This work was supported by National Science Foundation (MCB 1021831, JM) and J. &amp; E. Biomedical Research Program (Florida Department of Health, JM).

1. Sample Preparations
<ol>
	<li>Carry out the sample preparation and all sample manipulations in a dark room to prevent an unwanted uncaging.</li>
	<li>Solubilize DM-nitrophen ((1-(2-nitro-4,5-dimethoxyphenyl)-N,N,N',N'-tetrakis [(oxy-carbonyl) methyl]-1,2-ethanediamine) in 50 mM HEPES buffer, 100 mM KCl, pH 7.0 to a final concentration of 400 &#181;M (&#949;350nm = 4330 M-1cm-1 9).</li>
	<li>Add CaCl2 from the 0.1 M stock solution to achieve a desirable ratio of [Ca2+]:[DM-nitrophen]. For proteins with Kd for Ca2+ association larger than 10 &#181;M, the ratio of [Ca2+]:[DM-nitrophen] of 1:1 is preferable to prevent binding of photo-released Ca2+ to uncaged DM-nitrophen. Indeed, considering the Kd value for DM-nitrophen to be 10 nM and the total concentration of DM-nitrophen and Ca2+ to be 400 mM, ~90% of a calcium binding protein with Kd = 10 &#956;M will be in the apoform. On the other hand, for study of Ca2+ binding to proteins with Kd &#60; 10 &#181;M, it's preferable to decrease the [Ca2+]:[DM-nitrophen] ratio to 0.95 to prevent Ca2+ complexation with the apo-protein prior the cage photo-dissociation.</li>
	<li>Solubilize the reference compound, K3[Fe(III)(CN)6] or Na2CrO4, in the same buffer as for the sample.</li>
</ol>
2. Setting up the Experiment
<ol>
	<li>The basic experimental configuration is shown in Figure 2.</li>
	<li>Use a pin hole (P2) to adjust the diameter of the probe beam (632 nm output of He-Ne laser, ~5 mW laser power) to 1 mm and propagate the probe beam through the center of a cell placed in a temperature controlled cell holder using a M1 mirror.</li>
	<li>Use a mirror (M2) behind the sample to center the probe beam on a center of position sensitive detector.</li>
	<li>Focus the probe beam on the center of the detector in such way that the difference in the voltage between the top two diodes and bottom two diodes as well as the difference in the voltage between the two diodes on the left and right side of the detector is zero.</li>
	<li>Subsequently, shape a diameter of the pump beam, a 355 nm output of Q-switched Nd:YAG laser, FWHM 5 nsec) using a 3 mm pinhole (P1) placed between two 355 nm laser mirrors.</li>
	<li>Copropagate the pump beam through the center of the cuvette as demonstrated in Figure 2. It is important that both laser beams are propagated through the center of the optical cell in nearly colinear manner to obtain a measurable deflection angle and thus high amplitude of PBD signal. Under experimental conditions, the angle of the intersection of the probe and pump beams is less than 15&#176;.</li>
	<li>Use a reference compound to align the probe and pump beam to achieve a satisfactory PBD signal, i.e. a good S/N ratio and stable PBD amplitude on longer time-scales (~100 msec).</li>
	<li>Adjust the position of the pump beam with respect to the probe beam by an incremental adjustment of 355 nm laser mirrors.</li>
	<li>Measure the amplitude of the PBD reference signal as a difference in between two top and bottom photodiodes on the position sensitive detector. The PBD signal should exhibit a rapid increase in the amplitude on a fast time-scale (&#60;10 &#181;sec) and remain stable on 100 msec timescale as demonstrated in Figure 3. The shot to shot variability of the PDB amplitude is within 5% of the signal amplitude and the signal reproducibility is mainly affected by vibrations.</li>
	<li>Check the linearity in the PBD signal amplitude with respect to the released heat energy by measuring the linear dependence of the PBD signal on the excitation laser power and on the number of Einsteins absorbed, Ea = (1-10-A), where A corresponds to the reference absorbance at the excitation wavelength.</li>
	<li>Keep the laser power below approximately 1,000 &#181;J and absorbance of the sample/reference compound at the excitation wavelength less than 0.5 to prevent multiphoton absorption and decrease of the pump beam power, respectively, and ensure linearity of the PBD signal.</li>
</ol>
3. PBD Measurements
<ol>
	<li>Start with the measurement of the PBD traces for the reference. Place the solution of the reference compound in a 1.0 cm x 1.0 cm or 1.0 cm x 0.5 cm quartz cell and position the cell in the temperature controlled holder. Both path lengths provide comparable PBD amplitude.</li>
	<li>Detect the reference PBD signal as a function of temperature in the temperature range from 16-35 &#176;C with the temperature increment of 3 &#176;C.</li>
	<li>Upon each temperature change, check the position of the probe beam on the position sensitive detector and readjust the position to the center of the detector if necessary.</li>
	<li>Check the linearity of the PBD signal as a function of the [(dn/dt)/Cp&#961;] term according to Equation 2.</li>
	<li>Place the sample solution in the same optical cell as for the reference compound keeping the same orientation of the optical cell as for the reference measurement.</li>
	<li>Detect the sample PBD traces in the same temperature range as for the reference and check the linearity of the sample PBD amplitude with respect to the [(dn/dt)/Cp&#961;] term.</li>
</ol>
4. Data Analysis
The magnitude of the deflection is directly proportional to the volume change due to the sample heating (&#916;Vth) and nonthermal volume change (&#916;Vnonth) according to Equation 1: <img src="/files/ftp_upload/50969/50969eq1.jpg" alt="Equation 1" /> 
The amplitude of the sample (AS) and reference (Ar) PBD signal can be described using Equations 2 and 3, respectively.
 <img src="/files/ftp_upload/50969/50969eq2.jpg" alt="Equation 2" /> 
 <img src="/files/ftp_upload/50969/50969eq3.jpg" alt="Equation 3" /> 

