Estimates of the loss of main-chain conformational entropy of different residues on protein folding

The average contribution of conformational entropy for individual amino acid residues towards the free energy of protein folding is not well understood. We have developed empirical scales for the loss of the main-chain (torsion angles, phi and psi) conformational entropy by taking its side-chain into account. The analysis shows that the main-chain component of the total conformational entropy loss for a residue is significant and reflects intrinsic characteristics associated with individual residues. The values have direct correlation with the hydrophobicity values and this has important bearing on the folding process. Proteins 1999;36:332-339.

Packing of aromatic rings against tryptophan residues in proteins

The geometry of the interaction of the aromatic side chains of phenylalanine (Phe), tyrosine (Tyr), tryptophan (Trp) and histidine (His) with the indole ring of Trp has been analyzed using the structures in the Protein Data Bank in order to understand the dependence of the packing behaviour on the size and chemical nature of the aromatic rings. The Phe ring prefers to interact either perpendicularly, with its edge pointing towards the Trp face, or in an offset-stacked arrangement. The edge-to-face motif is typical of a Trp-Trp pair. While parallel stacking is the dominant feature of Trp-His interaction, Tyr packs in a more uniform manner around Trp with a higher than expected occurrence at the edge and a few cases of possible OH-pi interaction.

Graphical representation of the salient conformational features of protein residues

A composite plot for depicting in two dimensions the conformation and the secondary structural features of protein residues has been developed. Instead of presenting the exact values of the main- and side-chain torsion angles (φ, psi and chi(1)), it indicates the region in the three-dimensional conformational space to which a residue belongs. Other structural aspects, like the presence of a cis peptide bond and disulfide linkages, are also displayed. The plot may be used to recognize patterns in the backbone and side-chain conformation along a polypeptide chain and to compare protein structures derived from X-ray crystallography, NMR spectroscopy or molecular modelling studies and also to highlight the effect of mutation on structure.

Altered lipid peroxidation and antioxidant potential in human uterine tumors

A comparative study of lipid peroxidation and antioxidant potential has been made in human uterus and uterine tumor. Two types of uterine tumor used are: tumor (I), a fibroid which is the commonest benign solid tumor in uterus and tumor (II), an adenomyoma. Tumor microsomes are less susceptible to lipid peroxidation induced by both enzymic (NADPH-ADP-Fe3+ and xanthine-xanthine-oxidase) and non-enzymic (ascorbate-Fe2+) systems except in the case of tumor (II) microsomes when induced with xanthine-xanthine oxidase. Resistance of tumor microsomes to lipid peroxidation is associated with the low content of substrates in the form of polyunsaturated fatty acids (PUFAs), higher level of alpha-tocopherol, reduced glutathione and protein thiols and altered enzymic antioxidant potential (catalase and superoxide dismutase).

Isoniazid accumulation in Mycobacterium smegmatis is modulated by proton motive force-driven and ATP-dependent extrusion systems

Resistance to isoniazid (INH), a frontline, antituberculosis drug, presents a major problem in the chemotherapy of tuberculosis. Although several targets of INH have been identified, the mechanism of INH resistance remains incompletely understood. This report demonstrates that INH accumulation in Mycobacterium smegmatis is enhanced both upon addition of both a proton motive force (pmf) uncoupler, carbonylcyanide m-chlorophenylhydrazone (CCCP), and upon addition of ortho-vanadate, an inhibitor of ATP-dependent efflux pumps. Both the Deltapsi and DeltapH components of the pmf are likely to be involved as judged by the effects of valinomycin and nigericin, respectively. Reserpine, an inhibitor of the human MDR1 P-glycoprotein, enhances INH accumulation in a manner similar to o-vanadate. Verapamil, a calcium channel blocker, also enhances INH uptake. Taken together, the results provide evidence of the involvement of both pmf- and ATP-dependent extrusion systems in INH efflux in M. smegmatis, making it important to evaluate the role of such systems in INH resistance in pathogenic mycobacteria.

