bims-indpro 2022-09-18 papers

bims-indpro

Biomed News

on Intrinsically disordered proteins

Issue of 2022–09–18
fiveteen papers selected by
Sara Mingu, Johannes Gutenberg University

Direct Observation of 'Elongated' Conformational States in α-Synuclein upon Liquid-Liquid Phase Separation.
An integrated approach to identify intrinsically disordered regions in osteopontin with its interacting network in rheumatoid arthritis.
Regulating Phase Transition in Neurodegenerative Diseases by Nuclear Import Receptors.
Intrinsically disordered proteins in viral pathogenesis and infections.
Thermodynamics and Conformations of Single Polyalanine, Polyserine, and Polyglutamine Chains within the PRIME20 Model.
Amyloid fibril formation by αS1- and β-casein implies that fibril formation is a general property of all casein proteins.
Drugging the Undruggable: Targeting the N-Terminal Domain of Nuclear Hormone Receptors.
Hepatitis C Virus Infection and Intrinsic Disorder in the Signaling Pathways Induced by Toll-Like Receptors.
Carboxyl terminus of HOATZ is intrinsically disordered and interacts with heat shock protein A families.
Protein Condensation in the Nuclear Receptor Family; Implications for Transcriptional Output.
Phase separation of p53 induced by its unstructured basic region and prevented by oncogenic mutations in tetramerization domain.
ALS mutations in the TIA-1 prion-like domain trigger highly condensed pathogenic structures.
Micellization: A new principle in the formation of biomolecular condensates.
Uncovering the molecular mechanism for dual effect of ATP on phase separation in FUS solution.
A-type lamins involvement in transport and implications in cancer?

Angew Chem Int Ed Engl. 2022 Sep 17.

Direct Observation of 'Elongated' Conformational States in α-Synuclein upon Liquid-Liquid Phase Separation.

Daniele Ubbiali, Marta Fratini, Lolita Piersimoni, Christian Ihling, Marc Kipping, Ingo Heilmann, Claudio Iacobucci, Andrea Sinz.

  α-Synuclein (α-syn) is an intrinsically disordered protein (IDP) that undergoes liquid-liquid phase separation (LLPS), fibrillation, and forms insoluble intracellular Lewy's bodies in neurons, which are the hallmark of Parkinson's Disease (PD). Neurotoxicity precedes the formation of aggregates and might be related to α-syn LLPS. The molecular mechanisms underlying the early stages of LLPS are still elusive. To obtain structural insights into α-syn upon LLPS, we take advantage of cross-linking/mass spectrometry (XL-MS) and introduce an innovative approach, termed COMPASS (COMPetitive PAiring StatisticS). In this work, we show that the conformational ensemble of α-syn shifts from a 'hairpin-like' structure towards more 'elongated' conformational states upon LLPS. We obtain insights into the critical initial stages of LLPS and establish a novel mass spectrometry-based approach that will aid to solve open questions in LLPS structural biology.

Keywords:  Mass Spectrometry; Protein conformation; alpha-synuclein; cross-linking; intrinsically disordered proteins

DOI:  https://doi.org/10.1002/anie.202205726
Recent Adv Antiinfect Drug Discov. 2022 Sep 08.

An integrated approach to identify intrinsically disordered regions in osteopontin with its interacting network in rheumatoid arthritis.

Parul Johri, Sachidanand Singh, Prachi Sao, Sudeshana Banerjee, Mala Trivedi, Aditi Singh, Irena Kostova.

