Excitation and Electron Transfer

Excitation and Electron Transfer

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Phys 301: Computational Biological Physics – Winter 2004


Phys 4500: Computational Biological Physics – Winter 2005




University of Illinois at Urbana Champaign
Beckman Institute for Advanced Science and Technology
Theoretical and Computational Biophysics Group







Excitation and Electron Transfer





Chalermpol Kanchanawarin Melih Sener CONTENTS 2
Contents
1 Tutorial on Excitation Transfer 4
1.1 File Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.2 Architecture of Light Harvesting Complex II (LH II) . . . . . . . . . 4
1.2.1 Building block of LH II . . . . . . . . . . . . . . . . . . . . 5
1.2.2 Packing of two LH II structural units . . . . . . . . . . . . . 10
1.2.3 LH II ring . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
1.3 Excitation Transfer between two Bacteriochlorophyls in LH II . . . . 13
1.3.1 Orientation of BChl Transition Dipole Moments in LH II . . . 15
1.3.2 Calculation of Excitation transfer rate . . . . . . . . . . . . . 16
2 Tutorial on Electron Transfer 20
2.1 Starting your simulation . . . . . . . . . . . . . . . . . . . . . . . . 20
2.2 Interlude: Structure of cytochrome c . . . . . . . . . . . . . . . . . 212
2.3 a closer look at your configuration files . . . . . . . . . . . 22
2.4 Re running NAMD to read your previous trajectory . . . . . . . . . . 23
2.5 From the trajectory to the energy gap function . . . . . . . . . . . . . 24 CONTENTS 3
Introduction
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University of Illinois at Urbana-Champaign Beckman Institute for Advanced Science and Technology Theoretical and Computational Biophysics Group
Excitation and
Chalermpol Kanchanawarin
Electron
Transfer
Melih Sener
CONTENTS
Contents
1
2
Tutorial on Excitation Transfer 1.1 File Setup. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.2 Architecture of Light Harvesting Complex II (LH-II). . . . . . . 1.2.1 Building block of LH-II. . . . . . . . . . . . . . . . . . 1.2.2 Packing of two LH-II structural units. . . . . . . . . . . 1.2.3 LH-II ring. . . . . . . . . . . . . . . . . . . . . . . . . . 1.3 Excitation Transfer between two Bacteriochlorophyls in LH-II. . 1.3.1 Orientation of BChl Transition Dipole Moments in LH-II. 1.3.2 Calculation of Excitation transfer rate. . . . . . . . . . .
Tutorial on Electron Transfer 2.1 Starting your simulation. . . . . . . . . . . . . . . . . . . . . . 2.2 Interlude: Structure of cytochrome c2. . . . . . . . . . . . . . . 2.3 Interlude: a closer look at your conguration les. . . . . . . . . 2.4 Re-running NAMD to read your previous trajectory. . . . . . . . 2.5 From the trajectory to the energy gap function. . . . . . . . . . .
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CONTENTS
Introduction
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Life on earth is sustained through the harvesting of the energy of sunlight through photosynthesis, where the energy of an absorbed photon is rst converted to a (short lived) electronic excitation, which is then transferred to a reaction center, and later stored in a (longer lived) charge gradient across the membrane via an electron transfer. These two fundamental processes in photosynthetic light-harvesting form the subject matter of this tutorial. The rst section of this tutorial studies theexcitation transfer process in the pigment complex of the peripheral light-harvesting complex, LH-II, of the purple bacteriumRhodospirillum molischianum second section introduces. The electron transferin a a protein that shuttles electrons between different membrane proteins, namely cytochrome c2fromRhodobacter sphaeroides.
Getting started The two subdirectories:1-excitation,2-electroncontain the les required for the two sections of this tutorial.
If you ever get lost....Both tutorial directories contain an example-outputdirectory that has all intermediate and target les in it. You can restore your session to any intermediate stage by copying the les from this directory to your workspace. Simply typecp example-output/filename .in your working direc-tory.
1UTTORIALNOEXCITATIONTRANSFER
1 Tutorial on Excitation Transfer
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In this part of the tutorial, you will learn about the transfer of excitation energy between pairs of bacteriochlorophyl molecules (BChls) in light harvesting complex II (LH-II). The tutorial consists of two sections. In the rst section, you will use VMD to inves-tigate the structure of LH-II in order to see how proteins and pigments are organized in the complex. Then, in the second section you will calculate the rate of excitation energy transfer between pairs of BChls in LH-II using VMD and Mathematica.
