bims-indpro 2022-09-11 papers

bims-indpro

Biomed News

on Intrinsically disordered proteins

Issue of 2022–09–11
twelve papers selected by
Sara Mingu, Johannes Gutenberg University

Sequence-Dependent Backbone Dynamics of Intrinsically Disordered Proteins.
Surface Accessibility of an Intrinsically Disordered Protein Probed by 2D Time-Resolved Laser-Assisted NMR Spectroscopy.
Quantitative prediction of ensemble dynamics, shapes and contact propensities of intrinsically disordered proteins.
Developing Bonded Potentials for a Coarse-Grained Model of Intrinsically Disordered Proteins.
Thermodynamics of π-π Interactions of Benzene and Phenol in Water.
Toward Accurate Coarse-Grained Simulations of Disordered Proteins and Their Dynamic Interactions.
Coevolution of the Ess1-CTD axis in polar fungi suggests a role for phase separation in cold tolerance.
Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions.
Curcumin Interacts with α-Synuclein Condensates To Inhibit Amyloid Aggregation under Phase Separation.
In-solution structure and oligomerization of human histone deacetylase 6 - an integrative approach.
Tensin3 interaction with talin drives the formation of fibronectin-associated fibrillar adhesions.
Heat-shock chaperone HSPB1 regulates cytoplasmic TDP-43 phase separation and liquid-to-gel transition.

J Chem Theory Comput. 2022 Sep 09.

Sequence-Dependent Backbone Dynamics of Intrinsically Disordered Proteins.

Souvik Dey, Matthew MacAinsh, Huan-Xiang Zhou.

For intrinsically disordered proteins (IDPs), a pressing question is how sequence codes for function. Dynamics serves as a crucial link, reminiscent of the role of structure in sequence-function relations of structured proteins. To define general rules governing sequence-dependent backbone dynamics, we carried out long molecular dynamics simulations of eight IDPs. Blocks of residues exhibiting large amplitudes in slow dynamics are rigidified by local inter-residue interactions or secondary structures. A long region or an entire IDP can be slowed down by long-range contacts or secondary-structure packing. On the other hand, glycines promote fast dynamics and either demarcate rigid blocks or facilitate multiple modes of local and long-range inter-residue interactions. The sequence-dependent backbone dynamics endows IDPs with versatile response to binding partners, with some blocks recalcitrant while others readily adapting to intermolecular interactions.

DOI: https://doi.org/10.1021/acs.jctc.2c00328
J Am Chem Soc. 2022 Sep 09.

Surface Accessibility of an Intrinsically Disordered Protein Probed by 2D Time-Resolved Laser-Assisted NMR Spectroscopy.

Jonghyuk Im, Jongchan Lee, Jung Ho Lee.

Probing the protein surface accessibility of different residues is a powerful way of characterizing the overall conformation of intrinsically disordered proteins (IDPs). We present a two-dimensional (2D) time-resolved photo-CIDNP (TR-CIDNP) experiment suitable for IDP analysis. Pulse stretching of high-power laser pulses, band-selective decoupling of 13Cα, and simultaneous application of radiofrequency and laser pulses were implemented to quantitatively analyze the IDP surface at ultrahigh resolution. Comparative analysis with other methods that measure protein surface accessibility validated the newly developed method and emphasized the importance of dye charge in photo-CIDNP. Using the neutral riboflavin dye, surface accessibilities were measured to be nearly identical for the four Tyr residues of α-synuclein (α-Syn), whose 1Hα-13Cα correlations were well-resolved in the 2D TR-CIDNP spectrum. Having confirmed the similarity between the time-resolved and steady-state photo-CIDNP results for α-Syn, we used the more sensitive latter method to show that divalent cations induce compaction of the C-terminal region and release of the N-terminal region of α-Syn. The photo-CIDNP method presented herein can be used as an orthogonal and independent method for investigating important biological processes associated with changes in the overall IDP conformation.

