Biochemistry of Metabolism

Membrane Transport

Copyright 1999-2007 by Joyce J. Diwan. All rights reserved.

This discussion will focus on selected examples of transport catalysts for which structure/function relationships are relatively well understood. Transporters are of two general classes: carriers and channels. These are exemplified by two ionophores (ion carriers produced by microorganisms):

valinomycin (a carrier) gramicidin (a channel).

Valinomycin
H3C CH3 CH O N H H3C CH C O H C CH O C N H CH3 H3C H C CH CH3 O C O CH3 O CH C

L-valine

D-hydroxy-

D-valine

L-lactic

isovaleric acid

acid

Valinomycin is a carrier for K+.

It is a circular molecule, made up of 3 repeats of the sequence shown above.

Puckering of the ring, stabilized by H-bonds, allows valinomycin to closely surround a single unhydrated K+ ion. Six oxygen atoms of the ionophore interact with the bound K+, replacing O atoms of waters of hydration.

Valinomycin O O O
Hydrophobic

O O

Valinomycin is highly selective for K+ relative to Na+.

The smaller Na+ ion cannot simultaneously interact with all 6 oxygen atoms within valinomycin.

Thus it is energetically less favorable for Na+ to shed its waters of hydration to form a complex with valinomycin.

Valinomycin O O O
Hydrophobic

O O

Whereas the interior of the valinomycin-K+ complex is polar, the surface of the complex is hydrophobic.

This allows valinomycin to enter the lipid core of the bilayer, to solubilize K+ within this hydrophobic milieu.
Crystal structure (at Virtual Museum of Minerals & Molecules).

Val-K+

Val-K+

K+ Val membrane Val

K+

Valinomycin is a passive carrier for K+. It can bind or release K+ when it encounters the membrane surface. Valinomycin can catalyze net K+ transport because it can translocate either in the complexed or uncomplexed state. The direction of net flux depends on the electrochemical K+ gradient.

Proteins that act as carriers are too large to move across the membrane. They are transmembrane proteins, with fixed topology.

An example is the GLUT1 glucose carrier, in plasma membranes of various cells, including erythrocytes.
GLUT1 is a large integral protein, predicted via hydropathy plots to include 12 transmembrane a-helices.

conformation change

conformation change

Carrier-mediated solute transport

Carrier proteins cycle between conformations in which a solute binding site is accessible on one side of the membrane or the other. There may be an intermediate conformation in which a bound substrate is inaccessible to either aqueous phase. With carrier proteins, there is never an open channel all the way through the membrane.

conformation change

conformation change

Carrier-mediated solute transport

The transport rate mediated by carriers is faster than in the absence of a catalyst, but slower than with channels. A carrier transports one or few solute molecules per conformational cycle, whereas a single channel opening event may allow flux of many thousands of ions. Carriers exhibit Michaelis-Menten kinetics.

Uniport

Symport A B

Antiport A

Classes of carrier proteins

Uniport (facilitated diffusion) carriers mediate transport of a single solute. An example is the GLUT1 glucose carrier. The ionophore valinomycin is also a uniport carrier.

Uniport

Symport A B

An

Symport (cotransport) carriers bind two dissimilar solutes (substrates) & transport them together across a membrane. Transport of the two solutes is obligatorily coupled.

A gradient of one substrate, usually an ion, may drive uphill (against the gradient) transport of a co-substrate. It is sometimes referred to as secondary active transport. E.g: glucose-Na+ symport, in plasma membranes of some epithelial cells bacterial lactose permease, a H+ symport carrier.

Uniport A

Symport A B

Lactose permease catalyzes uptake of the disaccharide lactose into E. coli bacteria, along with H+, driven by a proton electrochemical gradient. It is the first carrier protein for which an atomic resolution structure has been determined. Lactose permease has been crystallized with thiodigalactoside (TDG), an analog of lactose.

The substrate binding site is at the apex of an aqueous cavity between two domains, each consisting of six transmembrane a-helices.

TDG substrate analog

Lactose Permease

PDB 1PV7

In the conformation observed in this crystal structure, the substrate analog is accessible only to what would be the cytosolic side of the intact membrane. Residues essential for H+ binding are are also near the middle of the membrane.

conformation change

conformation change

Carrier-mediated solute transport

As in simple models of carrier transport based on functional assays, the tilt of transmembrane a-helices is assumed to change, shifting access of lactose & H+ binding sites to the other side of the membrane during the transport cycle.

