Mesenchymal chondrosarcoma of the hyoid bone: a case report

Mesenchymal chondrosarcoma is a rare tumor that is distinctly different from classic chondrosarcoma. The prognosis of this tumor is poor, with a high incidence of locoregional and distant metastases. It shows a predilection for the head and neck, however mesenchymal chondrosarcoma of hyoid bone has rarely been reported. We experienced a case of mesenchymal chondrosarcoma of the hyoid bone in a 39-year-old woman. She underwent excision of the tumor by right hemihyoidectomy. Histologically, a combination of cellular zones composed of undifferentiated small cells and chondroid zones typically presented a bimorphic appearance. CD99 (DN16) immunohistochemical stain demonstrated that all undifferentiated small cells had strong reactivity with a distinct membranous pattern. There was microscopic tumor extension to the resection margin of the hyoid bone, however, no evidence of reccurence is noted at follow-up of 4 months with neck CT.

Cellular resistance to adriamycin conferred by enhanced Rb expression is associated with increased MDR1 expression

In order to investigate if the enhanced expression of Rb confers increased cellular resistance to adriamycin, we made Rb stable transfectants from colon carcinoma cells, SW620. Rb stable transfectants exhibited 5- to 10-fold more resistance to adriamycin than the control cells. To study the correlation between enhanced Rb expression and MDR1 expression, products of the Rb gene and the MDR1 gene in Rb stable transfectants were measured by Western blot analysis. These Rb transfectants showed increased MDR1 expression. Transient transfection of the MDR1 promoter-CAT reporter gene and the Rb gene demonstrated that Rb up-regulated MDR1 promoter activity in SW620 cells. Rb may, at least partly, contribute to a role in protecting cells from carcinogen exposure by up-regulating the MDR1 gene.

Prolactin-inducible enhancer activity of the first intron of the bovine beta-casein gene

We have analyzed the regulatory roles of the first intron (intron-1) of the bovine beta-casein gene in the bovine beta-casein/CAT expression system using a mouse mammary epithelial cell line, HC11. After a combined treatment of HC11 cells with insulin, dexamethasone and prolactin, the induced expression of p beta c1.8/+ICAT vector including 2 kb intron-1 and 1.8 kb promoter was greatly increased to 23.5 folds, while that of p beta ca.8CAT basic vector with 1.8 kb promoter only, was 6.5. A classical enhancer activity was shown in the 2 kb intron fragment from the experiment in which the orientation and the position of the intron-1 on the vectors were changed. The enhancer activity was largely dependent on the lactogenic hormones, especially prolactin. A stepwise reduction of the inducibility in the 5' to 3' deletion analysis of the intron-1 indicates the existence of several functional elements in the region. In particular, an internal fragment (+1071 to +1490) was important for the prolactin-dependent enhancing activity of the intron-1. These results suggest that several elements in the intron-1 of the bovine beta-casein gene cooperatively interact not only with each other but also with its promoter for hormonal induction.

Transcription activation via enhanced preinitiation complex assembly in a human cell-free system lacking TAFIIs

In contrast to previous findings in cell-free systems reconstituted with partially purified metazoan factors, we demonstrate dramatic activation of transcription in a TBP-dependent but TAFII-independent manner in HeLa nuclear extracts immunodepleted of TBP and major TAFIIs. Single-round transcription assays reveal that TAFII-independent activation is manifested at the level of productive preinitiation complex formation and that TAFIIs actually impair functional preinitiation complex assembly in a core promoter-specific manner. Furthermore, TAFIIs appear to elevate absolute levels of transcription under multiple-round transcription conditions, presumably by facilitating secondary initiation events. Finally, human coactivator activities related to those in yeast RNA polymerase II/mediator complexes appear to function in unfractionated HeLa nuclear extracts.

