Structural and computational characterization of the SHV-1 β-lactamase-β-lactamase inhibitor protein interface

Kimberly A. Reynolds, Jodi M. Thomson, Kevin D. Corbett, Christopher R. Bethel, James M. Berger, Jack F. Kirsch, Robert A. Bonomo, Tracy M. Handel

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Abstract

β-Lactamase inhibitor protein (BLIP) binds a variety of class A β-lactamases with affinities ranging from micromolar to picomolar. Whereas the TEM-1 and SHV-1 β-lactamases are almost structurally identical, BLIP binds TEM-1 ∼1000-fold tighter than SHV-1. Determining the underlying source of this affinity difference is important for understanding the molecular basis of β-lactamase inhibition and mechanisms of protein-protein interface specificity and affinity. Here we present the 1.6 Å resolution crystal structure of SHV-1·BLIP. In addition, a point mutation was identified, SHV D104E, that increases SHV·BLIP binding affinity from micromolar to nanomolar. Comparison of the SHV-1·BLIP structure with the published TEM-1·BLIP structure suggests that the increased volume of Glu-104 stabilizes a key binding loop in the interface. Solution of the 1.8 Å SHV D104K·BLIP crystal structure identifies a novel conformation in which this binding loop is removed from the interface. Using these structural data, we evaluated the ability of EGAD, a program developed for computational protein design, to calculate changes in the stability of mutant β- lactamase·BLIP complexes. Changes in binding affinity were calculated within an error of 1.6 kcal/mol of the experimental values for 112 mutations at the TEM-1·BLIP interface and within an error of 2.2 kcal/mol for 24 mutations at the SHV-1·BLIP interface. The reasonable success of EGAD in predicting changes in interface stability is a promising step toward understanding the stability of the β-lactamase·BLIP complexes and computationally assisted design of tight binding BLIP variants.

Original languageEnglish (US)
Pages (from-to)26745-26753
Number of pages9
JournalJournal of Biological Chemistry
Volume281
Issue number36
DOIs
StatePublished - Sep 8 2006

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ASJC Scopus subject areas

  • Biochemistry

Cite this

Reynolds, K. A., Thomson, J. M., Corbett, K. D., Bethel, C. R., Berger, J. M., Kirsch, J. F., Bonomo, R. A., & Handel, T. M. (2006). Structural and computational characterization of the SHV-1 β-lactamase-β-lactamase inhibitor protein interface. Journal of Biological Chemistry, 281(36), 26745-26753. https://doi.org/10.1074/jbc.M603878200