vanddraabe (version 1.1.1)

Mobility: Water Molecule Mobility

Description

Calculate the mobility values of waters for a structure.

Usage

Mobility(Bvalues, occupancy)

Arguments

Bvalues

B-value values from the imported PDB file(s)

occupancy

Occumpancy values from the imported PDB file(s)

Value

Vector of mobility values; unitless.

Details

The mobility of waters within a structure is normalization method to identify the amount of variance an atom has within a structure. In the case of waters, identified by an oxygen atom without hydrogen atoms, a water-oxygen atom with a mobility value of 0 is considered rigid and does not possess variance. The average mobility within a structure has value of 1 while an atom's mobility value of x is considered x-times as mobile as an average atom.

$$Mobility = \frac{\frac{B-value}{\mu_{B-value}}}{\frac{Occupancy}{\mu_{Occupancy}}}$$

Mobility is calculated using the B-value and occupancy values; these values are a byproduct of solving the 3D molecular structure from electron density maps. The mobility values allows us to compare atomic mobility between molecular structures solved using different structural refinement methods. Atoms, in this instance water-oxygens, with a mobility value greater than 2.0 are removed from analysis.

The mobility exclusion value is user defined within the main ConservedWaters() function but has a default value of 2.0.

References

Paul C Sanschagrin and Leslie A Kuhn. Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity. Protein Science, 1998, 7 (10), pp 2054-2064. DOI: 10.1002/pro.5560071002 PMID: 9792092 WatCH webpage

See Also

Other "Bound Water Environment": BoundWaterEnvironment.interact, BoundWaterEnvironment.quality, BoundWaterEnvironment, NormalizedBvalue, calcBvalue, calcNearbyHydrationFraction, calcNumHydrogenBonds

Examples

# NOT RUN {
  set.seed(13)
  sample.idc <- sample(1:nrow(thrombin.1hai$atom), 10)
  Bvalues <- thrombin.1hai$atom[sample.idc, "b"]
  Bvalues
  # [1] 45.73 45.40 20.24 39.30 35.53
  #     22.16 35.81 15.35 22.73 21.34
  occupancy <- thrombin.1hai$atom[sample.idc, "o"]
  occupancy
  # [1] 0.01 1.00 1.00 1.00 1.00
  #     1.00 1.00 1.00 1.00 1.00
  Mobility(Bvalues, occupancy)
  # [1] 135.7183 1.3474 0.6007 1.1664 1.0545
  #       0.6577 1.0628 0.4556 0.6746 0.6333

# }