   AIM: The aim of the study is to analyse the role of highly disordered proteins and its functional parameters in causing Rheumatoid Arthritis (RA).
BACKGROUND: Credentials of molecular diagnostic approaches is an important goal. Since protein-protein interaction (PPI) network analysis is a apposite method for molecular valuation, in the present research a PPI grid related to Intrinsically Disordered Proteins (IDPs) of RA was targeted.
METHOD: Cytoscape software helped in identifying the molecular interaction networks. Intrinsically disordered proteins lack higher order structure and has functional advantages, but their dysregulation can cause several diseases. All the significant proteins responsible for RA were identified. On the basis of data obtained, highly disordered proteins were selected. Further, MSA was done to find the similarity among the highly disordered protein and their functional partners were identified. To determine the most relevant functional partner(s) / interacting protein(s) out of large network three filters were introduced in the methodology.
RESULT: The two filtered protein IBSP and FGF2 have common functions and also play a vital role in the pathways of RA. Thus, gives an in-depth knowledge of molecular mechanisms involved in Rheumatoid Arthritis and targeted therapeutics.
CONCLUSION: The network analysis of these proteins has been explored using Cytoscape and the proteins with favourable values of graph centrality parameters such as IBSP and FGF2 are identified. Interesting functional cross talk such as Bio mineralization, Bone-remodelling, angiogenesis, cell differentiation etc. of SPP1 with IBSP and FGF2 are found, which throw light into the fact that these two proteins play a vital role in the pathways of RA.

Keywords:  Cytoscape; KEGG; Protein-Protein Interaction; Rheumatoid Arthritis; biological annotations; intrinsically disordered protein

DOI:  https://doi.org/10.2174/2772434417666220908122654
Biology (Basel). 2022 Jul 04. pii: 1009. [Epub ahead of print]11(7):

Regulating Phase Transition in Neurodegenerative Diseases by Nuclear Import Receptors.

Amandeep Girdhar, Lin Guo.

  RNA-binding proteins (RBPs) with a low-complexity prion-like domain (PLD) can undergo aberrant phase transitions and have been implicated in neurodegenerative diseases such as ALS and FTD. Several nuclear RBPs mislocalize to cytoplasmic inclusions in disease conditions. Impairment in nucleocytoplasmic transport is another major event observed in ageing and in neurodegenerative disorders. Nuclear import receptors (NIRs) regulate the nucleocytoplasmic transport of different RBPs bearing a nuclear localization signal by restoring their nuclear localization. NIRs can also specifically dissolve or prevent the aggregation and liquid-liquid phase separation of wild-type or disease-linked mutant RBPs, due to their chaperoning activity. This review focuses on the LLPS of intrinsically disordered proteins and the role of NIRs in regulating LLPS in neurodegeneration. This review also discusses the implication of NIRs as therapeutic agents in neurogenerative diseases.

Keywords:  ALS; FUS; Kapβ2; TDP-43; liquid–liquid phase separation; nuclear import receptor

DOI:  https://doi.org/10.3390/biology11071009
Adv Protein Chem Struct Biol. 2022 ;pii: S1876-1623(22)00055-4. [Epub ahead of print]132 221-242

Intrinsically disordered proteins in viral pathogenesis and infections.

Chandrabose Selvaraj, Muthuraja Arun Pravin, Wardah A Alhoqail, Anuraj Nayarisseri, Sanjeev Kumar Singh.

  Disordered proteins serve a crucial part in many biological processes that go beyond the capabilities of ordered proteins. A large number of virus-encoded proteins have extremely condensed proteomes and genomes, which results in highly disordered proteins. The presence of these IDPs allows them to rapidly adapt to changes in their biological environment and play a significant role in viral replication and down-regulation of host defense mechanisms. Since viruses undergo rapid evolution and have a high rate of mutation and accumulation in their proteome, IDPs' insights into viruses are critical for understanding how viruses hijack cells and cause disease. There are many conformational changes that IDPs can adopt in order to interact with different protein partners and thus stabilize the particular fold and withstand high mutation rates. This chapter explains the molecular mechanism behind viral IDPs, as well as the significance of recent research in the field of IDPs, with the goal of gaining a deeper comprehension of the essential roles and functions played by viral proteins.

Keywords:  Disorder proteins; Flavivirus; HIV-1; IDP; IDP servers; IPDs; Molecular dynamics; PONDR; Proteins; SARS-CoV-2; Viral proteome; Virulence; Virus

DOI:  https://doi.org/10.1016/bs.apcsb.2022.06.002
J Phys Chem B. 2022 Sep 14.

