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PubMed2003

Nuclear magnetic resonance structure of a prototype Lin12-Notch repeat module from human Notch1.

Notch1 is a member of a conserved family of large modular heterodimeric type 1 transmembrane receptors that control differentiation in multicellular animals. Receptor maturation is accompanied by a furin-dependent cleavage that converts the Notch1 precursor polypeptide into a heterodimer consisting of an extracellular ligand-binding subunit (NEC) and a transmembrane signaling subunit (NTM). Binding of a physiologic ligand to NEC induces signaling by triggering additional proteolytic cleavages in NTM, which allow its intracellular region to translocate to the nucleus where it participates in a transcriptional activation complex. In the absence of ligand, the three conserved LNR modules of the NEC subunit participate in maintaining the receptor in its resting conformation. Here, we report the solution structure of the first LNR module (LNR_A) of human Notch1, and identify residues of LNR_A perturbed by the presence of the adjacent module LNR_B. LNR_A is held together by a unique arrangement of three disulfide bonds and a single bound Ca(2+) ion, and adopts a novel fold that falls in the general class of irregular disulfide-bonded structures. Residues perturbed by the presence of the adjacent LNR_B module are predominantly hydrophobic, and lie on one face of the module. These studies represent an initial step toward understanding the structural interrelationships among the three contiguous LNR modules required for proper regulation of Notch signaling.

Amino Acid Sequence↗
PubMed2003

2.4 A resolution crystal structure of the prototypical hormone-processing protease Kex2 in complex with an Ala-Lys-Arg boronic acid inhibitor.

This paper reports the first structure of a member of the Kex2/furin family of eukaryotic pro-protein processing proteases, which cleave sites consisting of pairs or clusters of basic residues. Reported is the 2.4 A resolution crystal structure of the two-domain protein ssKex2 in complex with an Ac-Ala-Lys-boroArg inhibitor (R = 20.9%, R(free) = 24.5%). The Kex2 proteolytic domain is similar in its global fold to the subtilisin-like superfamily of degradative proteases. Analysis of the complex provides a structural basis for the extreme selectivity of this enzyme family that has evolved from a nonspecific subtilisin-like ancestor. The P-domain of ssKex2 has a novel jelly roll like fold consisting of nine beta strands and may potentially be involved, along with the buried Ca(2+) ion, in creating the highly determined binding site for P(1) arginine.

Amino Acid Sequence↗
PubMed2005

Folding and binding integrity of variants of a prototype ligand-binding module from the LDL receptor possessing multiple alanine substitutions.

The LA repeats that comprise the ligand-binding domain of the LDL receptor are among the most common autonomously structured extracellular modules found in the nonredundant protein sequence database. Here, we investigate the information content of the amino acid sequence of a typical LA module by constructing sequences with alanine residues at nonconserved positions in the module. Starting with the sequence of the fifth ligand-binding repeat of the LDL receptor (LA5), we created generic LA modules with alanine substitutions of nonconserved residues in only the N-terminal lobe, only the C-terminal lobe, and throughout both lobes of the module. LA variants with alanine residues at as many as 18 of 37 positions fold to a preferred disulfide isomer in the presence of calcium. Indeed, the six cysteines, the C-terminal calcium coordinating residues, two hydrophobic residues involved in packing, two glycines, and five other residues that form side chain-intramodule hydrogen bonds are alone sufficient to specify the fold of an LA module when alanine residues are present at all other positions. The LA variants with multiple alanines in either the N- or C-terminal lobe were then exploited to identify residues of LA5 that contribute to the binding of apoE-containing ligands in LDL receptor-derived "minireceptors", implicating nonconserved residues of the N-terminal lobe of LA5 in recognition of apoE-DMPC. Our library of LA modules with multiple alanine substitutions should be generally useful for probing the roles of nonconserved side chains in ligand recognition by proteins of the LDL receptor family.

Alanine↗
PubMed2007

High-risk HPV E6 oncoproteins assemble into large oligomers that allow localization of endogenous species in prototypic HPV-transformed cell lines.

