoral immunity against a tandem repeat epitope of human mucin MUC-1 in sera from breast, pancreatic, and colon cancer patients.

Using synthetic peptides 60,80, and 105 residues long, corresponding to 3, 4, and 5.25 tandem repeats of human mucin MUC-1 protein core, as antigens in a solid-phase enzyme-linked immunosorbent assay, we screened sera from 24 breast cancer patients, 10 colon cancer patients, and 12 pancreatic cancer patients, at various stages of disease, for the presence of mucin-specific antibodies. The 105-residue peptide was superior in allowing detection of high levels of anti-mucin antibodies in 10.9% of sera in each cancer group. Another 4.3% showed intermediate reactivity. Lower levels of detection were achieved with the 80-residue peptide, and no specific reactivity was detectable with the 60-residue peptide. Anti-mucin antibodies were previously undetectable when this assay was performed with purified whole mucin or short synthetic peptides. The presence or absence of antibody did not correlate with the levels of circulating mucin or stage of disease. One highly reactive serum sample was used to identify more precisely the epitope on the long synthetic peptide to which the reactivity was directed. The reactivity of this serum specific for the 105-residue peptide was blocked by a 9-residue peptide from the NH2-terminal region of the 20-residue tandem repeat containing the previously identified immunogenic epitope APDTRP. Another 9-residue mucin peptide, from the COOH-terminal region of the tandem repeat which does not contain the APDTRP epitope, had no effect. All the mucin-specific reactivity was found to be of the IgM isotype, indicating a helper T-cell-independent response, unusual for an antibody against a peptide epitope, but not unexpected for tandemly repeated epitopes.

N-acetylgalactosamine glycosylation of MUC1 tandem repeat peptides by pancreatic tumor cell extracts.

Synthetic peptides corresponding to the human mucin MUC1 tandem repeat domain (20 residues) were glycosylated in vitro by using UDP-N-[3H]acetyl-D-galactosamine (GalNAc) and lysates of pancreatic tumor cell lines. Results obtained with peptides of different lengths (from one to five repeats) suggest that increasing the number of tandem repeats has neither a positive nor a negative effect on the density of glycosylation along the MUC1 tandem repeat protein backbone. Purified glycopeptides were sequenced on a gas-phase sequencer, and glycosylated positions were determined by measuring the incorporated radioactivity in fractions collected following each round of Edman degradation. The results showed that two of three threonine residues on the MUC1 tandem repeat peptides were glycosylated by pancreatic tumor cell lysates at the following positons: GVTSAPDTRPAPGSTAPPAH (underlined T indicates position of GalNAc attachment). None of the serine residues were glycosylated. Determination of the mass of the glycopeptides by mass spectrometry confirmed that a maximum of two molecules of GalNAc were covalently linked to each 20-residue repeat unit in the peptides. The data presented here show that acceptor substrate specificity of the UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase detected in lysates of pancreatic and breast tumor cell lines is identical and is limited to some but not all threonines in the MUC1 tandem repeat peptide sequence. The influence of primary amino acid sequence on acceptor substrate activity was evaluated by using several peptides that contain single or double amino acid substitutions (relative to the native human MUC1 sequence). These included substitutions in the residues that were glycosylated and substitutions of the surrounding primary amino acid sequence. The results of these studies suggest that primary amino acid sequence, length, and relative position of the residue to be glycosylated dramatically affect the ability of peptides to serve as acceptor substrates for the UDP-GalNAc:polypeptide N-acetylgalatosaminyltransferase.

Design tools for proton therapy nozzles based on the double-scattering foil technique.

Proton therapy has been increasing over the past several years, with several new treatment facilities being built in Europe, Japan and the United States. In this work, analytical and Monte Carlo tools were combined to model the passively scattered neurosurgery treatment beamline of the Harvard Cyclotron Laboratory (Cambridge, MA). The predicted three-dimensional dose distributions agree with actual measurements to within 0.1 mm for all quantities considered in central-axis depth-dose curve and to within 2.1 mm for all quantities considered in the absorbed dose cross-field profile. The predicted neutron dose equivalent per therapeutic absorbed dose, H/D, was calculated at various locations representing clinically significant anatomical sites. Under typical treatment conditions, the average ratio of predicted-to-measured H/D is 1.8 in the gonadal region (50 cm from isocentre) and 3.4 in the thyroid region (21 cm from isocentre). The global ratio of predicted-to-measured H/D is 2.6.

