Name: direct-coupled electroretinogram (dc-erg) for recording the light-evoked electrical responses of the mouse retinal pigment epithelium
Uploaded: 2020-07-14T12:30:00
Description: Watch this Scientific Journal Video about Direct-Coupled Electroretinogram DC-ERG for Recording the Light-Evoked Electrical Responses of the Mouse Retinal Pigment Epithelium at JoVE.com

This work was supported by NEI intramural funds. The authors sincerely acknowledge Dr. Sheldon Miller for his scientific guidance, technical advice, and expertise in RPE physiology and disease. The authors thank Megan Kopera and the animal care staff for managing the mouse colonies, and Dr. Tarun Bansal, Raymond Zhou, and Yuan Wang for technical support.

This protocol follows the animal care guidelines outlined in the animal study protocol approved by the Animal Care and Use Committee of the National Eye Institute.
1. Importing light stimulation protocols for DC-ERG
NOTE: Follow the directions below to import the light stimulation protocols for the DC-ERG into the ERG system software (Table of Materials). The protocol consists of a 0.5 min pre-stimulus interval, followed by a step of light (10 cd/m<su...

<ol>
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S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Early+retinal+pigment+epithelium+dysfunction+is+concomitant+with+hyperglycemia+in+mouse+models+of+type+1+and+type+2+diabetes.">Early retinal pigment epithelium dysfunction is concomitant with hyperglycemia in mouse models of type 1 and type 2 diabetes.</a> Journal of Neurophysiology. 113 (4), 1085-1099 (2015).</li><li>Marmorstein, L. Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+light+peak+of+the+electroretinogram+is+dependent+on+voltage-gated+calcium+channels+and+antagonized+by+bestrophin+(best-1).">The light peak of the electroretinogram is dependent on voltage-gated calcium channels and antagonized by bestrophin (best-1).</a> Journal of General Physiology. 127 (5), 577-589 (2006).</li><li>Zhang, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Invest.+Ophtalmol.+Vis.+Sci.">Invest. Ophtalmol. Vis. Sci.</a> Annual Meeting for the Association for Research in Vision and Ophthalmology. , 3568 (2017).</li><li>Iacovelli, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Generation+of+Cre+transgenic+mice+with+postnatal+RPE-specific+ocular+expression.">Generation of Cre transgenic mice with postnatal RPE-specific ocular expression.</a> Investigative Ophthalmology and Visual Science. 52 (3), 1378-1383 (2011).</li><li>Wang, F. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MicroRNA-204/211+alters+epithelial+physiology.">MicroRNA-204/211 alters epithelial physiology.</a> FASEB Journal. 24 (5), 1552-1571 (2010).</li><li>He, L., Marioutina, M., Dunaief, J. L., Marneros, A. 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Critical Steps
A good DC-ERG recording requires stable electrodes that are free from bubbles that create artifacts and unwanted drift as they are extremely sensitive to outgassing and temperature changes. It is essential that a stable baseline is achieved when the electrodes are placed in the HBSS bath solution before proceeding forward with the mouse recording. Small bubbles tend to collect at the base of the capillary electrode or around the silicone gasket and are difficult...

The retinal pigment epithelium (RPE) is a monolayer of specialized cells that line the posterior segment of the eye and exert critical functions to maintain retinal homeostasis1. The RPE supports photoreceptors by regenerating their photon-capturing visual pigment in a process called the visual cycle2, by participating in the diurnal phagocytosis of shed outer segment tips3, and in the transport of nutrients and metabolic products between photoreceptors and the choriocapillaris4,5. Abnormalities in RPE function underlie numerous human retinal diseases, such as age-related macular degeneration6, Leber&#8217;s congenital amaurosis7,8 and Best vitelliform macular dystrophy9. As donor eye tissues are often difficult to obtain solely for research purposes, animal models with genetic modifications can provide an alternative way to study the development of retinal diseases10,11. Additionally, the emergence and application of CRISPR cas9 technology now permits genomic introductions (knock-in) or deletions (knock-out) in a simple, one-step process surpassing limitations of prior gene targeting technologies12. The boom in the availability of new mouse models13 necessitates a more efficient recording protocol to non-invasively evaluate RPE function.
Measurement of the light-evoked electrical responses of the RPE can be achieved using a direct-coupled electroretinogram (DC-ERG) technique. When used in combination with conventional ERG recordings that measure the photoreceptor (a-wave) and bipolar (b-wave) cell responses14, the DC-ERG can define how the response properties of the RPE change with retinal degeneration15,16,17 or whether RPE dysfunction precedes photoreceptor loss. This protocol describes a method adapted from the work of Marmorstein, Peachey, and colleagues who first developed the DC-ERG technique16,18,19,20 and improves upon the reproducibility and ease of use.
The DC-ERG recording is difficult to perform because of the long acquisition time (9 min) during which any interruption or introduction of noise can complicate the interpretation of the data. The advantage of this new method is that the baselines reach steady state within a shorter amount of time reducing the likelihood that the animal will awaken prematurely from anesthesia and is less prone to bubble formation in the capillary electrodes.

