bims-indpro Biomed News
on Intrinsically disordered proteins
Issue of 2022‒06‒26
thirteen papers selected by
Sara Mingu
Johannes Gutenberg University
  1. Artificial intelligence guided conformational mining of intrinsically disordered proteins.
  2. Dynamical Behavior of Disordered Regions in Disease-Related Proteins Revealed by Quasielastic Neutron Scattering.
  3. Affinity of disordered protein complexes is modulated by entropy-energy reinforcement.
  4. Electronic Polarization at the Interface between the p53 Transactivation Domain and Two Binding Partners.
  5. Intrinsic disorder, extraterrestrial peptides, and prebiotic life on the earth.
  6. AlphaFold2 models indicate that protein sequence determines both structure and dynamics.
  7. Structural dynamics of Zika virus NS1 via a reductionist approach reveal the disordered nature of its β-roll domain in isolation.
  8. Role of ergodicity, aging, and Gaussianity in resolving the origins of biomolecule subdiffusion.
  9. Production of native recombinant human ameloblastin.
  10. Structural Basis for Dityrosine-Mediated Inhibition of α-Synuclein Fibrillization.
  11. Integration of light and temperature sensing by liquid-liquid phase separation of phytochrome B.
  12. Dual Effects of Presynaptic Membrane Mimetics on α-Synuclein Amyloid Aggregation.
  13. Effects of pH alterations on stress- and aging-induced protein phase separation.
  1. Commun Biol. 2022 Jun 20. 5(1): 610
    Artificial intelligence guided conformational mining of intrinsically disordered proteins.
    Aayush Gupta, Souvik Dey, Alan Hicks, Huan-Xiang Zhou.
      Artificial intelligence recently achieved the breakthrough of predicting the three-dimensional structures of proteins. The next frontier is presented by intrinsically disordered proteins (IDPs), which, representing 30% to 50% of proteomes, readily access vast conformational space. Molecular dynamics (MD) simulations are promising in sampling IDP conformations, but only at extremely high computational cost. Here, we developed generative autoencoders that learn from short MD simulations and generate full conformational ensembles. An encoder represents IDP conformations as vectors in a reduced-dimensional latent space. The mean vector and covariance matrix of the training dataset are calculated to define a multivariate Gaussian distribution, from which vectors are sampled and fed to a decoder to generate new conformations. The ensembles of generated conformations cover those sampled by long MD simulations and are validated by small-angle X-ray scattering profile and NMR chemical shifts. This work illustrates the vast potential of artificial intelligence in conformational mining of IDPs.
    DOI:  https://doi.org/10.1038/s42003-022-03562-y
  2. Medicina (Kaunas). 2022 Jun 13. pii: 795. [Epub ahead of print]58(6):
    Dynamical Behavior of Disordered Regions in Disease-Related Proteins Revealed by Quasielastic Neutron Scattering.
    Satoru Fujiwara.
      Background and Objectives: Intrinsically disordered proteins (IDPs) and proteins containing intrinsically disordered regions (IDRs) are known to be involved in various human diseases. Since the IDPs/IDRs are fluctuating between many structural substrates, the dynamical behavior of the disease-related IDPs/IDRs needs to be characterized to elucidate the mechanisms of the pathogenesis of the diseases. As protein motions have a hierarchy ranging from local side-chain motions, through segmental motions of loops or disordered regions, to diffusive motions of entire molecules, segmental motions, as well as local motions, need to be characterized. Materials and Methods: Combined analysis of quasielastic neutron scattering (QENS) spectra with the structural data provides information on both the segmental motions and the local motions of the IDPs/IDRs. Here, this method is applied to re-analyze the QENS spectra of the troponin core domain (Tn-CD), various mutants of which cause the pathogenesis of familial cardiomyopathy (FCM), and α-synuclein (αSyn), amyloid fibril formation of which is closely related to the pathogenesis of Parkinson's disease, collected in the previous studies. The dynamical behavior of wild-type Tn-CD, FCM-related mutant Tn-CD, and αSyn in the different propensity states for fibril formation is characterized. Results: In the Tn-CD, the behavior of the segmental motions is shown to be different between the wild type and the mutant. This difference is likely to arise from changes in the intramolecular interactions, which are suggested to be related to the functional aberration of the mutant Tn-CD. In αSyn, concerted enhancement of the segmental motions and the local motions is observed with an increased propensity for fibril formation, suggesting the importance of these motions in fibril formation. Conclusions: Characterization of the segmental motions as well as the local motions is thus useful for discussing how the changes in dynamical behavior caused by the disease-related mutations and/or environmental changes could be related to the functional and/or behavioral aberrations of these proteins.
