Name: measuring biomolecular dsc profiles with thermolabile ligands to rapidly characterize folding and binding interactions
Uploaded: 2017-11-21T12:30:00.000+00:00
Duration: 9 min 15 s
Description: Watch this Scientific Journal Video about Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions at JoVE.com

r.w.h. V 得到加拿大麦吉尔自然科学和工程研究理事会 (NSERC) Bionanomachines 的培训项目的支持。a.k.m. 和 p.e.j. 得到了 NSERC 赠款 327028-09 (ak M) 和 238562 (p.e.j.) 的支持。

1. 样品制备
<ol><li>净化所需的生物13。 注: 本协议使用购买的可卡因结合 DNA 适 MN4 后, 交换2米氯化钠三次后, 三轮的去离子水使用离心过滤器与 3 kDa 分子量的截止膜。</li>
	<li>合成和纯化, 或购买所需的耐热配体13。 注: MN4 结合耐热配体可卡因。MN4 还结合奎宁, 这是作为一个负控制的配体 thermolability 在这些实验温度。</li>
	<li>准备用于透析纯化生物和配体溶解的缓冲剂 (20 毫米磷酸钠和140毫米氯化钠缓冲液, pH 7.4, 用于 MN4 和这里使用的配基)。</li>
	<li>透析生物对至少2升的缓冲使用透析管与 0.5-1.0 kDa 切断。</li>
	<li>通过已彻底平衡缓冲区的0.2 µm 筛选器筛选最终缓冲区 (称为工作缓冲区)。</li>
	<li>称量所需的配体质量, 并将其溶解在过滤工作缓冲中。如果所需的配体浓度要求太小而不能准确称量的质量, 就做一个浓缩的配体溶液 (例如 10x)。 注意: 至关重要的是, 所有的 DSC 实验使用相同的工作缓冲区的样品和配体,即, 从来没有执行的实验中, 配体被溶解在不同批次的工作缓冲区比生物, 因为这将导致缓冲区数据中的不匹配工件。</li>
	<li>通过使用工作缓冲区彻底平衡的0.2 µm 过滤器筛选生物库存解决方案。</li>
	<li>测定生物浓度 (260 nm 的核酸, 如 MN4 和 280 nm 的蛋白质)。</li>
	<li>将准备好的生物和配体储存在一个4° c 的冰箱 (适用于 MN4 和这里使用的配基), 或在-20 或-80 ° c 时, 如果生物和配位物耐受冷冻和长期贮存是必需的。在加载到 DSC 之前, 将缓冲、生物和配体解决方案放在表顶部气 (请参见材料表)。 注: 脱气有助于防止在较高温度下的 DSC 形成气泡。气泡导致的信号伪影模糊了 DSC 峰值形状和基线。</li>
</ol>2. DSC 制备
<ol><li>从 DSC 中拧下压力手柄 (请参阅材料表)。</li>
	<li>从工作缓冲器上运行硅管, 并将其连接到参考毛细管的前法兰 (金属开口) 上。</li>
	<li>通过将后参照法兰连接到前面的样品法兰, 在参照和样品毛细管之间创建一座桥。</li>
	<li>将一根硅管连接到后面的样品法兰上, 然后用真空管路连接到一个废弃烧瓶。</li>
	<li>打开真空线, 用200毫升的工作缓冲器冲洗 DSC。</li>
	<li>用工作缓冲器加载 DSC 的参考毛细管。在参考毛细管法兰上附加大约 3-5 厘米的硅管部分。</li>
	<li>插入一个1毫升吸管尖端到后方法兰的硅管。用吸管绘制0.8 毫升的工作缓冲器, 并将吸管尖端与缓冲器插入前参照法兰的硅管中。</li>
	<li>轻轻按下吸管柱塞, 通过前硅管的工作缓冲到参考毛细管, 并进入后方法兰的附加吸管尖端。按下吸管柱塞直到工作缓冲液位到达前硅管的上方, 然后松开吸管柱塞直到工作缓冲液位到达后硅管的正上方。<ol>
<li>重复通过工作缓冲器来回传递, 以清除气泡的参考毛细管中的体积。 注: 通常情况下, 来回10次的解决方案足以清除任何气泡。</li>
	</ol>
</li>
	<li>用拇指盖上吸管尖端, 然后轻轻地拉上吸管尖端和前吸管, 将它们从参照法兰上取下, 并附上硅管。</li>
	<li>在步骤 2.6-2.9 中加载带工作缓冲的样品毛细管。将黑色塑料盖放在后面的参照和样品法兰上, 留下前法兰。</li>
	<li>连接压力手柄。</li>
	<li>打开 DSC 软件 (请参阅材料表), 并在电源读数稳定后单击接口顶部的红色向上箭头来增压仪器;在接口的右上方的一个盒子里, 随着仪器温度和压力读数的变化, DSC 的功率被指示出来。 注: 监控功率读数为 DSC 加压。超过10µW 的功率变化表明, 毛细血管中的气泡形成, 这可能导致数据中的工件。在继续之前, 必须删除并脱解决方案。</li>
	<li>通过执行正向和反向扫描, 将 DSC 与工作缓冲器平衡。在屏幕左侧的 "实验方法" 选项卡中, 确保选中 "扫描" 选项以在温度扫描模式下运行 DSC。 注: 实验参数为温度扫描范围、扫描速率、低、高温平衡时间和扫描次数。<ol>
<li>在 "实验方法" 标签下的 "温度参数" 中, 单击 "加热" 按钮。进入1和100° c 为低和上部实验温度, 1 ° c/分钟为扫瞄率和六十年代为平衡期间。</li>