<table>
	<tbody>
		<tr>
			<td>Ag/AgCl (mouth) Electrode</td>
			<td>WPI Inc</td>
			<td>EP1</td>
			<td>Mouth reference electrode for mouse</td>
		</tr>
		<tr>
			<td>Ceramic Tile</td>
			<td>Sutter Instrument</td>
			<td>CTS</td>
			<td>Used to cut the glass capillary tube to an appropriate size</td>
		</tr>
		<tr>
			<td>Cotton Tipped Cleaning Stick</td>
			<td>Puritan Medical Products</td>
			<td>867-WC No Glue</td>
			<td>To be used as a spacer to improve the fit of the electrode holder assembly</td>
		</tr>
		<tr>
			<td>Electroretinogram (ERG) System</td>
			<td>Diagnosys LLC</td>
			<td>E3 System</td>
			<td>Visual electrophysiology system to diagnose ophthalmic conditions in vision research and drug trials</td>
		</tr>
		<tr>
			<td>Bunsen Burner</td>
			<td>Argos Technologies</td>
			<td>BW20002460</td>
			<td>Or equivlaent to shape glass under flame</td>
		</tr>
		<tr>
			<td>Glass Capillary Tube (1.5 mm)</td>
			<td>Sutter Instruments</td>
			<td>BF150-75</td>
			<td>For filling with HBSS and making contact to the cornea</td>
		</tr>
		<tr>
			<td>Hank&#8217;s Buffered Salt Solution (HBSS)</td>
			<td>Thermo Fisher Scientific Inc</td>
			<td>14175-095</td>
			<td>Commercially available. Maintain at RT</td>
		</tr>
		<tr>
			<td>In-Line Filter</td>
			<td>Whatman</td>
			<td>6722-5001</td>
			<td>To protect vacuum pump from aerosols</td>
		</tr>
		<tr>
			<td>Low Noise Cable for Microelectrode Holders</td>
			<td>WPI Inc</td>
			<td>5372</td>
			<td>Suggested for improving the length and placement of the cables and electrode holder assemblies</td>
		</tr>
		<tr>
			<td>Magnetic Ball Joint</td>
			<td>WPI Inc</td>
			<td>500871</td>
			<td>For magnetically positioning the electrode holder assembly on the stage</td>
		</tr>
		<tr>
			<td>MatLab</td>
			<td>Mathworks</td>
			<td></td>
			<td>MatLab: For editing the analysis software</td>
		</tr>
		<tr>
			<td>Matlab Curvefit Toolbox</td>
			<td>Mathworks</td>
			<td></td>
			<td>Toolbox for MatLab (only required for editing the analysis software)</td>
		</tr>
		<tr>
			<td>MatLab Compiler</td>
			<td>Mathworks</td>
			<td></td>
			<td>Toolbox for MatLab (only required for editing and re-releasing the analysis software)</td>
		</tr>
		<tr>
			<td>MatLab Runtime version 9.5</td>
			<td>Mathworks</td>
			<td>R2018b (9.5)</td>
			<td>Required to run the analysis software: https://www.mathworks.com/products/compiler/matlab-runtime.html</td>
		</tr>
		<tr>
			<td>Microelectrode Holders (45 degrees)</td>
			<td>WPI Inc</td>
			<td>MEH345-15</td>
			<td>For holding the capillaries</td>
		</tr>
		<tr>
			<td>Needle (25 ga)</td>
			<td>Covidien</td>
			<td>8881250313</td>
			<td>For filling the capillary tubes with HBSS</td>
		</tr>
		<tr>
			<td>needle (ground) electrode</td>
			<td>Rhythmlink</td>
			<td>13mm - one elctrode</td>
			<td>Subdermal needle electrode (ground) for mouse (13mm long, 0.4mm diameter needle, 1.5m leadwire)</td>
		</tr>
		<tr>
			<td>Regulator/Power Conditioner</td>
			<td>Furman</td>
			<td>P-1800</td>
			<td>Or equivalent to remove DC-offset from noise introduced through power line</td>
		</tr>
		<tr>
			<td>Syringe (12 mL)</td>
			<td>Monoject</td>
			<td>1181200777</td>
			<td>For filling the capillary tubes with HBSS</td>
		</tr>
		<tr>
			<td>T-clip</td>
			<td>Cole-Parmer</td>
			<td>06852-20</td>
			<td>For electrode holder assembly</td>
		</tr>
		<tr>
			<td>Vacuum Desiccator</td>
			<td>Bel-Art</td>
			<td>420120000</td>
			<td>Clear polycarbonate bottom &#38; cover</td>
		</tr>
		<tr>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Pharmacological treatment</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Lubricant eye gel</td>
			<td>Alcon</td>
			<td>0078-0429-47</td>
			<td>Helps lubricates corneal surface and maintain electrical contact with capillary electrodes</td>
		</tr>
		<tr>
			<td>Phenylephrine Hydrochloride 2.5%</td>
			<td>Akorn</td>
			<td>17478-201-15</td>
			<td>Short acting mydriatic eye drops (for pupil dilation)</td>
		</tr>
		<tr>
			<td>Proparacaine Hydrochloride 0.5%</td>
			<td>Akorn</td>
			<td>17478-263-12</td>
			<td>Local anesthetic for ophthalmic instillation</td>
		</tr>
		<tr>
			<td>Tropicamide 0.5%</td>
			<td>Akorn</td>
			<td>17478-101-12</td>
			<td>Short acting mydriatic eye drops (for pupil dilation)</td>
		</tr>
		<tr>
			<td>Xylazine</td>
			<td>AnaSed</td>
			<td>sc-362949Rx</td>
			<td>Analgesic and muscle relaxant</td>
		</tr>
		<tr>
			<td>Zetamine (Ketamine HCl)</td>
			<td>VetOne</td>
			<td>501072</td>
			<td>Anesthetic for intramuscular injections</td>
		</tr>
	</tbody>
</table>

