Unraveling the potential of segment scan mass spectral acquisition for chemical isotope labeling LC-MS-based metabolome analysis: Performance assessment across different types of biological samples

BACKGROUND

Chemical isotope labeling (CIL) LC-MS is a powerful tool for metabolome analysis with high metabolomic coverage and quantification accuracy. In CIL LC-MS, the overall metabolite detection efficiency using Orbitrap MS can be further improved by employing a segment scan method where the full m/z range is divided into multiple segments for spectral acquisition with a significant increase in the in-spectrum dynamic range. Considering the metabolic complexity in different types of biological samples (e.g., feces, urine, serum/plasma, cell/tissue extracts, saliva, etc.), we report the development and evaluation of the segment scan method for metabolome analysis of different sample types.

RESULTS

It was found that sample complexity significantly influenced the performance of the segment scan method. In metabolically complex samples such as feces and urine, the method yielded a substantial increase (up to 94 %) in detected peak pairs or metabolites, compared to conventional full scan. Conversely, less complex samples like saliva exhibited more modest gains (approximately 25 %). Based on the observations, a 120-m/z segment scan method was determined as a routine approach for CIL LC-Orbitrap-MS-based metabolomics with good compatibility with different types of biological samples. For this method, a further investigation on relative quantification accuracy was done. The peak area ratios of 12C-/13-labeled metabolites were slightly reduced with 72%-84 % of peak pairs falling within the ±25 % range of the anticipated peak ratio of 1.0 among different samples, as opposed to 81%-90 % in the full scan, which was attributed to the inclusion of more low-abundance peak pairs within the narrow MS segments. However, the overall peak ratio measurement precision was not significantly affected by the segment scan.

SIGNIFICANCE AND NOVELTY

The segment scan method was found to be useful for CIL LC-Orbitrap-MS-based metabolome analysis of different types of samples with significant improvement in metabolite detectability (25-94 % increase), compared to the conventional full scan method.

Sensitive poliovirus detection using nested PCR and nanopore sequencing: a prospective validation study

Timely detection of outbreaks is needed for poliovirus eradication, but gold standard detection in the Democratic Republic of the Congo takes 30 days (median). Direct molecular detection and nanopore sequencing (DDNS) of poliovirus in stool samples is a promising fast method. Here we report prospective testing of stool samples from suspected polio cases, and their contacts, in the Democratic Republic of the Congo between 10 August 2021 and 4 February 2022. DDNS detected polioviruses in 62/2,339 (2.7%) of samples, while gold standard combination of cell culture, quantitative PCR and Sanger sequencing detected polioviruses in 51/2,339 (2.2%) of the same samples. DDNS provided case confirmation in 7 days (median) in routine surveillance conditions. DDNS enabled confirmation of three serotype 2 circulating vaccine-derived poliovirus outbreaks 23 days (mean) earlier (range 6-30 days) than the gold standard method. The mean sequence similarity between sequences obtained by the two methods was 99.98%. Our data confirm the feasibility of implementing DDNS in a national poliovirus laboratory.

Molecularly Imprinted Nanogels Possessing Dansylamide Interaction Sites for Controlling Protein Corona In Situ by Cloaking Intrinsic Human Serum Albumin

Nanomaterials have become increasingly promising for biomedical applications owing to their specific biological characteristics. As drug delivery vehicles, nanomaterials have to circulate in the bloodstream to deliver the encapsulated components to the target tissues. Protein corona regulation is one of the promising approaches that gives stealth capability to avoid immune response. The aim of this study was to develop molecularly imprinted polymer nanogels (MIP-NGs) capable of protein corona regulation, using intrinsic human serum albumin (HSA) and with a functional monomer, dansylamide ethyl acrylamide (DAEAm), the dansylamide group serving as a ligand for HSA. The recognition capability of HSA for MIP-NGs was investigated by isothermal titration calorimetry (ITC). The affinity of the MIP-NGs prepared with DAEAm was then compared to that of the reference MIP-NGs prepared with pyrrolidyl acrylate developed in our previous study. Furthermore, we demonstrated that the concurrent use of these two different functional monomers for molecular imprinting was further effective to construct high-affinity recognition nanocavities for HSA and to form HSA-rich protein corona in the human plasma owing to the different interaction modes of the monomers. We believe that the molecular imprinting strategy developed through the use of ligand-based functional monomer is an effective strategy to create artificial molecular recognition materials.

Identifying lost surgical needles with visible and near infrared fluorescent light emitting microscale coating

BACKGROUND

Retained foreign bodies (RFOs) have substantial clinical and financial consequences. In laparoscopic surgery, RFOs can be a cause of needing to convert a minimally invasive surgery (MIS) procedure to an open operation. A coating for surgical models was developed to augment localization of needles using fluorescence appropriate for open and minimally invasive surgeries procedures.

METHODS

An epoxy matrix containing both dansyl chloride and indocyanine green was coated as visible and near infrared labels, respectively. With ultraviolet excitation, dansyl chloride emits green fluorescence and with NIR excitation, the ICG dye emits radiation observable with specialized near infrared capable laparoscopes. To evaluate the coatings, open and laproscopic surgeries were simulated in rabbits. Surgeons blinded to the type of needles (coated or non-coated) were timed while finding needles in standard conditions and with the use of the adjunct coatings. Control needles not located within 300 seconds were researched with the corresponding near infrared or ultraviolet light. Localization time was evaluated for statistical significance, P < .05.

RESULTS

All dual dye coated needles searched utilizing the near infrared camera (n = 26) or ultraviolet light (n= 26) were located within 300 seconds. Conversely, 9 needles in both control settings (no dye usage) were not located within 300 seconds. Mean time to locate control needles in open surgery and laparoscopic surgery was statistically 2-3× greater than time to localization with the use of dye as an adjunct (P = .0027 open, P < .001 laparoscopic).

CONCLUSION

Incorporation of a dual-dye fluorescent coating on surgical needles improved the efficiency of locating needles, may minimize the need to convert minimally invasive surgeries procedures to open, and may decrease the consequences of a missed RFO.

[Determination of 8 bisphenols in human breast milk by dansyl chloride derivatization-ultra performance liquid chromatography-tandem mass spectrometry]

OBJECTIVE

To establish a rapid and sensitive method for the analysis of eight bisphenols in breast milk using small amount of samples.