		<li>在平衡周期的输入字段下单击 "添加系列" 按钮。在弹出窗口中输入2到 "要添加的步骤" 字段 (对于一个加热和一个冷却扫描), 然后检查 "备用加热/冷却" 框。点击 "OK";添加的扫描显示在接口的下部。检查每个扫描的参数是否都是所需的。</li>
		<li>通过单击界面顶部的绿色 "播放" 按钮开始实验。导航到所需的文件夹, 并输入一个文件名, 以便在弹出式窗口中保存实验。通过单击 "实验方法" 选项卡右侧的 "数据" 选项卡, 查看实验进度。</li>
	</ol>
</li>
</ol>3. 收集耐热配体 DSC 数据集
注: 最小程序包括五实验: 具有和无配体的缓冲参考实验 (用于基线减法, 参见讨论), 样品实验与自由生物, 配体结合的生物, 和配体结合生物具有较长的高温平衡期。
<ol><li>为样本数据的基线减法运行参考实验。重新加载 DSC 与工作缓冲在两个毛细管和收集多个前和反向扫描在一个合适的温度范围在1° c 分钟-1与一个上层 (高温) 平衡时间的120s。<ol>
<li>通过逐个突出显示并单击接口的中间右边的红色 X, 从接口的下部删除以前的缓冲区平衡扫描。通过单击 "添加系列" 按钮添加新扫描, 在 "添加步骤" 字段中输入 20, 然后检查 "备用加热/冷却" 框。单击 "确定", 然后单击上面的 "绿色播放" 按钮运行实验。</li>
		<li>重复步骤 3.1-3.1.1 与工作缓冲, 其中含有所需的配体在两个毛细管的浓度, 以获得对配体的参考实验 (收集两个单独的实验使用120s 和600s 高温平衡时间分别用于获得耐热配体转换的速率常数。 注: 此处使用的扫描速率可确保后续实验中的生物在正向和反向扫描中处于热平衡状态 (请参见讨论)。扫描速率 < 0.1-0.2 ° c min-1导致噪音热, 不适用于 DSC 实验。温度应从远低于自由生物的熔化温度, 以及超过配体饱和生物 (~ 20-80 ° c MN4) 的熔化温度。验证扫描的重现性 (例如, 10 前向和10反向扫描20总共足够)。</li>
		<li>如果使用多个配体 (如可卡因和奎宁), 冲洗的 DSC 与200毫升的工作缓冲 (重复从步骤 2.5) 之间的运行, 以消除配剂从毛细血管和防止交叉污染。 注: 在配体结合的运行后, 对自由生物进行复制实验, 以检查前配体是否对毛细管壁吸附强, 并在缓冲冲洗时没有充分去除。如果游离生物的热在配体结合实验后出现了更大的变化和较高的变性温度, 那么很可能在冲洗后的量热计中仍然存在着前配体。用 20% Contrad-70 在60° c 时, 用塑料帽和压力手柄将毛细血管孵化, 除去吸附的配体。在 DSC 软件中, 在实验方法选项卡下将实验模式改为 "等温". 选择 3600 s 为期间和60° c 为等温温度, 以零进入平衡时间。单击 "添加到实验方法"。等温实验出现在屏幕的下部。完成后, 用2升去离子水冲洗仪器, 重复步骤2.5。</li>
	</ol>
</li>
	<li>使用与参考扫描相同的 DSC 加载过程和实验参数运行样品实验。对于自由生物数据集, 请确保参考毛细管包含工作缓冲区, 而样品毛细管则包含在工作缓冲中所需浓度的自由生物。<ol>
<li>在配体结合实验中, 确保配体在参考毛细管中处于工作缓冲中, 生物加配体在样品毛细管中处于工作缓冲中。在步骤2.5 中, 在不同配体的添加物之间冲洗系统。</li>
	</ol>
</li>
	<li>执行一个额外的实验与生物绑定到耐热配体的高温平衡期增加到600s 和所有其他实验参数是相同的步骤3.2.1。 注: 选择第二配体实验的高温平衡期的持续时间, 以确保配体比短平衡时间实验更迅速地耗尽。如果在第一个实验中, 配体结合的峰值衰减缓慢, 作为扫描数的函数 (例如, 连续峰值的差异是≤0.5 ° c), 估计在高温平衡期间增加10到20倍, 以在第二次试验中充分消耗配体。对配体转换速率常数的精确计算要求, 第二个实验的配体相对于第一个试验有更快的损耗。从两个实验的全球分析中提取的配体浓度将是相似的, 因此, 如果在第二个实验中配体损耗没有得到足够的加速, 就无法使用。</li>
</ol>4. 数据处理
<ol><li>在 dsc 数据分析软件中打开 dsc 实验文件 (请参阅材料表), 并将原始电源数据导出为电子表格。</li>
	<li>将包含原始电源数据的电子表格导入到软件中以进行数据拟合。</li>
	<li>基线减去从自由和配体结合的生物实验中减去缓冲功率数据的样本数据。 注: 对于耐热配体实验, 每次扫描时, 初始配体浓度均呈下降趋势。因此, 从样本扫描1中减去缓冲区扫描1是理想的, 等等。我们发现, 随着配体转换的进行, 与可卡因的缓冲扫描没有明显的变化, 因此一个单一的耐热配体缓冲扫描可以用来减去所有耐热配体的数据。</li>
	<li>将基线减去的采样功率数据转换为热容量。 注意: 转换需要生物的部分特定卷, 可以估计为14,15,16。将功率转换为热容量的公式已被描述为以前的17。</li>
</ol>5. 数据分析
<ol><li>全局拟合的短平衡时间耐热配体结合热容量数据集与一组基线, 配体浓度, 折叠, 和配体结合参数, 如前所述4。</li>
	<li>重复长平衡时间数据集的全局拟合, 以计算耐热配体转换的速率常数, 如前所述4。</li>
</ol>

