Conformational requirements of suramin to target angiogenic growth factors

The conformational requirements of suramin for its binding to basic fibroblast growth factor (bFGF) and platelet-derived growth factor (PDGF) were examined by molecular modeling and docking simulations using the conformational features of suramin determined by the present proton nuclear magnetic resonance (1H-NMR) studies and the crystal structures of growth factors reported previously. The assignment of resonances of suramin to individual protons was accomplished by the combined analysis of the coupling constants, two-dimensional correlated spectroscopy (COSY) and nuclear Overhauser effect spectroscopy (NOESY). The NOESY data obtained for suramin were utilized in a conformational search algorithm with constraints to generate a family of conformers which were further refined by restrained energy minimization. A family of nine conformers generated by restrained modeling falls primarily into one of two categories, either the conformer's two naphthyl rings are far apart, approximately 28-30 A, from one another or the conformer's two naphthyl rings are relatively close, approximately 16-18 A. The NMR data provide evidence for the presence of more than one conformer in solution. The modeling and docking simulation studies suggest that suramin binds efficiently to bFGF and PDGF by an induced-fit mechanism, wherein suramin complements bFGF or PDGF by adjusting its conformational freedom around the two pairs of single bonds that link the middle phenyl rings to the secondary amide backbone. The interaction of suramin with bFGF or PDGF primarily involves ion-pair, hydrophobic and hydrogen bonding interactions, in addition to van der Waals' contacts. The results indicate that suramin not only sterically blocks the receptor binding loop of the growth factors, but also competes for the binding sites of agonists such as heparin. The results suggest that suramin's propensity to bind to several polypeptides of varying size and structure is due to its conformational flexibility. Collectively, the data emphasize that conformationally constrained suramin analogs that selectively and competitively target angiogenic growth factors could be designed to reduce non-specific binding and, accordingly, toxicity.

Giant Hamartoma of the Breast

Hamartoma of the breast is a rare clinico-pathologic entity. Its clinical diagnosis can be extremely difficult; however, diagnosis is not difficult when it is made on the basis of a combination of radiologic and pathologic features. Its differential diagnosis includes a circumscribed fibrocystic mass, fibroadenoma, lipoma, cystosarcoma phylloides, and various carcinomas. A high index of suspicion is mandatory. In this study, we report a case of giant hamartoma of the breast in a young postlactational female patient, including treatment of the tumor by excisional biopsy and correction of the resulting breast deformity by mastopexy. Clinical, radiologic, and pathologic features are discussed.

Structure of human salivary histatin 5 in aqueous and nonaqueous solutions

The solution structure of human salivary histatin 5 (D-S-H-A-K-R-H-H-G-Y-K-R-K-F-H-E-K-H-H-S-H-R-G-Y) was examined in water (pH 3.8) and dimethyl sulfoxide solutions using 500 MHz homo- and heteronuclear two-dimensional (2D) nmr. The resonance assignment of peptide backbone and side-chain protons was accomplished by 2D total correlated spectroscopy and nuclear Overhauser effect (NOE) spectroscopy. The high JNH-C alpha H values (> or = 7.4 Hz), absence of any characteristic NH-NH (i, i + 1) or C alpha H-C beta H (i, i + 3) NOE connectivities, high d delta/dT values (> or = 0.004 ppm K-1) and the fast 1H/2H amide exchange suggest that histatin 5 molecules remain unstructured in aqueous solution at pH 3.8. In contrast, histatin 5 prefers largely alpha-helical conformation in dimethyl sulfoxide solution as evident from the JNH-C alpha H values (< or = 6.4 Hz), slow 1H/2H exchange, low d delta/dT values (< or = 0.003 ppm K-1) observed for amide resonances of residues 6-24, and the characteristic NH-NH (i, i + 1) and C alpha H-C beta H (i, i + 3) NOE connectivities. All backbone amide 15N-1H connectivities fall within 6 ppm on the 15N scale in the 2D heteronuclear single quantum correlated spectrum, and the restrained structure calculations using DIANA suggest the prevalence of alpha-helical conformations stabilized by 19 (5-->1) intramolecular backbone amide hydrogen bonds in polar aprotic medium such as dimethyl sulfoxide. The interside-chain hydrogen bonding and salt-bridge type interactions that normally stabilize the helical structure of linear peptides in aqueous solutions are not observed. Histatin 5, unlike other naturally occurring antimicrobial polypeptides such as magainins, defensins, and tachyplesins, does not adopt amphiphilic structure, precluding its insertion into microbial membranes and formation of ion channels across membranes. Electrostatic (ionic type) and hydrogen bonding interactions of the positively charged and polar residues with the head groups of microbial membranes or with a membrane-bound receptor could be the initial step involved in the mechanism of antimicrobial activity of histatins.

Reconstruction of 3-dimensional right ventricular shape and volume from 3 orthogonal planes

This study validates a reconstructive technique that describes 3-dimensional right ventricular (RV) shape and volume with the use of 3 standard echocardiographic planes. The volume of 24 cast models of lamb right ventricles (12 normal, 12 hypertensive) was determined by water displacement. Reconstruction of the cast shapes was calculated from 2 sets of digitized data: cast cross-sectional digitized tracings and echocardiographic cross-sectional tracings. Regional volume ratios from both data sets were assessed to quantitatively specify RV regional volume differences between normotensive and hypertensive right ventricles. This method described the 3-dimensional RV shape with no differences between reconstructed volumes and true volumes for either normotensive or hypertensive casts. Between hypertensive and normal groups, regional volume ratios yielded a difference in free wall ratios that was observed to be greater in the hypertensive cast group (P =.007).

