Nonpolar Side Chains Research Articles

Protein Folding and Binding Characterized by Mass Spectrometry

This presentation will illustrate how the combination of solution phase labeling with mass spectrometry (MS) can elucidate mechanistic aspects of protein behavior. We will focus on two ongoing projects in our laboratory. (A) The initial (submillisecond) stages of protein folding represent a formidable experimental challenge. We have begun to address this issue by using submillisecond mixing with laser-induced oxidative labeling. Apomyoglobin (aMb) serves as a model system for these measurements. Exposure of the protein to a brief pulse of hydroxyl radical (•OH) at different time points during folding introduces covalent modifications at solvent accessible side chains. The extent of labeling is monitored using MS-based peptide mapping, providing spatially-resolved measurements of changes in solvent accessibility. The technique introduced here is capable of providing in-depth structural information on time scales that have thus far been dominated by low resolution spectroscopic probes. (B) The bacterial protease ClpP is a multi-subunit complex with a central degradation chamber that can be accessed via axial pores. In free ClpP these pores are obstructed. Acyldepsipeptides (ADEPs) are antibacterial compounds that bind ClpP and cause the pores to open up. The ensuing uncontrolled degradation of intracellular proteins is responsible for the antibiotic activity of ADEPs. We use hydrogen/deuterium exchange MS to obtain insights into the ClpP behavior with and without ADEP1. Our data point to a mechanism where the pore opening mechanism is mediated primarily by changes in the packing of N-terminal nonpolar side chains. We propose that a “hydrophobic plug” causes pore blockage in ligand-free ClpP. ADEP1 binding provides new hydrophobic anchor points that nonpolar N-terminal residues can interact with. In this way ADEP1 triggers the transition to an open conformation, where nonpolar moieties are clustered around the rim of the pore.

Poly(4-styrenesulfonate) as an Inhibitor of Aβ40 Amyloid Fibril Formation

The formation of amyloid, a cross-β-sheet fibrillar aggregate of proteins, is associated with a variety of neurodegenerative diseases. Amyloidogenic proteins such as β-amyloid (Aβ) are known to exist with a large amount of polyelectrolyte macromolecules in vivo. The exact nature of Aβ-polyelectrolyte interactions and their roles in Aβ-aggregation are largely unknown. In this regard, we report the inhibiting effect of an anionic polyelectrolyte poly(4-styrenesulfonate) (PSS) on the aggregation of Aβ40 peptide. The results demonstrate the strong inhibition potential of PSS on the aggregation of Aβ40 and imply the dominant role of hydrophobicity of the polyelectrolyte in reducing the propensity of Aβ40 amyloid formation. Additional studies with poly(vinyl sulfate) (PVS) and p-toluenesulfonate (PTS), which share similar charge density with PSS except the former lacking the nonpolar aromatic side chain and the latter the aliphatic hydrocarbon backbone, reveal that the presence of both aliphatic backbone and aromatic side chain group in PSS is essential for its Aβ-aggregation inhibition activity. The interactions involved in the Aβ40-PSS complex were further investigated using molecular dynamics (MD) simulation. Our results provide new insights into the structural interplay between polyelectrolytes and Aβ peptide, facilitating the ultimate understanding of amyloid formation in Alzheimer's disease. The results should assist in developing novel polyelectrolytes as potential chemical tools to study amyloid aggregation.

