PLD holds the Canada Research Chair in Protein Engineering. This work was funded by a grant from the Canadian Institutes of Health Research to PLD. This work was also supported by a Grant-in-Aid for scientific research from the Japan Society for the Promotion of Science (JSPS) (No. 23310171) and from the Japan Bio-oriented Technology Research Advancement Institution (BRAIN). We are grateful to Drs. Chris Marshall and Mike Kuiper for pioneering work that led to FIPA. We are also grateful to Dr. Sakae Tsuda for providing facilities for some of this work&#160;and to Dr. Laurie Graham for setting up the fluorescent light excitation and emission filters.

1. Growing Single Ice Crystals
<ol>
	<li>Take a clean metal pan (15 cm diameter, 4.5 cm high) that fits into, and can float on, an ethylene glycol cooling bath.</li>
	<li>Prepare polyvinyl chloride (PVC) cylindrical molds, (4.5 cm diameter, 3-4 cm high, 4 mm thick), by sawing sections from a pipe.
	<ol>
		<li>Cut a notch, (1 mm wide, 2 mm high) on one side&#160;(Figure 1A).</li>
		<li>Prepare as many molds that can fit comfortably into the pan&#160;(Figure 1B). 
		Note: A study showed that polyvinyl alcohol (PVA) can affect ice nucleation22. However, in our open mold PVC system we have not encountered problems of atypical ice formation.&#160;</li>
	</ol>
	</li>
	<li>Apply a light film of vacuum grease to the bottom surface ring of each mold, which is the surface with the notch cut out. Seal this greased, notched surface onto a metal pan with the notches oriented away from the center of the pan. Be careful not to fill or obstruct the notches with grease.</li>
	<li>Add 0.22 &#956;m&#160;filtered and degassed/deionized water to the center of pan, but outside of the molds, and allow the water to slowly enter into the molds through the notches. Be careful not to introduce any bubbles. The water layer should be approximately 5 mm deep.</li>
	<li>Place the pan into a temperature-controlled ethylene glycol bath cooled to -0.5 &#176;C. The pan should be perfectly level. Add ballast weights to the sides of the pan if necessary.</li>
	<li>After the pan and water have reached -0.5 &#176;C, add a small piece of ice to the middle of the pan, outside of the molds.
	<ol>
		<li>This will nucleate ice growth in the supercooled water across the pan and into the molds. The small notch at the bottom of each mold allows only one ice crystal to propagate through, resulting in a single ice crystal in each mold.</li>
		<li>Incubate overnight to form a layer of ice.</li>
	</ol>
	</li>
	<li>Over the next three days add 13 ml of 4 &#176;C degassed/deionized water to each mold once a day and drop the temperature of the ethylene glycol bath after each addition to -0.8 &#176;C on day one, to -1.1 &#176;C on day two, and to -1.5 &#176;C on day three.
	<ol>
		<li>Incubate at those temperatures overnight.</li>
		<li>By day four, the molds should be completely filled with ice.</li>
	</ol>
	</li>
	<li>Pull the molds off the pan, push the ice crystals out of the molds, and store on a clean surface, such as a weighing boat, in a -20 &#176;C freezer for approximately 1 hr before handling.</li>
	<li>Rather than preparing many small single ice crystals, a large single ice crystal several liters in volume can be prepared in a constant temperature incubator as described by Knight23. The large ice crystal can be stored for a year or more if kept covered in a -15 to -20 &#176;C freezer. Portions of single crystal can be cut from the ice block with a saw as required.</li>
</ol>
2. Determining Singularity and Orientation of the Ice Crystal
<ol>
	<li>Determine if the ice expelled from the mold is a single crystal by observing in a freezer room, between two crossed polaroids&#160;(Figure 1D).
	<ol>
		<li>If the ice crystal is single, then no cracks or discontinuities should be seen, and the light direction should not change within the ice crystal. 
		Note: If a freezer room is not available, a cold room can be used instead in all required steps, being cautious to work quickly and handle the ice sparingly.</li>
	</ol>
	</li>
	<li>Due to the ice birefringence, one may determine orientation of the c-axis at the same time. Use the following information to determine the orientation:
	<ol>
		<li>When the c-axis is exactly parallel to the incident light, in theory, no light will pass through the crossed polaroids. If the incident light is titled slightly from parallel with the c-axis, a uniform multicolor spectrum of light is transmitted through the crystal when it is rotated between the crossed polaroids. This uniform transmittance arises from the optical inactivity of ice Ih&#160;along its c-axis24. The basal plane of the ice crystal is normal to the c-axis.</li>
		<li>When the c-axis is further from parallel to the incident light and the ice crystal is rotated between the crossed polaroids, the transmitted light will alternate between 0-100% transmittance with every 90&#176; of rotation of the crystal.</li>