Thermodynamics and Conformations of Single Polyalanine, Polyserine, and Polyglutamine Chains within the PRIME20 Model.

Arne Böker, Wolfgang Paul.

Understanding the conformational behavior of proteins has been a long-standing challenge to which computer simulations could contribute significantly. This concerns the folding behavior of proteins as well as the conformational statistics of intrinsically disordered proteins. A well-converged sampling of the conformational statistics over a broad range of control parameters is computationally extremely challenging and best addressed by coarse-grained modeling, for example, with an intermediate resolution model like the PRIME20 model. A comprehensive understanding of the thermodynamics and conformational statistics of individual protein chains is, however, not only a goal in itself but also a prerequisite for a better understanding of their aggregation tendency into oligomers and further into amyloid fibrils. We present here an extensive comparison of the ability of the PRIME20 model (in its documented variants in the literature) to faithfully reproduce the thermodynamics and statistics of three homopeptides having very different folding temperatures and different typical secondary structures.

DOI: https://doi.org/10.1021/acs.jpcb.2c04360
Biochim Biophys Acta Proteins Proteom. 2022 Sep 07. pii: S1570-9639(22)00101-7. [Epub ahead of print] 140854

Amyloid fibril formation by αS1- and β-casein implies that fibril formation is a general property of all casein proteins.

Elmira Bahraminejad, Devashi Paliwal, Margaret Sunde, Carl Holt, John A Carver, David C Thorn.

  Caseins are a diverse family of intrinsically disordered proteins present in the milks of all mammals. A property common to two cow paralogues, αS2- and κ-casein, is their propensity in vitro to form amyloid fibrils, the highly ordered protein aggregates associated with many age-related, including neurological, diseases. In this study, we explored whether amyloid fibril-forming propensity is a general feature of casein proteins by examining the other cow caseins (αS1 and β) as well as β-caseins from camel and goat. Small-angle X-ray scattering measurements indicated that cow αS1- and β-casein formed large spherical aggregates at neutral pH and 20°C. Upon incubation at 65°C, αS1- and β-casein underwent conversion to amyloid fibrils over the course of ten days, as shown by thioflavin T binding, transmission electron microscopy, and X-ray fibre diffraction. Far-UV circular dichroism spectroscopy indicated that fibril formation led to increased β-sheet structure from an initial, mostly disordered, state. At the lower temperature of 37°C where fibril formation was more limited, camel β-casein exhibited a greater fibril-forming propensity than its cow or goat orthologues. Limited proteolysis of cow and camel β-casein fibrils and analysis by mass spectrometry indicated a common amyloidogenic sequence in the proline, glutamine-rich, C-terminal region of β-casein. These findings highlight the persistence of amyloidogenic sequences within caseins, which likely contribute to their functional, heterotypic self-assembly; in all mammalian milks, at least two caseins coalesce to form casein micelles, implying that caseins diversified partly to avoid dysfunctional amyloid fibril formation.

Keywords:  Amyloid fibril; Amyloidogenic sequence; Functional amyloid; Intrinsically disordered protein; Oligomer; Polyproline-II helix; Proline/glutamine-rich; alphaS1-casein; beta-casein

DOI:  https://doi.org/10.1016/j.bbapap.2022.140854
Adv Exp Med Biol. 2022 ;1390 311-326

Drugging the Undruggable: Targeting the N-Terminal Domain of Nuclear Hormone Receptors.

Marianne D Sadar.

  This chapter focuses on the development of drugs targeting the N-terminal domain of nuclear hormone receptors, using progress with the androgen receptor as an example. Historically, development of therapies targeting nuclear hormone receptors has focused on the folded C-terminal ligand-binding domain. Therapies were traditionally not developed to target the intrinsically disordered N-terminal domain as it was considered "undruggable". Recent developments have now shown it is possible to direct therapies to the N-terminal domain. This chapter will provide an introduction of the structure and function of the domains of nuclear hormone receptors, followed by a discussion of the rationale supporting the development of N-terminal domain inhibitors. Chemistry and mechanisms of action of small molecule inhibitors will be described with emphasis on N-terminal domain inhibitors developed to the androgen receptor including those in clinical trials.

