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Atomic evidence: the foundations of structural molecular biology

Posted on 19. December, 2011.

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David S. Goodsell is an Associate Professor of Molecular Biology at the Scripps Research Institute, La Jolla, CA, USA (E-mail: In his research, he develops computational tools to study the basic principles of biomolecular structure and function. He is author of the Molecule of the Month at the Protein Data Bank, which presents the structure and function of a new protein each month. His illustrated books ‘‘The Machinery of Life’’ and ‘‘Our Molecular Nature’’ explore biological molecules and their diverse roles within living cells, and his book ‘‘Bionanotechnology: Lessons from Nature’’ presents the growing connections between biology and nanotechnology.

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David Goodsell

Structural molecular biology is one of the few fields of science where the primary scientific data is easily accessible to anyone who is interested. Techniques like X-ray crystallography, NMR spectroscopy and electron microscopy are used to determine the atomic structures of biological molecules. These structures are available in public databases such as the Protein Data Bank (PDB;, the Nucleic Acids Database (, and EM Databank (, and many excellent tools are freely available for exploring these structures.

Atomic structures provide the support for many of the basic functional principles of molecular biology. This support is particularly direct: the structures show the three-dimensional arrangement of atoms. Often, a structure will bring together decades of biochemical results, revealing the atomic basis of experimental observations and occasionally refuting theories based on more indirect results.

Atomic structures are limited, however. Often, they capture only one of many conformational states of the molecule, so dynamic processes must be inferred. Structures are difficult to obtain for large and flexible molecules, so structures may be obtained for stable fragments or individual subunits of a larger complex. In the case of enzymes, structures are often obtained for stable substrate analogs and inhibitors rather than the actual substrates and products of the reaction.
In spite of these limitations, many of the foundational concepts of molecular biology have been discovered through the determination of atomic structures. In this review, I will present some of the basic principles of biomolecular structure and function, and describe the structures that were instrumental in their discovery. Using resources like the Protein Data Bank, you can go directly to these structures and explore these atomic structures yourself.

DAVID S. GOODSELL (pictured inset)

Click here to download the full text article (doi: 10.3184/003685011X13201799666745)

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