TDG substrate analog

Lactose Permease

PDB 1PV7

Uniport

Symport

Antiport A

Antiport (exchange diffusion) carriers A A B exchange one solute for another across a membrane. Usually antiporters exhibit "ping pong" kinetics. A substrate binds & is transported.

Then another substrate binds & is transported in the other direction. Only exchange is catalyzed, not net transport. The carrier protein cannot undergo the conformational transition in the absence of bound substrate.

mitochondrial matrix ATP 4 ADP 3 adenine nucleotide translocase

Example of an antiport carrier:

Adenine nucleotide translocase (ADP/ATP exchanger) catalyzes 1:1 exchange of ADP for ATP across the inner mitochondrial membrane.

Active Transport

ADP + Pi

S1
ATP
Side 1 Side 2

S2

Active transport enzymes couple net solute movement across a membrane to ATP hydrolysis. An active transport pump may be a uniporter or antiporter.

ATP-dependent ion pumps are grouped into classes based on transport mechanism, as well as genetic & structural homology. Examples include: P-class pumps

F-class (e.g., F1Fo-ATPase to be discussed later) & related V-class pumps.

ABC (ATP binding cassette) transporters, which catalyze transmembrane movements of various organic compounds including amphipathic lipids and drugs, will not be discussed here.

P-class ion pumps are a gene family exhibiting sequence homology. They include: Na+,K+-ATPase, in plasma membranes of most animal cells is an antiport pump.

It catalyzes ATP-dependent transport of Na+ out of a cell in exchange for K+ entering.

(H+, K+)-ATPase, involved in acid secretion in the stomach is an antiport pump. It catalyzes transport of H+ out of the gastric parietal cell (toward the stomach lumen) in exchange for K+ entering the cell.

P-class pumps (cont):

Ca++-ATPases, in endoplasmic reticulum (ER) and plasma membranes, catalyze ATP-dependent transport of Ca++ away from the cytosol, into the ER lumen or out of the cell.
Some evidence indicates that these pumps are antiporters, transporting protons in the opposite direction. Ca++-ATPase pumps function to keep cytosolic Ca++ low, allowing Ca++ to serve as a signal.

O Enzyme-C ATP OH Pi H2O O Enzyme- C O O P OO-

The reaction mechanism for a P-class ion pump involves transient covalent modification of the enzyme.

ADP

P-Class Pumps

At one stage of the reaction cycle, phosphate is transferred from ATP to the carboxyl of a Glu or Asp side-chain, forming a high energy anhydride linkage (~P).

At a later stage in the reaction cycle, the Pi is released by hydrolysis.

E~P-Ca++2 ADP ATP 2Ca++ E Pi cytosol E-Ca++2

E~P-Ca++2 2Ca++

The ER Ca++ pump is called SERCA: Sarco(Endo)plasmic Reticulum Ca++-ATPase.

membrane

ER lumen

In this diagram of SERCA reaction cycle, conformational changes altering accessibility of Ca++-binding sites to the cytosol or ER lumen are depicted as positional changes.

Keep in mind that SERCA is a large protein that maintains its transmembrane orientation.

Reaction cycle:

E~P-Ca++2 ADP

E~P-Ca++2 2Ca++

1. 2 Ca++ bind tightly ATP E-Ca++ from the cytosolic 2 side, stabilizing the ++ 2Ca conformation that E allows ATP to react Pi with an active site cytosol membrane aspartate residue.

ER lumen

2. Phosphorylation of the active site aspartate induces a conformational change that shifts accessibility of the 2 Ca++ binding sites from one side of the membrane to the other, & lowers the affinity of the binding sites for Ca++.

E~P-Ca++2 ADP ATP 2Ca++ E Pi cytosol E-Ca++2

E~P-Ca++2 2Ca++

membrane

ER lumen

3. Ca++ dissociates into the ER lumen. 4. Ca++ dissociation promotes hydrolysis of Pi from the enzyme Asp conformational change (recovery) that causes Ca++ binding sites to be accessible again from the cytosol.

Asp351

This X-ray structure of muscle SERCA (Ca++-ATPase) shows 2 Ca++ ions (colored magenta) bound between transmembrane a-helices in the membrane domain.

cytosolic domain

2 Ca++

membrane domain

PDB 1EUL

Muscle SERCA

Active site Asp351, which is transiently phosphorylated during catalysis, is located in a cytosolic domain, far from the Ca++ binding sites.