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作者声明没有利益冲突。

修改和故障排除
在图 1 和图 2中使用的全局管接头分析的详细信息已被描述为以前的4。在这里, 我们概述了执行和分析 DSC 结合实验与耐热配体的实际方面。请注意, 仅为耐热配体获得的 DSC 基线从配体 + 生物数据集中减去, 有效地抵消热转换过程本身释放或吸收的热量。标准耐热配体全局拟合分析 (图 1 和图 2) 假定系统在整个温度扫描过程中处于热力学平衡状态, 并且耐热配体浓度是恒定的在每个热, 在高温平衡期间完全减少。我们以前已经表明, 这种假设适用于可卡因绑定 MN4, 并预计将举行任何耐热配体/生物系统与这些动力学类似。
然而, 在某些情况下, 系统不能被认为是在热力学平衡和/或浓度的配体不能被视为恒定在整个一次扫描。这些包括 i) 当配体热转换迅速相对于温度扫描率, ii) 当生物经历不可逆转的聚集在高温, iii) 当折叠/展开速率是缓慢的比扫描率, 和 iv)当配体缔/离解率比扫描速率慢时。在这些情况下, 系统是在动能, 而不是热力学控制, 并在参考4中所给的分析不能严格地适用。数据可以在图 3之后定量模拟, 如补充文件 1中所述。原则上, 这些 kinetics-based 计算可以用来拟合非平衡 DSC 数据, 有可能产生动能和热力学数据, 但是这一分析超出了本文的范围。相反, 我们提出一些有代表性的模拟 DSC 数据, 以协助读者识别非平衡情况。
一个热力学控制的理想例子如图 4a, b.DSC 热的自由生物是 superimposable (图 4a) 和扫描与耐热配体不显示滞后, 这样的熔融温度观察到的上扫描匹配的折叠温度前向下扫描 (图 4b)。当耐热配体转换迅速与扫描速度相比, 大的扭曲出现在热和热力学方程不占峰值形状, 如图 4c, d所示。这可以通过增加扫描速率来缓解。当生物聚集在温度依赖性的方式, DSC 踪影为自由生物显示连续的减少的大小 (图 4e), 而耐热配体的加法产生减少热档的模式与理想情况类似, 但按递减的生物浓度 (图 4f) 进行缩放。当折叠/展开动力学比扫描速度慢, 滞后是明显的 DSC 痕迹的自由生物, 使表面的变性温度上扫描高于明显的复温度在向下扫描 (图 4g)。添加一个耐热配体导致熟悉的模式减少热档, 特别是对向上扫描 (图 4h)。最后, 快速折叠和慢束缚的系统产生无滞后的 DSC 热为自由的生物 (图 4i), 但是数据与耐热配体显示滞后, 在表面熔化温度上扫描是高于上一个向下扫描的表观折叠温度 (图 4j)。然而, 在上扫描和下扫描中, 典型的降低热档的模式是明显的。在缓慢折叠或结合动力学的情况下, 非平衡行为可以通过降低扫描速率来缓解, 尽管这会在整个扫描过程中发生不可配体热转换的风险。在实际操作中, 可以手动调整扫描速率和上平衡温度, 以获取类似图 4ab的数据。
技术的局限
我们对耐热配体的 DSC 结合实验的热力学分析要求, 折叠和装订过程相对较快, 在每次扫描的高温部分之前, 耐热的配位转换是缓慢的。当折叠和/或绑定状态的生存期大于大约三十年代 (koff, ku < 0.03 s-1) 时, 在执行1° c min-1的扫描时, 迟滞变得可辨识。此外, 当配体转化率常数高于约 kc = 10-4 s-1在变性转变之前, 在单个扫描过程中, 配体可能会有明显的损耗。当不可逆聚集发生时, 我们的分析的应用也不适当。在这些情况下, 可以对数据应用更高级的建模。如果配体转换如此迅速, 在第一次变性转变之前就达到了完成, 那么就没有亲和性信息可用。
关于现有方法的意义
我们第一次的方法允许 DSC 用于测量高亲和性, 耐热配体的结合热力学。通过对所有扫描执行全局同时分析, 用高精度的20提取热力学参数。另外一个好处是, 如果热转换产品对自由生物没有亲和力, 则可以在很少的一个实验中收集完整的数据集。相比之下, 生产一个典型的 non-thermolabile 配体的实验 DSC 系列需要〜7-10 总实验。
未来应用
这种方法直接应用于描述药物发现运动中的致密、耐热抑制剂。一些治疗性的化合物, 如抗生素和苯被称为耐热, 接受快速水解或接近生理 pH 值和温度为60-70 ° c11。这一 DSC 方法很好地定位, 以识别和表征更多。同样, 如上所述, 对拟合协议的修改要考虑到系统的动力学, 而不是热力学的控制, 这有可能为更多的生物相关性系统打开大门。
协议中的关键步骤
其中一个最重要的实验程序要考虑的是透析或交换的生物和配体到相同的工作缓冲解决方案 (协议步骤 1.3-1.6)。配体和生物溶液之间的缓冲不匹配会导致基线和样本扫描中的大型工件, 这完全掩盖了相关的折叠数据。此外, 重要的是, 功率读数稳定之前, DSC 是加压, 使它可以在加压过程中监测 (协议步骤 2.3)。如果在加压过程中, 功率读数的变化超过了µW 10, 那么气泡很可能在毛细管中形成, 并可能导致数据中的大型工件。在这种情况下, 需要更彻底地脱解决方案。
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/55959/55959fig3.jpg"> 图3。生物分子折叠, 结合到耐热配体, 和不可逆转的聚集.耐热配体 (L) 以速率常数 kc转换为乘积 (X)。X 对生物没有亲和力。生物交换的绑定状态 (B) 与自由折叠状态 (F) 与速率常数 koff和 kon。F 与展开状态 (u) 交换, 速率常数 ku和 kf。U 不可逆转地将速率常数 kagg转换为聚合状态 (A)。<a href="//ecsource.jove.com/files/ftp_upload/55959/55959fig3large.jpg" target="_blank">请单击此处查看此图的较大版本.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/55959/55959fig4.jpg"> 图4。平衡和动力学控制的 DSC 实验的计算机模拟在缺席和存在耐热配体.(a) 平衡生物分子折叠。(b) 平衡折叠、耐热配体结合、慢耐热配体转换。(c) 平衡生物分子折叠。(d) 平衡折叠, 耐热配体结合, 快速耐热配体转换。(e) 平衡生物分子折叠和缓慢不可逆聚集。(f) 平衡折叠、装订、慢耐热配体转换和缓慢的不可逆聚合。(g) 缓慢的生物分子折叠。(h) 慢折叠、平衡结合、慢耐热配体转换。(i) 平衡生物分子折叠。(j) 平衡折叠、慢耐热配体结合、慢耐热配体转换。在所有面板中, 第一次和最后一次模拟的扫描分别是深红色和深蓝色。只显示光和深蓝色热的面板表示所有模拟的扫描都覆盖, 并且只有最后两个在图中可见。DSC 实验模拟了20扫描 (10 熔化和10退火) 在1° c min-1扫描率, 以温度范围0-80 ° c。某些面板显示较窄的温度范围, 以便更好地可视化模拟趋势。模拟中的生物和配体浓度分别为200µM 和10毫米。每一次实验都是在扫描前0° c 的600s 平衡时间和每个后续扫描之间的六十年代平衡时间模拟的。平衡结合和折叠的阿伦尼乌斯参数为on = 5 x 10-1 M-1 s-1,off = 1 x 1019 s-1, E上的=-20 焦摩尔-1, Ea关闭= 120 焦摩尔-1,折叠= 1 x10-14 s-1,展开= 5 x 1018, E折叠=-80 焦摩尔-1, 和 E展开= 120 焦摩尔-1.动力学控制的绑定和折叠的阿伦尼乌斯参数为on = 5 x 10-3 M-1 s-1,off = 1 x 1016 s-1, E在=-20 焦摩尔-1, Ea关闭= 120 焦摩尔-1,折叠= 1 x10-16 s-1,展开= 5 x 1016, E折叠=-80 焦摩尔-1, 和 E展开= 120 焦摩尔-1.阿伦尼乌斯参数的缓慢和快速耐热配体转换是一个慢= 7.509 x 1010 s-1, E慢= 94.65 焦摩尔-1, 和快速= 1 s-1, ea快速= 10 焦摩尔-1。慢不可逆聚合的阿伦尼乌斯参数为agg. = 5 x 107 s-1和 Eagg. = 80 焦摩尔-1。通过 hUF (展开)、hBF (绑定) 和 hAF (聚合) = 200、-140 和50焦摩尔-1分别计算了过量的热容量。用耐热配体的动力学控制 DSC 实验的理论描述和用于执行这些模拟的脚本 (以及必要的参数) 在补充文件 1中提供。<a href="//ecsource.jove.com/files/ftp_upload/55959/55959fig4large.jpg" target="_blank">请单击此处查看此图的较大版本.</a>

