bims-indpro 2022-03-27 papers

bims-indpro

Biomed News

on Intrinsically disordered proteins

Issue of 2022–03–27
twenty papers selected by
Sara Mingu, Johannes Gutenberg University

Atomic resolution dynamics of cohesive interactions in phase-separated Nup98 FG domains.
The auto-inhibition mechanism of transcription factor Ets-1 induced by phosphorylation on the intrinsically disordered region.
Intrinsic disorder in proteins associated with oxidative stress-induced JNK signaling.
Biophysical characterization of the interaction of Atg8 with a disordered region of Nup159 involved in selective autophagy of the nuclear pore complex.
Dilute phase oligomerization can oppose phase separation and modulate material properties of a ribonucleoprotein condensate.
Hyperphosphorylation tunes TDP-43 solubility.
Modeling the Dynamics of Protein-Protein Interfaces, How and Why?
The Amazing World of IDPs in Human Diseases II.
Small Molecules Modulate Liquid-to-Solid Transitions in Phase-separated Tau Condensates.
Urea ameliorates trimethylamine N-oxide-Induced aggregation of intrinsically disordered α-casein protein: the other side of the urea-methylamine counteraction.
The importance of the compact disordered state in the fuzzy interactions between intrinsically disordered proteins.
Different Oligomeric States of the Tumor Suppressor p53 Show Identical Binding Behavior Towards the S100β Homodimer.
Structural dynamics of the C-terminal X domain of Nipah and Hendra viruses controls the attachment to the C-terminal tail of the nucleocapsid protein.
Iron-induced NCOA4 condensation regulates ferritin fate and iron homeostasis.
Interaction kinetics reveal distinct properties of conformational ensembles of three-repeat and four-repeat tau proteins.
Identifying Intrinsically Disordered Protein Regions through a Deep Neural Network with Three Novel Sequence Features.
Initial heat analysis in dissociation isothermal titration calorimetry: An analytical tool for thermodynamic dissection of biomolecular condensates.
The Role of Post-Translational Modifications on the Structure and Function of Tau Protein.
How well does molecular simulation reproduce environment-specific conformations of the intrinsically disordered peptides PLP, TP2 and ONEG?
On the nuclear pore complex and its emerging role in cellular mechanotransduction.

Nat Commun. 2022 Mar 21. 13(1): 1494

Atomic resolution dynamics of cohesive interactions in phase-separated Nup98 FG domains.

Eszter E Najbauer, Sheung Chun Ng, Christian Griesinger, Dirk Görlich, Loren B Andreas.

Cohesive FG domains assemble into a condensed phase forming the selective permeability barrier of nuclear pore complexes. Nanoscopic insight into fundamental cohesive interactions has long been hampered by the sequence heterogeneity of native FG domains. We overcome this challenge by utilizing an engineered perfectly repetitive sequence and a combination of solution and magic angle spinning NMR spectroscopy. We map the dynamics of cohesive interactions in both phase-separated and soluble states at atomic resolution using TROSY for rotational correlation time (TRACT) measurements. We find that FG repeats exhibit nanosecond-range rotational correlation times and remain disordered in both states, although FRAP measurements show slow translation of phase-separated FG domains. NOESY measurements enable the direct detection of contacts involved in cohesive interactions. Finally, increasing salt concentration and temperature enhance phase separation and decrease local mobility of FG repeats. This lower critical solution temperature (LCST) behaviour indicates that cohesive interactions are driven by entropy.

DOI: https://doi.org/10.1038/s41467-022-28821-8
Comput Struct Biotechnol J. 2022 ;20 1132-1141

The auto-inhibition mechanism of transcription factor Ets-1 induced by phosphorylation on the intrinsically disordered region.

Shangbo Ning, Hong-Jun Chao, Shuangli Li, Rui Zhou, Lei Zou, Xu Zhang, Jun Liu, Dazhong Yan, Mojie Duan.