Synthesis and antibacterial activities of new carbapenems having a proline reverse amide moiety at the C-2 position

The synthesis of new 1 beta-methylcarbapenems (1a-l) having a proline reverse amide moiety at the C-2 position and their in vitro antibacterial activities are described. The compounds were evaluated by the Mueller-Hinton agar dilution method and compared with meropenem as control. Aliphatic amides (1a-h) are found to show greater antibacterial activity than aromatic amides (1i-l). Moreover, C-2 free amino compound (1m) reveals greater activity than any other amide compounds (1a-l).

p53 mutation and overexpression in hepatocellular carcinoma and dysplastic nodules in the liver

In hepatocarcinogenesis, both de novo and multistep pathways have been suggested and in the latter a dysplastic nodule is the proposed precancerous lesion. In this study, we tried to ascertain whether or not the p53 gene is altered in low-grade/high-grade dysplastic nodules (LDN/HDN) and to determine the role of p53 alteration in multistep hepatocarcinogenesis. Eight hepatocellular carcinomas (HCCs), 9 HDNs, 17 LDNs and 25 cirrhotic nodules (LCs) were examined by polymerase chain reaction-single strand conformation polymorphism/direct sequencing and immunohistochemical staining for p53. Four of the 8 HCCs (50%) revealed p53 overexpression and 2 (25%) had missense mutations. Four of the 9 HDNs (44%) showed weak and/or focal p53 overexpression but none had mutation in the exons examined. Neither p53 overexpression nor mutation was found in 17 LDNs and 25 LCs. These results suggest that p53 mutation might be an unusual event in precancerous lesions of multistep hepatocarcinogenesis (DN-HCC sequence) and may play a less crucial part than in colorectal carcinogenesis.

Paclitaxel-resistant human ovarian cancer cells have mutant beta-tubulins that exhibit impaired paclitaxel-driven polymerization

Acquired resistance to paclitaxel can be mediated by P-glycoprotein or by alterations involving tubulin. We report two paclitaxel-resistant sublines derived from 1A9 human ovarian carcinoma cells. Single-step paclitaxel selection with verapamil yielded two clones that are resistant to paclitaxel and collaterally sensitive to vinblastine. The resistant sublines are not paclitaxel-dependent, and resistance remained stable after 3 years of drug-free culture. All cell lines accumulate [3H]paclitaxel equally, and no MDR-1 mRNA was detected by polymerase chain reaction following reverse transcription. Total tubulin content is similar, but the polymerized fraction increased in parental but not in resistant cells following the paclitaxel addition. Purified tubulin from parental cells demonstrated paclitaxel-driven increased polymerization, in contrast to resistant cell tubulin, which did not polymerize under identical conditions. In contrast, epothilone B, an agent to which the resistant cells retained sensitivity, increased assembly. Comparable expression of beta-tubulin isotypes was found in parental and resistant cells, with predominant expression of the M40 and beta2 isotypes. Sequence analysis demonstrated acquired mutations in the M40 isotype at nucleotide 810 (T --> G; Phe270 --> Val) in 1A9PTX10 cells and nucleotide 1092 (G --> A; Ala364 --> Thr) in 1A9PTX22 cells. These results identify residues beta270 and beta364 as important modulators of paclitaxel's interaction with tubulin.

Identification of the secretory vesicle membrane binding region of chromogranin B

In the past a synthetic peptide representing the conserved near N-terminal region of chromogranin B (CGB) (residues 17-36) has been shown to interact with the vesicle membrane. Hence, it was necessary to confirm this observation with CGB deletion proteins. In order to address this need and to confirm the published sequence of CGB, we cloned a CGB gene and produced various CGB deletion proteins. The recombinant CGB protein lacking the first 15 (rCGB 16-626) or 16 amino acid residues (rCGB 17-626) bound to the vesicle membrane as well as the full-length CGB. However, rCGB 49-626, lacking the conserved near N-terminal region, failed to interact with the vesicle membrane, indicating an anchor role for the conserved near the N-terminal region.