差示扫描量热 (DSC) 是量化生物分子结合和折叠相互作用的有力方法1,2,3。DSC 的优点包括其阐明装订和折叠机制的能力, 并产生相应的热力学参数2,3。此外, DSC 可以在接近生理条件下的溶液中进行, 不需要生物或配体的标签,例如, 荧光, 旋转标签或核同位素4。该仪器在温度下进行扫描, 测量在存在和没有配体的情况下变性生物所需的热量。所产生的热被用来提取调节配体结合和折叠过程的热力学参数。DSC 或其他热力学技术提供的信息对于指导药物靶向生物分子的设计是至关重要的1,5,6,7,8。然而, 反复扫描到高温 (〜 60-100 ° c) 可能会有问题。例如, 许多药学重要化合物经过重排或分解后, 持续暴露在高温下9,10,11,即, 它们都是耐热的。通过 DSC 检查结合的相互作用通常需要多个正向和反向扫描, 以验证热的重现性, 用于热力学分析12。初始配体的热转化为次级形式, 具有改变的结合特性导致在连续热的形状和位置上明显的差异, 因为初始配体的浓度随着每次扫描而减小, 而热转换产品积累。这些数据集不适于传统的分析。
我们最近开发了一个耐热配体 DSC 数据集的全局拟合方法, 它产生了一套完整的热力学参数, 用于控制生物分子的折叠和结合作用, 从单个配体结合实验中引用免费生物的必要热4。与标准 DSC 方法相比, 该分析减少了10倍所需的实验时间和样品。我们已经考虑了配体热转换假设这发生在每个扫描的高温部分, 热不依赖于配体浓度。因此, 配体浓度是热部分中的常数, 用于提取热力学参数。通过对较长的高温平衡期进行一项补充试验, 进一步论证了配体热转换速率常数的计算方法。对于配体热转换较不依赖温度的系统 (即, 在所有温度下都能明显地发生), 可以对该分析进行修改, 使其包括可变配体浓度。在这里, 我们演示了这个过程的 DNA 适 MN4 存在的耐热配体可卡因, 迅速转换为 benzoylecgonine 在高温 (> 60 ° c)。奎宁是用于配体 thermolability 的负控制, 因为它不在这些实验温度下进行转换, 并且也结合到 MN4。我们描述了耐热配体 DSC 数据集的获取及其分析结果的热力学和动力学参数的折叠, 结合, 和配体转换过程。