PBD signal is directly proportional to the instrument response parameter (K) and the number of Einsteins absorbed (Ea). The first term in Equation 2, (dn/dt)(1/&#961;Cp)Q, corresponds to the signal change due to the heat released to the solvent. The dn/dt term represents the temperature-dependent change in the index of refraction, &#961; is the density of the solvent, Cp is the heat capacity. All parameters are known for the distilled water and can be determined for a buffer solution by comparing a PBD signal for the reference compound in distilled water and in an appropriate buffer. Q is the amount of heat returned to the solvent. The &#961; (dn/d &#961; ) term is a unit-less constant that is temperature-independent in the temperature range from 10-40 &#176;C 10. &#916;nabs term corresponds to the change in the index of refraction due to the presence of absorbing species in the solution and it's negligible if the wavelength of the probe beam is shifted relative to the absorption spectra of any species in the solution. The signal arising from the reference compound (Ar) is expressed by Equation 3 where Eh&#957; is the photon energy at the excitation wavelength, Eh&#957; = 80.5 kcal/mol for 355 nm excitation.
<ol>
	<li>Take the amplitude of the reference PBD signal as the difference between the pretrigger and post trigger PBD signal as demonstrated in Figure 3. In a similar way, determine the amplitude of the fast (Asfast) and slow phase (Asslow) of the sample PBD signal.</li>
	<li>To eliminate the instrument response parameter, K, scale the amplitude of the sample PBD signal by the amplitude of the PBD signal for the reference. The ratio of the sample signal to the reference signal gives Equation 4 and can be written as:
	 <img src="/files/ftp_upload/50969/50969eq4.jpg" alt="Equation 4" /> </li>
	<li>Using this equation, determine the heat released to the solution (Q) and nonthermal volume change (&#916;Vnonth) associated with a photo-initiated reaction from the slope and intercept, respectively, of a plot of [(As/Ar) Eh&#957;] term versus temperature dependent term [(dn/dt)(1/&#961;Cp)].</li>
	<li>To determine the reaction volume and enthalpy change for the fast and the slow process, scale the observed volume and enthalpy change to the appropriate quantum yield according to Equations 5-7.
		 <img src="/files/ftp_upload/50969/50969eq5.jpg" alt="Equation 5" /> 
		 <img src="/files/ftp_upload/50969/50969eq6.jpg" alt="Equation 6" /> 
		 <img src="/files/ftp_upload/50969/50969eq7.jpg" alt="Equation 7" /> 
		 For a multistep process with kinetics occurring on the time-scale between 10 &#181;sec~200 msec, the volume and enthalpy changes associated with the individual steps of the reaction can be determined. The amplitudes and lifetimes for the individual steps are analyzed by fitting the data to the function F(t) that describes the time profile of the volume and enthalpy changes. 
			<img alt="Equation 8" src="/files/ftp_upload/50969/50969eq8.jpg" /> 
		where &#945;0 corresponds to the Asfast and &#945;i corresponds to Asslow for each individual process and &#964; i are the lifetime of the individual reaction steps. From the temperature-dependence of the rate constant for individual processes (ki = 1/&#964;i) the activation enthalpy and entropy parameters can be readily determined using Eyring plots.</li>
</ol>

