PLD担任加拿大蛋白质工程研究主席。这项工作由加拿大卫生研究所向民盟提供的赠款资助。这项工作还得到了日本科学促进协会（JSPS）和日本生物导向技术研究促进机构（BRAIN）的科学研究资助。我们感谢克里斯·马歇尔博士和迈克·奎珀博士开创性的工作，导致FIPA。我们还感谢萨凯·齐达博士为这项工作提供设施，并感谢劳里·格雷厄姆博士为荧光灯激发和排放过滤器的建立提供便利。

1. 生长单一冰晶
<ol><li>拿一个干净的金属锅（直径15厘米，高4.5厘米），适合，可以漂浮在乙烯乙二醇冷却浴。</li>
	<li>准备聚氯乙烯 （PVC） 圆柱形模具，直径 4.5 厘米，高 3-4 厘米，厚 4 毫米），从管道锯断面。<ol>
<li>一侧切一个档次（1毫米宽，2毫米高）（图1A）。</li>
		<li>准备尽可能多的模具，可以舒适地放入锅（图1B）。 注：一项研究表明，聚乙烯醇（PVA）可以影响冰核22。然而，在我们的开放模具PVC系统中，我们没有遇到非典型冰层的问题。</li>
	</ol>
</li>
	<li>将真空润滑脂的光膜涂在每个模具的底部表面环上，即切出缺口的表面。将这个涂有油脂的凹面密封在金属平底锅上，凹槽定位于远离平底锅中心的地方。小心不要用油脂填充或阻塞凹槽。</li>
	<li>将 0.22 μm 过滤和脱气/除离子水添加到锅的中心，但在模具之外，并允许水通过凹槽慢慢进入模具。小心不要引入任何泡沫。水层应约5毫米深。</li>
	<li>将平底锅放入温度控制的乙二醇浴池中，冷却至-0.5 °C。 平底锅应该是完全水平的。如有必要，在平底锅两侧添加压载重量。</li>
	<li>锅和水达到 -0.5 °C 后，在锅中间和模具外加入一小块冰。<ol>
<li>这将核化冰在超冷水中的生长，穿过锅和模具。每个模具底部的小缺口只能通过一个冰晶传播，导致每个模具中只有一个冰晶。</li>
		<li>隔夜孵化形成一层冰。</li>
	</ol>
</li>
	<li>在接下来的三天里，每天向每个模具添加 13 毫升 4 °C 的脱气/除离子水，并在每增加一天后将乙二醇浴池的温度降至 -0.8 °C，第二天降至 -1.1 °C，第三天降至 -1.5 °C。<ol>
<li>在那些温度下孵化过夜。</li>
		<li>到第四天，模具应该完全装满冰。</li>
	</ol>
</li>
	<li>将模具从平底锅中拉下来，将冰晶从模具中推出，并存放在干净的表面（如称重船）中，在 -20 °C 冰柜中存放约 1 小时，然后再处理。</li>
	<li>与其准备许多小的单一冰晶，一个体积几升的大单冰晶可以在一个恒温孵化器中准备，正如骑士23所描述的。如果将大冰晶保存在 -15 至 -20 °C 的冰柜中，则可储存一年或更长期。单晶部分可根据需要用锯从冰块上切开。</li>
</ol>2. 确定冰晶的奇点和方向
<ol><li>通过在冰柜室中观察两个交叉的极性（图1D）来确定从模具中排出的冰是否是单个晶体。<ol>
<li>如果冰晶是单一的，则不应看到任何裂缝或不连续性，冰晶内的光向不应发生变化。 注意：如果没有冰柜室，可以在所有需要的步骤中使用冷室，谨慎地快速工作并谨慎处理冰。</li>
	</ol>
</li>
	<li>由于冰的裂口，可以同时确定 c轴的方向。使用以下信息确定方向：<ol>
<li>当 c轴与事件光完全平行时，理论上，没有光会穿过交叉的极性。如果事件光的标题与 c轴平行，则当光在交叉极性之间旋转时，均匀的多色光谱通过晶体传输。这种均匀的发射产生于冰Ih沿其 c轴24的光学不活动。冰晶的基底平面对 c轴是正常的。</li>
		<li>当 c轴与事件光进一步平行，冰晶在交叉极性之间旋转时，传输的光将每旋转 90°，传输的光将交替 0-100% 传输。</li>
		<li>最常见的情况是 ，c轴对圆柱形冰晶的圆形平面是正常的。</li>
	</ol>
</li>
	<li>通过将冰晶紧紧包裹在铝箔中，用针头将一个小孔戳入基底平面上的冰（对c轴正常），并将其置于真空中 20 分钟，从而确定 a 轴的方向。<ol>
<li>这种治疗将在基底平面上产生六边形对称性的蚀刻，其中A轴穿过六面星的顶点（图2A）。</li>
		<li>如果需要，冰晶可以用锯子平行或垂直于六边形的一侧切割，分别用垂直于冷手指的主棱镜或次要棱镜平面安装它（图3）。</li>
	</ol>
</li>
</ol>3. 将荧光标签防冻蛋白吸附到单一冰晶中
<ol><li>将单个冰晶安装到冷手指 上（图1C），首先将一个腔钻进水晶顶部。为此，用两根直径稍异但与冷指直径相似的铝棒交替融化冰层，形成冷手指可以容纳的腔。</li>
	<li>将冷手指冷却至-0.5 °C，放在冰腔中，并将冰晶保持原位，直到它冻结到金属（图2B）。将晶体连接到手指时避免气泡，因为它们会阻碍热量从手指到棒的有效传输。</li>
	<li>用过滤过的除离子水或缓冲器填充一个直径约为冰晶两倍的半球杯，冷却至约 4 °C。 将冰块冰晶浸入杯中，去除多余的水或缓冲液，使冰晶顶部与液层大致水平，冰不会接触杯壁。<ol>
<li>用绝缘材料盖住杯子，将温度降低到-5°C。</li>
		<li>等待大约1小时，冰晶形成一个半球，检查其状态大约每20分钟（图2C）。</li>
		<li>冰会通过融化和生长冰晶来形成半球杯的形状，但触摸杯壁绝不应过度生长。墙壁和半球之间至少应该有1厘米的缝隙，冷手指不应该从冰上伸出来。</li>
	</ol>
</li>
	<li>从冰晶中取出杯子，将荧光蛋白溶液加入最终体积为 25-30 毫升，并达到所需的分析浓度，小心保持杯中液体总体积不变。典型的 AFP 浓度为 0.1 毫克/毫升。<ol>
<li>将冰晶重新注入杯中，使冰晶顶部与液体处于水平，冰晶不会接触杯壁（图2D）。</li>
		<li>将冷手指温度降至 -8 °C，让蛋白质溶液冻结到冰晶中 2-3 小时，经常搅拌溶液。蛋白质溶液形成的冰在阻止冰生长之前应至少为5毫米。</li>
	</ol>
</li>
	<li>从杯子中取出冰晶，同时仍然附着在冷手指上。通过将冷却剂通过冷手指加热到略高于 0 °C，将冰从后者分离，并等待冰晶融化。</li>
	<li>将水晶平坦的一面放在干净的表面上，如称重盘，小心不要触摸新形成的冰，在交接前至少存放在-20°C。</li>
</ol>4. 防冻蛋白冰平面的可视化
<ol><li>荧光的可视化是在较暗的冰柜或冷室进行的，通过将冰晶平坦的一面放在带有波长特定激发滤光片的灯下，以激发荧光标签和相机发射过滤器以阻止任何其他非特定光。根据图案，可以估计受AFP约束的冰平面（图4）。</li>
	<li>如果没有波长特定的灯，则可以使用紫外线灯箱。</li>
	<li>传统的冰蚀刻也可以简单地通过允许冰半球在-20°C升华至少3小时，之后残留蛋白粉可能会在冰面上可见（图5）。</li>
	<li>可以重复第 2.3 步，以确定完成的冰半球 的斧头的方向。</li>
</ol>