Keywords:  Androgen receptor; Drugs; EPI-002; Intrinsically disordered protein; Ralaniten; Sintokamide

DOI:  https://doi.org/10.1007/978-3-031-11836-4_18
Biology (Basel). 2022 Jul 21. pii: 1091. [Epub ahead of print]11(7):

Hepatitis C Virus Infection and Intrinsic Disorder in the Signaling Pathways Induced by Toll-Like Receptors.

Elrashdy M Redwan, Abdullah A Aljadawi, Vladimir N Uversky.

  In this study, we examined the interplay between protein intrinsic disorder, hepatitis C virus (HCV) infection, and signaling pathways induced by Toll-like receptors (TLRs). To this end, 10 HCV proteins, 10 human TLRs, and 41 proteins from the TLR-induced downstream pathways were considered from the prevalence of intrinsic disorder. Mapping of the intrinsic disorder to the HCV-TLR interactome and to the TLR-based pathways of human innate immune response to the HCV infection demonstrates that substantial levels of intrinsic disorder are characteristic for proteins involved in the regulation and execution of these innate immunity pathways and in HCV-TLR interaction. Disordered regions, being commonly enriched in sites of various posttranslational modifications, may play important functional roles by promoting protein-protein interactions and support the binding of the analyzed proteins to other partners such as nucleic acids. It seems that this system represents an important illustration of the role of intrinsic disorder in virus-host warfare.

Keywords:  disorder-to-order transition; hepatitis C virus; intrinsically disordered protein; intrinsically disordered region; posttranslational modifications; protein–protein interactions; toll-like receptors

DOI:  https://doi.org/10.3390/biology11071091
Protein Pept Lett. 2022 Sep 12.

Carboxyl terminus of HOATZ is intrinsically disordered and interacts with heat shock protein A families.

Keishi Narita, Takuji Oyama.

   BACKGROUND: Hoatz is a vertebrate-specific gene, the defects of which results in hydrocephalus and oligo-astheno-teratozoospermia in mice. It encodes a 19-kDa protein lacking any domains of known function.
METHODS: To understand the protein activity, we purified the carboxyl-terminal fragment that is conserved among different species and analyzed its structure and potential binding proteins. A soluble 9.9-kDa HOATZ fragment, including a poly-histidine tag (designated HOATZ-C), was purified to homogeneity.
RESULTS: The gel filtration profile and circular dichroism spectra collectively indicated that HOATZ-C was intrinsically disordered. When HOATZ-C was mixed with cleared lysate from Hoatz-null mouse testis, several proteins, including two of ~70 kDa size, were specifically co-purified with HOATZ-C on a nickel column.
CONCLUSION: Based on the peptide mass fingerprinting of these bands, two members of heat-shock protein family A were identified. These data may indicate the role of HOATZ in stress regulation in cells characterized by motile cilia and flagella.

Keywords:  Motile cilia; circular dichroism; flagella; heat shock protein; stress regulation

DOI:  https://doi.org/10.2174/0929866529666220912115544
Adv Exp Med Biol. 2022 ;1390 243-253

Protein Condensation in the Nuclear Receptor Family; Implications for Transcriptional Output.

Monique D Appelman, Elle E Hollaar, Jurian Schuijers, Saskia W C van Mil.

  The nuclear receptor superfamily is a group of transcriptional regulators that orchestrate multiple vital processes such as inflammation, metabolism, and cell proliferation. In recent years, it has become clear that some nuclear receptors form condensates in living cells. These condensates contain high concentrations of proteins and can contain millions of molecules. At these sites, high concentrations of nuclear receptors and co-factors potentially contribute to efficient transcription. While condensate formation has been observed for some nuclear receptors, the majority have unknown condensate formation abilities. Condensate formation abilities for these NRs would implicate an additional layer of regulation for the entire nuclear receptor family. Here, we consider the nuclear receptor superfamily, the current evidence for condensate formation of some of its members and the potential of the whole superfamily to form condensates. Insights into the regulation of assembly or disassembly of nuclear receptor condensates and our considerations for the understudied family members imply that condensate biology might be an important aspect of nuclear receptor-regulated gene transcription.

