Search

In this article, we implement and compare 10 node removal (attack) strategies from the literature over the photosystem I (PSI) complex network of the common pea plant (Pisum sativum), representing the FRET energy transfer among its nodes/chromophores. We measure the network robustness (functioning) with four indicators. The node attack strategies and the network robustness indicators consider both the binary-topological and the weighted structure of the network. First, we find that the well-known node betweenness centrality attack, which has proven highly effective in dismantling most real-world networks' topological connectivity, is ineffective over the PSI network. Second, the degeneracy of the node properties caused by the PSI's higher network connectivity level induces a random-like node removal even when nodes are removed according to a specific node centrality measure. This phenomenon triggers a very low decrease of the PSI network functioning even when subjected to node attack. Such an outcome would indicate that the node attack strategies based on classic node properties, such as the degree or the betweenness centrality, may show low efficacy in dismantling real-world networks with very high connectivity levels. Last, the PSI network can be built by tuning a cut-off distance (CD) that defines the viable energy transfers among nodes/chromophores and progressively discards the lower energy transfer links among distant nodes/chromophores. This represents a 'weight thresholding' procedure allowing us to investigate the efficacy of the node attack strategies when links of lower weight are progressively pruned from the PSI network. We find that the best node attack strategies change by decreasing the CD, showing that the weight thresholding procedure affects the network response to node removal. This last outcome outlines the importance of investigating the stability of the system response for real-world weighted complex networks subjected to the weight thresholding procedure. [ABSTRACT FROM AUTHOR]

Due to the low temperature, the Antarctic marine environment is challenging for protein functioning. Cold-adapted organisms have evolved proteins endowed with higher flexibility and lower stability in comparison to their thermophilic homologs, resulting in enhanced reaction rates at low temperatures. The Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125) genome is one of the few examples of coexistence of multiple hemoglobin genes encoding, among others, two constitutively transcribed 2/2 hemoglobins (2/2Hbs), also named truncated Hbs (TrHbs), belonging to the Group II (or O), annotated as PSHAa0030 and PSHAa2217. In this work, we describe the ligand binding kinetics and their interrelationship with the dynamical properties of globin Ph-2/2HbO-2217 by combining experimental and computational approaches and implementing a new computational method to retrieve information from molecular dynamic trajectories. We show that our approach allows us to identify docking sites within the protein matrix that are potentially able to transiently accommodate ligands and migration pathways connecting them. Consistently with ligand rebinding studies, our modeling suggests that the distal heme pocket is connected to the solvent through a low energy barrier, while inner cavities play only a minor role in modulating rebinding kinetics., (© 2024 The Protein Society.)

Förster resonance energy transfer (FRET) is a widely-used and versatile technique for the structural characterization of biomolecules. Here, we introduce FRETpredict, an easy-to-use Python software to predict FRET efficiencies from ensembles of protein conformations. FRETpredict uses a rotamer library approach to describe the FRET probes covalently bound to the protein. The software efficiently and flexibly operates on large conformational ensembles such as those generated by molecular dynamics simulations to facilitate the validation or refinement of molecular models and the interpretation of experimental data. We provide access to rotamer libraries for many commonly used dyes and linkers and describe a general methodology to generate new rotamer libraries for FRET probes. We demonstrate the performance and accuracy of the software for different types of systems: a rigid peptide (polyproline 11), an intrinsically disordered protein (ACTR), and three folded proteins (HiSiaP, SBD2, and MalE). FRETpredict is open source (GPLv3) and is available at github.com/KULL-Centre/FRETpredict and as a Python PyPI package at pypi.org/project/FRETpredict ., (© 2024. The Author(s).)

The Fourth Cell Stress Society International workshop on small heat shock proteins (sHSPs), a follow-up to successful workshops held in 2014, 2016 and 2018, took place as a virtual meeting on the 17-18 November 2022. The meeting was designed to provide an opportunity for those working on sHSPs to reconnect and discuss their latest work. The diversity of research in the sHSP field is reflected in the breadth of topics covered in the talks presented at this meeting. Here we summarise the presentations at this meeting and provide some perspectives on exciting future topics to be addressed in the field., (© 2023. The Author(s).)

The biological functions of proteins closely depend on their conformational dynamics. This aspect is especially relevant for intrinsically disordered proteins (IDP) for which structural ensembles often offer more useful representations than individual conformations. Here we employ extensive enhanced sampling temperature replica-exchange atomistic simulations (TREMD) and deep learning dimensionality reduction to study the conformational ensembles of the human heat shock protein B8 and its pathological mutant K141E, for which no experimental 3D structures are available. First, we combined homology modelling with TREMD to generate high-dimensional data sets of 3D structures. Then, we employed a recently developed machine learning based post-processing algorithm, EncoderMap, to project the large conformational data sets into meaningful two-dimensional maps that helped us interpret the data and extract the most significant conformations adopted by both proteins during TREMD. These studies provide the first 3D structural characterization of HSPB8 and reveal the effects of the pathogenic K141E mutation on its conformational ensembles. In particular, this missense mutation appears to increase the compactness of the protein and its structural variability, at the same time rearranging the hydrophobic patches exposed on the protein surface. These results offer the possibility of rationalizing the pathogenic effects of the K141E mutation in terms of conformational changes., Competing Interests: The authors declare no conflict of interest., (This journal is © The Royal Society of Chemistry.)