Name: 3d printing of biomolecular models for research and pedagogy
Uploaded: 2017-03-13T14:00:00.000+00:00
Duration: 9 min 17 s
Description: Watch this Scientific Journal Video about 3D Printing of Biomolecular Models for Research and Pedagogy at JoVE.com

The authors are grateful for the support of Deis3D, the Brandeis 3D Printing Club, and members of Brandeis Library/LTS/Makerlab. This work was funded in part by a grant awarded to Pomeranz Krummel by the NSF, Award No. 1157892; an ESIT grant of the BMBF, awarded to the University of T&#252;bingen; and US Federal funds from the National Institutes of Health, Department of Health and Human Services, under Contract No. GS35F0373X. Molecular graphics and analyses were performed with the UCSF Chimera package. Chimera was developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311).

1.准备3D模型文件进行打印注:（1）在线使用NIH三维打印交换10的自动化工具，或（2）本地使用分子建模软件:生物分子的三维模型文件可以通过两种方法产生。自动生成的模型将使用在这个协议中详述创建打印表示的处理，但表示的细节不能由用户来选择。与此相反，自定义模型生成允许对生物分子的视觉属性的用户控件。单个原子，残基，以及键可以被显示，并且色带，债券的规模，并可以指定支柱。美国国立卫生研究院的3D打印交换的自动化工具和以下两个协议使用奇美拉UCSF一个自由和开放源码的分子建模软件包，11很适合于出口生物分子的3D文件。通过使用奇美拉对埃出口的所有3D文件距离单位。当这些文件被在1毫米/距离单位导入到切片软件，该机型将在1000万次的放大倍率进行缩放。 <ol><li> 自动生成与NIH 3D打印交易所3D打印模型 注意:美国国立卫生研究院的3D打印Exchange运行嵌合体的脚本，其类似于步骤1.2-1.3中描述的步骤。 <ol><li>找到生物分子结构的分子数据文件，从数据库，无论是PDB，EMDB或PubChem数据库（补充1.1）打印。记录感兴趣的生物分子的登记号。 </li><li>如果是第一次用户导航到NIH 3D打印交易所（3dprint.nih.gov），并创建一个新的用户帐户。 </li><li>导航到" 快速发布 "功能，进入生物分子加入代码，并点击提交。 </li><li>产生的生物分子的模型后，导航到模型页面并下载生物分子STL文件中的" 丝带"或" 面 "表示。继续执行该协议第2条。 </li></ol></li><li> 生成具有UCSF嵌合体定制的分子模型 注:使用奇美拉制作的3D模型，包括命令行等效很多步骤的更多细节，可以在补充1.2中找到。 <ol><li>下载并安装UCSF嵌合体（https://www.cgl.ucsf.edu/chimera/download.html）。 </li><li>使用奇美拉，通过执行下列操作之一检索分子数据文件: <ol><li> 由ID使用工具栏命令文件&gt;获取 ，输入PubChem数据库，PDB，或加入EMDB代码直接从数据库中检索的文件。 </li><li>使用工具栏命令文件&gt;打开 ，检索本地分子数据文件;默认情况下，分子将5立杆一个内显示配体蛋白质和核酸，原子彩带和债券，和残留物ð。 </li><li>使用奇美拉命令行中，通过转至收藏夹访问&gt;命令行 ，使用打开命令，并输入登录码。 </li></ol></li></ol></li><li> 准备一个生物分子的三维打印表示 注:有一个生物分子结构可以显示或代表的几种方法。要打印的特定表示的选择应基于如何最好地提供了最大的洞察生物分子结构与功能。常用的表示包括"带"，"面"，和"原子/债券"。不过，最好是使用这些表象的组合，显示选择侧链或配体探索。此外，三维印刷结构应该足够健壮要打印和处理时不会破裂。因此，要考虑这一点是很重要的选择表示或显示侧链时。阿尔斯o考虑引入支撑结构，或者"支柱"。最后，在打印模型时，这将是缩放重要的，以便所有的特征将正确打印。因此，对于较大的生物分子，完全在带或原子表示打印可能不是可行由于在这些需要被印刷的规模。 <ol><li>在"彩带"生成一个3D打印表示 注:更多详细信息可在补充1.2.1找到。 <ol><li>选择可见的" 溶剂 "，其中包括离子，通过选择&gt;结构&gt;溶剂 。 </li><li>隐藏选定的" 溶剂 "使用操作&gt;原子/债券&gt;隐藏 。 </li><li>加厚带的直径，以便它可以成功地打印。使用在工具&gt;描写 功能区样式编辑器菜单。 注意:苏ggested参数的初步尝试: 缩放选项卡下 ，更改每一个项目至少0.7以及每个设置的宽度至少有以下的高度 :0.7 线圈 ; 螺旋 1.4; 表 :1.4; 箭头（基地）:2.1; 箭头（TIP）0.7; 核酸 1.0。 </li><li>如果核酸存在，改变与操作&gt;原子/债券&gt;核苷酸对象&gt;设置的基本表示。改变糖/碱显示器梯子梯级半径0.6。 </li><li>可选:继续执行步骤1.3.3引进的支撑结构。 </li></ol></li><li>产生的分子的三维打印"的表面"表示 注:更多详细信息可在补充1.2.2找到。 <ol><li>隐藏所有先前的陈述。使用操作&gt;原子/债券&gt;隐藏和 操作&gt;丝带&gt;隐藏。 </li><li>当渲染原子作为球体，通过选择所需的原子（S）和去操作&gt;检查菜单调节半径。 注:更改默认的原子半径可以更容易地在印刷模式区分不同的原子类型。 </li><li>隐藏任何使用操作&gt;原子/债券&gt;隐藏和行动&gt;丝带&gt;隐藏显示的色带，原子，债券和pseudobonds。 </li><li>如果表面细节是理想的，添加的氢原子，以使表面的计算更准确。使用工具&gt;结构编辑&gt; ADDH。 </li><li>产生通过在命令行中输入冲浪＃0电网0.5的表面。 </li></ol></li><li>生成一个3D打印表示"原子/债券。" 注:更多详细信息可在补充1.2.3找到。 <ol><li>隐藏溶剂。使用选择&gt;结构&gt;溶剂中 ，然后操作&gt;原子/债券&gt;隐藏 。 </li><li>通过选择并显示出操作&gt;原子/债券&gt;显示它们显示特定的残留物和/或表示形式原子的配体和债券。原子表示方式可以在操作&gt;原子/债券下拉列表中选择棍，球和棍子 ，或球来改变。 </li><li>进行选择后，提高棒或球的半径，并与操作棒表示&gt;检查菜单。 </li><li>可选:继续执行步骤1.3.4引进的支撑结构。 </li></ol></li></ol></li><li> 添加结构支撑一个3D打印表示 注:更多详细信息可在补充1.2.4和1.2.5中找到。在此阶段，支柱可以被添加到3D模型。建议用于α-螺旋和β-折叠片的二级结构，以包括稳定骨干氢键，虽然小蛋白质（ 即，少于50个残基）通常表示为具有典型厚度的带状，并且可以打印良好，没有这样的支持。然而，对于较大的蛋白质，即使加入的氢键，许多色带车型仍然过于细腻要成功地打印。支柱是不反映任何分子属性但增加的机械强度，从而有利于印刷和处理模型中的物理连接。奇美提供了一个快速的方法来自动支柱的支柱命令通过命令行添加到模型和个体支柱也可能是使用手动工具的距离显示。 <ol><li>显示氢键准备一个坚固的打印。使用菜单工具&gt;结构分析&gt; FindHBond。 </li><li>使用工具&gt;常规续ROLS&gt; PseudoBond面板修改氢键。选择"氢键"pseudobonds，点击属性按钮，勾选" 组件PseudoBond属性 "对话框。在底部面板，改变从线债券的风格， 坚持从0.2到0.6的半径值。 </li><li>可选:添加支撑结构（S），或者"支柱"，使用Struts命令。与1.0在每个70个残基的碳阿尔法半径不超过8创建蓝支柱分开，使用命令: 支柱@ca长度8圈70色蓝色弧度1.0 fattenRibbon假的 。 </li><li>可选:要使用距离工具创建单独的支柱，选择每个人，请使用工具&gt;结构分析&gt;距离由移CTRL单击两个原子，然后单击创建添加pseudobond。 NAVIGAT以e为PseudoBond面板中选择"远程监控"pseudobonds，点击属性按钮，然后选中"组件PseudoBond属性 "对话框。在底部面板，改变从线债券的风格， 坚持从0.2到0.01的半径值。 </li><li>导出奇美拉渲染为STL的3D模型文件<ol><li>一旦获得所需的代表性，使用文件&gt;导出场景导出3D文件。 STL选择作为文件类型和名称，并保存模型。注:在协议的第2节这STL文件可以修复，导向，并打印。 </li></ol></li></ol></li></ol> 2.印刷工艺STL文件<ol><li> 与Autodesk Netfabb修复STL文件 注:模型可能需要维修时，它包含多个重叠的部分与INTErsecting几何形状，其通常是用丝带模型和原子模型的情况。重叠几何当文件被一些切片软件读，因为相交的区域可以解释为模型的外观可能会导致错误。更多详细信息可在补充2.1中找到。 <ol><li>下载并安装该软件的标准版本。 </li><li>打开程序并导入STL文件进行修复。如果有与该网格的问题，将显示一个警告信号。 </li><li>使用其他&gt;自动零件修理 ，选择扩展修复 ，然后等待文件处理;对于小机型，这将需要几秒钟，但对于大型模型，可能需要几分钟。 </li><li>在模型上单击鼠标右键，选择导出部分&gt;由于STL或使用项目&gt;导出工程为STL保存修复模型;该方案将增加" 修理 "到文件名从原始文件区分开来。 </li></ol></li><li> 东方模型与Autodesk Meshmixer打印 注:切片前一模型的最优取向将减少突出端的数量，因此，在印刷过程中需要支撑件的数量。一个最佳化模式将打印速度更快，使用更少的材料，并且不太可能在打印过程中失败。更多详细信息可在补充2.2中找到。 <ol><li>下载并安装软件</li><li>导入修复STL文件到程序中。 </li><li>选择分析&gt;方向 。 </li><li>强度重量值调整为100，支持卷重量值设置为0，支持单位面积质量为0，然后更新模型。这将旋转模型以最小化突出端的数目。接受由此带来的方向。 </li><li>使用文件&gt;导出 ，然后选择从下拉菜单中的二进制STL文件。保存文件。 </li></ol></li></ol> 3，切片和打印<ol><li> 选择灯丝材料 注意:一打印材料的选择应使用切片软件之前进行，因为打印设置将所选材料不同。被广泛使用的三种材料是聚乳酸（PLA），热塑性弹性体（TPE）和丙烯腈丁二烯苯乙烯（ABS）。 PLA一般是打印详细的分子模型最有效的材料，因为它冷却快，很好地粘附到构建板，很少扭曲。 TPE是类似的材料PLA和可以用来生产柔性的模型。推荐用于补充蛋白质表面模型或蛋白带状模型。 ABS更强，比PLA更灵活，但在打印时12它所产生潜在危险的颗粒。它一般不建议在打印分子模型，为更高的材料的温度会导致LESŞ精确的生产小的特点。更多详细信息可在补充3.1中找到。 <ol><li>与聚乳酸（PLA）打印。 <ol><li>设置喷嘴温度至210℃。为了确保部到床的粘附，设置的床温至70℃。如果使用未加热的床上，用画家的胶带覆盖。使用主动散热。 </li></ol></li><li>与热塑性弹性体印刷（TPE） <ol><li>重复步骤3.1.1.1。打印速度设置到1200毫米/分钟或更小。 </li></ol></li><li>与丙烯腈 - 丁二烯 - 苯乙烯印刷（ABS）的<ol><li>不要使用冷却。设置喷嘴温度至240℃。为了确保部到床的粘附，设置的床温至110℃。 </li></ol></li></ol></li><li> 生成的G代码 注:该模型将在倍放大倍率由默认为10万元左右进口。带状模型应该缩放至20万次（200％）或更高。表面模型公关在100％或更大诠释好。更多详细信息可在补充3.2中找到。 <ol><li>下载并安装打印软件的切片。 </li><li>使用文件&gt;导入模型并选择修理和面向STL文件。 </li><li>比例通过在模型上双击和在屏幕的右手侧上的窗口中输入的比例因子模型。 </li><li>生成的模型的支持结构。选择支持图标，并使用正常的支持下，为1的支柱分辨率和50°的最大角悬。 </li><li>点击生成所有支持。添加或删除支撑结构特性来定制的支持位置。 </li><li>选择一个进程，然后单击编辑流程设置 。 </li><li>配置为正在使用的打印机和材料的轮廓。 注:木筏和边缘应包括，和带状模式应在100％填充打印。详细介绍设置可以在suppleme找到NT 3.2。 </li><li>转换模型成可由打印机读取的G代码文件。点击" 准备打印 "按钮，选择包含打印机/材料的个人资料的过程。观察打印机喷头的路径，并检查其可能导致打印失败的错误。 注:错误可导致打印失败包括缺乏下悬过于薄打印支架，不希望的空腔，缺失层或区域。 </li><li>保存G代码文件保存到桌面，或直接到SD卡。 </li></ol></li><li> 操作打印机 注:每个打印机品牌或型号是独一无二的，它的准备和校准打印将相应变化。请参考手册打印机。 <ol><li>确保工作站连接到打印机或与GCODE SD卡在打印机中。 </li><li>准备通过加载灯丝，并确保该床是水平的打印机;有关这些过程的说明，请参阅打印机的说明书。 </li><li>开始从计算机或从本地通过打印机菜单SD卡打印。 </li><li>观看打印直到第一层已成功完成。如果在第一层的任何错误，中止并重新启动打印。 </li></ol></li></ol> 4.后期制作处理注:当然护理应该在这个取，最后，舞台。应该删除该模型支撑结构。这通常是手动完成的，虽然其他方法，如使用可溶解的支持，可以使用;见补充4。 <ol><li>轻轻侧身拉松脱，从构建盘打印。如果筏牢固地粘附到构建板，通过插入它们之间的尖锐边缘分开吧。 </li><li>从模型中取出支撑结构。许多载体可用手取出，通过断开它们关闭的部分和岭英尺灵活的模型可以拉动他们的部分离开分离。对于那些难以到达或连接到脆弱的结构，用剪钳夹所在的支持连接到部分点支撑。 </li></ol>

