bims-nucpor 2021-08-08 papers

Issue of 2021–08–08
four papers selected by
Sara Mingu, Johannes Gutenberg University

Biophys J. 2021 Jul 30. pii: S0006-3495(21)00633-0. [Epub ahead of print]

Free Energy Calculations Shed Light on the Nuclear Pore Complex's Selective Barrier Nature.

The nuclear pore complex (NPC) is the exclusive gateway for traffic control across the nuclear envelope. While smaller cargoes (less than 5-9 nm in size) can freely diffuse through the NPC, the passage of larger cargoes is restricted to those accompanied by nuclear transport receptors (NTRs). This selective barrier nature of the NPC is putatively associated with the intrinsically disordered, phenylalanine-glycine repeat domain containing nucleoporins, termed FG-Nups. The precise mechanism underlying how FG-Nups carry out such an exquisite task at high throughputs has, however, remained elusive and the subject of various hypotheses. From the thermodynamics perspective, free energy analysis can be a way to determine cargo's transportability since the traffic through the NPC must be in the direction of reducing the free energy. In this study, we developed a computational model to evaluate the free energy composed of the conformational entropy of FG-Nups and the energetic gain associated with binding interactions between FG-Nups and NTRs, and investigated whether these physical features can be the basis of NPC's selectivity. Our results showed that the reduction in conformational entropy by inserting a cargo into the NPC increased the free energy by an amount substantially greater than the thermal energy (≫kBT), while the free energy change was negligible (<kBT) for small cargoes (less than ∼6 nm in size), indicating the size-dependent selectivity emerges from the entropic effect. Our models suggested that the entropy-induced selectivity of the NPC depends sensitively upon the physical parameters such as the flexibility and the length of FG-Nups. On the other hand, the energetic gain via binding interactions effectively counteracted the entropic reduction, increasing the size limit of transportable cargoes up to the nuclear pore size. We further investigated the geometric effect of the binding spot spatial distribution, and found that the clustered binding spot distribution decreased the free energy more efficiently as compared to the scattered distribution.

DOI: https://doi.org/10.1016/j.bpj.2021.07.025

Sci Rep. 2021 Aug 02. 11(1): 15649

Distinct mutations in importin-β family nucleocytoplasmic transport receptors transportin-SR and importin-13 affect specific cargo binding.

Makoto Kimura, Kenichiro Imai, Yuriko Morinaka, Yoshiko Hosono-Sakuma, Paul Horton, Naoko Imamoto.

Importin-(Imp)β family nucleocytoplasmic transport receptors (NTRs) are supposed to bind to their cargoes through interaction between a confined interface on an NTR and a nuclear localization or export signal (NLS/NES) on a cargo. Although consensus NLS/NES sequence motifs have been defined for cargoes of some NTRs, many experimentally identified cargoes of those NTRs lack those motifs, and consensus NLSs/NESs have been reported for only a few NTRs. Crystal structures of NTR-cargo complexes have exemplified 3D structure-dependent binding of cargoes lacking a consensus NLS/NES to different sites on an NTR. Since only a limited number of NTR-cargo interactions have been studied, whether most cargoes lacking a consensus NLS/NES bind to the same confined interface or to various sites on an NTR is still unclear. Addressing this issue, we generated four mutants of transportin-(Trn)SR, of which many cargoes lack a consensus NLS, and eight mutants of Imp13, where no consensus NLS has been defined, and we analyzed their binding to as many as 40 cargo candidates that we previously identified by a nuclear import reaction-based method. The cargoes bind differently to the NTR mutants, suggesting that positions on an NTR contribute differently to the binding of respective cargoes.

DOI: https://doi.org/10.1038/s41598-021-94948-1

J Am Chem Soc. 2021 Aug 06.

Thermodynamic Models for Assembly of Intrinsically Disordered Protein Hubs with Multiple Interaction Partners.

ByeongJin Cho, Jaejun Choi, RyeongHyeon Kim, Jean Nyoung Yun, Yuri Choi, Hyung Ho Lee, Junseock Koh.

Prevalent in diverse protein interactomes, intrinsically disordered proteins or regions (IDPs or IDRs) often drive assembly of higher-order macromolecular complexes, using multiple target-binding motifs. Such IDP hubs are suggested to process various cellular signals and coordinate relevant biological processes. However, the mechanism of assembly and functional regulation of IDP hubs remains elusive due to the challenges in dissecting their intricate protein-protein interaction networks. Here we present basic thermodynamic models for the assembly of simple IDP hubs with multiple target proteins, constructing partition functions from fundamental binding parameters. We combined these basic functions to develop advanced thermodynamic models to analyze the assembly of the Nup153 hubs interacting with multiple karyopherin β1 (Kap) molecules, critical components of nucleocytoplasmic transport. The thermodynamic analysis revealed a complex organization of the Kap binding sites within the C-terminal IDR of Nup153 including a high-affinity 1:1 interaction site and a series of low-affinity sites for binding of multiple Kaps with negative cooperativity. The negative cooperativity arises from the overlapping nature of the low-affinity sites where Kap occupies multiple dipeptide motifs. The quantitative dissection culminated in construction of the Nup153 hub ensemble, elucidating how distribution among various Kap-bound states is modulated by Kap concentration and competing nuclear proteins. In particular, the Kap occupancy of the IDR can be fine-tuned by varying the location of competition within the overlapping sites, suggesting coupling of specific nuclear processes to distinct transport activities. In general, our results demonstrate the feasibility and a potential mechanism for manifold regulation of IDP functions by diverse cellular signals.

DOI: https://doi.org/10.1021/jacs.1c00811

Metab Brain Dis. 2021 Aug 04.

Intrinsically disordered proteins identified in the aggregate proteome serve as biomarkers of neurodegeneration.

Srinivas Ayyadevara, Akshatha Ganne, Meenakshisundaram Balasubramaniam, Robert J Shmookler Reis.

A protein's structure is determined by its amino acid sequence and post-translational modifications, and provides the basis for its physiological functions. Across all organisms, roughly a third of the proteome comprises proteins that contain highly unstructured or intrinsically disordered regions. Proteins comprising or containing extensive unstructured regions are referred to as intrinsically disordered proteins (IDPs). IDPs are believed to participate in complex physiological processes through refolding of IDP regions, dependent on their binding to a diverse array of potential protein partners. They thus play critical roles in the assembly and function of protein complexes. Recent advances in experimental and computational analyses predicted multiple interacting partners for the disordered regions of proteins, implying critical roles in signal transduction and regulation of biological processes. Numerous disordered proteins are sequestered into aggregates in neurodegenerative diseases such as Alzheimer's disease (AD) where they are enriched even in serum, making them good candidates for serum biomarkers to enable early detection of AD.

Keywords: Aggregate proteome; Biomarker; Intrinsically disordered proteins; Neurodegneration; Protein aggregation

DOI: https://doi.org/10.1007/s11011-021-00791-8