Structural Origins of Oxacillinase Specificity in Class D β-Lactamases

Since the discovery and use of penicillin, the increase of antibiotic resistance among bacterial pathogens has become a major health concern. The most prevalent resistance mechanism in Gram-negative bacteria is due to β-lactamase expression. Class D β-lactamases are of particular importance due to their presence in multidrug-resistant Acinetobacter baumannii and Pseudomonas aeruginosa. The class D enzymes were initially characterized by their ability to efficiently hydrolyze isoxazolyl-type β-lactams like oxacillin. Due to this substrate preference, these enzymes are traditionally referred to as oxacillinases or OXAs. However, this class is comprised of subfamilies characterized by diverse activities that include oxacillinase, carbapenemase, or cephalosporinase substrate specificity. OXA-1 represents one subtype of class D enzyme that efficiently hydrolyzes oxacillin, and OXA-24/40 represents another with weak oxacillinase, but increased carbapenemase, activity. To examine the structural basis for the substrate selectivity differences between OXA-1 and OXA-24/40, the X-ray crystal structures of deacylation-deficient mutants of these enzymes (Lys70Asp for OXA-1; Lys84Asp for OXA-24) in complexes with oxacillin were determined to 1.4 Å and 2.4 Å, respectively. In the OXA-24/40/oxacillin structure, the hydrophobic R1 side chain of oxacillin disrupts the bridge between Tyr112 and Met223 present in the apo OXA-24/40 structure, causing the main chain of the Met223-containing loop to adopt a completely different conformation. In contrast, in the OXA-1/oxacillin structure, a hydrophobic pocket consisting of Trp102, Met99, Phe217, Leu161, and Leu255 nicely complements oxacillin's nonpolar R1 side chain. Comparison of the OXA-1/oxacillin and OXA-24/40/oxacillin complexes provides novel insight on how substrate selectivity is achieved among subtypes of class D β-lactamases. By elucidating important active site interactions, these findings can also inform the design of novel antibiotics and inhibitors.

Activation of ClpP Protease by ADEP Antibiotics: Insights from Hydrogen Exchange Mass Spectrometry

The bacterial protease ClpP consists of 14 subunits that assemble into two stacked heptameric rings. The central degradation chamber can be accessed via axial pores. In free ClpP, these pores are obstructed by the N-terminal regions of the seven subunits at either end of the barrel. Acyldepsipeptides (ADEPs) are antibacterial compounds that bind in hydrophobic clefts surrounding the pore region, causing the pores to open up. The ensuing uncontrolled degradation of intracellular proteins is responsible for the antibiotic activity of ADEPs. Recently published X-ray structures yielded conflicting models regarding the conformation adopted by the N-terminal regions in the open state. Here, we use hydrogen/deuterium exchange (HDX) mass spectrometry to obtain complementary insights into the ClpP behavior with and without ADEP1. Ligand binding causes rigidification of the equatorial belt, accompanied by destabilization in the vicinity of the binding clefts. The N-terminal regions undergo rapid deuteration with only minor changes after ADEP1 binding, revealing a lack of stable H-bonding. Our data point to a mechanism where the pore opening mechanism is mediated primarily by changes in the packing of N-terminal nonpolar side chains. We propose that a “hydrophobic plug” causes pore blockage in ligand-free ClpP. ADEP1 binding provides new hydrophobic anchor points that nonpolar N-terminal residues can interact with. In this way, ADEP1 triggers the transition to an open conformation, where nonpolar moieties are clustered around the rim of the pore. This proposed mechanism helps reconcile the conflicting models that had been put forward earlier.

Amino acid/water interactions study: a new amino acid scale

Partition ratios of 8 free l-amino acids (Gln, Glu, His, Lys, Met, Ser, Thr, and Tyr) were measured in 10 different polymer/polymer aqueous two-phase systems containing 0.15 M NaCl in 0.01 M phosphate buffer, pH 7.4. The solute-specific coefficients representing the solute dipole/dipole, hydrogen-bonding and electrostatic interactions with the aqueous environment of the amino acids were determined by multiple linear regression analysis using a modified linear solvation energy relationship. The solute-specific coefficients determined in this study together with the solute-specific coefficients reported previously for amino acids with non-polar side-chains where used in a Quantitative Structure/Property Relationship analysis. It is shown that linear combinations of these solute-specific coefficients are correlated well with various physicochemical, structural, and biological properties of amino acids.