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The authors have nothing to disclose.

生物分子的物理3D模型的可视化的更常见的基于计算机的方法提供了一个有力的补充。物理3D表现的附加属性有助于生物分子结构的直观的了解。生物分子物理3D模型的建设可以通过使用，它利用人感发达模式的介质有利于他们的学习。 3D模型不仅作为一种辅助手段的研究人员，但也可以用来促进教学活动，并能增加实现的学习成果13，14，15。磁体可以加入到塑料模型以允许组装和拆卸，如图所示多肽16的模型。此外，3D印刷对象可以在研究中使用，无论是在制造的实验室设备17，以及使microfl对于小区18和19的晶体或神经元20款uidic设备。物理模型的操作可以有利于促进协作的讨论，可以激发新的见解。 在3D打印技术和减排的最新进展在打印机的费用由个人用户启用的生物分子的复杂的，物理的3D模型的创建。虽然FFF印刷技术是更常见的，比其他方法更便宜，它带来了一些限制。三维印刷工艺是费时的，并且不发生机械故障。 FFF打印机通常只能打印一种材料每部分限制的色彩信息的显示。对FFF打印机国产车型的分辨率较低，约为每层100微米。我们建议读者与这些限制工作，并为他们的利益的打印机和生物分子（S）的方法。我们已经提出了PROCE为用户所需的小规模企业开发自己感兴趣的生物分子的自定义3D表示是准确，翔实，并打印。正如任何新技术，经常有"成长的烦恼"，但必须其使用过程中克服。我们提供在哪里的问题可能在3D打印生物分子（见补充6）的过程中可能遇到的几个例子。 最后，通过这篇文章，我们的目标是促进从事生物分子的三维打印用户组成的社区的发展。重要的是，美国国立卫生研究院已经建立了一个数据库，供公众共享3D模型和使用的方法来打印这些10。我们强烈建议在这一独特的资源（见补充7如何上传3D模型打印和背景信息，美国国立卫生研究院的3D打印交易指令）的参与。