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L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Role+of+glycopeptides+and+peptides+in+inhibition+of+crystallization+of+water+in+polar+fishes.">Role of glycopeptides and peptides in inhibition of crystallization of water in polar fishes.</a> Philos. T Roy. Soc. B. 304 (1121), 575-588 (1984).</li><li>Pertaya, N., 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=Fluorescence+microscopy+evidence+for+quasi-permanent+attachment+of+antifreeze+proteins+to+ice+surfaces.">Fluorescence microscopy evidence for quasi-permanent attachment of antifreeze proteins to ice surfaces.</a> Biophys. 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F., 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=Structural+basis+for+the+superior+activity+of+the+large+isoform+of+snow+flea+antifreeze+protein.">Structural basis for the superior activity of the large isoform of snow flea antifreeze protein.</a> Biochemistry. 49 (11), 2593-2603 (2010).</li><li>Takamichi, M., Nishimiya, Y., Miura, A., Tsuda, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fully+active+qae+isoform+confers+thermal+hysteresis+activity+on+a+defective+sp+isoform+of+type+iii+antifreeze+protein.">Fully active qae isoform confers thermal hysteresis activity on a defective sp isoform of type iii antifreeze protein.</a> FEBS J. 276 (5), 1471-1479 (2009).</li><li>Bar-Dolev, M., Celik, Y., Wettlaufer, J. S., Davies, P. L., Braslavsky, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=New+insights+into+ice+growth+and+melting+modifications+by+antifreeze+proteins.">New insights into ice growth and melting modifications by antifreeze proteins.</a> J. R. Soc. Interface. 9 (77), 3249-3259 (2012).</li><li>Celik, 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=Microfluidic+experiments+reveal+that+antifreeze+proteins+bound+to+ice+crystals+suffice+to+prevent+their+growth.">Microfluidic experiments reveal that antifreeze proteins bound to ice crystals suffice to prevent their growth.</a> Proc. Natl. Acad. Sci. U.S.A. 110 (4), 1309-1314 (2013).</li><li>Garnham, C. P., Campbell, R. L., Walker, V. K., Davies, P. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Novel+dimeric+beta-helical+model+of+an+ice+nucleation+protein+with+bridged+active+sites.">Novel dimeric beta-helical model of an ice nucleation protein with bridged active sites.</a> BMC Struct. Biol. 11, (2011).</li></ol>