Identification of the secretory vesicle membrane binding region of chromogranin A

Since the conserved near N-terminal region (residues 18-37) of chromogranin A (CGA) has tentatively been identified as the vesicle membrane interacting region using synthetic peptides, it was necessary to confirm this finding with CGA deletion proteins. In order to address this need and to clarify the discrepancies of the published amino acid sequences of CGA, we cloned a CGA gene and produced CGA deletion proteins of various sizes. The recombinant CGA protein lacking the first 16 amino acid residues bound to the vesicle membrane as well as the full-length CGA at pH 5.5. However, the CGA protein lacking the first 39 amino acid residues, which include the conserved near N-terminal region (residues 17-38), failed to interact with the vesicle membrane at pH 5.5, clearly indicating the essential role of the conserved near N-terminal region in the pH-dependent interaction of CGA with the vesicle membrane.

Genetic evidence for the multicentric origin of synchronous multiple gastric carcinoma

Multiple gastric cancers, which constitute 4% to 10% of all gastric cancers, occur in older people and are associated with more extensive intestinal metaplasia. With regard to the genesis of multiple gastric cancers, multicentricity (independent origin) rather than multifocality (local or lateral spread of one cancer) has been the favored theory. Conventional morphologic study, however, has not been able to provide convincing evidence in support of multicentricity. The purpose of this study was to verify the multicentric origin of multiple gastric cancers at a genetic level. For this purpose, immunohistochemical and molecular techniques were used to define the mutation pattern of APC, MCC and p53 in multiple lesions of synchronous multiple gastric cancers. The study was based on a total of 30 gastric tumors from 13 patients, including 10 double tumors, 2 triple tumors, and 1 quadruple tumor. Single-strand conformation polymorphism and polymerase chain reaction direct sequencing were carried out for exons 5 to 8 of p53, and loss of heterozygosity was detected on the basis of polymerase chain reaction amplification of polymorphism in exon 10 of MCC and in exon 11 of APC. Twelve of 13 cases showed alteration in one or more genetic markers. Of these, three demonstrated a discordant mutation pattern of p53 in individual lesions, and another two revealed allelic loss of MCC in one lesion and p53 mutation in the other. In six other cases, only one lesion showed alteration of APC, MCC, or p53, and in the remaining case, one lesion carried p53 and MCC mutations and the other carried MCC loss of heterozygosity only. The results of this study showed discordance of the mutation pattern of APC, MCC, and p53 in individual lesions of multiple gastric cancers, providing genetic evidence for a multicentric origin of synchronous multiple gastric carcinomas. Collectively, these findings supported the theory of field cancerization in gastric carcinogenesis.

Establishment and characterization of human gastric carcinoma cell lines

We report 8 newly established gastric-carcinoma cell lines (SNU-216, 484, 520, 601, 620, 638, 668, 719) from Korean patients. Morphologic study was carried out using light and electron microscopes. CEA, alpha FP, and CA 19-9 and TPA in supernatant and in cell lysate were measured by radioimmunoassay. p53 and c-Ki-ras gene mutations were screened and confirmed by sequencing. The cell lines, derived from tumors with moderate differentiation, grew as a diffuse monolayer, and those from tumors with poor differentiation and minimal desmoplasia grew exclusively as non-adherent. Out of the 8 gastric-cancer cell lines, 5 had detectable levels of CEA both in supernatant and in cell lysate; there was no expression or secretion of alpha FP in these cells; 4 cell lines showed high levels of CA 19-9 in cell pellets. All cell lines except SNU-484 had high concentrations of TPA both in cell lysate and in supernatants. p53 mutation was found in 6 cell lines (75%): 2 (SNU-216 and SNU-668) had mutations in exon 6, and other 3 in exon 8. The c-Ki-ras mutation was found in 2 cell lines (25%), SNU-601 and SNU-668. The former showed GGT-to-GAT transition mutation at codon 12, while the latter showed CAA-to-AAA transversion mutation at codon 61. DNA profiles using restriction endonuclease HinfI and polymorphic DNA probes ChdTC-15 and ChdTC-114 showed different unique patterns; which suggests that these cell lines are unique and not cross-contaminated. We believe that the newly characterized gastric-cancer cell lines presented in this paper will provide a useful in vitro model for studies related to human gastric cancer.