The E6 oncoproteins of high-risk HPV types 16 and 18 are involved in the development of cervical cancer. Besides its determinant role in carcinogenic progression, HPV E6 oncoprotein has also been instrumental in elucidating fundamental aspects of p53 function and its ubiquitin-proteasome degradation, with counterpart activities in various DNA tumor viruses. Establishing the conformational state and cellular distribution unequivocally for the endogenous protein in HPV-transformed cell lines derived from carcinomas is essential for understanding the underlying mechanism. Recombinant E6 from high-risk strains 16 and 18 folds into soluble oligomers of approximately 1.2 MDa, which are thermostable and display cooperative loss of tertiary and secondary structure upon chemical denaturation. Antibodies raised against these assemblies locate E6 evenly distributed in the cells. By depleting the polyclonal serum by immunoblocking with monomeric E6, the nuclei of Hela and CaSki cells become completely devoid of label, indicating that monomeric species are mainly localized in the nucleus and that both monomers and oligomers share epitopes. The monomeric species promote degradation of p53 by the proteasome, which correlates with the nuclear localization we describe. In contrast, the oligomeric E6 does not promote p53 degradation, in agreement with its cytoplasmic localization inferred from the immunoneutralization experiments. Our results indicate that the cytoplasmic species contain conformational epitopes that may arise from yet undefined homo or hetero-oligomers, but its localization otherwise agrees with that of the other group of major E6 targets, those involving PDZ binding domains, which requires further investigation.

Base Sequence↗
PubMedDate not supplied

Microengineered surface topography facilitates cell grafting from a prototype hydrogel wound dressing with antibacterial capability.

Skin wounds derive therapeutic benefit from redeployment of dermal tissues, whether as split-thickness allo- and autografts or as biological dressings comprising cultured cells. However, the clinical outcome is strongly influenced by the techniques used for cell/tissue grafting and also the microbiological status of the wound. Here we report that microtopography incorporated into the surface of a novel polymeric material, derivatized with fibronectin to promote attachment and encourage motility, improved the efficiency of cell transfer onto de-epithelialized human skin ex vivo. The microtopography had two functions, first as a conduit for migrating cells to cross between the vehicle and recipient surface and second to shield adherent cells from destruction by mechanical shearing during handling and application. Quantitative analysis showed that topographic projections (columns) rather than recesses (pits) in the hydrogel surface achieved the highest efficiency of cell transfer. In order to address the crucial relevance of microbiological contamination to the success of wound grafting, the effect of iodine on several common bacterial pathogens was examined using an XTT+C(Q10) kinetic cell viability assay. Increasing concentrations of iodine initially stressed and after 0.5% v/v were subsequently bacteriocidal for Gram-negative Pseudomonas aeruginosa and Escherichia coli and Gram-positive Bacillus subtillis and Staphylococcus aureus. Slightly higher doses of iodine (approx 1-1.5% v/v) were required to kill HaCaT cells outright, but for both pro- and eukaryotes the major determinant of cytotoxicity was absolute dose rather than duration of exposure. Iodine delivered by the hydrogel at low concentration was bacteriostatic but not apparently cytotoxic to epithelial cells as measured by MTT end-point cell viability assay. Zone of inhibition studies confirmed that bacteriocidal quantities of neomycin, phenol red, and silver could also be delivered using the same hydrogel. This research suggests that grafting cell-based biological dressings to wounds using a topographically modified hydrogel dressing capable of simultaneous reducing the microbiological threat to a successful outcome may be a realistic clinical proposition.

Adult↗
PubMed2002

Thermally inert metal ammines as light-inducible DNA-targeted agents. Synthesis, photochemistry, and photobiology of a prototypical rhodium(III)-intercalator conjugate.

The recent discovery of the promising tumor cell kill by a novel platinum-acridine conjugate [Martins, E. T.; et al. J. Med. Chem. 2001, 44, 4492] has prompted us to explore the utility of analogous light-activatable rhodium(III) compounds as photocytotoxic agents. Here, the design and synthesis of [Rh(NH(3))(5)L](n)(+) complexes are described with L = 1,1,3,3-tetramethylthiourea (tmtu) or 1-[2-(acridin-9-ylamino)ethyl]-1,3,3-trimethylthiourea (2). The intercalator-based DNA-affinic carrier ligand 2 was synthesized from N-acridin-9-yl-N'-methylethane-1,2-diamine and dimethylthiocarbamoyl chloride and isolated as the hydrotriflate salt 2(CF(3)SO(3)). [Rh(NH(3))(5)(tmtu)](3+) (1) and [Rh(NH(3))(5)(2)](4+) (3) were obtained from the reactions of the trifluoromethanesulfonato complex [Rh(NH(3))(5)(OSO(2)CF(3))](CF(3)SO(3))(2) with the appropriate thiourea in noncoordinating solvents. All compounds were characterized by (1)H NMR and UV-vis spectroscopies and by elemental analyses. The single-crystal X-ray structures of 1(CF(3)SO(3))(3) x 2MeOH, 2(CF(3)SO(3)), and 3(CF(3)SO(3))(4) x H(2)O have been determined. Ligand-field photolysis of thermally inert 1 (lambda(max) = 378 nm) resulted in the aquation of 2 equiv of ammine ligand without noticeable release of sulfur-bound tmtu ((1)H NMR spectroscopy, NH(3)-sensitive electrode measurements). This was confirmed by (15)N[(1)H] NMR spectroscopy using (15)N-labeled [Rh((15)NH(3))(5)(tmtu)](3+) (1), which also indicated photoisomerization of the [RhN(5)S] moiety. Despite greatly accelerated ligand exchange, rhodium in 1 and 3 did not show light-enhanced formation of covalent adducts in calf thymus DNA. "Dark binding" levels of 3 in native DNA were slightly higher than for nontargeted 1, but significantly lower than those observed for analogous platinum-acridine. Agarose gel electrophoresis revealed photocleavage of supercoiled pUC19 plasmid DNA in the presence of hybrid 3 and its individual constituents 1 and 2. Simple 1 induced single-strand breaks while 3 produced complete degradation of the DNA after 24 h of continuous irradiation. Acridine 2 alone produced double-strand breaks. The extent of DNA damage observed for 1-3 correlates with the photocytotoxicity of the compounds in human leukemia cells, suggesting that DNA might be the cellular target of these agents.

