Optimization of a ß-sheet-cap for long loop closure.

Protein loops make up a large portion of the secondary structure in nature. But very little is known concerning loop closure dynamics and the effects of loop composition on fold stability. We have designed a small system with stable ß-sheet structures, including features that allow us to probe these questions. Using paired Trp residues that form aromatic clusters on folding, we are able to stabilize two ß-strands connected by varying loop lengths and composition (an example sequence: RWITVTI - loop - KKIRVWE). Using NMR and CD, both fold stability and folding dynamics can be investigated for these systems. With the 16 residue loop peptide (sequence: RWITVTI-(GGGGKK)2 GGGG-KKIRVWE) remaining folded (ΔGU = 1.6 kJ/mol at 295K). To increase stability and extend the series to longer loops, we added an additional Trp/Trp pair in the loop flanking position. With this addition to the strands, the 16 residue loop (sequence: RWITVRIW-(GGGGKK)2 GGGG-WKTIRVWE) supports a remarkably stable ß-sheet (ΔGU = 6.3 kJ/mol at 295 K, Tm = ∼55°C). Given the abundance of loops in binding motifs and between secondary structures, these constructs can be powerful tools for peptide chemists to study loop effects; with the Trp/Trp pair providing spectroscopic probes for assessing both stability and dynamics by NMR.

Nascent Hairpins in Proteins: Identifying Turn Loci and Quantitating Turn Contributions to Hairpin Stability.

Many factors influence the stability of hairpins that could appear as foldons in partially folded states of proteins; of these, the propensity of certain amino acid sequences to favor conformations that serve to align potential ß-strands for antiparallel association is likely the dominant feature. Quantitating turn propensities is viewed as the first step in developing an algorithm for locating nascent hairpins in protein sequences. Such nascent hairpins can serve to accelerate protein folding or, if they represent structural elements that differ from the final folded state, as kinetic traps. We have measured these "turn propensities" for the two most common turn types using a series of model peptide hairpins with four- and six-residue loops connecting the associated ß-strands. Loops of four to six residues with specific turn sequences containing only natural l-amino acids and glycine can provide as much as 15 kJ/mol of hairpin stabilization versus loops lacking the defined turn loci. Single-site mutations within some of the optimal connecting loops can have ΔΔG effects as large as 9-10 kJ/mol on hairpin stability. In contrast to the near universal II'/I' turns of model hairpins, a number of hairpin-supporting XZZG sequence ß-turns with αR and/or γR configurations at the ZZ unit were found. A series of turn replacements (four-residue ß-turns replaced by sequences that favor five- and six-residue reversing loops) using identical strands in our model systems have confirmed that several sequences have intrinsic turn propensities that could favor ß-strand association in a non-native strand register and thus serve as kinetic traps. These studies also indicate that aryl residues immediately flanking a turn sequence can alter relative turn propensities by as much as 9-11 kJ/mol and will need to be a part of any nascent hairpin recognition algorithm.

Peptide Inhibitors of the amyloidogenesis of IAPP: verification of the hairpin-binding geometry hypothesis.

Versions of a previously discovered ß-hairpin peptide inhibitor of IAPP aggregation that are stabilized in that conformation, or even forced to remain in the hairpin conformation by a backbone cyclization constraint, display superior activity as inhibitors. The cyclized hairpin, cyclo-WW2, displays inhibitory activity at substoichiometric concentrations relative to this amyloidogenic peptide. The hairpin-binding hypothesis stands confirmed.

Determination of methamphetamine enantiomer composition in human hair by non-chiral liquid chromatography-tandem mass spectrometry method.