direct-coupled electroretinogram (dc-erg) for recording the light-evoked electrical responses of the mouse retinal pigment epithelium

The retinal pigment epithelium (RPE) is a specialized monolayer of cells strategically located between the retina and the choriocapillaris that maintain the overall health and structural integrity of the photoreceptors. The RPE is polarized, exhibiting apically and basally located receptors or channels, and performs vectoral transport of water, ions, metabolites, and secretes several cytokines.
In vivo noninvasive measurements of RPE function can be made using direct-coupled ERGs (DC-ERGs). The methodology behind the DC-ERG was pioneered by Marmorstein, Peachey, and colleagues using a custom-built stimulation recording system and later demonstrated using a commercially available system. The DC-ERG technique uses glass capillaries filled with Hank&#8217;s buffered salt solution (HBSS) to measure the slower electrical responses of the RPE elicited from light-evoked concentration changes in the subretinal space due to photoreceptor activity. The prolonged light stimulus and length of the DC-ERG recording make it vulnerable to drift and noise resulting in a low yield of useable recordings. Here, we present a fast, reliable method for improving the stability of the recordings while reducing noise by using vacuum pressure to reduce/eliminate bubbles that result from outgassing of the HBSS and electrode holder. Additionally, power line artifacts are attenuated using a voltage regulator/power conditioner. We include the necessary light stimulation protocols for a commercially available ERG system as well as scripts for analysis of the DC-ERG components: c-wave, fast oscillation, light peak, and off response. Due to the improved ease of recordings and rapid analysis workflow, this simplified protocol is particularly useful in measuring age-related changes in RPE function, disease progression, and in the assessment of pharmacological intervention.

Figure 2 is a sample dataset from miR-204 ko/ko cre/+ (conditional KO) and wild type (WT) mice. MiR-204 ko/ko cre/+ are mice with a conditional knockout of microRNA 204 in the retinal pigment epithelium. These mice are generated by crossing floxed miR-204 mice (produced by NEIGEF)22 with VMD2-CRE mice23. MiR-204 is highly expressed in the RPE where it regulates the expression of proteins critical for epithelial function that maintain tight junc...

Watch this Scientific Journal Video about Direct-Coupled Electroretinogram DC-ERG for Recording the Light-Evoked Electrical Responses of the Mouse Retinal Pigment Epithelium at JoVE.com

Direct-Coupled Electroretinogram DC-ERG for Recording the Light-Evoked Electrical Responses of the Mouse Retinal Pigment Epithelium

Here, we present a method for recording light-evoked electrical responses of the retinal pigment epithelium (RPE) in mice using a technique known as DC-ERGs first described by Marmorstein, Peachey, and colleagues in the early 2000s.

Direct-Coupled Electroretinogram (DC-ERG) for Recording the Light-Evoked Electrical Responses of the Mouse Retinal Pigment Epithelium

The retinal pigment epithelium (RPE) is a specialized monolayer of cells strategically located between the retina and the choriocapillaris that maintain ...