    Keywords:  Parkinson’s disease; hypertrophic cardiomyopathy; intrinsically disordered protein; protein dynamics; quasielastic neutron scattering; synuclein; troponin
    DOI:  https://doi.org/10.3390/medicina58060795
  3. Proc Natl Acad Sci U S A. 2022 Jun 28. 119(26): e2120456119
    Affinity of disordered protein complexes is modulated by entropy-energy reinforcement.
    Milan Kumar Hazra, Yaakov Levy.
      The association between two intrinsically disordered proteins (IDPs) may produce a fuzzy complex characterized by a high binding affinity, similar to that found in the ultrastable complexes formed between two well-structured proteins. Here, using coarse-grained simulations, we quantified the biophysical forces driving the formation of such fuzzy complexes. We found that the high-affinity complex formed between the highly and oppositely charged H1 and ProTα proteins is sensitive to electrostatic interactions. We investigated 52 variants of the complex by swapping charges between the two oppositely charged proteins to produce sequences whose negatively or positively charged residue content was more homogeneous or heterogenous (i.e., polyelectrolytic or polyampholytic, having higher or lower absolute net charges, respectively) than the wild type. We also changed the distributions of oppositely charged residues within each participating sequence to produce variants in which the charges were segregated or well mixed. Both types of changes significantly affect binding affinity in fuzzy complexes, which is governed by both enthalpy and entropy. The formation of H1-ProTa is supported by an increase in configurational entropy and by entropy due to counterion release. The latter can be twice as large as the former, illustrating the dominance of counterion entropy in modulating the binding thermodynamics. Complexes formed between proteins with greater absolute net charges are more stable, both enthalpically and entropically, indicating that enthalpy and entropy have a mutually reinforcing effect. The sensitivity of the thermodynamics of the complex to net charge and the charge pattern within each of the binding constituents may provide a means to achieve binding specificity between IDPs.
    Keywords:  counterion entropy; high-affinity binding; intrinsically disordered proteins; polyelectrolytes; protein association
    DOI:  https://doi.org/10.1073/pnas.2120456119
  4. J Phys Chem B. 2022 Jun 24.
    Electronic Polarization at the Interface between the p53 Transactivation Domain and Two Binding Partners.
    Alexsandra N Corrigan, Justin A Lemkul.
      Intrinsically disordered proteins (IDPs) are an abundant class of highly charged proteins that participate in numerous crucial biological processes, often in regulatory roles. IDPs do not have one major free energy minimum with a dominant structure, instead existing as conformational ensembles of multiple semistable conformations. p53 is a prototypical protein with disordered regions and binds to many structurally diverse partners, making it a useful model for exploring the role of electrostatic interactions at IDP binding interfaces. In this study, we used the Drude-2019 force field to simulate the p53 transactivation domain with two protein partners to probe the role of electrostatic interactions in IDP protein-protein interactions. We found that the Drude-2019 polarizable force field reasonably reproduced experimental chemical shifts of the p53 transactivation domain (TAD) in one complex for which these data are available. We also found that the proteins in these complexes displayed dipole response at specific residues of each protein and that residues primarily involved in binding showed a large percent change in dipole moment between the unbound and complexed states. Probing the role of electrostatic interactions in IDP binding can allow us greater fundamental understanding of these interactions and may help with targeting p53 or its partners for drug design.
    DOI:  https://doi.org/10.1021/acs.jpcb.2c02268
  5. J Biomol Struct Dyn. 2022 Jun 20. 1-5
    Intrinsic disorder, extraterrestrial peptides, and prebiotic life on the earth.
    Prakash Kulkarni, Ravi Salgia, Vladimir N Uversky.