<ol>
	<li>Gensch, T., Viappiani, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Time-resolved+photothermal+methods:+accessing+time-resolved+thermodynamics+of+photoinduced+processes+in+chemistry+and+biology.">Time-resolved photothermal methods: accessing time-resolved thermodynamics of photoinduced processes in chemistry and biology.</a> Photochem. Photobiol. Sci. 2, 699-721 (2003).</li><li>Larsen, R. W., Mik&#353;ovsk&#225;, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Time+resolved+thermodynamics+of+ligand+binding+to+heme+proteins.">Time resolved thermodynamics of ligand binding to heme proteins.</a> Coord. Chem. Rev. 251 (9-10), 1101-1127 (2007).</li><li>Westrick, J. A., Peters, K. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+photoacoustic+calorimetric+study+of+horse+myoglobin.">A photoacoustic calorimetric study of horse myoglobin.</a> Bioph. Chem. 37 (1-3), 73-79 (1990).</li><li>Belogortseva, N., Rubio, M., Terrell, W., Miksovska, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+contribution+of+heme+propionate+groups+to+the+conformational+dynamics+associated+with+CO+photodissociation+from+horse+heart+myoglobin.">The contribution of heme propionate groups to the conformational dynamics associated with CO photodissociation from horse heart myoglobin.</a> J. Inorg. Biochem. 101 (7), 977-986 (2007).</li><li>Mik&#353;ovsk&#225;, J., Suquet, C., Satterlee, J. D., Larsen, R. 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The authors have nothing to disclose.

The physical principle behind photothermal methods is that a photo-excited molecule dissipates excess energy via vibrational relaxation to the ground state, resulting in thermal heating of the surrounding solvent1,12. For solvents such as water, this produces a rapid volume expansion (&#916;Vth). Excited-state molecules may also undergo photochemical processes that result in nonthermal volume changes (&#916;Vnonth) due to bond cleavage/formation and/or changes in molecular structure that ...

Photo-thermal methods such as photoacoustic calorimetry, photothermal beam deflection (PDB), and transient grating coupled with nanosecond laser excitation represent a powerful alternative to transient optical spectroscopies for time-resolved studies of short-lived intermediates1,2. In contrast to optical techniques, such as transient absorption and IR spectroscopy, that monitor the time profile of absorption changes in the chromophore surrounding; photothermal techniques detect the time-dependence of heat/volume changes and therefore are valuable tools for investigating time profiles of optically "silent" processes. So far, photoacoustic calorimetry and transient grating has been successfully applied to study conformational dynamics of photo-induced processes including diatomic ligand migration in globins3,4, ligand interactions with oxygen sensor protein FixL5, electron and proton transport in heme-copper oxidases6 and photosystem II as well as photo-isomerization in rhodopsin7 and conformational dynamics in cryptochrome8.
To expand the application of photothermal techniques to biological systems that are lacking an internal chromophore and/or fluorophore, the PBD technique was combined with the use of caged compound to photo-trigger an increase in ligand/substrate concentration within few microseconds or faster, depending on the caged compound. This approach allows monitoring of dynamics and energetics of structural changes associated with the ligand/substrate binding to proteins that are lacking an internal fluorophore or chromophore and on time-scale that are not accessible by commercial stop-flow instruments. Here an application of PBD to monitor the thermodynamics of the cage compound, Ca2+DM-nitrophen, photo-cleavage as well as the kinetics for Ca2+ association to the C-terminal domain of the neuronal calcium sensor Downstream Regulatory Element Antagonist Modulator (DREAM) is presented. The Ca2+ is photo-released from Ca2+DM-nitrophen within 10 &#956;sec and rebinds to an unphotolysed cage with a time constant of ~300 &#956;sec. On the other hand, in the presence of apoDREAM an additional kinetic occurring on the millisecond time-scale is observed and reflects the ligand binding to the protein. The application of PBD to probe conformational transitions in biological systems has been somehow limited due the instrumental difficulties; e.g. arduous alignment of the probe and pump beam to achieve a strong and reproducible PBD signal. However, a meticulous design of an instrumentation set-up, a precise control of the temperature, and a careful alignment of the probe and pump beam provide a consistent and robust PBD signal that allows monitoring of time-resolved volume and enthalpy changes on a broad time-scale from 10 &#181;sec to approximately 200 msec. In addition, modifications of the experimental procedure to assure the detection of sample and reference traces under identical temperature, buffer composition, optical cell orientation, laser power,&#160;etc. significantly reduces the experimental error in measured reaction volumes and enthalpies.

