Instructors: Jane and David Richardson

This is a seminar/lab course in the 3D structure of macromolecules, primarily using computer graphics. Class time is Thursday afternoons in room 132 Nanaline Duke Bldg., for discussion, reports, working/playing with brass or plastic molecular models, etc. For the first half of the course each week there is a homework exercise, primarily working with kinemages and the KiNG (or Mage) display program on Linux, Unix, Mac or Windows, or directly on the Web. Assistance with the exercises or software is available in the Richardson lab (132 Nanaline Duke) after class or on other afternoons. For the second half of the course students will work on projects.

The course web site contains the exercises, kinemage files, and other information. The site can be reached directly at, and has a link from the BIOCHEM.622 Sakai site.

Jane and Dave: , Rm 132 Nanaline Duke Bldg, 684-6010

Biophysical Highlights from 54 Years of Macromolecular Crystallography (preprint handout)

General references for course

J. S. Richardson (1981) "The Anatomy and Taxonomy of Protein Structure", Adv. Prot. Chem. 34, pp. 167-339.

This document is available in an online version, annotated annd somewhat updated from the original. Very thorough but old, and no nucleic acids.

C.I. Branden and J. Tooze (1999) Introduction to Protein Structure, Second Edition, Garland Publishing.

(Should be available in either the Duke or the Medical Center bookstores.) There is a "kinemage supplement" to each chapter of this text. We will use several of these kin files in the class exercises, and they are all available from the kinemage web site; use the link at left. Thorough intro to protein structure but little on RNA; good Structure/function, x-ray and NMR intro.

J. S. Richardson & D. C. Richardson (1989) "Principles and Patterns of Protein Conformation" in Prediction of Protein Structure and Principles of Protein Conformation, ed. G. D. Fasman, Plenum Press, pp. 1-98.

This is available in the Richardson lab, if you can't find it elsewhere. A few sections will be handed out, esp. about the structural roles of specific amino acids.

A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard (2009) Textbook of Structural Biology, World Scientific Publ. Co. Available on Amazon.

Good, brief intro to nucleic acids as well as proteins, plus structure/function examples; no experimental methodology.

Journal articles relevant to specific lessons will also be handed out during the course.

The initial lessons will refer to Anatomy & Taxonomy - for the first week, read the Background section (I.) of the on-line version. Any of the references constitute a background resource in which to look things up over the entire semester. The amount you make use of them will depend on your type and level of background. For the first week, use one or more of them to check out your familiarity with the terms and concepts (for example, amino-acid structures or cis peptides).