BCH 6746: Structural Biology Course Prerequisites: CRN 12063 Section 001, 3 Credit Hours

Total Page：16

File Type：pdf, Size：1020Kb

BCH 6746: Structural Biology Course Prerequisites: CRN 12063 Section 001, 3 Credit Hours

Please note: Each college and department may have their own requirements, in addition to those stated in the Syllabus Guidelines. BCH 6746: Structural Biology Course Prerequisites: CRN 12063 Section 001, 3 Credit hours College of Arts and Sciences, CMMB COURSE SYLLABUS Insert USF Logo here Instructor Name: Yu Chen Semester/Term & Year: Spring 2019 Class Meeting Days: TR Class Meeting Time: 11:00 – 12:20 pm Class Meeting Location: MDC 1507 Lab Meeting Location: N/A Delivery Method: Lecture I. Welcome! II. University Course Description The theory and application of modern physical biochemical techniques. III. Course Objectives This course focuses on relating theoretical concepts and experimental approaches to a wide range of potential research problems in the area of structural biology. The course aims to provide a solid foundation and breadth of understanding in structural biology that will facilitate application to current and future research problems. IV. Course Purpose Major Topics: Introduction to Structural Biology; From Structure to Function I; From Structure to Function II; From Structure to Function III; From Structure fo Function IV; Control of Protein Function I; Strategies for Protein Separation; Strategies for Protein Identification; Chemical and Immunochemical Probes of Structure; Methods in Structural Bio I, II, II; Structure Determination I, II, III, IV; Control of Protein Function II, III, IV V. Learning Outcomes Students will gain an understanding of the basic science of Protein Structure, including first principles of the physical interactions that maintain proteins and the mechanisms that make them tic. They will also learn about different techniques and experimental approaches that represent the state-of-the-art and are widely used in the study of proteins. The final session of the course will deal with different applications of protein structure. Importantly, with the Structural Biology course, the students will be offered a learning environment that should make the understanding of protein structure exciting, interesting, reachable and clearly relevant to their future careers. 1 .

Copy Link

Recommended publications

Structural Data in Synthetic Biology Approaches for Studying General Design Principles of Cellular Signaling Networks
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Structure Perspective Structural Data in Synthetic Biology Approaches for Studying General Design Principles of Cellular Signaling Networks Christina Kiel1,2,* and Luis Serrano1,2,3 1EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain 3ICREA, Pg. Lluı´s Companys 23, 08010 Barcelona, Spain *Correspondence: [email protected] http://dx.doi.org/10.1016/j.str.2012.10.002 In recent years, high-throughput discovery of macromolecular protein structures and complexes has played a major role in advancing a more systems-oriented view of protein interaction and signaling networks. The design of biological systems often employs structural information or structure-based protein design to successfully implement synthetic signaling circuits or for rewiring signaling ﬂows. Here, we summarize the latest advances in using structural information for studying protein interaction and signaling networks, and in synthetic biology approaches. We then provide a perspective of how combining structural biology with engineered cell signaling modules—using additional information from quantitative biochemistry and proteo- mics, gene evolution, and mathematical modeling—can provide insight into signaling modules and the general design principles of cell signaling. Ultimately, this will improve our understanding of cell- and tissue-type-speciﬁc signal transduction. Integrating the quantitative effects of disease mutations into these systems may provide a basis for elucidating the molecular mechanisms of diseases. Introduction further complicated by the fact that often proteins recruit binding There is growing three-dimensional (3D) structural information partners using several domain or linear motifs.