<table border="0" cellpadding="0" cellspacing="0" width="639">
	<colgroup>
		<col />
		<col />
		<col /> 
		<col />
	</colgroup>
	<tbody>
		<tr height="84">
			<td height="84" style="height:84px;width:216px;">1-(4,5-Dimethoxy-2-Nitrophenyl)-1,2-Diaminoethane-N,N,N&#39;,N&#39;-Tetraacetic Acid</td>
			<td style="width:84px;">Life Technologies</td>
			<td style="width:119px;">D-6814</td>
			<td style="width:220px;">DM-nitrophen, cage calcium compound, keep stock solutions in dark to prevent photodissociation,</td>
		</tr>
		<tr height="80">
			<td height="80" style="height:80px;width:216px;">4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid, N-(2-Hydroxyethyl)piperazine-N&#8242;-(2-ethanesulfonic acid)</td>
			<td style="width:84px;">Sigma Adrich</td>
			<td>0909C</td>
			<td>HEPES buffer</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Potassium ferricyanide(III)</td>
			<td style="width:84px;">Sigma Aldrich</td>
			<td style="width:119px;">702587</td>
			<td style="width:220px;">reference compound for PBD measurments</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;"> </td>
			<td style="width:84px;"> </td>
			<td style="width:119px;"> </td>
			<td style="width:220px;"> </td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Sodium chromate</td>
			<td style="width:84px;">Sigma Aldrich</td>
			<td style="width:119px;">307831</td>
			<td style="width:220px;">reference compound for PBD measurments</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">He-Ne Laser Diode 5mW 635nm </td>
			<td style="width:84px;">Edmund Optics</td>
			<td style="width:119px;">54-179</td>
			<td style="width:220px;">use as a probe beam for PBD measurments</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">Oscilloscope, </td>
			<td style="width:84px;">LeCroy</td>
			<td style="width:119px;">Wave Surfer 42Xs</td>
			<td style="width:220px;">400 MHz bandwith</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Nd:YAG laser</td>
			<td style="width:84px;">Continuum</td>
			<td style="width:119px;">ML II</td>
			<td>pump beam for PBD measurments</td>
		</tr>
		<tr height="44">
			<td height="44" style="height:44px;width:216px;">M355; Nd:YAG laser mirror</td>
			<td style="width:84px;">Edmund Optics</td>
			<td style="width:119px;">47-324</td>
			<td>laser mirror for 355 nm laser line</td>
		</tr>
		<tr height="44">
			<td height="44" style="height:44px;width:216px;">M1 and M2; Laser diode mirror</td>
			<td style="width:84px;">Edmund Optics</td>
			<td style="width:119px;">43-532</td>
			<td>visilbe laser flat mirror, wavelength range 300-700 nm</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">P1 and P2; Iris Diaphragm</td>
			<td style="width:84px;">Edmind Optics</td>
			<td style="width:119px;">62-649</td>
			<td style="width:220px;">pin hole to shape the probe and pum beams</td>
		</tr>
		<tr height="84">
			<td height="84" style="height:84px;">L1; bi-convex lens</td>
			<td style="width:84px;">Thorlabs</td>
			<td style="width:119px;">LB1844</td>
			<td style="width:220px;">a lens to focus the probe beam at the detector, EFL 50 mm, wavelength range 350 - 2000 nm</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">DM, dichroic mirror</td>
			<td style="width:84px;">Thorlab </td>
			<td style="width:119px;">DMLP505</td>
			<td style="width:220px;">a longpass dichroic mirror with a cutoff wavelength of 505 nm</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">F1; Edge filter</td>
			<td style="width:84px;">Andower </td>
			<td style="width:119px;">500FH90-25</td>
			<td>a long pass filter with a cutoff wavelength of 500 nm</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Temperature-controlled cuvette holder</td>
			<td style="width:84px;">Quantum Northwest</td>
			<td style="width:119px;">FLASH 300</td>
			<td></td>
		</tr>
	</tbody>
</table>

submillisecond conformational changes in proteins resolved by photothermal beam deflection

Photothermal beam deflection together with photo-acoustic calorimetry and thermal grating belongs to the family of photothermal methods that monitor the time-profile volume and enthalpy changes of light induced conformational changes in proteins on microsecond to millisecond time-scales that are not accessible using traditional stop-flow instruments. In addition, since overall changes in volume and/or enthalpy are probed, these techniques can be applied to proteins and other biomacromolecules that lack a fluorophore and or a chromophore label. To monitor dynamics and energetics of structural changes associated with Ca2+ binding to calcium transducers, such neuronal calcium sensors, a caged calcium compound, DM-nitrophen, is employed to photo-trigger a fast (&#964; &#60; 20 &#956;sec) increase in free calcium concentration and the associated volume and enthalpy changes are probed using photothermal beam deflection technique.

A representative example of PBD traces for Ca2+ photo-release from Ca2+DM-nitrophen is shown in Figure 3. The fast phase corresponds to the photo-cleavage of Ca2+DM-nitrophen and Ca2+ liberation, whereas the slow phase reflects Ca2+ binding to the nonphotolysed cage. The plot of the sample PBD amplitude for the fast and slow phase scaled to the amplitude of the reference compound as a function of the temperature depended factor [Cp&#961;/(...

