蛋白质表达，纯化和结晶实验在结构分子生物学中心（CSMB）进行，该中心是美国能源部橡树岭国家实验室生物与环境研究用户设施。中子衍射数据是在BL-11B MaNDi上收集的，位于ORNL的散裂中子源（SNS），由美国能源部基础能源科学办公室科学用户设施司赞助。作者感谢Brendan Sullivan在数据减少方面的帮助。X射线衍射数据是在北卡罗来纳州立大学的分子教育，技术和研究创新中心（METRIC）设施中收集的，该中心由北卡罗来纳州提供支持。GCS感谢南非国家研究基金会（NRF）和ORNL的毕业生机会（GO！）计划的部分支持。FM感谢美国农业部NIFA Hatch 211001的支持。

作者没有什么可透露的。

中子蛋白晶体学是一种高度灵敏的技术，用于探测蛋白质中的质子化状态和水分子取向。这些信息揭示了蛋白质催化机制，因为质子化和氢键相互作用的变化通常是酶化学的核心10。中子蛋白晶体学虽然是一种信息丰富的技术，但在计划进行中子衍射实验之前，应考虑许多因素，即:
<ol><li>需要大蛋白质晶体进行数据收集。</li>
	<li>氢和其他元素的散射性质，如金属离子。</li>
	<li>处理氘代样品时，结构细化和模型构建软件的局限性。</li>
</ol>中子蛋白晶体学是一种通量有限的技术。与X射线衍射数据集相比，由于技术固有的局限性（通量有限，准劳厄，更长波长），中子数据集预计会有更高的R因子和更低的完整性，冗余和信噪比。单个帧的数据收集通常为 12 – 18 小时。实验的成功很大程度上取决于样品大小和质量，0.1 mm3的晶体通常是最低要求3。中子衍射需要产生大量的蛋白质来建立10至800μL的结晶滴。生长足够大晶体的最小体积可以使用体积计算器估计，给定晶体和样品参数（https://neutrons.ornl.gov/imagine）。大晶体的生长最普遍地通过蒸汽扩散3完成。悬挂式滴结晶允许晶体在10-25 μL范围内的大液滴中生长，而使用市售的坐滴设备可以设置高达~50 μL的较大液滴14，54。硅化九孔玻璃板可用于设置非常大的液滴，体积高达800μL。这些玻璃板被放置在汉普顿研究公司市售的"三明治盒"中。进一步的结晶技术包括间歇结晶，其中液滴大小的限制由容器决定。批量结晶实验设置的范围可以从微升到毫升55。也可以使用透析技术进行结晶，其中蛋白质通过透析膜或沿沉淀剂浓度梯度或通过多孔塞（如琼脂糖）的反扩散与沉淀剂平衡56，57。播种提供了另一种获得所需体积的晶体的替代方法。微晶和晶状体已成功用于大晶体生长，包括NcLPMO9D45的大晶体。蛋白质相图的一些知识，包括温度对溶解度的影响，有助于大晶体生长。
在规划中子衍射实验时，必须优化蛋白质制备，以在衍射数据收集过程中最大限度地提高信噪比7。为了规避H原子引起的密度抵消和高不相干散射，可以通过用H原子交换其同位素D来改善中子SLD图谱，D具有正相干散射长度和低不相干散射长度。为此，对氢化蛋白质晶体进行蒸气交换以对抗氘化结晶缓冲液。这确保了溶剂分子和不稳定的可滴定蛋白H原子的H / D交换23。蒸汽交换是通过将氢化晶体安装到具有D2O基氘化结晶缓冲液"塞子"的石英毛细管中来进行的，它代表了一种有效，温和的技术，最常用于14，23，35。更换可能需要数周时间，最好需要频繁更换氘代缓冲液，以确保最大的H / D更换。H/ D交换也可以通过将晶体直接浸泡在氘代缓冲液中来进行。为避免将晶体置于由于D2O暴露而产生的应力下，应通过逐渐增加D2O:H2O比来逐渐进行浸泡过程58。除此之外，氢化蛋白的结晶也可以在氘代缓冲液中进行，用于在不稳定的H位点进行H / D交换22，59。然而，应该注意的是，基于D2O的缓冲液对蛋白质溶解度有影响，需要进一步调整已知的基于H2O的条件3，59。在某些情况下，基于D2O的缓冲液也会导致更小的晶体59。通过在氘化培养基中表达蛋白质以生成氘化样品，可以实现可滴定和碳结合的H原子与D的完全交换20。脱氘样品的中子SLD图谱将得到显着改善，不再显示氢化样品对应物的密度抵消。当表征在蛋白质或辅因子中不可交换位点结合的H / D时，这是有益的。然而，氘代蛋白的表达既高成本又低产量60。橡树岭国家实验室（ORNL）结构分子生物学中心（CSMB）为寻求生成氘化样本（https://www.ornl.gov/facility/csmb）的用户提供了氘传设施。纯化表达通常在1 L尺度上的生物反应器中进行，产生约50mg纯化蛋白61。