<table><tbody><tr><td>Sodium chloride</td><td>Chem Impex</td><td>#00829</td><td></td></tr><tr><td>Sodium phosphate monobasic dihydrate</td><td>Sigma Aldrich</td><td>71502</td><td></td></tr><tr><td>Sodium phosphate dibasic</td><td>Sigma Aldrich</td><td>S9763</td><td></td></tr><tr><td>Deioinized water for molecular biology</td><td>Millipore</td><td>H20MB1001</td><td></td></tr><tr><td>0.2 micron sterile syringe filters</td><td>VWR</td><td>CA28145-477</td><td></td></tr><tr><td>3 kDa centrifugal filters</td><td>Millipore</td><td>UFC900324</td><td></td></tr><tr><td>Dialysis tubing 0.5-1.0 kDa cutoff</td><td>Spectrum Laboratories</td><td>131048</td><td></td></tr><tr><td>Silicon tubing</td><td>VWR</td><td>89068-474</td><td></td></tr><tr><td>Plastic DSC flange caps</td><td>TA Instruments</td><td>6111</td><td></td></tr><tr><td>DNA aptamer MN4</td><td>Integrated DNA Technologies</td><td>https://www.idtdna.com/site/order/menu</td><td></td></tr><tr><td>Cocaine</td><td>Sigma Aldrich</td><td>C008</td><td></td></tr><tr><td>Quinine</td><td>Sigma Aldrich</td><td>22620</td><td></td></tr><tr><td>NanoDSC-III microcalorimeter</td><td>TA Instruments</td><td>http://www.tainstruments.com/nanodsc/</td><td></td></tr><tr><td>DSCRun software</td><td>TA Instruments</td><td>http://www.tainstruments.com/support/software-downloads-support/instruments-by-software/</td><td></td></tr><tr><td>NanoAnalyze software</td><td>TA Instruments</td><td>http://www.tainstruments.com/support/software-downloads-support/instruments-by-software/</td><td></td></tr><tr><td>Contrad-70</td><td>VWR</td><td>89233-152</td><td></td></tr></tbody></table>

measuring biomolecular dsc profiles with thermolabile ligands to rapidly characterize folding and binding interactions

差示扫描量热法 (DSC) 是一种用于量化生物分子折叠和结合相互作用的热力学参数的强大技术。这些信息对于新的药物化合物的设计是至关重要的。然而, 在 DSC 分析中使用的高温下, 许多药学相关配体在化学上不稳定。因此, 测量结合的相互作用是有挑战性的, 因为配体和热转换产品的浓度在热量计细胞内不断变化。在这里, 我们提出了一个协议使用耐热配体和 DSC 快速获得热力学和动力学信息的折叠, 结合, 和配基转换过程。我们已经将我们的方法应用于与耐热配体可卡因结合的 DNA 适 MN4。通过对耐热配体转换的新的全局拟合分析, 通过对 DSC 的实验, 得到了一套完整的折叠和结合参数。此外, 我们还证明了耐热配体转换的速率常数只能得到一个补充的 DSC 数据集。提出了识别和分析多个复杂场景中数据的准则, 包括生物的不可逆集合、慢折叠、慢束缚和耐热配体的快速损耗。