Watch this Scientific Journal Video about Submillisecond Conformational Changes in Proteins Resolved by Photothermal Beam Deflection at JoVE.com

Submillisecond Conformational Changes in Proteins Resolved by Photothermal Beam Deflection

Here we report an application of the photothermal beam deflection technique in combination with a caged calcium compound, DM-nitrophen, to monitor microsecond and millisecond dynamics and energetics of structural changes associated with the calcium association to a neuronal calcium sensor, Downstream Regulatory Element Antagonist Modulator.

Photothermal beam deflection together with photo-acoustic calorimetry and thermal grating belongs to the family of photothermal methods that monitor the ...

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8.9K Views.  Florida International University. Here we report an application of the photothermal beam deflection technique in combination with a caged calcium compound, DM-nitrophen, to monitor microsecond and millisecond dynamics and energetics of structural changes associated with the calcium association to a neuronal calcium sensor, Downstream Regulatory Element Antagonist Modulator. 

Video: Submillisecond Conformational Changes in Proteins Resolved by Photothermal Beam Deflection

Determining the Ice-binding Planes of Antifreeze Proteins by Fluorescence-based Ice Plane Affinity

Antifreeze proteins (AFPs) are expressed in a variety of cold-hardy organisms to prevent or slow internal ice growth. AFPs bind to specific planes of ice through their ice-binding surfaces. Fluorescence-based ice plane affinity (FIPA) analysis is a modified technique used to determine the ice planes to which the AFPs bind. FIPA is based on the original ice-etching method for determining AFP-bound ice-planes. It produces clearer images in a shortened experimental time. In FIPA analysis, AFPs are fluorescently labeled with a chimeric tag or a covalent dye then slowly incorporated into a macroscopic single ice crystal, which has been preformed into a hemisphere and oriented to determine the a- and c-axes. The AFP-bound ice hemisphere is imaged under UV light to visualize AFP-bound planes using filters to block out nonspecific light. Fluorescent labeling of the AFPs allows real-time monitoring of AFP adsorption into ice. The labels have been found not to influence the planes to which AFPs bind. FIPA analysis also introduces the option to bind more than one differently tagged AFP on the same single ice crystal to help differentiate their binding planes. These applications of FIPA are helping to advance our understanding of how AFPs bind to ice to halt its growth and why many AFP-producing organisms express multiple AFP isoforms.

Antifreeze proteins (AFPs) bind to specific planes of ice to prevent or slow ice growth. Fluorescence-based ice plane affinity (FIPA) analysis is a modification of the original ice-etching method for determination of AFP-bound ice planes. AFPs are fluorescently labeled, incorporated into macroscopic single ice crystals, and visualized under UV light.

Antifreeze proteins (AFPs) are expressed in a variety of cold-hardy organisms to prevent or slow internal ice growth. AFPs bind to specific planes of ice ...

The Use of Gas Chromatography to Analyze Compositional Changes of Fatty Acids in Rat Liver Tissue during Pregnancy

Gas chromatography (GC) is a highly sensitive method used to identify and quantify the fatty acid content of lipids from tissues, cells, and plasma/serum, yielding results with high accuracy and high reproducibility. In metabolic and nutrition studies GC allows assessment of changes in fatty acid concentrations following interventions or during changes in physiological state such as pregnancy. Solid phase extraction (SPE) using aminopropyl silica cartridges allows separation of the major lipid classes including triacylglycerols, different phospholipids, and cholesteryl esters (CE). GC combined with SPE was used to analyze the changes in fatty acid composition of the CE fraction in the livers of virgin and pregnant rats that had been fed various high and low fat diets. There are significant diet/pregnancy interaction effects upon the omega-3 and omega-6 fatty acid content of liver CE, indicating that pregnant females have a different response to dietary manipulation than is seen among virgin females.

Pregnancy leads to significant changes to the fatty acid composition of maternal tissues. Lipid profiles can be obtained via gas chromatography to allow identification and quantification of fatty acids in individual lipid classes among rats fed various high and low fat diets during pregnancy.

Gas chromatography (GC) is a highly sensitive method used to identify and quantify the fatty acid content of lipids from tissues, cells, and plasma/serum, ...