的功能和生物分子的活性的透彻理解要求其三维（3D）结构的测定。这是通过使用X-射线晶体学，NMR或电子显微镜常规实现。三维结构可以通过模型或类似它们代表1结构精确对象的感知来理解。从历史上看，物理3D模型的建设是必要的调查验证，探索和交流有关生物分子的功能所产生的假设。这些模型中，如沃森-克里克的DNA双螺旋和鲍林的α螺旋，提供了独特的洞察的结构-功能关系和分别枢轴于我们的核酸和蛋白质结构-功能2，3，4的早期理解。尽管复杂的蛋白质和核酸模型可以被创建时，时间和构建物理模型的成本最终被相对容易计算机辅助分子可视化抵消。 3D打印，也被称为添加剂制造的发展，已再次启用生物分子5物理模型建设。三维打印是通过顺序加入的材料（S）层的制造从一个数字文件的物理，3D对象的过程。各种机制在此过程中使用。直到最近，用于生产生物分子的物理模型的机器太贵被广泛使用。然而，在过去的十年中，3D印刷技术，熔融长丝制造（FFF）特别是已显著先进，使得它对于用户使用6访问。 FFF打印机现在在高中，图书馆，大学和实验室常用的。更大的负担能力和获得的3D打印技术使得有可能以数字化三维生物分子模型转换成精确的，物理的3D模型生物分子7，8，9。这些模型不仅包括单个生物分子的简单表示，但也复杂大分子组件，如核糖体和病毒衣壳的结构。然而，打印单张生物分子和大分子组装的过程中带来一些挑战，用热塑性挤压方法时尤为如此。尤其是生物分子的表现往往具有复杂几何形状难以对打印机的生产，以及创建和处理数字的模型，将成功打印需要与分子建模，3D建模和3D打印机软件技能。 三维工作流程大致印刷生物分子发生在四个步骤:（1）制备从三维打印其坐标文件生物分子模型;（2）进口生物分子模型变成了"切片"的软件来分割模型的打印机，并生成一个支撑结构，将身体撑起生物分子模型; （3）选择正确的长丝和打印三维模型;和（4）的后期制作处理的步骤，包括从模型移除支撑材料（ 图1和2）。第一步在此过程中，计算上操纵生物分子的坐标文件，是至关重要的。在此阶段，用户可以在支杆的形式建立模型加固，以及删除是无关的什么用户选择要显示的结构。另外，表示的选择在此阶段是由:是否显示该生物分子的全部或部分作为表面表示，色带，和/或单个原子。一旦必要的添加和/或内容的减法制成并且被选择的表示，该结构被保存为一个三维莫德尔文件。接着，该文件是在一个第二软件程序到模型转换成可打印的三维打印文件，逐层，进入生物分子的一个塑料复制品打开。 我们的协议的目标是使分子模型的制造中可访问的大量用户的谁有权访问FFF打印机，但不以更昂贵的三维打印技术。在这里，我们提供了从3D分子数据的生物分子的三维打印指导，与那些为FFF打印优化方法。我们详细介绍了如何最大限度地提高生物分子的复杂结构的可印刷性和保证物理模型的简单的后期处理。常见的几种印刷材料或长丝的性能进行比较，并在它们的使用的建议来创建提供灵活的印刷品。最后，我们展示了一系列的演示使用不同的分子表征的3D打印生物分子模型的例子。

<table><tbody><tr><td>&lt;strong&gt;Filament&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>PLA 3D Printing Filament (1.0 kg Roll)</td><td>Quantum3D Printing</td><td>http://quantum3dprinting.com/</td><td>Very good quality PLA filament, strongly recomended</td></tr><tr><td>NinjaFlex Flexible 3D Printing Filament</td><td>Ninjatek</td><td>https://ninjatek.com/</td><td>High quality flexible filament</td></tr><tr><td>PLA Filaments PrimaValue &amp;amp; PrimaSelect</td><td>3DPrima</td><td>http://3dprima.com/</td><td>High quality European supplier of filament</td></tr><tr><td>&lt;strong&gt;Printers&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Prusa I3 MK2 3D Printer</td><td>Prusa Research</td><td>http://www.prusa3d.com/</td><td>A popular 3D printer</td></tr><tr><td>MakerGear M2 Revision E (M2e)</td><td>MakerGear</td><td>http://www.makergear.com/</td><td>Closed source, very high quality printer</td></tr><tr><td>Ultimaker 2</td><td>Ultimaker</td><td>https://ultimaker.com/</td><td>Very reliable, easy to use printer, highest rating on 3Dhubs.com</td></tr><tr><td>Flashforge Creator Pro</td><td>Flashforge</td><td>http://www.flashforge-usa.com</td><td>Reliable, dual extrusion printer, highest rating on 3Dhubs.com</td></tr><tr><td>&lt;strong&gt;Software&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Simplify3D Slicer</td><td>Simplify3D</td><td>https://www.simplify3d.com/</td><td>Excellent slicing software</td></tr><tr><td>Netfabb</td><td>Autodesk</td><td>http://www.autodesk.com/education/free-software/netfabb</td><td>Mesh repair software, available free of cost for educational purposes</td></tr><tr><td>Chimera</td><td>University of California, San Francisco</td><td>https://www.cgl.ucsf.edu/chimera/</td><td>Chimera molecular vizualizer</td></tr><tr><td>Meshmixer</td><td>Autodesk</td><td>http://www.meshmixer.com/</td><td>Used for orienting models, but has other features</td></tr></tbody></table>

3d printing of biomolecular models for research and pedagogy

The construction of physical three-dimensional (3D) models of biomolecules can uniquely contribute to the study of the structure-function relationship. 3D structures are most often perceived using the two-dimensional and exclusively visual medium of the computer screen. Converting digital 3D molecular data into real objects enables information to be perceived through an expanded range of human senses, including direct stereoscopic vision, touch, and interaction. Such tangible models facilitate new insights, enable hypothesis testing, and serve as psychological or sensory anchors for conceptual information about the functions of biomolecules. Recent advances in consumer 3D printing technology enable, for the first time, the cost-effective fabrication of high-quality and scientifically accurate models of biomolecules in a variety of molecular representations. However, the optimization of the virtual model and its printing parameters is difficult and time consuming without detailed guidance. Here, we provide a guide on the digital design and physical fabrication of biomolecule models for research and pedagogy using open source or low-cost software and low-cost 3D printers that use fused filament fabrication technology.