Acridines↗
PubMed2001

Alamethicin-leucine zipper hybrid peptide: a prototype for the design of artificial receptors and ion channels.

In this report, we describe a novel concept of extramembrane control of channel peptide assembly and the eventual channel current modulation. Alamethicin is a peptide antibiotic, which usually forms ion channels in various association states. By introducing an extramembrane leucine zipper segment (Alm-LeuZ), the association number of alamethicin was effectively controlled to produce a single predominant channel open state. The assembly was estimated to be a tetramer, by comparison of the channel conductance with that of the template-assembled Alm-LeuZ tetramer, which was prepared by the conjugation of a maleimide-functionalized peptide template with cysteine-derivatized Alm-LeuZ segments. Employment of an extramembrane segment of a random conformation provided higher levels of channel conductance. The result exemplified the possibility of channel current control by a conformational switch of the extramembrane segments.

Alamethicin↗
PubMed2002

A prototype for catalyzed amide bond cleavage: production of the [NH(3), H(2)O](*)(+) dimer from ionized formamide and its carbene isomer.

The reaction of ionized formamide H(2)NCHO(*)(+) with water leads to an exclusive loss of CO from the complex. This contrasts with the unimolecular reaction of low-energy ionized formamide, which loses exclusively one hydrogen atom. The unimolecular loss of CO is not observed because it involves several H-transfers corresponding to high-energy barriers. Experimental and theoretical studies of the role of solvation by water on the fragmentation of ionized formamide leads to three different results: (i) In contrast with different systems previously studied, in which solvation plays only a role on one or two steps of a reaction, a molecule of water is efficient in the catalysis of the decarbonylation process because water catalyzes all the steps of the reaction of ionized formamide, including the final dissociation of the amide bond. (ii) The catalyzed isomerization of carbonylic radical cations into their carbene counterparts is shown to be an important step in the process. To study this step, a precise probe, characterizing the carbene structure by ion-molecule reaction, is for the first time described. (iii) Finally, decarbonylation of ionized formamide yields the [NH(3), H(2)O](*)(+) ion, which has not been generated and experimentally studied previously. By this method, the [NH(3), H(2)O](*)(+) ion is generated in abundance and with a low internal energy content, allowing one either to prepare, by ligand exchange, a series of other solvated radical cations or to generate covalent structures such as distonic ions. First results on related systems indicate that the conclusions obtained for ionized formamide are widespread.

Journal Article↗
PubMed2003

Competition between C-C and C-H insertion in prototype transition metal-hydrocarbon reactions.

The competition between C-C and C-H insertion in model transition-metal reactions with cyclopropane and propene (C3H6) was studied as a function of total energy. Insertion of neutral transition metal atoms M (= Y, Zr, Nb, and Mo*) into the C-C bonds of cyclopropane led to formation of MCH2 + C2H4, whereas C-H insertion produced MC3H4 + H2. The measured product branching ratios verify the relative potential energy barrier heights for C-C and C-H insertion predicted by ab initio calculations.

Journal Article↗
PubMed2003

Modeling H-bonding and solvent effects in the alkylation of pyrimidine bases by a prototype quinone methide: a DFT study.