		<li>Most commonly, the c-axis will be normal to the circular plane of the cylindrical ice crystal.</li>
	</ol>
	</li>
	<li>Determine the orientation of the a-axes by ice pitting25 which is done by wrapping the ice crystal tightly in aluminum foil, poking a small hole with a needle through the foil into the ice on the basal plane (normal to the c-axis), and placing it under vacuum for 20 min.
	<ol>
		<li>This treatment will produce an etch with hexagonal symmetry on the basal plane, where the a-axes run through the vertices of the six-sided star (Figure 2A).</li>
		<li>If desired, the ice crystal can be cut with a saw either parallel or perpendicular to one side of the hexagon to mount it with a primary or secondary prism plane perpendicular to the cold finger, respectively (Figure 3).</li>
	</ol>
	</li>
</ol>
3. Adsorption of Fluorescently Labeled Antifreeze Proteins to a Single Ice Crystal
<ol>
	<li>Mount a single ice crystal onto the cold finger (Figure 1C)&#160;by first boring a cavity into the top of the crystal. To do this, alternate melting the ice with a two aluminum rods of slightly different diameter, but similar to the diameter of the cold finger, to form the cavity into which the cold finger can fit.</li>
	<li>Cool the cold finger to -0.5 &#176;C, place in the ice cavity, and hold the ice crystal in place until it freezes to the metal&#160;(Figure 2B). Avoid air bubbles when attaching the crystal to the finger as they hinder efficient transfer of heat from the finger to the rod.</li>
	<li>Fill a hemispherical cup that is approximately twice the diameter of the ice crystal with filtered deionized water or buffer, cooled to approximately 4 &#176;C. Submerge the cold finger-bound ice crystal into the cup and remove excess water or buffer such that the top of the ice crystal is approximately level with the liquid layer and the ice is not touching the cup walls.
	<ol>
		<li>Cover the cup with insulation and lower the temperature to -5 &#176;C.</li>
		<li>Wait approximately 1 hr for the ice crystal to form into a hemisphere, checking its status approximately every 20 min&#160;(Figure 2C).</li>
		<li>The ice will take the shape of the hemispherical cup by melting and growing the ice crystal, but it should never overgrow to touch the cup walls. There should be at least a 1 cm gap between the wall and hemisphere and the cold finger should not protrude from the ice.</li>
	</ol>
	</li>
	<li>Remove the cup from the ice crystal and add the fluorescent protein solution to a final volume of 25-30 ml and desired analysis concentration, being careful to keep the total liquid volume in the cup unchanged. A typical AFP concentration is 0.1 mg/ml.
	<ol>
		<li>Resubmerge the ice crystal into the cup so that the top of the ice crystal is at level with the liquid and the ice crystal is not touching the cup walls&#160;(Figure 2D).</li>
		<li>Drop the cold finger temperature to -8 &#176;C and let the protein solution freeze into the ice crystal for 2-3 hr, stirring the solution often. The ice formed from the protein solution should be at least 5 mm before stopping ice growth.</li>
	</ol>
	</li>
	<li>Remove the ice crystal from the cup while still attached to the cold finger. Detach the ice from the latter by warming the coolant through the cold finger to just above 0 &#176;C and wait until the ice crystal melts off.</li>
	<li>Place the crystal flat side down onto a clean surface, such as a weighing dish, being careful not to touch the newly form ice and store at -20 &#176;C for at least 20 min before handing.</li>
</ol>
4. Visualization of Antifreeze-protein-bound Planes of Ice
<ol>
	<li>Visualization of fluorescence is done in a darkened freezer or cold room, by placing the ice crystal flat side down under lamps with wavelength specific excitation filters to excite the fluorescent label and camera emission filters to block out any other nonspecific light. Based on the pattern, the ice planes that are bound by AFPs can be estimated (Figure 4).</li>
	<li>If wavelength specific lights are not available a UV light box can be used instead.</li>
	<li>Traditional ice etches can also be performed simply by allowing the ice hemisphere to sublimate at -20 &#176;C for at least 3 hr, after which residual protein powder may become visible on the ice surface (Figure 5).</li>
	<li>Step 2.3 can be repeated in order to determine the orientation of the a-axes of the completed ice hemisphere.</li>
</ol>

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No conflicts of interest declared.

Development of the ice-etching method by Charles Knight for determination of AFP-bound ice planes greatly advanced studies on the mechanism of ice binding by AFPs. Whereas structures of AFPs could be solved by X-ray&#160;crystallography26,27 there was no obvious method for deducing the complementary surface on ice to which the AFP bound. When type I AFP from winter flounder was initially characterized, it was hypothesized to bind to the primary prism planes of ice28. However, Knight&#39;s ground bre...

