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. In this course we identify reoccurring structural principles and motifs and show how proteins with unrelated functions are built up from combinations of these. We then introduce methods of structure determination by X-ray crystallography and NMR. Finally, we use specific examples from the current literature to 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, both for class exercises and for projects.
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.
258CourseSummary.pdf (76KB)
258GenInfo20080825.pdf (84KB)
258ClassSchedule20080825.pdf (112KB)
Mon - 8/25/2008
Macromolecular computer graphics
KiNG basics
3D literacy
WrkSht1_Intro2008.pdf (120KB pdf) | Demo5_4a-KiNG.kin (100KB)
KiNG basics | QuickStartKing.pdf (36KB pdf)
LectureNotesMonAug25-2008.pdf (56KB pdf)
Wed - 08/27/2008
Peptide geometry & handedness
Wrksht2_handedAAroles2008.pdf (148KB)
LectureNotesWedAug27-2008.pdf (60KB)
c1Basics-A-KiNG.kin (120KB)
Fri - 08/29/2008
Polypeptide chain & amino-acids
howdotswork3KiNG.kin (515KB)
(requires mage) ala_dipept_geom_dotball5.1.kin (4.9MB)
(requires mage) idealpolyala12.kin (16KB)
(requires mage) appendstuff2.kin (3.8MB)
c1Basics-B-KiNG.kin (16KB)
Wrksht3-DihedralsHanded2008.pdf (120KB)
4FXN.pdb (120KB)
LectureNotesFriAug29-2008.pdf (60KB)
Mon - 09/01/2008
Labor Day -- (no class)
Wed - 09/03/2008
Secondary structures, motifs, models, & kinemages
WrkSht4-makeKins2008.pdf (140 KB)
LectureNotesWedSept03-2008.pdf (60KB)
Fri - 09/05/2008
Structural Motifs & Domains
WrkSht5-StructClasses2008.pdf (110KB)
c2Motifs.kin (248KB)
c3Alpha.kin (352KB)
c4Al_Bet.kin (348KB)
c5Beta.kin (408KB)
WrkSht5-StructClasses2008.pdf (140 KB)
LectureNotesFriSept05-2008.pdf (60KB)
Mon - 09/08/2008
Structural Classification, The Coloring Book
LectureNotesMonSept08-2008.pdf (60KB)
Wed - 09/10/2008
Hydrogens: all-atom contacts,
H-bonds, & waters
WrkSht6-H-bonds2008.pdf (150KB)
HbondPractice-KiNG.kin (100KB)
LectureNotesWedSept10-2008.pdf (60KB)
Fri - 09/12/2008
Roles of amino acids and mutations to replace them
WrkSht7-mutants2008.pdf (120KB)
1lmb6_85aH.kin (185KB)
1lmb6_85aH.pdb (120KB)
2simHdot.kin (5.3MB)
2simH.pdb (520KB)
LectureNotesFriSept12-2008.pdf (60KB)
Mon - 09/15/2008
Motions, Alternative Conformations, & Ensembles
WrkSht8-motions2008.pdf (130KB)
c6FldFlx-KiNG.kin (800KB)
HbAllo-KiNG.kin (120KB)
LectureNotesMonSept15-2008.pdf (60KB)
The following kins & maps are optional:
2dn1H-OXY-KiNG.kin (1.4MB) | 2dn1.omap.gz (1.6MB)
2dn2H-Deoxy-KiNG.kin (1.4MB) | 2dn2.omap.gz (2.7MB)
Davis_Backrub_kinSup.kin (2.2MB)
Wed - 09/17/08 (Coloring Books due)
Protein-nucleic acid recognition:
General Principles
Prot-DNAInteractionsWksht.pdf (32KB)
258protDNAinter.kin (240KB)
c7DNA.kin (156KB)
c8HthTF.kin (312KB)
Fri - 09/19/08
Sequence-specific DNA recognition:
Procaryotic and eucaryotic transcription factors
Prot-DNAInteractionsWksht.pdf (32KB)
258protDNAinter.kin (240KB)
c9EuTF.kin (316KB)
c10TFfam.kin (312KB)
Mon - 09/22/08
Enzyme catalysis:
DNA polymerases & HIV-1 reverse transcriptase
Polymerase movie
(local download) polymerase.mov (10.6MB)
Wed - 09/24/08
Structure determination by X-ray crystallography
c18StDet.kin (204KB)
Fri - 09/26/08
Structure determination (continued)
Mon - 09/29/08
The Ribosome
Ribosome movie ribosome.mov (32.4MB)
1ffk.bb.kin (704KB)
1ffk_hlx7H.kin (1.3MB)
1ffk_5Sto38.kin (436KB)
1ffk_pieceH.kin (116KB)
1ffk5S_mcdots.kin (1.1MB)
1ffk5SHstack.kin (1.9MB)
1JJ2s.L24.kin (72KB)
Wed - 10/01/08
Enzyme catalysis: Serine & HIV-1 proteases
Wkst-SerineProtease.pdf (36KB)
c11SerPr.kin (316KB)
Fri - 10/03/08 (Protein-DNA interactions worksheet due)
Structure determination by NMR
Mon - 10/06/08
Immunoglobins
Wed - 10/08/08
Frontiers in Structural Biology
Fri - 10/10/08
Biochemistry Departmental Retreat
(no class)
Mon - 10/13/08
Duke Fall Break
(no class)
Wed - 10/15/08 - start BCH259 session (258 reports due)
Resources on using KiNG and kinemages
makeKinTut_inKiNG.pdf (84KB)
format-kinemage.pdf (144KB)
king-manual.pdf (244KB)