METHODS

Breast milk samples were extracted by acetonitrile and the lipid substances were removed by freezing under-20 ℃ condition. Then the samples were derivatized with dansyl chloride and analyzed by ultra-performance liquid chromatography-tandem mass spectrometry( UPLCMS/MS). The seperation was performed on an ACQUITY UPLC BEH Phenyl column( 2. 1 mm × 100 mm, 1. 7 μm) with methanol and 0. 1% formic acid in water as mobile phase. The electrospray source was in the positive ion mode and monitored in the multiple reactions monitoring mode. Isotope internal standard dilution technique was used for the quantification analysis. At last, the methodology was studied.

RESULTS

The linear range of 8 bisphenols was 0. 010-10. 00 μg/L. The recoveries of the three spiked levels were84. 6%-108. 1%, with the relative standard deviations no more than 12%( n = 6). 30 samples of breast milk were analyzed, in which BPA was detected in 11 breast milk samples, and the concentrations ranged from 0. 13 μg/L to 2. 25 μg/L. BPAF was detected in 1 breast milk sample, and the concentration was 0. 02 μg/L.

CONCLUSION

The established method using a small amount of breast milk is highly sensitive, simple and fast, and can be used for the simultaneous determination of 8 bisphenols in breast milk.

[Simultaneous determination of salidroside and tyrosol in Beagle dog plasma using UHPLC-MS/MS after pre-column dansyl chloride derivatization]

A pre-column derivatization method combined with UHPLC-MS/MS was developed for the simultaneous determination of salidroside and tyrosol in Beagle dog plasma. After protein precipitation by acetonitrile, the liquid supernatant was treated with dansyl chloride under dark conditions at 60 ℃ for 30 min, and then, the sample solution was extracted using methyl tertiary butyl ether. The multiple reaction monitoring in positive ion mode was used for MS detection of the tested analytes with the specific ion transitions of m/z 534.2→372.0 for salidroside derivative, m/z 372.0→171.0 for tyrosol derivative and m/z 506.0→171.0 for arbutin derivative. The chromatograph separation was achieved on an ACQUITY UPLC® BEH C18 column (100 mm × 2.1 mm, 1.7 μm) with a gradient mobile phase consisting of acetonitrile (0.1% formic acid)-water (10% acetonitrile, 0.1% formic acid) for 9 min. The assay showed a good linearity over the range of 0.02/0.1 − 20/10 μmol·L−1 with a lower limit of quantitation of 0.02 and 0.1 μmol·L−1 for salidroside and tyrosol in dog plasma, respectively. The intra- and inter-day precisions were all less than 8.68%, and the accuracy was within ±11.4%. The established method with a high sensitivity, good specificity and reliability was appropriate for simultaneous determination of salidroside and tyrosol in dog plasma and successfully applied to a pharmacokinetic study after intragastric administration of salidroside to Beagle dogs.

Staining of Lipid Droplets with Monodansylpentane

Monodansylpentane (MDH) is a fluorophore that displays selective labeling of lipid droplets (LDs). The dye preferentially segregates into the neutral lipid cores of LDs and emits blue fluorescence, compatible with the simultaneous use of green and red fluorescent reporters in multi-color live-cell imaging. MDH can be used for visualizing LDs not only in cell cultures, but also in fixed tissues such as the fat body and ovaries from Drosophila. MDH is therefore a versatile marker for LDs in fluorescence microscopy.

Sulfation of Lower Chlorinated Polychlorinated Biphenyls Increases Their Affinity for the Major Drug-Binding Sites of Human Serum Albumin

The disposition of toxicants is often affected by their binding to serum proteins, of which the most abundant in humans is serum albumin (HSA). There is increasing interest in the toxicities of environmentally persistent polychlorinated biphenyls (PCBs) with lower numbers of chlorine atoms (LC-PCBs) due to their presence in both indoor and outdoor air. PCB sulfates derived from metabolic hydroxylation and sulfation of LC-PCBs have been implicated in endocrine disruption due to high affinity-binding to the thyroxine-carrying protein, transthyretin. Interactions of these sulfated metabolites of LC-PCBs with HSA, however, have not been previously explored. We have now determined the relative HSA-binding affinities for a group of LC-PCBs and their hydroxylated and sulfated derivatives by selective displacement of the fluorescent probes 5-dimethylamino-1-naphthalenesulfonamide and dansyl-l-proline from the two major drug-binding sites on HSA (previously designated as Site I and Site II). Values for half-maximal displacement of the probes indicated that the relative binding affinities were generally PCB sulfate ≥ OH-PCB > PCB, although this affinity was site- and congener-selective. Moreover, specificity for Site II increased as the numbers of chlorine atoms increased. Thus, hydroxylation and sulfation of LC-PCBs result in selective interactions with HSA which may affect their overall retention and toxicity.

Determination and characterization of oxy-naphthenic acids in oilfield wastewater

Oxy-naphthenic acids (oxy-NAs) are one of the major components of NA mixtures in wastewaters from petroleum industries. The limited available data indicated that oxy-NAs were considered as a potential marker for the degradation of NAs, and some oxy-NAs exhibited endocrine disrupting activities. However, the lack of information on the structures and occurrences of oxy-NAs in oilfield wastewaters limited the interpretations of the biotransformation pathways of NAs and structure-specific toxicity. A sensitive method for simultaneous determination of oxy-NAs together with NAs was developed by combining MAX extraction column and UPLC-ESI(-)-QTOF-MS. The 2000-fold SPE preconcentration step was highly specific for acids and the prewash solvent greatly reduced matrix effects in the UPLC-ESI(-)-QTOF-MS analysis, resulting in an increase in sensitivity down to detection limits in the ng/L range. To provide structural information within each oxy-NA isomer class, a new method was developed by derivatizing oxy-NAs with dansyl chloride by UPLC-ESI(+)-QTOF-MS. The molecular ion dansyl derivatives from the corresponding oxy-NAs and characteristic fragmentation ions, not detected before derivatization, were observed in the extracts of oilfield wastewater, providing evidence that O3-NAs and O4-NAs were mainly composed of OH-NAs and (OH)2-NAs, respectively. Semiquantification of oxy-NAs and NAs in various oilfield wastewaters revealed NAs, O3-NAs, and O4-NAs present at concentrations of 187-397, 44-146, and 40-108 μg/L, respectively. Significantly different profiles of NA mixtures were observed in petroleum refinery wastewater and oil sands extraction water, but the profile of oxy-NAs was similar to NAs in different wastewaters suggesting the existence of biotransformation between NAs and oxy-NAs in the environment, and hydroxylation could be one of the major biotransformation pathways of NAs.

