What follows is the extracted content from a series of lectures given by Prof. Clarence E. Schutt in the Spring Term 2011 at Princeton University. The ‘Structural Biology of Neurodevelopmental Disorders’ is organized around the analysis of crystal structures of biological molecules that play crucial roles in the development and operation of the nervous system. Generally, the topics were chosen because of a direct connection to the discoveries emerging from genetic analysis of autism spectrum disorders. The premise of the course is that by reading papers and reviews from the original research literature a student can build up their own ‘architectonic’ picture of the molecular reality of autism. Central to carrying out this process is to develop a capacity to build molecular models in the computer of the relevant structures, such as neurotransmitter receptors, scaffolding proteins, and repressor-DNA complexes. The Study Guides provide a sign-posted path through a series of research papers with detailed instructions on building illustrative atomic models.
Getting Started. A set of completed Study Guide exercises is available online at the Proteopedia website. Please go there now and type ‘autism’ in the search box. A good structure to begin with is neurexin:neuroligin. When the window opens there will be a molecular image of this complex rotating in the graphics window on the right. As you scroll down the text window you will notice highlighted words. When you click on them, new molecular images will appear in the graphics window. These images will illustrate key molecular interactions and structural features important for understanding how these molecules function.
1. Genes, proteins & neurons. There is a vast imaginative gap between genes and behavior. We are told that genes code for proteins, ‘the work-horses of the cell’, but we need much more than this humble metaphor to begin to grasp how inherited genetic propensities, or de novo errors in gene transcription, can give rise to the devastating social and communicative consequences of autism. What roles do proteins play as structural scaffolds, catalysts, signaling elements, energy converters, and translators of the information encoded in DNA structure in the human organism? The neuron, strictly the broad set of different kinds of neurons, is the key organizing principle of the nervous system. That neurons are born with pluri-potency, the ability to become any type of cell, and differentiate into specialized subtypes each with complex dendritic ‘tree-like’ arborizations and unique electrochemical signaling properties, is amazing enough. But, how does the brain build language circuits that can internalize language and edit its own efforts to speak via auditory pathways? How does it learn to use and control the neuromuscular systems in the throat and mouth, key adaptive processes involved in integrating an individual human being into his family and culture?
2. Crystallography. Structural Biology is a branch of investigative science that aims to provide pictures, detailed atomic descriptions, of the molecules of life and their mutual patterns of association, DNA:protein interactions serving as a conspicuous example, which are so essential for understanding the gene-protein coding connection. (For more information, please visit Dr. Schutt's Princeton faculty website). A powerful tool of this discipline is x-ray crystallography, a technique based on the elegant mathematics of Fourier analysis and its formal relationship to optical imaging. If a crystal of an interesting substance is available, its three-dimensional organization can be imaged (with computer calculations of ‘Fourier maps’ serving in the role of the lenses of conventional light microscopes). As surprising as it may seem, many of the most complicated molecules (proteins) and molecular assemblies (viruses, ribosomes, photosynthetic systems, neuro-transmitter receptors) from living systems can self-associate into beautiful three-dimensional crystals.
3. Animal models. The availability of crystal structures itself can begin a discourse on the question of how mutations in proteins, or deletions and duplications in chromosomes, can give rise to a neurological disorder. The functional role of each molecule must be determined in its biological context, often in organizational centers like the chemical synapses between neurons. The incredible correspondence of genetic programs of development, certainly between mouse and human, but even down to the lowliest of organisms, the acorn worm, enables biologists to introduce mutations into animals at highly relevant genetic checkpoints and functional networks based on the rich genetic data emerging about neurological diseases. Genes can be engineered so as to be turned on or off at specific points of development and changes in neurotransmission or cell motility or any other relevant change can be studied in organo-typic slices or in living animals. A truly difficult problem is to discover precisely in what cell types a given mutation exerts its influence. The example of dysfunctional dopamine producing cells in a small cluster of cells in the brain stem, the substantial nigra, in the case of Parkinson’s Disease gives hope that repairing damage to or modulating just one or a few microcircuits might be one day feasible in the case of autism.
4. Study Guides. Weekly exercises successively introduce molecular modeling exercises involving molecules of neuro-biological interest, so that by the time the course is completed it is possible to produce professional quality images, and carry out sophisticated structural analyses, as one is actively reading about a structure. The Study Guides provide step-by-step instructions on how to access the results of x-ray crystallographic studies. These are concisely expressed in terms of the three-dimensional coordinates of the atoms comprising each molecule in computer files (.pdb file) downloadable from an open access website, the RCSB Protein Data Bank website. Structures can be visualized with a program, Swiss PDBViewer, also downloadable from the SIB Swiss Institute of Bioinformatics website. This website contains a downloadable user’s manual and tutorial.
Click here to access the Study Guides.
5. Answers to Study Guides. Concise answers to the Study Guide questions and molecular images resulting from the modeling exercises are available on the Proteopedia website. In the Navigation Panel in the upper left hand corner select ‘Table of Contents’, or simply type in ‘autism’ in the search bar. In the Table of Contents, select ‘Neurodevelopmental Disorders’ and you will be directed to a list of pages, each devoted to a crystal structure of relevance for understanding autism spectrum disorders. As each page is downloaded, a molecular image of the featured structure, say MeCP2 in the case of Rett Syndrome, will be seen rotating in the image window on the right. As you scroll down the page, you will find highlighted words, such as ‘ST-motif’, which when clicked upon will activate a new image on the right, usually at a much greater level of chemical detail. (These pages were created by David Canner).