Keywords:  Biomolecular condensates; Condensate formation; Liquid-liquid phase separation; Nuclear receptors; Transcriptional regulation; intrinsically disordered regions

DOI:  https://doi.org/10.1007/978-3-031-11836-4_14
Int J Biol Macromol. 2022 Sep 12. pii: S0141-8130(22)02018-9. [Epub ahead of print]

Phase separation of p53 induced by its unstructured basic region and prevented by oncogenic mutations in tetramerization domain.

Chen Chen, Gaohong Fu, Quanqiang Guo, Song Xue, Shi-Zhong Luo.

  Liquid-liquid phase separation (LLPS) drives the formation of extensive membrane-less compartments to regulate various cellular biological activities both physiologically and pathologically. It has been widely accepted that LLPS is closely related to amyloid diseases and increasing reports have linked this phenomenon to cancers. Mutations of tumor suppressor protein p53 exist in more than half of malignant tumors, making the protein vitally important in cancer research. Recently, p53 was reported to undergo phase separation, which may regulate the function of p53. The molecular mechanism of p53 phase separation and how this process relates to cancer remains largely unclear. Herein, we find that the disordered unstructured basic region (UBR) plays a crucial role in p53 LLPS, driven by electrostatic and hydrophobic interactions. Mutations in the tetramerization domain (TD) disrupt p53 phase separation by preventing the tetramer formation. Furthermore, our results have revealed that, in response to DNA damage in cell, the wild type (WT) p53 undergoes LLPS, while LLPS in oncogenic mutations is diminished or eliminated. The expression of the target gene of p53 decreased significantly with the mutations and cell survival increased with the mutations. Thus, we propose a novel mechanism of p53 carcinogenesis, whereby oncogenic mutations in TD impair the formation of p53 condensates, decreasing the activation of target genes and promoting cancer progression. This study helps to understand the behavior and function of p53 in a different aspect and may provide insights into cancer therapies targeting p53.

Keywords:  Liquid-liquid phase separation; Oncogenic mutations; Tetramerization domain; Unstructured basic region; p53

DOI:  https://doi.org/10.1016/j.ijbiomac.2022.09.087
Proc Natl Acad Sci U S A. 2022 Sep 20. 119(38): e2122523119

ALS mutations in the TIA-1 prion-like domain trigger highly condensed pathogenic structures.

Naotaka Sekiyama, Kiyofumi Takaba, Saori Maki-Yonekura, Ken-Ichi Akagi, Yasuko Ohtani, Kayo Imamura, Tsuyoshi Terakawa, Keitaro Yamashita, Daigo Inaoka, Koji Yonekura, Takashi S Kodama, Hidehito Tochio.

  T cell intracellular antigen-1 (TIA-1) plays a central role in stress granule (SG) formation by self-assembly via the prion-like domain (PLD). In the TIA-1 PLD, amino acid mutations associated with neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) or Welander distal myopathy (WDM), have been identified. However, how these mutations affect PLD self-assembly properties has remained elusive. In this study, we uncovered the implicit pathogenic structures caused by the mutations. NMR analysis indicated that the dynamic structures of the PLD are synergistically determined by the physicochemical properties of amino acids in units of five residues. Molecular dynamics simulations and three-dimensional electron crystallography, together with biochemical assays, revealed that the WDM mutation E384K attenuated the sticky properties, whereas the ALS mutations P362L and A381T enhanced the self-assembly by inducing β-sheet interactions and highly condensed assembly, respectively. These results suggest that the P362L and A381T mutations increase the likelihood of irreversible amyloid fibrillization after phase-separated droplet formation, and this process may lead to pathogenicity.

Keywords:  intrinsically disordered protein regions; liquid–liquid phase separation; neurodegenerative diseases

DOI:  https://doi.org/10.1073/pnas.2122523119
Front Mol Biosci. 2022 ;9 974772

Micellization: A new principle in the formation of biomolecular condensates.

