―To solve a basic problem in medicine,‖ Kornberg told the commencement audience, ―don’t study it directly; rather, pursue a curiosity about nature and the rest will follow.‖


2. The c rotation is passed to Gamma and Epsilon, causing conformational changes in Alpha/Beta. Rotation forces one of 3 catalytic sites into an opened conformation. Synthesized ATP is released, and Pi/ADP are bound instead.
Nobel Price in Chemistry, 2006

In 2001, Kornberg published the first molecular snapshot of the protein machinery responsible — RNA polymerase — in action. The finding helped explain how cells express all the information in the human genome, and how that expression sometimes goes awry, leading to cancer, birth defects and other disorders.
1.2. 能量转换
1.2.1.生物能的产生

古细菌 Bacteriorhodopsin （光能至化学梯度势 能）
Photocycle & proton pumping
Hundreds of protons per sec.
Conformational changes & proton affinity jump
第三章：纳米生物学的功 能原理
第一节：纳米生物材料的 基本功能
宏观功能vs微观功能
1.1. 信息驱动
1.1.1. 信息的载体

DNA RNA
Chinese: ―dian, heng, shu, pie, na,,,‖ English:― a, b, c, d,,,,z‖ Computers: ―1,0‖
•;
2007, Cell 129, 1299–1309
Sliding clamp
E.Coli. Human
2008, Cell 132, 43–54
1.1.3. 信息的传递（读）

RNA Transcription ( HHMI video)
RNA polymerase

RNA polymerases are very large enzymes, consisting of 12-17 subunits with a total molecular weight of 0.5-0.7 Mega Dalton. They transiently assemble with many additional factors into large transcription machineries of changing composition.
J. Mol. Biol. (2007) 366, 790–805 Biophysical Journal (2009) 96, 2779–2788
Water in proton channel
Life needs water
Energy flow
Photon 光能
Isomerization 键能 Conformational changes 动能 Proton gradient 化学梯度势能


3. Rotation goes further, Gamma subunit turns another 120 degrees forcing the next site into the opened conformation, and the ADP and phosphate bound to the previous opened site are occluded and ATP synthesis takes place. The ATP molecule formed is released when the Gamma subunit makes one 360 degrees turn and once again opens the site.

ATP hydrolysis

fof1_rot_2700nm.mov The energy of ATP hydrolysis can drive the reverse rotation of the F1 motor and subsequently pump protons against their electrochemical gradient.
Updated on 10.31.2012/10.09.2013
1.2.2. 生物能转化
ATP synthase

Fo: proton channel F1: synthase

β: catalytic sites γ: rotation axle c: rotated by proton
RNA Translocation and Unwinding Mechanism of HCV NS3 Helicase and its Coordination by ATP. 2006. Nature 439: 105.

PNAS 2005 vol. 102 3623–3626
•Sequence dependent (GC rich/AT rich) •DNA polymerase coupled
What can we learn (may do)?

E=hv=hc/λ =(6.626E10-34 J· s)(3E8m/s) /(5E10-7m ) =4E-19J (2.5eV) =40E-20J E of (N-H…O)~=8kJ/mol ~=1.3E-20J (O-H…N)~=29KJ/mol ~=4.8E-20J Covalent bonds: ~hundreds of KJ/mol
1.1.2. 信息的复制(a HHMI video)





DNA polymerase DNA template DNA helicase (Werner syndrome: premature aging) DNA primase dNTP Single strand DNA binding protein RNaseH Ligase Sliding clamp
Unique features compared to replication


ed when breaking dsDNA Bind dsDNA No sliding clamp needed ~50bp/sec …
Questions ?

Do we need energy?
DNA replication model
Helicase

Binds single strand DNA Motor protein: ATP hydrolysis 1000bp/sec (E. Coli)

Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped t7 helicase. 2007. Cell 129 (7): 1299–309.
(N-H…O)
~8kJ/mol (O-H…N)~29KJ/mol
Milestone works:



Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution. Science. 2009; 324 (5931): 1203-1206 Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science. 2001; 292 (5523): 1863-76 Architecture of RNA polymerase II and implications for the transcription mechanism. Science. 2000; 288 (5466): 640-9

Milestone work and stories



Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J Mol Biol. 1990. 213:899-929 (2394/2626 cited) Surface of bacteriorhodopsin revealed by highresolution electron crystallography. Nature. 1997.389:206-211 (415/453 cited) Structure of bacteriorhodopsin at 1.55 A resolution. J Mol Biol. 1999. 291:899-911 (1061/1172 cited) X-ray structure of bacteriorhodopsin at 2.5 angstroms from microcrystals grown in lipidic cubic phases. Science. 1997. 277:1676-81. (797/870 cited)