Structure-based design of peptides that recognize the CD4 binding domain of HIV-1 gp120.

DESIGN: Envelope protein-specific antiviral peptides, called mucibodies, that can specifically recognize and bind to the surface unit protein gp120 of HIV-1 were designed. The initial mucibody binding target was the V3 loop of HIV-1 gp120. Here, the gp120-CD4 binding domain was chosen as the site of mucibody binding. The CD4 binding domain of gp120 is known to be a conformational epitope and is involved in the earliest events of viral entry into many cells. METHODS: The design of the mucibody antivirals was based on previous observations that antibody complementarity determining regions (CDR) are generally similar to the repeating loops or knob structures found in the 20-residue tandem repeat domain of human mucin MUC1. The heavy chain CDR3 from the bacteriophage display antibody b12 was used to construct two mucibodies, b12-CDR1 and b12-26. RESULTS: Peptides corresponding to three tandem repeats were shown to bind directly to the CD4 binding domain of HIV-1 gp120 in a solid-phase enzyme-linked immunosorbent assay. These mucibody peptides also disrupted the gp120-CD4 interaction in a solution-phase inhibition assay. Finally, mucibodies neutralized primary and laboratory macrophage-tropic isolates of HIV-1. CONCLUSIONS: There is a potential for medical use of these peptides as topical vaginal microbicides in preventing HIV-1 transmission during sexual contact. These results also suggest that multivalent, non-immunogenic binding proteins of virtually any specificity could be constructed for use in therapeutic applications involving infectious diseases and immune system dysfunction.

Presentation of HIV V3 loop epitopes for enhanced antigenicity, immunogenicity and diagnostic potential.

OBJECTIVE: To evaluate the immunological properties of a panel of human mucin MUC1/HIV V3 loop chimeras. DESIGN: The immunodominant epitope of MUC1 (APDTR) was found to be structurally isomorphous with the tip of the principle neutralizing determinant (PND) of HIV-1 (MN) (GPGRA). A panel of 120 residue, six tandem repeat (TR) and 60 residue, three TR chimeric antigens were constructed in which the repeating MUC1 epitope is replaced by HIV-1 PND. Each 20 residue TR contains one PND epitope. The PND of HIV-1 is presented in the native beta-turn conformation at the crest of each repeating knob structure of the mucin-like protein. METHODS: The antigenicity of the chimeric antigens were compared using enzyme-linked immunosorbent assay (ELISA) and HIV-infected patient sera. Structural effects of antibody-antigen interactions were determined using surface plasmon resonance, with human monoclonal antibodies, chimeric antigens and the cyclic and linear V3 loops. Immunogenicity of three versus six TR was measured in mice. RESULTS: Nine residues of the HIV PND substituted into the mucin backbone were equivalent to the 36 residue cyclic V3 loop in ELISA. The 120 residue antigens induced high titer, immunoglobulin (Ig) M and IgG, and HIV-specific antibodies in mice. CONCLUSIONS: MUC1/V3 chimeras efficiently detect HIV-specific antibodies in patient sera. Multivalent presentation of the PND is advantageous for higher affinity antibody-antigen interactions and for inducing HIV-specific IgM and IgG antibodies.

Isolation and characterization of a proteoglycan variant from human aorta exhibiting a marked affinity for low density lipoprotein and demonstration of its enhanced expression in atherosclerotic plaques.

