Light. Structure-Function Relationship of Retinal Proteins. Retinal Proteins -- Rhodopsins. Structure of Retinal Proteins [H + ]

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1 Structure-Function Relationship of Retinal Proteins Structure of Retinal Proteins A B D E F G GPRs Retinal proteins or rhodopsins belong to the superfamily of seventransmembrane helical (7TM) proteins. Seven, with -terminus on the extracellular side and -terminus on the cytoplasmic side of the membrane (not necessarily G-protein coupled) Retinal Proteins -- Rhodopsins Bacteriorhodopsin -- br The simplest ion pump in biology The simplest photosynthetic center The best characterized membrane protein Technological applications in molecular electronics hromophore ovalently linked to a lysine Usually protonated Schiff base all-trans and 11-cis isomers The first membrane protein with a known atomic-detail 3D structures br role in Bioenergetics alobacterium Salinarum Light Schematic proton path in bacteriorhodopsin ytoplasmic side Asp 96 The Purple mbrane [ ] ytoplasmic side ADP ATP hv ATP Synthase Water Proton Gradient [ ] Arg 82

2 Active hannels eed a Switch chanism Photocycle of br Photo-induced 1 µs What is the switch in br? ow does it work? 40 µs All intermediates are trapped in low temperature and have been characterized by vibrational and absorption spectroscopy. o membrane protein has been studied as extensively as br Photo-induced Schematic proton path in bacteriorhodopsin hv ytoplasmic side Asp 96 1 µs Water 40 µs All intermediates have also been characterized by X-ray crystallography! Arg 82 -D96 -D96 br 568 BR s Photocycle BR s Photocycle D85- D85- cytoplasmic -E204 -E K D96 -D96 -D96 br 568 K 603 -D96 D85- D85- D85- D85- -E204 -E204 -E204 -E204 1µs 1µs -D96 -D96 -D96 -D96 D85- -E204 D85- -E204 D85- -E204 D85- -E204 extracellular 550 -D96 L µs 550 -D96 L µs light driven proton pump D85- -E204 M 410 onformational hange of elices Kuhlbarandt, ature, 406,569 (2000) D85- -E204 M 410

3 Study of br at three levels Retinoids yhromophore Analysis of the structure alculation of excited state dynamics yprotein hromophore-protein interaction QM-MM calculations MD simulation of the photocycle Retinal Schiff base mbrane, covalently bound, chromophore Retinal ybr in the purple membrane Modeling of the protein in lipid bilayers Retinoic Acid ucleus, receptor site, ligand (no photoactivity) Unconventioanl chemistry Effect of onjugation on pk a (Gas Phase Proton Affinity) The necessity of quantum mechanical treatment of the chromophore: onjugated π-electronic system, delocalization The effect of protein matrix on the ligand QM is expensive Most of the time, one needs to use models PA* PA*(zpe) PA** PA**(zpe) o. of conjugated double bonds syn anti PA= E A -(E A E ) Effect of the methyl groups on pk a What is the effect of isomerization? Species 6-31G* 6-31G* (zpe) 6-31G** 6-31G** (zpe) PSB6 4-met met met met cis-met trans-met B1 2 B3 4 B B2 B4 B6 -met ,8-dimet ,12-dimet ,4,8-trimet ,8,12,12-tetramet PA= E A -(E A E ),4,8,12,12-pentamet met-retinal Schiff base o more room for additional methyl groups on the backbone

4 Isomerization State and Proton Affinity 255 What is the effect of isomerization? cc ct tc tt syn anti o. of conjugated double bonds cc: B2,B3-di-cis isomer tc: B2-strans, B3-cis isomer ct: B2-s-cis, B3-trans isomer tt: all-trans isomer. PA= E A -(E A E ) Isomerization does not have a strong impact on PA! Retinal binding pocket in br Effect of the environment on PA ounterion: Asp85 & Asp212 Water λ max : ~ psin shift pk a : ~ ε acetate SB SB SB SB SB SB Water WATER PMET RSB PA= E A -(E A E ) In situ isomerization and pk a 290 oupling of electronic excitation and conformational change in br 280 PSB3 PSB4 S 1 S Dielectric onstant ε=6.0 BR K = 14 -trans 13 = 14 -cis ε=2.0 Asp

5 Ground and Excited State Potential Energy Surfaces of Retinal Ab Initio QM/MM Excited State MD Simulation QM trans cis Quantum mechanical (QM) treatment of the chromophore, and force field (MM) treatment of the embedding protein Isomerization Barriers in retinal B B2 B4 B1 B3 B5 PA= E A -(E A E ) A twisted chromophore in br? PA (kcal/mole) all-trans B1-90 B2-90 B3-90 B4-90 B5-90 B6-90 Rotated bond Low barriers against double bond isomerization B7-90 B8-90 B9-90 B10-90 Ground state isomerization 177 A twisted chromophore is also experimentally reported. X-ray structures of br report the twisted form of chromophore The twist is found around the terminal double bonds It may influence pk a of the chromophore