[Show full text]
Synthetic Biology Applying Engineering to Biology
Synthetic Biology Applying Engineering to Biology Report of a NEST High-Level Expert Group EUR 21796 PROJECT REPORT Interested in European research? RTD info is our quarterly magazine keeping you in touch with main developments (results, programmes, events, etc). It is available in English, French and German. A free sample copy or free subscription can be obtained from: European Commission Directorate-General for Research Information and Communication Unit B-1049 Brussels Fax : (32-2) 29-58220 E-mail: [email protected] Internet: http://europa.eu.int/comm/research/rtdinfo/index_en.html EUROPEAN COMMISSION Directorate-General for Research Directorate B — Structuring the European Research Area Unit B1 — Anticipation of Scientific and Technological Needs (NEST activity); Basic Research E-mail: [email protected] Contact: Christian Krassnig European Commission Office SDME 01/37 B-1049 Brussels Tel. (32-2) 29-86445 Fax (32-2) 29-93173 E-mail: [email protected] For further information on the NEST activity please refer to the following website: http://www.cordis.lu/nest/home.html EUROPEAN COMMISSION Synthetic Biology Applying Engineering to Biology Report of a NEST High-Level Expert Group NEST - New and Energing Science and Technology - is a research activity under the European Community’s 6th Framework Programme Directorate-General for Research Structuring the European Research Area 2005 Anticipating Scientific and Technological Needs; Basic Research EUR 21796 Europe Direct is a service to help you find answers to your questions about the European Union Freephone number: 00 800 6 7 8 9 10 11 LEGAL NOTICE: Neither the European Commission nor any person acting on behalf of the Commission is responsible for the use which might be made of the following information.
[Show full text]
Biochemistry Biotechnology Cell Biology
Undergraduate Biochemistry Opportunities www.ed.ac.uk/biology Biotechnology Cell Biology Biochem_Biotech_CellBio_A5.indd 1 21/05/2019 14:25 Biochemistry The programme combines coverage of the Biochemistry is the study of living systems at basic principles and knowledge underpinning the cellular and molecular level. This dynamic biotechnology and an appreciation of the field draws on a variety of subjects and has processes involved in converting an idea widespread application. Biochemistry applies a into a product. The objective is to provide a knowledge of chemistry and physical sciences firm foundation in molecular and microbial to investigate basic life processes. The subject biotechnology through compulsory sections has a major impact on modern medical research dealing with topics such as expression vectors, and upon the pharmaceutical, bioengineering, microbial fermentation, protein structure, drug agricultural and environmental industries. design and the development of antimicrobials and vaccines. The programme encourages the critical assessment of current developments in areas of Cell Biology biological interest. Modern cell biology is a dynamic discipline that combines the interests and techniques of many Biotechnology scientific fields. Cell biologists investigate the Biotechnology is concerned with industrial basic structural and functional units of life, the and biomedical applications of fundamental cells that compose all living organisms. They aim knowledge derived from biology. This covers to understand: cellular structure, composition many facets from making useful products and regulation, the organelles that cells contain, using microbial, plant or animal cells to using cell growth, nuclear and cellular division, and bioinformatics and structural biology to design cell death. Understanding how cells work is new drugs. Biotechnology is an exciting area fundamental to many areas of biology and is of with new developments each year in areas that particular importance to fields such as cancer affect us all.
[Show full text]
MATHEMATICAL TECHNIQUES in STRUCTURAL BIOLOGY Contents 0. Introduction 4 1. Molecular Genetics: DNA 6 1.1. Genetic Code 6 1.2. T
MATHEMATICAL TECHNIQUES IN STRUCTURAL BIOLOGY J. R. QUINE Contents 0. Introduction 4 1. Molecular Genetics: DNA 6 1.1. Genetic code 6 1.2. The geometry of DNA 6 1.3. The double helix 6 1.4. Larger organization of DNA 7 1.5. DNA and proteins 7 1.6. Problems 7 2. Molecular Genetics: Proteins 10 2.1. Amino Acids 10 2.2. The genetic code 10 2.3. Amino acid template 11 2.4. Tetrahedral geometry 11 2.5. Amino acid structure 13 2.6. The peptide bond 13 2.7. Protein structure 14 2.8. Secondary structure 14 3. Frames and moving frames 19 3.1. Basic definitions 19 3.2. Frames and gram matrices 19 3.3. Frames and rotations 20 3.4. Frames fixed at a point 20 3.5. The Frenet Frame 20 3.6. The coiled-coil 22 3.7. The Frenet formula 22 3.8. Problems 24 4. Orthogonal transformations and Rotations 25 4.1. The rotation group 25 4.2. Complex form of a rotation 28 4.3. Eigenvalues of a rotation 28 4.4. Properties of rotations 29 4.5. Problems 30 5. Torsion angles and pdb files 33 5.1. Torsion Angles 33 5.2. The arg function 34 5.3. The torsion angle formula 34 5.4. Protein torsion angles. 35 5.5. Protein Data Bank files. 35 1 2 J. R. QUINE 5.6. Ramachandran diagram 36 5.7. Torsion angles on the diamond packing 37 5.8. Appendix, properties of cross product 38 5.9. Problems 38 6.