  As the most abundant post-translation modifications (PTMs), the phosphorylation usually occurred on the intrinsically disordered regions (IDRs). The regulation on the structures and interactions of IDRs induced by phosphorylation is critical to the function performing. The eukaryotic transcription factor 1 (Ets-1) is a member of transcription factor family, which participates in many important biological processes. The DNA-binding ability of Ets-1 is auto-inhibited by a disordered serine-rich region (SRR) on the Ets-1. The inhibition ability of SRR is greatly enhanced by the phosphorylation of the serine on the SRR. Nevertheless, the molecular mechanisms of the phosphorylation regulation on the structure and activity of Ets-1 are still unclear and under debates. By using both of the molecular simulations and biochemical experiments, we studied the molecule mechanism of phosphorylation regulation on the auto-inhibition of the Ets-1. The reasons of stabilization of Ets-1 core by phosphorylation on SRR region were elucidated. More important, the free energy landscapes (FEL) show that both of the steric hindrance and allosteric regulation are responsible for the DNA-binding inhibitory induced by phosphorylation, but the steric effects contribute greater than the allosteric regulation. The phosphorylation not only enhances the electrostatic interactions to facilitate the steric impedance, but also promotes the formation of hydrophobic residue clusters, which provide major driven force for the allosteric regulation. The structural basis of auto-inhibition of Ets-1 induced by the phosphorylation revealed in this study would great help the developing of inhibitor for the cancer therapy.

Keywords:  BE, Biased-exchange; CD, Circular dichroism; CS, Chemical shift; DCC, Dynamic correlation coefficient; EMSA, Electrophoretic mobility shift assay; FEL, Free energy landscape; HRC, Hydrophobic residue clusters; IDRs, Intrinsically disordered regions; IM, Inhibitory module; PT-WTE, Parallel tempering Well-Tempered Ensemble; PTMs, Post-translation modifications; RMSE, Root-mean-square error; SRR, Serine-rich region

DOI:  https://doi.org/10.1016/j.csbj.2022.02.025
Cell Mol Life Sci. 2022 Mar 24. 79(4): 202

Intrinsic disorder in proteins associated with oxidative stress-induced JNK signaling.

Bhuvaneshwari R Gehi, Kundlik Gadhave, Vladimir N Uversky, Rajanish Giri.

  The c-Jun N-terminal kinase (JNK) signaling cascade is a mitogen-activated protein kinase (MAPK) signaling pathway that can be activated in response to a wide range of environmental stimuli. Based on the type, degree, and duration of the stimulus, the JNK signaling cascade dictates the fate of the cell by influencing gene expression through its substrate transcription factors. Oxidative stress is a result of a disturbance in the pro-oxidant/antioxidant homeostasis of the cell and is associated with a large number of diseases, such as neurodegenerative disorders, cancer, diabetes, cardiovascular diseases, and disorders of the immune system, where it activates the JNK signaling pathway. Among different biological roles ascribed to the intrinsically disordered proteins (IDPs) and hybrid proteins containing ordered domains and intrinsically disordered protein regions (IDPRs) are signaling hub functions, as intrinsic disorder allows proteins to undertake multiple interactions, each with a different consequence. In order to ensure precise signaling, the cellular abundance of IDPs is highly regulated, and mutations or changes in abundance of IDPs/IDPRs are often associated with disease. In this study, we have used a combination of six disorder predictors to evaluate the presence of intrinsic disorder in proteins of the oxidative stress-induced JNK signaling cascade, and as per our findings, none of the 18 proteins involved in this pathway are ordered. The highest level of intrinsic disorder was observed in the scaffold proteins, JIP1, JIP2, JIP3; dual specificity phosphatases, MKP5, MKP7; 14-3-3ζ and transcription factor c-Jun. The MAP3Ks, MAP2Ks, MAPKs, TRAFs, and thioredoxin were the proteins that were predicted to be moderately disordered. Furthermore, to characterize the predicted IDPs/IDPRs in the proteins of the JNK signaling cascade, we identified the molecular recognition features (MoRFs), posttranslational modification (PTM) sites, and short linear motifs (SLiMs) associated with the disordered regions. These findings will serve as a foundation for experimental characterization of disordered regions in these proteins, which represents a crucial step for a better understanding of the roles of IDPRs in diseases associated with this important pathway.

Keywords:  Intrinsically disordered protein regions; Intrinsically disordered proteins; Molecular recognition features; Oxidative stress; Posttranslational modifications; Short linear Motifs; c-Jun N-terminal kinase (JNK) signaling pathway

DOI:  https://doi.org/10.1007/s00018-022-04230-4
Biochem Biophys Res Commun. 2022 Mar 12. pii: S0006-291X(22)00388-6. [Epub ahead of print]604 172-178

Biophysical characterization of the interaction of Atg8 with a disordered region of Nup159 involved in selective autophagy of the nuclear pore complex.