在收集中子衍射数据后，进行细化和交互式模型构建。可以使用多个软件套件运行细化，包括phenix.refine，nCNS或SHELXL28，31，32，33。Phenix套件是最常用的软件，用于与Coot一起优化中子衍射数据，Coot用于从中子SLD图手动构建模型34。虽然Phenix和Coot都允许处理中子衍射数据，但它们可能缺乏处理与中子数据和氘化样品相关的特性所必需的某些特征。例如，Coot 不包含氘代残留物的几何优化，这可能导致模型构建过程中的复杂情况，因为"真实空间细化"特征会导致"爆炸"残留物（补充图 26）62。这可以通过为所有氘代残留物生成约束文件来解决。但是，这是一个密集的过程，此类库目前尚未公开。在Phenix中执行优化时，H和D的可交换H / D站点最初将设置为0.50占用。随着细化，H和D的占用将根据中子SLD图进行细化。在交互式模型构建过程中，差密度 Fo-Fc 图在评估 H/D 占用率方面非常有用。地图可用于确定哪些位点具有高D占用率，这在质子化状态具有催化相关性的活动位点尤其有用63。然而，当H:D占用率接近0.70:0.30，这导致中子SLD图中的信号完全消除64。还应该考虑到，准劳埃中子数据集的完整性通常在80%左右，低于X射线衍射数据的常规观测≥98%。因此，在Phenix中细化中子衍射数据时，从模型中计算出缺失的观测振幅（Fo）以完成反射列表，从而引入模型偏差。为了解释这种潜在的偏差，应在交互式模型构建期间检查"no_fill"地图，而不是"填充"地图。
用户可以选择对其结构进行联合X射线/中子数据细化，或仅对中子数据进行细化。可视化中子SLD图谱，特别是在较低分辨率下，最初可能令人不安，特别是对于氢化蛋白质，尽管H / D蒸汽交换，H仍存在于不可交换的位点。这导致中子密度图取消，给人的印象是不连续的图65，66。收集相应的X射线数据集有利地补充了联合细化中的这些取消（图13A和图13B）。联合细化策略通常涉及根据X射线数据提炼蛋白质骨架坐标，而中子衍射数据用于细化H / D原子在可交换位点的位置和占用28。由于在可交换地点引入联合H/D占用增加了正在改进的参数数量，因此使用X射线数据的联合细化也增加了数据与参数的比率。联合细化需要在相同温度下在同一晶体或相同条件下生长的晶体上收集相应的X射线数据集。对于在室温（300K）下收集的中子衍射数据，应使用低剂量数据收集策略在室温下收集相应的X射线数据集，以限制辐射损伤。相比之下，经过氚化的样品提供改进的连续中子SLD图谱，因为它们不具有相同幅度的H / D信号消除。然而，包括金属和硫在内的某些元素的中子散射长度使它们在中子SLD图中不可见，即使蛋白质已经氘化（图13C-F）18。如果需要表征金属，最好在联合细化中利用X射线衍射或应用光谱技术来补充衍射实验。仅中子数据优化通常在中子数据集具有高分辨率或使用过氘蛋白质时执行。此外，如果正在研究对辐射损伤高度敏感的蛋白质，仅中子数据改进特别有用，因为X射线衍生的结构可能具有辐射诱导的伪影。如果要进行仅中子数据的细化，则必须确定相应的中子数据集是否具有足够的完整性和分辨率。
ORNL提供了两个用于收集中子衍射数据的设施:HFIR的IMAGINE光束线以及SNS36，67的MaNDi光束线。虽然这两种仪器都为使用类似原理收集中子衍射数据集提供了有效的手段，但每种仪器都有独特的规格，在应用光束时间时应予以考虑。IMAGINE 收集准劳厄数据，并针对晶胞高达 ~100 Å 的晶体的室温数据收集进行了优化。MaNDi可用于收集室温和低温数据，采用TOF-Laue收集方法收集晶胞高达约300 Å的晶体。在收集完整的数据集之前，对晶体进行测试以评估获得的衍射图的质量，其中晶体暴露于中子束中单帧。如果晶体质量足够高，将收集完整的中子衍射数据集，将其索引，集成，缩放和合并，该过程类似于X射线数据处理。IMAGINE利用Lauegen和Lscale，MaNDi利用Mantid封装并采用三维轮廓拟合48，50，51，68，69，70。成为这些设施用户的科学家将获得MTZ或HDL格式的数据集，以进行进一步分析。
中子衍射是一种非破坏性、高度灵敏的技术，用于探测生物大分子的质子化状态和氢键相互作用。它对光敏蛋白和金属蛋白特别有用。在进行实验之前，必须考虑有关该技术以及数据处理的几个考虑因素，但是结果产生的结果可能会对感兴趣蛋白质的催化机制提供有价值的见解。中子蛋白晶体学是对计算、结构、生化和光谱研究的补充，使其成为生物学家用于表征生物大分子的技术工具箱中的宝贵工具。