      The discovery of mechanisms for the synthesis of homo-polymeric oligopeptides, such as polyglycine under conditions relevant to the astrophysical environment as well as in scenarios resembling primordial conditions that prevailed soon after Earth was formed, raises hopes in the search of extraterrestrial life. It also raises the possibility of extraterrestrial contribution to origin of life on Earth in the form of simple polypeptides. Bioinformatics analyses strongly predict such homo-polymeric peptides to be intrinsically disordered underscoring the potential involvement of IDPs in the origin of life which, even in its simplest form, could emerge spontaneously by autocatalysis of the primordial IDPs in self-organizing systems that evolved over time following natural selection.Communicated by Ramaswamy H. Sarma.
    Keywords:  Extraterrestrial life; aminoketene condensation; intrinsically disordered proteins; polyglycine; prebiotic evolution
    DOI:  https://doi.org/10.1080/07391102.2022.2088619
  6. Sci Rep. 2022 Jun 23. 12(1): 10696
    AlphaFold2 models indicate that protein sequence determines both structure and dynamics.
    Hao-Bo Guo, Alexander Perminov, Selemon Bekele, Gary Kedziora, Sanaz Farajollahi, Vanessa Varaljay, Kevin Hinkle, Valeria Molinero, Konrad Meister, Chia Hung, Patrick Dennis, Nancy Kelley-Loughnane, Rajiv Berry.
      AlphaFold 2 (AF2) has placed Molecular Biology in a new era where we can visualize, analyze and interpret the structures and functions of all proteins solely from their primary sequences. We performed AF2 structure predictions for various protein systems, including globular proteins, a multi-domain protein, an intrinsically disordered protein (IDP), a randomized protein, two larger proteins (> 1000 AA), a heterodimer and a homodimer protein complex. Our results show that along with the three dimensional (3D) structures, AF2 also decodes protein sequences into residue flexibilities via both the predicted local distance difference test (pLDDT) scores of the models, and the predicted aligned error (PAE) maps. We show that PAE maps from AF2 are correlated with the distance variation (DV) matrices from molecular dynamics (MD) simulations, which reveals that the PAE maps can predict the dynamical nature of protein residues. Here, we introduce the AF2-scores, which are simply derived from pLDDT scores and are in the range of [0, 1]. We found that for most protein models, including large proteins and protein complexes, the AF2-scores are highly correlated with the root mean square fluctuations (RMSF) calculated from MD simulations. However, for an IDP and a randomized protein, the AF2-scores do not correlate with the RMSF from MD, especially for the IDP. Our results indicate that the protein structures predicted by AF2 also convey information of the residue flexibility, i.e., protein dynamics.
    DOI:  https://doi.org/10.1038/s41598-022-14382-9
  7. Virology. 2022 Jun 14. pii: S0042-6822(22)00097-6. [Epub ahead of print]573 72-83
    Structural dynamics of Zika virus NS1 via a reductionist approach reveal the disordered nature of its β-roll domain in isolation.
    Shivani Krishna Kapuganti, Prateek Kumar, Rajanish Giri.
      Flavivirus Non-structural 1 (NS1) protein performs multiple functions and it is highly plausible that significant structural and folding dynamics of NS1 might play a role in its multifunctionality. It is important to understand the structural conformations of NS1 and its domains in isolation, possibly highlighting the implications on the overall NS1 protein dynamics. Therefore, we have employed extensively long molecular dynamic (MD) simulations in understanding the dynamics of the three structural domains (i.e., β-roll, wing, and β-ladder) in isolation, as a reductionist approach. We also found that the β-ladder domain is highly flexible, while the β-roll domain is disordered during long simulations. Further, we experimentally validated our findings using CD spectroscopy and confirmed the intrinsically disordered behavior of NS1 β-roll in isolation and lipid mimetic environments. Therefore, we believe this study may have implications for significant dynamics played by NS1 protein, specifically during oligomerization of NS1.
    Keywords:  Conformational dynamics; Lipid mimetics; Molecular dynamics simulations; Structural disorder
    DOI:  https://doi.org/10.1016/j.virol.2022.06.005
  8. Phys Chem Chem Phys. 2022 Jun 22.
    Role of ergodicity, aging, and Gaussianity in resolving the origins of biomolecule subdiffusion.
    Jun Li.
