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)
258GenInfo20090824.pdf (84KB)
258ClassSchedule20090824.pdf (112KB)
258_report_09-NOTES.pdf (40KB)
protein_structure_coloring_book.pdf (412KB)
Mon - 8/24/2009
Macromolecular computer graphics
KiNG basics
3D literacy
WrkSht1_Intro2009.pdf (120KB pdf) | Demo5_4a-KiNG.kin (100KB)
WrkSht1_Intro2009.doc (120KB pdf)
KiNG basics | QuickStartKing.pdf (36KB pdf)
LectureNotesMonAug24-2009.pdf (56KB pdf)
3Dlit2a-exercise-KiNG.pdf (24KB pdf) | 3Dlit2a-exercise-KiNG.kin (20KB)
Wed - 08/26/2009
Peptide geometry & handedness
Wrksht2_DihedralsHanded2009.pdf (148KB)
Wrksht2_DihedralsHanded2009.doc (148KB)
LectureNotesWedAug26-2009.pdf (60KB)
c1Basics-1n6-KiNG.kin (120KB)
4FXN.pdb (120KB)
Fri - 08/28/2009
Polypeptide chain & amino-acids
c1Basics-2-5-QKiNG.kin (16KB)
Wrksht3-handedAAroles2009.pdf (120KB)
Wrksht3-handedAAroles2009.doc (120KB)
LectureNotesFriAug28-2009.pdf (60KB)
LectureNotesFriAug28-2009.doc (60KB)
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 - 08/31/2009
Secondary structures, motifs, models, & kinemages
WrkSht4-MakingKinemages2009.pdf (140 KB)
LectureNotesMonAug31-2009.pdf (60KB)
WrkSht4-MakingKinemages2009.doc (140 KB)
LectureNotesMonAug31-2009.doc (60KB)
Wed - 09/03/2009
Structural Motifs & Domains
WrkSht5-StructClasses2009.pdf (110KB)
WrkSht5-StructClasses2009.doc (110KB)
c2Motifs.kin (248KB)
c3Alpha.kin (352KB)
c4Al_Bet.kin (348KB)
c5Beta.kin (408KB)
LectureNotesWedSept03-2009.pdf (60KB)
LectureNotesWedSept03-2009.doc (60KB)
Fri - 09/04/2009
Structural Classification, The Coloring Book,
Hydrogens: all-atom contacts,
H-bonds, & waters
LectureNotesFriSept04-2009.pdf (60KB)
LectureNotesFriSept04-2009.doc (60KB)
WrkSht6-H-bonds2009.pdf (150KB)
WrkSht6-H-bonds2009.doc (150KB)
HbondPractice-KiNG.kin (100KB)
Wed - 09/09/2009
Roles of amino acids and mutations to replace them
WrkSht7-mutants2009.pdf (120KB)
WrkSht7-mutants2009.doc (120KB)
1lmb6_85aH.kin (185KB)
1lmb6_85aH.pdb (120KB)
2simHdot.kin (5.3MB)
2simH.pdb (520KB)
LectureNotesWedSept09-2009.pdf (60KB)
LectureNotesWedSept09-2009.doc (60KB)
Fri - 09/11/2009
Motions, Alternative Conformations, & Ensembles
WrkSht8-motions2009.pdf (130KB)
WrkSht8-motions2009.doc (130KB)
c6FldFlx-KiNG.kin (800KB)
Davis_Backrub_kinSup.kin (2.2MB)
HbAllo-KiNG.kin (120KB)
LectureNotesFriSept11-2009.pdf (60KB)
LectureNotesFriSept11-2009.doc (60KB)
Mon - 09/14/2009
Motions, Allostery
The following kins & maps were shown in class:
2dn1H-OXY-KiNG.kin (1.4MB) | 2dn1.omap.gz (1.6MB)
2dn2H-Deoxy-KiNG.kin (1.4MB) | 2dn2.omap.gz (2.7MB)
Wed - 09/16/09 (Coloring Books due)
Protein-nucleic acid recognition:
General Principles
Prot-DNAInteractionsWksht.pdf (32KB)
258protDNAinter.kin (240KB)
c7DNA.kin (156KB)
c8HthTF.kin (312KB)
Fri - 09/18/09
Sequence-specific DNA recognition:
Procaryotic and eucaryotic transcription factors
Prot-DNAInteractionsWksht.pdf (32KB)
258protDNAinter.kin (240KB)
c9EuTF.kin (316KB)
c10TFfam.kin (312KB)
Mon - 09/21/09
Enzyme catalysis: Serine & HIV-1 proteases
Wkst-SerineProtease.pdf (36KB)
c11SerPr.kin (316KB)
Wed - 09/23/09
Enzyme catalysis:
DNA polymerases & HIV-1 reverse transcriptase
Polymerase movie
(local download) polymerase.mov (10.6MB)
Fri - 09/25/09
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)
Mon - 09/28/09
Structure determination by X-ray crystallography
c18StDet.kin (204KB)
Wed - 09/30/09
Structure determination (continued)
Fri - 10/02/09 (Protein-DNA interactions worksheet due)
Frontiers in Structural Biology
Mon - 10/05/09
Duke Fall Break
(no class)
Wed - 10/07/09 - Pei Zhou, lecturer
Structure determination by NMR
Fri - 10/09/09
Immunoglobins
Mon - 10/12/09 - start BCH259 session (258 reports due)
Resources on using KiNG and kinemages
makeKinTut_inKiNG.pdf (84KB)
format-kinemage.pdf (144KB)
king-manual.pdf (244KB)