Chiral separation is crucial for investigating methamphetamine positive cases. While (S)-(+)-enantiomer of methamphetamine (S-MAMP) is a schedule II controlled substance, (R)-(-)-enantiomer (R-MAMP) is an active ingredient of a few over-the-counter drugs in the United States. Among biological specimen types, hair provides greater detection window than blood, urine or oral fluid, and are therefore regarded with particular interest. Herein we describe a novel non-chiral liquid chromatography-tandem mass spectrometry (LC-MS/MS) method to directly determine methamphetamine enantiomeric composition (percentage) in hair specimens. Hair samples were washed once with acetone, powdered, incubated overnight at 53°C in 0.1M hydrochloric acid (HCl), and subjected to a solid phase extraction (SPE). The extracts were derivatized using Marfey's reagent at 53°C for 60min. The final mixture was analyzed by LC-MS/MS. Chromatographic separation was achieved using a C18 Kinetex analytical column and 60% (v/v) aqueous methanol as mobile phase (isocratic). Triple quadrupole mass spectrometer was equipped with an electro-spray ionization (ESI) source operating in negative mode and the chromatograms were acquired using a multiple-reaction monitoring (MRM) approach. The results were expressed as ratio of R- to S-MAMP and then derived to composition percentages without requiring quantitating each enantiomer. The method was precise and accurate across 0-100% S-composition at a range of 80-18,000pg/mg. The performance of the new method was compared with an (S)-(-)-N-trifluoroacetylprolyl chloride (S-TPC) derivatization and gas chromatography-mass spectrometry (GC-MS) method on authentic methamphetamine-positive hair samples. Not only the new Marfey's reagent approach presented satisfactory correlation with the S-TPC approach, but it also exhibited significantly improved quality (e.g., S/N) of the chromatograms. In summary, our protocol employs cost effective and minimally hazardous Marfey's reagent to derivatize trace amounts of methamphetamine extracted from hair samples and a non-chiral LC-MS/MS approach to separate and identify the two enantiomers. The method allows determination of the methamphetamine enantiomeric composition without requiring quantitation of each enantiomer and is therefore well suited for further investigate previously determined methamphetamine positive cases. This method represents a viable tool for evaluation of long-term drug exposure.

Aryl-aryl interactions in designed peptide folds: Spectroscopic characteristics and optimal placement for structure stabilization.

We have extended our studies of Trp/Trp to other Aryl/Aryl through-space interactions that stabilize hairpins and other small polypeptide folds. Herein we detail the NMR and CD spectroscopic features of these types of interactions. NMR data remains the best diagnostic for characterizing the common T-shape orientation. Designated as an edge-to-face (EtF or FtE) interaction, large ring current shifts are produced at the edge aryl ring hydrogens and, in most cases, large exciton couplets appear in the far UV circular dichroic (CD) spectrum. The preference for the face aryl in FtE clusters is W ≫ Y ≥ F (there are some exceptions in the Y/F order); this sequence corresponds to the order of fold stability enhancement and always predicts the amplitude of the lower energy feature of the exciton couplet in the CD spectrum. The CD spectra for FtE W/W, W/Y, Y/W, and Y/Y pairs all include an intense feature at 225-232 nm. An additional couplet feature seen for W/Y, W/F, Y/Y, and F/Y clusters, is a negative feature at 197-200 nm. Tyr/Tyr (as well as F/Y and F/F) interactions produce much smaller exciton couplet amplitudes. The Trp-cage fold was employed to search for the CD effects of other Trp/Trp and Trp/Tyr cluster geometries: several were identified. In this account, we provide additional examples of the application of cross-strand aryl/aryl clusters for the design of stable ß-sheet models and a scale of fold stability increments associated with all possible FtE Ar/Ar clusters in several structural contexts. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 337-356, 2016.

Detection of Drugs in Nails: Three Year Experience.