RyeongHyeon Kim, Junseock Koh.

  A functional proteome in the cell is maintained by coordinate regulation of biogenesis, folding, and degradation of cellular proteins. Although the degradation pathways have been extensively characterized for various substrates, it remains elusive how large multiprotein complexes are selectively degraded. Recent investigations have discovered selective autophagic degradation of the yeast Nuclear Pore Complex (NPC) consisting of ∼500 proteins and mediating selective nucleocytoplasmic transport. To understand the underlying molecular mechanism of NPC-phagy, we performed biophysical characterization of the interaction between Atg8 and an intrinsically disordered region (IDR) of Nup159 involved in the initial recognition step. In particular, from the systematic isothermal titration calorimetry (ITC) experiments, we determined the thermodynamic parameters and discovered a significant negative heat capacity change (ΔCp°) for the interaction. Furthermore, the heat capacity change becomes more negative at higher temperatures, yielding a negative curvature in the observed enthalpy change (ΔH°) with respect to temperature. This thermodynamic feature was analyzed in terms of coupling between binding and conformational equilibria of Atg8 and/or Nup159 IDR. We interpret the coupled conformational equilibria as disorder-to-order transitions or local stabilizations of Nup159 IDR and/or partially unfolded Atg8 upon binding. A potential impact of the proposed coupling in the initial step of NPC-phagy is discussed. In a broader view, our study demonstrates that a negative curvature of ΔH° can be used as a probe for conformational selection processes in the interactions of IDRs with their target proteins.

Keywords:  Atg8; Coupled conformational change; Heat capacity change; Intrinsically disordered region; Nucleoporin; Selective autophagy

DOI:  https://doi.org/10.1016/j.bbrc.2022.03.056
Proc Natl Acad Sci U S A. 2022 Mar 29. 119(13): e2120799119

Dilute phase oligomerization can oppose phase separation and modulate material properties of a ribonucleoprotein condensate.

Ian Seim, Ammon E Posey, Wilton T Snead, Benjamin M Stormo, Daphne Klotsa, Rohit V Pappu, Amy S Gladfelter.

  SignificanceA large subclass of biomolecular condensates are linked to RNA regulation and are known as ribonucleoprotein (RNP) bodies. While extensive work has identified driving forces for biomolecular condensate formation, relatively little is known about forces that oppose assembly. Here, using a fungal RNP protein, Whi3, we show that a portion of its intrinsically disordered, glutamine-rich region modulates phase separation by forming transient alpha helical structures that promote the assembly of dilute phase oligomers. These oligomers detour Whi3 proteins from condensates, thereby impacting the driving forces for phase separation, the protein-to-RNA ratio in condensates, and the material properties of condensates. Our findings show how nanoscale conformational and oligomerization equilibria can influence mesoscale phase equilibria.

Keywords:  oligomerization; phase separation; ribonucleoprotein complexes

DOI:  https://doi.org/10.1073/pnas.2120799119
EMBO J. 2022 Mar 21. e111062

Hyperphosphorylation tunes TDP-43 solubility.

Garrett M Ginell, Alex S Holehouse.

Post-translational modifications of intrinsically disordered regions (IDRs) enable changes in sequence chemistry, which in turn can tune conformational behavior and molecular interactions. In this issue of The EMBO Journal, Gruijs da Silva et al disentangle the effect of hyperphosphorylation on the C-terminal domain of TDP-43, a key IDR implicated in Amyotrophic Lateral Sclerosis (ALS).

DOI: https://doi.org/10.15252/embj.2022111062
Molecules. 2022 Mar 11. pii: 1841. [Epub ahead of print]27(6):

Modeling the Dynamics of Protein-Protein Interfaces, How and Why?

Ezgi Karaca, Chantal Prévost, Sophie Sacquin-Mora.

