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Robust identification of binding hot spots using continuum electrostatics: application to hen egg-white lysozyme.

(2011) J Am Chem Soc 133

PubMed: 22092261 | PubMedCentral: PMC3244821 | DOI: 10.1021/ja207914y

In short, the structure derived from PDB entry 2LYO corresponds to the experiment of Wang et al.,( 13 ) with the singly bound CCN molecule residing in site C; the corresponding apo structure is also l... sted (PDB entry 2LYM ).

Table 1 Rankings of Hot Spots Identified by FTMap and Their Respective Numbers of Probe Clusters       secondary sites a     PDB entry structural notes site C a site B site D total probe cluster count distance to CCN (Å) b 2LYO holo, CCN bound 1 (34), 6 (4) 3 (13) 2 (16) 67 1.1 2LYM apo 1 (22), 3 (13), 6 (6) 2 (15), 7 (5) 4 (12) 73 1.4 1IR8 Ile58 → Met58 1 (33), 7 (2) 3 (11), 5 (10) 2 (14) 67 1.6 1IR9 Ile98 → Met98 1 (25), 6 (6) 2 (18) 4 (11) 60 2.5 1LSY Asp52 → Ser52 1 (34), 6 (5) 2 (13) 3 (12) 64 1.3 1LSZ Asp52 → Ser52, holo 1 (32), 8 (3) 2 (11), 4 (10) 3 (11), 5 (6) 73 1.2 1XEI 17.6% dehydrated 1 (34) 4 (11) 2 (14) 59 1.1 1XEJ 16.9% dehydrated 1 (35), 6 (6)   4 (10) 51 0.7 1XEK 9.4% dehydrated 1 (18), 5 (7), 9 (4)   3 (12) 41 1.3 a The number shown in parentheses after each ranking number is the total probe cluster count for that particular CS.

In each case, the probe representative located closest to that from the 2LYO structure has the lowest energy.

b The distance is that between the center carbons of the CCN molecules from the 2LYO structure and the lowest-energy CCN from mapping results.

Figure 4 Mapping results for the 2LYM structure using FTMap (A) are shown in comparison to those obtained using MD simulations on the 2LYO structure (B).

13 , 3 Furthermore, each top-ranked CS included at least one cluster of CCN molecules in close proximity to the experimentally determined position of CCN in the 2LYO structure.

14 , 15 FTMap also predicted that the top CS, CS1, contains at least one cluster of CCN molecules for each of the nine structures, with the mapping results from the 2LYO , 1IR8 , 1LSY , 1XEI , and 1XEJ structures containing two CCN clusters.

This site is the same identified by Wang et al. as binding a single CCN molecule (PDB entry 2LYO ).

To quantify the position of CCN within each cluster in relation to that found in the bound structure (PDB entry 2LYO ), the distance between the middle carbons of the lowest-energy CCN probe in the highest ranking FTMap-predicted cluster and the CCN molecule from the 2LYO structure was measured for each structure (Table 1 ).

Publication Year: 2011