Proteoglycans (PG) are implicated in the pathophysiology of atherosclerosis due to their ability to complex with plasma low density lipoproteins (LDL). Studies were conducted to determine whether human aorta contains PG subclasses that exhibit enhanced LDL binding ability. PG were isolated from normal and atherosclerotic aortas by a combination of dissociative extraction and ion-exchange chromatography. The PG were further subfractionated on an LDL affinity column based on their binding affinity to LDL. Two PG fractions exhibiting high-affinity binding to LDL, as evidenced by their elution at 1.0 and 1.5 M NaCl, respectively, were isolated from both normal and atherosclerotic tissue. Compared with normal tissue, atherosclerotic tissue showed a twofold increase in the high-affinity PG that eluted at 1.5 M NaCl. Gel filtration of the high-affinity PG from normal tissue yielded two peaks (nPG2 and nPG3), while the high-affinity PG from plaque tissue was resolved into three peaks (pPG1, pPG2, and pPG3). pPG1 eluted at the void volume of the column, indicating that it was of very large molecular size. The hydrodynamic size of pPG2 was larger than that of the corresponding nPG2 (Kav = 0.44 versus 0.51), while pPG3 had the same hydrodynamic size as nPG3 (Kav = 0.86). The high-affinity PG subfractions from normal aorta contained varying proportions of chondroitin sulfates, dermatan sulfates, and heparan sulfate. In contrast, the PG subfractions from plaque tissue contained predominantly chondroitin sulfates and heparan sulfate. In vitro complexes of LDL and the high-affinity PG fractions from normal aorta and plaque tissue stimulated cholesteryl ester synthesis in human monocyte-derived macrophages. However, the LDL-plaque PG complex was significantly more potent than the LDL-normal aorta PG complex in this respect. These results indicate that PG subclasses with enhanced binding affinity to LDL occur in the normal human aorta and that their concentration increases significantly in atherosclerotic lesions. In addition, the high-affinity PG in plaque tissue have altered characteristics and increased ability to stimulate LDL-mediated cholesterol ester synthesis in macrophages. This could lead to increased lipid deposition during atherogenesis.

Structure and self assembly of a retrovirus (FeLV) proline rich neutralization domain.

The 60 amino acid proline-rich neutralization domain of the external surface unit glycoprotein of feline leukemia virus was chemically synthesized in total and in fragments. We examined the ability of these retroviral peptides to form ordered conformations using 1H-NMR, circular dichroism spectroscopy, and intrinsic viscosity measurements. One dimensional nuclear magnetic resonance spectroscopy revealed that the 60 amino acid peptide could form a stable, folded structure that was long-lived, as shown by the ability to protect amide-protons in D20. Peptides corresponding to the N-terminal 42, N-terminal 20 amino acids, and middle 20 amino acid sections could also form stable structures. The C-terminal segment did not protect any protons in D20. Interestingly, self assembly of the N-terminal 42 and C-terminal 16 amino acid peptides into a structure very close to that of the 60 amino acid domain was observed. The circular dichroism results reveals a large negative cotton effect at 198 nm that is characteristic of the proline-rich beta-turn helixes which consist predominantly of trans-proline. The intrinsic viscosity results suggest a non-random coil structure that is rod shaped. Our conclusion is that PRN60 forms a beta-turn helix and that this region of FeLV-gp70 is a separate folding domain of the retroviral surface unit glycoprotein. The unique conformational properties of PRN60 and its critical role as the predominant target for neutralizing antibody responses suggest that this peptide is a reasonable candidate for producing a synthetic peptide vaccine for FeLV.

Structure of a tumor associated antigen containing a tandemly repeated immunodominant epitope.

Human mucins are T or S glycosylated tandem repeat proteins. In breast cancer, mucins become under or unglycosylated. Two-dimensional nuclear magnetic resonance experiments are performed on chemically synthesized mucin tandem repeat polypeptides, (PDTRPAPGST-APPAHGVTSA)n the unglycosylated form for n=1,3 where (APDTR) constitutes the antigenic sites for the antibodies isolated form the tumors in the breast cancer patients. These studies demonstrate how the tandem repeats assemble in space giving rise to the overall tertiary structure, and the local structure and presentation of the antigenic site(APDTR) at the junction of two neighboring repeats. The NMR data reveal repeating knob-like structures connected by extended spacers. The knobs protrude away from the long-axis of Muc-1 and the predominant antigenic site (APDTR) forms the accessible tip of the knob. Multiple tandem repeats enhance the rigidity and presentation of the knob-like structures.

Overestimation of hemoglobin in a patient with an IgA-kappa monoclonal gammopathy.

A patient with multiple myeloma had an automated blood count performed on a Coulter STK-S counter that repeatedly failed internal limits for both mean corpuscular hemoglobin and mean corpuscular hemoglobin concentration. The calculated hematocrit agreed with a spun hematocrit, suggesting that the hemoglobin concentration was being overestimated by the automated counter. Measurement of the plasma hemoglobin concentration of the sample, which showed no visible hemolysis, gave a hemoglobin concentration of 32 g/L on the STK-S analyzer. Correction of the whole blood hemoglobin using the plasma hemoglobin gave a value consistent with the hematocrit. The corrected mean corpuscular hemoglobin and mean corpuscular hemoglobin concentration values were within standard limits. This patient's paraprotein was characterized as IgA-kappa and was present at a concentration of 61 g/L. The hemoglobin concentration measured on whole blood by Sysmex NE 8000 and Technicon H*1E autoanalyzers agreed reasonably well with the corrected result from the STK-S.