  Protein-protein assemblies act as a key component in numerous cellular processes. Their accurate modeling at the atomic level remains a challenge for structural biology. To address this challenge, several docking and a handful of deep learning methodologies focus on modeling protein-protein interfaces. Although the outcome of these methods has been assessed using static reference structures, more and more data point to the fact that the interaction stability and specificity is encoded in the dynamics of these interfaces. Therefore, this dynamics information must be taken into account when modeling and assessing protein interactions at the atomistic scale. Expanding on this, our review initially focuses on the recent computational strategies aiming at investigating protein-protein interfaces in a dynamic fashion using enhanced sampling, multi-scale modeling, and experimental data integration. Then, we discuss how interface dynamics report on the function of protein assemblies in globular complexes, in fuzzy complexes containing intrinsically disordered proteins, as well as in active complexes, where chemical reactions take place across the protein-protein interface.

Keywords:  molecular modeling; protein docking; protein dynamics; protein interactions; protein interfaces

DOI:  https://doi.org/10.3390/molecules27061841
Biomolecules. 2022 Feb 25. pii: 369. [Epub ahead of print]12(3):

The Amazing World of IDPs in Human Diseases II.

Simona Maria Monti, Giuseppina De Simone, Emma Langella.

Intrinsically Disordered Proteins (IDPs) lack stable tertiary and secondary structures and are extensively distributed across eukaryotic cells, playing critical roles in cell signaling and regulation [...].

DOI: https://doi.org/10.3390/biom12030369
Angew Chem Int Ed Engl. 2022 Mar 23.

Small Molecules Modulate Liquid-to-Solid Transitions in Phase-separated Tau Condensates.

Sagun Jonchhe, Wei Pan, Pravin Pokhrel, Hanbin Mao.

  In Tau protein condensates formed by the Liquid-Liquid Phase Separation (LLPS) process, liquid-to-solid transitions lead to the formation of fibrils implicated in Alzheimer's disease. Here, by tracking two contacting Tau-rich droplets using a simple and nonintrusive video microscopy, we found that the halftime of the liquid-to-solid transition in the Tau condensate is affected by the Hofmeister series according to the solvation energy of anions. After dissecting functional groups of physiologically relevant small molecules using a multivariate approach, we found that charged groups facilitate the liquid-to-solid transition in a manner similar to the Hofmeister effect whereas hydrophobic alkyl chains and aromatic rings inhibit the transition. Our results not only elucidate the driving force of the liquid-to-solid transition in Tau condensates, but also provide guidelines to design small molecules to modulate this important transition for many biological functions for the first time.

Keywords:  liquid-liquid phase separation, liquid-to-solid transition, Tau condensates, Hofmeister effect, small-molecule modulation

DOI:  https://doi.org/10.1002/anie.202113156
J Biomol Struct Dyn. 2022 Mar 22. 1-8

Urea ameliorates trimethylamine N-oxide-Induced aggregation of intrinsically disordered α-casein protein: the other side of the urea-methylamine counteraction.

Mohd Younus Bhat, Irfan Ahmad Mir, Mahboob Ul Hussain, Laishram Rajendrakumar Singh, Tanveer Ali Dar.

  Trimethylamine N-oxide (TMAO) is generally accumulated by organisms and cells to cope with denaturing effects of urea/hydrodynamic pressure on proteins and can even reverse misfolded or aggregated proteins so as to sustain proteostasis. However, most of the work regarding this urea-TMAO counteraction has been performed on folded proteins. Compelling evidence of aggregation of intrinsically disordered proteins (IDPs) like tau, α-synuclein, amyloid β etc., by TMAO and its potential to impact various protein processes in absence of stressing agents (such as urea) suggests that the contrary feature of interaction profiles of urea and TMAO maximizes their chances of offsetting the perturbing effects of each other. Recently, our lab observed that TMAO induces aggregation of α-casein, a model IDP. In this context, the present study, for the first time, evaluated urea for its potential to counteract the TMAO-induced aggregation of α-casein. It was observed that, at the biologically relevant ratios of 2:1 or 3:1 (urea:TMAO), urea was able to inhibit TMAO-induced aggregation of α-casein. However, urea did not reverse the effects of TMAO on α-casein. In addition to this, α-casein in presence of 1:1 and 2:1 urea:TMAO working ratios show aggregation-induced cytotoxic effect on HEK-293, Neuro2A and HCT-116 cell lines but not in presence of 3:1 working ratio, as there was no aggregation at all. The study infers that the accumulation of TMAO alone in the cells, in absence of stress (such as urea), might result in loss of conformational flexibility and aggregation of IDPs in TMAO accumulating organisms.Communicated by Ramaswamy H. Sarma.