中子大分子晶体学是一种技术，为蛋白质的结构和潜在化学提供了一个独特的窗口。在概念上与X射线衍射相似，中子衍射提供了大分子结构的原子细节，然而，中子与原子核的相互作用使轻原子的定位成为可能，通常很难用X射线衍射检测到1。在 X 射线衍射过程中，X 射线从电子云中散射，使得氢 （H） 等轻原子在没有接近亚 Ångström 分辨率的电子密度图中不可见2。相反，中子的散射强度取决于与原子核的复杂相互作用，同一元素的同位素显示出不同的散射长度。因此，轻原子及其同位素，如氢（1H）和氘（2H或D），在中子散射长度密度（SLD）图中具有与骨架碳，氮和氧原子相当的可见性。此外，由于中子散射的大小与电子的数量无关，因此当轻元素彼此靠近时，轻元素的散射不会被重元素遮挡，正如在X射线散射中观察到的那样。H及其同位素D在采用中子衍射时的能见度增强，提供了有关催化重要残基、辅因子和配体质子化状态的宝贵信息，并有助于水分子的取向，揭示了有关催化机理和蛋白质化学的重要信息3。中子衍射还具有非破坏性技术的优点，特别适用于对电离敏感的生物样品，例如具有金属中心的蛋白质或光敏氧化还原辅因子2。本文的主要重点是概述获得高质量中子蛋白晶体结构的工作流程。我们将感兴趣的读者推荐给Podjarny et al.4，Blakeley5，Blakeley et al.6和O'Dell et al.3，以很好地概述中子蛋白衍射和Ashkar等人7对中子散射的进一步应用。
中子主要在核反应过程中产生，采用两个过程之一:反应堆源的核裂变或加速器源的散裂8。反应堆源通过利用 235U同位素的核裂变来提供连续的中子束，而散裂中子源通过用质子轰击目标（例如液态金属，如汞）来产生脉冲中子束9。位于田纳西州橡树岭的橡树岭国家实验室（ORNL）在高通量同位素反应堆（HFIR）拥有稳态中子源，在散裂中子源（SNS）拥有60 Hz脉冲源。位于HFIR的IMAGINE光束线是针对生物大分子优化的中子衍射仪（补充图1）10。IMAGINE采用中子成像板探测器，使用2.8 – 4.5 Å范围内的窄带通测量准Laue数据，该带通来自具有单元单元边缘<150 Å的单晶。位于SNS的高分子中子衍射仪（MaNDi）是一种飞行时间（TOF）劳埃中子衍射仪，配有球形探测器阵列框架（DAF）（补充图2）11。MaNDi 采用 2.0 – 6.0 Å12 之间的可调 2 Å 波长带宽，测量来自具有 10 – 300 Å 范围内单元边缘的单晶的数据。
产生中子的过程是高度能量密集型的，与同步子源处的X射线束通量相比，导致中子束通量相对较弱13。为了确保在数据收集过程中具有足够的信噪比，有必要生长合适尺寸和质量的晶体14。通常，需要体积>0.1 mm3的晶体来收集具有足够统计数据的数据15。除了较低的通量外，还必须考虑中子与样品核之间相互作用的固有特性16。对于同一元素的同位素，中子的散射长度不同，这一特性可以在小角度中子散射（SANS）中得到有利利用，以掩盖或突出显示样品的区域 - 这一过程称为对比度匹配17。在衍射实验中，H的负相干中子散射长度（-3.741 fm表示1H）可导致中子散射密度图特征的抵消，因为其他生物相关原子的相干中子散射长度包括碳（12C为6.6511 fm），氮（14N为9.37 fm），氧（16O为5.803 fm）， 磷（31P为5.13 fm）和硫（32S为2.804 fm）为正（表1）12，14。此外，H （25.274 fm） 的大不相干散射长度增加了数据收集过程中的背景，影响了数据集的质量并影响了数据分辨率7。为了规避H引入的这些限制，对于中子衍射，有必要将H换成其同位素氘2H（D），其具有正相干中子散射长度（6.671 fm）和显着降低的非相干散射长度（4.04 fm）19。这可以通过氘散来实现，在氘透过程中，蛋白质由在完全氘代培养基中生长的生物体表达，确保在H位点20完全掺入D。也可以通过仅在可交换位点（可滴定基团）处用D代替H来部分氘化蛋白质，而不可交换的碳结合位点保持氢化21。这可以通过在氘代母液中生长氢化蛋白质晶体来实现22。然而，最常见的是，氢化蛋白的H / D交换是在基于H2O的缓冲液中生长适当大的晶体23之后通过蒸汽交换进行的。在这种情况下，晶体安装在石英毛细管中，并与基于D20的母液进行蒸汽平衡。
中子源的中子通量有限，导致数据收集时间更长，从几天到几周不等24。在ORNL，IMAGINE和MaNDi都采用2-6 Å范围内的窄波长带通来优化数据收集25。数据可以在室温或低温下收集。冷冻数据收集可以潜在地提高数据质量，并为冷冻捕获催化中间体开辟可能性。在收集中子衍射数据之后，通常在相同温度下在同一晶体上或在相同条件下生长的晶体上收集X射线数据集26。在相同温度下收集数据允许针对X射线和中子数据进行结构细化，防止任何潜在的温度引起的伪影，例如水的能见度和位置的变化或具有交替构象的残留物的占用27。联合X射线中子数据细化增加了数据与参数的比率，并提供了允许根据X射线数据细化蛋白质骨架坐标的优势，而中子衍射数据用于细化H / D原子的位置28。当使用部分氘代样品时，这特别有用，其中由于蛋白质上不可交换位点处的H原子存在密度抵消。虽然X射线结构的数量远远超过蛋白质数据库（PDB）中沉积的中子结构的数量，但最初设计用于改进X射线数据的软件包已经扩展到包括中子数据3，29，30。在数据收集之后，可以使用phenix.refine，CNSsolve（nCNS）或SHELXL28，31，32，33等细化包来优化模型。在细化过程中，可以使用COOT34可视化中子散射密度图，以便手动拟合。按照结构解决方案，坐标以及中子和/或X射线衍射数据文件可以提交给PDB，PDB将验证并存放模型，使其可供公众访问18，29，30。
蛋白质的结构分析是一种多方面的方法，其中许多技术用于探测其功能和机制35。中子蛋白晶体学提供了有价值的化学见解，以扩展和补充其他研究的发现，如X射线衍射，光谱学，核磁共振（NMR）或微晶电子衍射（microED）36。中子蛋白衍射具有独特的优势，可以提供对酶学机制的见解，因为H原子是其化学的核心。没有中子诱导的辐射损伤使它们成为特别适合研究金属蛋白的探针37。我们在这里展示了从样品制备到数据收集，细化和分析的中子蛋白衍射过程的代表性示例（图1）。已经生长了足够大小的晶体，用于中子衍射实验的金属蛋白神经孢子菌LPMO9D（NcLPMO9D）。数控LPMO9D是一种含铜的金属蛋白，通过在糖苷键处插入氧原子来参与顽固纤维素的降解38，39。NcLPMO9D活性位点在由N端组氨酸和第二保守组氨酸组成的特征性"组氨酸支撑"内包含一个单核铜中心（补充图3）40。真菌LPMO的N端被甲基化，但在酵母的重组表达过程中不会发生过渡后修饰。在NcLPMO9D静息状态下，铜中心以Cu2+氧化态存在，并通过单电子还原为Cu1 +被激活，允许分子氧结合并通过迅速还原为超氧化物物种而被激活41，42。整个NcLPMO9D反应需要进一步添加一个电子和两个质子以形成羟基化多糖产物43。负责从多糖底物中提取氢原子（HAA）的活性氧物种的身份尚未确定，目前正在进行密集的结构和计算研究44，45。鉴于NcLPMO9D活性位点的氧化还原化学性质，减轻辐射损伤尤其重要。我们在这里说明在NcLPMO9D晶体上的室温和低温数据收集，以确定NcLPMO9D结构在静止状态和活化还原形式中分别46。重点将放在蛋白质晶体安装，用于数据收集的光束线仪器设置，数据和坐标文件的准备以及建模全原子中子结构所需的改进步骤。