DOI: https://doi.org/10.1021/jacs.2c06309
PLoS Comput Biol. 2022 Sep 09. 18(9): e1010036

Quantitative prediction of ensemble dynamics, shapes and contact propensities of intrinsically disordered proteins.

Lei Yu, Rafael Brüschweiler.

Intrinsically disordered proteins (IDPs) are highly dynamic systems that play an important role in cell signaling processes and their misfunction often causes human disease. Proper understanding of IDP function not only requires the realistic characterization of their three-dimensional conformational ensembles at atomic-level resolution but also of the time scales of interconversion between their conformational substates. Large sets of experimental data are often used in combination with molecular modeling to restrain or bias models to improve agreement with experiment. It is shown here for the N-terminal transactivation domain of p53 (p53TAD) and Pup, which are two IDPs that fold upon binding to their targets, how the latest advancements in molecular dynamics (MD) simulations methodology produces native conformational ensembles by combining replica exchange with series of microsecond MD simulations. They closely reproduce experimental data at the global conformational ensemble level, in terms of the distribution properties of the radius of gyration tensor, and at the local level, in terms of NMR properties including 15N spin relaxation, without the need for reweighting. Further inspection revealed that 10-20% of the individual MD trajectories display the formation of secondary structures not observed in the experimental NMR data. The IDP ensembles were analyzed by graph theory to identify dominant inter-residue contact clusters and characteristic amino-acid contact propensities. These findings indicate that modern MD force fields with residue-specific backbone potentials can produce highly realistic IDP ensembles sampling a hierarchy of nano- and picosecond time scales providing new insights into their biological function.

DOI: https://doi.org/10.1371/journal.pcbi.1010036
J Chem Inf Model. 2022 Sep 06.

Developing Bonded Potentials for a Coarse-Grained Model of Intrinsically Disordered Proteins.

Azamat Rizuan, Nina Jovic, Tien M Phan, Young C Kim, Jeetain Mittal.

Recent advances in residue-level coarse-grained (CG) computational models have enabled molecular-level insights into biological condensates of intrinsically disordered proteins (IDPs), shedding light on the sequence determinants of their phase separation. The existing CG models that treat protein chains as flexible molecules connected via harmonic bonds cannot populate common secondary-structure elements. Here, we present a CG dihedral angle potential between four neighboring beads centered at Cα atoms to faithfully capture the transient helical structures of IDPs. In order to parameterize and validate our new model, we propose Cα-based helix assignment rules based on dihedral angles that succeed in reproducing the atomistic helicity results of a polyalanine peptide and folded proteins. We then introduce sequence-dependent dihedral angle potential parameters (εd) and use experimentally available helical propensities of naturally occurring 20 amino acids to find their optimal values. The single-chain helical propensities from the CG simulations for commonly studied prion-like IDPs are in excellent agreement with the NMR-based α-helix fraction, demonstrating that the new HPS-SS model can accurately produce structural features of IDPs. Furthermore, this model can be easily implemented for large-scale assembly simulations due to its simplicity.

DOI: https://doi.org/10.1021/acs.jcim.2c00450
Int J Mol Sci. 2022 Aug 29. pii: 9811. [Epub ahead of print]23(17):

Thermodynamics of π-π Interactions of Benzene and Phenol in Water.

Dooam Paik, Hankyul Lee, Hyungjun Kim, Jeong-Mo Choi.

  The π-π interaction is a major driving force that stabilizes protein assemblies during protein folding. Recent studies have additionally demonstrated its involvement in the liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs). As the participating residues in IDPs are exposed to water, π-π interactions for LLPS must be modeled in water, as opposed to the interactions that are often established at the hydrophobic domains of folded proteins. Thus, we investigated the association of free energies of benzene and phenol dimers in water by integrating van der Waals (vdW)-corrected density functional theory (DFT) and DFT in classical explicit solvents (DFT-CES). By comparing the vdW-corrected DFT and DFT-CES results with high-level wavefunction calculations and experimental solvation free energies, respectively, we established the quantitative credibility of these approaches, enabling a reliable prediction of the benzene and phenol dimer association free energies in water. We discovered that solvation influences dimer association free energies, but not significantly when no direct hydrogen-bond-type interaction exists between two monomeric units, which can be explained by the enthalpy-entropy compensation. Our comprehensive computational study of the solvation effect on π-π interactions in water could help us understand the molecular-level driving mechanism underlying the IDP phase behaviors.