Keywords:  TMAO; Urea; aggregation; counteraction; intrinsically disordered proteins

DOI:  https://doi.org/10.1080/07391102.2022.2053744
Chem Sci. 2022 Feb 23. 13(8): 2363-2377

The importance of the compact disordered state in the fuzzy interactions between intrinsically disordered proteins.

Dan Wang, Shaowen Wu, Dongdong Wang, Xingyu Song, Maohua Yang, Wolun Zhang, Shaohui Huang, Jingwei Weng, Zhijun Liu, Wenning Wang.

The intrinsically disordered C-terminal domain (CTD) of protein 4.1G is able to specifically bind a 26-residue intrinsically disordered region of NuMA, forming a dynamic fuzzy complex. As one of a few cases of extremely fuzzy interactions between two intrinsically disordered proteins/regions (IDPs/IDRs) without induced folding, the principle of the binding is unknown. Here, we combined experimental and computational methods to explore the detailed mechanism of the interaction between 4.1G-CTD and NuMA. MD simulations suggest that the kinetic hub states in the structure ensemble of 4.1G-CTD are favorable in the fuzzy complex. The feature of these hub states is that the binding 'hot spot' motifs βA and βB exhibit β strand propensities and are well packed to each other. The binding between 4.1G-CTD and NuMA is disrupted at low pH, which changes the intramolecular packing of 4.1G-CTD and weakens the packing between βA and βB motifs. Low pH conditions also lead to increased hydrodynamic radius and acceleration of backbone dynamics of 4.1G-CTD. All these results underscore the importance of tertiary structural arrangements and overall compactness of 4.1G-CTD in its binding to NuMA, i.e. the compact disordered state of 4.1G-CTD is crucial for binding. Different from the short linear motifs (SLiMs) that are often found to mediate IDP interactions, 4.1G-CTD functions as an intrinsically disordered domain (IDD), which is a functional and structural unit similar to conventional protein domains. This work sheds light on the molecular recognition mechanism of IDPs/IDRs and expands the conventional structure-function paradigm in protein biochemistry.

DOI: https://doi.org/10.1039/d1sc06825c
Chembiochem. 2022 Mar 25.

Different Oligomeric States of the Tumor Suppressor p53 Show Identical Binding Behavior Towards the S100β Homodimer.

Andrea Sinz, Alan An Jung Wei, Claudio Iacobucci, Wiebke Schultze, Christian H Ihling, Christian Arlt.

  The tumor suppressor protein p53 is a transcription factor that is referred to as the "guardian of the genome" and plays an important role in cancer development. P53 is active as a homotetramer;the S100β homodimer binds to the intrinsically disordered C -terminus of p53 affecting its transcriptional activity.The p53/S100β complex is regarded as highly promising therapeutic target in cancer. It has been suggested that S100β exerts its oncogenic effects by altering the p53 oligomeric state. Our aim was to study the structures and oligomerization behavior of different p53/S100β complexes by ESI-MS, XL-MS, and SPR. Wild-type p53 and single amino acid variants, representing different oligomeric states of p53 were individually investigated regarding their binding behavior towards S100β. The stoichiometry of the different p53/S100β complexes were determined by ESI-MS showing that tetrameric, dimeric, and monomeric p53 variants all bind to an S100β dimer. In addition, XL-MS revealed the topologies of the p53/S100β complexes to be independent of p53's oligomeric state. With SPR, the thermodynamic parameters were determined for S100β binding to tetrameric, dimeric or monomeric p53 variants. Our data prove that the S100β homodimer binds to different oligomeric states of p53 irrespective of p53´s oligomerization state and similar binding affinities were observed. This emphasizes the need for alternative explanations to describe the molecular mechanisms underlying p53/S100β interaction.

Keywords:  Mass spectrometry; S100β; intrinsically disordered proteins; p53; tumor suppressor

DOI:  https://doi.org/10.1002/cbic.202100665
J Mol Biol. 2022 Mar 19. pii: S0022-2836(22)00125-5. [Epub ahead of print] 167551

Structural dynamics of the C-terminal X domain of Nipah and Hendra viruses controls the attachment to the C-terminal tail of the nucleocapsid protein.