Influence of variation of a side chain on the folding equilibrium of a β‐peptide: Limitations of one‐step perturbation

In a recent study (Lin et al., Helv. Chim. Acta 2011, 94, 597), the one-step perturbation method was applied to tackle a challenging computational problem, that is, the calculation of the folding free enthalpies ΔGF,U of six hepta-β-peptides with different, Ala, Val, Leu, Ile, Ser, or Thr, side chains in the fifth residue. The ΔGF,U values obtained using one-step perturbation based on a single molecular dynamics simulation of a judiciously chosen reference state with soft-core atoms in the side chain of the fifth residue showed an overall accuracy of about kB T for the four peptides with nonpolar side chains, but twice as large deviations were observed for the peptides with polar side chains. Here, alternative reference-state Hamiltonians that better cover the conformational space relevant to these peptides are investigated, and post simulation rotational sampling of the χ1 and χ2 torsional angles of the fifth residue is carried out to sample different orientations of the side chain. A reference state with rather soft atoms yields accurate ΔGF,U values for the peptides with the Ser and Thr side chains, but it failed to correctly predict the folding free enthalpy for one peptide with a nonpolar side chain, that is, Leu. Based on the results and those of earlier studies, possible ways to improve the accuracy of the efficient one-step perturbation technique to compute free enthalpies of folding are discussed.

Role of Rhodobacter sphaeroides Photosynthetic Reaction Center Residue M214 in the Composition, Absorbance Properties, and Conformations of HA and BA Cofactors

In the native reaction center (RC) of Rhodobacter sphaeroides, the side chain of (M)L214 projects orthogonally toward the plane and into the center of the A branch bacteriopheophytin (BPhe) macrocycle. The possibility that this side chain is responsible for the dechelation of the central Mg(2+) of bacteriochlorophyll (BChl) was investigated by replacement of (M)214 with residues possessing small, nonpolar side chains that can neither coordinate nor block access to the central metal ion. The (M)L214 side chain was also replaced with Cys, Gln, and Asn to evaluate further the requirements for assembly of the RC with BChl in the HA pocket. Photoheterotrophic growth studies showed no difference in growth rates of the (M)214 nonpolar mutants at a low light intensity, but the growth of the amide-containing mutants was impaired. The absorbance spectra of purified RCs indicated that although absorbance changes are associated with the nonpolar mutations, the nonpolar mutant RC pigment compositions are the same as in the wild-type protein. Crystal structures of the (M)L214G, (M)L214A, and (M)L214N mutants were determined (determined to 2.2-2.85 Å resolution), confirming the presence of BPhe in the HA pocket and revealing alternative conformations of the phytyl tail of the accessory BChl in the BA site of these nonpolar mutants. Our results demonstrate that (i) BChl is converted to BPhe in a manner independent of the aliphatic side chain length of nonpolar residues replacing (M)214, (ii) BChl replaces BPhe if residue (M)214 has an amide-bearing side chain, (iii) (M)214 side chains containing sulfur are not sufficient to bind BChl in the HA pocket, and (iv) the (M)214 side chain influences the conformation of the phytyl tail of the BA BChl.

Conserved Regional 3′ Grouping of Rare Codons in the Coding Sequence of Ocular Prosecretory Mitogen Lacritin

Lacritin is a prosecretory mitogen in tears and, although a tear protein, it promotes basal tearing and lacrimal gland secretion. Since scale up is relevant to its potential use in the treatment of dry eye, we explored various mutagenic strategies to alter the stability, solubility, and translational efficiency of nascent lacritin, and discovered 3' clustering of rare human codons. Site-directed mutagenesis of lacritin coding cDNA "pLAC" generated 24 different nonsynonymous and 13 synonymous mutations. Nonsynonymous mutations altered amino acids with nonpolar, basic or acidic side chains to serine. Synonymous mutation progressively optimized human codons that are rare or uncommon in Escherichia coli without changing the amino acid specified. These changes were validated by sequencing and protein production, and analyzed via the "rare codon calculator" (RCC). Nonhuman primate and nonprimate lacritin coding sequences were extracted from Ensembl, and analyzed via RCC using codon usage appropriate for each species. Superior yields were obtained by modification of individual hydrophobic residues or a predicted salt bridge, suggesting that production was limited by lacritin stability. Accordingly, elimination of rare codons increased yields less effectively. Importantly, RCC analysis of human, nonhuman primate (mouse lemur) and nonprimate (cat, tree shrew) lacritin coding sequences revealed remarkable 3' clustering of rare codons, unlike human lipocalin-1 and 21 other widely expressed human tear genes. Lacritin protein yields were improved primarily by hydrophobic or salt bridge mutagenesis and less so by elimination of rare codons. The 3' clustering of rare codons is conserved in all lacritin orthologs examined.

