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148 Benoit Roux-I I I I II I I I II’I I I I-110II I I I I10-11I I I I II I-:;I0-110-10 20 40 60 80 100t In ps-v-4I- L ,II 0-I 4RelativeProbabilityFigure 6-3. Projection of the water orientation vector along the channel axis as a function oftime during the simulation. The ordering corresponds to: number 1 is a mouth water;number 2 to 11 are the 10 waters inside the channel, (number 6 and 7 are at the inter-monomerjunction); number 12 is a bulk water included for comparison. Water number 2 is hydrogenbonded with ethanolamine of monomer 1 which undergo a conformational change at 25 psand shows an increase in fluctuations compared to water number 11, the equivalent entrancewater of monomer 2.I
6 Theory of Transport in Ion Channels 149waters, consistent with the dimer symmetry. Such differences may be due to severalfactors: Firstly, it has been observed that the structure and dynamics of the internalwater is very sensitive to the flexibility of the channel [32]; secondly, it may be thatthe dynamics and structure of the internal waters depends on detailed aspects of thepotential function, in particular those representing the hydrogen bonding interaction.6.3.2.4 Rare Events : Ethanolamine Tail IsomerizationObservation of rare events in a simulation, even though they are not statisticallysignificant, can give useful information. During the 100 ps trajectory, the ethanolaminetail of one of the monomers changed its conformation (the ethanol is locatedat x = + 1.4 nm and is labeled residue + 16). As can be seen in Figure 6-4, the transitionsof the three dihedral angles take place in a concerted fashion. The changes inthe successive dihedral angles are anticorrelated along the ethanolamine tail. Thiscan be observed clearly for the major transition at 25 ps and, to a lesser degree,around 50 ps for the second transition of the angle ty. The anticorrelation is relatedto the fact that the transition takes place without large and sudden displacements ofthe 0 - H group at the end of the tail [78]. The hydrogen bond with the entrancewater is lost in the time interval from 20 to 25 ps (see water 2 in Figure 6-3). Thelatter shows an increase in fluctuations compared to the water at the other entrance(water 11) which does not lose its ethanolamine hydrogen bond. From 25 to 50 psthe ethanolamine hydrogen bonds alternately to the three mouth waters and the twor 360 300 180r---12040030050 -P'CI 0 -.-L".ran -120 .-"-10 10 30 50 70 SO 110 -10 10 30 50 70 SO 110t in pat in paE *0°8:u 100c-r.x o-1 00-200 ..-10 10 30 50 70 SO 110t in psFigure 6-4. Dihedral angle transitions of the ethanolamine of monomer 1, ( -CNC,CBOH).The angles are defined as CN%,CB, NC,%BO and C,CDYOH.
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Computer Modellingin Molecular Biol
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Professor Julia M. GoodfellowDepart
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ContentsColour Illustrations ......
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XContributorsBenoit RouxGroupe de R
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Colour IllustrationsXI11Figure 4-4.
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XVIColour IllustrationsFigure 7-18.
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2 Julia M. Goodfellow and Mark A. W
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Computer Modelling in Molecular Bio
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2 Modellinn Protein Structures 11su
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2 Modelling Protein Structures 13St
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2 Modelling Protein Structures 15Th
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2 Modelling Protein Structures 17Th
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2 Modelling Protein Structures 19Fa
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2 Modellinn Protein Structures 21th
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2 Modelling Protein Structures 23ho
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2 Modelling Protein Structures 25Wo
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2 Modelling Protein Structures 271.
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2.3.3 Available Modelling Programs2
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2 Modelling Protein Structures 31sp
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2 Modellina Protein Structures 33Ac
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2 Modelling Protein Structures 35[8
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38 D. J Osmthorue and I? K. C Paul3
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~443.3.1D. J. Osnuthorpe and I? K.
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Computer Modelling in Molecular Bio
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4 Molecular Dynamics and Free Energ
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4 Molecular Dvnamics and Free Enera
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4 Molecular Dynamics and Free Enerw
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4 Molecular Dynamics and Free Enern
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Page 144 and 145: 134 Benoft Roux6.1 IntroductionThe
Page 146 and 147: 136 Benoit Roux[18-201. The gramici
Page 148 and 149: 138 Benoft Rouxwhere D (x) is the l
Page 150 and 151: 140 Benoft Roux“one-ion” conduc
Page 152 and 153: 142 Benoft RouxTable 6-1. Interacti
Page 154 and 155: 144 Benoit RouxFigure 6-2. Solvated
Page 156 and 157: 146 Benoit Rouxwater box equilibrat
Page 160 and 161: 150 Benoi’t Rouxbulk waters. A st
Page 162 and 163: 152 Benoit RouxOne advantage of thi
Page 164 and 165: 154 Benoft Roux-.3.-15-c 10 -h5 5 -
Page 166 and 167: 156 Benoft Rouxwhere x and v are th
Page 168 and 169: 158 Benoit RouxReactant to ProductO
Page 170 and 171: 160 Benoit Rouxremain in close cont
Page 172 and 173: 162 Benoit Rouxis the deviation of
Page 174 and 175: 164 Benoft RouxTable 6-3. Pre-expon
Page 176 and 177: 166 Benoft RouxThis chapter demonst
Page 178 and 179: 168 Benoft Rouxproximately one Kf c
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7 Major Histocompatibility Complex
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HLA-B*270 IHLA-B*2702HLA-B*2703HLA-
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7 Maior Histocomvatibilitv Comrdex
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216 Oliver S. Smart8.1 Introduction
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218 Oliver S. Smartvolving large mo
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220 Oliver S. Smart8.2 TheoryConsid
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222 Oliver S. Smart(8-2)and applyin
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224 Oliver S. SmartThe repulsion te
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226 Oliver S. Smart8.4 Applications
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228 Oliver S. Smartrigid-body penal
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230 Oliver S. Smart216 252 200 324
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232 Oliver S. SmartrbFigure 8-5. A
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234 Oliver S. Smartlink the eoc and
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236 Oliver S. Smarttermediates mark
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238 Oliver S. Smartmoving conformat
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240 Oliver S. Smart[39] Halgren, T.
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242 IndexGGramicidin A 134- NMR dat
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