<table>
	<tbody>
		<tr>
			<td>Absorbent Paper Points Size #30-#40, 60 mm length</td>
			<td>DiaDent/DiaVet</td>
			<td>218-292</td>
			<td></td>
		</tr>
		<tr>
			<td>Capillary wax</td>
			<td>Hampton</td>
			<td>HR4-328</td>
			<td></td>
		</tr>
		<tr>
			<td>CCP4</td>
			<td></td>
			<td>Version 7.0.077</td>
			<td></td>
		</tr>
		<tr>
			<td>Conical Centrifuge Tubes (15 mL)</td>
			<td>Corning</td>
			<td>CLS430790</td>
			<td></td>
		</tr>
		<tr>
			<td>Conical Centrifuge Tubes (50mL)</td>
			<td>Corning</td>
			<td>CLS430828</td>
			<td></td>
		</tr>
		<tr>
			<td>Coot</td>
			<td></td>
			<td>Version 0.8.9.2</td>
			<td></td>
		</tr>
		<tr>
			<td>CrystalCap ALS</td>
			<td>Hampton</td>
			<td>HR4-779</td>
			<td></td>
		</tr>
		<tr>
			<td>Curved-Tip Forceps</td>
			<td>Mitegen</td>
			<td>TW-CTF-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Deuterium chloride solution, 35 wt. % in D2O, &#8805;99 atom % D</td>
			<td>Sigma-Aldrich</td>
			<td>543047</td>
			<td></td>
		</tr>
		<tr>
			<td>Deuterium oxide 99.9 atom % D</td>
			<td>Sigma-Aldrich</td>
			<td>151882</td>
			<td></td>
		</tr>
		<tr>
			<td>Dual Thickness MicroLoops 1000 &#181;m</td>
			<td>Mitegen</td>
			<td>M5-L18SP-1000</td>
			<td></td>
		</tr>
		<tr>
			<td>FiveEasy pH meter F20-Std-Kit</td>
			<td>Mettler Toledo</td>
			<td>30266626</td>
			<td></td>
		</tr>
		<tr>
			<td>Foam Dewars Standard Vessel 800 ml</td>
			<td>Spearlab</td>
			<td>M-FD-800</td>
			<td></td>
		</tr>
		<tr>
			<td>Four Color Mounting Clay</td>
			<td>Hampton</td>
			<td>HR4-326</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES, BioUltra, for molecular biology, &#8805;99.5% (T),</td>
			<td>Sigma-Aldrich</td>
			<td>54457</td>
			<td></td>
		</tr>
		<tr>
			<td>High flux rotating anode X-ray diffractomemeter with EIGER 4M detector</td>
			<td>Rigaku, Oxford Cryostream and Dectris</td>
			<td>XtaLAB Synergy-R</td>
			<td>Home source X-ray diffractometer</td>
		</tr>
		<tr>
			<td>Magnetic Wand Straight</td>
			<td>Mitegen</td>
			<td>M-R-1013198</td>
			<td></td>
		</tr>
		<tr>
			<td>Microloader, tip for filling Femtotips and other glass microcapillaries (for research use only), 0.5 &#8211; 20 &#181;L, 100 mm, light gray, 192 pcs. (2 racks &#215; 96 pcs.)</td>
			<td>Eppendorf</td>
			<td>930001007</td>
			<td></td>
		</tr>
		<tr>
			<td>Microtubes volume 1.5 mL</td>
			<td>Eppendorf</td>
			<td>Z606340</td>
			<td></td>
		</tr>
		<tr>
			<td>Petri Dishes with Clear Lid 100 mm diameter</td>
			<td>Fischerbrand</td>
			<td>FB0875713</td>
			<td></td>
		</tr>
		<tr>
			<td>Phenix</td>
			<td></td>
			<td>Version 1.14-3260</td>
			<td></td>
		</tr>
		<tr>
			<td>Pin Tong 18 mm</td>
			<td>Mitegen</td>
			<td>M-R-1013196</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipette Volume 0.1-2.5 &#956;L</td>
			<td>Eppendorf Research</td>
			<td>Z683779</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipette Volume 100-1000 &#956;L</td>
			<td>Eppendorf Research</td>
			<td>Z683825</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipette Volume 10-100 &#956;L</td>
			<td>Eppendorf Research</td>
			<td>Z683809</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipette Volume 20-200 &#956;L</td>
			<td>Eppendorf Research</td>
			<td>Z683817</td>
			<td></td>
		</tr>
		<tr>
			<td>Poly(ethylene glycol) BioXtra, average mol wt 3,350, powder</td>
			<td>Sigma-Aldrich</td>
			<td>P4338</td>
			<td></td>
		</tr>
		<tr>
			<td>Quartz Capillary , 1.00 mm inner diameter, 80 mm length</td>
			<td>Hampton</td>
			<td>HR6-146</td>
			<td>Thin-walled capillary</td>
		</tr>
		<tr>
			<td>Research Stereomicroscope System</td>
			<td>Olympus</td>
			<td>SZX16</td>
			<td></td>
		</tr>
		<tr>
			<td>Reusable B3 (SSRL/SAM Style) Goniometer Bases</td>
			<td>Mitegen</td>
			<td>GB-B3-R</td>
			<td></td>
		</tr>
		<tr>
			<td>Round - Miniature Hollow Glass Tubing (VitroTubes) Clear Fused Quartz / 1.00 mm inner diameter, 100 mm length</td>
			<td>VitroCom</td>
			<td>CV1012</td>
			<td>Thick-walled capillary</td>
		</tr>
		<tr>
			<td>Sandwich Box with cover</td>
			<td>Hampton</td>
			<td>HR3-132</td>
			<td></td>
		</tr>
		<tr>
			<td>Siliconized 9 Well Glass Plate</td>
			<td>Hampton</td>
			<td>HR3-134</td>
			<td></td>
		</tr>
		<tr>
			<td>Sitting Drop Crystallization Plate (24 Big Well)</td>
			<td>Mitegen</td>
			<td>XQ-P-24S-A</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium deuteroxide solution, 40 wt. % in D2O, 99 atom % D</td>
			<td>Sigma-Aldrich</td>
			<td>176788</td>
			<td></td>
		</tr>
		<tr>
			<td>Thick Siliconized circle cover slides (22 mm x 0.96 mm)</td>
			<td>Hampton</td>
			<td>HR3-247</td>
			<td></td>
		</tr>
		<tr>
			<td>Universal Pipet Tips, 0.1 - 10 &#181;L</td>
			<td>VWR</td>
			<td>76322-528</td>
			<td></td>
		</tr>
		<tr>
			<td>Universal Pipet Tips, 1 - 100 &#181;L</td>
			<td>VWR</td>
			<td>76322-136</td>
			<td></td>
		</tr>
		<tr>
			<td>Universal Pipet Tips, 100 - 1000 &#181;L</td>
			<td>VWR</td>
			<td>76322-154</td>
			<td></td>
		</tr>
		<tr>
			<td>Universal Pipet Tips, 20 - 200 &#181;L</td>
			<td>VWR</td>
			<td>76322-150</td>
			<td></td>
		</tr>
		<tr>
			<td>Universal Pipet Tips, 1 - 20 &#181;L</td>
			<td>VWR</td>
			<td>76322-134</td>
			<td></td>
		</tr>
		<tr>
			<td>Wax pen</td>
			<td>Hampton</td>
			<td>HR4-342</td>
			<td></td>
		</tr>
	</tbody>
</table>