Nails (fingernails and toenails) are made of keratin. As the nail grows, substances incorporate into the keratin fibers where they can be detected 3-6 months after use. Samples are collected by clipping of 2-3 mm of nail from all fingers (100 mg). We present drug testing results from 10,349 nail samples collected from high-risk cases during a 3-year period of time. Samples were analyzed by validated analytical methods. The initial testing was performed mostly using enzyme-linked immunosorbent assay, but by liquid chromatography-tandem mass spectrometry (LC-MS-MS) as well. Presumptive positive samples were subjected to confirmatory testing with sample preparation procedures including washing, pulverizing, digestion and extraction optimized for each drug class. The total of 7,799 samples was analyzed for amphetamines. The concentrations ranged from 40 to 572,865 pg/mg (median, 100-3,687) for all amphetamine analytes. Amphetamine and methamphetamine were present in 14% of the samples, 22 samples were positive for 3,4-methylenedioxymethamphetamine (0.3%), 7 for methylenedioxyamphetamine (0.09%) and 4 for 3,4-methylenedioxy-N-ethylamphetamine (0.05%). Cocaine and related analytes were found in 5% samples (7,787 total), and the concentration range was 20-265,063 pg/mg (median 84-1,768). Opioids overall ranged from 40 to 118,229 pg/mg (median 123-830). The most prevalent opioid was oxycodone (15.1%) and hydrocodone (11.4%) compared with 1.0-3.6% for the others, including morphine, codeine, hydromorphone, methadone, 2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine and oxymorphone. Carboxy-Δ-9-tetrahydrocannabinol positivity rate was 18.1% (0.04-262 pg/mg, median 6.41). Out of 3,039 samples, 756 were positive (24.9%) for ethyl glucuronide (20-3,754 pg/mg, median 88). Other drugs found in nails included barbiturates, benzodiazepines, ketamine, meperidine, tramadol, zolpidem, propoxyphene, naltrexone and buprenorphine. Nail analyses have become a reliable way of determining the long-term use and abuse of drugs. Extraction techniques are simple and produce accurate and precise results. Sensitive analytical instrumentation, mainly LC-MS-MS, allows for detection of femtogram (10(-15) g) quantities of substances in nails. Samples were from a high-risk population, therefore the extraordinary positivity rate was observed.

Analytical performance of QMS everolimus assay on ortho Vitros 5,1 FS fusion analyzer: measuring everolimus trough levels for solid organ transplant recipients.

BACKGROUND: Everolimus has recently been approved by Food and Drug Administration for graft maintenance in liver transplant recipients. This drug has a narrow therapeutic index and benefits from close blood level monitoring. Currently, in the United States, the Thermo Fisher Scientific Quantitative Microsphere System (QMS) Everolimus Immunoassay is the only Food and Drug Administration-cleared immunoassay for monitoring everolimus in renal transplant recipients. However, studies on this assay adapted to the Ortho Vitros 5,1 FS chemistry analyzer have not been published, and data of this assay applied to monitoring drug levels in liver transplant recipients are limited. Here, the authors evaluated and validated the QMS everolimus assay on the Vitros analyzer and its application to supporting the immunosuppressant management of mainly liver transplant recipients. METHODS: The analysis was performed according to the QMS assay package insert. The method was compared with a liquid chromatography-tandem mass spectrometry method from a reference laboratory using a total of 34 samples from 1 double lung and liver, 8 liver, and 3 kidney recipients. The method comparison was assessed by Deming regression. Proficiency test materials issued by Everolimus TDM Proficiency Support Program were tested and compared with the peer group results of using the QMS kits. RESULTS: The assay was linear in the range of 0.75-20.0 ng/mL. Limit of detection was 0.70 ng/mL and lower limit of quantitation was 0.75 ng/mL. Within-day and between-day (20 days) coefficients of variation were between 3.1% and 16.5% at mean levels of 5.3, 12.0, and 17.2 ng/mL, respectively. We obtained a Deming regression of y = 1.271 - 0.666 (r = 0.880) when comparing with the liquid chromatography-tandem mass spectrometry method. CONCLUSIONS: The authors concluded that the analytical performance of the QMS everolimus immunoassay by the Vitros 5,1 FS analyzer was satisfactory for monitoring drug levels of solid organ transplant patients.