      The internal motions of biomolecules are essential to their function. Although biological macromolecules conventionally show subdiffusive dynamics, only recently has subdiffusion been associated with non-ergodicity. These findings have stimulated new questions in biophysics and statistical mechanics. Is non-ergodic subdiffusion a general strategy shared by biomolecules? What underlying mechanisms are responsible for it? Here, we performed extensive molecular dynamics (MD) simulations to characterize the internal dynamics of six different biomolecules, ranging from single or double-stranded DNA, a single domain protein (KRAS), two globular proteins (PGK and SHP2), to an intrinsically disordered protein (SNAP-25). We found that the subdiffusive behavior of these biomolecules falls into two classes. The internal motion of the first three cases is ergodic subdiffusion and can be interpreted by fractional Brownian motion (FBM), while the latter three cases involve non-ergodic subdiffusion and can be modeled by mixed origins of continuous-time random walk (CTRW) and FBM.
    DOI:  https://doi.org/10.1039/d2cp01161a
  9. Protein Expr Purif. 2022 Jun 21. pii: S1046-5928(22)00090-0. [Epub ahead of print] 106133
    Production of native recombinant human ameloblastin.
    V Vetyskova, M Zouharova, K Bousova.
      Ameloblastin (Ambn) is an intrinsically disordered protein (IDP) with a specific function of forming heterogenous homooligomers. The oligomeric function is led through a specific sequence encoded by exon 5 of Ambn. Due to the IDP character of Ambn to form oligomers, protein purification is subject to many challenges. Human ameloblastin (AMBN) and its two isoforms, I and II have already been purified as a recombinant protein in a bacterial expression system and functionally characterized in vitro. However, here we present a new purification protocol for the production of native AMBN in its original formation as a homooligomeric heterogeneous IDP. The purification process consists of three chromatographic steps utilizing His-tag and Twin Strep-tag affinity chromatography, along with size exclusion and reverse affinity chromatography. The presented workflow offers the production of AMBN in sufficient yield for in vitro protein characterizations and can be used to produce both AMBN isoforms I and II.
    Keywords:  Ameloblastin; Oligomerization; Protein native conditions; Purification; Twin strep-tag
    DOI:  https://doi.org/10.1016/j.pep.2022.106133
  10. J Am Chem Soc. 2022 Jun 24.
    Structural Basis for Dityrosine-Mediated Inhibition of α-Synuclein Fibrillization.
    Cagla Sahin, Eva Christina Østerlund, Nicklas Österlund, Joana Costeira-Paulo, Jannik Nedergaard Pedersen, Gunna Christiansen, Janni Nielsen, Anne Louise Grønnemose, Søren Kirk Amstrup, Manish K Tiwari, R Shyama Prasad Rao, Morten Jannik Bjerrum, Leopold L Ilag, Michael J Davies, Erik G Marklund, Jan Skov Pedersen, Michael Landreh, Ian Max Møller, Thomas J D Jørgensen, Daniel Erik Otzen.
      α-Synuclein (α-Syn) is an intrinsically disordered protein which self-assembles into highly organized β-sheet structures that accumulate in plaques in brains of Parkinson's disease patients. Oxidative stress influences α-Syn structure and self-assembly; however, the basis for this remains unclear. Here we characterize the chemical and physical effects of mild oxidation on monomeric α-Syn and its aggregation. Using a combination of biophysical methods, small-angle X-ray scattering, and native ion mobility mass spectrometry, we find that oxidation leads to formation of intramolecular dityrosine cross-linkages and a compaction of the α-Syn monomer by a factor of √2. Oxidation-induced compaction is shown to inhibit ordered self-assembly and amyloid formation by steric hindrance, suggesting an important role of mild oxidation in preventing amyloid formation.
    DOI:  https://doi.org/10.1021/jacs.2c03607
  11. Mol Cell. 2022 Jun 12. pii: S1097-2765(22)00493-2. [Epub ahead of print]
    Integration of light and temperature sensing by liquid-liquid phase separation of phytochrome B.
    Di Chen, Mohan Lyu, Xiaoxia Kou, Jing Li, Zhixuan Yang, Lulu Gao, Yue Li, Liu-Min Fan, Hui Shi, Shangwei Zhong.
