CH2 lecture May 19 2009 - Information Management ...chem2/Bioenergetics 5-19-09.pdfCh/APh2...
Transcript of CH2 lecture May 19 2009 - Information Management ...chem2/Bioenergetics 5-19-09.pdfCh/APh2...
Ch/APh2 Bioenergetics Section Lecture of May 19, 2009 Introduction to bioenergetics. The thermodynamics of biological energy production. Kinetic aspects of bioenergetic processes. Energy transfer Electron transfer The molecular and cellular organization of bioenergetic systems. Membrane transport Ion Channels, transporters Photosynthesis Respiration and ATP synthesis Haber-Bosch process and biological nitrogen fixation
Kinetics of Bioenergetics
light energy transfer
electron transfer
diffusion
distance, time and driving force dependences
Dutton et al. Adv. Prot. Chem. 63 (2003)
Photon absorption and de-excitation
phosphorescence
time scale ~sec
fluorescence
time scale ~ ns
radiationless transfer
time scale ~ ns
absorption and fluorescence of bacteriochlorophyll
Qy
Qx
light (resonance) energy transfer
Donor absorbs at higher energy (shorter ) than Acceptor.
rate of transfer ~ (R0/R)6
R0 depends on spectral overlap and quantum yields; typically ~ 10 - 50+ Å
basis of “spectroscopic ruler”
acceptor donor
Fluorescence resonance energy transfer (FRET)
measure fluorescence yield of the donor in the absence and presence of the acceptor:
efficiency = Ro6/(Ro
6 + R6)
R0 ~ 34Å
energy transfer in bacterial RC/LHC complexes
Sundstrom et al. JPC B103, 2327 (1999)
(RC absorbs ~ 870 nm)
photosynthetic systems have a common core structure
bacterial
plants: PSI and PSII
Dutton et al. Adv. Prot. Chem. 63, 71 (2003)
bacterial photosynthetic reaction center (RC)
three subunits: L, M and H
A
BCD
E
A’
B’
C’
D’
E’
PDB IDs 2PRC; 1AIJ
view down membrane normalview in plane of membrane
organization of cofactors in the RC
Bchl2
BchlChl
BphBph
Bchl2
QBQA
B branchA branch
carotenoid
photosynthesis - the reaction center
membrane
Bchl2
QA QB
Bchl
Bph
h
Bchl -chlorophyll
Bph - bacteriopheophytin
Q - quinone
Fe
QuickTime™ and aQuickDraw decompressor
are needed to see this picture.
(Bchl)2
Bph
Bchl
QAQBFe
5 Å
10 Å
5 Å
13 Å10 Å
5 Å
5 Å
why is the B branch so much slower than the A branch?
why is the back reaction (to (Bchl)2+) so unfavorable?
Bph
Bchl
Incident solar radiation ~1 photon/RC/sec
Cycling time for the RC is ~ 10-3 sec;
Use light harvesting/antennae complexes to transfer light energy to RC
Mechanism of light energy transfer is not quantitatively understood:
After absorption of a photon, the excited state likely becomes delocalized around the electronically coupled chromophores.
http://www.chem.gla.ac.uk/protein/LH2/migrate.html
h
Electron Transfer Kinetics: classical Marcus theory
(Marcus and Sutin, BBA 811, 265 (1985))www.nobel.se/chemistry/laureates/1992/marcus-lecture.html
activation energy for exchange reaction (ET rate)
kET = A e-(∆G*/RT)
http://iriaxp.iri.tudelft.nl/~scwww/candeias/bio-et/kinetic.html
calculation of activation energy - classical model
∆G* = (1+∆G˚/ )2/4
kET = Ae-(∆G*/RT)
max. rate when ∆G˚= -
Gray & Winkler Ann. Rev. Biochem. 65, 537 (1996)
= energy to distort reactant into product geometry
the inverted region
distance dependence of electron transfer kinetics
kET = A(r) e-(∆G*)/RT
Tunneling timetable for ET in Ru-modified proteins (open symbols), water (light blue, = 1.61-1.75 Å1), and vacuum (dark blue, = 3.0-4.0 Å1) (adapted from ref. 36). Most coupling-limited electron tunneling times in proteins [cyt c (); azurin (); cyt b562 (); myoglobin (); and high-potential iron-sulfur protein ()] fall in the 1.0- to 1.2-Å1 wedge (pale blue solid lines; pale blue dashed line is the average of 1.1 Å1). Colored circles (*Zn-cyt c Fe(III)-cyt c, green and Fe(II)-cytc Zn-cyt c+, red) are interprotein time constants.