生物分子的稳定和翔实的三维打印模型可以如下制备:（ⅰ）增稠键以提供稳定性，（ⅱ）仔细选择二级结构表示类型或风格，将提供最大的洞察力和稳定性，（ⅲ）印刷生物分子在多于一个的分子表示，（ⅳ）使用长丝，将呈现所有的或柔性的生物分子的一部分，或（v）产生一复杂的组件，其是模块化（ 即，在连接件）。 为了说明如何打印这样的信息和稳定的模型，我们专注于染色质的组件和生产上的染色质的假设模型。染色质是一个高度复杂的蛋白-DNA装配。染色质的基本蛋白质亚基是组蛋白。有四个组蛋白，各由一个螺旋-loop - 螺旋（一个"组蛋白折叠"），接着是延长的α螺旋和第二"组蛋白折叠"。组蛋白蛋白质的结构可以很容易地通过使用"色带"表示（ 图3A）来制造。可替代地，可以仅使用其表面（ 图3B）被显示的组蛋白结构。有四个组蛋白，其组装以形成球状的组蛋白八聚体的两个副本。组蛋白八聚体过大，无法完全打印为带状或棒表示，由于较大的规模在这些功能需要打印。因此，这样的大的蛋白装配，使用表面表示（ 图3C）最好显示。将DNA图表周围组蛋白八聚体的路径，形成纳米直径的10核小颗粒。 DNA的路径可以最好通过印刷两个单独的模型，并使用该DNA（ 图3D）的柔性长丝被显示。核小颗粒堆叠在彼此以形成一个高阶组件，纳米直径30"纤维"左手suprahelical结构。到最好的说明如何在10纳米的核小体核心颗粒可以堆叠以形成一个30纳米染色质装配，打印个人"二核"颗粒（ 图3E），然后打印（ 图3F）后它们堆叠。 一旦掌握上述的单一挤压表面和色带的工作流程，探索使一个范围的原子，分子，和复合模式的，如在图4中示出。例如，结合表面和色带表示设置一个复杂的分开不同部位（参见DNA聚合酶， 图4B）。通过使用双挤出打印机可同时熔融两个灯丝成一个单一的3D对象做出更多指导性和吸引人的模型（参见图4C）。另外，该机型的油漆部分（见关INE和α螺旋， 图4A）。印刷和装配的蛋白复合物的亚基，如钠通道，或将其进一步通过印刷复杂的不同的部分，并稍后将它们组装成一个较大的，多色模型（见的HIV抗体和核糖体复合物， 图4C）。这种复合模型能够更好相比单丝打印到显示功能特征。不同的颜色可以突出，例如，糖基化与蛋白质（HIV模型）或RNA与蛋白质（见核糖体模型， 图4C）。它们还允许创建的教育三维拼图，像抗体结合对HIV表面（见gp120的抗体结合， 图4C），其中只有一个三维配置提供两个零件的紧密配合。上打印这些机型的使用说明可以补充5.此外可以发现，我们提供了一个补充说明视频的第一个3D模型的构建È佛将其印刷在片和组装以这样的方式，以便它可以概括发生在此酶催化机制转动机构/ F1的质子ATP合酶。 <img alt="图1" src="/files/ftp_upload/55427/55427fig1.jpg" /> 图1. 工作流程准备和打印三维模型。示出是在制造一个物理3D生物分子印记的阶段:（i）制备的模型，其中包括选择所述表示; （ 二 ）在打开模型的保存.STL文件，并使用切片软件处理文件; （ 三 ）在打印模型和选择材料或长丝;最后，（ⅳ）执行的后期制作步骤。<a href="http://ecsource.jove.com/files/ftp_upload/55427/55427fig1large.jpg" target="_blank">请点击此处查看该图的放大版本。</a> <img alt="图2" src="/files/ftp_upload/55427/55427fig2.jpg" /> 图2. 型号不同表示的视觉编写的各个阶段。上排:两种机型（泛素（PDB 1UBQ）和精氨酸）共同表示使用该程序奇美拉可视化。 中排 :从奇美拉STL模型生成的刀具路径印刷，泛素和精氨酸的功能型有色（橙色:填充图案;深蓝色:外壳;浅蓝:内壳）。 下排:泛素和精氨酸的最终印刷品。泛蛋白的表面和两个色带机型打印在默认嵌合STL输出的300％（嵌合体默认是模型1nm且在印刷1厘米），而精氨酸W型印在1000％。嵌合体默认带状或棍模型太薄正确打印，但加厚版本将可靠地打印。 <a href="http://ecsource.jove.com/files/ftp_upload/55427/55427fig2large.jpg" target="_blank">请点击此处查看该图的放大版本。</a> <img alt="图3" src="/files/ftp_upload/55427/55427fig3.jpg" /> 图3. 核小体的案例研究 。 （一）由增厚呈现单组蛋白H3蛋白"丝带"，印在300％。 （B）的组蛋白H3蛋白质"表面"表示，在200％的印刷。八聚体在100％印刷的（C）的组蛋白的蛋白质。在具有柔性的DNA（白色）配合物（D）的组蛋白八聚体蛋白（橙色）在100％的打印。印有一个默认的探针半径（E）Dinucleosome表面模型，并在100％的比例打印。 （F）A M通过手动堆叠"10纳米"dinucleosome，其中该表面用3埃的探针半径呈现时，在50％和25％的尺寸印刷的单独打印模型产生的染色质"30纳米纤维"Odel等，并保持再加上播放，卫生署。从dinucleosome（PDB 1ZBB）模型生成的3D打印。所有型号都可以免费下载在NIH 3D打印兑换11。 <a href="http://ecsource.jove.com/files/ftp_upload/55427/55427fig3large.jpg" target="_blank">请点击此处查看该图的放大版本。</a> <img alt="图4" src="/files/ftp_upload/55427/55427fig4.jpg" /> 图4. 三维打印模型的示例使用灯丝的打印机产生的。 （A）的左，在六角形冰晶（双灯丝打印）一个水分子的球棒模型。中东，核苷酸（鸟嘌呤）的模型。对，一个蛋白α^ h<html> ELIX骨干，只有模型显示了氢键（黑色）。鸟嘌呤和α螺旋用骗子手动着色。 （B）的左，钠通道，4个亚单位可结合在一起组成（PDB 3E89）。中东， 恶性疟原虫 L-乳酸脱氢酶（PDB 1T2D）打印为丝带。右，模型中的DNA聚合酶的活性位点（PDB 1KLN），显示出DNA为表面蛋白丝带。 （C）左，艾滋病毒脂质包膜糖蛋白（PDB 5FUU）由抗体（PDB 1IGT），在15％的印刷约束。中间，在150％的糖蛋白抗原表面的细节，示出为带（PDB 5FYJ）抗体的可变区。细菌70S核糖体（PDB 4V5D）的右边，模型在40％和20％。百分数是指标准嵌合体输出，其中100％是指在分子打印1毫米1纳米。所有型号都可以免费下载在NIH 3D打印兑换11。OAD / 55427 / 55427fig4large.jpg"目标="_空白"&gt;点击此处查看该图的放大版本。