Single-arc volumetric-modulated arc therapy can provide dose distributions equivalent to fixed-beam intensity-modulated radiation therapy for prostatic irradiation with seminal vesicle and/or lymph node involvement.

OBJECTIVES: Volumetric-modulated arc therapy (VMAT) is becoming an increasingly utilised modality for treating a variety of anatomical sites. However, the efficacy of single-arc VMAT to treat prostate cancer suspicious for extraprostatic extension was heretofore unknown. In this work, we report our institutional experience with single-arc VMAT and fixed-beam intensity-modulated radiation therapy (IMRT) for prostate cancer patients treated for seminal vesicle and/or lymph node involvement. METHODS: Single-arc VMAT and 7- or 9-field IMRT treatment plans were compared for 10 prostate cancer patients treated for seminal vesicle involvement and/or lymph node involvement. All treatment plans were constructed using the Philips Pinnacle treatment planning system (v.9.0, Fitchburg, WI) and delivered on an Elekta Infinity radiotherapy accelerator (Crawley, UK). Resulting plans were compared using metrics that characterised dosimetry and delivery efficiency. RESULTS: No statistically significant differences in target coverage, target homogeneity or normal tissue doses were noted between the plans (p>0.05). For prostate patients treated for seminal vesicle involvement, VMAT plans were delivered in 1.4±0.1 min (vs 9.5±2.4 min for fixed-beam IMRT) (p<0.01) and required approximately 20% fewer monitor units (p=0.01). For prostate patients treated for lymph node involvement, VMAT plans were delivered in 1.4±0.1 min (vs 11.7±1.3 min for fixed-beam IMRT) (p<0.01) and required approximately 45% fewer monitor units (p<0.01). CONCLUSION: Single-arc VMAT plans were dosimetrically equivalent to fixed-beam IMRT plans with significantly improved delivery efficiency.

Proline-rich tandem repeats of antibody complementarity-determining regions bind and neutralize human immunodeficiency virus type 1 particles.

The proline-rich tandem repeat domain of human mucin MUC1 forms an extended structure containing large repeating loops that are crested by a turn. We show that the repeating-loop structure of MUC1 can be replaced by an antibody complementarity-determining region loop of a human immunodeficiency virus type 1 (HIV-1)-specific neutralizing antibody to create a chimeric, multivalent, mucin-like, anti-HIV-1 compound. We used 8 residues of an antibody molecule to replace 8 of 20 residues of the MUC1 tandem-repeat sequence. The antiviral peptide discussed here contains three copies of a 20-residue tandem repeat, (IYYDYEEDPAPGSTAPPAHG)3, for a total of 60 residues. We demonstrate that the mucin-antibody chimera retains the binding specificity of the parent antibody (monoclonal antibody F58), GPGR of the HIV-1 gp120 V3 neutralizing epitope, and the ability to neutralize virus particles. In inhibition enzyme-linked immunosorbent assay, the mucin-antibody chimeric peptide could inhibit 71 to 84% of binding to a V3 loop peptide by monoclonal antibodies known to be specific for GPGR in the V3 loop. The mucin-antibody chimeric peptide could also inhibit monoclonal antibody binding to native gp120 captured from virus particles. In addition, the chimeric peptide neutralized the homologous HIV-IIIB virus in a standard neutralization assay. The methods of antiviral peptide design and construction presented here are general and theoretically limited only by the size of the antibody repertoire. This approach could be used to synthesize peptides for a variety of therapeutic applications.

Sulfated polysaccharides block chlamydia infection in vitro, but do not protect mice from vaginal inoculation.

There is considerable interest in developing a vaginal product that women could use to protect themselves from sexually transmitted pathogens, including chlamydia. It has been suggested that sulfated polysaccharides would be effective in a prophylactic product because they have been shown to block infection of cultured cells by sexually transmitted pathogens, including chlamydia. In order to compare in vitro findings with animals, we placed sulfated polysaccharides into the vaginae of mice prior to inoculation with chlamydia. The surfactant nonoxynol 9 (N9) was used as a positive control as it has been previously shown to protect mice from infection by chlamydia. In this study, N9 also protected the mice from infection. However, sulfated polysaccharides which had been shown to be efficacious in vitro did not block infection.