Breast cancer screening, diagnosis, and treatment

The incidence of breast cancer in US women remains disturbingly high, and unfortunately primary care physicians still frequently encounter patients in whom the disease is suspected or, even worse, confirmed. Fortunately, however, the body of knowledge surrounding the disease has grown dramatically during the past decade, and major advances have been made in the understanding of breast cancer risk, prevention, diagnosis, and treatment. Controversies persist, particularly those concerning the screening of younger women, but consensus now exists regarding many clinical issues relevant to primary care practice. Although multidisciplinary subspecialty expertise must be made available to all women with known or suspected breast cancer, the primary care physician has an important role to play when dealing with patients with this condition. The following article focuses on what primary care practitioners need to know to expertly contribute to the diagnosis, counseling, and initial treatment of women with this disease.

How confounding are breast pain confounders?

Nine thousand four hundred evaluable patients with breast complaints were consecutively studied from 1984 to 1994. Their ages ranged between 15-65 years with a median of 33 years. Five thousand, six hundred and seventy-five of these presented on account of pain and a mass was the cause of pain in 74%. Gross fibrocystic disease of the breast was the commonest tumour encountered in this group. Seven hundred and thirty eight patients were found to have 'referred' pain, and splenomegaly was the commonest cause of this 'referred' pain. At present, a simple breast biopsy remains the cheapest and most effective method of investigating this organ in most developing countries.

Delineation of an active fragment and poly(L-proline) II conformation for candidacidal activity of bactenecin 5

Bactenecin 5 and its fragments [BN22 (1-22), BN16 (7-22), and BC24 (20-43)] were synthesized by solid-phase methods. Their antifungal activities on Candida albicans have been studied and compared with those of the native bactenecin 5. The conformational preferences of these peptides in aqueous and nonaqueous solutions and in lipid vesicles were examined by circular dichroism. The highly active N-terminal fragment (BN16) was examined in aqueous solution using 500 MHz two-dimensional NMR. Bactenecin 5 and its fragments are potent candidacidal agents against C. albicans. The N-terminal fragments (BN22 and BN16) of bactenecin 5 are relatively more active than the C-terminal fragment BC24, especially at lower concentrations. The N-terminal region (7-22) which retains the activity of the whole molecule appears to be the functional domain for candidacidal activity. The CD spectra of bactenecin 5 and its fragments are reminiscent of the CD spectrum of poly(L-proline) type II structure in aqueous and nonaqueous solutions and also in lipid vesicles. The temperature dependence of NH chemical shifts and 1H/2H exchange effect on amide resonances suggest the absence of intramolecularly hydrogen-bonded NH groups. The coupling constant (JNH-CalphaH) values, conformational restriction offered by the Pro residues (phi = -60 degrees +/- 15 degrees), the set of medium- and short-range nuclear Overhauser effects observed for the active N-terminal fragment (BN16), and the restrained structure calculation using DIANA suggest that poly(L-proline) type II conformers of the peptide molecules could be significantly populated in aqueous solution. The ability of bactenecin peptides to induce disruption of lipid vesicles correlates well with their activity. Our results suggest that poly(L-proline) type II structure may, indeed, be the biologically active conformation for candidacidal activity of bactenecin peptides.

Finding the global minimum: a fuzzy end elimination implementation

The 'fuzzy end elimination theorem' (FEE) is a mathematically proven theorem that identifies rotameric states in proteins which are incompatible with the global minimum energy conformation. While implementing the FEE we noticed two different aspects that directly affected the final results at convergence. First, the identification of a single dead-ending rotameric state can trigger a 'domino effect' that initiates the identification of additional rotameric states which become dead-ending. A recursive check for dead-ending rotameric states is therefore necessary every time a dead-ending rotameric state is identified. It is shown that, if the recursive check is omitted, it is possible to miss the identification of some dead-ending rotameric states causing a premature termination of the elimination process. Second, we examined the effects of removing dead-ending rotameric states from further considerations at different moments of time. Two different methods of rotameric state removal were examined for an order dependence. In one case, each rotamer found to be incompatible with the global minimum energy conformation was removed immediately following its identification. In the other, dead-ending rotamers were marked for deletion but retained during the search, so that they influenced the evaluation of other rotameric states. When the search was completed, all marked rotamers were removed simultaneously. In addition, to expand further the usefulness of the FEE, a novel method is presented that allows for further reduction in the remaining set of conformations at the FEE convergence. In this method, called a tree-based search, each dead-ending pair of rotamers which does not lead to the direct removal of either rotameric state is used to reduce significantly the number of remaining conformations. In the future this method can also be expanded to triplet and quadruplet sets of rotameric states. We tested our implementation of the FEE by exhaustively searching ten protein segments and found that the FEE identified the global minimum every time. For each segment, the global minimum was exhaustively searched in two different environments: (i) the segments were extracted from the protein and exhaustively searched in the absence of the surrounding residues; (ii) the segments were exhaustively searched in the presence of the remaining residues fixed at crystal structure conformations. We also evaluated the performance of the method for accurately predicting side chain conformations. We examined the influence of factors such as type and accuracy of backbone template used, and the restrictions imposed by the choice of potential function, parameterization and rotamer database. Conclusions are drawn on these results and future prospects are given.