未声明任何利益冲突。

查尔斯·奈特研制的冰蚀方法，用于确定法新社的冰平面，大大推进了对AFP冰结合机理的研究。虽然AFP的结构可以通过X射线晶体学26，27 来解决，但没有明显的方法来推断AFP绑定在冰上的互补表面。当I型法新社从冬季比目鱼的最初特征，它被假设绑定到冰28的主要棱镜平面。然而，奈特的破冰实验I型法新社显示，他们与冰13金字塔平面结合。这一结果促使法新社研究界重?...

抗冻蛋白（AFPs）的产生是生活在冰层中环境中的一些生物体的重要生存机制。直到最近，人们还认为AFP的唯一功能是防止或减缓内部冰晶的生长，这些冰晶会阻断循环，造成组织损伤和渗透应激。不能容忍任何程度的冰冻的生物，如鱼，表达AFP，以完全抑制冰晶生长1。其他，如草，是耐冻和表达AFP，以抑制冰的再封装，减少形成大冰晶在他们的组织2。在低温下稳定膜是另一个功能，建议为AFP3。最近，一个新的角色被建议为法新社的南极细菌， 马里诺莫纳斯原始，从冰覆盖的咸水湖4。这个AFP是一个更大的粘合蛋白5的一部分，被认为是附加细菌到冰上，以更好地获得氧气和营养物质6。其他微生物已知分泌AFP，这可能改变它们生活7的冰的结构。
在一些鱼类、昆虫、植物、藻类、细菌、硅藻和真菌中发现了AFP。它们具有显著不同的序列和结构，与不同祖先在不同场合的进化相一致：然而，它们都与冰结合，并通过吸附抑制机制8抑制其生长。AFP各有一个特定的表面，作为其冰结合点（IBS）。这些通常通过9-11表面残留物的现场定向突变来识别。IBS 假设将水分子排列在与特定冰平面相匹配的冰样图案中。因此，法新社形成其配体之前，绑定到它5，12。冰飞机可以通过米勒指数来定义，不同的AFP可以与不同的平面结合。因此，I型法新社从冬季比目鱼绑定到20-21金字塔平面13，III型法新社结合主棱镜和金字塔平面使用复合冰结合表面11，14，而云杉芽虫法新社，一个过度活跃的法新社，同时结合到主平面和基底平面15，16。其他过度活跃的AFP，如 MpAFP，与多个冰平面结合，如它们对单个冰晶半球5，17的完全覆盖所示。据推测，超活性AFP结合基底平面和其他飞机的能力，可能占其活性的10倍，比适度活跃的AFP18。虽然超活性AFP的效率是有据可查的，但它们与多个冰层结合的能力仍然不为人所知。
确定法新社飞往冰上飞机的最初方法是由查尔斯·奈特13，19开发的。在这种方法中，一个宏观的单一冰晶被安装在一个空心金属棒（冷手指）上，通过将其浸入装满脱气水的半球杯中形成半球。然后，半球被淹没在AFP的稀释溶液中，在几个小时内，由通过冷手指循环的乙二醇温度控制，从法新社溶液中长出一层冰到冰晶半球。冰晶从溶液中取出，从冷手指上分离出来，放置在-10至-15°C的冰柜室中。表面用锋利的刀片刮去防冻蛋白溶液的冷冻表面薄膜，冰晶允许升华至少3小时。升华后，由AFP绑定的冰平面可视为从残余蛋白质中提取的白色蚀刻图案。冰半球可以定向到其 c轴和 斧头，定位冰的基础平面和棱镜平面，并确定蚀刻补丁的米勒指数。
在这里，我们描述了对确定法新社绑定冰平面的原始方法的修改，我们称之为荧光基冰平面亲和力（FIPA）11。AFP 的荧光标记要么带有钟音标签，如绿色荧光蛋白 （GFP）11，16，17，20，要么与荧光染料共价绑定到 AFP5，21。荧光标记的AFP被吸收到一个冰晶中，并且使用与原始冰蚀实验相同的实验程序过度生长。在整个实验中，可以使用紫外线（UV）灯监测与生长的冰半球结合的AFP的程度。实验完成后，半球可以直接从冷手指上取下并成像，无需升华。然而，如果需要，半球可以留给升华，以可视化传统的冰蚀刻。对FIPA方法的修改将传统的冰蚀协议缩短了几个小时。此外，还有可能同时成像几个具有不同荧光标签的 AFP，以可视化 AFP 绑定冰平面的重叠模式。

