Manual

In this module, you can set some options affecting both the model building and the hydrodynamic computations stages. The Calculate vbar checkbox allows the computation of the partial specific volume (vbar) in standard conditions (water @ 20°C) of the structure from its composition, using the residues' values stored in the residue table (default: active). Alternatively, a vbar value (vbar(ent), either computed by other means or measured) can be entered in the Enter a vbar value (cm^3/g) field. For instance, if a significant number of non-coded or incomplete residues are skipped when parsing the PDB file, the computed vbar could be not correct; likewise, if the Automatic Bead Builder is used for non-coded residues, the vbar could also be incorrect. In these cases, entering an experimental value will be the best option. Importantly, the temperature T(ent) at which the entered vbar(ent) has been measured/computed must be entered in the Vbar measured/computed at T=°C: field. The vbar(ent) and T(ent) values will be then used by the Hydrodynamic Computation Options module to calculate an operational vbar valid for the temperature conditions to which the hydrodynamic computations are referred. If a vbar value is entered in this field (and the Calculate vbar checkbox is deselected), a message will be displayed in the progress window ("ATTENTION: vbar = ") when the model is being built. This should avoid the use of incorrect external vbar values resulting by inadvertently leaving the Calculate vbar checkbox deselected from a previous model-generating session.
The Select vbar button will instead load a vbar value calculated from protein sequence by using the UltraScan vbar calculation routine. WARNING: whenever possible, use experimental vbar values, as many factors can affect its computation!!!! The routines provided here should be considered just as a best approximation in absence of experimental data.

The Hydration Water Vol. (A^3) field sets the volume of the water of hydration molecules, which has been found (Gerstein and Chothia, Proc. Natl. Acad. Sci. USA 93:10167-10172, 1996) to be on average 24.5 A³, different from that of either bulk (29.7 A³) or isolated (11.5 A³) water molecules (default: 24.041 A³).

The Enable Peptide Bond Rule checkbox controls if the peptide bond rule is used by the SoMo method. With this rule, the peptide bond segment is used for the main chain beads of a protein structure. These beads are thus positioned at the cog of the (CA-C-O)_n-(N)_(n+1) atoms, except when PRO is the (n+1) residue. In this case, the peptide bond bead is positioned at the cog of the (CA-C-O)_n atoms. Additional rules control the generation of the OXT bead and of the first N atom at the beginning of each protein chain. All these rules are controlled by "special" residues in the somo.residue table. To gain total control over the positioning, volumes and masses of every bead, the Enable Peptide Bond Rule checkbox should be deselected. In this case, the descriptions present in the somo.residue table are fully effective. (default: selected).

The Average Parameters for Automatic Bead Builder: submenu contains a series of fields governing the average parameters that will be used by the Automatic Bead Builder routine when this option is selected (see here) for non-coded residues.

• Average atomic radius (A):. This is the radius used by the ASA routines (see here) to compute the accessible surface area of the non-coded residue. The default value (1.68 A) was derived by averaging the atomic radii of the C,O,P,N,S elements present in the current (April 2009) version of the default somo.atom table. Averaging over all elements produced essentially the same value, 1.67 A.
• Average atomic mass (Da):. This is an average atomic mass for atoms within non-coded residues used in the computation of the total mass of the model. The default value (16 Da) was derived by averaging the atomic masses of the C,O,P,N,S elements present in the current (April 2009) version of the default somo.atom table. Including all elements produced a slightly larger value, 17.6 Da. In any case, we strongly suggest to enter a global value in the Total Mass of Model field in the SOMO Hydrodynamic Calculation Options panel when dealing with structures containing non-coded residues.
• Average atomic hydration:. This value will be multiplied by the number of atoms present in the non-coded residue to determine an hydration number (which will be rounded to the closest integer). The volume calculated from this hydration number multiplied by the hydration water volume (see above) will be added to the anhydrous bead volume (see below) to determine the final volume of the bead. The default value (0.4) is a compromise between the value derived for amino acids and carbohydrates (0.3) and that for nucleotides/nucleosides and prosthetic groups, 0.5. These number were calculated by averaging the hydration number of a bead divided by the number of atoms assigned to it for the beads defined in the current (April 2009) version of the default somo.residue table. This value should perhaps be adapted to the kind of non-coded residue(s) being roughly modeled by the Automatic Bead Builder.
• Average bead/atom volume:. This value will be multiplied by the number of atoms present in the non-coded residue to determine the anhydrous volume of the bead that will represent them, to which the volume of the water of hydration will be then added (see above). The default value (15.3 A³) was derived by averaging the bead volume divided by the number of atoms assigned to it for each bead present in the current (April 2009) version of the default somo.residue table. Volumes by categories are: 17.8 A³ for amino acids, 15.3 A³ for carbohdrates, 14.7 A³ for nucleotides/nucleosides, and 11.8 A³ for prosthetic groups.
• Average Residue vbar:. This value will be used in the computation of the global vbar of the model. The default value (0.72 cm³/g) is that of the average protein. It could be changed when dealing with other kind of biomacromolecules. In any case, we strongly suggest to enter a global (better if experimental) value for vbar in the Enter vbar: field above when dealing with structures containing non-coded residues.

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Last modified on January 27, 2010.