Tezcan et al. PNAS 98, 5002 (2001)
distance dependence of electron transfer A(r) ~ 1013 e-r s-1
= 1.1 Å-1
Page et al. Nature 402, 47 (1999)hopping vs jumping…
Using ~ 1.1 Å-1, ket for electron transfer over 10 Å, 15 Å, 20 Å, 25 Å, and 30 Å, are calculatedto be approximately 8.8 x 109, 3.6x107, 1.5x105, 6.0x102, 2.5 sec-1, respectively. From thesevalues, the time required for electron transfer over 30 Å by either hopping in three 10 Å steps, orby tunneling directly, are calculated to be:
t1 / 2 , hopping ~ 18.8109 ln 2 (31) 3.11010 sec
t1/ 2, tunneling ~1
2.5ln 2 (11) 0.28 sec
kET = 1013 e-r e-(∆G*)/RT s-1
Kinetic aspects of getting a molecule or ion across a membrane
Thermodynamic driving forces:concentration gradientsmembrane potential (charged species)
Pore geometry (radius, length, electrostatics)
kinetics are governed by fundamental empirical laws that relate fluxes (flows) to driving forces
Ohm’s law relates forces (V) and flows (I) of electrical current
I = (1/R) V
Fick’s laws of diffusion relate forces and flows of particles
In general, the flux is proportional to the driving force
J = L F
J L
and J = L F
L F = c v
F = (c/L) v f v f = frictional coefficient
ie at steady state, F ~ velocity, not acceleration!
J = particles/unit area/unit time = molecules cm-2 sec-1
= concentration x velocity = c v
total current = J x Area
Basic equations of microscopic diffusion: Fick’s First Law
The basic diffusion equation may be derived from random walk considerations
area = AN(x) N(x+)
Consider how many particles will move across from point x to point x+ per unitarea per unit time - ie, what is the net flux J in the x direction?
For a random walk, where N(x) is the number of particles at x,during the next step
(1/2)N(x) will move from x to x+(1/2)N(x+) will move from x+ to x(1/2)[N(x)-N(x+)] will be the net movement from x to x+
= -(1/2)[N(x+)-N(x)]
cellular and molecular architecture of bioenergetic systems
(sub)cellular organization
Buchanan, Gruissem, JonesBiochemistry and Molecular Biology of Plants
organization of phospholipid membranes
S.J. Singer’s fluid mosaic model Science 175, 720 (1972)
phospholipids assemble into a bilayer through the “hydrophobic effect”; the apolar interior of the membrane is largely impermeable to water, ions and other polar molecules. Membrane proteins are required for transport of these species into and out of cells
Chandler, Nature 417, 491 (2002)
• Mitochondria: respiratory organelle, generates ~body weight of ATP daily
• Contains an outer membrane and a highly convoluted inner membrane with respiratory complexes
• Total surface area of inner membranes in humans is estimated to be 14,000 m2. (Rich, Nature 421, 583 (2003)
E. coli has two cell membranes
membrane spanning
polypeptide conformations
Looking at Macromolecular Structures
Viewer
SwissPDB
Rasmol
iMol
PyMOL
etc….