Tomohiro Yamazaki, Tetsuya Yamamoto, Tetsuro Hirose.

  Phase separation is a fundamental mechanism for compartmentalization in cells and leads to the formation of biomolecular condensates, generally containing various RNA molecules. RNAs are biomolecules that can serve as suitable scaffolds for biomolecular condensates and determine their forms and functions. Many studies have focused on biomolecular condensates formed by liquid-liquid phase separation (LLPS), one type of intracellular phase separation mechanism. We recently identified that paraspeckle nuclear bodies use an intracellular phase separation mechanism called micellization of block copolymers in their formation. The paraspeckles are scaffolded by NEAT1_2 long non-coding RNAs (lncRNAs) and their partner RNA-binding proteins (NEAT1_2 RNA-protein complexes [RNPs]). The NEAT1_2 RNPs act as block copolymers and the paraspeckles assemble through micellization. In LLPS, condensates grow without bound as long as components are available and typically have spherical shapes to minimize surface tension. In contrast, the size, shape, and internal morphology of the condensates are more strictly controlled in micellization. Here, we discuss the potential importance and future perspectives of micellization of block copolymers of RNPs in cells, including the construction of designer condensates with optimal internal organization, shape, and size according to design guidelines of block copolymers.

Keywords:  NEAT1; architectural RNA (arcRNA); biomolecular condensate; block copolymer (BCP); long non-coding RNA (lncRNA); micellization; paraspeckle; phase separation

DOI:  https://doi.org/10.3389/fmolb.2022.974772
Sci Adv. 2022 Sep 16. 8(37): eabo7885

Uncovering the molecular mechanism for dual effect of ATP on phase separation in FUS solution.

Chun-Lai Ren, Yue Shan, Pengfei Zhang, Hong-Ming Ding, Yu-Qiang Ma.

Recent studies reported that adenosine triphosphate (ATP) could inhibit and enhance the phase separation in prion-like proteins. The molecular mechanism underlying such a puzzling phenomenon remains elusive. Here, taking the fused in sarcoma (FUS) solution as an example, we comprehensively reveal the underlying mechanism by which ATP regulates phase separation by combining the semiempirical quantum mechanical method, mean-field theory, and molecular simulation. At the microscopic level, ATP acts as a bivalent or trivalent binder; at the macroscopic level, the reentrant phase separation occurs in dilute FUS solutions, resulting from the ATP concentration-dependent binding ability under different conditions. The ATP concentration for dissolving the protein condensates is about 10 mM, agreeing with experimental results. Furthermore, from a dynamic point of view, the effect of ATP on phase separation is also nonmonotonic. This work provides a clear physical description of the microscopic interaction and macroscopic phase diagram of the ATP-modulated phase separation.

DOI: https://doi.org/10.1126/sciadv.abo7885
Nucleus. 2022 Dec;13(1): 221-235

A-type lamins involvement in transport and implications in cancer?

Nicholas R Scott, Sapun H Parekh.

  Nuclear lamins and transport are intrinsically linked, but their relationship is yet to be fully unraveled. A multitude of complex, coupled interactions between lamins and nucleoporins (Nups), which mediate active transport into and out of the nucleus, combined with well documented dysregulation of lamins in many cancers, suggests that lamins and nuclear transport may play a pivotal role in carcinogenesis and the preservation of cancer. Changes of function related to lamin/Nup activity can principally lead to DNA damage, further increasing the genetic diversity within a tumor, which could lead to the reduction the effectiveness of antineoplastic treatments. This review discusses and synthesizes different connections of lamins to nuclear transport and offers a number of outlook questions, the answers to which could reveal a new perspective on the connection of lamins to molecular transport of cancer therapeutics, in addition to their established role in nuclear mechanics.

Keywords:  A-type lamins; cancer; lamin A/C; membrane diffusion; nuclear trafficking; nuclear transport; nucleoporins; nucleus; size dependent transport; transport in cancer

DOI:  https://doi.org/10.1080/19491034.2022.2118418