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To study the nature of antigenic recognition, antibodies have been prepared against a set of peptide sequences representing both highly mobile and well-ordered regions of myohaemerythrin, based on X-ray crystallographic temperature factors. Anti-peptide antibodies against highly mobile regions react strongly with the native protein; anti-peptide antibodies from well-ordered regions do not. Mobility is a major factor in the recognition of the native protein by anti-peptide antibodies; this may be of general significance in protein-protein interactions.

Resistance to chemotherapeutic drugs often limits their clinical efficacy. Previous studies have implicated the bioactive sphingolipid sphingosine-1-phosphate (S-1-P) in regulating sensitivity to cisplatin [cis-diamminedichloroplatinum(II)] and showed that modulating the S-1-P lyase can alter cisplatin sensitivity. Here, we show that the members of the sphingosine kinase (SphK1 and SphK2) and dihydroceramide synthase (LASS1/CerS1, LASS4/CerS4, and LASS5/CerS5) enzyme families each have a unique role in regulating sensitivity to cisplatin and other drugs. Thus, expression of SphK1 decreases sensitivity to cisplatin, carboplatin, doxorubicin, and vincristine, whereas expression of SphK2 increases sensitivity. Expression of LASS1/CerS1 increases the sensitivity to all the drugs tested, whereas LASS5/CerS5 only increases sensitivity to doxorubicin and vincristine. LASS4/CerS4 expression has no effect on the sensitivity to any drug tested. Reflecting this, we show that the activation of the p38 mitogen-activated protein (MAP) kinase is increased only by LASS1/CerS1, and not by LASS4/CerS4 or LASS5/CerS5. Cisplatin was shown to cause a specific translocation of LASS1/CerS1, but not LASS4/CerS4 or LASS5/CerS5, from the endoplasmic reticulum (ER) to the Golgi apparatus. Supporting the hypothesis that this translocation is mechanistically involved in the response to cisplatin, we showed that expression of SphK1, but not SphK2, abrogates both the increased cisplatin sensitivity in cells stably expressing LASS1/CerS and the translocation of the LASS1/CerS1. The data suggest that the enzymes of the sphingolipid metabolic pathway can be manipulated to improve sensitivity to the widely used drug cisplatin. (Mol Cancer Res 2007;5(8):801 -12)

Thirteen peptides corresponding to amino acid sequences predicted from the nucleotide sequence ofthe hepatitis B surface antigen were synthesized chemically. The free or carrier-linked synthetic peptides were injected into rabbits, and 7 of the 13 elicited an antipeptide response. Antisera against four of the six soluble peptides longer than 10 amino acids were reactive with native antigen and specifically precipitated the 23,000-and 28,000-dalton forms from Dane particles. As the hepatitis molecule had not been chosen for study because of any structural feature suggesting unique opportunities for success, these results suggest that the strategy is general and should work for any protein as long as enough domains are studied. Peptides such as these could prove to be ideal vaccines. The cloning and sequence determination of genes have greatly increased our knowledge of the structure of proteins and suggested mechanisms by which some are synthesized, processed, and transported. As we move to the study of uncharted genetic regions, however, we encounter a gap between the ease with which a gene can be cloned and sequenced and the unequivocal assignment of its protein product. Recently, a solution to this problem was offered that demonstrated that one could produce antibodies to a few chemically synthesized peptides predicted from newly solved nucleotide sequences and then use these antibodies to define the protein product ofthe gene in question (1-3). The most important feature ofantibodies made in this way is that they are directed against a small region of the protein, determined in advance by the investigator, and are thus unique biochemical reagents. Because this technology could have significant implications, it was important to learn whether the somewhat limited experience could be generalized and any "rules" that might be derived concerning which regions of proteins offered the best possibilities for selection ofpeptides likely to yield useful antibodies. We selected as models two genes whose nucleotide sequences were known and whose protein products were of both theoretical and practical interest. The first was the major envelope protein of the hepatitis B genome, a molecule that, because of its extreme hydrophobicity, offered an interesting challenge to the technology. The second was the hemagglutinin of influenza virus because its complete crystallographic structure is known (4); thus, one could correlate how antibodies to protein domains ofknown molecular location perturb virus infectivity and, in fact, what the structural correlates ofantigenicity are for the molecule. We report here our studies on the hepatitis B surface antigen (HBsAg).HBsAg is a glycosylated protein and the major surface antigen of the 42-nm particles (Dane particle) of hepatitis B virus (5-7). The HBsAg contains group-and type-specific determinants and is thought to be the major target of neutralizing antibody (6). Purified preparations of HBsAg are physically heterogenous and consist of at least seven polypeptides ranging i...

Purpose: Proteomic analysis of breast nipple aspirate fluid (NAF) holds promise as a noninvasive method to identify markers of breast cancer. The objectives of the study were to: (a) describe the NAF proteome, (b) identify candidate markers of breast cancer in NAF by using proteomic analysis, and (c) validate the markers identified by using a quantitative, high-throughput ELISA analysis.Experimental Design: For proteome analysis, NAF proteins from a single subject without breast cancer were separated by two-dimensional PAGE and were subjected to matrix-assisted laser desorption ionization time-of-flight mass spectometry identification. A total of 41 different proteins were identified, 25 of which were known to be secreted. To identify breast cancer markers, we separated 20 NAF samples (10 normal, 10 cancer) by two-dimensional PAGE. Three protein spots were detected that were up-regulated in three or more cancer samples. These spots were identified to be gross cystic disease fluid protein (GCDFP)-15, apolipoprotein D (apoD), and ␣1-acid glycoprotein (AAG). To validate these three potential biomarkers, 105 samples (53 from benign breasts and 52 from breasts with cancer) were analyzed using ELISA.Results: Among all of the subjects, GCDFP-15 levels were lower (P < 0.001) and AAG levels were higher (P ‫؍‬ 0.001) in breasts with cancer. This was also true in premenopausal (GCDFP-15, P ‫؍‬ 0.011; AAG, P ‫؍‬ 0.002) but not in postmenopausal women. GCDFP-15 levels were lowest (P ‫؍‬ 0.003) and AAG levels highest (P < 0.001) in women with ductal carcinoma in situ (DCIS). Menopausal status influenced GCDFP-15 and AAG more in women without breast cancer than in women with breast cancer. apoD levels did not correlate significantly with breast cancer.Conclusions: Our study revealed that the NAF proteome, as defined by two-dimensional PAGE, consists of a limited number of proteins, and that the expression of AAG and GCDFP-15 correlates with disease presence and stage.

The chemistry of antibody recognition was studied by mapping the antigenicity of the protein myohemerythrin with peptide homologs of the protein sequence. The results suggest that the entire protein surface is antigenic, but the probability of there being antibodies to a given site is influenced by local stereochemistry. Although accessible to an antibody binding domain, the least reactive positions cluster in the most tightly packed and least mobile regions and are closely associated with narrow, concave grooves in the molecular surface containing bound water molecules. The most frequently recognized sites form three-dimensional superassemblies characterized by high local mobility, convex surface shape, and often by negative electrostatic potential.

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