Primary malignant lymphomas of the stomach. Pathological and clinical analyses of 38 resected cases

The stomach is the most frequent site of extranodal lymphoma and primary gastric lymphoma might be distinguished from the nodal lymphoma by its different pathogenesis and prognosis. Based on the Isaacson's classification, clinico-pathologic reviews of 38 resected primary gastric lymphomas were done. Immunohistochemical stainings for PCNA, B and T cell markers, bcl-2 and p53 were performed. Eighteen were of low grade and 20 were of high grade. There were significant differences between low and high graders in the aspect of the size, depth of lesion, gross type, immunophenotype, staining intensity for PCNA, expressions of bcl-2 and p53. The overall 2-year survival rate was 85.3%. Factors with prognostic significance on survival by univariate analyses included immunophenotype, histologic grading and PCNA staining pattern. After multivariate analyses, immunophenotype proved to be a significant factor. We think that the histologic grading by Isaacson's classification and the immunohistochemical stainings performed were useful in pathologic and/or clinical aspects. The excellent survival rate in this study was partly due to the selection of resectable cases. However, earlier diagnosis and appropriate treatment might have contributed to the improved prognosis of gastric lymphoma in recent years.

Cloning and characterization of cDNAs coding for heavy and light chains of a monoclonal antibody (MabB23) specific for human plasma apolipoprotein B-100

We have determined the nucleotide sequences encoding the heavy and light chains of the Fab fragment of murine monoclonal antibody MabB23(gamma2b,lambda), which is specific for human plasma apolipoprotein B-100 of low-density lipoproteins. The sequence analyses revealed that the variable regions of the heavy and light chains are members of mouse heavy-chain subgroup I(B) and lambda light-chain, respectively. A few unusual amino acids in the framework and constant regions of the heavy-chain were also noticed.

Sensitive assay for verapamil in plasma using gas-liquid chromatography with nitrogen-phosphorus detection

A sensitive gas-chromatographic method for quantitative analysis of verapamil in human plasma is described. The method involves a single extraction procedure, followed by separation on a capillary column and detection with a nitrogen-phosphorus detector. The detection limit, based upon an assayed plasma volume of 0.5 ml, is 2 ng/ml. The standard curve is linear in the concentration range of 2 to 1000 ng/ml. The recovery of verapamil by pentane-isopropanol extraction was found to be 95%. Zipeprol is used as the internal standard. No interference from drugs needed for the associated cancer therapy has been found. Serum verapamil concentrations are determined by this method in fourteen cancer patients undergoing treatment with adriamycin.

Clinical reversal of multidrug resistance

Reversal of drug resistance offers the hope of increasing the efficacy of conventional chemotherapy. We tested dexverapamil as a P-glycoprotein antagonist in combination with EPOCH chemotherapy in refractory non-Hodgkin's lymphoma. In a cross-over design, dexverapamil was added to EPOCH after disease stabilization or progression occurred. Objective responses were observed in 10 of 41 assessable patients. Biopsies for mdr-1 were obtained before EPOCH treatment and at the time of cross-over to dexverapamil. Levels of mdr-1 were low before EPOCH, but increased four-fold or more in 42% of patients in whom serial samples were obtained. Pharmacokinetic analysis revealed median peak concentrations of dexverapamil and its metabolite, nor-dexverapamil, of 1.66 mumol/l and 1.58 mumol/l, respectively. Since both are comparable antagonists, a median peak total reversing concentration of 3.24 mumol/l was achieved. Pharmacokinetic analysis of doxorubicin and etoposide levels confirmed a delay in the clearance of doxorubicin ranging from 5% to 24%; no change in the pharmacokinetics of etoposide was observed. This study provides sufficient rationale for testing dexverapamil in a randomized clinical trial.