Investigation of the Mechanism of Protein Denaturation by Guanidine Hydrochloride-Induced Dissociation of Inhibitor-Protease Complexes

In this communication we describe an approach in which guanidine hydrochloride-induced dissociation of a protein inhibitor-serine protease complex is used to explore the molecular basis of protein denaturation. The rationale behind this approach is that the inhibitor-protease complex is stabilized by the same types of non-covalent interactions that stabilize the native state of a protein. The dissociation of inhibitor-protease complex can be performed at concentrations of guanidine hydrochloride at which the inhibitor and the protease retain their native conformations. Here, we present our results on the effect of 0.1 M to 0.4 M guanidine hydrochloride concentrations on the association equilibrium constants (reciprocal of dissociation constant) of P₁G, P₁A, P₁V, P₁N, and P₁S variants of turkey ovomucoid third domain with bovine α-chymotrypsin. We use these results to calculate the free energy change in the dissociation of inhibitor-protease complexes (the m value) per mol of guanidine hydrochloride concentration. Our results agree with the general consensus that the denaturing effect of guanidine hydrochloride is due to its favorable interaction with the polar parts of proteins and that the non-polar side chains have no or little favorable interaction with guanidine hydrochloride.

Effect of the Chain Length on the Structure of Ionic Liquids: from Spatial Heterogeneity to Ionic Liquid Crystals

Ionic liquids with intermediate nonpolar cationic side-chain lengths are known to have nanoscale spatial heterogeneities with nonpolar tail domains separated by a continuous polar network. In this work, we use coarse-grained molecular dynamics simulations to show that, when the nonpolar cationic side chain is sufficiently long, due to the stronger van der Waals interactions between the side chains, the structure of ionic liquids goes through a transition from spatially heterogeneous to liquid crystalline-like. For XMIm(+)/NO(3)(-) ionic liquids, change occurs when the number of carbon groups on the cationic side chain varies from 14 to 16. In the liquid crystal-like phase, the cationic side chains tend to be parallel to each other, while the cationic head groups and anions, although being mostly layered perpendicularly to the direction along the side chains, still form a continuous polar network.

Synthesis and Characterization of DNA Minor Groove Binding Alkylating Agents

Derivatives of methyl 3-(1-methyl-5-(1-methyl-5-(propylcarbamoyl)-1H-pyrrol-3-ylcarbamoyl)-1H-pyrrol-3-ylamino)-3-oxopropane-1-sulfonate (1), a peptide-based DNA minor groove binding methylating agent, were synthesized and characterized. In all cases, the N-terminus was appended with an O-methyl sulfonate ester, while the C-terminus group was varied with nonpolar and polar side chains. In addition, the number of pyrrole rings was varied from 2 (dipeptide) to 3 (tripeptide). The ability of the different analogues to efficiently generate N3-methyladenine was demonstrated as was their selectivity for minor groove (N3-methyladenine) versus major groove (N7-methylguanine) methylation. Induced circular dichroism studies were used to measure the DNA equilibrium binding properties of the stable sulfone analogues; the tripeptide binds with affinity that is >10-fold higher than that of the dipeptide. The toxicities of the compounds were evaluated in alkA/tag glycosylase mutant E. coli and in human WT glioma cells and in cells overexpressing and under-expressing N-methylpurine-DNA glycosylase, which excises N3-methyladenine from DNA. The results show that equilibrium binding correlates with the levels of N3-methyladenine produced and cellular toxicity. The toxicity of 1 was inversely related to the expression of MPG in both the bacterial and mammalian cell lines. The enhanced toxicity parallels the reduced activation of PARP and the diminished rate of formation of aldehyde reactive sites observed in the MPG knockdown cells. It is proposed that unrepaired N3-methyladenine is toxic due to its ability to directly block DNA polymerization.