Synthesis of large multideterminant peptide immunogens using a poly-proline beta-turn helix motif.

We report the synthesis and characterization of a novel secondary structural motif, the poly-proline beta-turn helix. This motif is found in the proline-rich immunogenic domains of feline retroviruses, mucins and many proline-rich tandem repeat-containing surface proteins. We describe the synthetic methodology to directly synthesize natural and engineered immunogens of up to 100+ amino acids. Using manual solid-phase peptide synthesis modified for optimal efficiency, we directly synthesized 1, 2, 3, 4 and 5.25 tandem repeats corresponding to 20, 40, 60, 80, 105 amino acids of the human mucin muc-1, the complete 60 amino acid proline-rich neutralization domain of feline leukemia virus, and 70 and 72 amino acids of two very hydrophobic engineered tandem repeat proteins. High pressure liquid chromatography and mass spectrometry results indicate that the desired peptide can be synthesized up to 92% pure. The secondary structures of these peptides were studied using circular dichroism (CD) spectroscopy. The CD spectra revealed a characteristic intense negative band at 198 nm. A melting of structure could be demonstrated with increasing temperature as measured by decreasing molar ellipticity at 198 nm. The intensity of the molar ellipticity at 198 nm, as compared to the molar ellipticity of random coil, non-proline-containing peptides, led to the conclusion that the large, intense negative band at 198 nm is diagnostic of the poly-proline beta-turn helix.(ABSTRACT TRUNCATED AT 250 WORDS)

Evaluation of feline immunodeficiency virus and feline leukemia virus transmembrane peptides for serological diagnosis.

The general model for retrovirus transmembrane (TM) proteins proposed by Gallaher et al. (W. R. Gallaher, J. M. Ball, R. F. Garry, M. C. Griffin, and R. C. Montelaro, AIDS Res. Hum. Retroviruses 5:431-440, 1989) suggests that all retrovirus TM proteins may contain an immunodominant domain (Imd-TM peptide) located at the apex of the TM polypeptide. Although this Imd-TM peptide has been shown to be immunodominant in a variety of lentivirus infections, there has not been a detailed serological analysis of an oncovirus Imd-TM peptide as a diagnostic agent. We describe here an analysis of the antigenic properties and diagnostic potentials of the predicted Imd-TM peptides of feline immunodeficiency virus (FIV) and feline leukemia virus (FeLV) in serological assays of sera from infected cats. The results of these studies demonstrate that antibodies specific to the FIV Imd-TM peptide are detected within 2 weeks postinfection, are maintained at high levels for extended periods, and are not detectable in uninfected or FeLV-infected cats. In marked contrast, the FeLV Imd-TM peptide displayed only negligible levels of serological reactivity in FeLV-infected cats. These studies indicate that the peptide is a useful reagent for the detection of antibodies to FIV.

Marked alteration of proteoglycan metabolism in cholesterol-enriched human arterial smooth muscle cells.

To elucidate the correlation between vascular cholesterol metabolism and proteoglycan (PrGl) biosynthesis, we investigated PrGl synthesis in human aortic smooth muscle cells (SMCs) after cholesterol enrichment with cationized low-density lipoproteins (LDL). Compared with normal SMCs, total PrGl synthesis by cholesterol-enriched cells decreased 2.4-fold (11874 +/- 530 d.p.m. per 10(5) cells compared with 4890 +/- 385 d.p.m. per 10(5) cells). This was the net result of a 6.9-fold reduction in medium PrGl (11000 +/- 490 d.p.m. per 10(5) cells compared with 1580 +/- 246 d.p.m. per 10(5) cells) and a 3.8-fold increase in cellular PrGl over controls (874 +/- 27 d.p.m. per 10(5) cells compared with 3310 +/- 193 d.p.m. per 10(5) cells). Prior incubation of SMCs with native LDL had no effect on PrGl synthesis by these cells. The decrease in PrGl synthesis in cholesterol-enriched cells correlated with a 90% and 20% reduction in the steady-state level of mRNA for biglycan and decorin respectively, and a virtual elimination of the steady-state level of mRNA for versican over controls. Despite the down-regulation of PrGl synthesis, cholesterol-loaded cells produced a 2-fold increase in a PrGl subfraction with high affinity for LDL. Compared with the corresponding PrGl subfraction from normal cells, that from the cholesterol-enriched cells exhibited increased charge density and a higher molecular mass and contained relatively larger proportions of chondroitin 6-sulphate and dermatan sulphate. These results show that PrGl metabolism is dramatically altered in cholesterol-enriched human SMCs.

