Molecular Dynamics of AChBP: Water in the Binding Pocket

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Molecular Dynamics of AChBP Water in the
Binding Pocket

• Shiva Amiri
• http//sbcb.bioch.ox.ac.uk/amiri.php
• Biophysical Society Annual Meeting, February, 2006

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AChBP nAChR Ligand Binding Domain Homologue

• a ligand gated ion channel (LGIC) found in
  central and peripheral nervous system
• mutations lead to various diseases such as
  epilepsy, myasthenic syndromes, etc.
• implicated in Alzheimers disease and Parkinsons
  disease
• mediates nicotine addiction

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• Studying the behaviour of the binding pocket in
  the presence
• and absence of ligands
• 1. The structure of the binding pocket
  (distances, dihedrals, structural integrity)
• 2. The role of water in the binding of ligand to
  the binding site

Loop F
Loop C
Loop E
Loop D
CYS Loop
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Molecular Dynamics

• Molecular Dynamics (MD) simulations of AChBP
  using GROMACS (GROMOS96)
• Focus on structural changes and ligand/protein
  interactions in the binding pocket

• Describe the forces on all atoms
• bonded (bonds, angles, dihedrals)
• non-bonded (van der Waals, electrostatics)
• Result positions of all atoms during a few
  nanoseconds

Simulation PDB code Ligand?
NCT 1UW6 Nicotine
NCT-Apo 1UW6 -
CCE 1UV6 Carbamylcholine
CCE-Apo 1UV6 -
All simulations were run for 10 ns
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Global Motions
1UW6 without Nicotine
1UV6 without Carbamylcholine
1UW6 with Nicotine
MSF (Å)
0.6 0.8 1 1.2
1.4
1UV6 with Carbamylcholine
0 2
4 6
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Time (ns)

• Simulations with ligands have lower mean square
  fluctuation (MSF) values than those without
  ligand
• 10 ns is not enough to see the full range of
  motions involved in the function of the receptor
  (ie. channel gating)

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Binding Pocket Motions

• Several atoms involved in the binding of the
  ligand were used to carry out RMSD calculations

• The residues of the binding pocket are more
  constrained in the presence of a ligand

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Persistent Waters
Time-averaged water density plots for AChBP with
Carbamylcholine bound

• Higher density of water molecules in the
  binding sites of ligand bound AChBP

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Persistent Waters

• Several zones identified in the binding site
  where water molecules persist for gt 40 of the
  duration of the simulation

ZONE Average for NCT Average for CCE
1 92 92.5
2 45 79.5
3 40 89.5
4 60 76
5 55 50
Zone 1
Zone 2
Zone 4
Water densities in the binding site
Zone 5
Zone 3
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Water molecules which remain in their position in
the binding pocket with Nicotine bound
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Bridging Waters

• Ligand-protein interactions via water
  molecules in the binding site
• Many of these waters remain for gt40 (some gt
  90) of the simulation, suggesting functional
  importance

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Bridging Waters
Waters Between LEU103 and MET115

• Following waters in one of the zones of
  persistent waters.
• - A water situated between LEU103 and MET115
  leaves the site and is instantly replaced by
  another water molecule
• - When both waters are gone, the space between
  the two residues is decreased and the
  interactions with the ligand are affected
  (decreased)

Time (ns)
Distance between LEU103 and MET115 on loop E
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Conclusions

• AChBP has greater global flexibility in the
  non-ligand bound state
• - the binding of a ligand adds structural
  integrity to the ion channel
• The binding pocket is less flexible in the
  presence of a ligand
• There are positionally conserved waters in the
  binding pocket, higher in quantity and more
  persistent in the presence of a ligand
• Several water molecules bridge the ligand to
  neighbouring residues in the binding site
• These waters plays a structural role in the
  binding pocket, adding rigidity that may extend
  beyond the binding site to functionally relevant
  loops

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Acknowledgements

• Prof. Mark S. P. Sansom
• Dr. Philip C. Biggin
• Dr. Alessandro Grottesi
• Dr. Kaihsu Tai
• Dr. Zara Sands
• Dr. Oliver Beckstein
• Dr. Jorge Pikunic
• Dr. Andy Hung
• Dr. Shozeb Haider
• Dr. Syma Khalid
• Dr. Pete Bond
• Dr. Kia Balali-Mood
• Dr. Hiunji Kim
• Dr. Martin Ulmschneider
• Dr. Daniele Bemporad
• Dr. Bing Wu
• Sundeep Deol
• Yalini Pathy

• Jennifer Johnston
• Katherine Cox
• Robert DRozario
• Jeff Campbell
• Loredana Vaccaro
• John Holyoake
• Tony Ivetac
• Samantha Kaye
• Sylvanna Ho
• Benjamin Hall
• Tim Carpenter
• Emi Psachoulia
• Chze Ling Wee
• Ranjit Vijayan
• Michael Kohl

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The Ligands

• Nicotine is less flexible in the binding
  pocket than carbamylcholine
• There seems to be one mode of binding for
  Nicotine

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Distances between residues in the BP
Carbamylcholine
Nicotine
Distance between CYS 188 and THR 145
Distance between CYS 188 and THR 145
APO Nicotine
APO Carbamylcholine
Distance between CYS 188 and THR 145
Distance between CYS 188 and THR 145
Time (ns)
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Loop C of AChBP (1UV6) With and Without
Carbamylcholine
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Carbamylcholine
Nicotine
Water molecule Residue 1 Residue 2 Number of occurences
SOL1256 MET 527 NCT 18814 1870
SOL7253 MET 527 NCT 18814 1342
SOL1078 MET 115 NCT 18817 1056
SOL1078 TRP 968 NCT 18817 620
SOL5732 NCT 18813 SER 143 308
SOL13378 NCT 18817 TRP 968 188
SOL1256 TRP 350 NCT 18814 147
SOL7253 TRP 350 NCT 18814 130
SOL17829 TYR 165 NCT 18817 100
SOL6834 NCT 18816 TRP 762 79
Water molecule Residue 1 Residue 2 Number of Occurences
SOL9297 MET 729 CCE 1026 2003
SOL14171 CCE 1027 TRP 758 1387
SOL14171 CCE 1027 TYR 807 1386
SOL1428 CCE 1026 TYR 602 580
SOL6702 CCE 1027 TRP 758 505
SOL1428 CCE 1026 TRP 553 429
SOL1428 CCE 1026 THR 554 403
SOL6702 CCE 1027 TYR 807 377
SOL11808 MET 934 CCE 1027 354
SOL16192 CCE 1027 TYR 807 315
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