Fast mass spectrometry-based enantiomeric excess determination of proteinogenic amino acids

A rapid determination of the enantiomeric excess of proteinogenic amino acids is of great importance in various fields of chemical and biologic research and industries. Owing to their different biologic effects, enantiomers are interesting research subjects in drug development for the design of new and more efficient pharmaceuticals. Usually, the enantiomeric composition of amino acids is determined by conventional analytical methods such as liquid or gas chromatography or capillary electrophoresis. These analytical techniques do not fulfill the requirements of high-throughput screening due to their relative long analysis times. The method presented allows a fast analysis of chiral amino acids without previous time consuming chromatographic separation. The analytical measurements base on parallel kinetic resolution with pseudoenantiomeric mass tagged auxiliaries and were carried out by mass spectrometry with electrospray ionization. All 19 chiral proteinogenic amino acids were tested and Pro, Ser, Trp, His, and Glu were selected as model substrates for verification measurements. The enantiomeric excesses of amino acids with non-polar and aliphatic side chains as well as Trp and Phe (aromatic side chains) were determined with maximum deviations of the expected value less than or equal to 10ee%. Ser, Cys, His, Glu, and Asp were determined with deviations lower or equal to 14ee% and the enantiomeric excess of Tyr were calculated with 17ee% deviation. The total screening process is fully automated from the sample pretreatment to the data processing. The method presented enables fast measurement times about 1.38 min per sample and is applicable in the scope of high-throughput screenings.

Analysis of amino acid–water interactions by partitioning in aqueous two-phase systems. I—Amino acids with non-polar side-chains

Partition ratios of 10 l-amino acids with non-polar side chains (Gly, Ala, Val, nor-Val, Ile, Leu, nor-Leu, Phe, Trp and Pro) were measured in ten different polymer/polymer aqueous two-phase systems (ATPS) containing 0.15M NaCl in 0.01M phosphate buffer, pH 7.4. The solute-specific coefficients representing the solute dipole–dipole, hydrogen bonding and electrostatic interactions with aqueous environment for the compounds examined were determined by the multiple linear regression analysis using the modified linear solvation energy relationship equation. It is shown that linear combinations of these coefficients are correlated with the amino acid lipophilicity/hydrophobicity scales reported in the literature. The results obtained imply that the solute-specific coefficients may be used as solute descriptors for quantitative structure–property relationship (QSPR) analysis.

Investigation of the Mechanism of Protein Denaturation by Guanidine Hydrochloride-Induced Dissociation of Inhibitor-Protease Complexes

In this communication we describe an approach in which guanidine hydrochloride-induced dissociation of a protein inhibitor-serine protease complex is used to explore the molecular basis of protein denaturation. The rationale behind this approach is that the inhibitor-protease complex is stabilized by the same types of non-covalent interactions that stabilize the native state of a protein. The dissociation of inhibitor-protease complex can be performed at concentrations of guanidine hydrochloride at which the inhibitor and the protease retain their native conformations. Here, we present our results on the effect of 0.1M to 0.4M guanidine hydrochloride concentrations on the association equilibrium constants (reciprocal of dissociation constant) of P1G, P1A, P1V, P1N, and P1S variants of turkey ovomucoid third domain with bovine α-chymotrypsin. We use these results to calculate the free energy change in the dissociation of inhibitor-protease complexes (the m value) per mol of guanidine hydrochloride concentration. Our results agree with the general consensus that the denaturing effect of guanidine hydrochloride is due to its favorable interaction with the polar parts of proteins and that the non-polar side chains have no or little favorable interaction with guanidine hydrochloride. Keywords: Chymotrypsin, denaturation, osmolytes, protease inhibitor, serine proteases, turkey ovomucoid third domain