The DC-ERG technique can be used for the non-evasive evaluation of retinal pigment epithelium function to monitor age-related changes or disease progression and to assess pharmacological intervention effects. This technique improves upon DC-ERG reproduce ability and the easy of use by simplifying the capillary electrode preparation. It can also be supplemented with a standard ohm software application to facilitate analysis.Begin by carefully sliding a 25-gauge syringe needle through the silicone rubber gasket to the back wall of the electrode holder. Fill the base of the electrode holder with degassed HBSS while slowly retracting the needle, taking care not to introduce bubbles, and replace the threaded cap without tightening. Reinsert the syringe needle to fill the empty space within the gap with HBSS and hold the capillary horizontally while filling to prevent solution escaping from the other end.Grasping the filled capillary at the bent end, slowly insert the other end through the loosened cap and tighten the screw cap into place. Tilt the electrode holders with the capillary electrodes facing up to allow any bubbles to flow out and degas the capillaries in a vacuum chamber for five to 10 minutes. Then, slowly release the vacuum and refill the electrode holders and glass capillaries, as demonstrated.To make a custom stand for the microelectrode holder, remove the black polyacetal clips from one side of a number eight T-clip and use a cylinder base with magnetic ball joints machined in half to adjust the height. Secure the modified T-clips to the magnetic ball mounting screws with M3-size nuts and a slide in approximately one-inch tapered wooden handle, modified from a cotton tip cleaning stick, into the stand at an angle to secure the microelectrode holder into the custom-made T-clip magnetic ball joint stand. Then, use the rare-earth magnets cylinder base to securely position the customized electrode holder stand onto the metal plate of the stage, enabling a 360-degree rotation on a 180-degree axis.To perform an electrode test, first, gently lower the fully assembled HBSS-filled capillary microelectrodes into a small container of HBSS. Place the needle ground electrode and the silver, silver chloride centered pellet reference electrode in the same HBSS to complete the circuit and select or create an appropriate identifier to describe the mouse to be tested. To select the direct coupled electroretinogram protocol to be performed, click protocols and select DC-ERG.Click run. A dialog box will pop up with the patient information. If the information is correct, click yes and proceed to steps one of six.Close the doors to the Faraday cage and click impedance to display the impedance mode. Verify that the values for the mouth reference, tail ground and recording electrodes are acceptable and click step to proceed to step four of six to test the baseline stability. To begin viewing the traces, click preview.The traces should be low noise with a peak-to-peak amplitude of less than 200 microvolts. To position the mouse and electrodes for an experiment, anesthetize the cornea of a sedated mouse with a drop of 5%proparacaine hydrochloric acid before dilating the cornea with a drop of 2.5%phenylephrine HCL and 5%tropicamide. In the ERG system software, verify that the correct patient is selected.Click protocols. Under protocol description, select DC-ERG and click run. Click yes to verify that the correct test is being performed.Use step one of six to turn on a dim red light inside the dome and place the mouse on a heated recording table. Use forceps to carefully tent the skin of the rear leg. And using one hand to firmly hold the needle electrode, use the other hand to insert the electrode subcutaneously into the rear leg to secure the electrode into place.Place the reference silver, silver chloride electrode into the animal's mouth so that the centered pellet rests along the back cheek and is held in place behind the teeth. Before placing the capillary electrodes onto the eye, position the electrode holder with the glass capillaries oriented vertically and flick the electrode holder with an index finger to remove any bubbles that may have been introduced. Use a 25-gauge needle to fill the capillary tips with HBSS and inspect the capillaries to ensure that there are no air bubbles trapped in the tips.Position the electrode holder stand so that the open tips of the HBSS-filled capillaries are in gentle contact with the cornea. And taking care to avoid introducing bubbles, invert the lubricant eye gel dispenser to discard the initial drops. Then, place a drop of lubricant eye gel onto each eye to maintain conductivity and to prevent desiccation during the recording.To record the DC-ERGs, click step to select step five of six and click impedance to use the impedance checking screen to examine the resistances of the left and right eyes. The impedance values for the recording electrodes at each eye should be similar. And the impedance values for both the ground and reference electrodes should be less than 10 kilohms.Click preview to view the traces for the left and right eyes and wait up to 10 minutes for a stable baseline to be achieved. Then, click stop to exit the trace preview and click run to start the recording. Here, a sample dataset from conditional knockout and wild-type mice is shown.In this analysis, the trace suffered from minute bubbles in the electrode. It increased the peak-to-peak noise in the trace. In a separate analysis, the bubbles were eliminated using the vacuum chamber prior to assembling the microelectrodes within the electrode holder stands.The best fit lines to the initial 25 seconds can be calculated, allowing the drift-corrected responses to be replotted and the amplitudes of the DC-ERG components to be identified. As expected, reduced expression of cure 7.1 potassium channels in the RPE greatly attenuates the c-wave and fast oscillation, indicating a significant impairment of the retinal pigment epithelium electrical properties. Here, the relative amplitudes of the DC-ERG components, normalized to wild-type and plotted against the relative two largest light-evoked a-wave amplitudes, are shown.This form of analysis can determine whether the reduced electrical responses of the RPE can be accounted for by the reduction of photoreceptor activity alone. Or if there is an underlying defect that originates in the RPE. Remember to achieve a stable baseline prior to moving on to the mouse recording and to reinspect the electrodes periodically for bubbles that may have been introduced.Dark-adapted ERGs can be recorded prior to the DC-ERG to measure the cone-driven retinal function. Light-adapted ERGs can also be performed after the DC-ERG to evaluate the cone-driven retinal responses.