1.1 File Setup The working directory for this tutorial is at 1-excitation It contains ve les and one directory. 1.lh2.pdbis a pdb le for LH-II. 2.TwoDimer.vmdis a VMD state le for two LH-II structural units. 3.EightDimer.vmdis a VMD state le for LH-II ring. 4.lh2-dipole.vmdis a VMD state le for showing direction of transition dipole moments of BChls in LH-II. 5.transfer.nbis a Mathematica le for excitation transfer rate calculation. 6.example-outputis a directory containing example output les e.g.OneD-imer.vmdVMD state le for an LH-II structural unit.is a
1.2 Architecture of Light Harvesting Complex II (LH-II) In this section, you are going to view and investigate the three dimensional structure of the light harvesting complex II from Rhodospirillum (Rh.) molischianum using VMD.
Your objective in this section is to see how proteins and pigments (BChls and carotenoids) are arranged in LH-II by using VMD. It should take you about 45 minutes to complete.
LH-II fromRh. molischianuma membrane protein complex which absorbs lightis and transfers its energy to a reaction center in a photosynthetic unit. It consists of eight copies of a basic structural unit (building block) containing a heterodimer of two protein subunits (α-apoprotein andβ-apoprotein), three bacteriochlorophyls (BChls named B850a, B850b and B800, according to their absorption wavelength in nm) and one carotenoid. Eight of these units are assembled into the LH-II ring as shown in Figure1. In total, there are 16 protein segments, 24 BChls (each contains a Mg2+ion at its center) and 8 carotenoids.
You will start from viewing a building block of LH-II. From there, you will then examine how two heterodimers t together in LH-II. Finally, you will investigate the complete LH-II ring which is made of eight of these heterodimers.
swhlhritidesidueeerhidniudivCBladeachconsistsoftCB2A.,..,.CB8Ana
Figure 1: Top and side view of a light harvesting complex II fromRh. molischianum.
Light-harvesting antennae: why so many chlorophyls?.Light-harvesting complexes contain many pigments for light absorp-tion. However, most of these pigments are not directly involved with storing the absorbed light energy in the form of a membrane charge. Most pigments function as auxilliary antennae that trans-fer their excitation through their neighbors to a reaction center, that converts light energy into electron transfer and, thereby, into a membrane charge. The number of chlorophylls can be explained by the rate of absorption under dim light conditions: to charge the membrane at the needed rate,200 chlorophylls are needed to absorb enough sun light per time.
1.2.1 Building block of LH-II In this subsection, you will examine the building block of LH-II as shown in Figure2 and investigate how the two proteins and the four pigments are arranged.
NOTE.If you want you may skip the rendering of LH-II building block by loading the VMD stateOneDimer.vmdin the directory 1-excitation/example-outputof the system shown in Fig-ure2 You canto save time for later subsections in the tutorial. start to answer questions in this subsection.
95sID)r(Re8and57,5ctaneitmueboinn5NOITATICREFSNARTLAIRXENO1OTUTpo-aotprofeseαththgiipocereheeraALP2,...mesALP1,geemtnaniewntishb),t2.pdI(lhLH-IelfodpbtnehIopsenidngiegrgth.,..T8BEhe.TrrcogeemtnanemBsAC,1oupsofBChlshaveshtfoseiprpopa-βeanP8AL.,cohtigdeBsTEanem2T.,,1EBnwitoteimenthseg
1 TUTORIAL ON EXCITATION TRANSFER
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corresponding to BChls B850b, B800 and B850a respectively. Finally there are eight carotenoids with segment names LYC8 ..,LYC1, LYC2,...
Figure 2: Building Block of LH-II.
You will rst render a heterodimer of the two proteins made of the segmentALP1 andBET1inCartoonrepresentation and color theα- andβ-apoproteins in blue and purple respectively according to their segment names. You will then render the four pigments contained in the heterodimer in Licorice representation using various ways of coloring methods which allow you to color the carotenoid in yellow and color BChl B850a, B850b and B800 (resid 59,57 and 58) in red, green and pink, respectively, to
1UTOTIRALONEXCITATIONTRANSFER7
show their locations relative to each other. Finally, you will render the two proteins inSurfrepresentation and color them so that you can learn how they pack with each other and with the four pigments. Here is one way how to do this all.
1 Open VMD and load the LH-II coordinate lelh2.pdb.Open a terminal and change directory to the Excitation Transfer tutorial directory. tbss> cd/oriown.ssbtotutlairhp/k-otoxc-eatitil-f/1es Open a VMD session and load the LH-II coordinate lelh2.pdb. tbss> vmd lh2.pdb 2 Select theα-apoprotein with segment nameALP1to be displayed in the VMD OpenGL Window.In theSelected Atomstext entry of theGraphical Representation Window, delete the wordalland typesegname ALP1and then pressEnter.