neutron crystallography data collection and processing for modelling hydrogen atoms in protein structures

中子晶体学是一种结构技术，可以确定生物大分子内的氢原子位置，产生有关质子化和水合状态的机械重要信息，同时不会引起辐射损伤。相比之下，X射线衍射仅提供有关光原子位置的有限信息，并且X射线束会迅速引起光敏辅助因子和金属中心的辐射损伤。这里介绍的是橡树岭国家实验室（ORNL）的IMAGINE和MaNDi光束线所采用的工作流程，一旦生长出合适尺寸（>0.1 mm3）的蛋白质晶体，就可以获得中子衍射结构。我们展示了在石英毛细管中安装氢化蛋白质晶体，用于中子衍射数据收集。还介绍了用含D2O的缓冲液安装的晶体的蒸汽交换过程，以确保用氘替换可交换位点的氢原子。氘的掺入减少了氢原子不相干散射产生的背景，并防止了由其负相干散射长度引起的密度抵消。在高通量同位素反应器（HFIR）的IMAGINE上使用准Laue数据收集来说明样品对准和室温数据收集策略。此外，在散裂中子源（SNS）的MaNDi飞行时间仪器上演示了晶体镶样和液氮中的快速冷冻，用于冷冻数据收集以捕获不稳定的反应中间体。还将处理模型坐标和衍射数据文件的准备以及中子散射长度密度（SLD）图的可视化。最后将讨论针对中子数据或针对联合X射线/中子数据的结构细化，以获得目标蛋白质的全原子结构。确定中子结构的过程将使用裂解多糖单加氧酶 Neurospora crassa LPMO9D的晶体进行演示，LPMO9D是一种含铜的金属蛋白， 通过 糖苷键的氧化切割参与顽固性多糖的降解。

Watch this Scientific Journal Video about Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures at JoVE.com

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

中子蛋白晶体学是一种结构技术，允许氢原子的定位，从而提供蛋白质功能的重要机制细节。我们在这里介绍了用于安装蛋白质晶体，中子衍射数据收集，结构细化以及中子散射长度密度图分析的工作流程。

中子晶体学数据收集和处理，用于蛋白质结构中氢原子的建模

Neutron crystallography is a structural technique that allows determination of hydrogen atom positions within biological macromolecules, yielding ...