Total synthesis of N,O,O,O-tetraacetyl-d-ribo-phytosphingosine and its 2-epi-congener

AbstractTotal synthesis of the natural d-ribo-phytosphingosine I and its 2-epimer III in the protected form was achieved through a common strategy. The aza-Claisen rearrangement of allylic thiocyanate (Z)-V incorporated the new stereogenic centre with nitrogen and the subsequent Wittig olefination constructed a non-polar side chain. Hydrogenation, followed by removal of protecting groups, completed the syntheses of I and III.

Mapping the Active Site Helix-to-Strand Conversion of CxxxxC Peroxiredoxin Q Enzymes

Peroxiredoxins (Prx) make up a family of enzymes that reduce peroxides using a peroxidatic cysteine residue; among these, members of the PrxQ subfamily are proposed to be the most ancestral-like yet are among the least characterized. In many PrxQ enzymes, a second "resolving" cysteine is located five residues downstream from the peroxidatic Cys, and these residues form a disulfide during the catalytic cycle. Here, we describe three hyperthermophilic PrxQ crystal structures originally determined by the RIKEN structural genomics group. We reprocessed the diffraction data and conducted further refinement to yield models with R(free) values lowered by 2.3-7.2% and resolution extended by 0.2-0.3 Å, making one, at 1.4 Å, one of the best resolved peroxiredoxins to date. Comparisons of two matched thiol and disulfide forms reveal that the active site conformational change required for disulfide formation involves a transition of ~20 residues from a pair of α-helices to a β-hairpin and 3(10)-helix. Each conformation has ~10 residues with a high level of disorder providing slack that allows the dramatic shift, and the two conformations are anchored to the protein core by distinct nonpolar side chains that fill three hydrophobic pockets. Sequence conservation patterns confirm the importance of these and a few additional residues for function. From a broader perspective, this study raises the provocative question of how to make use of the valuable information in the Protein Data Bank generated by structural genomics projects but not described in the literature, perhaps remaining unrecognized and certainly underutilized.

Estimation of the “hydrophobic reactivity” of SDS micelles by the use of BPh4− anions

Above the cmc, aqueous solution of sodium dodecyl sulfate SDS is an ionic mixture constituted of micelles of apparent charge number Zap, free counterions Na+ and free monomers SD-. The degree of micellization and the degree of condensation of Na+ on the micelles are calculated according to the mass-action model and by the generalization of the Fuoss ionic association theory.In the first part of this work, conductance data of this mixture are analyzed within the framework of the Onsager–Kim–MSA conductivity theory of mixed electrolytes and that of the Zwanzig dielectric friction theory. It appears that the micellization process is a progressive continuous “micro-phase transition” highly correlated to the degree of condensation of counterions. In the second part, we show how (in contrast with spectroscopic techniques) the high precision conductivity technique, combined to the theories mentioned above, can detect the absorption of the hydrophobic BPh4- anions by SDS micelles in dilute aqueous solutions: Because of the affinity of the BPh4- ions to the nonpolar side chains inside SDS, each micelle incorporates nBPh4–anions (hydrophobic reactivity). This number is determined by adjusting theoretical specific conductance to its corresponding experimental value. Results show that Na+ condensation facilitates this absorption and that “nBPh4–” increases with dilution.