[Show full text]
The Institute of Botany
FEATURE ARTICLE Taiwan’s Academia Sinica Forges Ahead Research in the life sciences has expanded and improved, and is conforming to international standards institutes and research projects, to promote academic collaboration between Taiwan and other countries, and to make plans for academic development when requested by the government. It is also responsible for nominating three candidates for the presidency when the president vacates, as well as formulation of rules pertaining to the Academia. The Central Advisory Committee consists of chairpersons of the advisory committee of the individual institutes, and two to three specialists from each of the Academia’s three divisions. One of the vice presidents of the Academia serves as its chairperson. The committee recruits national and international specialists for the Academia and also creates long-term interdisciplinary research plans. It is also he development of science and 188 associate research fellows, 134 responsible for evaluating and promoting T technology has been given much assistant research fellows, 123 assistant inter-institutional large-scale research importance by the Taiwan government in fellows, and 20 research assistants. projects, evaluating applications of recent years. This can be seen from the postdoctoral researchers, and selecting Organization increased expenditure on science and winners for the Academia’s annual technology, and the annual increase in The Academia is headed by Dr. Yuan- awards for outstanding publications by national R&D budget. The government Tseh Lee, its president. Dr. Lee is the junior research faculties. is determined to improve the quality of 1986 Nobel Laureate in Chemistry. He Division of Life Sciences research carried out in the country.
[Show full text]
Journal of Molecular Biology
JOURNAL OF MOLECULAR BIOLOGY AUTHOR INFORMATION PACK TABLE OF CONTENTS XXX . • Description p.1 • Audience p.2 • Impact Factor p.2 • Abstracting and Indexing p.2 • Editorial Board p.2 • Guide for Authors p.6 ISSN: 0022-2836 DESCRIPTION . Journal of Molecular Biology (JMB) provides high quality, comprehensive and broad coverage in all areas of molecular biology. The journal publishes original scientific research papers that provide mechanistic and functional insights and report a significant advance to the field. The journal encourages the submission of multidisciplinary studies that use complementary experimental and computational approaches to address challenging biological questions. Research areas include but are not limited to: Biomolecular interactions, signaling networks, systems biology Cell cycle, cell growth, cell differentiation Cell death, autophagy Cell signaling and regulation Chemical biology Computational biology, in combination with experimental studies DNA replication, repair, and recombination Development, regenerative biology, mechanistic and functional studies of stem cells Epigenetics, chromatin structure and function Gene expression Receptors, channels, and transporters Membrane processes Cell surface proteins and cell adhesion Methodological advances, both experimental and theoretical, including databases Microbiology, virology, and interactions with the host or environment Microbiota mechanistic and functional studies Nuclear organization Post-translational modifications, proteomics Processing and function of biologically
[Show full text]
States of Origin: Influences on Research Into the Origins of Life
COPYRIGHT AND USE OF THIS THESIS This thesis must be used in accordance with the provisions of the Copyright Act 1968. Reproduction of material protected by copyright may be an infringement of copyright and copyright owners may be entitled to take legal action against persons who infringe their copyright. Section 51 (2) of the Copyright Act permits an authorized officer of a university library or archives to provide a copy (by communication or otherwise) of an unpublished thesis kept in the library or archives, to a person who satisfies the authorized officer that he or she requires the reproduction for the purposes of research or study. The Copyright Act grants the creator of a work a number of moral rights, specifically the right of attribution, the right against false attribution and the right of integrity. You may infringe the author’s moral rights if you: - fail to acknowledge the author of this thesis if you quote sections from the work - attribute this thesis to another author - subject this thesis to derogatory treatment which may prejudice the author’s reputation For further information contact the University’s Director of Copyright Services sydney.edu.au/copyright Influences on Research into the Origins of Life. Idan Ben-Barak Unit for the History and Philosophy of Science Faculty of Science The University of Sydney A thesis submitted to the University of Sydney as fulfilment of the requirements for the degree of Doctor of Philosophy 2014 Declaration I hereby declare that this submission is my own work and that, to the best of my knowledge and belief, it contains no material previously published or written by another person, nor material which to a substantial extent has been accepted for the award of any other degree or diploma of a University or other institute of higher learning.