C--H...O hydrogen bond involving proline residues in alpha-helices

Despite proline being assumed to be a helix-breaker, a large number of alpha-helices are found to contain Pro in globular as well as membrane proteins. Proline has no free NH group and therefore cannot form the conventional intra-helical NH.O=C hydrogen bond. An analysis of known protein structures has shown that the Cdelta protons are involved in C--H...O hydrogen bonds, usually two, with the carbonyl groups in the preceding turn of the helix (four and three residues away). These interactions satisfy the hydrogen bond forming potential of the carbonyl groups, which would otherwise, in the case of membrane-bound helices, be unfavorably exposed to hydrophobic surroundings. Depending on the type (based on the location of the carbonyl group, usually three, four or five residues preceding Pro) of C--H...O interactions, the kink in the helix may be of different magnitude. The puckering (UP or DOWN) of the pyrrolidine ring of Pro residues is controlled by the type of the C--H...O bond present, and the form that provides a better hydrogen bond geometry is preferred.

Delta-aminolevulinic acid-mediated photosensitization of prostate cell lines: implication for photodynamic therapy of prostate cancer

BACKGROUND

Delta-aminolevulinic acid (ALA)-mediated photodynamic therapy (PDT) is currently being investigated for the treatment of prostate diseases. In this study, we evaluate 1) the in vitro production of protoporphyrin IX (PPIX) (the active photosensitizing agent of ALA-mediated PDT) by two different prostate cancer cell lines (LNCaP and PC-3) and a benign, modified, prostatic cell line (TP-2), and 2) the extent of PDT-induced cell injury, as determined by electron microscopy (EM) and cell survival.

METHODS

The cell lines were assigned into four treatment groups: group 1, control, no ALA and no light irradiation; group 2, dark control, ALA only; group 3, light control, radiation only; and group 4, PDT, ALA followed by irradiation (630 nm, 3 joules/cm2). The experiments were performed in triplicate. ALA concentration was 50 microg/ml of media in all instances.

RESULTS

Following incubation with ALA, PPIX production was significantly increased in the three cell lines studied, and more notably in the PC-3 cell line. Compared to controls, EM and cell survival studies demonstrated significant mitochondrial damage and decreased survival, respectively, in the cells treated with PDT. This was also more evident in the PC-3 cell line.

CONCLUSIONS

Our results demonstrate that prostate cells differ in their response to ALA-mediated PDT. This response appears to depend on the intracellular production of PPIX and the cell type, i.e., on the functional and structural characteristics of the cell mitochondria. In addition, our results suggest that PDT might be effective at killing prostate cancer cells.

Main-chain conformational features at different conformations of the side-chains in proteins

An analysis of the known protein structures has shown that the main-chain torsion angles, phi and psi of a residue can be affected by the side-chain torsion angle, chi1. The (chi1, psi) plot of all residues (except Gly, Ala and Pro) show six distinct regions where points are concentrated-although some of these regions are nearly absent in specific cases. The mean of these clusters can show a shift along the psi axis by as much as 30 degrees as chi1 is changed from around 180 to -60 to 60 degrees. Because of the lesser steric constraint points are more diffused along the psi axis when chi1 is approximately -60 degrees. Although points are more spread out along the phi axis in the (chi1, phi) plot, the dependence of phi on chi1 shows up in a shortened phi range (by about 30 degrees) when chi1 is around -60 degrees, and a distinct tendency of clustering of points into two regions when chi1 is approximately equal to 60 degrees, especially for the aromatic residues. Based on the dependence of the backbone conformation on its side-chain the 17 amino acids can be grouped into five classes: (i) aliphatic residues branched at the Cbeta position (although Thr is atypical), (ii) Leu (branched at the Cgamma position), (iii) aromatic residues (Trp can show some deviations), (iv) short polar residues (Asp and Asn), and (v) the remaining linear-chain residues, mainly polar. Ser and Thr have the highest inclination to occur with two different orientations of the side-chain that can be located through crystallography. Such residues exhibiting two chi1 angles have their phi and psi angles in a region that is common to the Ramachandran plots at the two different chi1 angles. The dependence of phi and psi angles on chi1 can be used to understand the helical propensities of some residues. Moreover, the average phi, psi values in the alpha-helices vary with the side-chain conformation.