direct-coupled-electroretinogram-dc-erg-for-recording-light-evoked

Research

JoVE Journal

Chemistry

LabVIEW-operated Novel Nanoliter Osmometer for Ice Binding Protein Investigations

Ice-binding proteins (IBPs), including antifreeze proteins, ice structuring proteins, thermal hysteresis proteins, and ice recrystallization inhibition proteins, are found in cold-adapted organisms and protect them from freeze injuries by interacting with ice crystals. IBPs are found in a variety of organism, including fish1, plants2, 3, arthropods4, 5, fungi6, and bacteria7. IBPs adsorb to the surfaces of ice crystals and prevent water molecules from joining the ice lattice at the IBP adsorption location. Ice that grows on the crystal surface between the adsorbed IBPs develops a high curvature that lowers the temperature at which the ice crystals grow, a phenomenon referred to as the Gibbs-Thomson effect. This depression creates a gap (thermal hysteresis, TH) between the melting point and the nonequilibrium freezing point, within which ice growth is arrested8-10, see Figure 1. One of the main tools used in IBP research is the nanoliter osmometer, which facilitates measurements of the TH activities of IBP solutions. Nanoliter osmometers, such as the Clifton instrument (Clifton Technical Physics, Hartford, NY,) and Otago instrument (Otago Osmometers, Dunedin, New Zealand), were designed to measure the osmolarity of a solution by measuring the melting point depression of droplets with nanoliter volumes. These devices were used to measure the osmolarities of biological samples, such as tears11, and were found to be useful in IBP research. Manual control over these nanoliter osmometers limited the experimental possibilities. Temperature rate changes could not be controlled reliably, the temperature range of the Clifton instrument was limited to 4,000 mOsmol (about -7.5 &deg;C), and temperature recordings as a function of time were not an available option for these instruments.
We designed a custom-made computer-controlled nanoliter osmometer system using a LabVIEW platform (National Instruments). The cold stage, described previously9, 10, contains a metal block through which water circulates, thereby functioning as a heat sink, see Figure 2. Attached to this block are thermoelectric coolers that may be driven using a commercial temperature controller that can be controlled via LabVIEW modules, see Figure 3. Further details are provided below. The major advantage of this system is its sensitive temperature control, see Figure 4. Automated temperature control permits the coordination of a fixed temperature ramp with a video microscopy output containing additional experimental details.
To study the time dependence of the TH activity, we tested a 58 kDa hyperactive IBP from the Antarctic bacterium Marinomonas primoryensis (MpIBP)12. This protein was tagged with enhanced green fluorescence proteins (eGFP) in a construct developed by Peter Davies' group (Queens University)10. We showed that the temperature change profile affected the TH activity. Excellent control over the temperature profile in these experiments significantly improved the TH measurements. The nanoliter osmometer additionally allowed us to test the recrystallization inhibition of IBPs5, 13. In general, recrystallization is a phenomenon in which large crystals grow larger at the expense of small crystals. IBPs efficiently inhibit recrystallization, even at low concentrations14, 15. We used our LabVIEW-controlled osmometer to quantitatively follow the recrystallization of ice and to enforce a constant ice fraction using simultaneous real-time video analysis of the images and temperature feedback from the sample chamber13. The real-time calculations offer additional control options during an experimental procedure. A stage for an inverted microscope was developed to accommodate temperature-controlled microfluidic devices, which will be described elsewhere16.
The Cold Stage System
The cold stage assembly (Figure 2) consists of a set of thermoelectric coolers that cool a copper plate. Heat is removed from the stage by flowing cold water through a closed compartment under the thermoelectric coolers. A 4 mm diameter hole in the middle of the copper plate serves as a viewing window. A 1 mm diameter in-plane hole was drilled to fit the thermistor. A custom-made copper disc (7 mm in diameter) with several holes (500 &mu;m in diameter) was placed on the copper plate and aligned with the viewing window. Air was pumped at a flow rate of 35 ml/sec and dried using Drierite (W.A. Hammond). The dry air was used to ensure a dry environment at the cooling stage. The stage was connected via a 9 pin connection outlet to a temperature controller (Model 3040 or 3150, Newport Corporation, Irvine, California, US). The temperature controller was connected via a cable to a computer GPIB-PCI card (National instruments, Austin, Texas, USA).

Ice binding proteins (IBPs), also known as antifreeze proteins, inhibit ice growth and are a promising additive for use in the cryopreservation of tissues. The main tool used to investigate IBPs is the nanoliter osmometer. We developed a home-designed cooling stage mounted on an optical microscope and controlled using a custom-built LabVIEW routine. The nanoliter osmometer described here manipulated the sample temperature in an ultra-sensitive manner.

Ice-binding proteins (IBPs), including antifreeze proteins, ice structuring proteins, thermal hysteresis proteins, and ice recrystallization inhibition ...