Local and global structural properties of the HIV-MN V3 loop.

Studies of the feasibility of a subunit vaccine to protect against human immunodeficiency virus (HIV) infection have principally focused on the third variable (V3) loop. The principal neutralizing determinant (PND) of HIV-1 is located inside the V3 loop of the surface envelope glycoprotein, gp120. However, progress toward a PND-based vaccine has been impeded by the amino acid sequence variability in the V3 loops of different HIV isolates. Theoretical studies revealed that the variability in sequence and structure of the V3 loop is confined to the N- and C-terminal sides of the conserved GPG crest. This leaves three regions of the V3 loop conserved both in sequence and secondary structure. We present the results of NMR studies that test the validity of our theoretical predictions. Structural studies are reported for the HIV-V3 loop (HIV-MN) in the linear and cyclic (S-S-bridged) forms. For the V3 loop sequence of the HIV-MN isolate, the three conserved secondary structural elements are as underlined below: turns turn helix CTRPNYNKRKRIHIGPGRAFYTTKNIIGTIROAHC Finally, the conformational requirement of the PND in the V3 loop-antibody interaction is tested by monitoring the monoclonal antibody binding to the HIV-MN V3 loop in the linear and cyclic forms by enzyme-linked immunosorbent assay. The binding data reveal that the cyclic V3 loop is a better ligand for the monoclonal antibodies than the linear form although the latter has the same sequence. This means that the monoclonal antibodies recognize the PNDs as conformational epitopes.

A survey of potential problems and quality control in peptide synthesis by the fluorenylmethoxycarbonyl procedure.

The routine production of peptides by manual or automated solid-phase synthesis protocols has gained widespread usage among a variety of biological scientists as new synthetic procedures have been introduced over the past several years. We report here a detailed analysis of Fmoc synthesis procedures to identify problematic reactions and to evaluate analytical procedures for monitoring the quality of peptides during and after synthesis. The results of these studies demonstrate double additions of particular amino acids during single coupling cycles, frequent incomplete deblocking of peptides by standard piperidine reactions, and the failure of the Kaiser ninhydrin test to detect free amino groups of certain amino acids at the N-terminus of synthetic peptides. These results suggest the need for more careful monitoring of Fmoc synthesis reactions than previously recognized or recommended in standard protocols. We demonstrate the utility of plasma desorption mass spectrometry (PDMS) in analyzing peptide products and recommend a minimum sequence of analytical quality control including HPLC and PDMS.

Antibodies reactive with the protein core of MUC1 mucin are present in ovarian cancer patients and healthy women.

Antibodies reactive with peptide epitopes on the core protein of MUC1 epithelial mucin have been demonstrated in some patients with adenocarcinomas. Because these epitopes can be exposed on MUC1 in the serum of healthy women, we measured concentrations of MUC1-reactive antibodies in the serum of healthy pregnant and non-pregnant women, and in patients with benign and malignant ovarian tumours. Antibodies were measured in an enzyme-linked immunosorbent assay utilising a synthetic peptide corresponding to a 105-amino-acid segment of the MUC1 tandem repeat region (5.25 repeats). MUC1-reactive antibodies were always of an IgM isotype and concentrations were highest in young healthy women and declined progressively with age (P=0.0006) concomitantly with increasing serum MUC1 levels (P=0.003). Regardless of age, antibody levels were lower in cancer patients than in healthy women (P<0.0001), but MUC1 levels were much higher in cancer patients (P<0.0001). Although high antibody levels were associated with greater survival in ovarian cancer (P=0.015), multivariate regression analysis showed that this was not a significant independent prognostic indicator after consideration of the International Federation of Gynaecology and Obstetrics (FIGO) stage, histological type, serum MUC1 levels and age. Serial measurement of MUC1 and MUC1 antibodies during treatment in 18 patients with ovarian cancer and throughout pregnancy in 10 women showed a negative correlation between alterations in MUC1 and MUC1 antibodies. These results show that MUC1-peptide-reactive antibodies are present in the serum of healthy women and women with cancer and that they probably form immune complexes with MUC1, but provide no evidence for an augmentation of the humoral immune response to MUC1 in ovarian cancer