<table border="0" cellpadding="0" cellspacing="0" width="605">
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			<td height="42" style="height:42px;width:177px;">NESLAB RTE Refrigerating Bath/Circulators</td>
			<td style="width:95px;">Thermo Scientific</td>
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			<td style="width:189px;"></td>
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			<td height="48" style="height:48px;width:177px;">Ethylene glycol, Premixed Antifreeze/Coolant</td>
			<td style="width:95px;">Certified</td>
			<td style="width:145px;">29-3037-0</td>
			<td style="width:189px;">Common automotive antifreeze</td>
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			<td height="65" style="height:65px;width:177px;">Cold finger</td>
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			<td style="width:189px;">Custom made with brass (9 cm long, 1.5 cm outer diameter)</td>
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			<td height="67" style="height:67px;width:177px;">Hemispherical cup</td>
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			<td style="width:189px;">Custom made with resin (8 cm outer diameter, 6 cm inner diameter)</td>
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			<td height="84" style="height:84px;width:177px;">High Dual Output Lighting System</td>
			<td style="width:95px;">Lightools Research</td>
			<td style="width:145px;">LT-99D2, Illumatools DLS 120 volts AC, LT-9470FX, LT-9549FX</td>
			<td style="width:189px;">Additional and custom excitation filters can be purchased from Lightools Research</td>
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			<td height="40" rowspan="2" style="height:40px;width:177px;">Camera</td>
			<td rowspan="2" style="width:95px;">Canon</td>
			<td rowspan="2" style="width:145px;">EOS 50D</td>
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			<td height="79" style="height:79px;width:177px;">Emission Filters</td>
			<td style="width:95px;">Lightools Research</td>
			<td style="width:145px;">LT-9EFPVG, LT-9GFPVG, LT-9RFPVG</td>
			<td style="width:189px;">Filter ring adapter may be required to fit filter onto camera lens</td>
		</tr>
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</table>

determining the ice-binding planes of antifreeze proteins by fluorescence-based ice plane affinity

防冻蛋白 （AFP） 表现在各种冷硬生物体中，以防止或减缓内部冰的生长。AFP 通过冰结合表面与特定的冰平面结合。基于荧光的冰平面亲和力 （FIPA） 分析是一种用于确定 AFP 与之结合的冰平面的修改技术。FIPA 基于确定法新社绑定冰平面的原始冰蚀方法。它在缩短的实验时间内产生更清晰的图像。在 FIPA 分析中，AFP 被荧光标记为有幻想标记或共价染料，然后慢慢融入宏观单一冰晶中，该晶体已预制成半球，并定向以确定 a 轴 和 c 轴。法新社的冰半球在紫外线下被成像，使用过滤器来阻挡非特异性光，以可视化法新社的平面。AFP 的荧光标签允许实时监控 AFP 吸附到冰中。已发现这些标签不会影响 AFP 绑定的平面。FIPA 分析还引入了将多个不同标签的 AFP 绑在同一个单一冰晶上的选项，以帮助区分其绑定平面。FIPA的这些应用有助于增进我们对AFP如何与冰结合以阻止其生长的理解，以及为什么许多产生AFF的生物会表达多种AFP等形。

单个冰晶的准备和安装是 FIPA 程序的两个步骤，其中最常出错。确定准备好的冰晶是否为单一的，通过交叉极性体（图1D）检查它，如协议部分的第2.1步所概述。如果用于 FIPA 分析的多晶冰晶，则结果将是非晶体在半球的不连续绑定，而没有连贯的结合模式 （图 6B）。如果冰晶接口位于法新社绑定的冰层周围，最终结果可能无法解释。因此，在进入下一步之前，应仔细检...

