Combining molecular visualization with bench methods in a hypothesis-driven undergraduate biochemistry lab course
Combining molecular visualization with bench methods in a hypothesis-driven undergraduate biochemistry lab course
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在假设驱动的本科生物化学实验课程中将分子可视化与实验台方法相结合
DOI：
10.1096/fasebj.30.1_supplement.666.2
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发表时间：
2016
期刊：
影响因子：
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通讯作者：
Pikaart, Michael J
中科院分区：
文献类型：
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作者：
Craig, Paul A;Mills, Jeffrey L;Daubner, Colette;Pikaart, Michael J
我们正在寻求将真实的调查纳入本科生生物化学实验室课程。六个校区的学生正在结合计算（“在硅片”）和湿实验室（“在体外”）技术，因为他们表征蛋白质的三维结构是已知的，但其功能还没有被归因于以前。这些模块包括PyMOL蛋白质可视化，Dali和ProMOL结构比对，BLAST和Pfam序列探索，PyRX和Autodock维纳配体对接。目标是预测蛋白质的功能，并确定活性位点的最有希望的底物。在湿实验室中，学生表达和纯化他们的目标蛋白质，然后用从对接研究中选择的底物进行酶动力学。他们作为学生的学习和作为科学家的成长正在从研究方法、可视化、生物背景和蛋白质功能机制方面进行评估。实验室课程是RIT和道林学院成功的本科研究成果的延伸。将通过一个网站（promol.org）向科学界传播所开发的模块，包括所涉技术的规程和带字幕的视频教学。在该项目的过程中，我们还将遵循教师和教学助理能力在两个领域的变化：有效的教学与结构生物学工具和技能的发展，在测量学生的学习收益的领域。当我们在这些不同的校园进行实验室，我们也将专注于我们的方法和障碍，以实现存在于每个校园的优势，从学生接受和教师培训的水平，需要在部门和机构层面的文化变化的资源。当我们分析这种方法在其他校园的可行性时，我们将寻求其他潜在采用者对他们的兴趣水平和他们在校园中预期的障碍的投入。支持或资助信息该项目部分由NSF IUSE 1503811支持。
We are seeking to incorporate authentic inquiry into an undergraduate biochemistry lab course. Students on six campuses are combining computational (“in silico”) and wet lab (“in vitro”) techniques as they characterize proteins whose three dimensional structures are known but to which functions have not been previously ascribed. Thein silicomodules include protein visualization with PyMOL, structural alignment using Dali and ProMOL, sequence exploration with BLAST and Pfam, and ligand docking with PyRX and Autodock Vina. The goal is to predict the function of the protein and to identify the most promising substrates for the active sites. In the wet lab, students express and purify their target proteins, then conduct enzyme kinetics with substrates selected from their docking studies. Their learning as students and their growth as scientists is being assessed in terms of research methods, visualization, biological context, and mechanism of protein function. The lab course is an extension of successful undergraduate research efforts at RIT and Dowling College. The modules that are developed will be disseminated to the scientific community via a web site (promol.org), including both protocols and captioned video instruction in the techniques involved. Over the course of the project, we will also be following changes in faculty and teaching assistant competence in two areas: effective teaching with structural biology tools and the development of skills in the area of measuring learning gains by students. As we conduct the lab on these different campuses, we will also focus on advantages of our approach and barriers to implementation that exist on each campus, from the level of student acceptance and faculty training, to resources that are needed to changes in the culture at the departmental and institutional levels. As we analyze the feasibility of this approach on other campuses, we will seek input from other potential adopters about their level of interest and the barriers that they anticipate on their campuses.Support or Funding InformationThis project is supported in part by NSF IUSE 1503811.