耐热配体 DSC 的代表性数据如图 1所示。在每次扫描 (图 1a) 中, 随着耐热配体的耗尽, 耐热配体结合峰的位置和高度先后向未绑定的生物转移。自由变性剖面被用作耐热配体转换终点 (图 1b) 的参考。MN4 绑定到奎宁的数据显示为耐热配体转换的负控制 (图 1b)。最后的耐热配体扫描有略高的过渡中点和峰值高度相对于未绑定的 MN4, 表明耐热配体转换产品 (benzoylecgonine) 有弱亲和力 MN4。图 1中的数据集的全局分析所产生的热力学参数列在表 1中。MN4 的折叠参数在存在的可卡因或奎宁是相同的错误, 正如预期的, 因为稀小分子预计不会扰乱自由生物的折叠热力学。结合参数与等温滴定量热法 (ITC)18一致, 表明 MN4's 对可卡因的偏爱是由更有利的结合焓驱动的。在图 2中, 增加高温平衡周期会使每个扫描相对于短平衡周期数据集的耐热配体浓度更明显地降低。利用两个数据集的最佳全局拟合浓度参数, 从图 2嵌入线的斜率计算高平衡温度下配体转换的速率常数。
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/55959/55959fig1.jpg"> 图1。耐热配体 DSC.(a) 热 MN4 (83 µM) 与可卡因 (初始浓度778µM) 的结合。第一次和最后一次扫描的 MN4 在存在的配体显示为深红色和蓝色的圆圈, 而相应的配合显示为有色线。(b) 热的自由 MN4 (83 µM、黑眼圈) 和连续扫描, 以奎宁 (880 µM, 彩色圆圈) 为约束。适合自由和奎宁绑定数据集分别显示为黑色和彩色线条。从参考文献4获得皇家化学学会的许可。<a href="//cloudflare.jove.com/files/ftp_upload/55959/55959fig1large.jpg" target="_blank">请单击此处查看此图的较大版本.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/55959/55959fig2.jpg"> 图2。测量耐热配体转化率常数.(a) 套热, MN4 与短 (120s, 暗红色) 和长 (600s, 深蓝色) 的可卡因的平衡时间分别为80° c。(b) 从 (a) 中的数据集的全局分析中提取的可卡因的浓度作为扫描数字的函数。实验点和指数拟合分别显示为彩色圆圈和线。该插页显示了一个线性适合先前描述的补充 Eq. 19 从哈克尼斯et al.使用优化的全球适合可卡因浓度的两个数据集4。以80° c 的配体热转换速率常数作为直线的斜率计算。给出了耐热配体转换速率常数的误差为±两个标准差。从参考文献4获得皇家化学学会的许可。<a href="//cloudflare.jove.com/files/ftp_upload/55959/55959fig2large.jpg" target="_blank">请单击此处查看此图的较大版本.</a>
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always"><tbody>
<tr>
<td>适合参数</td>
			<td>添加的可卡因</td>
			<td>奎宁添加</td>
		</tr>
<tr>
<td>∆HUF</td>
			<td>271.3±1。8</td>
			<td>272.5±4。0</td>
		</tr>
<tr>
<td>∆SUF</td>
			<td>824.4±5。1</td>
			<td>827.9±10。9</td>
		</tr>
<tr>
<td>a∆G超滤</td>
			<td>21.6±0。2</td>
			<td>21.6±0。9</td>
		</tr>
<tr>
<td>a∆HB1F</td>
			<td>-75.2±1。6</td>
			<td>-101.0±4。0</td>
		</tr>
<tr>
<td>a∆SB1F</td>
			<td>-154.2±5。0</td>
			<td>-213.7±12。0</td>
		</tr>
<tr>
<td>∆CpB1F</td>
			<td>-1.5±0。1</td>
			<td>-1.2±0。1</td>
		</tr>
<tr>
<td>a∆GB1F</td>
			<td>-28.5±0。2</td>
			<td>-36.2±0。7</td>
		</tr>
<tr>
<td>a∆HB2F</td>
			<td>-33.7±1。8</td>
			<td>-</td>
		</tr>
<tr>
<td>a∆SB2F</td>
			<td>-49.9±5。2</td>
			<td>-</td>
		</tr>
<tr>
<td>∆CpB2F</td>
			<td>-2.2±0。1</td>
			<td>-</td>
		</tr>
<tr>
<td>a∆GB2F</td>
			<td>-18.6±0。3</td>
			<td>-</td>
		</tr>
</tbody></table>表1。从全球分析的热力学参数 MN4 DSC 数据集使用可卡因和奎宁配体。参数在30° c 时计算。B1F 指的是可卡因或奎宁结合的折叠状态, B2F 指的是 benzoylecgonine 束缚的折叠态。δH和δG以焦/摩尔表示, ΔS 以 J/摩尔/k 表示, δCp 以焦/摩尔/k 值表示, 根据方差/协方法19计算。

Watch this Scientific Journal Video about Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions at JoVE.com

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions

我们提出了一个协议, 快速表征生物分子折叠和约束力的相互作用与耐热配体使用差分扫描量热法。

用耐热配体测量生物分子 DSC 剖面快速表征折叠和结合的相互作用

Differential scanning calorimetry (DSC) is a powerful technique for quantifying thermodynamic parameters governing biomolecular folding and binding ...

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Nanyang Technological University

Research

JoVE Journal

Biochemistry

8.2K 次观看.  McGill University. 我们提出了一个协议, 快速表征生物分子折叠和约束力的相互作用与耐热配体使用差分扫描量热法。

视频: Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions

Bio-layer Interferometry for Measuring Kinetics of Protein-protein Interactions and Allosteric Ligand Effects

We describe the use of Bio-layer Interferometry to study inhibitory interactions of subunit &#949;&#160;with the catalytic complex of Escherichia coli&#160;ATP synthase. Bacterial F-type ATP synthase is the target of a new, FDA-approved antibiotic to combat drug-resistant tuberculosis. Understanding bacteria-specific auto-inhibition of ATP synthase by the C-terminal domain of subunit &#949;&#160;could provide a new means to target the enzyme for discovery of antibacterial drugs. The C-terminal domain of &#949;&#160;undergoes a dramatic conformational change when the enzyme transitions between the active and inactive states, and catalytic-site ligands can influence which of &#949;&#39;s conformations is predominant. The assay measures kinetics of &#949;&#39;s binding/dissociation with the catalytic complex, and indirectly measures the shift of enzyme-bound &#949;&#160;to and from the apparently nondissociable inhibitory conformation. The Bio-layer Interferometry signal is not overly sensitive to solution composition, so it can also be used to monitor allosteric effects of catalytic-site ligands on &#949;&#39;s conformational changes.

The protocols here describe kinetic assays of protein-protein interactions with Bio-layer Interferometry. F-type ATP synthase, which is involved in cellular energy metabolism, can be inhibited by its &#949; subunit in bacteria. We have adapted Bio-layer Interferometry to study interactions of the catalytic complex with &#949;&#8217;s inhibitory C-terminal domain.

生物层干涉测量的蛋白质 - 蛋白质相互作用和变构配体反应动力学的影响

We describe the use of Bio-layer Interferometry to study inhibitory interactions of subunit &#949;&#160;with the catalytic complex of Escherichia ...

