Uncovering channels in photosystem II by computer modelling: current progress, future prospects, and lessons from analogous systems.
Even prior to the publication of the crystal structures for photosystem II (PSII), it had already been suggested that water, O(2) and H(+) channels exist in PSII to achieve directed transport of these molecules, and to avoid undesirable side reactions. Computational efforts to uncover these channels and investigate their properties are still at early stages, and have so far only been based on the static PSII structure. The rationale behind the proposals for such channels and the computer modelling studies thus far are reviewed here. The need to take the dynamic protein into account is then highlighted with reference to the specific issues and techniques applicable to the simulation of each of the three channels. In particular, lessons are drawn from simulation studies on other protein systems containing similar channels.
Ho
Felix M
FM
Department of Photochemistry and Molecular Science, The Angström Laboratory, Uppsala University, Uppsala, Sweden. Felix.Ho@fotomol.uu.se
D020346:Aquaporins / Q000378:metabolism*; D003198:Computer Simulation; D003460:Crystallization; D008954:Models, Biological; D010100:Oxygen / Q000378:metabolism*; D045332:Photosystem II Protein Complex / Q000378:metabolism*; D011487:Protein Conformation; D017494:Proton Pumps / Q000378:metabolism; D014867:Water / Q000378:metabolism*
D020346:Aquaporins; D045332:Photosystem II Protein Complex; D017494:Proton Pumps; D014867:Water; D010100:Oxygen
Biophys J. 2004 Jan;86(1 Pt 1):50-7
14695248
Biochim Biophys Acta. 2008 Feb;1777(2):196-201
18155154
Philos Trans R Soc Lond B Biol Sci. 2002 Oct 29;357(1426):1421-30; discussion 1469-70
12437881
Biochemistry. 2007 Jul 3;46(26):7865-74
17559194
Biochemistry. 2000 Apr 18;39(15):4399-405
10757989
Biochemistry. 1992 Dec 8;31(48):12204-10
1457417
Biochim Biophys Acta. 2006 Aug;1757(8):886-912
16934216
Coord Chem Rev. 2008 Feb;252(3-4):395-415
19190716
Biochim Biophys Acta. 2004 Apr 12;1655(1-3):123-32
15100024
Biochim Biophys Acta. 2004 Apr 12;1655(1-3):13-28
15100012
Philos Trans R Soc Lond B Biol Sci. 2008 Mar 27;363(1494):1229-34; discussion 1234-5
17954434
FEBS Lett. 2001 Aug 31;504(3):212-8
11532456
Nature. 2005 Dec 15;438(7070):1040-4
16355230
Science. 1998 Jun 12;280(5370):1723-9
9624044
J Biol Chem. 2007 Jun 15;282(24):17767-76
17409383
Biochemistry. 2000 Jul 11;39(27):7863-7
10891065
Biochim Biophys Acta. 2003 Jun 5;1604(2):61-5
12765763
Biochemistry. 2005 Jun 21;44(24):8817-25
15952788
Biochim Biophys Acta. 2003 Aug 18;1605(1-3):1-13
12907296
J Mol Biol. 2002 Aug 9;321(2):329-39
12144789
J Mol Biol. 2004 Oct 15;343(2):493-510
15451676
Chem Rev. 2006 Nov;106(11):4455-83
17091926
Philos Trans R Soc Lond B Biol Sci. 2008 Mar 27;363(1494):1149-56; discussion 1156
17971333
J Mol Biol. 2003 Oct 17;333(2):279-93
14529616
Biochem Soc Trans. 2005 Feb;33(Pt 1):80-2
15667271
Biophys J. 2006 May 1;90(9):3062-73
16461403
Biochim Biophys Acta. 2008 Feb;1777(2):140-53
17964532
Science. 2001 Dec 14;294(5550):2353-7
11743202
Biochemistry. 2002 May 7;41(18):5830-43
11980487
Science. 2004 Mar 19;303(5665):1831-8
14764885
Biochemistry. 1996 Oct 8;35(40):13089-93
8855945
Nature. 2001 Dec 20-27;414(6866):872-8
11780053
Biochemistry. 2006 Apr 4;45(13):4128-30
16566586
FEBS Lett. 2001 Jan 12;488(1-2):1-4
11163784
J Mol Biol. 2003 Mar 7;326(5):1635-50
12595270
Nature. 2000 Oct 5;407(6804):599-605
11034202
Biochemistry. 1998 Aug 18;37(33):11405-11
9708975
Biochemistry. 2002 Nov 5;41(44):13328-34
12403635
Photosynth Res. 1993 Jan;38(3):279-96
24317981
FEBS Lett. 1991 Jul 29;286(1-2):209-13
1864370
Biochim Biophys Acta. 2006 Aug;1757(8):1052-63
16824482
Biochemistry. 2000 Jun 13;39(23):6756-62
10841754
Philos Trans R Soc Lond B Biol Sci. 2002 Oct 29;357(1426):1383-94; discussion 1394, 1419-20
12437877
Science. 2002 Apr 19;296(5567):525-30
11964478
Proc Natl Acad Sci U S A. 1999 May 25;96(11):6183-8
10339562
Biophys J. 2003 Dec;85(6):3696-706
14645061
FEBS Lett. 1990 Dec 17;277(1-2):69-74
2176622
J Phys Chem B. 2008 Jan 17;112(2):467-82
17999484
Annu Rev Biochem. 2006;75:165-87
