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5 Modelling Nucleic Acids 1235.12 MD of the Anticodon Hairpin withImplicit Solvent TreatmentSeveral molecular dynamics simulations were performed on the anticodon stem (i. e.the five base pair helix with the seven residues loop) of the yeast tRNA-asp undervarious conditions (Rubin-Carrez and Westhof, in preparation). Without counterions(Figure 5-12), the use of dielectric functions equal to r or to 4r leads a completeloss of anticodon-like conformation of the loop in which the bases splay apart andpoint independently toward the solvent. At the same time, there is a strong unwindingof the helix. With the sigmoidal dielectric function, the system evolves to aglobular and compact state in which the sugar-phosphate backbone of the loop foldsback on the deep an narrow groove of the helix. Whatever the dielectric function,the addition of counterions accelerates this phenomenum of molecular collapse bybridging the phosphate groups of the 5’-helical strand and the 3’-end of the loop.What are the origins of this molecular contraction? RNA helices are characterizedby a deep and narrow groove with a shallow and large groove corresponding,respectively, to the large and minor grooves of the B-DNA helix. This geometricaldifference arises from the displacement of the base pairs away from the helical axisand toward the minor groove side. Such a movement fills in the minor groove anddeepens the major groove sides, leading to an asymmetric distribution of matter,especially in a helix with less than one turn. In the simulations performed, it is apparentthat the weakest electrostatic dampening (E = r) leads to the least dramaticresults, emphasizing the fact that electrostatic repulsion keeps the strands apart insuch simulations, but without warranting realistic dynamic behaviors. Or, in otherwords, implicit treatment of the screening of electrostatic repulsions by the solventgives too much weigth to the van der Waals attraction and leads to a globularmolecule in the absence of the space-filling property of bulk solvent.5.13 MD of the Anticodon Hairpin withExplicit Solvent TreatmentEven in aqueous solutions, simulations of the anticodon hairpin lead to severedistortions of the helical parameters. It should be reminded, however, that the sequenceof the anticodon helix contains a wobble G-U base pair which forms theepicentre of distortion. Also, the helix is only 5 base pairs, barely half a helical turn,and this could be responsible for artefactual values. The most deviant globalparameters (with respect to the helical axis) are the inclination and the tip, i.e. the
124 E. Westhof; C. Rubin-Carrez, and K Fritsch(a)E=rT=300K(c)E = mT=300KFigure 5-12. Stereo views of the anticodon hairpin after 50 ps of MD simulation in V~CUOwith different dielectric functions. (From Rubin-Carrez [67]).
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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 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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40 D. J; Osnuthorue and I? K. C. Pa
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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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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
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Page 152 and 153: 142 Benoft RouxTable 6-1. Interacti
Page 154 and 155: 144 Benoit RouxFigure 6-2. Solvated
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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
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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 HistocompatibiIity Complex
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7 Maior Histocompatibility Complex
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7 Major Histocompatibility Complex
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7 Maior Histocomuatibilitv Cornulex
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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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