科研

化学

Differential Scanning Calorimetry &#8212; A Method for Assessing the Thermal Stability and Conformation of Protein Antigen

Differential scanning calorimetry (DSC) is an analytical technique that measures the molar heat capacity of samples as a function of temperature. In the case of protein samples, DSC profiles provide information about thermal stability, and to some extent serves as a structural &#8220;fingerprint&#8221; that can be used to assess structural conformation. It is performed using a differential scanning calorimeter that measures the thermal transition temperature (melting temperature; Tm) and the energy required to disrupt the interactions stabilizing the tertiary structure (enthalpy; &#8710;H) of proteins. Comparisons are made between formulations as well as production lots, and differences in derived values indicate differences in thermal stability and structural conformation. Data illustrating the use of DSC in an industrial setting for stability studies as well as monitoring key manufacturing steps are provided as proof of the effectiveness of this protocol. In comparison to other methods for assessing the thermal stability of protein conformations, DSC is cost-effective, requires few sample preparation steps, and also provides a complete thermodynamic profile of the protein unfolding process.

Differential scanning calorimetry measures the thermal transition temperature(s) and total heat energy required to denature a protein. Results obtained are used to assess the thermal stability of protein antigens in vaccine formulations.

差示扫描量热 - 用于评估蛋白质抗原的热稳定性和构象的方法

Differential scanning calorimetry (DSC) is an analytical technique that measures the molar heat capacity of samples as a function of temperature. In the ...

生物化学

Measuring Interactions of Globular and Filamentous Proteins by Nuclear Magnetic Resonance Spectroscopy (NMR) and Microscale Thermophoresis (MST)

Filamentous proteins such as vimentin provide organization within cells by providing a structural scaffold with sites that bind proteins containing plakin repeats. Here, a protocol for detecting and measuring such interactions is described using the globular plakin repeat domain of envoplakin and the helical coil of vimentin. This provides a basis for determining whether a protein binds vimentin (or similar filamentous proteins) and for measurement of the affinity of the interaction. The globular protein of interest is labeled with 15N and titrated with vimentin protein in solution. A two-dimensional NMR spectrum is acquired to detect interactions by observing changes in peak shape or chemical shifts, and to elucidate effects of solution conditions including salt levels, which influence vimentin quaternary structure. If the protein of interest binds the filamentous ligand, the binding interaction is quantified by MST using the purified proteins. The approach is a straightforward way for determining whether a protein of interest binds a filament, and for assessing how alterations, such as mutations or solution conditions, affect the interaction.

Measuring Interactions of Globular and Filamentous Proteins by Nuclear Magnetic Resonance Spectroscopy NMR and Microscale Thermophoresis MST

Here, we present a protocol for the production and purification of proteins that are labeled with stable isotopes, and subsequent characterization of protein-protein interactions using Nuclear Magnetic Resonance (NMR) spectroscopy and MicroScale Thermophoresis (MST) experiments.

用核磁共振 (nmr) 和微尺度热能 (mst) 测量球状和丝状蛋白的相互作用

Filamentous proteins such as vimentin provide organization within cells by providing a structural scaffold with sites that bind proteins containing plakin ...

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Proteins are an important class of biological macromolecules that play many key roles in cellular functions including gene expression, catalyzing metabolic reactions, DNA repair and replication. Therefore, a detailed understanding of these processes provides critical information on how cells function. Integrative structural MS methods offer structural and dynamical information on protein complex assembly, complex connectivity, subunit stoichiometry, protein oligomerization and ligand binding. Recent advances in integrative structural MS have allowed for the characterization of challenging biological systems including large DNA binding proteins and membrane proteins. This protocol describes how to integrate diverse MS data such as native MS and ion mobility-mass spectrometry (IM-MS) with molecular dynamics simulations to gain insights into a helicase-nuclease DNA repair protein complex. The resulting approach provides a framework for detailed studies of ligand binding to other protein complexes involved in important biological processes.

Mass spectrometry (MS) has emerged as an important tool for the investigation of structure and dynamics of macromolecular assemblies. Here, we integrate MS-based approaches to interrogate protein complex formation and ligand binding.

综合结构质谱分析蛋白质结构和蛋白质配体配合物

Proteins are an important class of biological macromolecules that play many key roles in cellular functions including gene expression, catalyzing ...

Use of Microscale Thermophoresis to Measure Protein-Lipid Interactions

The ability to determine the binding affinity of lipids to proteins is an essential part of understanding protein-lipid interactions in membrane trafficking, signal transduction and cytoskeletal remodeling. Classic tools for measuring such interactions include surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC). While powerful tools, these approaches have setbacks. ITC requires large amounts of purified protein as well as lipids, which can be costly and difficult to produce. Furthermore, ITC as well as SPR are very time consuming, which could add significantly to the cost of performing these experiments. One way to bypass these restrictions is to use the relatively new technique of microscale thermophoresis (MST). MST is fast and cost effective using small amounts of sample to obtain a saturation curve for a given binding event. There currently are two types of MST systems available. One type of MST requires labeling with a fluorophore in the blue or red spectrum. The second system relies on the intrinsic fluorescence of aromatic amino acids in the UV range. Both systems detect the movement of molecules in response to localized induction of heat from an infrared laser. Each approach has its advantages and disadvantages. Label-free MST can use untagged native proteins; however, many analytes, including pharmaceuticals, fluoresce in the UV range, which can interfere with determination of accurate KD values. In comparison, labeled MST allows for a greater diversity of measurable pairwise interactions utilizing fluorescently labeled probes attached to ligands with measurable absorbances in the visible range as opposed to UV, limiting the potential for interfering signals from analytes.

Microscale thermophoresis obtains binding constants quickly at low material cost. Either labeled or label free microscale thermophoresis is commercially available; however, label free thermophoresis is not capable of the diversity of interaction measurements that can be performed using fluorescent labels. We provide a protocol for labeled thermophoresis measurements.