Lymphangiosarcoma following mastectomy

This study reviews 16 cases of lymphangiosarcoma of the upper extremity after mastectomy for breast cancer (Stewart-Treves syndrome) was done at the author's institution from 1970 to 1992. Lymphangiosarcoma was diagnosed an average of 10.6 years (range, 5.6-18 years) after the diagnosis of breast cancer. Presenting signs included a bruise (6 patients); increased swelling (4); a red, raised lesion (2); a palpable mass (2); a blister appearance (1); and a non-healing eschar with continual bleeding (1). After biopsy, surgical treatment included forequarter amputation (8 patients), wide excision with grafting (5), and above-elbow amputation (1). Local recurrence of the lymphangiosarcoma occurred on the chest wall in 11 of the 16 patients after an average of 10.9 months. Metastasis occurred in 11 patients. (Metastasis occurred in 1 patient without local recurrence, and 1 patient with locally recurrent lymphangiosarcoma died of breast cancer before evidence of metastatic lymphangiosarcoma.) There are 2 long-term survivors who have lived 9.3 and 6 years, respectively, since the operation. One had been treated with a forequarter amputation and the other with wide excision. Early recognition and surgical treatment seem to offer the only chance for long-term survival.

Conformation and activity of +H2-Pro-Leu-Gly-NH2 and its analogues modified at the leucyl residue

In order to investigate the relation between the conformation and the ability to modulate dopamine receptors, conformational free-energy calculations using an empirical potential (ECEPP/3) and hydration shell model were carried out on the tripeptide +H2-Pro-Leu-Gly-NH2 (PLG) and its analogues in which the Leu residue is replaced with Phe, Ahx (L-2-aminohexanoic acid), Ile, Abu and Ala residues in the unhydrated and hydrated states. PLG and two tripeptides possessing Phe and Ahx residues show dopamine receptor modulating activity, while the other tripeptides do not. Irrespective of activities, PLG and its analogues are found to have the high probabilities to form beta-bends of types II and I in the unhydrated state. However, in the hydrated state, the beta-bend probabilities of the PLG analogues decrease significantly compared with those in the unhydrated state. These results indicate that the beta-bend structure is a necessary factor for the PLG analogues to be active, but not a sufficient factor, and that the interactions of water molecules with the backbone may force the tripeptides to be more distorted or extended. The size and the orientation of the hydrophobic moiety of the second residue seem to be of consequence in eliciting the activity of the tripeptides.

Expression of mdr-1 in refractory lymphoma: quantitation by polymerase chain reaction and validation of the assay

Measurement of P-glycoprotein and the gene that encodes it, mdr-1, is an important tool for assessing the impact of multidrug resistance in clinical cancer. We evaluated mdr-1 expression by a quantitative polymerase chain reaction (PCR) assay in 78 biopsy samples from 48 patients with refractory lymphoma enrolled on a trial of infusional chemotherapy (EPOCH) in which R-verapamil was added as an antagonist of P-glycoprotein in a subset of patients whose tumors were unresponsive to treatment. Expression of mdr-1 was detectable in all biopsies at the time of enrollment on study, and a fourfold or greater increase in mdr-1 expression was noted in 42% of patients at the time of treatment failure. Expression of mdr-1 was also detectable in biopsies from patients at the time of diagnosis of lymphoma. An endogenous control gene, beta 2-microglobulin, was quantitated for normalization of the mdr-1 values. The use of beta 2-microglobulin expression for normalization was validated in a subset of samples by comparing Northern blots detecting beta 2-microglobulin, beta actin, and GAPDH gene expression. Immunoblot analysis suggested that no major discrepancy was present between mRNA expression and protein level. Immunophenotyping of lymphomatous lymph nodes showed that infiltration of tumor cells ranged from 8% to 95% and of normal T cells from 1% to 83%. Expression of mdr-1 in normal T cells and monocytes was also shown to be low. The mdr-1 levels in patient samples were independent of T-cell contamination, suggesting that the presence of normal cells has at best a small impact on mdr-1 measurements. Expression of mdr-1 in lymphoma can be quantitated by PCR, and wide variations in expression can be observed. Increased expression in patients with refractory disease supports an important role for Pgp in drug resistance in lymphoma. These studies will aid in the design and interpretation of clinical trials in lymphoma.