      Light and temperature in plants are perceived by a common receptor, phytochrome B (phyB). How phyB distinguishes these signals remains elusive. Here, we report that phyB spontaneously undergoes phase separation to assemble liquid-like droplets. This capacity is driven by its C terminus through self-association, whereas the intrinsically disordered N-terminal extension (NTE) functions as a biophysical modulator of phase separation. Light exposure triggers a conformational change to subsequently alter phyB condensate assembly, while temperature sensation is directly mediated by the NTE to modulate the phase behavior of phyB droplets. Multiple signaling components are selectively incorporated into phyB droplets to form concentrated microreactors, allowing switch-like control of phyB signaling activity through phase transitions. Therefore, light and temperature cues are separately read out by phyB via allosteric changes and spontaneous phase separation, respectively. We provide a conceptual framework showing how the distinct but highly correlated physical signals are interpreted and sorted by one receptor.
    Keywords:  biomolecular condensates; oligomerization; photoreceptor; signal clustering; thermosensor
    DOI:  https://doi.org/10.1016/j.molcel.2022.05.026
  12. Front Cell Dev Biol. 2022 ;10 707417
    Dual Effects of Presynaptic Membrane Mimetics on α-Synuclein Amyloid Aggregation.
    Yuxi Lin, Dai Ito, Je Min Yoo, Mi Hee Lim, Wookyung Yu, Yasushi Kawata, Young-Ho Lee.
      Aggregation of intrinsically disordered α-synuclein (αSN) under various conditions is closely related to synucleinopathies. Although various biological membranes have shown to alter the structure and aggregation propensity of αSN, a thorough understanding of the molecular and mechanical mechanism of amyloidogenesis in membranes remains unanswered. Herein, we examined the structural changes, binding properties, and amyloidogenicity of three variations of αSN mutants under two types of liposomes, 1,2-Dioleoyl-sn-glycero-3-Phosphocholine (DOPC) and presynaptic vesicle mimetic (Mimic) membranes. While neutrally charged DOPC membranes elicited marginal changes in the structure and amyloid fibrillation of αSNs, negatively charged Mimic membranes induced dramatic helical folding and biphasic amyloid generation. At low concentration of Mimic membranes, the amyloid fibrillation of αSNs was promoted in a dose-dependent manner. However, further increases in the concentration constrained the fibrillation process. These results suggest the dual effect of Mimic membranes on regulating the amyloidogenesis of αSN, which is rationalized by the amyloidogenic structure of αSN and condensation-dilution of local αSN concentration. Finally, we propose physicochemical properties of αSN and membrane surfaces, and their propensity to drive electrostatic interactions as decisive factors of amyloidogenesis.
    Keywords:  Parkinson’s disease; amyloid fibril; electrostatic interaction; helical structure; intermolecular interaction; membrane mimetic; presynaptic vesicle; α-Synuclein
    DOI:  https://doi.org/10.3389/fcell.2022.707417
  13. Cell Mol Life Sci. 2022 Jun 24. 79(7): 380
    Effects of pH alterations on stress- and aging-induced protein phase separation.
    Xuejiao Jin, Min Zhou, Shuxin Chen, Danqi Li, Xiuling Cao, Beidong Liu.
      Upon stress challenges, proteins/RNAs undergo liquid-liquid phase separation (LLPS) to fine-tune cell physiology and metabolism to help cells adapt to adverse environments. The formation of LLPS has been recently linked with intracellular pH, and maintaining proper intracellular pH homeostasis is known to be essential for the survival of organisms. However, organisms are constantly exposed to diverse stresses, which are accompanied by alterations in the intracellular pH. Aging processes and human diseases are also intimately linked with intracellular pH alterations. In this review, we summarize stress-, aging-, and cancer-associated pH changes together with the mechanisms by which cells regulate cytosolic pH homeostasis. How critical cell components undergo LLPS in response to pH alterations is also discussed, along with the functional roles of intracellular pH fluctuation in the regulation of LLPS. Further studies investigating the interplay of pH with other stressors in LLPS regulation and identifying protein responses to different pH levels will provide an in-depth understanding of the mechanisms underlying pH-driven LLPS in cell adaptation. Moreover, deciphering aging and disease-associated pH changes that influence LLPS condensate formation could lead to a deeper understanding of the functional roles of biomolecular condensates in aging and aging-related diseases.
    Keywords:  Acidification; Membrane-less compartment; Neurodegenerative disease; Protein aggregation; Tumorigenesis
    DOI:  https://doi.org/10.1007/s00018-022-04393-0
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