Different types of interactions involving cysteine sulfhydryl group in proteins

Various types of interactions involving the sulfhydryl group of free cysteine residues have been analyzed using known protein structures. In a hydrogen bond the -SH group is more amenable to donating its proton to a carbonyl group, rather than acting as a proton acceptor. It rarely interacts with a carboxylate group, and is a poor ligand to bind an anionic substrate. It is quite prone to make contacts that are definitely non-hydrogen bond type. In the S...C=O interaction the S atom is placed on the face of an amide group (mostly from the main-chain, but there are cases from the side-chain also) close to the C atom. Cases of S...N interaction, where the S atom is on top of the N atom of another residue (both main-, as well as side-chains, including the guanidinium group) are also observed. A considerable number of Cys residues have aromatic residues as neighbors, and here too, the preferred mode of interaction is along the face. The intra-residue S...C=O interaction constrains the main-chain and side-chain torsion angles (psi and chi1), whereas the inter-residue interactions are non-local and stabilize the tertiary structure. The S...C=O interaction may have a role in lowering the pKa values of the Cys residues in enzyme active sites.

Naive human T cells develop into Th1 or Th0 effectors and exhibit cytotoxicity early after stimulation with Leishmania-infected macrophages

Studies of human disease suggest that naturally acquired immunity is the predominant outcome of Leishmania infection. Normally protective immune mechanisms activated during asymptomatic or self-healing infections may be minimal in patients who develop disease. To explore early immune responses, an in vitro model of human Leishmania infection was developed in which naive T cells were sensitized with Leishmania-infected macrophages. An analysis of Leishmania-specific cytokine production by these T cell lines revealed that most individuals developed Th1 or Th0 responses early after infection. Infected macrophages from Th1 responders produced interleukin-12. Th0 responders who produced little or no endogenous interleukin-12 could be converted to the Th1 phenotype by addition of interleukin-12 during priming. Finally, infection-sensitized T cells specifically lysed Leishmania-infected macrophages. Thus, this in vitro model system can be used to delineate protective human immune responses against Leishmania induced early after infection.

Characterization of a porin from Mycobacterium smegmatis

A pore-forming protein with an Mr of 40,000 has been extracted from the cell wall of Mycobacterium smegmatis with buffer containing the detergent Zwittergent 3-12 and 0.5 M NaCl and purified on an anion-exchange column. Although the pore diameter was large (2 nm), the specific activity was much lower than those of nonspecific porin channels of enteric bacteria. The channel allowed the permeation of small hydrophilic molecules such as sugars and amino acids. Its N-terminal sequence did not show any similarity to those of other porins sequenced so far.

Involvement of a 43-kilodalton outer membrane protein in beta-lactam resistance of Shigella dysenteriae

A beta-lactam-sensitive strain (C152) of Shigella dysenteriae showed two major outer membrane proteins (OMPs) with M(r)s of 43,000 and 38,000, while the clinical isolate M2 lacked the 43,000-Mr OMP, which acted as a channel for beta-lactam antibiotics. Permeability of beta-lactams across the outer membrane (OM) of M2 was lower than that across the OM of C152. Mutants deficient in the 43-kDa OMP could be selected in vitro from strain C152 in the presence of cefoxitin. All beta-lactam-resistant strains were sensitive to imipenem.

Altered permeability and beta-lactam resistance in a mutant of Mycobacterium smegmatis

Beta-lactam resistance in mycobacteria results from an interplay between the following: (i) beta-lactamase production, (ii) affinity of the penicillin-binding proteins (PBPs) for the drugs, and (iii) permeation of the drugs. A laboratory mutant of Mycobacterium smegmatis was studied in order to evaluate the roles of these factors in beta-lactam resistance. Mutant M13 was between 7- and 78-fold more resistant than the wild type to cephaloridine, cefoxitin, cefazolin, cefamandole, and cephalothin. Increased beta-lactamase activity toward these antibiotics was not observed in the mutant. The PBP profiles of the wild type and M13 were comparable. However, the affinities of PBP 1 for the beta-lactams tested were lower for the mutant than for the wild type. The permeation of the drugs measured in intact cells was lower for M13 than for the parent strain. The liposome swelling technique, which could be used for cephaloridine, also supported this view. Reduced permeation was not restricted to the beta-lactams alone. Glycine uptake was also lower in M13. Taken together, the results suggest that decreased affinities of PBP 1 for beta-lactams, combined with the decreased permeability of the cell wall of the mutant, lead to the development of high-level acquired beta-lactam resistance.

Dual multimodular class A penicillin-binding proteins in Mycobacterium leprae

The ponA gene of cosmid L222 of the Mycobacterium leprae genome library encodes a multimodular class A penicillin-binding protein (PBP), PBP1. The PBP, labelled with a polyhistidine sequence, has been produced in Escherichia coli, extracted from the membranes with 3-[(3-cholamidopropyl)-dimethylammonio]-1-propane-sulfonate (CHAPS) and purified by Ni2(+)-nitrilotriacetic acid-agarose chromatography. In contrast to the pon1-encoded class A PBP1, PBP1 undergoes denaturation at temperatures higher than 25 degrees C, it catalyzes acyl transfer reactions on properly structured thiolesters, and it binds penicillin with high affinity.