Coordinates
PDB - the Protein Data Bank - operated by the Research Collaboratory for Structural Bioinformatics
http://www.rcsb.org/pdb
Rich, Nature 421, 583 (2003)
Abeles, Nature 420, 27 (2002)
If N(x) N(x ) , then there will be a net flux through an area elementperpendicular to x between x and x+ that is given by Fick’s first law.
J D dcdx
; if dcdx
constant, J = constant
Cb
ba
Ca
there is a next flux from right to left, simply because there are more particles onthe right than on the left.
This flux depends only on the gradient, and not the value of c. This drive towardsequalizing the concentrations (chemical potential) will tend to flatten allconcentration gradients, and is principally entropic in origin.
Just as Newton’s laws give forces are derivatives of energy, the force from aconcentration gradient can be expressed as a derivative of the chemicalpotential.
Looking at Macromolecular Structures
Viewer
SwissPDB
PyMOL
etc….
Coordinates
PDB - the Protein Data Bank - operated by the Research Collaboratory for Structural Bioinformatics
http://www.rcsb.org/pdb
membrane spanning
polypeptide conformations
electron transfer complexestransporterschannels
matter, energy, information
inside
outside
Membrane proteins are the basic circuit elements of bioenergetic processes
∆µ
KcsA potassium channel
Doyle et al. Science 280, 69 (1998)
PDB ID: 1BL8
tetramer
K+ ion coordination. Zhou et al. Nature 414, 43 (2000).
PDB ID 1K4C
potassium permeation pathway
Morais-Cabral et al. Nature 414, 317 (2001)
mechanism of K+ permeation: conduction state diagram
MthK channel
Ca+2 mediated gating through a K+ channel
Jiang et al.Nature 417, 505 (2002)
PDB ID 1LNQ
Voltage gating in Kv potassium channels
opening and closing the channel in response to changes in membrane potential: the charged S4 helix
“voltage sensor paddles operate somewhat like hydrophobic cations attached to levers, enabling the membrane electric field to open and close the pore”
Jiang et al. Nature 423, 33; 42 (2003)
closed open
mechanosensitive channel of small conductance MscS
3.9 Å resolutionBass et al. Science 298, 1582 (2002)
membrane spanning domain
cytoplasmic domain
L105L109
N-terminal
C-terminal
TM1
TM2
TM3
middle
C-terminaldomain
MscS gating mechanismmechanosensitivity - open state has larger cross-sectional area
voltage sensitivity - open state has (+) charges moving away from cytoplasm
TM1 and TM2 likely serve as coupled tension and voltage sensorsTM3 forms the pore
R46
R74
R88
conformational variability in TM region of MscS
coloring by B factor (low to high)
How are concentration gradients generated in the first place?
Alberts et al. Essential Cell Biology
Na+,K+ ATPase
Two gate mechanism of pumps
ABC transporters andthe ATP-binding cassette:
importers and exporters of a diverseset of substrates
contain two copies each ofconserved ABC domainsmembrane spanning domains (diverse)
The Escherichia coli B12 uptake system Btu
Experimentalelectron density
3.5 Å resolutioncontour level=1
BtuCD architecture
cytoplasm
BtuC BtuC
BtuD BtuD3.2 Å resolutionLocher et al. Science 296, 1091 (2002)
periplasm
exit pathway
gate
translocation pathway
membrane spanning BtuC subunits
BtuCD structural organization
mechanistic issues• consequences of ATP binding and hydrolysis? • coupling of ABC and TM domains?• role of binding protein BtuF?
ATP-binding cassettes (BtuD subunits)
ABC signature motif
Walker-B
P-loops (Walker-A)
Proposed B12 transport mechanism
BtuF-B12
BtuCD
“alternating access” or “airlock” model
Channels and Transporters - summary
channels and transporters have common architectural features, namely:
translocation pathwayclosed with either one gate (channels) or two (transporters)
specificity elements (eg selectivity filter/binding proteins)
gating sensors