What is ProMode-Elastic
ProMode-Elastic is a database of normal mode analysis (NMA) of PDB data using a program PDBETA we have developed. PDBETA is a program of Elastic-network-model based normal mode analysis in Torsional Angle space for PDB data. PDBETA can describe molecular structures with relatively smaller number of degrees of freedom even in a full-atom model, and take into computation not only proteins but also DNA, RNA, and ligand molecules (hydrogen atoms and water molecules are excluded currently to suppress the number of variables).
(1) Independent variables and representation of molecular structures
A dihedral angle is used as an independent variable. A chemical-bond length and a chemical-bond angle are fixed to the corresponding values in PDB data. In the NMA calculation using the dihedral angle as independent variable it is necessary to represent molecules as a tree in a graph theory sense. A rigid body part (that is composed of one or more atoms) corresponds to a vertex and a rotatable bond connecting the rigid body parts corresponds to an edge in the tree representation.
For representing molecules as a tree, there is a severe restriction. That is, a closing loop containing any rotatable chemical bonds is not allowed. There is no problem with a ring structure that is considered as a rigid body. Therefore, most of the ring structures such as aromatic rings in amino acids and base rings in nucleotides are treated as a rigid body. The exception is a sugar ring in a nucleotide. In order to consider its puckering, one of the chemical bonds in the ring is regarded as non-bonded, but alternatively, the strong restriction is imposed on the distance between the atoms forming that bond using the pseudo-potential of type K (dij - dijPDB)2. Similarly, for a loop structure formed by more than one residue (for example, a loop formed by a disulfide bond), one of the chemical bonds in the loop (for example, an S-S bond) is regarded as non-bonded, but alternatively, the strong restiction is imposed on the distance between the atoms forming that bond using the pseudo-potential of the same type.
(2) Potential function
Potential function is given in a very simple form:
E (dij) = K exp{-(dij)2/a2} (dij - dijPDB)2
dij is a distance between atoms i and j in a calculated conformation.
dijPDB is a distance between atoms i and j in the PDB conformation.
K and a are parameters determined independently of the atomic types of i, and j. They can be determined properly by a user.
Obviously, the PDB conformation is the energy-minimum one for this potential function.
(3) Fluctuation amplitude or temperature
Since the potential function is artificial (i.e., the parameters in the potential function are not determined based on the conventional molecular mechanics theory), there is no realistic sense in temperature. Neither is fluctuation amplitude determined by the temperature. Consequently, a user should specify the fluctuation amplitude arbitrarily, irrespective of temperature. Information about the amplitude specified in the calculation is given in the Calculation note in each protein page.
It should be noted that the fluctuation set to any proteins are much larger than the ones at ordinary temperature. Such exaggerated fluctuation is necessary for animation, because the fluctuation at ordinary temperature is too small for a user to recognize.
(4) Information provided in ProMode-Elastic
a) Fluctuation of atoms. Time average and data for the 3 lowest-frequency normal modes are given by graphs.
b) Fluctuation of dihedral angles. Time average and data for the 3 lowest-frequency normal modes are given by graphs.
c) Correlation between fluctuating atoms. Time average and data for the 10 lowest-frequency normal modes are given by a triangle map.
For a reference, a distance map between residues are given also by a triangle map.
d) Animation of fluctuating molecules displayed on the viewers, jV (PDBj) and Jmol, for the 10 lowest-frequency normal modes.
GIF animation is also presented.
e) Displacement vectors exhibited on the viewers, jV (PDBj) and Jmol, for the 10 lowest-frequency normal modes.
Static images for displacement vectors are also presented.
f) Some numerical data are downloadable.
(1) Independent variables and representation of molecular structures
A dihedral angle is used as an independent variable. A chemical-bond length and a chemical-bond angle are fixed to the corresponding values in PDB data. In the NMA calculation using the dihedral angle as independent variable it is necessary to represent molecules as a tree in a graph theory sense. A rigid body part (that is composed of one or more atoms) corresponds to a vertex and a rotatable bond connecting the rigid body parts corresponds to an edge in the tree representation.
For representing molecules as a tree, there is a severe restriction. That is, a closing loop containing any rotatable chemical bonds is not allowed. There is no problem with a ring structure that is considered as a rigid body. Therefore, most of the ring structures such as aromatic rings in amino acids and base rings in nucleotides are treated as a rigid body. The exception is a sugar ring in a nucleotide. In order to consider its puckering, one of the chemical bonds in the ring is regarded as non-bonded, but alternatively, the strong restriction is imposed on the distance between the atoms forming that bond using the pseudo-potential of type K (dij - dijPDB)2. Similarly, for a loop structure formed by more than one residue (for example, a loop formed by a disulfide bond), one of the chemical bonds in the loop (for example, an S-S bond) is regarded as non-bonded, but alternatively, the strong restiction is imposed on the distance between the atoms forming that bond using the pseudo-potential of the same type.
(2) Potential function
Potential function is given in a very simple form:
E (dij) = K exp{-(dij)2/a2} (dij - dijPDB)2
dij is a distance between atoms i and j in a calculated conformation.
dijPDB is a distance between atoms i and j in the PDB conformation.
K and a are parameters determined independently of the atomic types of i, and j. They can be determined properly by a user.
Obviously, the PDB conformation is the energy-minimum one for this potential function.
(3) Fluctuation amplitude or temperature
Since the potential function is artificial (i.e., the parameters in the potential function are not determined based on the conventional molecular mechanics theory), there is no realistic sense in temperature. Neither is fluctuation amplitude determined by the temperature. Consequently, a user should specify the fluctuation amplitude arbitrarily, irrespective of temperature. Information about the amplitude specified in the calculation is given in the Calculation note in each protein page.
It should be noted that the fluctuation set to any proteins are much larger than the ones at ordinary temperature. Such exaggerated fluctuation is necessary for animation, because the fluctuation at ordinary temperature is too small for a user to recognize.
(4) Information provided in ProMode-Elastic
a) Fluctuation of atoms. Time average and data for the 3 lowest-frequency normal modes are given by graphs.
b) Fluctuation of dihedral angles. Time average and data for the 3 lowest-frequency normal modes are given by graphs.
c) Correlation between fluctuating atoms. Time average and data for the 10 lowest-frequency normal modes are given by a triangle map.
For a reference, a distance map between residues are given also by a triangle map.
d) Animation of fluctuating molecules displayed on the viewers, jV (PDBj) and Jmol, for the 10 lowest-frequency normal modes.
GIF animation is also presented.
e) Displacement vectors exhibited on the viewers, jV (PDBj) and Jmol, for the 10 lowest-frequency normal modes.
Static images for displacement vectors are also presented.
f) Some numerical data are downloadable.
Created: 2013-03-21 (last edited: more than 1 year ago)
