Biology subjects

Fraternali, F.

Publications and source records attributed to Fraternali, F..

3 recordsLinked to original sources

bioRxiv2018

Functional cross-talk between allosteric effects of activating and inhibiting ligands underlies PKM2 regulation

Allosteric regulation is central to the role of the glycolytic enzyme pyruvate kinase M2 (PKM2) in cellular metabolism. Multiple activating and inhibitory allosteric ligands regulate PKM2 activity by controlling the equilibrium between high activity tetramers and low activity dimers and monomers. However, it remains elusive how allosteric inputs upon simultaneous binding of different ligands are integrated to regulate PKM2 activity. Here, we show that, in the presence of the allosteric inhibitor L-phenylalanine (Phe), the activator fructose 1,6-bisphosphate (FBP) can induce PKM2 tetramerisation, but fails to maximally increase enzymatic activity. Guided by a new computational framework we developed to identify residues that mediate FBP-induced allostery, we generated two PKM2 mutants, A327S and C358A, in which activation by FBP remains intact but cannot be attenuated by Phe. Our findings demonstrate a role for residues involved in FBP-induced allostery in enabling the integration of allosteric input from Phe and reveal a mechanism that underlies the co-ordinate regulation of PKM2 activity by multiple allosteric ligands.

biochemistry↗

bioRxiv2018

Short loop motif profiling of protein interaction networks in acute myeloid leukaemia

Recent advances in biotechnologies for genomics and proteomics have expanded our understanding of biological components which play crucial roles in complex mechanisms related to cancer. However, it is still challenging to extract from the available knowledge reliable targets to use in a translational setting. The reasons for this are manifold, but essentially distilling real biological signal from heterogeneous \"big data\" collections is the major hurdle. Here, we aim to establish an in-silico pipeline to explore mutations and their effects on protein-protein interactions, with a focus on acute myeloid leukaemia (AML), one of the most common blood cancers with the highest mortality rate. Our method, based on cyclic interactions of a small number of proteins topologically linked in the network (short loop network motifs), highlights specific protein-protein interactions (PPIs) and their functions in AML when compared with other leukaemias. We also developed a new property named short loop commonality to measure indirect PPIs occurring via common short loop interactions. This new method detects \"modules\" of PPI networks (PPINs) enriched with common biological functions which have proteins that contain mutation hotspots. We further perform 3D structural modelling to extract atomistic details, which shows that such hotspots map to PPI interfaces as well as active sites. Thus, our study proposes a framework for the macroscopic and microscopic investigation of PPINs, their relation to cancers, and highlights important functional modules in the network to be exploited in targeted drug screening.

bioinformatics↗

bioRxiv2018

Identifying the genetic basis of variation in cell behaviour in human iPS cell lines from healthy donors

Large cohorts of human iPSCs from healthy donors are potentially a powerful tool for investigating the relationship between genetic variants and cellular phenotypes. Here we integrate high content imaging, gene expression and DNA sequence datasets for over 100 human iPSC lines to identify the genetic basis of inter-individual variability in cell behaviour. By applying a dimensionality reduction approach, Probabilistic Estimation of Expression Residuals (PEER), we identified genes that correlated in expression with intrinsic (genetic) and extrinsic (ECM) factors. However, variation in mRNA levels could not account for outlier cell behaviour. Instead, we identified rare, deleterious SNVs in the coding sequence of genes involved in ECM adhesion that occurred in cell lines that were outliers for one or more phenotypes such as cell spreading. These also correlated with altered germ layer differentiation on micropatterned surfaces. Our study thus establishes a strategy for integrating genetic and cell biological measurements for high-throughput analysis.

cell biology↗