Sequences responsible for transcription termination of the mouse gastrin gene

To identify the transcription termination elements in the mouse gastrin gene, we examined RNA transcripts after stable transfection of gastrin expression plasmids into the NIH3T3 cell line. The GT-repeat region at the 3'-flanking sequence of the mouse gastrin gene acted as a transcription terminator. When the GT-repeat unit was deleted from its site, the effect of termination disappeared. Further experiment, using serial deletion mutants, revealed that the 56-38 nucleotide upstream region from the GT-repeat unit also participated in transcription termination. We propose that the upstream region of the GT-repeat unit might be recognized as a pause site by the RNA polymerase II, and an abnormal DNA structure, derived from the GT-repeat unit, might function as a blockage of polymerase processivity.

Different effects of base analog substitutions in BamHI restriction site on recognition by BamHI endonuclease and BamHI methylase

BamHI endonuclease and BamHI methylase were used to investigate their specific interaction with the common recognition sequence, GGATCC. Five derivatives of the oligonucleotide, GACGGATCCGTC, containing a variety of single-base analog substitutions within the hexameric recognition core were synthesized. Steady-state kinetics for the reaction of the endonuclease and the methylase showed that both enzymes recognize the sequences by contacting with functional groups exposed in both major and minor grooves of the site but in different ways. Removal or substitution of the 5-methyl group in thymidine blocked the endonuclease reaction completely but still allowed the methylase reaction with less efficiency. The data also showed that the methylase made a critical minor groove contact with the 2-amino group of the first G but the endonuclease did with that of the second G.

Adult T-cell leukemia/lymphoma in a Korean--a case report

The clinicopathologic features of a Korean patient with adult T-cell leukemia/lymphoma(ATLL) are presented. A 51-year-old man, who has lived in Korea since birth, had multiple cutaneous nodules and multiple lymphadenopathy for the previous two months. A histopathologic study of the lymph node and skin lesion revealed T-cell non-Hodgkin's lymphoma of pleomorphic type, medium and large cell type. Peripheral blood examination showed leukemic features with 30% of abnormal lymphoid cells. HTLV-I proviral DNA pX region was detected in the DNA from peripheral blood mononuclear cells(PBMC) and the specific gag, pol, and env HTLV-I sequences were detected in the lymph node using polymerase chain reaction technique. Human T-cell leukemia/lymphoma type I(HTLV-I) antibodies were present in the serum. An immunophenotypic study of the lymph node revealed CD4 positive and CD8 negative helper/inducer T cell type surface markers. This case is the acute type, i.e. prototypic ATLL. He was treated with an intensive chemotherapy including cyclophosphamide, etoposide, doxorubicin, vincristine, and prednisone. Despite initial transient improvement, the tumor progressed after three cycles of the regimen and became refractory to further chemotherapy. These clinicopathologic findings, including the immunophenotypic analysis, established with certainty the diagnosis of HTLV-I-induced adult T-cell leukemia/lymphoma.

Conformation and sweet tastes of L-aspartyl dipeptide methyl esters

In order to investigate the conformational preferences to elicit tastes, conformational free energy calculations using an empirical potential (ECEPP/2) and the hydration shell model were carried out on the L-aspartyl dipeptide methyl esters, L-(+)HAsp(-)-L-Xaa-OMe, in the hydrated state, where Xaa includes sweet (Phe, Tyr, Met, and Gly), bitter (Ala, Trp, Val, Leu, and Ile), and tasteless (Ser, Thr, and Abu) residues. The refined preferred conformation of the Phe dipeptide (aspartame) with side chain chi 1/2 conformation g- is g-Fg- in the hydrated state, which is consistent with the structure deduced from 1H-nmr experiments. Irrespective of the Xaa and taste, all the dipeptides have the same conformation for the Asp residue, which is attributable to the hydrogen bond between protonated amino hydrogen and carboxylate oxygen and the favored hydration of the carboxylate group. This implies that the L-aspartyl residue is a necessary factor for the dipeptides to be sweet not a sufficient factor. The computed conformational preferences for sweet, bitter, and tasteless dipeptides in the hydrated state indicate to us that the conformation about the N--C alpha bond of the Xaa residue, i.e., the orientation of the hydrophobic moiety with respect to the AH/B functionalities in the aspartyl moiety, seems to be crucial to elicit the tastes. In addition, the hydrophobicity and the size of the Xaa residue are found to play a major role in determining the tastes. These well accord with the related works reported previously.