[Detection of monoamine neurotransmitters and its metabolites by high performance liquid chromatograph after pre-column derivatization of dansyl chloride column]

OBJECTIVE

To develop a high performance liquid chromatography (HPLC) for detection of monoamine neurotransmitters and its metabolites after pre-column derivatization with dansyl chloride.

METHODS

The C(18) chromatograph column (150 mm×4.6 mm×5 µm) was selected for detection, and derived by dansyl chloride (10 mg/ml) under the condition of 50°C water bath by pH11 buffer solution. 20 µl acetic acid acetone solution (1.0 mol/L) was then mixed in for termination of the reaction. Then the solution was cooling to room temperature, 0.1 mol/L acetic acid zinc-acetonitrile-tetrahydrofuran solution was adopted for mobile phrase, with the volume ratio at 62:35:3. The flow rate was 1.0 ml/min between 0-10 min, 2.0 ml/min between 10-35 min. The ultraviolet detection wavelength was 286 nm. The above method separately detected monoamine neurotransmitters and its metabolites and evaluated the limit of detection, accurate degree and accuracy degree.

RESULTS

The linear relations between each component was good in the range of 1 - 20 µg/ml (r = 0.999). The lowest detection limit of norepinephrine, dopamine, 5-hydroxytryptamine and the metabolites 3-methoxy-4-benzoglycols, homovanillic acid and 5-heteroauxin were separately 0.60, 0.80, 0.41, 0.21, 0.19 and 0.1 µg/ml; while the average recovery rates were between 78.5% - 95.9%, and the relative standard deviation (RSD) was 6.62%, 7.64%, 2.98%, 3.60%, 5.09% and 3.09%, respectively. In the process of selection and optimization of the chromatographic conditions, we observed the importance of metal ions to discretion, and discussed the temperature, pH of the buffer solution and dosage of dansyl chloride in derivation. Under the above conditions, the reaction was perfect, and the baseline of the detected materials thoroughly separated.

CONCLUSION

The method to detect monoamine neurotransmitters and its metabolites by HPLC and pre-column derivatization with dansyl chloride was established; and this method could provide reference for the detection of polyamine by HPLC.

Qualitative metabolome analysis of human cerebrospinal fluid by 13C-/12C-isotope dansylation labeling combined with liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry

Metabolome analysis of human cerebrospinal fluid (CSF) is challenging because of low abundance of metabolites present in a small volume of sample. We describe and apply a sensitive isotope labeling LC-MS technique for qualitative analysis of the CSF metabolome. After a CSF sample is divided into two aliquots, they are labeled by (13)C-dansyl and (12)C-dansyl chloride, respectively. The differentially labeled aliquots are then mixed and subjected to LC-MS using Fourier-transform ion cyclotron resonance mass spectrometry (FTICR MS). Dansylation offers significant improvement in the performance of chromatography separation and detection sensitivity. Moreover, peaks detected in the mass spectra can be readily analyzed for ion pair recognition and database search based on accurate mass and/or retention time information. It is shown that about 14,000 features can be detected in a 25-min LC-FTICR MS run of a dansyl-labeled CSF sample, from which about 500 metabolites can be profiled. Results from four CSF samples are compared to gauge the detectability of metabolites by this method. About 261 metabolites are commonly detected in replicate runs of four samples. In total, 1132 unique metabolite ion pairs are detected and 347 pairs (31%) matched with at least one metabolite in the Human Metabolome Database. We also report a dansylation library of 220 standard compounds and, using this library, about 85 metabolites can be positively identified. Among them, 21 metabolites have never been reported to be associated with CSF. These results illustrate that the dansylation LC-FTICR MS method can be used to analyze the CSF metabolome in a more comprehensive manner.

Novel fluorescence molecular imaging of chemotherapy-induced intestinal apoptosis

Chemotherapy-induced enteropathy (CIE) is one of the most serious complications of anticancer therapy, and tools for its early detection and monitoring are highly needed. We report on a novel fluorescence method for detection of CIE, based on molecular imaging of the related apoptotic process. The method comprises systemic intravenous administration of the ApoSense fluorescent biomarker (N,N(')-didansyl-L-cystine DDC) in vivo and subsequent fluorescence imaging of the intestinal mucosa. In the reported proof-of-concept studies, mice were treated with either taxol+cyclophosphamide or doxil. DDC was administered in vivo at various time points after drug administration, and tracer uptake by ileum tissue was subsequently evaluated by ex vivo fluorescent microscopy. Chemotherapy caused marked and selective uptake of DDC in ileal epithelial cells, in correlation with other hallmarks of apoptosis (i.e., DNA fragmentation and Annexin-V binding). Induction of DDC uptake occurred early after chemotherapy, and its temporal profile was parallel to that of the apoptotic process, as assessed histologically. DDC may therefore serve as a useful tool for detection of CIE. Future potential integration of this method with fluorescent endoscopic techniques, or development of radio-labeled derivatives of DDC for emission tomography, may advance early diagnosis and monitoring of this severe adverse effect of chemotherapy.

S-carboxymethylcysteine sulfone: instability to acid hydrolysis and unreactivity with N-terminal reagents

An examination of the properties and reactivity of S-carboxymethylcysteine sulfone indicated that, unlike S-carboxymethylcysteine, the sulfone is not stable under acid hydrolysis conditions and decomposes to yield alanine. Unlike S-carboxymethylcysteine, the sulfone is resistant to N-derivatization by the dansyl reagent or by phenylisothiocyanate. Efforts were made to determine if spontaneous cyclization of the sulfone to the corresponding thiazane (lactam) accounts for lack of reactivity. These included i.r. spectroscopy, natural abundance 13C-n.m.r. spectroscopy and differential scanning calorimetry, but yielded equivocal results concerning the existence of the cyclic form in solution. Solubility behavior of the sulfone after lyophilization from strongly acid solutions was consistent with conversion of the open chain form to the cyclic form on addition of water.

A rapid LC-FTMS method for the analysis of cysteine, cystine and cysteine/cystine steady-state redox potential in human plasma

BACKGROUND

The steady-state redox potential of the cysteine/cystine couple in human plasma provides a measure of oxidative stress, yet available assays are limited by either specificity or speed of assay.

METHOD

The present study evaluated the use of LC-FTMS for identification based on accurate mass combined with quantification by stable isotopic dilution to rapidly determine cysteine and cystine concentration and cysteine/cystine steady-state redox potential in human plasma.