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

防冻蛋白 （AFP） 与特定的冰平面结合，以防止或减缓冰的生长。基于荧光的冰平面亲和力 （FIPA） 分析是对确定 AFP 绑定冰平面的原始冰蚀刻方法的修改。AFP 采用荧光标记，并融入宏观单一冰晶中，并在紫外线下可视化。

通过荧光基冰平面亲和力确定防冻蛋白的冰结合平面

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

8.9K 次观看.  Queen's University. 防冻蛋白 （AFP） 与特定的冰平面结合，以防止或减缓冰的生长。基于荧光的冰平面亲和力 （FIPA） 分析是对确定 AFP 绑定冰平面的原始冰蚀刻方法的修改。AFP 采用荧光标记，并融入宏观单一冰晶中，并在紫外线下可视化。

视频: 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.

LabVIEW操作的新型纳升渗透压仪冰结合蛋白的调查

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

科研

化学

Methods to Identify the NMR Resonances of the 13C-Dimethyl N-terminal Amine on Reductively Methylated Proteins

Nuclear magnetic resonance (NMR) spectroscopy is a proven technique for protein structure and dynamic studies. To study proteins with NMR, stable magnetic isotopes are typically incorporated metabolically to improve the sensitivity and allow for sequential resonance assignment. Reductive 13C-methylation is an alternative labeling method for proteins that are not amenable to bacterial host over-expression, the most common method of isotope incorporation. Reductive 13C-methylation is a chemical reaction performed under mild conditions that modifies a protein&#39;s primary amino groups (lysine &#949;-amino groups and the N-terminal &#945;-amino group) to 13C-dimethylamino groups. The structure and function of most proteins are not altered by the modification, making it a viable alternative to metabolic labeling. Because reductive 13C-methylation adds sparse, isotopic labels, traditional methods of assigning the NMR signals are not applicable. An alternative assignment method using mass spectrometry (MS) to aid in the assignment of protein 13C-dimethylamine NMR signals has been developed. The method relies on partial and different amounts of 13C-labeling at each primary amino group. One limitation of the method arises when the protein&#39;s N-terminal residue is a lysine because the &#945;- and &#949;-dimethylamino groups of Lys1 cannot be individually measured with MS. To circumvent this limitation, two methods are described to identify the NMR resonance of the 13C-dimethylamines associated with both the N-terminal &#945;-amine and the side chain &#949;-amine. The NMR signals of the N-terminal &#945;-dimethylamine and the side chain &#949;-dimethylamine of hen egg white lysozyme, Lys1, are identified in 1H-13C heteronuclear single-quantum coherence spectra.

Methods to Identify the NMR Resonances of the 13C-Dimethyl N-terminal Amine on Reductively Methylated Proteins

Two methods for assigning the &#945;- and &#949;-dimethylamine nuclear magnetic resonance signals of a reductively 13C-methylated N-terminal lysine are described. One method utilizes the pH-induced selectivity of the reductive methylation reaction, and the other uses aminopeptidase to selectively remove the N-terminal lysine.

Nuclear magnetic resonance (NMR) spectroscopy is a proven technique for protein structure and dynamic studies. To study proteins with NMR, stable magnetic ...

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.

生物分子有序结构由短肽的自组装形成

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.

亚毫秒构象变化蛋白的光热光束偏转已解决

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.

PAD4活动通过亲荧光底物类似物基于荧光监测

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.

优化合成蛋白质：Interpositional依赖性的鉴定指示在结构和/或功能性连接的残留

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.

在水中水合蛋白原位表征SALVI和TOF-SIMS

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.

使用Photoredox催化剂蠕虫状胶束的简便合成可见光介导的分散聚合

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.

确定缓蚀剂/金属界面的化学成分与XPS：最小化后浸入氧化

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.

液相色谱离子迁移 QTOF 质谱测定蛋白质生物中宿主细胞蛋白的 HS-MRM 法

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