16756489
Nature. 2001 Nov 8;414(6860):188-90
11700553
Biochemistry. 2005 Feb 8;44(5):1708-18
15683255
Biochemistry. 1999 Feb 2;38(5):1582-8
9931025
Proc Natl Acad Sci U S A. 1992 Feb 15;89(4):1408-12
11607279
J Phys Chem B. 2007 May 3;111(17):4300-14
17429993
Biochemistry. 2003 May 27;42(20):6209-17
12755624
Biochim Biophys Acta. 2001 Jan 5;1503(1-2):246-59
11115637
Proc Natl Acad Sci U S A. 2004 Aug 10;101(32):11617-21
15289603
Biochim Biophys Acta. 2004 Apr 12;1655(1-3):241-7
15100038
Trends Biochem Sci. 2001 Jun;26(6):341-4
11406392
Biochim Biophys Acta. 2008 Jun;1777(6):525-31
18452701
J Struct Biol. 2007 Aug;159(2):228-37
17369049
Biochim Biophys Acta. 2007 Oct;1767(10):1200-14
17689487
Photochem Photobiol Sci. 2005 Dec;4(12):940-9
16307106
Biochemistry. 2004 Jul 13;43(27):8607-15
15236568
Biochemistry. 2002 Nov 12;41(45):13417-23
12416987
Annu Rev Physiol. 2004;66:665-88
14977418
Science. 1995 Aug 25;269(5227):1069-74
7652554
Biophys J. 2001 Aug;81(2):715-24
11463620
Biochemistry. 1989 Nov 28;28(24):9459-64
2558720
BMC Bioinformatics. 2006 Jun 22;7:316
16792811
Proteins. 2004 May 1;55(2):223-8
15048815
Nat Struct Biol. 2002 Sep;9(9):646-52
12198485
J Biol Chem. 2001 Dec 14;276(50):46917-24
11595731
Photochem Photobiol Sci. 2005 Dec;4(12):950-6
16307107
Proc Natl Acad Sci U S A. 1995 Apr 11;92(8):3209-13
11607525
Biochim Biophys Acta. 2006 Aug;1757(8):876-85
16414007
Science. 1991 Aug 23;253(5022):872-9
1678899
Proteins. 2005 Feb 15;58(3):528-37
15609339
Curr Opin Struct Biol. 2007 Apr;17(2):173-80
17395452
Biophys J. 2004 Apr;86(4):1873-89
15041635
J Biol Chem. 2005 Jun 24;280(25):23791-6
15849358
J Biol Chem. 2008 May 9;283(19):13330-40
18332136
Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15304-9
14673090
Biochemistry. 2008 May 13;47(19):5368-77
18410129
Biochemistry. 2006 Feb 21;45(7):2063-71
16475795
Biochemistry. 1989 Nov 14;28(23):8984-9
2557913
Proc Natl Acad Sci U S A. 1998 Aug 4;95(16):9280-3
9689071
Science. 1996 May 24;272(5265):1136-44
8638158
Proc Natl Acad Sci U S A. 2002 May 14;99(10):6731-6
11997475
Biochemistry. 1998 Dec 1;37(48):16908-14
9836583
Photosynth Res. 2004;81(3):329-43
16034536
Biochim Biophys Acta. 2002 Oct 11;1565(2):144-67
12409192
Biochemistry. 2007 Oct 30;46(43):11987-97
17915952
FEBS Lett. 2005 Apr 11;579(10):2026-34
15811313
Curr Opin Struct Biol. 2005 Apr;15(2):176-83
15837176
Proc Natl Acad Sci U S A. 2007 Aug 14;104(33):13319-24
17675410
Biochim Biophys Acta. 2007 Jan;1767(1):79-87
17123463
Biochim Biophys Acta. 2006 Aug;1757(8):942-68
16905113
J Am Chem Soc. 2008 Mar 19;130(11):3428-42
18290643
Phys Biol. 2004 Jun;1(1-2):42-52
16204821
Structure. 2004 Aug;12(8):1343-51
15296727
Proc Natl Acad Sci U S A. 2005 Jul 26;102(30):10478-81
16014708
Chem Rev. 2007 Nov;107(11):5004-64
17999556
Biochim Biophys Acta. 2006 Aug;1757(8):1012-8
16376293
Proc Natl Acad Sci U S A. 2005 May 10;102(19):6795-800
15857953
Acc Chem Res. 2002 Jun;35(6):332-40
12069617
Nature. 2001 Feb 8;409(6821):739-43
11217865
Biochim Biophys Acta. 2006 Jul;1757(7):852-9
16815239
Structure. 2005 Sep;13(9):1321-9
16154089
Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6500-5
16614069
Biochim Biophys Acta. 2007 Sep;1767(9):1102-6
17706938
Biochim Biophys Acta. 2007 Mar;1767(3):244-60
17350588
Curr Opin Struct Biol. 2006 Aug;16(4):465-72
16842995
Biochim Biophys Acta. 2004 Feb 15;1608(2-3):171-80
14871495
FEBS Lett. 1999 Dec 17;463(3):199-204
10606721
Biophys J. 2007 Nov 15;93(10):3591-600
17693478
Biophys J. 2006 Sep 1;91(5):1844-57
16751246
Biochim Biophys Acta. 1996 Jul 18;1275(1-2):1-4
8688439
J Am Chem Soc. 2007 Mar 14;129(10):2910-3
17309257
Trends Biochem Sci. 1989 Jun;14(6):227-32
2669240
Proteins. 1998 Jan;30(1):100-7
9443344
Biochemistry. 1999 Jun 29;38(26):8189-95
10387064
Biochemistry. 1986 Jan 14;25(1):125-30
3954986
J Chem Theory Comput. 2006 Jul;2(4):1119-34
26633071
Structure. 2004 Jan;12(1):65-74
14725766
Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15543-7
14676323
Structure. 2007 Nov;15(11):1357-63
17997961
Biochim Biophys Acta. 2004 Jun 7;1656(2-3):189-202
15178480
Biochemistry. 1991 May 14;30(19):4734-9
1851435