Dataset Information

Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases.

ABSTRACT: Beta-lactamases represent the main bacterial mechanism of resistance to beta-lactam antibiotics and are a significant challenge to modern medicine. We have developed an automated classification and analysis protocol that exploits structure- and sequence-based approaches and which allows us to propose a grouping of serine beta-lactamases that more consistently captures and rationalizes the existing three classification schemes: Classes, (A, C and D, which vary in their implementation of the mechanism of action); Types (that largely reflect evolutionary distance measured by sequence similarity); and Variant groups (which largely correspond with the Bush-Jacoby clinical groups). Our analysis platform exploits a suite of in-house and public tools to identify Functional Determinants (FDs), i.e. residue sites, responsible for conferring different phenotypes between different classes, different types and different variants. We focused on Class A beta-lactamases, the most highly populated and clinically relevant class, to identify FDs implicated in the distinct phenotypes associated with different Class A Types and Variants. We show that our FunFHMMer method can separate the known beta-lactamase classes and identify those positions likely to be responsible for the different implementations of the mechanism of action in these enzymes. Two novel algorithms, ASSP and SSPA, allow detection of FD sites likely to contribute to the broadening of the substrate profiles. Using our approaches, we recognise 151 Class A types in UniProt. Finally, we used our beta-lactamase FunFams and ASSP profiles to detect 4 novel Class A types in microbiome samples. Our platforms have been validated by literature studies, in silico analysis and some targeted experimental verification. Although developed for the serine beta-lactamases they could be used to classify and analyse any diverse protein superfamily where sub-families have diverged over both long and short evolutionary timescales.

SUBMITTER: Lee D

PROVIDER: S-EPMC4917113 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

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Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases.

Lee David D Das Sayoni S Dawson Natalie L NL Dobrijevic Dragana D Ward John J Orengo Christine C

PLoS computational biology 20160622 6

Beta-lactamases represent the main bacterial mechanism of resistance to beta-lactam antibiotics and are a significant challenge to modern medicine. We have developed an automated classification and analysis protocol that exploits structure- and sequence-based approaches and which allows us to propose a grouping of serine beta-lactamases that more consistently captures and rationalizes the existing three classification schemes: Classes, (A, C and D, which vary in their implementation of the mecha ...[more]

PMID: 27332861

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Project description:BackgroundThe half-life of a protein is regulated by a range of system properties, including the abundance of components of the degradative machinery and protein modifiers. It is also influenced by protein-specific properties, such as a protein's structural make-up and interaction partners. New experimental techniques coupled with powerful data integration methods now enable us to not only investigate what features govern protein stability in general, but also to build models that identify what properties determine each protein's metabolic stability.ResultsIn this work we present five groups of features useful for predicting protein stability: (1) post-translational modifications, (2) domain types, (3) structural disorder, (4) the identity of a protein's N-terminal residue and (5) amino acid sequence. We incorporate these features into a predictive model with promising accuracy. At a 20% false positive rate, the model exhibits an 80% true positive rate, outperforming the only previously proposed stability predictor. We also investigate the impact of N-terminal protein tagging as used to generate the data set, in particular the impact it may have on the measurements for secreted and transmembrane proteins; we train and test our model on a subset of the data with those proteins removed, and show that the model sustains high accuracy. Finally, we estimate system-wide metabolic stability by surveying the whole human proteome.ConclusionsWe describe a variety of protein features that are significantly over- or under-represented in stable and unstable proteins, including phosphorylation, acetylation and destabilizing N-terminal residues. Bayesian networks are ideal for combining these features into a predictive model with superior accuracy and transparency compared to the only other proposed stability predictor. Furthermore, our stability predictions of the human proteome will find application in the analysis of functionally related proteins, shedding new light on regulation by protein synthesis and degradation.

Dataset Information

Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases.

Publications

Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases.

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