Watch this Scientific Journal Video about 3D Printing of Biomolecular Models for Research and Pedagogy at JoVE.com

3D Printing of Biomolecular Models for Research and Pedagogy

Physical models of biomolecules can facilitate an understanding of their structure-function for the researcher, aid in communication between researchers, and serve as an educational tool in pedagogical endeavors. Here, we provide detailed guidance for the 3D printing of accurate models of biomolecules using fused filament fabrication desktop 3D printers.

生物分子模型的3D打印技术的研究与教学

The construction of physical three-dimensional (3D) models of biomolecules can uniquely contribute to the study of the structure-function relationship. 3D ...

3d-printing-of-biomolecular-models-for-research-and-pedagogy

Nanyang Technological University

Research

JoVE Journal

Engineering

23.6K 次观看.  Brandeis University. Physical models of biomolecules can facilitate an understanding of their structure-function for the researcher, aid in communication between researchers, and serve as an educational tool in pedagogical endeavors. Here, we provide detailed guidance for the 3D printing of accurate models of biomolecules using fused filament fabrication desktop 3D printers.

视频: 3D Printing of Biomolecular Models for Research and Pedagogy

Multimodal 3D Printing of Phantoms to Simulate Biological Tissue

Biomedical optical imaging is playing an important role in diagnosis and treatment of various diseases. However, the accuracy and the reproducibility of an optical imaging device are greatly affected by the performance characteristics of its components, the test environment, and the operations. Therefore, it is necessary to calibrate these devices by traceable phantom standards. However, most of the currently available phantoms are homogeneous phantoms that cannot simulate multimodal and dynamic characteristics of biological tissue. Here, we show the fabrication of heterogeneous tissue-simulating phantoms using a production line integrating a spin coating module, a polyjet module, a fused deposition modeling (FDM) module, and an automatic control framework. The structural information and the optical parameters of a &#34;digital optical phantom&#34; are defined in a prototype file, imported to the production line, and fabricated layer-by-layer with sequential switch between different printing modalities. Technical capability of such a production line is exemplified by the automatic printing of skin-simulating phantoms that comprise the epidermis, dermis, subcutaneous tissue, and an embedded tumor.

Spin coating, polyjet printing, and fused deposition modeling are integrated to produce multilayered heterogeneous phantoms that simulate structural and functional properties of biological tissue.

幻影的多模态3D打印模拟生物组织

Biomedical optical imaging is playing an important role in diagnosis and treatment of various diseases. However, the accuracy and the reproducibility of ...

科研

工程学

Interactive Molecular Model Assembly with 3D Printing

With the growth in accessibility of 3D printing, there has been a growing application of and interest in additive manufacturing processes in chemical laboratories and chemical education. Building on the long and successful history of physical modeling of molecular systems, we present select models along with a protocol to facilitate 3D printing of molecular structures that are able to do more than represent shape and connectivity. Models assembled as described incorporate dynamic aspects and degrees of freedom into saturated hydrocarbon structures. As a representative example, cyclohexane was assembled from parts printed and finished using different thermoplastics, and the resulting models retain their functionality at a variety of scales. The resulting structures show configurational space accessibility consistent with calculations and literature, and versions of these structures can be used as aids to illustrate concepts that are difficult to convey in other ways. This exercise enables us to evaluate successful printing protocols, make practical recommendations for assembly, and outline design principles for physical modeling of molecular systems. The provided structures, procedures, and results provide a foundation for individual manufacture and exploration of molecular structure and dynamics with 3D printing.

Physical modeling of microscopic systems helps obtain insights that are difficult to gain by other means. To facilitate the construction of physical molecular models, we demonstrate how 3D printing can be used to assemble functional macroscopic models that capture qualities of molecular systems in a tactile way.

带 3D 打印的交互式分子模型组件

With the growth in accessibility of 3D printing, there has been a growing application of and interest in additive manufacturing processes in chemical ...