[Show full text]
Program Overview
plant biology di vision of biology & biomedical sciences program overview The WUSTL Graduate Program in Plant Biology provides training in the use of vascular plants, mosses, algae, photosynthetic prokaryotes, and other microbes as experimental organisms to address both fundamental and applied biological questions. Contemporary research on plant and microbial systems adds to our knowledge of basic biology, informs our understanding of the natural world, and leads to innovations in biomedicine, agriculture, and energy production. Washington University graduate students have unparalleled opportunities to pursue multidisciplinary training in genetics, biochemistry, cell biology, development, molecular evolution, and physiology, capitalizing on current Research Environment interest and investment in biological research, and fueled by experimental resources found at WUSTL. Researchers in the Program in Plant Biology investigate fundamental and Students primarily interested in plant population biology, taxonomy, applied biological problems using systematics, economic botany, ecology, or conservation biology should apply to plants and/or microbes. the Evolution, Ecology and Population Biology Program. Current research programs include what is plant biology? studies of: Modern plant biology is the study of plants and other photosynthetic organisms with • The mechanisms by which plant the goal of elucidating their unique biology and biochemistry to address important growth, differentiation, and questions about biological regulation and complexity
[Show full text]
The Protein-Imaging Technique Taking Over Structural
manipulating peer review to boost their From 2014 to 2018, Chou was named as a microscopes and more sophisticated soft- citations. Chou’s case is the first to be highly cited researcher in a list produced by ware for transforming the images they cap- revealed since that announcement. “While Clarivate Analytics, an information-services tured into sharper molecular structures. thankfully rare, such practices are an abuse firm in Philadelphia, Pennsylvania, that owns That paved the way for the current growth of the peer-review system and undermine the the citation database Web of Science. But his of cryo-EM, says Sjors Scheres, a structural hard work and commitment that editors and name does not appear on the 2019 list; last biologist and specialist in the technique at the reviewers devote to ensuring the integrity of year, Clarivate decided to remove scientists MRC Laboratory of Molecular Biology (LMB) the scholarly record,” a spokesperson says. whose papers showed “unusually high levels in Cambridge, UK. “Elsevier has developed analytical tools to of self-citation”. Richard Henderson, an LMB structural help detect such practices and is committed Elsevier hasn’t yet decided what to do about biologist who shared the 2017 Nobel Prize in to implementing technology to flag citation papers that Chou handled that liberally cite his Chemistry for his work developing the tech- manipulation before publication.” work, the spokesperson says. nique, says that even after these advances, growth was slow at first, because only a small number of labs had access to the equipment. But when they started using cryo-EM to pro- duce detailed maps of molecules such as the ribosome — cells’ protein-making machines THE PROTEIN-IMAGING — other scientists, as well as their institutions and funders, quickly took notice.
[Show full text]
Nulabs Courses.Xlsx
Current IBiS and IGP Course Offerings Instructor Course # Title Type QUARTER Description Course Structure and function of cells and their organelles. Morphological, molecular, and physiological approaches to IGP 405 Cell Biology CORE - Cell Biology Mitchell / Kosak Winter solving cell-biological problems. Structure and function, taxonomy and replication of infectious agents. Host-parasite interactions and microbial IGP 442 Microbiology Core - Cell Biology Satchell Spring diseases. Prerequisites: IGP 405, IGP 410, and IGP 401 or equivalent. Biology of cell organelles including translocation of proteins through membranes, protein secretion, organelle IBIS 406 Cell Biology CORE - Cell Biology Horvath Spring inheritance during mitosis, membrane trafficking etc. Molecular Biology & CORE - Molecular