neutron-crystallography-data-collection-processing-for-modelling

Universidad de Cartagena UDEC

Research

JoVE Journal

Chemistry

4.8K 次观看.  North Carolina State University. 中子蛋白晶体学是一种结构技术，允许氢原子的定位，从而提供蛋白质功能的重要机制细节。我们在这里介绍了用于安装蛋白质晶体，中子衍射数据收集，结构细化以及中子散射长度密度图分析的工作流程。

视频: Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry

All cellular processes depend on the functionality of proteins. Although the functionality of a given protein is the direct consequence of its unique amino acid sequence, it is only realized by the folding of the polypeptide chain into a single defined three-dimensional arrangement or more commonly into an ensemble of interconverting conformations. Investigating the connection between protein conformation and its function is therefore essential for a complete understanding of how proteins are able to fulfill their great variety of tasks. One possibility to study conformational changes a protein undergoes while progressing through its functional cycle is hydrogen-1H/2H-exchange in combination with high-resolution mass spectrometry (HX-MS). HX-MS is a versatile and robust method that adds a new dimension to structural information obtained by e.g. crystallography. It is used to study protein folding and unfolding, binding of small molecule ligands, protein-protein interactions, conformational changes linked to enzyme catalysis, and allostery. In addition, HX-MS is often used when the amount of protein is very limited or crystallization of the protein is not feasible. Here we provide a general protocol for studying protein dynamics with HX-MS and describe as an example how to reveal the interaction interface of two proteins in a complex. &#160;&#160;

Protein conformation and dynamics are key to understanding the relationship between protein structure and function. Hydrogen exchange coupled with high-resolution mass spectrometry is a versatile method to study the conformational dynamics of proteins as well as characterizing protein-ligand and protein-protein interactions, including contact interfaces and allosteric effects.

使用氢交换质谱分析蛋白质动力学

All cellular processes depend on the functionality of proteins. Although the functionality of a given protein is the direct consequence of its unique ...

科研

化学

Supercritical Nitrogen Processing for the Purification of Reactive Porous Materials

Supercritical fluid extraction and drying methods are well established in numerous applications for the synthesis and processing of porous materials. Herein, nitrogen is presented as a novel supercritical drying fluid for specialized applications such as in the processing of reactive porous materials, where carbon dioxide and other fluids are not appropriate due to their higher chemical reactivity. Nitrogen exhibits similar physical properties in the near-critical region of its phase diagram as compared to carbon dioxide: a widely tunable density up to ~1 g ml-1, modest critical pressure (3.4 MPa), and small molecular diameter of ~3.6 &#197;. The key to achieving a high solvation power of nitrogen is to apply a processing temperature in the range of 80-150 K, where the density of nitrogen is an order of magnitude higher than at similar pressures near ambient temperature. The detailed solvation properties of nitrogen, and especially its selectivity, across a wide range of common target species of extraction still require further investigation. Herein we describe a protocol for the supercritical nitrogen processing of porous magnesium borohydride.

Nitrogen is an effective supercritical fluid for extraction or drying processes due to its small molecular size, high density in the near-liquid supercritical regime, and chemical inertness. We present a supercritical nitrogen drying protocol for the purification treatment of reactive, porous materials.

超临界氮处理的活性多孔材料的净化

Supercritical fluid extraction and drying methods are well established in numerous applications for the synthesis and processing of porous materials. ...

Functionalization of Single-walled Carbon Nanotubes with Thermo-reversible Block Copolymers and Characterization by Small-angle Neutron Scattering

We demonstrate a protocol for single-walled carbon nanotube functionalization using thermo-sensitive PEO-PPO-PEO triblock copolymers in an aqueous solution. In a carbon nanotube/PEO105-PPO70-PEO105 (poloxamer 407) aqueous solution, the amphiphilic poloxamer 407 adsorbs onto the carbon nanotube surfaces and self-assembles into continuous layers, driven by intermolecular interactions between constituent molecules. The addition of 5-methylsalicylic acid changes the self-assembled structure from spherical-micellar to a cylindrical morphology. The fabricated poloxamer 407/carbon nanotube hybrid particles exhibit thermo-responsive structural features so that the density and thickness of poloxamer 407 layers are also reversibly controllable by varying temperature. The detailed structural properties of the poloxamer 407/carbon nanotube particles in suspension can be characterized by small-angle neutron scattering experiments and model fit analyses. The distinct curve shapes of the scattering intensities depending on temperature control or addition of aromatic additives are well described by a modified core-shell cylinder model consisting of a carbon nanotube core cylinder, a hydrophobic shell, and a hydrated polymer layer. This method can provide a simple but efficient way for the fabrication and in-situ characterization of carbon nanotube-based nano particles with a structure-tunable encapsulation.

A method for the functionalization of carbon nanotubes with structure-tunable polymeric encapsulation layers and structural characterization using small-angle neutron scattering is presented.

单壁碳纳米管与热可逆嵌段共聚物及表征功能化小角度中子散射

We demonstrate a protocol for single-walled carbon nanotube functionalization using thermo-sensitive PEO-PPO-PEO triblock copolymers in an aqueous ...

X-ray Powder Diffraction in Conservation Science: Towards Routine Crystal Structure Determination of Corrosion Products on Heritage Art Objects

The crystal structure determination and refinement process of corrosion products on historic art objects using laboratory high-resolution X-ray powder diffraction (XRPD) is presented in detail via two case studies.
The first material under investigation was sodium copper formate hydroxide oxide hydrate, Cu4Na4O(HCOO)8(OH)2&#8729;4H2O (sample 1) which forms on soda glass/copper alloy composite historic objects (e.g., enamels) in museum collections, exposed to formaldehyde and formic acid emitted from wooden storage cabinets, adhesives, etc. This degradation phenomenon has recently been characterized as &#34;glass induced metal corrosion&#34;.
For the second case study, thecotrichite, Ca3(CH3COO)3Cl(NO3)2&#8729;6H2O (sample 2), was chosen, which is an efflorescent salt forming needlelike crystallites on tiles and limestone objects which are stored in wooden cabinets and display cases. In this case, the wood acts as source for acetic acid which reacts with soluble chloride and nitrate salts from the artifact or its environment.
The knowledge of the geometrical structure helps conservation science to better understand production and decay reactions and to allow for full quantitative analysis in the frequent case of mixtures.

