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BCH 258
Structural Biochemistry I

1st-half Fall Semester
MWF 3:05-3:55
Nanaline Duke 437
Course Director: Lorena Beese

pol A ribbon on diffraction pattern

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.

BEWARE: This website will be updated as we go...

Lecture titles updated 2011/09/05

assignments updated sometimes after the lecture...

I - Chemistry becomes Biochemistry, Richardson & Oas section

Mon - 8/29/2011

3D and thermodynamic literacy
Macromolecular computer graphics & KiNG

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

Wed - 08/31/2011

Peptide geometry & handedness

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

Fri - 09/02/2011

Secondary structures

download arrow c1Basics-2-5-QKiNG.kin (16KB)
download arrow Wrksht3-handedAAroles2009.pdf (120KB)
download arrow Wrksht3-handedAAroles2009.doc (120KB)
download arrow howdotswork3KiNG.kin (515KB)
(requires mage) download arrow ala_dipept_geom_dotball5.1.kin (4.9MB)
(requires mage) download arrow idealpolyala12.kin (16KB)
(requires mage) download arrow 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.
download arrow WrkSht5-StructClasses2009.pdf (110KB)
download arrow WrkSht5-StructClasses2009.doc (110KB)
download arrow c2Motifs.kin (248KB)
download arrow c3Alpha.kin (352KB)
download arrow c4Al_Bet.kin (348KB)
download arrow c5Beta.kin (408KB)

Wed - 09/07/2011

Structure stabilizing interactions

download arrow 258LectureNotes2011-Sep07Wednesday.pdf (60KB)
download arrow WrkSht6-H-bonds2011.pdf (150KB)
download arrow 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:
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 (Revised 20110913)
You will see that the questions in this PS are quite trivial. This is mainly an exercise to acquaint you with Mathematica.

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

Mon - 09/12/2011

Roles of amino acids and mutations

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

Wed - 09/14/2011

Ligand binding

download arrow 258ClassNotes110914.pdf (60KB)
download arrow 258OasLecture2.pdf (60KB)

Fri - 09/16/2011


download arrow 258OasLecture3.pdf (60KB)
download arrow CantorSchimmelCh15.pdf (60KB)
download arrow CantorSchimmelCh17.pdf (60KB)

Mon - 09/19/2011

Structural View of allostery

download arrow WrkSht8-motions2009.pdf (130KB)
download arrow WrkSht8-motions2009.doc (130KB)
download arrow c6FldFlx-KiNG.kin (800KB)
download arrow HbAllo-KiNG.kin (120KB)

Wed - 09/21/2011

More on Allostery...

(Fri - 09/23/2011

in-class EXAM (individual laptops!)

download arrow 2p8oFH-exam.kin (800KB)

II - Structure meets Biology - Beese section

Mon - 09/26/11

Principles of protein-nucleic acid recognition:
Procaryotic transcription factors

download arrow Prot-DNAInteractionsWksht.pdf (32KB)
download arrow 258protDNAinter.kin (240KB)
download arrow c7DNA.kin (156KB)
download arrow c8HthTF.kin (312KB)

Wed - 09/28/11

Eucaryotic transcription

download arrow Prot-DNAInteractionsWksht.pdf (32KB)
download arrow 258protDNAinter.kin (240KB)
download arrow c9EuTF.kin (316KB)
download arrow c10TFfam.kin (312KB)

Fri - 09/30/11

Enzyme catalysis: Serine & HIV proteases

download arrow Wkst-SerineProtease.pdf (36KB)
download arrow c11SerPr.kin (316KB)

Mon - 10/03/11

Enzyme catalysis:
DNA polymerases & HIV-1 reverse transcriptase

Polymerase movie

(local download)
download arrow (10.6MB)

Wed - 10/05/11

The Ribosome

Ribosome movie download arrow (32.4MB)
download arrow (704KB)
download arrow 1ffk_hlx7H.kin (1.3MB)
download arrow 1ffk_5Sto38.kin (436KB)
download arrow 1ffk_pieceH.kin (116KB)
download arrow 1ffk5S_mcdots.kin (1.1MB)
download arrow 1ffk5SHstack.kin (1.9MB)
download arrow 1JJ2s.L24.kin (72KB)

Fri - 10/07/11  (Protein-DNA interactions worksheet due)

Structure determination methodology - Part I

download arrow c18StDet.kin (204KB)

Mon - 10/10/11

Duke Fall Break
(no class)

Wed - 10/12/11

Structure determination methodology - Part II

Thu - 10/13/11  (Time to be determined)

Frontiers of Structural Biology

Resources on using KiNG and kinemages