Nucleophilicity of NH(2), N3, and O(2) centers of cytosine toward a model quinone methide (o-QM) as alkylating agent has been studied using DFT computational analysis [at the B3LYP/6-311+G(d,p) level]. Specific and bulk effects of water (by C-PCM model) on the alkylation pathways have been evaluated by analyzing both unassisted and water-assisted reaction mechanisms. An ancillary water molecule, H-bonded to the alkylating agent, may interact monofunctionally with the o-QM oxygen atom (passive mechanisms) or may participate bifunctionally in cyclic hydrogen-bonded structures as a proton shuttle (active mechanisms). A comparison of the unassisted with the water-assisted reaction mechanisms has been made on the basis of activation Gibbs free energies (DeltaG(++)). The gas-phase alkylation reaction at N3 does proceed through a passive mechanism that is preferred over both the active (by -6.3 kcal mol(-1)) and the unassisted process. In contrast, in the gas phase, the active assisted processes at NH(2) and O(2) centers are both favored over their unassisted counterparts by -4.0 and -2.2 kcal mol(-1), respectively. The catalytic effect of a water molecule, in gas phase, reduces the gap between the TSs of the O(2) and NH(2) reaction pathways, but the former remains more stable. Water bulk effect significantly modifies the relative importance of the unassisted and water-assisted alkylation mechanisms, favoring the former, in comparison to the gas-phase reactions. In particular, the unassisted alkylation becomes the preferred mechanism for the reaction at both the exocyclic (NH(2)) and the heterocyclic (N3) nitrogen atoms. By contrast, alkylation at the cytosine oxygen atom is a water-catalyzed process, since in water the active water-assisted mechanism is still favored. As far as competition, among all the possible mechanisms, our calculations unambiguously suggest that the most nucleophilic site both in gas phase (naked reagents: N3 >> O(2) >or= NH(2)) and in water solution (solvated reagents: N3 >> NH(2) >> O(2)) is the heterocyclic nitrogen atom (N3) (DeltaG(++)(gas) = +7.1 kcal mol(-1), and DeltaG(++)(solv) = +13.7 kcal mol(-1)). Our investigation explains the high reactivity and selectivity of the cytosine moiety toward o-QM-like structures both in deoxymononucleoside and in a single-stranded DNA, on the basis of strong H-bonding interactions between reactants and solvent bulk effect. It also offers two general reactivity models in water, uncatalyzed and active water-catalyzed mechanisms (for nitrogen and oxygen nucleophiles, respectively), which should provide a general tool for the planning of nucleic acid modification.

Alkylation↗
PubMed2003

Hybridization-based unquenching of DNA hairpins on au surfaces: prototypical "molecular beacon" biosensors.

There is a keen interest in developing techniques for rapid genetic analysis that do not require labeling of an analyte. Here we demonstrate that fluorophore-tagged DNA hairpins attached to gold films can function as immobilized "molecular beacons". Two DNA hairpins incorporating portions of the Staphlococcus aureus FemA and mecR methicillin-resistance genes were attached to a gold substrate. Upon exposure to the complement, a approximately 26-fold increase in fluorescence intensity was measured corresponding to a 96 +/- 5% quenching efficiency. Studies with nonspecific DNA indicate that DNA hairpins immobilized on a gold surface retain their ability to bind complementary DNA sequences selectively.

Bacterial Proteins↗
PubMed2004

Solid-state Ru-99 NMR spectroscopy: a useful tool for characterizing prototypal diamagnetic ruthenium compounds.

The feasibility of (99)Ru NMR spectroscopy as a tool to characterize solid compounds is demonstrated. Results of the first solid-state (99)Ru NMR investigation of diamagnetic compounds are presented for Ru(NH(3))(6)Cl(2), K(4)Ru(CN)(6). xH(2)O (x = 0, 3), LaKRu(CN)(6), and Ru(3)(CO)(12). The sensitivity of the ruthenium magnetic shielding tensor to subtle changes in the local structure about the ruthenium nucleus is highlighted by comparing the (99)Ru isotropic chemical shift of Ru(NH(3))(6)Cl(2) in aqueous solutions and in the solid state. The narrow isotropic (99)Ru NMR peak observed for solid Ru(NH(3))(6)Cl(2) indicates that this compound is an ideal secondary reference sample for solid-state (99)Ru NMR studies. The isotropic (99)Ru chemical shift, (99)Ru nuclear quadrupolar coupling constant, C(Q), and quadrupolar asymmetry parameter of K(4)Ru(CN)(6). xH(2)O (x = 0, 3) are shown to be sensitive to x. For Ru(3)(CO)(12), the magnetic shielding tensors of each of the three nonequivalent Ru nuclei have spans of 1300-1400 ppm, and the (99)Ru C(Q) values are also similar, 1.36-1.85 MHz, and are surprisingly small given that (99)Ru has a moderate nuclear quadrupole moment. Information about the relative orientation of the Ru magnetic shielding and electric field gradient tensors has been determined for Ru(3)(CO)(12) from experimental (99)Ru NMR spectra as well as quantum chemical calculations.

Journal Article↗