The dataset contains 145 holo proteins. The majority of these structures are enzymes, and their distribution among different enzymatic classes is shown in the lower pie chart. Functional annotation was done using UniProt and PDB (Berman et al., 2000; Jain et al., 2009). See also Table S1, Table S2, and TableS3.

A-D. Fluctuation profiles obtained by the GNM for four metal-binding proteins in holo form: A. 1MUC a muconate lactonizing enzyme with bound Mn²⁺; B. 1VLX an electron transport protein with bound Co²⁺; C. 1JFZ an RNase III endonuclease with bound Mn²⁺; and D. 1HP7 an anti-trypsin binding Zn²⁺. The curves represent the normalized distributions, or histograms, of square fluctuations, as a function of residue number, in the softest modes accessible to each structure. The yellow markers show the loci of metal-binding residues. These tend to occupy positions near local or global minima. Panels A and B compare the profiles for the holo (red dashed curve) and apo (blue curve) forms and illlustrate that the two forms show minimal, if any, change in their global mode profile. A′, B′, C′, D′. Ribbon diagrams of the four proteins in their holo forms, color-coded according to GNM softest mode profiles in panels A-D, from blue (most rigid) to red (most mobile). The metal-binding sites are shown in space-filling representation, and the metal ions in pink. Note that metal-binding sites are highly constrained in general (shown in blue), except for the structure in panel A/A′. See also Table S1, Table S2, and TableS3.

A. Histograms of mobilities for three different groups of residues: metal-binding CHED, all CHED (green) and all (blue) residues. Mobilities are normalized in the range [0, 1], and results are shown for 21 bins at an interval of 0.05; the first bin refers to the count of residues having mobilities in the range from 0.00 to 0.05 and so on, expressed as probabilistic occurrence on the ordinate. B. Cumulative distributions of mobilities for the same three groups of residues. C-F. Same as in panel A, for specific amino acids at metal-binding and other (green) locations. Metal-binding ‘HED’ residues exhibit mobilities significantly lower than their non-metal-binding counterparts, while cysteines (‘C’) show the opposite trend. See Table S4 for the number of residues in each subset, along with the mean and covariance values corresponding to the histograms in panels A, C-F. The numbers in parenthesis in the insets show average mobilities. See also Table S4, Table S5, Figure S1, and Figure S2.

A. Histograms of solvent accessibilities for CHED residues in the two groups. B. Cumulative distributions for two groups of CHED residues, indicating the strong propensity of metal-binding CHED residues to be buried. C-F. Same as panel A, for each of the CHED residues. Solvent accessibility was calculated using the constrained Voronoi procedure described in McConkey et al. (2002), and Eyal et al. (2004). The numbers in parenthesis on the legend show average solvent accessibility.

A. Hitting time H(i,j) map as a metric of the average duration of time, or number of steps, required to transmit signals from residue i to residue j, predicted by a Markovian model of communication (see Eq. 5). Blue and red regions correspond to shortest and longest hit times, respectively. B. Commute times C(i,j) = H(i,j) + H(j,i) (see Eq. 6). C. Average hit time vs residue number, evaluated from the average of H(i,j) over all starting points j. Red markers show the metal binding residues. Almost all of them occur at the minima of the curve, pointing to the efficient signal transmission properties of metal-binding sites. D. Average hit time vs its variance for each residue. The residues that participate in metal binding (shown in red markers) exhibit small average hit time along with small standard deviations. See also Figure S3 and Figure S4.

Results are displayed for all residues in 145 holo metal-binding proteins. The abscissa shows the average hit-time, and the ordinate shows the variance in the hit-times, both quantities being normalized with respect to the cumulative degree of the proteins. A. The black markers show the position of metal-binding CHED residues; colored points refer to all other residues. B The black markers show the position of non metal-binding CHED. A few outliers are highlighted in panel A. See also Figure S4 and Figure S5.

A. Global fluctuation profiles predicted by the GNM for 1OVU – a four-helix bundle binding Co²⁺ (top) and 1HZ8 – a dimetal Zn²⁺ binding protein (bottom). Metal binding sites are shown by the red markers. B. Average hitting times vs their covariance plot, for all residues in these two cases. Metal-binding residues (red circles) lie at the shortest hitting times and smallest variance region. C. Ribbon diagram color-coded by signal propagation properties with the blue regions indicating fast and efficient communication, and red regions the poorest communication properties. Metal-binding residues are shown by space-filling representation, and metals are shown by the red spheres. The metal binding sites were identified using Ligand Explorer in the PDB.