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Distinct Binding Mechanisms for Allosteric Sodium Ion In Cannabinoid Receptors

final_MSM_obj.pkl

This file can be downloaded from https://uofi.box.com/s/n8a15pcabkh8fzd42hecxh2mkhz1fzh3. It contains optimal MSM object for CB1 and CB2.

bootstraping

This folder can be downloaded from https://uofi.box.com/s/n8a15pcabkh8fzd42hecxh2mkhz1fzh3. It contains 200 bootstrap samples for CB1 and CB2 and corresponding MSMs with same state index as reference MSM.

Figure_1

  • Figure_1.vmd: Visulazation states of CB1 and CB2 inactive structures as shown in Figure 1.

Figure_2

  • Figure_2C.vmd: Visulazation states of CB1 structures as shown in Figure 2C with orthosteric pocket volume.
  • Figure_2D.vmd: Visulazation states of CB2 structures as shown in Figure 2D with orthosteric pocket volume.

Figure_3

  • Figure_3A.vmd: Visulazation states of CB1 structures as shown in Figure 3A with Na+ bound in N-terminus.
  • Figure_3B.vmd: Visulazation states of CB2 structures as shown in Figure 3B with Na+ bound in ECL1
  • Figure_3C.py: Python code to generate box plot for Figure 3C
  • Figure_3D.py: Python code to generate box plot for Figure 3D

Figure_4

  • Figure_4A.py: python code to generate two dimentional free energy landscape as shown in Figure 4A
  • Figure_4B.py: python code to generate two dimentional free energy landscape as shown in Figure 4B
  • Figure_4C.vmd : Visulazation states of CB1 with Na+ in orthosteric binding pocket as shown in Figure 4C.
  • Figure_4D.vmd : Visulazation states of CB1 with Na+ in orthosteric binding pocket as shown in Figure 4D.

Figure_5

  • Figure_5A.py: python code to estimating MFPT calculations for CB1 as shown in Figure 5A
  • Figure_5B.py: python code to estimating MFPT calculations for CB2 as shown in Figure 5B
  • Figure_5C.vmd: Visulazation states of Na+ binding from orthosteric binding pocket to secondary Na+ binding as shown in Figure 5C.
  • Figure_5D.vmd: Visulazation states of Na+ binding from orthosteric binding pocket to primary Na+ binding as shown in Figure 5D.

Figure_6

  • Figure_6A.py: python code to generate two dimentional free energy landscape as shown in Figure 6A
  • Figure_6B.py: python code to generate two dimentional free energy landscape as shown in Figure 6B
  • Figure_6C.vmd, Figure_6D.vmd: Visulazation states of CB1 and CB2 structures with Y7.53 and N7.49 in different poses as shown in Figure 6C, 6D.

Figure_7

  • Figure_7.py: python code to calculate secondary pocket volume as shown in Figure 5A
  • Figure_7_CB1.vmd, Figure_7_CB2.vmd: Visulazation states of CB1 and CB2 structures with calculated secondary pocket volume as shown in inlet figures.

Figure_8

  • Figure_8A.py: python code to generate two dimentional free energy landscape as shown in Figure 8A
  • Figure_8B.py: python code to generate two dimentional free energy landscape as shown in Figure 8B -Visulazation states of CB1 and CB2 structures to depict sodium binding from intracellular direction as shown in Figure 8A, 8B.

##Videos

  • Extracellular binding video Na+ to CB1 structure (with truncated N-terminus): CB1_original_extracellular_binding.mpg
  • Intracellular binding video Na+ to CB1 structure (with truncated N-terminus): CB1_original_intracellular_binding.mpg
  • Extracellular binding video Na+ to CB2 structure (with truncated N-terminus): CB2_original_extracellular_binding.mpg
  • Extracellular binding video Na+ to CB1 structure (with fully modeled N-terminus): CB1_model_1.mpg
  • Extracellular binding video Na+ to CB1 structure (with fully modeled N-terminus): CB1_model_2.mpg
  • Extracellular binding video Na+ to CB2 structure (with fully modeled N-terminus): CB2_model_1.mpg

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