The production of antifreeze proteins (AFPs) is an important survival mechanism of some organisms that live in ice-laden environments. Until recently, it was thought that the sole function of AFPs was to prevent or slow the growth of internal ice crystals that would block circulation, cause tissue damage, and osmotic stress. Organisms that cannot tolerate any degree of freezing, such as fish, express AFPs to completely inhibit ice crystal growth1. Others, such as grass, are freeze tolerant and express AFPs to inhibit ice recrystallization which reduces the formation of large ice crystals in their tissues2. Stabilization of membranes in low temperature is yet another function that was suggested for the AFPs3. Recently, a novel role was suggested for the AFP of an Antarctic bacterium, Marinomonas primoryensis, from ice-covered brackish lakes4. This AFP is part of a much larger adhesin protein5&#160;that is thought to attach the bacterium to ice for better access to oxygen and nutrients6. Other microbes are known to secrete AFPs, which might alter the structure of the ice in which they live7.
AFPs have been found in some fish, insects, plants, algae, bacteria, diatoms, and fungi. They have remarkably divergent sequences and structures consistent with their evolution from different progenitors on various occasions; and yet they all bind to ice and inhibit its growth by the adsorption-inhibition mechanism8. The AFPs each have a specific surface that acts as its ice-binding site (IBS). These have typically been identified by site-directed mutagenesis of surface residues9-11. The IBS is hypothesized to arrange water molecules in an ice-like pattern that matches specific planes of ice. Thus the AFP forms its ligand before binding to it5, 12. Ice planes can be defined by their Miller indices, and different AFPs can bind to different planes. Thus, type I AFP from winter flounder binds to the 20-21 pyramidal planes13, type III AFP binds both primary prism and pyramidal planes using a compound ice-binding surface11,14, while the spruce budworm AFP, a hyperactive AFP, binds simultaneously to both the primary and basal planes15,16. Other hyperactive AFPs, such as MpAFP, bind to multiple ice planes as shown by their complete coverage of single ice crystal hemispheres5,17. It is hypothesized, that the ability of hyperactive AFPs to bind the basal plane, as well as other planes, may account for their 10-fold higher activity over moderately active AFPs18. Though the efficiency of hyperactive AFPs is well documented, their ability to bind to multiple ice planes is still not understood.
The original method for determining the AFP-bound ice planes was developed by Charles Knight13,19. In this method, a macroscopic single ice crystal is mounted onto a hollow metal rod (cold finger) and formed into a hemisphere by submerging it into a hemispherical cup filled with degassed water. Then, the hemisphere is submerged into a dilute solution of AFPs and a layer of ice is grown from the AFP solution onto the ice crystal hemisphere over several hours controlled by the temperature of the ethylene glycol circulating through the cold finger. The ice crystal is removed from the solution, detached from the cold finger, and placed in a -10 to -15 &#176;C freezer room. The surface is scraped with a sharp blade to remove the frozen surface film of antifreeze protein solution and the ice crystal is allowed to sublimate for at least 3 hr. After sublimation, the ice planes bound by AFPs can be seen as white etched patterns&#160;derived from residual protein. The ice hemisphere can be oriented to its c-axis and a-axes, to locate the basal and prism planes of ice, and determine the Miller indices of the etched patches.
Here we describe a modification of the original method for determining AFP-bound planes of ice, a method we refer to as fluorescence-based ice plane affinity (FIPA)11. The AFPs are fluorescently labeled with either a chimeric tag, such as green fluorescent protein (GFP)11,16,17,20, or with a fluorescent dye covalently bound to the AFP5,21. The fluorescently labeled AFPs are adsorbed to a single ice crystal and overgrown using the same experimental procedure as the original ice-etching experiments. The extent of AFP binding to the growing ice hemisphere can be monitored throughout the experiment using an ultraviolet (UV) lamp. After the experiment is complete, the hemisphere can be directly taken off of the cold finger and imaged, without sublimation. However, if desired, the hemisphere can be left to sublimate to visualize a traditional ice etch. Modifications introduced to the FIPA methodology shorten the traditional ice-etching protocol by several hours. Additionally, there is the potential for simultaneously imaging several AFPs, each with a different fluorescent label, to visualize the overlapping patterns of AFP-bound ice planes.

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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.

Preparation and mounting of the single ice crystal are the two steps of the FIPA procedure where errors are most commonly made. Determining if the prepared ice crystal is single is done by examining it through crossed polaroids&#160;(Figure 1D), as outlined in step 2.1 of the protocol section. If a multicrystalline ice crystal is used for the FIPA analysis, the result will be discontinuous binding of the AFPs on the hemisphere without a coherent binding pattern (Figure 6B). If the ice cr...