An electrophile-nucleophile interaction in metalloprotein structures

A new attractive interaction in metalloprotein structures, between the thiolate anion of a metal-bound cysteine (acting as a nucleophile) and a carbonyl carbon of a peptide group (an electrophile), has been identified. From 82 cases extracted from 23 metalloprotein structures, the interacting S and C atoms are found to be at a distance of 3.2 (+/-2) A, such that the angle S ... C-O is 109 degrees (+/-15 degrees). Usually, the interacting atoms are from the same Cys residue, and to allow the S to interact with the carbonyl group the side-chain and the main-chain torsion angles deviate from those found in cysteines not bound by metals. There is a good correlation between the S...C distance and the angular deviation of the S...C vector from the normal to the peptide plane. Various data points may be envisaged to represent "snapshots" along the reaction coordinate for the intra-residue attack of Cys S on the CO group.

Tiazofurin-induced autosecretion of IL-6 and hemoglobin production in K562 human leukemia cells

Previous reports have established the synthesis of interleukin-6 (IL-6) and IL-6 receptors (IL-6R) in several human leukemia cells and found that IL-6 and the IL-6R could be expressed in cell lines with erythroid/megakaryocytic features. IL-6 is a pleiotropic cytokine involved in megakaryocytic differentiation. The finding that endogenous IL-6 levels in serum increased after 5-fluorouracil (5-FU) treatment suggests that IL-6 may play some role in the recovery of hematopoietic systems. This observation may assist the understanding of erythroid regeneration caused by antineoplastic agents such as tiazofurin. Tiazofurin inhibits the activity of IMP dehydrogenase. Its exposure to K562 cells at 10 microM tiazofurin stimulates erythroid differentiation. Stimulation of cells with tiazofurin gave a significant increase in IL-6 production. Its levels were quadrupled after 2 days of culture. Tiazofurin also caused a trivial reduction in the percentage of cells with the IL-6R. This evidence implies that tiazofurin produced no significant effect on the IL-6R. Tiazofurin also increased the percentage of benzidine-positive cells representing hemoglobin production, confirmed by GpA expression. We concluded that IL-6 is rate limiting in regard to hemoglobin production and that IL-3 could be used for clinical benefit to stimulate erythropoiesis and synergize with tiazofurin.

Metal binding properties of a monoclonal antibody directed toward metal-chelate complexes

A monoclonal antibody that recognizes cadmium-EDTA complexes has been produced by the injection of BALB/c mice with a metal-chelate complex covalently coupled to a carrier protein. The ability of purified antibody to recognize 16 different metal-EDTA complexes was assessed by measuring equilibrium binding constants using a KinExATM immunoassay instrument. The antibody bound to cadmium- and mercury-EDTA complexes with equilibrium dissociation constants of 21 and 26 nM, respectively. All other metal-EDTA complexes tested, including those of Mn(II), In(III), Ni(II), Zn(II), Co(II), Cu(II), Ag(I), Fe(III), Pb(II), Au(III), Tb(III), Ga(III), Mg(II), and Al(III) bound with affinities from 20- to 40,000-fold less than that determined for the cadmium-EDTA complex. With the exception of mercury and magnesium, the binding of divalent metal-chelate complexes was well-correlated with the size of the metal ion. The amino acid sequences of the heavy and light chain variable regions were deduced from polymerase chain reaction-amplified regions of the corresponding genes and subsequently used to construct molecular models of the antigen binding region. The key residue for cadmium binding in the model for 2A81G5 appeared to be histidine 96 in the heavy chain.

Optical characterization and coagulation performance of side-emitting fiber delivery systems for laser therapy of benign prostatic hyperplasia: a comparative study

OBJECTIVES

Currently, various side-emitting optical fibers with different tip geometry are used transurethrally to deliver laser radiation for treatment of benign prostatic hyperplasia (BPH). Since fiber tip design could profoundly affect the size and profile of the emitted laser beam, and consequently the tissue response and the extent of tissue coagulation, we evaluted commercially available fibers in regard to their optical characteristics and their ability to coagulate tissue in a controlled experimental setting.