13C structuring shifts for the analysis of model ß-hairpins and ß-sheets in proteins: diagnostic shifts appear only at the cross-strand H-bonded residues.

The present studies have shown that (13)C=O, (13)C(α) and (13)C(ß) of H-bonded strand residues in ß-hairpins provide additional probes for quantitating the extent of folding in ß-hairpins and other ß-sheet models. Large differences in the structuring shifts (CSDs) of these (13)C sites in H-bonded versus non-H-bonded sites are observed: the differences between H-bonded and non-H-bonded sites are greater than 1.2 ppm for all three (13)C probes. This prompts us to suggest that efforts to determine the extent of hairpin folding from (13)C shifts should be based exclusively on the observation at the cross-strand H-bonded sites. Furthermore, the statistics suggest the (13)C' and (13)C(ß) CSDs will provide the best differentiation with 100%-folded CSD values approaching -2.6 and +3 ppm, respectively, for the H-bonded sites. These conclusions can be extended to edge-strands of protein ß-sheets. Our survey of reported (13)C shifts in ß-proteins indicates that some of the currently employed random coil values need to be adjusted, particularly for ionization-induced effects.

Simultaneous serum nicotine, cotinine, and trans-3'-hydroxycotinine quantitation with minimal sample volume for tobacco exposure status of solid organ transplant patients.

Concentrations of nicotine and its metabolites in blood are indicative of patients' current tobacco exposure, and their quantifications have been clinically applied to multiple assessments including demonstration of abstinence prior to heart-lung transplantation. For the purpose of transplant evaluation, the laboratory work up is extensive; thereby an assay with minimal sample volume is preferred. We developed and validated a rapid LC-MS/MS assay to simultaneously quantitate nicotine and its major metabolites, Cotinine and trans-3'-OH-cotinine (3-OH-Cot), in serum. 100µL of serum was spiked with deuterated internal standards and extracted by Oasis HLB solid phase extraction cartridge. Nicotine and metabolites in the reconstituted serum extract were separated by Agilent Eclipse XDB-C8 3.5µm 2.1mm×50mm HPLC column within 4.7min, and quantified by MS/MS with positive mode electrospray ionization and multiple reaction monitoring. Ion suppression was insignificant, and extraction efficiency was 79-110% at 50ng/mL for all compounds. Limit of detection was 1.0ng/mL for nicotine and 3-OH-Cot, and <0.5ng/mL for Cotinine. Linearity ranges for nicotine, cotinine and 3-OH-Cot were 2-100, 2-1000, and 5-1000ng/mL with recoveries of 86-115%. Within-day and twenty-day imprecision at nicotine/cotinine/3-OH-Cot levels of 22/150/90, 37/250/150, and 50/800/500ng/mL were all 1.1-6.5%. The reconstituted serum extracts were stable for at least 7 days stored in the HPLC autosampler at 5°C. Our method correlates well with alternative LC-MS/MS methods. We successfully developed and validated an LC-MS/MS assay to quantitate concentrations of nicotine and its metabolites in serum with minimal sample volume to assess tobacco exposure of heart-lung transplant patients.

Mutational effects on the folding dynamics of a minimized hairpin.

The fold stabilities and folding dynamics of a series of mutants of a model hairpin, KTW-NPATGK-WTE (HP7), are reported. The parent system and the corresponding DPATGK loop species display submicrosecond folding time constants. The mutational studies revealed that ultrafast folding requires both some prestructuring of the loop and a favorable interaction between the chain termini in the transition state. In the case of YY-DPETGT-WY, another submicrosecond folding species [Davis, C. M., Xiao, S., Raleigh, D. P., and Dyer, R. B. (2012) J. Am. Chem. Soc. 134, 14476-14482], a hydrophobic cluster provides the latter. In the case of HP7, the Coulombic interaction between the terminal NH3(+) and CO2(-) units provides this; a C-terminal Glu to amidated Ala mutation results in a 5-fold retardation of the folding rate. The effects of mutations within the reversing loop indicate the balance between loop flexibility (favoring fast conformational searching) and turn formation in the unfolded state is a major factor in determining the folding dynamics. The -NAAAKX- loops examined display no detectable turn formation propensity in other hairpin constructs but do result in stable analogues of HP7. Peptide KTW-NAAAKK-WTE displays the same fold stability as HP7, but both the folding and unfolding time constants are greater by a factor of 20.

