Molecular Machines Mechanism and Structure (M3S) Training Program

项目摘要 细胞的分子机器包括诸如核糖体和蛋白体等工厂，以及众多的 分子发动机、开关、泵、时钟和信息处理器，它们的功能构成了所有细胞的基础。 生物学分子机器机制和结构（M3 S）培训补助金的目标是统一 宾夕法尼亚州立大学的生物物理学社区，并培养一批不同的跨学科学生 了解分子机器内部运作所需的基本知识， 细胞功能培训补助金包括来自三个研究生课程的教师和学生：生物化学， 微生物学和分子生物学（BMMB）;化学（CHEM）;和生物医学工程（BME）。八 学生将被录取，每年在他们的博士课程的第一年年底，和培训组 将包括16名学生，在他们的博士学位的第二和第三年支持。学生将在三个培训 领域：结构、功能和模拟。首先，学生将接触到尖端的结构生物学 工具，如低温电子显微镜，X射线晶体学和核磁共振，以发展他们的能力， 理解组成分子机器的组成部分的原子结构。二是 将学习显微镜仪器和图像分析的基础，基础单分子和 分子机器功能动力学的超分辨率成像。最后，他们将学习 分子动力学，布朗动力学和随机模拟的基础知识，使他们能够使用 计算工具，以开发机械假说，整合和解释实验结果 模拟分子机器的结构和功能。在秋季和春季学期，学生将 每周见面，作为名为“机械车间”的1-cr课程的一部分。教学将围绕一个单一的主题， 每个月，例如一个生物学问题，一种技术或一种特定的分子。在此基础上，四 教师培训师将导致：i）一个关于RCR，严谨性和再现性，专业发展，或相关的教程 培训; ii）期刊俱乐部; iii）学生演讲;以及iv）所有学生/教师活动，例如教师 演讲，外部演讲者，大学可用资源的教程或相关活动。 夏季活动将包括研讨会和务虚会。此外，学生将接受3D分子技术培训， 动画，这将：i）发展他们的科学沟通技能; ii）建立他们对动态的直觉 分子在纳米和微米/毫秒时间尺度上的相互作用，以及：iii）加强使用 计算，以了解分子机器的结构和动力学的相互关系。最后， 学生将接受科学写作训练，并在第三年撰写一份6页的提案。M3 S培训 该计划将积极招募代表性不足的少数民族学生和残疾学生，并将 努力发展一个安全和包容的校园社区，最大限度地提高学生的归属感和保留率。

Project Summary The molecular machines of the cell include factories such as the ribosome and proteosome, and the numerous molecular motors, switches, pumps, clocks, and information processors whose functions underlie all of cell biology. The goals of the Molecular Machines Mechanism and Structure (M3S) Training Grant are to unify the biophysics community at Penn State University and to train a diverse cohort of interdisciplinary students the fundamental knowledge needed to understand the inner workings of the molecular machines that power cell function. The training grant includes faculty and students from three graduate programs: Biochemistry, Microbiology and Molecular Biology (BMMB); Chemistry (CHEM); and Biomedical Engineering (BME). Eight students will be admitted every year at the end of the 1st year of their PhD program, and the training group will consist of 16 students, supported in the 2nd and 3rd year of their PhD. Students will be trained in three areas: structure, function, and simulations. First, students will be exposed to cutting edge structural biology tools such as cryo-electron microscopy, X-ray crystallography and NMR in order to develop their ability to understand the atomic structures of the component parts that make up molecular machines. Second, they will learn the foundations of microscopy instrumentation and image analysis that underlie single-molecule and super-resolution imaging of the functional dynamics of molecular machines. Finally, they will learn the fundamentals of Molecular Dynamics, Brownian Dynamics, and stochastic simulations, empowering them use computational tools to develop mechanistic hypotheses and to integrate and interpret experimental results into simulations of molecular machine structure and function. During Fall and Spring semesters, students will meet weekly as part of a 1-cr course titled ‘Machine Shop’. Instruction will revolve around a single theme for each month, such as a biological question, a technique, or a specific molecule. Building on this theme, four faculty trainers will lead: i) a tutorial on RCR, rigor and reproducibility, professional development, or a related training; ii) a journal club; iii) a student presentation; and iv) an all student/faculty event such as a faculty presentation, an outside speaker, a tutorial on available resources at the university, or a related activity. Summer activities will include workshops and a retreat. Additionally, students will be trained in 3D molecular animations, which will: i) develop their science communication skills; ii) build their intuition about the dynamic interactions of molecules at nanometer and micro/millisecond timescales, and: iii) reinforce the theme of using computation to understand the interrelationship of the structure and dynamics of molecular machines. Finally, students will be trained in scientific writing and will write a 6-page proposal in their 3rd year. The M3S Training Program will aggressively recruit underrepresented minority students and students with disabilities, and will work to develop a safe and inclusive campus community that maximizes student belonging and retention.