Modern high resolution X-ray powder diffraction (XRPD) in the laboratory is used as an efficient tool to determine crystal structures of long-known corrosion products on historic objects.

X射线粉末衍射在保护科学:迈向文物艺术品腐蚀产物的常规晶体结构测定

The crystal structure determination and refinement process of corrosion products on historic art objects using laboratory high-resolution X-ray powder ...

Highly Stable, Functional Hairy Nanoparticles and Biopolymers from Wood Fibers: Towards Sustainable Nanotechnology

Nanoparticles, as one of the key materials in nanotechnology and nanomedicine, have gained significant importance during the past decade. While metal-based nanoparticles are associated with synthetic and environmental hassles, cellulose introduces a green, sustainable alternative for nanoparticle synthesis. Here, we present the chemical synthesis and separation procedures to produce new classes of hairy nanoparticles (bearing both amorphous and crystalline regions) and biopolymers based on wood fibers. Through periodate oxidation of soft wood pulp, the glucose ring of cellulose is opened at the C2-C3 bond to form 2,3-dialdehyde groups. Further heating of the partially oxidized fibers (e.g., T = 80 &#176;C) results in three products, namely fibrous oxidized cellulose, sterically stabilized nanocrystalline cellulose (SNCC), and dissolved dialdehyde modified cellulose (DAMC), which are well separated by intermittent centrifugation and co-solvent addition. The partially oxidized fibers (without heating) were used as a highly reactive intermediate to react with chlorite for converting almost all aldehyde to carboxyl groups. Co-solvent precipitation and centrifugation resulted in electrosterically stabilized nanocrystalline cellulose (ENCC) and dicarboxylated cellulose (DCC). The aldehyde content of SNCC and consequently surface charge of ENCC (carboxyl content) were precisely controlled by controlling the periodate oxidation reaction time, resulting in highly stable nanoparticles bearing more than 7 mmol functional groups per gram of nanoparticles (e.g., as compared to conventional NCC bearing &#60;&#60; 1 mmol functional group/g). Atomic force microscopy (AFM), transmission electron microscopy (TEM), and scanning electron microscopy (SEM) attested to the rod-like morphology. Conductometric titration, Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance (NMR), dynamic light scattering (DLS), electrokinetic-sonic-amplitude (ESA) and acoustic attenuation spectroscopy shed light on the superior properties of these nanomaterials.

Synthesis schemes to prepare highly stable wood fiber-based hairy nanoparticles and functional cellulose-based biopolymers have been detailed.

高稳定性，功能性毛纳米粒子和木纤维生物聚合物:迈向可持续纳米技术

Nanoparticles, as one of the key materials in nanotechnology and nanomedicine, have gained significant importance during the past decade. While ...

Synthesis of Protein Bioconjugates via Cysteine-maleimide Chemistry

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

Synthesis of Protein Bioconjugates via Cysteine-maleimide Chemistry

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

蛋白质生物缀合物的合成<em&gt;通过</em&gt;半胱氨酸马来酰亚胺化学

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

Electrochemical Impedance Spectroscopy as a Tool for Electrochemical Rate Constant Estimation

Electrochemical impedance spectroscopy (EIS) was used for advanced characterization of organic electroactive compounds along with cyclic voltammetry (CV). In the case of fast reversible electrochemical processes, current is predominantly affected by the rate of diffusion, which is the slowest and limiting stage. EIS is a powerful technique that allows separate analysis of stages of charge transfer that have different AC frequency response. The capability of the method was used to extract the value of charge transfer resistance, which characterizes the rate of charge exchange on the electrode-solution interface. The application of this technique is broad, from biochemistry up to organic electronics. In this work, we are presenting the method of analysis of organic compounds for optoelectronic applications.

Electrochemical impedance spectroscopy (EIS) of species that undergo reversible oxidation or reduction in solution was used for determination of rate constants of oxidation or reduction.

电化学阻抗谱作为电化学速率常数估计的一种工具

Electrochemical impedance spectroscopy (EIS) was used for advanced characterization of organic electroactive compounds along with cyclic voltammetry (CV). ...

Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography

This protocol describes fabricating microfluidic devices with low X-ray background optimized for goniometer based fixed target serial crystallography. The devices are patterned from epoxy glue using soft lithography and are suitable for in situ X-ray diffraction experiments at room temperature. The sample wells are lidded on both sides with polymeric polyimide foil windows that allow diffraction data collection with low X-ray background. This fabrication method is undemanding and inexpensive. After the sourcing of a SU-8 master wafer, all fabrication can be completed outside of a cleanroom in a typical research lab environment. The chip design and fabrication protocol utilize capillary valving to microfluidically split an aqueous reaction into defined nanoliter sized droplets. This loading mechanism avoids the sample loss from channel dead-volume and can easily be performed manually without using pumps or other equipment for fluid actuation. We describe how isolated nanoliter sized drops of protein solution can be monitored in situ by dynamic light scattering to control protein crystal nucleation and growth. After suitable crystals are grown, complete X-ray diffraction datasets can be collected using goniometer based in situ fixed target serial X-ray crystallography at room temperature. The protocol provides custom scripts to process diffraction datasets using a suite of software tools to solve and refine the protein crystal structure. This approach avoids the artefacts possibly induced during cryo-preservation or manual crystal handling in conventional crystallography experiments. We present and compare three protein structures that were solved using small crystals with dimensions of approximately 10-20 &#181;m grown in chip. By crystallizing and diffracting in situ, handling and hence mechanical disturbances of fragile crystals is minimized. The protocol details how to fabricate a custom X-ray transparent microfluidic chip suitable for in situ serial crystallography. As almost every crystal can be used for diffraction data collection, these microfluidic chips are a very efficient crystal delivery method.

Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography

This protocol describes in detail how to fabricate and operate microfluidic devices for X-ray diffraction data collection at room temperature. Additionally, it describes how to monitor protein crystallization by dynamic light scattering and how to process and analyze obtained diffraction data.

用于原位晶体 x 射线衍射和原位的微流控芯片系列晶体学的动态光散射

This protocol describes fabricating microfluidic devices with low X-ray background optimized for goniometer based fixed target serial crystallography. The ...

U2O5 Film Preparation via UO2 Deposition by Direct Current Sputtering and Successive Oxidation and Reduction with Atomic Oxygen and Atomic Hydrogen

We describe a method to produce U2O5 films in situ using the Labstation, a modular machine developed at JRC Karlsruhe. The Labstation, an essential part of the Properties of Actinides under Extreme Conditions laboratory (PAMEC), allows the preparation of films and studies of sample surfaces using surface analytical techniques such as X-ray and ultra-violet photoemission spectroscopy (XPS and UPS, respectively). All studies are made in situ, and the films, transferred under ultra-high vacuum from their preparation to an analyses chamber, are never in contact with the atmosphere. Initially, a film of UO2 is prepared by direct current (DC) sputter deposition on a gold (Au) foil then oxidized by atomic oxygen to produce a UO3 film. This latter is then reduced with atomic hydrogen to U2O5. Analyses are performed after each step involving oxidation and reduction, using high-resolution photoelectron spectroscopy to examine the oxidation state of uranium. Indeed, the oxidation and reduction times and corresponding temperature of the substrate during this process have severe effects on the resulting oxidation state of the uranium. Stopping the reduction of UO3 to U2O5 with single U(V) is quite challenging; first, uranium-oxygen systems exist in numerous intermediate phases. Second, differentiation of the oxidation states of uranium is mainly based on satellite peaks, whose intensity peaks are weak. Also, experimenters should be aware that X-ray spectroscopy (XPS) is a technique with an atomic sensitivity of 1% to 5%. Thus, it is important to obtain a complete picture of the uranium oxidation state with the entire spectra obtained on U4f, O1s, and the valence band (VB). Programs used in the Labstation include a linear transfer program developed by an outside company (see Table of Materials) as well as data acquisition and sputter source programs, both developed in-house.

U2O5 Film Preparation via UO2 Deposition by Direct Current Sputtering and Successive Oxidation and Reduction with Atomic Oxygen and Atomic Hydrogen

This protocol presents the preparation of U2O5 thin films obtained in situ under ultra-high vacuum. The process involves oxidation and reduction of UO2 films with atomic oxygen and atomic hydrogen, respectively.

利用uo2沉积制备 u2o5 薄膜, 利用原子氧和原子氢连续氧化还原

We describe a method to produce U2O5 films in situ using the Labstation, a modular machine developed at JRC Karlsruhe. The Labstation, an essential part ...

Experimental Methods for Efficient Solar Hydrogen Production in Microgravity Environment

Long-term space flights and cis-lunar research platforms require a sustainable and light life-support hardware which can be reliably employed outside the Earth's atmosphere. So-called 'solar fuel' devices, currently developed for terrestrial applications in the quest for realizing a sustainable energy economy on Earth, provide promising alternative systems to existing air-revitalization units employed on the International Space Station (ISS) through photoelectrochemical water-splitting and hydrogen production. One obstacle for water (photo-) electrolysis in reduced gravity environments is the absence of buoyancy and the consequential, hindered gas bubble release from the electrode surface. This causes the formation of gas bubble froth layers in proximity to the electrode surface, leading to an increase in ohmic resistance and cell-efficiency loss due to reduced mass transfer of substrates and products to and from the electrode. Recently, we have demonstrated efficient solar hydrogen production in microgravity environment, using an integrated semiconductor-electrocatalyst system with p-type indium phosphide as the light-absorber and a rhodium electrocatalyst. By nanostructuring the electrocatalyst using shadow nanosphere lithography and thereby creating catalytic 'hot spots' on the photoelectrode surface, we could overcome gas bubble coalescence and mass transfer limitations and demonstrated efficient hydrogen production at high current densities in reduced gravitation. Here, the experimental details are described for the preparations of these nanostructured devices and further on, the procedure for their testing in microgravity environment, realized at the Bremen Drop Tower during 9.3 s of free fall.

Efficient solar-hydrogen production has recently been realized on functionalized semiconductor-electrocatalyst systems in a photoelectrochemical half-cell in microgravity environment at the Bremen Drop Tower. Here, we report the experimental procedures for manufacturing the semiconductor-electrocatalyst device, details of the experimental set-up in the drop capsule and the experimental sequence during free fall.

微重力环境下高效太阳能氢气生产的实验方法

Long-term space flights and cis-lunar research platforms require a sustainable and light life-support hardware which can be reliably employed outside the ...

中子晶体学数据收集和处理，用于蛋白质结构中氢原子的建模

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