Biology subjects

Timr, S.

Publications and source records attributed to Timr, S..

3 recordsLinked to original sources

bioRxiv2025

Beyond contacts: the important role of the support region to distinguish stable and transient protein interfaces

Protein-protein interactions (PPIs) are fundamental to virtually all cellular processes; however, elucidating the principles that govern protein association into complexes remains a significant challenge. In this study, we present a comparative analysis of stable and transient protein interfaces, offering a detailed perspective on the interactions that form them. Moving beyond the traditional focus on pairs of neighboring residues, we examine interacting pairs by identifying their distinct non-bonded interactions. Additionally, we account for the contextual dependence of these interactions by analyzing the regions of the interface where they occur. Our approach quantifies the diversity of pairs in each region, considering the type of interface. Furthermore, we introduce an innovative strategy to analyze pair co-occurrence, enabling a comparison of the inner local organization of stable and transient interfaces. Our findings reveal that stable and transient interfaces differ not in overall residue composition, but in the residue- and interaction-partitioning patterns across the variably hydrated regions of the interface. These results underscore the importance of considering the contextual environment in which pairs interact and identify the support region as a key determinant for distinguishing transient and stable protein complexes. The software package developed for this analysis is available as open source.

bioinformatics↗

bioRxiv2025

Directionality of two-photon absorption in representative fluorescent proteins

Molecules of fluorescent proteins (FPs) exhibit anisotropic optical properties. While the directionality of single-photon (1P) absorption and emission in the most commonly used FPs has already been characterized, directionality of their two-photon (2P) excitation remains poorly understood, even though it offers higher sensitivity to molecular orientation and promises to yield more information on molecular orientational distributions than the 1P processes. By measuring optical properties of FP crystals, we have now determined the two-photon absorptivity tensors (2PATs) of the FPs mTurquoise2, eGFP and mCherry. Our results demonstrate the feasibility of experimental 2PAT determinations, provide new insights into molecular mechanisms of 2P absorption in FPs, open a new avenue to rational development of novel biosensors and allow detailed structural interpretation of results obtained with such biosensors.

biophysics↗

bioRxiv2024

Structural basis for allosteric regulation of human phosphofructokinase-1

Phosphofructokinase-1 (PFK1) catalyzes the rate-limiting step of glycolysis, committing glucose to conversion into cellular energy. PFK1 is highly regulated to respond to the changing energy needs of the cell. In bacteria, the structural basis of PFK1 regulation is a textbook example of allostery; molecular signals of low and high cellular energy promote transition between an active R-state and inactive T-state conformation, respectively. Little is known, however, about the structural basis for regulation of eukaryotic PFK1. Here, we determine structures of the human liver isoform of PFK1 (PFKL) in the R- and T-state by cryoEM, providing insight into eukaryotic PFK1 allosteric regulatory mechanisms. The T-state structure reveals conformational differences between the bacterial and eukaryotic enzyme, the mechanisms of allosteric inhibition by ATP binding at multiple sites, and an autoinhibitory role of the C-terminus in stabilizing the T-state. We also determine structures of PFKL filaments that define the mechanism of higher-order assembly and demonstrate that these structures are necessary for higher-order assembly of PFKL in cells.

biochemistry↗