RESULTS

A simple extraction procedure followed by a rapid LC separation eluted cysteine in 4 min and cystine in 1.5 min with simultaneous measurement of glutathione (GSH) and glutathione disulfide (GSSG). A study of five young (mean age=25.7) subjects and 5 older (mean age=67.8 y) subjects showed an increased oxidation with age.

CONCLUSIONS

The analysis by LC-FTMS is suitable for high-throughput analysis of plasma cysteine, cystine and cysteine/cystine steady-state redox potential as clinical measures of oxidative stress.

Transport and hydrolysis of peptides by microorganisms

The structural specificities of the dipeptide and oligopeptide permeases of E. coli are briefly reviewed and related to the requirements found for other microorganisms. New, quick, sensitive methods for studying peptide transport are described, based on the following: (i) peptide-dependent incorporation of free radioactive amino acid into newly synthesized protein by a double amino acid auxotroph, (ii) colorimetric assay of peptide-dependent enzyme synthesis by an amino acid auxotroph, (iii) dansyl fingerprint technique. These approaches provide information on peptide binding affinity to a permease and rates of peptide uptake and amino acid efflux. Among current and future research areas considered are: the influence of the pKb of the N-terminal amino group on transport, generality of peptide transport in microorganisms, energy coupling and regulation, involvement of binding proteins, and the 'smugglin' concept. Peptide hydrolysis, and nutritional ultilization of peptides, by microorganisms are briefly discussed.

High selectivity in new chiral separations of dansyl amino acids by cyclodextrin derivatives in electrokinetic chromatography

Enantiomeric pairs of 11 dansyl derivatives of alpha-amino acids were used as analytes in electrokinetic chromatography to test the ability as chiral selectors of two pure derivatives of beta-cyclodextrin: the ethylendiamine derivative in primary position (CDen) and a member of a new class of receptors, the cysteamine-bridged hemispherodextrin THCMH. The selectivity obtained by the presence of the hemispherodextrin, appears particularly promising as shown by the large values of resolution obtained. The importance of a detailed analysis of these data is discussed in terms of suggestions for a rational approach to separation science.

Novel molecular imaging of cell death in experimental cerebral stroke

Cell death is the basic neuropathological substrate in cerebral ischemia, and its non-invasive imaging may improve diagnosis and treatment for stroke patients. ApoSense is a novel family of low-molecular weight compounds for detection and imaging of cell death in vivo. We now report on imaging of cell death and monitoring of efficacy of neuroprotective treatment in vivo by intravenous administration of the ApoSense compound DDC (didansylcystine), in experimental stroke in rodents. Rats and mice were subjected to a short-term (2 h) or permanent occlusion of the middle cerebral artery (MCA) and injected with DDC or 3H-labeled DDC. Fluorescent and autoradiographic studies, respectively, were performed ex vivo, comprising assessment of DDC uptake in the infarct region, in correlation with tissue histopathology. Neuroprotection was induced by a caspase inhibitor (Q-VD-OPH), and its effect was monitored by DDC. Following its intravenous administration, DDC accumulated selectively in injured neurons within the region of infarct. Caspase inhibition exerted a 45% reduction in infarct volume, which was well reported by DDC. This is the first report on a small molecule probe for detection in vivo of cell death in cerebral stroke. DDC may potentially assist in addressing the current "neuroimaging/neurohistology gap", for molecular assessment of the extent of stroke-related cell death.

Analysis of 3-aminopropionamide: A potential precursor of acrylamide

An analytical method for the analysis of 3-aminopropionamide (3-APA) based on derivatization with dansyl chloride and liquid chromatography/fluorescence detection was developed. We have analysed 3-APA formation in raw potatoes, grown and stored under different condition, green and roasted coffee beans and in freeze dried mixtures of asparagine with sucrose and glucose in molar ratio of 1:0.5, 1:1, and 1:1.5. In potatoes the 3-APA content varied depending on the potato variety. We detected 3-APA in potatoes up to 14 microg/g fresh weight. In the model experiment glucose had a stronger capacity to form 3-APA. The substance was formed at temperatures as low as 130 degrees C. However, in the model experiment with sucrose 3-APA was formed not below 150 degrees C. In heated mixtures with increasing molar ratio of sucrose at 170 degrees C we noticed a decrease of 3-APA and in the same mixtures at 150 degrees C we observed an increase of 3-APA. In coffee 3-APA was not formed, neither in green nor in roasted beans.

Identification of elastic fibers and lamellae in porcine pericardium and aorta by confocal, fluorescence and polarized light microscopy

Pericardial connective tissue has been used to construct bioprostheses to repair various types of injuries, including aortic wall repairs. The arrangement and the distribution of elastic and collagen staple fibers are related directly to the biomechanical properties of the tissue and thus determine the choice tissue for the construction of bioprostheses. Although elastic fibers can be visualized using several histochemical methods, the specificity and mechanism of binding involved remain to be clarified. In this work, we compared the elastic net of the porcine pericardial matrix with that of the aortic wall using 1-anilino-8-naphthalene sulfonate (ANS) and dansyl chloride (DCl) as fluorescent probes and the permanganate-bisulfite-toluidine (PBT) method. Polarized light and fluorescence microscopy were simultaneously used to analyze the tissues. Some samples also were examined using confocal microscopy. Aorta and pericardium treated with ANS and DCl showed elastic fibers and lamellae with an intense blue fluorescence. When stained with the PBT method, the aortic elastic lamellae were clearly metachromatic and, under polarized light, they showed a greenish birefringence. DCl provided clearer fluorescent labelling of elastic fibers when examined using confocal microscopy.

An alternative approach to amyloid fibrils morphology: CdSe/ZnS quantum dots labelled beta-amyloid peptide fragments Abeta (31-35), Abeta (1-40) and Abeta (1-42)

Abeta (31-35) peptide and control peptides as well as full length Abeta (1-40) and Abeta (1-42) peptides were labelled with luminescent CdSe/ZnS quantum dots (QDs) to observe the morphology of amyloid fibers. A comparison was made between QDs and an organic dye, namely Dansyl group, which showed that the QDs present a much better contrast for imaging than the organic dye.

