Structure-function relations in Beta-Lactamases: classes A and C

GUZOVSKY AB, SIMONETTI F, PARRA RG, FERREIRO DU

Rosario

Congreso; 4to Congreso de la Sociedad Iberoamericana de Bioinformática (SOIBIO) y 4to Congreso de Biología Computacional y Bioinformática; 2013

Asociación Argentina de Bioinformática y Biología Computacional

Ever since the decade of 1940, beta-lactamic antibiotics have been critical for the clinical treatment of bacterial infections. However, the use of these antibiotics, many times in excess and without control, selects the proliferation of resistant bacterial strains. The incidence of these resistant strains is extremely high in countries with low economic resources, especially in South America, and the therapeutical options are very limited. The wide and quick spread of beta-lactamase activities is one of the most important mechanisms of antibiotic resistance in gram negative pathogens, since these enzymes hydrolize the beta- lactamic of these antibiotics . The beta-lactamase family has been greatly characterized, as more than 470 beta-lactamases have been identified and more than 350 structures have been solved to date. Nevertheless, this information has yet to be systematically ordered and articulated. In that spirit, a local database was built including sequences and structures of beta-lactamases, using both natural and recombinant proteins from PFAM families PF0144 and PF13354. This database also includes biochemical and physicochemical data. The sequences contained in the database were classified according to the Ambler scheme, which divides beta-lactamases into 4 classes. Protein structures belonging to classes A, C and D have similar folds and a mechanism that involves a catalytic serine residue, while class B enzymes are metallobetalactamases and have a distinct fold and mechanism. It was found that while both proteins from classes A and C were correctly identified, this scheme is not useful for classifying most of the betalactamases. Therefore, it was decided to focus the rest of this work on the classes A and C. Although the beta-lactamases have been largely studied, many questions still arise regarding their function and evolution mechanisms. Statistical analyses relating protein sequence, structure and fuction both in the whole family and within each class would be useful to approach these topics. Conservation, coevolution and energetic data was gathered using sequences and structures from both classes. We seek to relate this data to biological, biochemical and biophysical measurements such as MIC, KM and Kcat using a standard numeration of the class A beta-lactamases. We extended the analysis to class C, using phylogenetic relationships. We aim for identifying target regions sites that have not been studied yet, which could be related to the evolution of beta-lactamic antibiotic resistance mechanisms and the rise of new activities. In particular, we expect that the analysis of the local frustration patterns will inform about yet uncovered relationships between structure, conformational dynamics and catalytic mechanisms.