Keywords:  QM/MM; enthalpy–entropy compensation; intrinsically disordered proteins; pi–pi interaction; solvation effects

DOI:  https://doi.org/10.3390/ijms23179811
J Chem Inf Model. 2022 Sep 09.

Toward Accurate Coarse-Grained Simulations of Disordered Proteins and Their Dynamic Interactions.

Yumeng Zhang, Xiaorong Liu, Jianhan Chen.

Intrinsically disordered proteins (IDPs) play crucial roles in cellular regulatory networks and are now recognized to often remain highly dynamic even in specific interactions and assemblies. Accurate description of these dynamic interactions is extremely challenging using atomistic simulations because of the prohibitive computational cost. Efficient coarse-grained approaches could offer an effective solution to overcome this bottleneck if they could provide an accurate description of key local and global properties of IDPs in both unbound and bound states. The recently developed hybrid-resolution (HyRes) protein model has been shown to be capable of providing a semiquantitative description of the secondary structure propensities of IDPs. Here, we show that greatly improved description of global structures and transient interactions can be achieved by introducing a solvent-accessible surface area-based implicit solvent term followed by reoptimization of effective interaction strengths. The new model, termed HyRes II, can semiquantitatively reproduce a wide range of local and global structural properties of a set of IDPs of various lengths and complexities. It can also distinguish the level of compaction between folded proteins and IDPs. In particular, applied to the disordered N-terminal transactivation domain (TAD) of tumor suppressor p53, HyRes II is able to recapitulate various nontrivial structural properties compared to experimental results, some of them to a level of accuracy that is almost comparable to results from atomistic explicit solvent simulations. Furthermore, we demonstrate that HyRes II can be used to simulate the dynamic interactions of TAD with the DNA-binding domain of p53, generating structural ensembles that are highly consistent with existing NMR data. We anticipate that HyRes II will provide an efficient and relatively reliable tool toward accurate coarse-grained simulations of dynamic protein interactions.

DOI: https://doi.org/10.1021/acs.jcim.2c00974
Sci Adv. 2022 Sep 09. 8(36): eabq3235

Coevolution of the Ess1-CTD axis in polar fungi suggests a role for phase separation in cold tolerance.

Ryan J Palumbo, Nathan McKean, Erinn Leatherman, Kevin E W Namitz, Laurie Connell, Aaron Wolfe, Kelsey Moody, Cene Gostinčar, Nina Gunde-Cimerman, Alaji Bah, Steven D Hanes.

Most of the world's biodiversity lives in cold (-2° to 4°C) and hypersaline environments. To understand how cells adapt to such conditions, we isolated two key components of the transcription machinery from fungal species that live in extreme polar environments: the Ess1 prolyl isomerase and its target, the carboxy-terminal domain (CTD) of RNA polymerase II. Polar Ess1 enzymes are conserved and functional in the model yeast, Saccharomyces cerevisiae. By contrast, polar CTDs diverge from the consensus (YSPTSPS)26 and are not fully functional in S. cerevisiae. These CTDs retain the critical Ess1 Ser-Pro target motifs, but substitutions at Y1, T4, and S7 profoundly affected their ability to undergo phase separation in vitro and localize in vivo. We propose that environmentally tuned phase separation by the CTD and other intrinsically disordered regions plays an adaptive role in cold tolerance by concentrating enzymes and substrates to overcome energetic barriers to metabolic activity.

DOI: https://doi.org/10.1126/sciadv.abq3235
Molecules. 2022 Sep 05. pii: 5726. [Epub ahead of print]27(17):

Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions.

