Analysis of the Binding Forces Driving the Tight Interactions between β-Lactamase Inhibitory Protein-II (BLIP-II) and Class A β-Lactamases

Abstract

␤-Lactamases hydrolyze ␤-lactam antibiotics to provide drug resistance to bacteria. ␤-Lactamase inhibitory protein-II (BLIP-II) is a potent proteinaceous inhibitor that exhibits low picomolar affinity for class A ␤-lactamases. This study examines the driving forces for binding between BLIP-II and ␤-lactamases using a combination of presteady state kinetics, isothermal titration calorimetry, and x-ray crystallography. The measured dissociation rate constants for BLIP-II and various ␤-lactamases ranged from 10 ؊4 to 10 ؊7 s ؊1 and are comparable with those found in some of the tightest known protein-protein interactions. The crystal structures of BLIP-II alone and in complex with Bacillus anthracis Bla1 ␤-lactamase revealed no significant side-chain movement in BLIP-II in the complex versus the monomer. The structural rigidity of BLIP-II minimizes the loss of the entropy upon complex formation and, as indicated by thermodynamics experiments, may be a key determinant of the observed potent inhibition of ␤-lactamases.Protein-protein interactions govern many cellular processes, and an understanding of the determinants of molecular recognition would facilitate the rationale design of interactions for therapeutic purposes. Detailed examination of kinetic constants and thermodynamic driving forces, however, has been performed for relatively few protein-protein interaction complexes. Although significant progress has been made in the understanding and prediction of association rate constants, the determinants of dissociation rates remain poorly understood (1-5). The ability to predict the kinetic constants would be a significant contribution to the understanding of interaction networks in the systems biology era (6). Several model systems have been developed to analyze the principles of protein-protein interactions, and one such model is the interaction between ␤-lactamase enzymes and a set of ␤-lactamase inhibitory proteins (BLIPs) 3 (7, 8). ␤-Lactamases act by hydrolyzing the four-membered ring of ␤-lactam antibiotics, e.g. penicillins and cephalosporins, rendering the drugs inactive (9, 10). There are four classes of ␤-lactamases (A-D) based on primary amino acid sequences (11,12). Class B ␤-lactamases are metalloenzymes that use a zinc-coordinated catalytic water to hydrolyze the ␤-lactam ring whereas classes A, C, and D are serine hydrolyases (13-15). Class A ␤-lactamases are widespread in both Gram-positive and Gramnegative bacteria and exhibit broad substrate hydrolysis profiles that include penicillins, cephalosporins, and for a few enzymes, carbapenems (12,14).The catalytic mechanism of serine ␤-lactamases is divided into two stages, acylation and deacylation (16). In class A enzymes, the catalytic Ser-70 residue nucleophilically attacks the carbonyl of the ␤-lactam and forms an acyl-intermediate (17,18). An essential Glu-166 residue activates a highly coordinated water for deacylation (18,19). Substitutions at Glu-166 result in an acylated, inactive enzyme (20 -22).Clinically available mechanism-based inhibitor...

Identification of the β-Lactamase Inhibitor Protein-II (BLIP-II) Interface Residues Essential for Binding Affinity and Specificity for Class A β-Lactamases

“…Protein Purification-The BLIP-II wild-type and alaninesubstituted proteins were purified as previously described (27,29). In short, the BLIP-II variants were purified using Talon metal affinity resin (Clontech) using a C-terminal His 6 tag.…”

“…Construction of Alanine Mutants-The BLIP-II residues chosen for alanine substitutions were based on the previously performed cluster analysis of the BLIP-II-TEM-1 and BLIP-II-Bla1 interfaces (27). The BLIP-II interface residues were mutated to alanine by site-directed mutagenesis using the QuikChange method (Stratagene).…”

“…Pre-steady state kinetic experiments demonstrated that association rate constants for BLIP-II and BLIP binding to TEM-1 ␤-lactamase are similar to each other and to most protein-protein interactions, but it is the exceptionally slow dissociation rate constants of BLIP-II that make it one of the tightest protein-protein interactions known (27). This slow dissociation rate is not associated with significant changes to the structure of BLIP-II as shown by crystal structures of BLIP-II monomer and in complex with ␤-lactamase (27). However, the binding contributions of the individual BLIP-II contact residues to affinity and specificity of binding to class A ␤-lactamases remain largely unknown (8,11,22,30,33).…”

“…In addition, BLIP-II exhibits a much narrower range of binding affinity for ␤-lactamases (range of 2 orders of magnitude) when compared with BLIP (range of 6 orders of magnitude) (8,27,29). Pre-steady state kinetic experiments demonstrated that association rate constants for BLIP-II and BLIP binding to TEM-1 ␤-lactamase are similar to each other and to most protein-protein interactions, but it is the exceptionally slow dissociation rate constants of BLIP-II that make it one of the tightest protein-protein interactions known (27). This slow dissociation rate is not associated with significant changes to the structure of BLIP-II as shown by crystal structures of BLIP-II monomer and in complex with ␤-lactamase (27).…”

“…1B) (20,27). BLIP-II utilizes the numerous ␤-turns of the seven-bladed ␤-propeller structure to bind the loop-helix region and to sterically block the ␤-lactamase active site (27,28).…”