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.
In columnar format below, is the tentative class schedule. 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. Immediately below are PDFs with general information about the course. Then in columnar format is the tentative class schedule (exact content of topics or resources may continue to change). Listed with the date and topic are downloadable resources - PDFs, kinemages, and text files; 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 to download, 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.
258CrsSum07.pdf (48KB)
258GenInfo07.pdf (56KB)
258projInst.pdf (120KB)
Mon - 8/27/07
Macromolecular computer graphics
KiNG basics
3D literacy
WrkSht1_Intro2007.pdf (116KB pdf) | Demo5_4a-KiNG.kin (95KB)
KiNG basics | QuickStartKing.pdf (36KB pdf)
3Dlit2a-exercise-KiNG.pdf (24KB pdf) | 3Dlit2a-exercise-KiNG.kin (20KB)
Wed - 08/29/07
Peptide geometry & handedness
Wrksht2_handedAAroles2007.pdf (135KB)
LectureNotesAug29.pdf (64KB)
c1Basics-A-KiNG.kin (120KB)
Fri - 08/31/07
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-DihedralsHanded2007.pdf (120KB)
4FXN.pdb (120KB)
Mon - 09/03/07
Labor Day -- (no class)
Wed - 09/05/07
Secondary structures & motifs
WrkSht4-makeKins2007.pdf (140 KB)
Fri - 09/07/07
Domains, Subunits & Superfolds
WrkSht5-StructClasses2007.pdf (110KB)
c2Motifs.kin (248KB)
c3Alpha.kin (352KB)
c4Al_Bet.kin (348KB)
c5Beta.kin (408KB)
Mon - 09/10/07
Hydrogens: all-atom contacts,
H-bonds, & waters
WrkSht6-H-bonds2007.pdf (150KB)
HbondPractice-KiNG.kin (100KB)
Wed - 09/12/07
Structural roles of the amino acids
WrkSht7-mutants2007.pdf (120KB)
1lmb6_85aH.kin (185KB)
1lmb6_85aH.pdb (120KB)
2simHdot.kin (5.3MB)
2simH.pdb (520KB)
Fri - 09/14/07
Motions
WrkSht8-motions2007.pdf (130KB)
c6FldFlx-KiNG.kin (800KB)
HbAllo-KiNG.kin (120KB)
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)
Mon - 09/17/07
Protein-nucleic acid recognition:
General Principles
Prot-DNAInteractionsWksht.pdf (32KB)
258protDNAinter.kin (240KB)
c7DNA.kin (156KB)
c8HthTF.kin (312KB)
Wed - 09/19/07
Sequence-specific DNA recognition:
Procaryotic and eucaryotic transcription factors
Prot-DNAInteractionsWksht.pdf (32KB)
258protDNAinter.kin (240KB)
c9EuTF.kin (316KB)
c10TFfam.kin (312KB)
Fri-09/21/07
Enzyme catalysis: Serine & HIV-1 proteases
Wkst-SerineProtease.pdf (36KB)
c11SerPr.kin (316KB)
Mon - 09/24/07
Enzyme catalysis:
DNA polymerases & HIV-1 reverse transcriptase
Polymerase movie
(local download) polymerase.mov (10.6MB)
Wed - 09/26/07
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)
Fri - 09/28/07
Structure determination by X-ray crystallography
c18StDet.kin (204KB)
Mon - 10/01/07
Structure determination (continued)
Wed - 10/03/07
Structure determination by NMR
Fri - 10/05/07
Immunoglobins
Mon - 10/08/07
Fall Break(no class)
Wed-10/10/07
Frontiers in Structural Biology
Fri - 10/12/07
Biochemistry Departmental Retreat
(no class)
Resources on using KiNG and kinemages
makeKinTut_inKiNG.pdf (84KB)
format-kinemage.pdf (144KB)
king-manual.pdf (244KB)