化学

Scaled Anatomical Model Creation of Biomedical Tomographic Imaging Data and Associated Labels for Subsequent Sub-surface Laser Engraving (SSLE) of Glass Crystals

Biomedical imaging modalities like computed tomography (CT) and magnetic resonance (MR) provide excellent platforms for collecting three-dimensional data sets of patient or specimen anatomy in clinical or preclinical settings. However, the use of a virtual, on-screen display limits the ability of these tomographic images to fully convey the anatomical information embedded within. One solution is to interface a biomedical imaging data set with 3D printing technology to generate a physical replica. Here we detail a complementary method to visualize tomographic imaging data with a hand-held model: Sub Surface Laser Engraving (SSLE) of crystal glass. SSLE offers several unique benefits including: the facile ability to include anatomical labels, as well as a scale bar; streamlined multipart assembly of complex structures in one medium; high resolution in the X, Y, and Z planes; and semi-transparent shells for visualization of internal anatomical substructures. Here we demonstrate the process of SSLE with CT data sets derived from pre-clinical and clinical sources. This protocol will serve as a powerful and inexpensive new tool with which to visualize complex anatomical structures for scientists and students in a number of educational and research settings.

Scaled Anatomical Model Creation of Biomedical Tomographic Imaging Data and Associated Labels for Subsequent Sub-surface Laser Engraving SSLE of Glass Crystals

A methodology is described herein for representing anatomical imaging data within crystals. We create scaled three-dimensional models of biomedical imaging data for use in Sub-Surface Laser Engraving (SSLE) of crystal glass. This tool offers a useful complement to computational display or three-dimensionally printed models used within clinical or educational settings.

缩放生物医学层析成像数据的解剖模型的创建和相关联的标签玻璃晶体的随后的子表面激光雕刻（SSLE）

Biomedical imaging modalities like computed tomography (CT) and magnetic resonance (MR) provide excellent platforms for collecting three-dimensional data ...

生物工程

Bioprintable Alginate/Gelatin Hydrogel 3D In Vitro Model Systems Induce Cell Spheroid Formation

The cellular, biochemical, and biophysical heterogeneity of the native tumor microenvironment is not recapitulated by growing immortalized cancer cell lines using conventional two-dimensional (2D) cell culture. These challenges can be overcome by using bioprinting techniques to build heterogeneous three-dimensional (3D) tumor models whereby different types of cells are embedded. Alginate and gelatin are two of the most common biomaterials employed in bioprinting due to their biocompatibility, biomimicry, and mechanical properties. By combining the two polymers, we achieved a bioprintable composite hydrogel with similarities to the microscopic architecture of a native tumor stroma. We studied the printability of the composite hydrogel via rheology and obtained the optimal printing window. Breast cancer cells and fibroblasts were embedded in the hydrogels and printed to form a 3D model mimicking the in vivo microenvironment. The bioprinted heterogeneous model achieves a high viability for long-term cell culture (&#62; 30 days) and promotes the self-assembly of breast cancer cells into multicellular tumor spheroids (MCTS). We observed the migration and interaction of the cancer-associated fibroblast cells (CAFs) with the MCTS in this model. By using bioprinted cell culture platforms as co-culture systems, it offers a unique tool to study the dependence of tumorigenesis on the stroma composition. This technique features a high-throughput, low cost, and high reproducibility, and it can also provide an alternative model to conventional cell monolayer cultures and animal tumor models to study cancer biology.

Bioprintable Alginate/Gelatin Hydrogel 3D In Vitro Model Systems Induce Cell Spheroid Formation

We developed a heterogeneous breast cancer model consisting of immortalized tumor and fibroblast cells embedded in a bioprintable alginate/gelatin bioink. The model recapitulates the in vivo tumor microenvironment and facilitates the formation of multicellular tumor spheroids, yielding insight into the mechanisms driving tumorigenesis.

Bioprintable 藻酸盐/明胶水凝胶 3D体外模型诱导细胞球形形成

The cellular, biochemical, and biophysical heterogeneity of the native tumor microenvironment is not recapitulated by growing immortalized cancer cell ...

Three-dimensional Patterning of Engineered Biofilms with a Do-it-yourself Bioprinter

Biofilms are aggregates of bacteria embedded in a self-produced spatially-patterned extracellular matrix. Bacteria within a biofilm develop enhanced antibiotic resistance, which poses potential health dangers, but can also be beneficial for environmental applications such as purification of drinking water. The further development of anti-bacterial therapeutics and biofilm-inspired applications will require the development of reproducible, engineerable methods for biofilm creation. Recently, a novel method of biofilm preparation using a modified three-dimensional (3D) printer with a bacterial ink has been developed. This article describes the steps necessary to build this efficient, low-cost 3D bioprinter that offers multiple applications in bacterially-induced materials processing. The protocol begins with an adapted commercial 3D printer in which the extruder has been replaced with a bio-ink dispenser connected to a syringe pump system enabling a controllable, continuous flow of bio-ink. To develop a bio-ink suitable for biofilm printing, engineered Escherichia coli bacteria were suspended in a solution of alginate, so that they solidify in contact with a surface containing calcium. The inclusion of an inducer chemical within the printing substrate drives expression of biofilm proteins within the printed bio-ink. This method enables 3D printing of various spatial patterns composed of discrete layers of printed biofilms. Such spatially-controlled biofilms can serve as model systems and can find applications in multiple fields that have a wide-ranging impact on society, including antibiotic resistance prevention or drinking water purification, among others.

This article describes a method of transforming a low-cost commercial 3D printer into a bacterial 3D printer that can facilitate printing of patterned biofilms. All necessary aspects of preparing the bioprinter and bio-ink are described, as well as verification methods to assess the formation of biofilms.

工程生物膜的三维造型

Biofilms are aggregates of bacteria embedded in a self-produced spatially-patterned extracellular matrix. Bacteria within a biofilm develop enhanced ...

