ryr1

For an overview on the ryanodine receptor (RyR1) being a Ca+2 channel that facilitates skeletal muscle excitation and contraction, we can refer to this paper.

Excellent reviews on ryanodine receptors (RYRs) , dihydropyridine receptors (DHPRs) and Disease-causing mutations of calcium channels.

In this project, we are calculating the energy landscapes using Multi-Conformer Continuum Electrostatics (MCCE). Calculations are done with two datasets. One set involves the RyR1 macromolecules in equilibrium with a thermal bath sans the activation of ligands; the other involves the RyR1 macromolecules in equilibrium with both a thermal bath as well as a reservoir of the activated ligands calcium, ATP, and caffeine.

testing/ligand_binding_sites:

These PDB files were prepared by Danya Ben Hail. There are 50 files labeled frame_01 to frame_50. The structure of this data set is modified such that only the activation core is calculated. Each frame_0i directory contains an input pdb, here highlighted in blue.

Activation core top view	Activation core side view

Figure 1: Activation core (PDBID: 5t9r). Residues B3614-B5102 The generated output files are titled head3.lst and fort.38.

All 50 frames

Figure 2: Binding energy (kCal/mol) data between Ca+2 and the activation core of ryr1

Note: special thanks to Ashley Roberts who helped me edit some of the work in here.