Watch this Scientific Journal Video about Determining the Ice-binding Planes of Antifreeze Proteins by Fluorescence-based Ice Plane Affinity at JoVE.com

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

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 ...

determining-ice-binding-planes-antifreeze-proteins-fluorescence-based

Research

JoVE Journal

Chemistry

9.0K 조회수.  Queen's University. 부동액 단백질(AfP)은 얼음 의 특정 평면에 결합하여 얼음 성장을 방지하거나 느리게 합니다. 형광계 얼음 비행기 선호도(FIPA) 분석은 AFP 바인딩 된 얼음 비행기의 측정을위한 원래 얼음 에칭 방법을 수정한 것입니다. AFP는 형광으로 표시되고, 거시적 단일 얼음 결정에 통합되고, UV 빛 아래에서 시각화됩니다.

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

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 ...

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 ...

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.

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 ...

Fluorescence-based Monitoring of PAD4 Activity via a Pro-fluorescence Substrate Analog

Post-translational modifications may lead to altered protein functional states by increasing the covalent variations on the side chains of many protein substrates. The histone tails represent one of the most heavily modified stretches within all human proteins. Peptidyl-arginine deiminase 4 (PAD4) has been shown to convert arginine residues into the non-genetically encoded citrulline residue. Few assays described to date have been operationally facile with satisfactory sensitivity. Thus, the lack of adequate assays has likely contributed to the absence of potent non-covalent PAD4 inhibitors. Herein a novel fluorescence-based assay that allows for the monitoring of PAD4 activity is described. A pro-fluorescent substrate analog was designed to link PAD4 enzymatic activity to fluorescence liberation upon the addition of the protease trypsin. It was shown that the assay is compatible with high-throughput screening conditions and has a strong signal-to-noise ratio. Furthermore, the assay can also be performed with crude cell lysates containing over-expressed PAD4.

PAD4 is an enzyme responsible for the conversion of peptidyl-arginine to peptidyl-citrulline. Dysregulation of PAD4 has been implicated in a number of human diseases. A facile and high-throughput compatible fluorescence based PAD4 assay is described.

Post-translational modifications may lead to altered protein functional states by increasing the covalent variations on the side chains of many protein ...

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 ...

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 ...

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 ...

Determining the Chemical Composition of Corrosion Inhibitor/Metal Interfaces with XPS: Minimizing Post Immersion Oxidation

An approach for acquiring more reliable X-ray photoelectron spectroscopy data from corrosion inhibitor/metal interfaces is described. More specifically, the focus is on metallic substrates immersed in acidic solutions containing organic corrosion inhibitors, as these systems can be particularly sensitive to oxidation following removal from solution. To minimize the likelihood of such degradation, samples are removed from solution within a glove box purged with inert gas, either N2 or Ar. The glove box is directly attached to the load-lock of the ultra-high vacuum X-ray photoelectron spectroscopy instrument, avoiding any exposure to the ambient laboratory atmosphere, and thus reducing the possibility of post immersion substrate oxidation. On this basis, one can be more certain that the X-ray photoelectron spectroscopy features observed are likely to be representative of the in situ submerged scenario, e.g. the oxidation state of the metal is not modified.

A protocol to avoid the oxidation of metallic substrates during sample transfer from an inhibited acidic solution to an X-ray photoelectron spectrometer is presented.

An approach for acquiring more reliable X-ray photoelectron spectroscopy data from corrosion inhibitor/metal interfaces is described. More specifically, ...

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 ...

Achieving Moderate Pressures in Sealed Vessels Using Dry Ice As a Solid CO2 Source

Herein is presented a general strategy to perform reactions under mild to moderate CO2 pressures with dry ice. This technique obviates the need for specialized equipment to achieve modest pressures, and can even be used to achieve higher pressures in more specialized equipment and sturdier reaction vessels. At the end of the reaction, the vials can be easily depressurized by opening at room temperature. In the present example CO2 serves as both a putative directing group as well as a way to passivate amine substrates, thereby preventing oxidation during the organometallic reaction. In addition to being easily added, the directing group is also removed under vacuum, obviating the need for extensive purification to remove the directing group. This strategy allows the facile &#947;-C(sp3)-H arylation of aliphatic amines and has the potential to be applied to a variety of other amine-based reactions.

Achieving Moderate Pressures in Sealed Vessels Using Dry Ice As a Solid CO2 Source

Here we present a protocol for performing reactions in simple reaction vessels under low-to-moderate pressures of CO2. The reactions can be performed in a variety of vessels simply by administering the carbon dioxide in the form of dry ice, without the need for costly or elaborate equipment or set-ups.

Herein is presented a general strategy to perform reactions under mild to moderate CO2 pressures with dry ice. This technique obviates the need for ...