Daiki Matsubara, Kento Kasahara, Hisham M Dokainish, Hiraku Oshima, Yuji Sugita.

  Proper balance between protein-protein and protein-water interactions is vital for atomistic molecular dynamics (MD) simulations of globular proteins as well as intrinsically disordered proteins (IDPs). The overestimation of protein-protein interactions tends to make IDPs more compact than those in experiments. Likewise, multiple proteins in crowded solutions are aggregated with each other too strongly. To optimize the balance, Lennard-Jones (LJ) interactions between protein and water are often increased about 10% (with a scaling parameter, λ = 1.1) from the existing force fields. Here, we explore the optimal scaling parameter of protein-water LJ interactions for CHARMM36m in conjunction with the modified TIP3P water model, by performing enhanced sampling MD simulations of several peptides in dilute solutions and conventional MD simulations of globular proteins in dilute and crowded solutions. In our simulations, 10% increase of protein-water LJ interaction for the CHARMM36m cannot maintain stability of a small helical peptide, (AAQAA)3 in a dilute solution and only a small modification of protein-water LJ interaction up to the 3% increase (λ = 1.03) is allowed. The modified protein-water interactions are applicable to other peptides and globular proteins in dilute solutions without changing thermodynamic properties from the original CHARMM36m. However, it has a great impact on the diffusive properties of proteins in crowded solutions, avoiding the formation of too sticky protein-protein interactions.

Keywords:  CHARMM36m; NBFIX; crowding simulations; enhanced sampling method; intrinsically disordered proteins; molecular dynamics simulation; molecular force fields; van der Waals interaction

DOI:  https://doi.org/10.3390/molecules27175726
ACS Omega. 2022 Aug 30. 7(34): 30281-30290

Curcumin Interacts with α-Synuclein Condensates To Inhibit Amyloid Aggregation under Phase Separation.

Bingkuan Xu, Jing Chen, Yinghui Liu.

The amyloid aggregation of α-synuclein (α-Syn) is highly associated with Parkinson's disease (PD). Discovering α-Syn amyloid inhibitors is one of the strategies for PD therapies. Recent studies suggested that α-Syn undergoes phase separation to accelerate amyloid aggregation. Molecules modulating α-Syn phase separation or transition have the potential to regulate amyloid aggregation. Here, we discovered that curcumin, a small natural molecule, interacts with α-Syn during phase separation. Our study showed that curcumin neither affects the formation of α-Syn condensates nor influences the initial morphology of α-Syn condensates. However, curcumin decreases the fluidity of α-Syn inside the condensates and efficiently inhibits α-Syn from turning into an amyloid. It also inhibits the amyloid aggregations of PD disease-related α-Syn E46K and H50Q mutants under phase separation. Furthermore, curcumin can destabilize preformed α-Syn amyloid aggregates in the condensates. Together, our findings demonstrate that curcumin regulates α-Syn amyloid formation during protein phase separation and reveal that α-Syn amyloid aggregation under phase separation can be modulated by small molecules.

DOI: https://doi.org/10.1021/acsomega.2c03534
FEBS J. 2022 Sep 05.

In-solution structure and oligomerization of human histone deacetylase 6 - an integrative approach.

Shivam Shukla, Jan Komarek, Zora Novakova, Jana Nedvedova, Kseniya Ustinova, Pavla Vankova, Alan Kadek, Charlotte Uetrecht, Haydyn Mertens, Cyril Barinka.

  Human histone deacetylase 6 (HDAC6) is a structurally unique, multidomain protein implicated in a variety of physiological processes including cytoskeletal remodeling and the maintenance of cellular homeostasis. Our current understanding of the HDAC6 structure is limited to isolated domains and a holistic picture of the full-length protein structure, including possible domain interactions, is missing. Here, we used an integrative structural biology approach to build a solution model of HDAC6 by combining experimental data from several orthogonal biophysical techniques complemented by molecular modeling. We show that HDAC6 is best described as a mosaic of folded and intrinsically disordered domains that in-solution adopts an ensemble of conformations without any stable interactions between structured domains. Furthermore, HDAC6 forms dimers/higher oligomers in a concentration-dependent manner and its oligomerization is mediated via the positively charged N-terminal microtubule-binding domain. Our findings provide the first insights into the structure of full-length human HDAC6 and can be used as a basis for further research into structure-function and physiological studies of this unique deacetylase.