Production of Disulfide-stabilized Transmembrane Peptide Complexes for Structural Studies

Physical interactions among the lipid-embedded alpha-helical domains of membrane proteins play a crucial role in folding and assembly of membrane protein complexes and in dynamic processes such as transmembrane (TM) signaling and regulation of cell-surface protein levels. Understanding the structural features driving the association of particular sequences requires sophisticated biophysical and biochemical analyses of TM peptide complexes. However, the extreme hydrophobicity of TM domains makes them very difficult to manipulate using standard peptide chemistry techniques, and production of suitable study material often proves prohibitively challenging. Identifying conditions under which peptides can adopt stable helical conformations and form complexes spontaneously adds a further level of difficulty. Here we present a procedure for the production of homo- or hetero-dimeric TM peptide complexes from materials that are expressed in E. coli, thus allowing incorporation of stable isotope labels for nuclear magnetic resonance (NMR) or non-natural amino acids for other applications relatively inexpensively. The key innovation in this method is that TM complexes are produced and purified as covalently associated (disulfide-crosslinked) assemblies that can form stable, stoichiometric and homogeneous structures when reconstituted into detergent, lipid or other membrane-mimetic materials. We also present carefully optimized procedures for expression and purification that are equally applicable whether producing single TM domains or crosslinked complexes and provide advice for adapting these methods to new TM sequences.

Biophysical and biochemical studies of interactions among membrane-embedded protein domains face many technical challenges, the first of which is obtaining appropriate study material. This article describes a protocol for producing and purifying disulfide-stabilized transmembrane peptide complexes that are suitable for structural analysis by solution nuclear magnetic resonance (NMR) and other analytical applications.

Physical  interactions among the lipid-embedded alpha-helical domains of membrane  proteins play a crucial role in folding and assembly of membrane ...

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Copper (I) binding by metallochaperone transport proteins prevents copper oxidation and release of the toxic ions that may participate in harmful redox reactions. The Cu (I) complex of the peptide model of a Cu (I) binding metallochaperone protein, which includes the sequence MTCSGCSRPG (underlined is conserved), was determined in solution under inert conditions by NMR spectroscopy.
NMR is a widely accepted technique for the determination of solution structures of proteins and peptides. Due to difficulty in crystallization to provide single crystals suitable for X-ray crystallography, the NMR technique is extremely valuable, especially as it provides information on the solution state rather than the solid state. Herein we describe all steps that are required for full three-dimensional structure determinations by NMR. The protocol includes sample preparation in an NMR tube, 1D and 2D data collection and processing, peak assignment and integration, molecular mechanics calculations, and structure analysis. Importantly, the analysis was first conducted without any preset metal-ligand bonds, to assure a reliable structure determination in an unbiased manner.

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

The NMR-solution structure of a metallochaperone model peptide with Cu (I) was determined, and a detailed protocol from sample preparation and 1D and 2D data collection to a three-dimensional structure is described.

Copper (I) binding by metallochaperone transport proteins prevents copper oxidation and release of the toxic ions that may participate in harmful redox ...

A High-throughput-compatible FRET-based Platform for Identification and Characterization of Botulinum Neurotoxin Light Chain Modulators

Botulinum neurotoxin (BoNT) is a potent and potentially lethal bacterial toxin that binds to host motor neurons, is internalized into the cell, and cleaves intracellular proteins that are essential for neurotransmitter release. BoNT is comprised of a heavy chain (HC), which mediates host cell binding and internalization, and a light chain (LC), which cleaves intracellular host proteins essential for acetylcholine release. While therapies that inhibit toxin binding/internalization have a small time window of administration, compounds that target intracellular LC activity have a much larger time window of administrations, particularly relevant given the extremely long half-life of the toxin. In recent years, small molecules have been heavily analyzed as potential LC inhibitors based on their increased cellular permeability relative to larger therapeutics (peptides, aptamers, etc.). Lead identification often involves high-throughput screening (HTS), where large libraries of small molecules are screened based on their ability to modulate therapeutic target function. Here we describe a FRET-based assay with a commercial BoNT/A LC substrate and recombinant LC that can be automated for HTS of potential BoNT inhibitors. Moreover, we describe a manual technique that can be used for follow-up secondary screening, or for comparing the potency of several candidate compounds.

The botulinum neurotoxin type A light chain (BoNT/A LC) is a metalloprotease that enters motor neurons, cleaves its substrate SNAP-25, and disrupts neurotransmission, thereby resulting in flaccid paralysis. Utilizing a high-throughput-compatible FRET-based assay, large libraries of small molecules can be screened for their impact on BoNT/A LC enzymatic activity.

Botulinum neurotoxin (BoNT) is a potent and potentially lethal bacterial toxin that binds to host motor neurons, is internalized into the cell, and ...