Fluorescence of tryptophan in designed hairpin and Trp-cage miniproteins: measurements of fluorescence yields and calculations by quantum mechanical molecular dynamics simulations.

The quantum yield of tryptophan (Trp) fluorescence was measured in 30 designed miniproteins (17 ß-hairpins and 13 Trp-cage peptides), each containing a single Trp residue. Measurements were made in D(2)O and H(2)O to distinguish between fluorescence quenching mechanisms involving electron and proton transfer in the hairpin peptides, and at two temperatures to check for effects of partial unfolding of the Trp-cage peptides. The extent of folding of all the peptides also was measured by NMR. The fluorescence yields ranged from 0.01 in some of the Trp-cage peptides to 0.27 in some hairpins. Fluorescence quenching was found to occur by electron transfer from the excited indole ring of the Trp to a backbone amide group or the protonated side chain of a nearby histidine, glutamate, aspartate, tyrosine, or cysteine residue. Ionized tyrosine side chains quenched strongly by resonance energy transfer or electron transfer to the excited indole ring. Hybrid classical/quantum mechanical molecular dynamics simulations were performed by a method that optimized induced electric dipoles separately for the ground and excited states in multiple π-π* and charge-transfer (CT) excitations. Twenty 0.5 ns trajectories in the tryptophan's lowest excited singlet π-π* state were run for each peptide, beginning by projections from trajectories in the ground state. Fluorescence quenching was correlated with the availability of a CT or exciton state that was strongly coupled to the π-π* state and that matched or fell below the π-π* state in energy. The fluorescence yields predicted by summing the calculated rates of charge and energy transfer are in good accord with the measured yields.

ß-Sheet 13C structuring shifts appear only at the H-bonded sites of hairpins.

The (13)C chemical shifts measured for designed ß-hairpins indicate that the structuring shifts (upfield for Cα and C', downfield for Cß) previously reported as diagnostic for ß-structuring in proteins appear only at the H-bonded strand residues. The resulting periodicity of structuring shift magnitudes is not, however, a consequence of H-bonding status; rather, it reflects a previously unrecognized alternation in the backbone torsion angles of ß-strands. This feature of hairpins is also likely to be present in proteins. The study provides reference values for the expectation shifts for (13)C sites in ß-structures that should prove useful in the characterization of the folding equilibria of ß-sheet models.

Stabilizing capping motif for beta-hairpins and sheets.

Although much has been learned about the design of models of beta-sheets during the last decade, modest fold stabilities in water and terminal fraying remain a feature of most beta-hairpin peptides. In the case of hairpin capping, nature did not provide guidance for solving the problem. Some observations from prior turn capping designs, with further optimization, have provided a generally applicable, "unnatural" beta cap motif (alkanoyl-Trp at the N terminus and Trp-Thr-Gly at the C terminus) that provides a net contribution of 6 + kJ/mol to beta-hairpin stability, surpassing all other interactions that stabilize beta-hairpins including the covalent disulfide bond. The motif, made up entirely of natural residues, is specific to the termini of antiparallel beta-strands and reduces fraying at the ends of hairpins and other beta-sheet models. Utilizing this motif, 10- to 22-residue peptide scaffolds of defined stereochemistry that are greater than 98% folded in water have been prepared. The beta-cap can also be used to staple together short antiparallel beta-strands connected by a long flexible loop.