Keywords:  Acetylation; analytical ultracentrifugation; hydrogen/deuterium exchange; intrinsically disordered regions; oligomerization; small-angle X-ray scattering

DOI:  https://doi.org/10.1111/febs.16616
J Cell Biol. 2022 Oct 03. pii: e202107022. [Epub ahead of print]221(10):

Tensin3 interaction with talin drives the formation of fibronectin-associated fibrillar adhesions.

Paul Atherton, Rafaella Konstantinou, Suat Peng Neo, Emily Wang, Eleonora Balloi, Marina Ptushkina, Hayley Bennett, Kath Clark, Jayantha Gunaratne, David Critchley, Igor Barsukov, Edward Manser, Christoph Ballestrem.

The formation of healthy tissue involves continuous remodeling of the extracellular matrix (ECM). Whilst it is known that this requires integrin-associated cell-ECM adhesion sites (CMAs) and actomyosin-mediated forces, the underlying mechanisms remain unclear. Here, we examine how tensin3 contributes to the formation of fibrillar adhesions (FBs) and fibronectin fibrillogenesis. Using BioID mass spectrometry and a mitochondrial targeting assay, we establish that tensin3 associates with the mechanosensors such as talin and vinculin. We show that the talin R11 rod domain binds directly to a helical motif within the central intrinsically disordered region (IDR) of tensin3, whilst vinculin binds indirectly to tensin3 via talin. Using CRISPR knock-out cells in combination with defined tensin3 mutations, we show (i) that tensin3 is critical for the formation of α5β1-integrin FBs and for fibronectin fibrillogenesis, and (ii) the talin/tensin3 interaction drives this process, with vinculin acting to potentiate it.

DOI: https://doi.org/10.1083/jcb.202107022
Nat Cell Biol. 2022 Sep 08.

Heat-shock chaperone HSPB1 regulates cytoplasmic TDP-43 phase separation and liquid-to-gel transition.

Shan Lu, Jiaojiao Hu, Olubankole Aladesuyi Arogundade, Alexander Goginashvili, Sonia Vazquez-Sanchez, Jolene K Diedrich, Jinge Gu, Jacob Blum, Spencer Oung, Qiaozhen Ye, Haiyang Yu, John Ravits, Cong Liu, John R Yates, Don W Cleveland.

While acetylated, RNA-binding-deficient TDP-43 reversibly phase separates within nuclei into complex droplets (anisosomes) comprised of TDP-43-containing liquid outer shells and liquid centres of HSP70-family chaperones, cytoplasmic aggregates of TDP-43 are hallmarks of multiple neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Here we show that transient oxidative stress, proteasome inhibition or inhibition of the ATP-dependent chaperone activity of HSP70 provokes reversible cytoplasmic TDP-43 de-mixing and transition from liquid to gel/solid, independently of RNA binding or stress granules. Isotope labelling mass spectrometry was used to identify that phase-separated cytoplasmic TDP-43 is bound by the small heat-shock protein HSPB1. Binding is direct, mediated through TDP-43's RNA binding and low-complexity domains. HSPB1 partitions into TDP-43 droplets, inhibits TDP-43 assembly into fibrils, and is essential for disassembly of stress-induced TDP-43 droplets. A decrease in HSPB1 promotes cytoplasmic TDP-43 de-mixing and mislocalization. HSPB1 depletion was identified in spinal motor neurons of patients with ALS containing aggregated TDP-43. These findings identify HSPB1 to be a regulator of cytoplasmic TDP-43 phase separation and aggregation.

DOI: https://doi.org/10.1038/s41556-022-00988-8