Voxel Printing Anatomy: Design and Fabrication of Realistic, Presurgical Planning Models through Bitmap Printing

Most applications of 3-dimensional (3D) printing for presurgical planning have been limited to bony structures and simple morphological descriptions of complex organs due to the fundamental limitations in accuracy, quality, and efficiency of the current modeling paradigm. This has largely ignored the soft tissue critical to most surgical specialties where the interior of an object matters and anatomical boundaries transition gradually. Therefore, the needs of the biomedical industry to replicate human tissue, which displays multiple scales of organization and varying material distributions, necessitate new forms of representation. 
Presented here is a novel technique to create 3D models directly from medical images, which are superior in spatial and contrast resolution to current 3D modeling methods and contain previously unachievable spatial fidelity and soft tissue differentiation. Also presented are empirical measurements of novel, additively manufactured composites that span the gamut of material stiffnesses seen in soft biological tissues from MRI and CT. These unique volumetric design and printing methods allow for deterministic and continuous adjustment of material stiffness and color. This capability enables an entirely new application of additive manufacturing to presurgical planning: mechanical realism. As a natural complement to existing models that provide appearance matching, these new models also allow medical professionals to "feel" the spatially varying material properties of a tissue simulant-a critical addition to a field in which tactile sensation plays a key role.

This method demonstrates a voxel-based 3D printing workflow, which prints directly from medical images with exact spatial fidelity and spatial/contrast resolution. This enables the precise, graduated control of material distributions through morphologically complex, graduated materials correlated to radiodensity without loss or alteration of data.

体素打印剖析:通过位图打印设计和制作逼真的、外科手术前规划模型

Most applications of 3-dimensional (3D) printing for presurgical planning have been limited to bony structures and simple morphological descriptions of ...

3D Printing of Preclinical X-ray Computed Tomographic Data Sets

Three-dimensional printing allows for the production of highly detailed objects through a process known as additive manufacturing. Traditional, mold-injection methods to create models or parts have several limitations, the most important of which is a difficulty in making highly complex products in a timely, cost-effective manner.1 However, gradual improvements in three-dimensional printing technology have resulted in both high-end and economy instruments that are now available for the facile production of customized models.2 These printers have the ability to extrude high-resolution objects with enough detail to accurately represent in vivo images generated from a preclinical X-ray CT scanner. With proper data collection, surface rendering, and stereolithographic editing, it is now possible and inexpensive to rapidly produce detailed skeletal and soft tissue structures from X-ray CT data. Even in the early stages of development, the anatomical models produced by three-dimensional printing appeal to both educators and researchers who can utilize the technology to improve visualization proficiency. 3, 4 The real benefits of this method result from the tangible experience a researcher can have with data that cannot be adequately conveyed through a computer screen. The translation of pre-clinical 3D data to a physical object that is an exact copy of the test subject is a powerful tool for visualization and communication, especially for relating imaging research to students, or those in other fields. Here, we provide a detailed method for printing plastic models of bone and organ structures derived from X-ray CT scans utilizing an Albira X-ray CT system in conjunction with PMOD, ImageJ, Meshlab, Netfabb, and ReplicatorG software packages.

Using modern plastic extrusion and printing technologies, it is now possible to quickly and inexpensively produce physical models of X-ray CT data taken in a laboratory. The three -dimensional printing of tomographic data is a powerful visualization, research, and educational tool that may now be accessed by the preclinical imaging community.

基础X射线计算机断层数据的三维打印设置

Three-dimensional printing allows for the production of highly detailed objects through a process known as additive manufacturing.  Traditional, ...

生物学

在水凝胶基质中生物打印细菌，用于研究运动和生长

3D Printing Bacteria to Study Motility and Growth in Complex 3D Porous Media

Bacteria are ubiquitous in complex three-dimensional (3D) porous environments, such as biological tissues and gels, and subsurface soils and sediments. However, the majority of previous work has focused on studies of cells in bulk liquids or at flat surfaces, which do not fully recapitulate the complexity of many natural bacterial habitats. Here, this gap in knowledge is addressed by describing the development of a method to 3D-print dense colonies of bacteria into jammed granular hydrogel matrices. These matrices have tunable pore sizes and mechanical properties; they physically confine the cells, thus supporting them in 3D. They are optically transparent, allowing for direct visualization of bacterial spreading through their surroundings using imaging. As a proof of this principle, here, the capability of this protocol is demonstrated by 3D printing and imaging non-motile and motile Vibro cholerae, as well as non-motile Escherichia coli, in jammed granular hydrogel matrices with varying interstitial pore sizes.

作者聚焦:研究 3D 水凝胶基质中的细菌生长

This protocol describes a procedure for three-dimensional (3D) printing of bacterial colonies to study their motility and growth in complex 3D porous hydrogel matrices that are more akin to their natural habitats than conventional liquid cultures or Petri dishes.

3D打印细菌研究复杂3D多孔介质中的运动和生长

Bacteria are ubiquitous in complex three-dimensional (3D) porous environments, such as biological tissues and gels, and subsurface soils and sediments. ...

生物分子模型的3D打印技术的研究与教学

摘要

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此视频中的章节

幻影的多模态3D打印模拟生物组织

带 3D 打印的交互式分子模型组件

缩放生物医学层析成像数据的解剖模型的创建和相关联的标签玻璃晶体的随后的子表面激光雕刻（SSLE）

Bioprintable 藻酸盐/明胶水凝胶 3D体外模型诱导细胞球形形成

工程生物膜的三维造型

体素打印剖析:通过位图打印设计和制作逼真的、外科手术前规划模型

基础X射线计算机断层数据的三维打印设置

3D打印细菌研究复杂3D多孔介质中的运动和生长

3D打印细菌研究复杂3D多孔介质中的运动和生长

3D打印细菌研究复杂3D多孔介质中的运动和生长