Jean-Marie Bourhis, Filip Yabukarski, Guillaume Communie, Robert Schneider, Valentina A Volchkova, Mickaël Frénéat, Francine Gérard, Corinne Ducournau, Caroline Mas, Nicolas Tarbouriech, Malene Ringkjøbing Jensen, Viktor E Volchkov, Martin Blackledge, Marc Jamin.

  To understand the dynamic interactions between the phosphoprotein (P) and the nucleoprotein (N) within the transcription/replication complex of the Paramyxoviridae and to decipher their roles in regulating viral multiplication, we characterized the structural properties of the C-terminal X domain (PXD) of Nipah (NiV) and Hendra virus (HeV) P protein. In crystals, isolated NiV PXD adopted a two-helix dimeric conformation, which was incompetent for binding its partners, but in complex with the C-terminal intrinsically disordered tail of the N protein (NTAIL), it folded into a canonical 3H bundle conformation. In solution, SEC-MALLS, SAXS and NMR spectroscopy experiments indicated that both NiV and HeV PXD were larger in size than expected for compact proteins of the same molecular mass and were in conformational exchange between a compact three-helix (3H) bundle and partially unfolded conformations, where helix α3 is detached from the other two. Some measurements also provided strong evidence for dimerization of NiV PXD in solution but not for HeV PXD. Ensemble modeling of experimental SAXS data and statistical-dynamical modeling reconciled all these data, yielding a model where NiV and HeV PXD exchanged between different conformations, and where NiV but not HeV PXD formed dimers. Finally, recombinant NiV comprising a chimeric P carrying HeV PXD was rescued and compared with parental NiV. Experiments carried out in cellula demonstrated that the replacement of PXD did not significantly affect the replication dynamics while caused a slight virus attenuation, suggesting a possible role of the dimerization of NiV PXD in viral replication.

Keywords:  Mononegavirales; Nipah virus; X-ray crystallography; intrinsically disordered protein; nuclear magnetic resonance; phosphoprotein; small-angle X-ray scattering

DOI:  https://doi.org/10.1016/j.jmb.2022.167551
EMBO Rep. 2022 Mar 23. e54278

Iron-induced NCOA4 condensation regulates ferritin fate and iron homeostasis.

Sota Kuno, Hiroaki Fujita, Yu-Ki Tanaka, Yasumitsu Ogra, Kazuhiro Iwai.

  Iron is not only essential but also a toxic trace element. Under iron repletion, ferritin maintains cellular iron homeostasis by storing iron to avoid iron toxicity. Under iron depletion, the ferritin-specific autophagy adaptor NCOA4 delivers ferritin to lysosomes via macroautophagy to enable cells to use stored iron. Here, we show that NCOA4 also plays crucial roles in the regulation of ferritin fate under iron repletion. NCOA4 forms insoluble condensates via multivalent interactions generated by the binding of iron to its intrinsically disordered region. This sequesters NCOA4 away from ferritin and allows ferritin accumulation in the early phase of iron repletion. Under prolonged iron repletion, NCOA4 condensates can deliver ferritin to lysosomes via a TAX1BP1-dependent non-canonical autophagy pathway, thereby preventing relative iron deficiency due to excessive iron storage and reduced iron uptake. Together, these observations suggest that the NCOA4-ferritin axis modulates intracellular iron homeostasis in accordance with cellular iron availability.

Keywords:  NCOA4; autophagy; ferritin; iron metabolism; phase separation

DOI:  https://doi.org/10.15252/embr.202154278
FEBS Lett. 2022 Mar 24.

Interaction kinetics reveal distinct properties of conformational ensembles of three-repeat and four-repeat tau proteins.

Lenka Hornakova, Jakub Sinsky, Maria Janubova, Anna Mederlyova, Natalia Paulenka Ivanovova, Juraj Piestansky, Andrej Kovac, Jaroslav Galba, Rostislav Skrabana, Ondrej Cehlar.

  Tau protein is an intrinsically disordered protein. Its physiological state is best described as a conformational ensemble (CE) of metastable structures interconverting on the local and molecular scale. The monoclonal antibody DC39C recognizes a linear C-terminal tau epitope, and as the tau interaction partner, its binding parameters report about tau CE. Association kinetics of DC39C binding, together with crosslinking mass spectrometry, show differences in the accessibility of the C-terminus in CEs of tau isoforms. Furthermore, removal of the C-terminus accelerated the aggregation kinetics of three-repeat tau proteins. Our results suggest a novel mechanism of splicing-driven regulation of the tau C-terminal domain with consequences on the specific roles of tau isoforms in microtubule assembly and pathological aggregation.