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

In nature, complex functional structures are formed by the self-assembly of biomolecules under mild conditions. Understanding the forces that control self-assembly and mimicking this process in vitro will bring about major advances in the areas of materials science and nanotechnology. Among the available biological building blocks, peptides have several advantages as they present substantial diversity, their synthesis in large scale is straightforward, and they can easily be modified with biological and chemical entities1,2. Several classes of designed peptides such as cyclic peptides, amphiphile peptides and peptide-conjugates self-assemble into ordered structures in solution. Homoaromatic dipeptides, are a class of short self-assembled peptides that contain all the molecular information needed to form ordered structures such as nanotubes, spheres and fibrils3-8. A large variety of these peptides is commercially available.
This paper presents a procedure that leads to the formation of ordered structures by the self-assembly of homoaromatic peptides. The protocol requires only commercial reagents and basic laboratory equipment. In addition, the paper describes some of the methods available for the characterization of peptide-based assemblies. These methods include electron and atomic force microscopy and Fourier-Transform Infrared Spectroscopy (FT-IR). Moreover, the manuscript demonstrates the blending of peptides (coassembly) and the formation of a &#34;beads on a string&#34;-like structure by this process.9 The protocols presented here can be adapted to other classes of peptides or biological building blocks and can potentially lead to the discovery of new peptide-based structures and to better control of their assembly.

This paper describes the formation of highly ordered peptide-based structures by the spontaneous process of self-assembly. The method utilizes commercially available peptides and common lab equipment. This technique can be applied to a large variety of peptides and may lead to the discovery of new peptide-based assemblies.

In nature, complex functional structures are formed by the self-assembly of biomolecules under mild conditions. Understanding the forces that control ...

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Protein alignments are commonly used to evaluate the similarity of protein residues, and the derived consensus sequence used for identifying functional units (e.g., domains). Traditional consensus-building models fail to account for interpositional dependencies &#8211; functionally required covariation of residues that tend to appear simultaneously throughout evolution and across the phylogentic tree. These relationships can reveal important clues about the processes of protein folding, thermostability, and the formation of functional sites, which in turn can be used to inform the engineering of synthetic proteins. Unfortunately, these relationships essentially form sub-motifs which cannot be predicted by simple &#8220;majority rule&#8221; or even HMM-based consensus models, and the result can be a biologically invalid &#8220;consensus&#8221; which is not only never seen in nature but is less viable than any extant protein. We have developed a visual analytics tool, StickWRLD, which creates an interactive 3D representation of a protein alignment and clearly displays covarying residues. The user has the ability to pan and zoom, as well as dynamically change the statistical threshold underlying the identification of covariants. StickWRLD has previously been successfully used to identify functionally-required covarying residues in proteins such as Adenylate Kinase and in DNA sequences such as endonuclease target sites.

Synthetic protein sequences based on consensus motifs typically ignore co-evolving residues, that imply interpositional dependencies (IPDs). IPDs can be essential to activity, and designs that disregard them may result in suboptimal results. This protocol uses StickWRLD to identify IPDs and help inform rational protein design, resulting in more efficient results.

Protein alignments are commonly used to evaluate the similarity of protein residues, and the derived consensus sequence used for identifying functional ...

Synthesis of Protein Bioconjugates via Cysteine-maleimide Chemistry

The chemical linking or bioconjugation of proteins to fluorescent dyes, drugs, polymers and other proteins has a broad range of applications, such as the development of antibody drug conjugates (ADCs) and nanomedicine, fluorescent microscopy and systems chemistry. For many of these applications, specificity of the bioconjugation method used is of prime concern. The Michael addition of maleimides with cysteine(s) on the target proteins is highly selective and proceeds rapidly under mild conditions, making it one of the most popular methods for protein bioconjugation.
We demonstrate here the modification of the only surface-accessible cysteine residue on yeast cytochrome c with a ruthenium(II) bisterpyridine maleimide. The protein bioconjugation is verified by gel electrophoresis and purified by aqueous-based fast protein liquid chromatography in 27% yield of isolated protein material. Structural characterization with MALDI-TOF MS and UV-Vis is then used to verify that the bioconjugation is successful. The protocol shown here is easily applicable to other cysteine - maleimide coupling of proteins to other proteins, dyes, drugs or polymers.

Synthesis of Protein Bioconjugates via Cysteine-maleimide Chemistry

This protocol details the important steps required for the bioconjugation of a cysteine containing protein to a maleimide, including reagent purification, reaction conditions, bioconjugate purification and bioconjugate characterization.

The chemical linking or bioconjugation of proteins to fluorescent dyes, drugs, polymers and other proteins has a broad range of applications, such as the ...