Fetus in fetu: a case with complete umbilical cord and fetal sac

The authors present a retroperitoneal fetus in fetus in a 3-month-old girl. A 15-cm cystic mass with a monstrous fetuslike structure surrounded by a complete sac containing serous fluid was removed from the left retroperitoneal space. The draining vessel of the cystic mass was connected to the right renal vein of the host. The included fetus weighed 380 g. It had a well-developed umbilical cord, four extremities, head, buttock, and vertebral bodies with a meningomyelocele. The thoracic cavity of the included fetus had only a saclike foregut structure, but the abdominal cavity revealed a full length of intestine with a Meckel diverticulum, bilateral ovaries, urinary bladder, and cloaca with external opening. The cephalic end was composed of well-developed tooth germs, tongue and buccopharynx, mandible, maxilla, sphenoid bone, and salivary glands. Chromosomal study showed 46,XX with a normal G banding pattern. We report this case as an example of fetus in fetu with a complete umbilical cord and fetal membrane.

Effects of base analog substitutions in the sequence, CCGG, on the cleavage and methylation reactions of HpaII and MspI endonucleases and their cognate methylases

HpaII endonuclease, HpaII methylase, MspI endonuclease, and MspI methylase were used to investigate their specific interactions with the common recognition sequence, CCGG. Six derivatives of the oligonucleotide, AGCCCGGGCT, containing a variety of single base analog substitutions within the tetrameric recognition core were synthesized. Steady state kinetic values for the reactions of all 4 enzymes with these oligonucleotide substrates were obtained. Our data suggest that there are close contacts between the C5 positions of both cytosine residues and the enzymes except that MspI endonuclease can accommodate a methyl group at the C5 position of the second cytosine residue. The data also showed that minor groove interactions between the 2-amino group of both G residues and the HpaII or MspI endonuclease were essential for activity. However, these interactions were not essential for methylase activity except that the oligonucleotide substituted with inosine nucleotide at the first G position did not react with MspI methylase.

Conformational study on trans- and cis-N-acetyl-N'-methylamides of Pro-Xaa dipeptides

Conformational free energy calculations using an empirical potential (ECEPP/2) and the hydration shell model were carried out on the N-acetyl-N'-methylamides of Pro-Xaa dipeptides (Xaa = Ala, Leu, Val, Gly, Cys, Met, Phe, Tyr, Asn, Asp, and Ser) with trans and cis peptide bonds preceding proline residue in the unhydrated and hydrated states. As compared with the results obtained by using the earlier version of ECEPP, the values of beta-bend probabilities are doubled. The average calculated population of cis-dipeptide is about 4%, which is close to the abundance obtained from the analysis of X-ray crystal structures of proteins. The beta-bends are the most dominant structures of cis-dipeptides. Type I, usually having intramolecular hydrogen bonds, contributes greatly to the beta-bend conformations of trans- and cis-dipeptides. However, type I beta-bends of cis-dipeptides do not have any hydrogen bonds. By including the hydration, the beta-bend probabilities for trans- and cis-dipeptides decreased, indicating that the interactions of water molecules with a backbone or side-chain may force the dipeptides to be more distorted or extended. In particular, type II is found to be a dominant beta-bend conformation of trans- and cis-Pro-Gly dipeptides in both the unhydrated and hydrated states. In general, the calculated propensities for Pro-Xaa dipeptides to adopt beta-bend conformations are reasonably consistent with available experimental data. From comparing conformations of Pro and Xaa residues in the dipeptides and single residues, we found that inter-residue interactions and hydration are of importance in determining the conformational properties of the Pro-Xaa dipeptide.