BCH258 -- Structural Biochemistry I

This course introduces students to the principles of modern structural biology. The objective is to convey the importance of understanding fundamental biological processes in terms of the atomic properties of the macromolecules that participate in them, and develop a feeling for the spatial and conceptual relationships of these molecular systems. In this course we identify reoccurring structural principles and motifs and show how proteins with unrelated functions are built up from combinations of these. A brief introduction to methods of structure determination by X-ray crystallography and NMR is included. Specific examples from the literature illustrate general structural principles.

Immediately below are PDFs with general information about the course. Following the general info is the tentative class schedule in columnar format. Listed with the date and topic are downloadable resources - PDFs, kinemages, and text files. The topics and/or resources may change during the course of the course. An assigned worksheet is generally expected to be done between the day it is listed and the following class. After the class schedule are links to additional resources on using kinemages and KiNG.

Be attentive with your downloads! Kinemage files are text files and may display in the browser. If necessary, use some type of "right-click"; option-click; shift-right elbow-click combo to download the file or link. This may be true for some browsers even with PDF files.

General Info 258GenInfo20110829.pdf (84KB)
Class Schedule 258ClassSchedule20110829.pdf (112KB)
Coloring Book: protein_structure_coloring_book.pdf (412KB)

I - Chemistry becomes Biochemistry, Richardson & Oas section

Mon - 8/29/2011

3D and thermodynamic literacy
Macromolecular computer graphics & KiNG

WrkSht1_Intro2011.pdf (120KB pdf) | WrkSht1_Intro2011.doc (120KB pdf)
Demo5_4a-KiNG.kin (100KB)
Link to online Quick Start KiNG | QuickStartKing.pdf (36KB pdf)
3Dlit2a-exercise-KiNG.pdf (24KB pdf) | 3Dlit2a-exercise-KiNG.kin (20KB)

Wed - 08/31/2011

Peptide geometry & handedness

Wrksht2_DihedralsHanded2009.pdf (148KB)
Wrksht2_DihedralsHanded2009.doc (148KB)
c1Basics-1n6-KiNG.kin (120KB) 4FXN.pdb (120KB)

Fri - 09/02/2011

Secondary structures

c1Basics-2-5-QKiNG.kin (16KB)
Wrksht3-handedAAroles2009.pdf (120KB)
Wrksht3-handedAAroles2009.doc (120KB)
howdotswork3KiNG.kin (515KB)
(requires mage)  ala_dipept_geom_dotball5.1.kin (4.9MB)
(requires mage)  idealpolyala12.kin (16KB)
(requires mage)  appendstuff2.kin (3.8MB)

Mon - 09/05/2011 (Duke classes are in session on Labor Day)

Structural Motifs & Domains;
Structural Classification

The on-line HTML version of the annotated Anatomy and Taxonomy of Protein Structure.
WrkSht5-StructClasses2009.pdf (110KB)
WrkSht5-StructClasses2009.doc (110KB)
c2Motifs.kin (248KB)
c3Alpha.kin (352KB)
c4Al_Bet.kin (348KB)
c5Beta.kin (408KB)

Wed - 09/07/2011

Structure stabilizing interactions

258LectureNotes2011-Sep07Wednesday.pdf (60KB)
WrkSht6-H-bonds2011.pdf (150KB)
HbondPractice-KiNG.kin (100KB)

Fri - 09/09/2011

Conformational thermodynamics

Mathmatica Assignment: due Wednesday Sept 14

Oas Problem Set #1 comes in the form of a Mathematica notebook. In order to use it you must first download Mathematica from the OIT software website at:
https://oit.duke.edu/comp-print/software/license/detail.php?id=18
When you have properly installed Mathematica you should be able to open PS1.nb and follow the instructions within it. When you are done save it to PS1.nb and e-mail it to Terry at oas@duke.edu. (Revised 20110913)
You will see that the questions in this PS are quite trivial. This is mainly an exercise to acquaint you with Mathematica.

258MathmaticaNB-20110909rev13-PS1.nb (25KB)

Mon - 09/12/2011

Roles of amino acids and mutations

WrkSht7-mutants2009.pdf (120KB)
WrkSht7-mutants2009.doc (120KB)
1lmb6_85aH.kin (185KB)
1lmb6_85aH.pdb (120KB)
2simHdot.kin (5.3MB)
2simH.pdb (520KB)
258LectureNotes2011-Sep12Monday.pdf (60KB)