3 Render theα-protein inCartoonrepresentation and color it in blue accord-ing to its segment name.In theDraw styletab of theGraphical Representa-tion Window, selectCartoonasDrawing MethodandSegnameasColoring Method. Theα-apoprotein should be colored in blue by default.
4 Reduce the distortion of the displayed protein due toPerspectiveviewing mode by changing it toOrthographic.In theVMD Main Menu Window, click the third pull-down menuDisplayand clickOrthographicin the second box. Orthographic mode renders three dimensional structure of the proteins by projecting them normally onto the screen.
5 Make a new representation and select theβ-apoprotein with segment name BET1.In theGraphical Representation Window, clickCreate Repto cre-ate a new representation. In theSelected Atomstext entry, deleteALP1and typeBET1and then pressEnter sure that the. Makeβ-apoprotein is drawn in Cartoonrepresentation.
6 Color theβpurple according to its segment name.-apoprotein in In theVMD Main Window, click the third pull down menuGraphicsand select the second optionColorsto open aColor Controls Window the rst column. InCate-goriesof theColor Controls Window, scroll down and clickSegname. In the second columnNames, clickBET1. In the third columnColors, select11 purple. Q1: What is the main secondary structure ofα- andβ-apoproteins?
7 Change the drawing method for the two proteins toSurfrepresentation to see how both proteins are packed with each other.NOTE: Surface rendering may take a-little while.
NOITNARTXENOATICTOTUALRI18SFERentationewrepresrCaeetnageaNem11inrdoSgtemthcoaccdnaroloatnenoitpresonreartostoCetnipoorehwtoftrodthMengwiraeDthegnahC01edneehtrretnR21.nLaiorichlBC50B8maBeACa1ytepesng9.PressEndresid5eled,yrtnetxetsmndsardwoheltalteoi.ntntaeresrwpedAtoecteeSelInthndWi,cowcklieaCreRetcotptaerenaeyed.IntheGraphiclaeRrpseneatitnoA1BCmenaidesdRanot95DIeualpsidebelecandsBChltthewati8B05emtnshgegoteesrithofoleCehtntsrulocaCnm,scrolldownandclrooCtnorsliWdnwocondcosemeNamnluahCnokciehtnI.nidcolthirolorumnCciok,slctnehXnI.itirderndnanolocntseioatericreeptnehrDwaahniDII.ngtoitsCac-cordigniwarDsaecirocitLecel,sabetylstdoI.eMhtirgnoColinasdChaodanMeth1Red.
NOTE: To delete the labels of atoms and distances on theVMD OpenGL Display, ClickGraphicsin theVMD Main Windowand selectLabels. SelectAtomsto see a list of atom labels. Select atom names, then clickDelete. SelectBondsto see a list of distance labels. Select pairs of atom names, then clickDelete.
You can see thatα- andβ-apoproteins are transmembrane proteins which consist mainly ofα also might have -helices. Younoticed that there is sufcient space in the middle of the heterodimer to accommodate 3 BChls and 1 carotenoid molecule. Now, let’s have a look at how pigments are arranged in the heterodimer.
s,select
9 Change theDrawing Methodfor the two proteins toTracerepresentation and useBondslabelling to measure the distance between the transmem-brane helices on theα- andβ-apoproteins.To useBondsLlabelling, click Mousein theVMD MainWindow. Then click and holdLabeland selectBonds 2. The mouse arrow should change to a cross sign +. This will provide a sep-aration distance of any two atoms you click. A quick and easy way to use this BondsLabelling is to press the button2on your keyboard. Q4: What is the approximate distance between the transmembrane helices ofα- and β-apoproteins?
Q5: Can you show that the N-terminals of both proteins are on the same side of the membrane while their C-terminals are on the other side.
Q2: Where doα- andβ-apoproteins make contact with each other?
8 Change the coloring method for the two proteins toResTypeto see how polar and non-polar residues are distributed on the two proteins. Q3: Can you tell thatα- orβ-apoproteins are transmembrane proteins?
1TUTORIALNOXEICATITONTRANSFER9
13 Create a new representation and select the BChl B850b with segment name BCA1 and residue ID 57 to be displayed.
14 Render the BChl B850b inLicorice representationand color it in green according to itsResidue Type.In theDraw style tab, selectLicoriceas Drawing MethodandResTypeasColoring Method. In the rst columnCat-egoriesof theColor Controls Window, scroll down and click onResType. In the second columnNames, click onUnassigned. In the third columnColors, select7 green. 15 Create a new representation and select the BChls B800 with segment name BCA1 and Residue ID 58 to be displayed.