Radiolabeling and Quantification of Cellular Levels of Phosphoinositides by High Performance Liquid Chromatography-coupled Flow Scintillation

Phosphoinositides (PtdInsPs) are essential signaling lipids responsible for recruiting specific effectors and conferring organelles with molecular identity and function. Each of the seven PtdInsPs varies in their distribution and abundance, which are tightly regulated by specific kinases and phosphatases. The abundance of PtdInsPs can change abruptly in response to various signaling events or disturbance of the regulatory machinery. To understand how these events lead to changes in the amount of PtdInsPs and their resulting impact, it is important to quantify PtdInsP levels before and after a signaling event or between control and abnormal conditions. However, due to their low abundance and similarity, quantifying the relative amounts of each PtdInsP can be challenging. This article describes a method for quantifying PtdInsP levels by metabolically labeling cells with 3H-myo-inositol, which is incorporated into PtdInsPs. Phospholipids are then precipitated and deacylated. The resulting soluble 3H-glycero-inositides are further extracted, separated by high-performance liquid chromatography (HPLC), and detected by flow scintillation. The labeling and processing of yeast samples is described in detail, as well as the instrumental setup for the HPLC and flow scintillator. Despite losing structural information regarding acyl chain content, this method is sensitive and can be optimized to concurrently quantify all seven PtdInsPs in cells.

Phosphoinositides are signaling lipids whose relative abundance rapidly changes in response to various stimuli. This article describes a method to measure the abundance of phosphoinositides by metabolically labeling cells with 3H-myo-inositol, followed by extraction and deacylation. Extracted glycero-inositides are then separated by high-performance liquid chromatography and quantified by flow scintillation.

Phosphoinositides (PtdInsPs) are essential signaling lipids responsible for recruiting specific effectors and conferring organelles with molecular ...

In Situ Characterization of Hydrated Proteins in Water by SALVI and ToF-SIMS

This work demonstrates in situ characterization of protein biomolecules in the aqueous solution using the System for Analysis at the Liquid Vacuum Interface (SALVI) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). The fibronectin protein film was immobilized on the silicon nitride (SiN) membrane that forms the SALVI detection area. During ToF-SIMS analysis, three modes of analysis were conducted including high spatial resolution mass spectrometry, two-dimensional (2D) imaging, and depth profiling. Mass spectra were acquired in both positive and negative modes. Deionized water was also analyzed as a reference sample. Our results show that the fibronectin film in water has more distinct and stronger water cluster peaks compared to water alone. Characteristic peaks of amino acid fragments are also observable in the hydrated protein ToF-SIMS spectra. These results illustrate that protein molecule adsorption on a surface can be studied dynamically using SALVI and ToF-SIMS in the liquid environment for the first time.

In Situ Characterization of Hydrated Proteins in Water by SALVI and ToF-SIMS

This work presents a protocol for liquid handling and sample introduction to a microchannel for in situ time-of-flight secondary ion mass spectrometry analysis of protein biomolecules in an aqueous solution.

This work demonstrates in situ characterization of protein biomolecules in the aqueous solution using the System for Analysis at the Liquid Vacuum ...

An HS-MRM Assay for the Quantification of Host-cell Proteins in Protein Biopharmaceuticals by Liquid Chromatography Ion Mobility QTOF Mass Spectrometry

The analysis of low-level (1-100 ppm) protein impurities (e.g., host-cell proteins (HCPs)) in protein biotherapeutics is a challenging assay requiring high sensitivity and a wide dynamic range. Mass spectrometry-based quantification assays for proteins typically involve protein digestion followed by the selective reaction monitoring/multiple reaction monitoring (SRM/MRM) quantification of peptides using a low-resolution (Rs ~1,000) tandem quadrupole mass spectrometer. One of the limitations of this approach is the interference phenomenon observed when the peptide of interest has the "same" precursor and fragment mass (in terms of m/z values) as other co-eluting peptides present in the sample (within a 1-Da window). To avoid this phenomenon, we propose an alternative mass spectrometric approach, a high selectivity (HS) MRM assay that combines the ion mobility separation of peptide precursors with the high-resolution (Rs ~30,000) MS detection of peptide fragments. We explored the capabilities of this approach to quantify low-abundance peptide standards spiked in a monoclonal antibody (mAb) digest and demonstrated that it has the sensitivity and dynamic range (at least 3 orders of magnitude) typically achieved in HCP analysis. All six peptide standards were detected at concentrations as low as 0.1 nM (1 femtomole loaded on a 2.1-mm ID chromatographic column) in the presence of a high-abundance peptide background (2 &#181;g of a mAb digest loaded on-column). When considering the MW of rabbit phosphorylase (97.2 kDa), from which the spiked peptides were derived, the LOQ of this assay is lower than 50 ppm. Relative standard deviations (RSD) of peak areas (n = 4 replicates) were less than 15% across the entire concentration range investigated (0.1-100 nM or 1-1,000 ppm) in this study.

Here, we describe a chromatographic assay coupled with the ion mobility separation of peptide precursors followed by the high-resolution (~30,000) MS-detection of peptide fragments for the quantification of spiked peptide standards in a monoclonal antibody digest.

The analysis of low-level (1-100 ppm) protein impurities (e.g., host-cell proteins (HCPs)) in protein biotherapeutics is a challenging assay requiring ...