Facile Synthesis of Worm-like Micelles by Visible Light Mediated Dispersion Polymerization Using Photoredox Catalyst

Presented herein is a protocol for the facile synthesis of worm-like micelles by visible light mediated dispersion polymerization. This approach begins with the synthesis of a hydrophilic poly(oligo(ethylene glycol) methyl ether methacrylate) (POEGMA) homopolymer using reversible addition-fragmentation chain-transfer (RAFT) polymerization. Under mild visible light irradiation (&#955; = 460 nm, 0.7 mW/cm2), this macro-chain transfer agent (macro-CTA) in the presence of a ruthenium based photoredox catalyst, Ru(bpy)3Cl2 can be chain extended with a second monomer to form a well-defined block copolymer in a process known as Photoinduced Electron Transfer RAFT (PET-RAFT). When PET-RAFT is used to chain extend POEGMA with benzyl methacrylate (BzMA) in ethanol (EtOH), polymeric nanoparticles with different morphologies are formed in situ according to a polymerization-induced self-assembly (PISA) mechanism. Self-assembly into nanoparticles presenting POEGMA chains at the corona and poly(benzyl methacrylate) (PBzMA) chains in the core occurs in situ due to the growing insolubility of the PBzMA block in ethanol. Interestingly, the formation of highly pure worm-like micelles can be readily monitored by observing the onset of a highly viscous gel in situ due to nanoparticle entanglements occurring during the polymerization. This process thereby allows for a more reproducible synthesis of worm-like micelles simply by monitoring the solution viscosity during the course of the polymerization. In addition, the light stimulus can be intermittently applied in an ON/OFF manner demonstrating temporal control over the nanoparticle morphology.

This article describes a process for producing polymeric self-assembled nanoparticles using visible light mediated dispersion polymerization. Using low energy visible light to control the polymerization allows for the reproducible formation of self-assembled worm-like micelles at high solids content.

Presented herein is a protocol for the facile synthesis of worm-like micelles by visible light mediated dispersion polymerization. This approach begins ...

Using Capillary Electrophoresis to Quantify Organic Acids from Plant Tissue: A Test Case Examining Coffea arabica Seeds

Carboxylic acids are organic acids containing one or more terminal carboxyl (COOH) functional groups. Short chain carboxylic acids (SCCAs; carboxylic acids containing three to six carbons), such as malate and citrate, are critical to the proper functioning of many biological systems, where they function in cellular respiration and can serve as indicators of cell health. In foods, organic acid content can have significant impact on taste, with increased SCCA levels resulting in a sour or &#34;acid&#34; taste. Because of this, methods for the rapid analysis of organic acid levels are of particular interest to the food and beverage industries. Unfortunately, however, most methods used for SCCA quantification are dependent on time-consuming protocols requiring the derivatization of samples with hazardous reagents, followed by costly chromatographic and/or mass spectrometric analyses. This method details an alternate method for the detection and quantification of organic acids from plant material and food samples using free zonal capillary electrophoresis (CZE), sometimes simply referred to as capillary electrophoresis (CE). CZE provides a cost-effective method for measuring SCCAs with a low limit of detection (0.005 mg/ml). This article details the extraction and quantification of SCCAs from plant samples. While the method provided focuses on measurement of SCCAs from coffee beans, the method provided can be applied to multiple plant-based food materials.

Using Capillary Electrophoresis to Quantify Organic Acids from Plant Tissue: A Test Case Examining Coffea arabica Seeds

This article presents a method for the detection and quantification of organic acids from plant material using free zonal capillary electrophoresis. An example of the potential application of this method, determining the effects of a secondary fermentation on organic acid levels in coffee seeds, is provided.

Carboxylic acids are organic acids containing one or more terminal carboxyl (COOH) functional groups. Short chain carboxylic acids (SCCAs; carboxylic ...

Insights into the Interactions of Amino Acids and Peptides with Inorganic Materials Using Single-Molecule Force Spectroscopy

The interactions between proteins or peptides and inorganic materials lead to several interesting processes. For example, combining proteins with minerals leads to the formation of composite materials with unique properties. In addition, the undesirable process of biofouling is initiated by the adsorption of biomolecules, mainly proteins, on surfaces. This organic layer is an adhesion layer for bacteria and allows them to interact with the surface. Understanding the fundamental forces that govern the interactions at the organic-inorganic interface is therefore important for many areas of research and could lead to the design of new materials for optical, mechanical and biomedical applications. This paper demonstrates a single-molecule force spectroscopy technique that utilizes an AFM to measure the adhesion force between either peptides or amino acids and well-defined inorganic surfaces. This technique involves a protocol for attaching the biomolecule to the AFM tip through a covalent flexible linker and single-molecule force spectroscopy measurements by atomic force microscope. In addition, an analysis of these measurements is included.

Here we present a protocol to measure the force of interactions between a well-defined inorganic surface and either peptides or amino acids by single-molecule force spectroscopy measurements using an atomic force microscope (AFM). The information obtained from the measurement is important to better understand the peptide-inorganic material interphase.

The interactions between proteins or peptides and inorganic materials lead to several interesting processes. For example, combining proteins with minerals ...