16 Render the BChl B800 inLicorice representationand color it in pink ac-cording to itsResidue Name.In theDraw style tab, selectLicoriceas Drawing MethodandResNameasColoring Method. In the rst columnCat-egoriesof theColor Controls Window, scroll down and click onResname. In the second columnNames, click onBCA. In the third columnColors, select 9 pink. 17 Create a new representation and select the Carotenoid with segment name LYC1 to be displayed.
18 Render the Carotenoid inLicorice representationand color it in yellow according to itsResidue Name.In theDraw style tab, selectLicoriceas Drawing MethodandResNameasColoring Method. In the rst columnCat-egoriesof theColor Controls Window, scroll down and click onResname. In the second columnNames, click onLYC. In the third columnColors, select 4 yellow. 19 Create another representation and select the three magnesium ions in the segment name BCA1 to be displayed.In theGraphical Representation Win-dow, clickCreate Repto create a new representation. In theSelected Atoms text entry, delete all the words in the entry and typename MG and segname BCA1and then pressEnter. 20 Render the three magnesium ions on the BChls inVDW representation and color them in white according to atom name.In theDraw style tab, selectVDWasDrawing MethodandNameasColoring Method. In the rst columnCategoriesof theColor Controls Window, scroll down and click on Name the second column. InNames, click onM. In the third columnColors select8 white. Your LH-II structural unit should look like what is shown in Figure2except that your BChls are rendered in their full chemical structure.
21 Use theBondsLabelling to measure the distances between BChls.
1UTOTIRLANOXECITATIONTRANSFER01
Q6: What are the distances between (1) BChls B850a and B850b; (2) BChls B850a and B800; (3) BChls B850b and B800?
22 Change theDrawing Methodfor the two proteins toVDWrepresentation and color them according to Residue Type. Q7: What are the polar protein residues which make close contact with the three BChls?
You can see that the BChls B850a (red), B850b (green) and the carotenoid (yellow) are packed in the space between theα- andβ-apoproteins (blue and purple) while BChl B800 make a contact to the N-terminal helix of theα-apoprotein. It can be seen that there are two histidine side chains: one (αHis34) contacta BChl B850a and the other (βHis35) contacts BChl B850b. 800 (pink) is coordinated by an aspar- BChl tate (αAsp6). A very important is how two of these building blocks assemble together. Experimentally, it has been shown that these proteins actively self-assemble into LH-II.
23 Before you proceed to the next subsection, save your work as a VMD state my-lh2-unit.vmdand delete the LH-II unit system.From theVMD Main Window, clickFileand then selectSave State. Typemy-lh2-unit.vmd and clickOK. In theVMD Main Window, highlightlh2.pdb. ClickMolecule and then selectDelete Molecule.
1.2.2 Packing of two LH-II structural units In this section, you will study two LH-II structural units from a VMD state prepared by us. You will then investigate the packing of proteins and pigments between them.
24 Load the VMD stateTwoDimer.vmdof two LH-II structural units.In the VMD Main Window, clickFileand then selectLoad Stateto open a le se-lection window. ClickTwoDimer.vmdand then clickOK. You should see two copies of the LH-II structural unit which you rendered in the previous section (see Figure3 the tails and ). Allbranches of the BChls have been removed to make it easier for viewing the system. 25 Change the drawing method for all the proteins toSurfrepresentation. Take a look at the system particularly at the interface between two proteins to see how they pack. Q1: How well do the twoαpack with each other? How about the packing-apoproteins between the twoβ-apoproteins?
26 Now render all the proteins inTracerepresentation.
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TUTORIAL ON EXCITATION TRANSFER
Figure 3: Packing of two LH-II structural units.
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Q2: What is the distance in  A (1) between twoα-apoproteins; (2) between twoβ-apoproteins?
27 Hide all the proteins and carotenoids.
Q3: What is the distance in  A between (1) two BChls B850a (red); (2) two BChls B850b (green); (3) BChls B850a (red, BCA1) and B850b’(green, BCA2) ; (4) B800 (pink, BCA1) and B850b’; (5) B800 and B850a’ (red, BCA2)?
It can be seen that the transmembrane helices of theα-apoproteins are packed closely while the transmembrane helices of theβ-apoproteins make very little contact with each other. The termini of both proteins also make extensive contact with each other.