Time-resolved Photophysical Characterization of Triplet-harvesting Organic Compounds at an Oxygen-free Environment Using an iCCD Camera

Here, we present a sensible method of the acquisition and analysis of time-resolved photoluminescence using an ultrafast iCCD camera. This system enables the acquisition of photoluminescence spectra covering the time regime from nanoseconds up to 0.1 s. This enables us to follow the changes in the intensity (decay) and emission of the spectra over time. Using this method, it is possible to study diverse photophysical phenomena, such as the emission of phosphorescence, and the contributions of prompt and delayed fluorescence in molecules showing thermally activated delayed fluorescence (TADF). Remarkably, all spectra and decays are obtained in a single experiment. This can be done for solids (thin film, powder, crystal) and liquid samples, where the only limitations are the spectral sensitivity of the camera and the excitation wavelength (532 nm, 355 nm, 337 nm, and 266 nm). This technique is, thus, very important when investigating the excited state dynamics in organic emitters for their application in organic light-emitting diodes and other areas where triplet harvesting is of paramount importance. Since triplet states are strongly quenched by oxygen, emitters with efficient TADF luminescence, or those showing room temperature phosphorescence (RTP), must be correctly prepared in order to remove any dissolved oxygen from solutions and films. Otherwise, no long-lived emission will be observed. The method of degassing solid samples as presented in this work is basic and simple, but the degassing of liquid samples creates additional difficulties and is particularly interesting. A method of minimizing solvent loss and changing the sample concentration, while still enabling to remove oxygen in a very efficient and a repeatable manner, is presented in this work.

Here, we present a method of the spectroscopic characterization of organic molecules by means of time-resolved photoluminescence spectroscopy on the nanosecond-to-millisecond timescale in oxygen-free conditions. Methods to efficiently remove oxygen from the samples and, thus, limit luminescence quenching are also described.

Here, we present a sensible method of the acquisition and analysis of time-resolved photoluminescence using an ultrafast iCCD camera. This system enables ...

DNA-magnetic Particle Binding Analysis by Dynamic and Electrophoretic Light Scattering

Isolation of DNA using magnetic particles is a field of high importance in biotechnology and molecular biology research. This protocol describes the evaluation of DNA-magnetic particles binding via dynamic light scattering (DLS) and electrophoretic light scattering (ELS). Analysis by DLS provides valuable information on the physicochemical properties of particles including particle size, polydispersity, and zeta potential. The latter describes the surface charge of the particle which plays major role in electrostatic binding of materials such as DNA. Here, a comparative analysis exploits three chemical modifications of nanoparticles and microparticles and their effects on DNA binding and elution. Chemical modifications by branched polyethylenimine, tetraethyl orthosilicate and (3-aminopropyl)triethoxysilane are investigated. Since DNA exhibits a negative charge, it is expected that zeta potential of particle surface will decrease upon binding of DNA. Forming of clusters should also affect particle size. In order to investigate the efficiency of these particles in isolation and elution of DNA, the particles are mixed with DNA in low pH (~6), high ionic strength and dehydration environment. Particles are washed on magnet and then DNA is eluted by Tris-HCl buffer (pH = 8). DNA copy number is estimated using quantitative polymerase chain reaction (PCR). Zeta potential, particle size, polydispersity and quantitative PCR data are evaluated and compared. DLS is an insightful and supporting method of analysis that adds a new perspective to the process of screening of particles for DNA isolation.

This protocol describes the synthesis of magnetic particles and evaluation of their DNA-binding properties via dynamic and electrophoretic light scattering. This method focuses on monitoring changes in particle size, their polydispersity and zeta potential of particle surface which play major role in binding of materials such as DNA.

Isolation of DNA using magnetic particles is a field of high importance in biotechnology and molecular biology research. This protocol describes the ...

Co-expression of Multiple Chimeric Fluorescent Fusion Proteins in an Efficient Way in Plants

Information about the spatiotemporal subcellular localization(s) of a protein is critical to understand its physiological functions in cells. Fluorescent proteins and generation of fluorescent fusion proteins have been wildly used as an effective tool to directly visualize the protein localization and dynamics in cells. It is especially useful to compare them with well-known organelle markers after co-expression with the protein of interest. Nevertheless, classical approaches for protein co-expression in plants usually involve multiple independent expression plasmids, and therefore have drawbacks that include low co-expression efficiency, expression-level variation, and high time expenditure in genetic crossing and screening. In this study, we describe a robust and novel method for co-expression of multiple chimeric fluorescent proteins in plants. It overcomes the limitations of the conventional methods by using a single expression vector that is composed of multiple semi-independent expressing cassettes. Each protein expression cassette contains its own functional protein expression elements, and therefore it can be flexibly adjusted to meet diverse expression demand. Also, it is easy and convenient to perform the assembly and manipulation of DNA fragments in the expression plasmid by using an optimized one-step reaction without additional digestion and ligation steps. Furthermore, it is fully compatible with current fluorescent protein derived bio-imaging technologies and applications, such as FRET and BiFC. As a validation of the method, we employed this new system to co-express fluorescently fused vacuolar sorting receptor and secretory carrier membrane proteins. The results show that their perspective subcellular localizations are the same as in previous studies by both transient expression and genetic transformation in plants.