A single lysyl residue defines the binding specificity of a human odorant-binding protein for aldehydes

Odorant-binding proteins (OBPs) are small abundant soluble proteins belonging to the lipocalin superfamily, which are thought to carry hydrophobic odorants through aqueous mucus towards olfactory receptors. Human variant hOBP-2A has been demonstrated to bind numerous odorants of different chemical classes with a higher affinity for aldehydes and fatty acids. Three lysyl residues of the binding pocket (Lys62, Lys82 and Lys112) have been suggested as candidates for playing such a role. Here, using site-directed mutagenesis and fluorescent probe displacements, we show that Lys112 is the major determinant for governing hOBP-2A specificity towards aldehydes and small carboxylic acids.

Type and location of fluorescent probes incorporated into the potent mu-opioid peptide [Dmt1]DALDA affect potency, receptor selectivity and intrinsic efficacy*

The dermorphin-derived tetrapeptide H-Dmt-d-Arg-Phe-Lys-NH(2) (Dmt = 2',6'-dimethyltyrosine) ([Dmt(1)]DALDA) is a highly potent and selective mu-opioid agonist capable of crossing the blood-brain barrier and producing a potent, centrally mediated analgesic effect when given systemically. For the purpose of biodistribution studies by fluorescence techniques, [Dmt(1)]DALDA analogues containing various fluorescent labels [dansyl, anthraniloyl (atn), fluorescein, or 6-dimethylamino-2'-naphthoyl] in several different locations of the peptide were synthesized and characterized in vitro in the guinea-pig ileum and mouse vas deferens assays, and in mu-, delta- and kappa-opioid receptor-binding assays. The analogues showed various degrees of mu receptor-binding selectivity, but all of them were less mu-selective than the [Dmt(1)]DALDA parent peptide. Most analogues retained potent, full mu-agonist activity, except for one with fluorescein attached at the C-terminus (3a) (partial mu-agonist) and one containing beta-(6'-dimethylamino-2'-naphthoyl)alanine (aladan) in place of Phe(3) (4) (mu- and kappa-antagonist). The obtained data indicate that the receptor-binding affinity, receptor selectivity and intrinsic efficacy of the prepared analogues vary very significantly, depending on the type of fluorescent label used and on its location in the peptide. The results suggest that the biological activity profile of fluorescence-labeled peptide analogues should always be carefully determined prior to their use in biodistribution studies or other studies. One of the analogues containing the atn group (2a) proved highly useful in a study of cellular uptake and intracellular distribution by confocal laser scanning microscopy.

Abnormal cardiac wall motion and early matrix metalloproteinase activity

Activation of matrix metalloproteinases (MMPs) in the heart is known to facilitate cardiac remodeling and progression to failure. We hypothesized that regional dyskinetic wall motion of the left ventricle would stimulate activation of MMPs. Abnormal wall motion at a target site on the anterior lateral wall of the left ventricle was induced by pacing atrial and ventricular sites of five open-chest anesthetized dogs. Changes in shortening at the left ventricular (LV) pacing site and at a remote site at the anterior base of the left ventricle were monitored with piezoelectric crystals. Simultaneous atrial and ventricular pacing resulted in abnormal motion at the LV pacing site, yielding early shortening and late systolic lengthening, whereas the shortening pattern at the remote site remained unaffected. Assessment of global myocardial MMP activity showed a sevenfold increase in substrate cleavage ( P < 0.02) at the LV pacing site relative to the remote site. Gelatin zymography revealed increases in 92-kDa MMP-9 activity and 86-kDa MMP-9 activity at the LV pacing site relative to the remote site, whereas MMP-2 activity was unaffected. Abnormal wall motion was associated with increases in collagen degradation (∼2-fold; P < 0.03), plasmin activity (∼1.5-fold; P < 0.05), nitrotyrosine levels (∼20-fold; P = 0.05), and inflammatory infiltrate (∼2-fold; P < 0.02) relative to the remote site. Results indicate that regional dyskinesis induced by epicardial activation is sufficient to stimulate significant MMP activity in the heart, suggesting that abnormal wall motion is a stimulus for MMP activation.

Subsecond chiral separations on a microchip

Fast chiral separation of DNS-amino acids could be realized using microchip electrophoresis with fluorescence detection. For this purpose, highly sulfated cyclodextrins (HS-gamma-CD) were used as chiral selectors enabling high selectivity. Even subsecond separation of DNS-tryptophan, DNS-norleucine, DNS-phenylalanine, DNS-methionine, and DNS-aspartic acid could be achieved. Baseline separation could be accomplished within 720 ms, which is the fastest separation of enantiomers reported to date. A more complex mixture consisting of three chiral DNS-amino acids could be separated within 3.3 s utilizing a separation length of only 7 mm and an electrical field strength of 2012 V/cm.

Assay of plasma semicarbazide-sensitive amine oxidase and determination of its endogenous substrate methylamine by liquid chromatography

Semicarbazide-sensitive amine oxidase (SSAO) is present in plasma, as well as in other tissues. Previous studies indicated that SSAO is of important physiological and pathophysiological functions. HPLC methods were developed for the assay of SSAO in plasma, and for the determination of plasma methylamine, an SSAO's endogenous substrate. Benzylamine was used as artificial substrate for the enzyme activity assay of SSAO. A 0.2-ml aliquot of plasma was incubated with benzylamine at 37 degrees C for 30min. Benzaldehyde, the enzymatic reaction product, was derivatized with 2,4-dinitrophenylhydrazine (DNPH), and analyzed with HPLC and UV detection. SSAO enzyme activity is defined as benzaldehyde (nmol) formed per ml plasma per hour. Recoveries of benzaldehyde spiked to plasma were between 63.5 and 68.2% with relative standard deviation less than 3%. To determine methylamine in plasma, a 0.1-ml aliquot of plasma was deproteinized by trichloroacetic acid and centrifugation. The supernatant was derivatized with dansyl chloride and analyzed by HPLC with fluorescence detection. Recoveries of spiked methylamine at ppb (ng/ml) level were between 93.7 and 97.6% with relative standard deviation less than 2.5%.

Free and conjugated biogenic amines in green and roasted coffee beans

This work reports the composition of arabica and robusta coffees in terms of biogenic amines. The analyses were conducted before and after acid hydrolysis with the aim of the determining both free and conjugated forms in green and roasted coffee beans. The amines (putrescine, cadaverine, serotonin, tyramine, spermidine, and spermine) were determined by reverse-phase high-performance liquid chromatography (RP-HPLC) after derivatization with dansyl chloride. Multivariate analyses were applied in order to evaluate the possible use of these amines as chemical descriptors for arabica and robusta coffees. It was found that putrescine, the main biogenic amine present in the green beans, could be used in the discrimination of the referred species. There is also some evidence that these compounds can be used for discrimination between green coffees subjected to different postharvest processes and that tyramine can be considered a chemical marker for Angolan robustas. The variations in biogenic amine levels after roasts is also discussed, but the statistical significance for species discrimination is reduced.