Keywords:  Tau protein isoforms; aggregation; conformational ensemble; crosslinking mass spectrometry; interaction kinetics; intrinsically disordered proteins; microscale thermophoresis; monoclonal antibody; surface plasmon resonance

DOI:  https://doi.org/10.1002/1873-3468.14339
Life (Basel). 2022 Feb 26. pii: 345. [Epub ahead of print]12(3):

Identifying Intrinsically Disordered Protein Regions through a Deep Neural Network with Three Novel Sequence Features.

Jiaxiang Zhao, Zengke Wang.

  The fast, reliable, and accurate identification of IDPRs is essential, as in recent years it has come to be recognized more and more that IDPRs have a wide impact on many important physiological processes, such as molecular recognition and molecular assembly, the regulation of transcription and translation, protein phosphorylation, cellular signal transduction, etc. For the sake of cost-effectiveness, it is imperative to develop computational approaches for identifying IDPRs. In this study, a deep neural structure where a variant VGG19 is situated between two MLP networks is developed for identifying IDPRs. Furthermore, for the first time, three novel sequence features-i.e., persistent entropy and the probabilities associated with two and three consecutive amino acids of the protein sequence-are introduced for identifying IDPRs. The simulation results show that our neural structure either performs considerably better than other known methods or, when relying on a much smaller training set, attains a similar performance. Our deep neural structure, which exploits the VGG19 structure, is effective for identifying IDPRs. Furthermore, three novel sequence features-i.e., the persistent entropy and the probabilities associated with two and three consecutive amino acids of the protein sequence-could be used as valuable sequence features in the further development of identifying IDPRs.

Keywords:  VGG19; intrinsically disordered proteins; the persistent entropy; the probabilities associated with two and three consecutive amino acids

DOI:  https://doi.org/10.3390/life12030345
Biochem Biophys Res Commun. 2022 Mar 15. pii: S0006-291X(22)00394-1. [Epub ahead of print]605 127-133

Initial heat analysis in dissociation isothermal titration calorimetry: An analytical tool for thermodynamic dissection of biomolecular condensates.

Jean Nyoung Yun, Junseock Koh.

  Multi-domain proteins or intrinsically disordered proteins (IDPs) often undergo liquid-liquid phase separation (LLPS) and form membraneless organelles or protein condensates. Such compartmentalization is considered critical in many cellular processes dynamically modulated by various external signals. However, molecular mechanisms underlying potential regulatory functions of the protein condensates remain obscure due to a limited understanding of the driving forces for their assembly. Here we propose isothermal titration calorimetry (ITC) as an efficient analytical tool to dissociate condensates and measure the corresponding dissociation heat. Subsequent analysis of the initial dissociation heat as a function of total protein concentration allows simple and accurate determination of the thermodynamic parameters for cooperative condensate formations including the dissociation (or condensation) enthalpy and the critical protein concentration. By performing systematic simulations, we further demonstrate that the initial heat analysis is sufficiently robust to quantitatively dissect protein condensates with a broad range of thermodynamic properties. Therefore, our proposed method analyzing the initial heat measured in dissociation ITC provides opportunities to further scrutinize the thermodynamic quantities as functions of solution variables to explore the molecular driving forces of LLPS.

Keywords:  Biomolecular condensates; Critical protein concentration; Dissociation enthalpy; Initial heat analysis; Isothermal titration calorimetry; Liquid liquid phase separation

DOI:  https://doi.org/10.1016/j.bbrc.2022.03.063
J Mol Neurosci. 2022 Mar 24.

The Role of Post-Translational Modifications on the Structure and Function of Tau Protein.

Haiqiong Ye, Yue Han, Ping Li, Zhengding Su, Yongqi Huang.