METHODS

Thirteen fibers manufactured by different companies and clinically used at the present time were tested using a surgical neodymium: yttrium-aluminum-garnet laser. The profile of the laser beam delivered via each fiber was imaged on a CCD camera at various distances and evaluated by means of a laser beam analyzer. Beam divergence angle was then calculated for each tip. Tissue coagulation effects were assessed by irradiating samples of beef muscle immersed in water at 37 degrees C. The fiber tip was kept 2.5 mm away from the tissue and irrigation was maintained at flow rate of 350 to 400 cc/min during irradation. Laser powers of 20, 40, and 60 W were used for 180, 90, and 60 seconds, respectively, delivering a total energy of 3600 J.

RESULTS

The results of the optical evaluation divided the fibers into two major groups: broad beam with large divergence angle and narrow beam with small divergence angle. Statistical analysis of the data (using analysis of variance) showed that volumes of coagulated tissue were significantly larger for broad beam fibers than for narrow beam fibers (1.15 +/- 0.32 versus 0.89 +/- 0.34 cm 3; P < 0.05). Also, significantly larger volumes were obtained for 20 W when compared with 60 W (1.08 +/- 0.43 versus 0.88 +/- 0.27 cm 3; P < 0.05).

CONCLUSIONS

The laser power density delivered by individual fibers to the prostate tissue may vary significantly, thus greatly affecting the extent of tissue coagulation. Therefore, irradiation parameters must be optimized for each fiber type.

Identification and overexpression in Escherichia coli of a Mycobacterium leprae gene, pon1, encoding a high-molecular-mass class A penicillin-binding protein, PBP1

Cosmid B577, a member of the collection of ordered clones corresponding to the genome of Mycobacterium leprae, contains a gene, provisionally called pon1, that encodes an 821-amino-acid-residue high-molecular-mass class A penicillin-binding protein, provisionally called PBP1. With similar amino acid sequences and modular designs, M. leprae PBP1 is related to Escherichia coli PBP1a and PBP1b, bienzymatic proteins with transglycosylase and transpeptidase activities. When produced in E. coli, His tag-labelled derivatives of M. leprae PBP1 adopt the correct membrane topology, with the bulk of the polypeptide chain on the surface of the plasma membrane. They defy attempts at solubilization with all the detergents tested except cetyltrimethylammonium bromide. The solubilized PBP1 derivatives can be purified by affinity chromatography on Ni2+-nitrilotriacetic acid agarose. They have low affinities for the usual penicillins and cephalosporins.

Laser irradiation for the treatment of benign prostatic hyperplasia

Benign prostatic hyperplasia (BPH) is one of the most common medical problems encountered in the United States. For many years, transurethral resection of the prostate (TURP) has been the mainstay of treatment for symptomatic BPH. In recent times, newer modalities of treatment in the form of drugs (a- blockers, LHRH-agonist, anti-androgens, 5 a-reductase inhibitors), microwave hyperthermia, prostatic stents, balloon urethroplasty, laser prostatectomy, and most recently High Intensity Focal Ultrasound (HIFU) and Trans Urethral Needle Ablation (TUNA) are challenging TURP as the gold standard therapy for BPH. Today, laser prostatectomy holds a special place in therapy of BPH, as it is easy to perform, safe to apply with a vastly improved patient compliance, and is the first choice in certain special circumstances, e.g., patients on anticoagulants. In this chapter we discuss the present status of laser prostatectomy for BPH.

CH/pi interaction in the packing of the adenine ring in protein structures

One of the weak but directional interactions in protein structures involves the O-H or N-H bond that is oriented along the center of a benzene ring. Even a CH group can have enthalpically favorable interaction with an aromatic ring if the latter is made electron-rich by incorporating nitrogen atoms. This CH/pi interaction is brought into play in the binding of the adenine rings, which are sandwiched between protein residues such that saturated carbon atoms are on top of ring nitrogen atoms at distances of approximately 3.7 A. There is a preponderance of residues with branched side-chains that have specific locations on the tertiary fold that is employed for binding the adenine-containing cofactors. In addition to the conventional hydrogen bonding, the CH/pi interaction can be important for the recognition of DNA and RNA molecules by proteins. The main- and the side-chain atoms of the same residue can participate in both types of interaction, so that a protein can engage an adenine moiety by employing only a limited number of residues.