Allosteric Modification of Factor XIa Functional Activity upon Binding to Polyanions

The effects of several polyanions on the hydrolysis of the chromogenic substrate L-pyroglutamyl-L-prolyl-L-arginyl-p-nitroaniline (S-2366) and on the activation of factor IX by factor XIa have been investigated. Two forms of dextran sulfate (M(r) approximately 500000 and M(r) approximately 10000, DX10) and two forms of heparin (64 disaccharide units, M(r) approximately 14000, and hypersulfated heparin, S-Hep, M(r) approximately 12000) inhibited both factor XIa amidolytic activity and factor IX activation in a concentration-dependent manner. The inhibitory effect was not due to binding of either substrate by the polyanions since only a decrease in V(max) without any effect on K(m) was observed in kinetic assays. Steric inhibition is unlikely since the concentrations of polyanions required for inhibition of small peptide hydrolysis were lower than those required for macromolecular substrate cleavage. In contrast, an allosteric inhibitory mechanism was supported by an enhancement of the dansyl fluorescence of 5-(dimethylamino)-1-(naphthalenesulfonyl)glutamylglycylarginyl- (DEGR-) factor XIa observed when the fluorophore was in complex with either DX10 or S-Hep. Moreover, in the presence of a polyanion the fluorophore was far more resistant to quenching by acrylamide. These results provide compelling evidence that factor XIa binding to the polyanions, dextran sulfate and heparin, results in inhibition of the enzyme by an allosteric mechanism.

Differences between biogenic amine detection by HPLC methods using OPA and dansyl derivates

Biogenic amines can be formed and degraded as a result of normal metabolic activity in animals, plants, and microorganisms and are usually produced by the decarboxylation of amino acids. Recent trends in food security are promoting an increasing search for trace compounds that can affect human health. Although they are present in fermented foods and beverages in low quantities, they exhibit interactions with normal human metabolism (e.g., having vasoactive or psychoactive properties) that justify the research on their presence in foods and the possible related toxicological effects that they may cause. Estimation of the biogenic amines histamine, tyramine, agmatine, putrescine, and cadaverine is important not only from the point of view of their toxicity, but also because they can be used as indicators of the degree of freshness or spoilage of food. Until recently, because of the difficulty in detecting and quantifying amines reliably we have had insufficient information about their occurrence in different types of foods and beverages. These problems are related to matrix interference (e.g., the presence of free amino acids) and the low levels at which the amines are found. Early techniques for the determination of biogenic amines in foods were based on thin-layer chromatography. More modern analytical techniques have since been developed that allow the acquisition of reliable quantitative data and better separation/resolution of various amines. The quantitative determination of biogenic amines is generally accomplished by overpressure-layer chromatography, high-performance liquid chromatography (HPLC), and gas chromatography. The use of reverse-phase column and precolumn derivatization was more efficient and faster than the conventional ion-exchange techniques. This study was conducted to evaluate two HPLC derivatization methods for quantitative determination of biogenic amines: the method described by Gonzales de Llano et al. for amino acid analysis and the method described by Eerola et al.

Interaction of apolipoprotein A-I with lecithin-cholesterol vesicles in the presence of phospholipase C

Here we study the anti-nucleating mechanism of apolipoprotein A-I (apo A-I) on model biliary vesicles in the presence of phospholipase C (PLC) utilizing dynamic light scattering (DLS), steady-state fluorescence spectroscopy, cryogenic transmission electron microscopy (cryo-TEM), and UV/Vis spectroscopy. PLC induces aggregation of cholesterol-free lecithin vesicles from an initial, average size of 100 nm to a maximal size of 600 nm. The presence of apo A-I likely inhibits vesicle aggregation by shielding the PLC-generated hydrophobic moieties, which results in vesicles of an average size of 200 nm. A similar phenomenon is observed in cholesterol-enriched lecithin vesicles. Whereas PLC alone produces aggregates of 300 nm, no aggregation is observed when apo A-I is present along with PLC. However, the ability of apo A-I to inhibit aggregation is temporary, and after 8 h, a broad particle size distribution with sizes as high as 800 nm is observed. Apo A-I possibly induces the formation of small apo A-I/lecithin/cholesterol complexes of about 5-20 nm similar to the discoidal pre-HDL complexes found in blood when it can no longer effectively shield all the DAG molecules. Concomitant with formation of complexes, DAG molecules coalesce into large oil droplets, which account for the large particles observed by light scattering. Thus, apo A-I acts as an anti-nucleating agent by two mechanisms, anti-aggregation and microstructural transition. The mode of protection is dependent on the cholesterol content and the relative amounts of DAG and apo A-I present. This study supports the possibility of apo A-I solubilizing lipids in bile in a similar fashion as it does in blood and also delineates the mechanism of formation of the complexes.

Synthesis and evaluation of peptidomimetics that bind DNA

A peptidomimetic template, consisting of a hydrophobic scaffold, a dansyl fluorophore, and an Arg-His recognition strand, was tested as a simple mimic of zinc finger 2 of the Zif268 protein. Association constants (K(A)'s) were on the order of 10(5) M(-1) for complexes formed between the mimetic and duplexes d(CGGGAATTCCCG)(2) and d(AAAAAAAAATTTTTTTTT)(2). Modest selectivity was observed for the GC-rich DNA in a 0.5M NaCl/buffer (0.1M phosphate, pH 7.0) solution. Differences in K(A)'s along with observed CD profiles suggest that the mimetic associated with the duplexes using different binding modes. The DNA duplexes had weaker interactions with the free Arg-His recognition strand, the dansyl functional group, and a scaffold that contained only glycines as the recognition strand. The scaffold most likely provides for greater van der Waal's interactions, a larger hydrophobic effect upon association, and reduces the freedom of motion of the side chains. This last effect was confirmed by molecular mechanics calculations and by the fact that the mimetic suffered a smaller loss of entropic energy upon association than the free recognition strand. These studies show that the synthetic scaffold is a promising platform in which peptides can be attached to increase their affinity and possibly selectivity for DNA targets.