SERCA structure has been determined in the presence & absence of Ca++, with or without substrate or product analogs and inhibitors.
Substantial differences in conformation have been interpreted as corresponding to different stages of the reaction cycle. Large conformational changes in the cytosolic domain of SERCA are accompanied by deformation & changes in position & tilt of transmembrane a-helices. The data indicate that when Ca++ dissociates: water molecules enter Ca++ binding sites charge compensation is provided by protonation of Ca++-binding residues.

Ca

++

SERCA Conformational Cycle

enzyme phosphorylation

phosphate hydrolysis

This simplified cartoon represents the proposed variation in accessibility & affinity of Ca++-binding sites during the reaction cycle. Only 2 transmembrane a-helices are represented, and the cytosolic domain of SERCA is omitted.

More complex diagrams & animations have been created by several laboratories, based on available structural evidence. E.g.: animation (lab of D. H. MacLennan) diagram (by C. Toyoshima, in a website of the Society of General
Physiologists - select Poster).

website of the Toyoshima Lab (select Resources for movies).

conformation change

Ion Channels

closed

open

Channels cycle between open & closed conformations. When open, a channel provides a continuous pathway through the bilayer, allowing flux of many ions.

Gramicidin is an example of a channel.

Gramicidin is an unusual peptide, with alternating D & L amino acids. In lipid bilayer membranes, gramicidin dimerizes & folds as a right-handed b-helix. The dimer just spans the bilayer. Primary structure of gramicidin (A):
HCO-L-Val-Gly-L-Ala-D-Leu-L-Ala-D-Val-L-Val-D-Val-L-TrpD-Leu-L-Trp-D-Leu-L-Trp-D-Leu-L-Trp-NHCH2CH2OH Note: The amino acids are all hydrophobic; both peptide ends are modified (blocked).
Gramicidin dimer (PDB file 1MAG)

The outer surface of the gramicidin dimer, which interacts with the core of the lipid bilayer, is hydrophobic. Ions pass through the more polar lumen of the helix. Ion flow through individual gramicidin channels can be observed if a small number of gramicidin molecules is present in a lipid bilayer separating 2 compartments containing salt solutions.

Gramicidin dimer (PDB file 1MAG)

ion flow through one channel time

With voltage clamped at some value, current (ion flow through the membrane) fluctuates. Each fluctuation, attributed to opening or closing of one channel, is the same magnitude.

The current increment corresponds to current flow through a single channel (drawing - not actual data).

current

Proposed mechanism of gramicidin gating

Gating (opening & closing) of a gramicidin channel is thought to involve reversible dimerization.

open

closed

An open channel forms when two gramicidin molecules join end to end to span the membrane.
This model is consistent with the finding that at high [gramicidin] overall transport rate depends on [gramicidin]2.

Channels that are proteins

Cellular channels usually consist of large protein complexes with multiple transmembrane a-helices. Their gating mechanisms must differ from that of gramicidin. Control of channel gating is a form of allosteric regulation. Conformational changes associated with channel opening may be regulated by: Voltage Binding of a ligand (a regulatory molecule) Membrane stretch (e.g., via link to cytoskeleton)

A
electrode glass pipet

Patch Clamping

B
electrode electrode

The technique of patch clamping is used to study ion channel activity. A narrow bore micropipet may be pushed up against a cell or vesicle, and then pulled back, capturing a fragment of membrane across the pipet tip.

amplifier with voltage control

Patch Clamping

reference electrode

electrode in patch pipet membrane patch

salt solution

A voltage is imposed between an electrode inside the patch pipet and a reference electrode in contact with surrounding solution. Current is carried by ions flowing through the membrane.

open

current

closed time

If a membrane patch contains a single channel with 2 conformational states, the current will fluctuate between 2 levels as the channel opens and closes. The increment in current between open & closed states reflects the rate of ion flux through one channel. View a video of an oscilloscope image during a patch clamp recording.

20 pA

102 msec per trace

Patch clamp recording at 60 mV. Consecutive traces are shown. Note that at a negative voltage, increased current is a downward deflection.

Current Amplitude Histogram

Occupancy of current levels

Occupancy of different current levels during the time period of a recording is plotted against current in picoAmperes (1012 Amp). Peaks represent open & closed states (note scale). Baseline current, when the channel is closed, is due to leakage of the patch seal and membrane permeability.

-60 -55 -50 Amplitude in pAmp

-45