Topics in molecular biology and the mechanisms of gene and cellular regulation. Prerequisites: Past or simultaneous IGP 410 Klumpp Fall Genetics Biology enrollment in IGP 401 or equivalent. This course introduces regulatory pathways and molecular themes employed in signal transduction and their Signal Transduction and CORE - Molecular IGP 426 Watterson Winter modulation by pharmacological agents. The molecular basis of diverse diseases and existing therapies for them Molecular Pharmacology Biology engage the various pathways that will be covered in the course. Receptors and Signaling CORE - Molecular Integrated discussion of different superfamilies of signaling receptors and their effectors. Pathways discussed IGP 435 Stern, Kiyokawa Spring Mechanisms
[Show full text]
Booklet-The-Structures-Of-Life.Pdf
The Structures of Life U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES NIH Publication No. 07-2778 National Institutes of Health Reprinted July 2007 National Institute of General Medical Sciences http://www.nigms.nih.gov Contents PREFACE: WHY STRUCTURE? iv CHAPTER 1: PROTEINS ARE THE BODY’S WORKER MOLECULES 2 Proteins Are Made From Small Building Blocks 3 Proteins in All Shapes and Sizes 4 Computer Graphics Advance Research 4 Small Errors in Proteins Can Cause Disease 6 Parts of Some Proteins Fold Into Corkscrews 7 Mountain Climbing and Computational Modeling 8 The Problem of Protein Folding 8 Provocative Proteins 9 Structural Genomics: From Gene to Structure, and Perhaps Function 10 The Genetic Code 12 CHAPTER 2: X-RAY CRYSTALLOGRAPHY: ART MARRIES SCIENCE 14 Viral Voyages 15 Crystal Cookery 16 Calling All Crystals 17 Student Snapshot: Science Brought One Student From the Coast of Venezuela to the Heart of Texas 18 Why X-Rays? 20 Synchrotron Radiation—One of the Brightest Lights on Earth 21 Peering Into Protein Factories 23 Scientists Get MAD at the Synchrotron 24 CHAPTER 3: THE WORLD OF NMR: MAGNETS, RADIO WAVES, AND DETECTIVE WORK 26 A Slam Dunk for Enzymes 27 NMR Spectroscopists Use Tailor-Made Proteins 28 NMR Magic Is in the Magnets 29 The Many Dimensions of NMR 30 NMR Tunes in on Radio Waves 31 Spectroscopists Get NOESY for Structures 32 The Wiggling World of Proteins 32 Untangling Protein Folding 33 Student Snapshot: The Sweetest Puzzle 34 CHAPTER 4: STRUCTURE-BASED DRUG DESIGN: FROM THE COMPUTER TO THE CLINIC 36 The Life of an AIDS
[Show full text]
Foundations of Structural Biology I
Foundations of Structural Biology II: GMS BY 763 Computation, Nuclear Magnetic Resonance, Thermodynamics and Spectroscopy in Structural Biology Spring Semester 2015: Monday 1:00 – 3:00 pm Course Director: Dr. Atkinson, W302, 8-4015 5 January Dr. Atkinson Introduction, Structural Databases and Tools: Protein Data Bank (PDB), PDB structure files, EM Structure repository (EMDataBank) 12 January Dr. Atkinson Structural Computational Biology I Macromolecular graphics, structure visualization and analysis. 19 January Martin Luther King Day – no class 26 January Dr. Atkinson Structural Computational Biology II Molecular Mechanics and Dynamics 2 February Dr. Gursky Thermodynamic Methods I Protein Energetics - what is it good for? Protein folding, stability and alternative conformations. Free energy landscape. Thermodynamic and kinetic stability; Gibbs and Eyring equations. Statistical weight and probability; extensive &intensive variables, state functions. Three laws of thermodynamics. Entropy S in spontaneous and equilibrium processes 9 February Dr. Gursky Thermodynamic Methods II A Long Way to Gibbs-Helmholtz Equation: Le Chatelier’s principle. Internal energy E and enthalpy H. Heat capacity - microscopic meaning, typical values. Effect of apolar compounds on Cp of liquid water. Protein unfolding as a 1st order phase transition. Gibbs free energy G and its linkage to H and S. Typical values of Delta S, Delta H and DeltaG for globular proteins. Entropy-enthalpy compensation in globular proteins. 16 February President’s Day – no class 23 February Dr. Gursky Thermodynamic Methods III Cool and Hot Methods in Protein Thermodynamics Gibbs-Helmholtz equation and its application to proteins. Cold denaturation. Plot G(T) and geometrical interpretation of Tm, Tc, S, H, and Cp Differential scanning calorimetry (DSC) – principle, advantages and limitations.
[Show full text]