Interaction of singlet molecular oxygen with double fluorescent and spin sensors

Double fluorescent and spin sensors were recently used to detect transient oxidants via simultaneous fluorescence change and production of the nitroxide radical detected by electron paramagnetic resonance. One such oxidant, singlet molecular oxygen ((1)O(2)), was detected in thylakoid membrane using these probes. In the present study, we investigated the total (physical and chemical) quenching of (1)O(2) phosphorescence by sensors composed of the 2,5-dihydro-2,2,5,5-tetramethyl-1H-pyrrole moiety attached to xanthene or dansyl fluorophores. We found that the quenching rate constants were in the range (2-7) x 10(7) M(-1)s(-1) in acetonitrile and D(2)O. Quenching of (1)O(2) is usually an additive process in which different functional groups may contribute. We estimated that the (1)O(2) quenching by the amine fragments was ca. one to two orders of magnitude lower than that for the complete molecules. Our data suggest that the incorporation of a fluorescent chromophore results in additional strong quenching of (1)O(2), which may in turn decrease the nitroxide yield via the (1)O(2) chemical path, possibly having an effect on quantitative interpretations. We have also found that probes with the dansyl fluorophore photosensitized (1)O(2) upon UV excitation with the quantum yield of 0.087 in acetonitrile at 366 nm. This result shows that care must be taken when the dansyl-based sensors are used in experiments requiring UV irradiation. We hope that our results will contribute to a better characterization and wider use of these novel double sensors.

Effects of water soluble phosphotidylserine on bovine factor Xa: functional and structural changes plus dimerization

Previous work has shown that two molecules of a soluble form of phosphatidylserine, C6PS, bind to human and bovine factor X(a). Activity measurements along with the fluorescence of active-site-labeled human factor X(a) showed that two linked sites specifically regulate the active site conformation and proteolytic activity of the human enzyme. These results imply, but cannot demonstrate, a C6PS-induced factor X(a) conformational change. The purpose of this paper is to extend these observations to bovine factor X(a) and to demonstrate that they do reflect conformational changes. We report that the fluorescence of active-site-labeled bovine factor X(a) also varied with C6PS concentration in a sigmoidal manner, whereas amidolytic activity of unlabeled enzyme varied in a simple hyperbolic fashion, also as seen for human factor X(a). C6PS induced a 70-fold increase in bovine factor X(a)'s autolytic activity, consistent with the 60-fold increase in proteolytic activity reported for human factor X(a). In addition, circular dichroism spectroscopy clearly demonstrated that C6PS binding to bovine factor X(a) induces secondary structural changes. In addition, C6PS binding to the tighter of the two sites triggered structural changes that lead to Ca(2+)-dependent dimer formation, as demonstrated by changes in intrinsic fluorescence and quantitative native gel electrophoresis. Dimerization produced further change in secondary structure, either inter- or intramolecularly. These results, along with results presented previously, support a model in which C6PS binds in a roughly sequential fashion to two linked sites whose occupancy in both human and bovine factor X(a) elicits different structural and functional responses.

Properties of palmitoyl phosphatidylcholine, sphingomyelin, and dihydrosphingomyelin bilayer membranes as reported by different fluorescent reporter molecules

The properties of vesicle membranes prepared from 16:0-SM, 16:0-DHSM, or DPPC were characterized using steady-state and time-resolved fluorescence spectroscopy and different fluorescent reporter molecules. The acyl-chain region was probed using free and phospholipid-bound 1,6-diphenyl-1,3,5-hexatriene. 16:0-DHSM was found to be the more ordered than both DPPC and 16:0-SM 5 degrees C below and above melting temperature. Interfacial properties of the phospholipid bilayers were examined using 6-dodecanoyl-2-dimethyl-aminonaphthalene (Laurdan), 6-propionyl-2-dimethyl-amino-naphthalene (Prodan), and dansyl-PE. Laurdan and Prodan reported that the two sphingomyelin (SM) membrane interfaces were clearly different from the DPPC membrane interface, whereas the two SM membrane interfaces had more similar properties (both in gel and liquid-crystalline phase). Prodan partition studies showed that membrane resistance to Prodan partitioning increased in the order: 16:0-SM < DPPC < 16:0-DHSM. The degree to which dansyl-PE is exposed to water reflects the structural properties of the membrane-water interface. By comparing the lifetime of dansyl-PE in water and deuterium oxide solution, we could show that the degree to which the dansyl moiety was exposed to water in the membranes increased in the order: 16:0-SM < DPPC < 16:0-DHSM. In conclusion, this study has shown that DHSM forms more ordered bilayers than acyl-chain matched SM or phosphatidylcholine, even in the liquid-crystalline state.

A streamlined method for the isolation and quantitation of nanomole levels of exported polyamines in cell culture media

A number of years ago, our laboratory published a method for the isolation of small amounts of polyamines from cell culture media using the ion-exchange resin Bio-Rex 70. We have used this technique extensively to study the export of putrescine and cadaverine from cultured mammalian cells. Unfortunately, this method was highly inefficient in isolating the polyamines spermidine and spermine and was incapable of recovering the acetylated polyamine N(1)-acetylspermidine. In response to these shortcomings, we modified our previous protocol to quantitatively isolate the polyamines N(1)-acetylspermidine, putrescine, cadaverine, N(1)-acetylspermine, spermidine, and spermine. The new method, which is much faster to perform and more efficient than the one previously described, employs the use of disposable minicolumns and a single resin washing step using a weak solution of sodium carbonate at pH 9.3. This new protocol also eliminates the column elution step in favor of directly derivatizing the polyamines with dansyl chloride on the ion-exchange resin. High-performance liquid chromatography analysis of the dansylated polyamines isolated by this procedure showed that 75% of N(1)-acetylspermidine and nearly 100% of the other polyamines present in nanomolar levels were recovered from small amounts of cell culture medium. This new protocol is a valuable new tool for the study of the intracellular/extracellular dynamics of polyamine pools in cultured cells. [A detailed laboratory protocol for this procedure (containing all of the information in this paper but in a condensed form) can be requested by e-mailing the authors.]