  Involving addition of chemical groups or protein units to specific residues of the target protein, post-translational modifications (PTMs) alter the charge, hydrophobicity, and conformation of a protein, which in tune influences protein function, protein - protein interaction, and protein aggregation. While the occurrence of PTMs is dynamic and subject to regulations, conformational disorder of the target protein facilitates PTMs. The microtubule-associated protein tau is a typical intrinsically disordered protein that undergoes a variety of PTMs including phosphorylation, acetylation, ubiquitination, methylation, and oxidation. Accumulated evidence shows that these PTMs play a critical role in regulating tau-microtubule interaction, tau localization, tau degradation and aggregation, and reinforces the correlation between tau PTMs and pathogenesis of neurodegenerative disease. Here, we review tau PTMs with an emphasis on their influence on tau structure. With available biophysical characterization results, we describe how PTMs induce conformational changes in tau monomer and regulate tau aggregation. Compared to functional analysis of tau PTMs, biophysical characterization of tau PTMs is lagging. While it is challenging, characterizing the specific effects of PTMs on tau conformation and interaction is indispensable to unravel the tau PTM code.

Keywords:  Neurodegenerative disease; Post-translational modification; Protein aggregation; Tau protein; Tauopathies

DOI:  https://doi.org/10.1007/s12031-022-02002-0
Chem Sci. 2022 Feb 16. 13(7): 1957-1971

How well does molecular simulation reproduce environment-specific conformations of the intrinsically disordered peptides PLP, TP2 and ONEG?

Lauren M Reid, Ileana Guzzetti, Tor Svensson, Anna-Carin Carlsson, Wu Su, Tomas Leek, Lena von Sydow, Werngard Czechtizky, Marija Miljak, Chandra Verma, Leonardo De Maria, Jonathan W Essex.

Understanding the conformational ensembles of intrinsically disordered proteins and peptides (IDPs) in their various biological environments is essential for understanding their mechanisms and functional roles in the proteome, leading to a greater knowledge of, and potential treatments for, a broad range of diseases. To determine whether molecular simulation is able to generate accurate conformational ensembles of IDPs, we explore the structural landscape of the PLP peptide (an intrinsically disordered region of the proteolipid membrane protein) in aqueous and membrane-mimicking solvents, using replica exchange with solute scaling (REST2), and examine the ability of four force fields (ff14SB, ff14IDPSFF, CHARMM36 and CHARMM36m) to reproduce literature circular dichroism (CD) data. Results from variable temperature (VT) 1H and Rotating frame Overhauser Effect SpectroscopY (ROESY) nuclear magnetic resonance (NMR) experiments are also presented and are consistent with the structural observations obtained from the simulations and CD. We also apply the optimum simulation protocol to TP2 and ONEG (a cell-penetrating peptide (CPP) and a negative control peptide, respectively) to gain insight into the structural differences that may account for the observed difference in their membrane-penetrating abilities. Of the tested force fields, we find that CHARMM36 and CHARMM36m are best suited to the study of IDPs, and accurately predict a disordered to helical conformational transition of the PLP peptide accompanying the change from aqueous to membrane-mimicking solvents. We also identify an α-helical structure of TP2 in the membrane-mimicking solvents and provide a discussion of the mechanistic implications of this observation with reference to the previous literature on the peptide. From these results, we recommend the use of CHARMM36m with the REST2 protocol for the study of environment-specific IDP conformations. We believe that the simulation protocol will allow the study of a broad range of IDPs that undergo conformational transitions in different biological environments.

DOI: https://doi.org/10.1039/d1sc03496k
APL Bioeng. 2022 Mar;6(1): 011504

On the nuclear pore complex and its emerging role in cellular mechanotransduction.

Atsushi Matsuda, Mohammad R K Mofrad.

The nuclear pore complex (NPC) is a large protein assembly that perforates the nuclear envelope and provides a sole gateway for traffic between the cytoplasm and the nucleus. The NPC controls the nucleocytoplasmic transport by selectively allowing cargoes such as proteins and mRNA to pass through its central channel, thereby playing a vital role in protecting the nuclear component and regulating gene expression and protein synthesis. The selective transport through the NPC originates from its exquisite molecular structure featuring a large scaffold and the intrinsically disordered central channel domain, but the exact mechanism underlying the selective transport remains elusive and is the subject of various, often conflicting, hypotheses. Moreover, recent studies have suggested a new role for the NPC as a mechanosensor, where the NPC changes its channel diameter depending on the nuclear envelope tension, altering the molecular transportability through this nanopore. In this mini-review, we summarize the current understandings of the selective nature of the NPC and discuss its emerging role in cellular mechanotransduction.

DOI: https://doi.org/10.1063/5.0080480