We have developed a novel method for co-expressing multiple chimeric fluorescent fusion proteins in plants to overcome the difficulties of conventional methods. It takes advantage of using a single expression plasmid that contains multiple functionally independent protein expressing cassettes to achieve protein co-expression.

Information about the spatiotemporal subcellular localization(s) of a protein is critical to understand its physiological functions in cells. Fluorescent ...

Photoelectron Imaging of Anions Illustrated by 310 Nm Detachment of F&#8722;

Anion photoelectron imaging is a very efficient method for the study of energy states of bound negative ions, neutral species and interactions of unbound electrons with neutral molecules/atoms. State-of-the-art in vacuo anion generation techniques allow application to a broad range of atomic, molecular, and cluster anion systems. These are separated and selected using time-of-flight mass spectrometry. Electrons are removed by linearly polarized photons (photo detachment) using table-top laser sources which provide ready access to excitation energies from the infra-red to the near ultraviolet. Detecting the photoelectrons with a velocity mapped imaging lens and position sensitive detector means that, in principle, every photoelectron reaches the detector and the detection efficiency is uniform for all kinetic energies. Photoelectron spectra extracted from the images via mathematical reconstruction using an inverse Abel transformation reveal details of the anion internal energy state distribution and the resultant neutral energy states. At low electron kinetic energy, typical resolution is sufficient to reveal energy level differences on the order of a few millielectron-volts, i.e., different vibrational levels for molecular species or spin-orbit splitting in atoms. Photoelectron angular distributions extracted from the inverse Abel transformation represent the signatures of the bound electron orbital, allowing more detailed probing of electronic structure. The spectra and angular distributions also encode details of the interactions between the outgoing electron and the residual neutral species subsequent to excitation. The technique is illustrated by the application to an atomic anion (F&#8722;), but it can also be applied to the measurement of molecular anion spectroscopy, the study of low lying anion resonances (as an alternative to scattering experiments) and femtosecond (fs) time resolved studies of the dynamic evolution of anions.

Photoelectron Imaging of Anions Illustrated by 310 Nm Detachment of F&lt;sup&gt;&amp;#8722;&lt;/sup&gt;

Here, we present a protocol for photoelectron imaging of anionic species. Anions generated in vacuo and separated by mass spectrometry are probed using velocity mapped photoelectron imaging, providing details of anion and neutral energy levels, anion and neutral structure and the nature of the anion electronic state.

Anion photoelectron imaging is a very efficient method for the study of energy states of bound negative ions, neutral species and interactions of unbound ...

Improving High Viscosity Extrusion of Microcrystals for Time-resolved Serial Femtosecond Crystallography at X-ray Lasers

High-viscosity micro-extrusion injectors have dramatically reduced sample consumption in serial femtosecond crystallographic experiments (SFX) at X-ray free electron lasers (XFELs). A series of experiments using the light-driven proton pump bacteriorhodopsin have further established these injectors as a preferred option to deliver crystals for time-resolved serial femtosecond crystallography (TR-SFX) to resolve structural changes of proteins after photoactivation. To obtain multiple structural snapshots of high quality, it is essential to collect large amounts of data and ensure clearance of crystals between every pump laser pulse. Here, we describe in detail how we optimized the extrusion of bacteriorhodopsin microcrystals for our recent TR-SFX experiments at the Linac Coherent Light Source (LCLS). The goal of the method is to optimize extrusion for a stable and continuous flow while maintaining a high density of crystals to increase the rate at which data can be collected in a TR-SFX experiment. We achieve this goal by preparing lipidic cubic phase with a homogenous distribution of crystals using a novel three-way syringe coupling device followed by adjusting the sample composition based on measurements of the extrusion stability taken with a high-speed camera setup. The methodology can be adapted to optimize the flow of other microcrystals. The setup will be available for users of the new Swiss Free Electron Laser facility.

The success of a time-resolved serial femtosecond crystallography experiment is dependent on efficient sample delivery. Here, we describe protocols to optimize the extrusion of bacteriorhodopsin microcrystals from a high viscosity micro-extrusion injector. The methodology relies on sample homogenization with a novel three-way coupler and visualization with a high-speed camera.

High-viscosity micro-extrusion injectors have dramatically reduced sample consumption in serial femtosecond crystallographic experiments (SFX) at X-ray ...