使用微尺度热泳测量蛋白质-脂质相互作用

The ability to determine the binding affinity of lipids to proteins is an essential part of understanding protein-lipid interactions in membrane ...

Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery

Thermal shift assays (TSAs) examine how the melting temperature (Tm) of a target protein changes in response to changes in its environment (e.g., buffer composition). The utility of TSA, and specifically of nano-Differential Scanning Fluorimetry (nano-DSF), has been established over the years, both for finding conditions that help stabilize a specific protein and for looking at ligand binding by monitoring changes in the apparent Tm. This paper presents an efficient screening of the Diamond-SGC-iNEXT Poised (DSi-Poised) fragment library (768 compounds) by the use of nano-DSF, monitoring Tm to identify potential fragment binding. The prerequisites regarding protein quality and concentration for performing nano-DSF experiments are briefly outlined followed by a step-by-step protocol that uses a nano-liter robotic dispenser commonly used in structural biology laboratories for preparing the required samples in 96-well plates. The protocol describes how the reagent mixtures are transferred to the capillaries needed for nano-DSF measurements. In addition, this paper provides protocols to measure thermal denaturation (monitoring intrinsic tryptophan fluorescence) and aggregation (monitoring light back-scattering) and the subsequent steps for data transfer and analysis. Finally, screening experiments with three different protein targets are discussed to illustrate the use of this procedure in the context of lead discovery campaigns. The overall principle of the method described can be easily transferred to other fragment libraries or adapted to other instruments.

Monitoring changes in the melting temperature of a target protein (i.e., thermal shift assay, TSA) is an efficient method for screening fragment libraries of a few hundred compounds. We present a TSA protocol implementing robotics-assisted nano-Differential Scanning Fluorimetry (nano-DSF) for monitoring intrinsic tryptophan fluorescence and light back-scattering for fragment screening.

纳米微分扫描荧光仪，用于在基于碎片的铅发现中筛选

Thermal shift assays (TSAs) examine how the melting temperature (Tm) of a target protein changes in response to changes in its environment (e.g., buffer ...

<meta charset="utf8"></head><body>用于蛋白质-配体相互作用的高通量热位移检测

Utilizing Thermal Shift Assay to Probe Substrate Binding to Selenoprotein O

Defining the biological importance of proteins with unknown functions poses a significant obstacle in understanding cellular processes. Although bioinformatic and structural predictions have contributed to the study of unknown proteins, in vitro experimental validations are often hampered by the optimal conditions and cofactors required for biochemical activity. Cofactor binding is not only essential for the activity of some enzymes but may also enhance the thermal stability of the protein. One practical application of this phenomenon lies in utilizing the change in thermal stability, as measured by alterations in the protein's melting temperature, to probe ligand binding. 
Thermal shift assay (TSA) can be used to analyze the binding of different ligands to the protein of interest or find a stabilizing condition to perform experiments such as X-ray crystallography. Here we will describe a protocol for TSA utilizing the pseudokinase, Selenoprotein O (SelO), for a simple and high-throughput method for testing metal and nucleotide binding. In contrast to canonical kinases, SelO binds ATP in an inverted orientation to catalyze the transfer of AMP to the hydroxyl side chains of proteins in a posttranslational modification known as protein AMPylation. By leveraging the shift in the melting temperatures, we provide crucial insights into the molecular interactions underlying SelO function.

<meta charset="utf8"></head><body>作者聚焦：通过热位移分析推进蛋白质的结构和生化研究

Here, we present the thermal shift assay, a high-throughput, fluorescence-based technique used to investigate the binding of small molecules to proteins of interest.

利用 Thermal Shift 分析探测底物与 Selenoprotein O 的结合

Defining the biological importance of proteins with unknown functions poses a significant obstacle in understanding cellular processes. Although ...

Isothermal Titration Calorimetry for Measuring Macromolecule-Ligand Affinity

Isothermal titration calorimetry (ITC) is a useful tool for understanding the complete thermodynamic picture of a binding reaction. In biological sciences, macromolecular interactions are essential in understanding the machinery of the cell. Experimental conditions, such as buffer and temperature, can be tailored to the particular binding system being studied. However, careful planning is needed since certain ligand and macromolecule concentration ranges are necessary to obtain useful data. Concentrations of the macromolecule and ligand need to be accurately determined for reliable results. Care also needs to be taken when preparing the samples as impurities can significantly affect the experiment. When ITC experiments, along with controls, are performed properly, useful binding information, such as the stoichiometry, affinity and enthalpy, are obtained. By running additional experiments under different buffer or temperature conditions, more detailed information can be obtained about the system. A protocol for the basic setup of an ITC experiment is given.

A general protocol for the use of isothermal titration calorimetry to monitor the binding thermodynamics for biological systems with moderate binding affinities is presented.

用耐热配体测量生物分子 DSC 剖面快速表征折叠和结合的相互作用

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此视频中的章节

生物层干涉测量的蛋白质 - 蛋白质相互作用和变构配体反应动力学的影响

差示扫描量热 - 用于评估蛋白质抗原的热稳定性和构象的方法

用核磁共振 (nmr) 和微尺度热能 (mst) 测量球状和丝状蛋白的相互作用

综合结构质谱分析蛋白质结构和蛋白质配体配合物

使用微尺度热泳测量蛋白质-脂质相互作用

纳米微分扫描荧光仪，用于在基于碎片的铅发现中筛选

利用 Thermal Shift 分析探测底物与 Selenoprotein O 的结合

利用 Thermal Shift 分析探测底物与 Selenoprotein O 的结合

利用 Thermal Shift 分析探测底物与 Selenoprotein O 的结合

用于测量高分子配体亲和等温滴定量热