Structural effects of cofilin on longitudinal contacts in F-actin

Structural effects of yeast cofilin on skeletal muscle and yeast actin were examined in solution. Cofilin binding to native actin was non-cooperative and saturated at a 1:1 molar ratio, with K(d)<or=0.05 microM for both CaATP-G-actin and F-actin. Cofilin binding enhanced the fluorescence of dansyl ethylenediamine (DED) attached to Gln41 on the DNase I binding loop of skeletal muscle F-actin and decreased the fluorescence of AEDANS at Cys41 on yeast Q41C/C374S mutant F-actin. However, cofilin had no effect on the spectral properties of DED or AEDANS on CaATP-G-actin. Fluorescence energy transfer (FRET) from tryptophan residues to DED at Gln41 on skeletal muscle actin and to AEDANS at Cys41 on yeast Q41C/C374S actin was decreased by cofilin binding to F- but not to G-actin. Cofilin inhibited strongly the rate of interprotomer disulfide cross-linking of Cys41 to Cys374 on yeast Q41C mutant F-actin. Binding of cofilin enhanced excimer formation between pyrene probes attached to Cys41 and Cys374 on Q41C F-actin. These results indicate that cofilin alters the interface between subdomains 1 and 2 and shifts the DNase I binding loop away from subdomain 1 of an adjacent actin protomer. Cofilin reduced FRET from tryptophan residues to 4-azido-2-nitrophenyl-putrescine (ANP) at Gln41 in skeletal muscle F-but not in G-actin. However, following the interprotomer cross-linking of Gln41 to Cys374 in F-actin by ANP, cofilin binding did not change FRET from the tryptophan residues to ANP. This suggests that cofilin binding and the conformational effect on F-actin are not coupled tightly. Overall, this study provides solution evidence for the weakening of longitudinal, subdomain 2/1 contacts in F-actin by cofilin.

High-performance liquid chromatographic determination of biogenic amines in poultry carcasses

Biogenic amines, produced by bacterial decarboxylation of amino acids, have been associated with toxicological symptoms in broilers fed various poultry byproducts. A reversed-phase high-performance liquid chromatographic method is described for the quantitation of eight biogenic amines (tryptamine, phenylethylamine, putrescine, cadaverine, histamine, tyramine, spermidine, and spermine) in chicken carcasses. Amines were extracted with perchloric acid, derivatized with dansyl chloride, separated using gradient elution (methanol and water), and detected by fluorescence. Benzylamine was used as the internal standard. Linearity, repeatability, and recovery of the method were evaluated. The method was linear for all of the amines studied at concentrations ranging from 0.05 to 25 microg/mL. Average recoveries ranged from 92.6% to 96.8% for all amines except for histamine, which was 74.6%.

Early kinetic intermediate in the folding of acyl-CoA binding protein detected by fluorescence labeling and ultrarapid mixing

Early conformational events during folding of acyl-CoA binding protein (ACBP), an 86-residue alpha-helical protein, were explored by using a continuous-flow mixing apparatus with a dead time of 70 micros to measure changes in intrinsic tryptophan fluorescence and tryptophan-dansyl fluorescence energy transfer. Although the folding of ACBP was initially described as a concerted two-state process, the tryptophan fluorescence measurements revealed a previously unresolved phase with a time constant tau = 80 micros, indicating formation of an intermediate with only slightly enhanced fluorescence of Trp-55 and Trp-58 relative to the unfolded state. To amplify this phase, a dansyl fluorophore was introduced at the C terminus by labeling an I86C mutant of ACBP with 5-IAEDANS [5-((((2-iodoacetyl)amino)ethyl)amino)naphthalene-1-sulfonic acid]. Continuous-flow refolding of guanidine HCl-denatured ACBP showed a major increase in tryptophan-dansyl fluorescence energy transfer, indicating formation of a partially collapsed ensemble of states on the 100-micros time scale. A subsequent decrease in dansyl fluorescence is attributed to intramolecular quenching of donor fluorescence on formation of the native state. The kinetic data are fully accounted for by three-state mechanisms with either on- or off-pathway intermediates. The intermediate accumulates to a maximum population of 40%, and its stability depends only weakly on denaturant concentration, which is consistent with a marginally stable ensemble of partially collapsed states with approximately 1/3 of the solvent-accessible surface buried. The findings indicate that ultrafast mixing methods combined with sensitive conformational probes can reveal transient accumulation of intermediate states in proteins with apparent two-state folding mechanisms.

Translocation of protegrin I through phospholipid membranes: role of peptide folding

The protegrin PG-1, belonging to the family of beta-stranded antimicrobial peptides, exerts its activity by forming pores in the target biological membranes. Linear analogues derived from PG-1 do not form pores in the phospholipid membranes and have been used successfully to deliver therapeutic compounds into eucaryotic cells. In this paper, the translocation of PG-1 and of a linear analogue through artificial phospholipid membranes was investigated, leading to a possible mechanism for the activity of these peptidic vectors. We report here that [12W]PG-1, a fluorescent analogue of PG-1, is able to translocate through lipid bilayers and we demonstrate that this property depends on its secondary structure. Our results agree with the recent mechanism proposed for the translocation and permeabilisation activities of several helical and beta-stranded peptides. In addition, our data corroborate recent work suggesting that certain protegrin-derived vectors enter into endothelial cells by adsorptive-mediated endocytosis.

Biological properties of a new fluorescent biphalin fragment analogue

Previous studies of structure-activity of biphalin defined fragments which expressed the full biological potency of the parent compound. The most simple fragment was Tyr-D-Ala-Gly-Phe-NH-NH<--X, where X=Phe, but it also could be other hydrophobic amino acids. This paper presents data that replacement of the phenylalanine with a dansyl (X=DNS) groups gives an analogue (AA2016) that fully preserves the high affinity of the initial analogue for both mu and delta opioid receptors. In the tail flick test in rats, intrathecal injection of the compound produces strong antinociception, comparable to the parent biphalin. Because AA2016 contains a strong fluorescent group, it can be a very useful tool for prospective studies in vivo, including biological barrier permeability, tissue distribution, metabolism and receptor-ligand complex formation.

ATP reorients the neck linker of kinesin in two sequential steps

Recent models of the kinesin mechanochemical cycle provide some conflicting information on how the neck linker contributes to movement. Some spectroscopic approaches suggest a nucleotide-induced order-to-disorder transition in the neck linker. However, cryoelectron microscopic imaging suggests instead that nucleotide alters the orientation of the neck linker when docked on the microtubule surface. Furthermore, since these studies utilized transition state or non-hydrolyzable nucleotide analogs, it is not clear at what point in the ATPase cycle this reorientation of the neck linker occurs. We have addressed this issue by developing a strategy to examine the effect of nucleotide on the orientation of the neck linker based on the technique of fluorescence resonance energy transfer. Transient kinetic studies utilizing this approach support a model in which ATP binding leads to two sequential isomerizations, the second of which reorients the neck linker in relation to the microtubule surface.