Correlating ETD fragment ion intensities with peptide ion conformational and electronic structure

Amino acid residues affect the formation of backbone fragments upon electron transfer dissociation of doubly charged peptide ions of the AAXAR type. Peptide ions having non-polar residues (X=A, V, L, M, W) undergo backbone dissociations near the protonated N- and C-termini, forming mainly z1 and z4 fragment ions. Polar residues (X=H, D) prefer backbone dissociations occurring next to the polar residue, forming z2 and z3 fragment ions. Computational analysis, combining molecular dynamics, semi-empirical, density functional theory, and Møller–Plesset theory of precursor ion conformational space, identified the thermodynamically most stable tautomers and conformers for (AAVAR+2H)2+, (AAHAR+2H)2+, and (AADAR+2H)2+ precursor ions. Analysis of electronic states and potential energy surfaces for charge-reduced cation-radicals was used to interpret the ETD fragmentations. Electron attachment to (AAVAR+2H)2+ and (AAHAR+2H)2+ forms zwitterionic tautomers of charge-reduced cation-radicals as local energy minima in the ground electronic state. These are dynamically unstable with respect to exothermic ammonium proton migration forming aminoketyl intermediates. Direct NCα bond cleavage in the zwitterion requires an energy barrier which makes it noncompetitive with the proton migration. This bears on the long-standing chicken-and-egg problem of the ExD dissociation mechanisms according to the Utah–Washington model. Migration of a proton from a proximate neutral amide group was found to form a dynamically unstable enolimidate intermediate that cannot undergo NCα bond cleavage according to the Murrell–Laidler rule of reaction dynamics. According to electronic structure analysis in a conformationally defined peptide ion, the non-polar side chain in charge-reduced (AAVAR+2H)+ has only a spectator role in isomerizations and backbone dissociations. This casts doubt on the “hydrophobic” effect of amino acid residues on electron-based fragmentations proposed previously.

Interactions and Ordering of Ionic Liquids at a Metal Surface.

An atomistic force field for ionic liquids interacting with a metal surface is built on the basis of quantum methods. Density functional calculations of alkylammonium cations and alkylsulfonate anions interacting with a cluster of iron atoms were performed, at a series of distances and orientations, using the M06 functional that represents noncovalent interactions. A site-site potential function was then adjusted to the BSSE-corrected DFT interaction energies. Finally, the polarization of the metal by the ions was taken into account using induced dipoles to reproduce the interaction energy between charges and a conductor surface. When combined with a molecular force field for the ionic liquid and a suitable potential for metals, our model allows the computer simulation of heterogeneous systems containing metal surfaces or nanoparticles in the presence of ionic liquids. Our aim is to study tribological systems with ionic lubricants. We report molecular dynamics results on the structure of the interfacial layer of several alkylammonium alkylsulfonate ionic liquids at a flat iron surface, including analyses of the positional and orientational ordering of the ions near the surface, and charge density profiles. Both anions and cations are found in the first ordered layer of ions near the surface, with the oxygen atoms of the sulfonyl groups interacting more strongly with the metal. The interfacial layer is essentially one ion thick, except for very short chain ionic liquids in which a second layer is observed. The effects of different lengths of the nonpolar alkyl side chains on the cation and the anion are different: whereas butyl chains on the sulfonate anions tend to be directed away from the surface, those on ammonium cations lie more parallel to the surface.

Evaluation of the cytotoxic activity of new jadomycin derivatives reveals the potential to improve its selectivity against tumor cells

The jadomycins are a unique family of angucycline-derived antibiotics with interesting cytotoxic activities. In this work, six new jadomycin derivatives were produced in vivo by providing non-natural amino acids in fermentation media. They were further purified and identified by MS and NMR analyses. The cytotoxicities of these derivatives were evaluated against tumor cell lines MCF-7 and HCT116, as well as the normal human microvascular epithelial cells. The derivatives with alkyl side chains showed similar levels of cytotoxicity as jadomycin B and other known derivatives with nonpolar side chains, with IC(50) ranging from 1.3 to 10 μM; but the activities are not selective as these compounds also showed similar levels of cytotoxicity toward the normal human microvascular epithelial cells in the same concentration range. For the first time, derivatives with amino side chains (jadomycin Orn and K) were prepared and evaluated. Significantly, jadomycin Orn showed differential activity against normal and tumor cell lines. This result points to a new direction to modify jadomycin structure. The insights on the structure-activity relationship of jadomycins will guide further efforts to generate new and improved jadomycin derivatives against tumor cells.