A targeted bioinformatics approach identifies highly variable cell surface proteins that are unique to Glomeromycotina

AbstractDiversity in arbuscular mycorrhizal fungi (AMF) contributes to biodiversity and resilience in natural environments and healthy agricultural systems. Functional complementarity exists among species of AMF in symbiosis with their plant hosts, but the molecular basis of this is not known. We hypothesise this is in part due to the difficulties that current sequence assembly methodologies have assembling sequences for intrinsically disordered proteins (IDPs) due to their low sequence complexity. IDPs are potential candidates for functional complementarity because they often exist as extended (non-globular) proteins providing additional amino acids for molecular interactions. Rhizophagus irregularis arabinogalactan-protein-like proteins (AGLs) are small secreted IDPs with no known orthologues in AMF or other fungi. We developed a targeted bioinformatics approach to identify highly variable AGLs/IDPs in RNA-sequence datasets. The approach includes a modified multiple k-mer assembly approach (Oases) to identify candidate sequences, followed by targeted sequence capture and assembly (mirabait-mira). All AMF species analysed, including the ancestral family Paraglomeraceae, have small families of proteins rich in disorder promoting amino acids such as proline and glycine, or glycine and asparagine. Glycine- and asparagine-rich proteins also were found in Geosiphon pyriformis (an obligate symbiont of a cyanobacterium), from the same subphylum (Glomeromycotina) as AMF. The sequence diversity of AGLs likely translates to functional diversity, based on predicted physical properties of tandem repeats (elastic, amyloid, or interchangeable) and their broad pI ranges. We envisage that AGLs/IDPs could contribute to functional complementarity in AMF through processes such as self-recognition, retention of nutrients, soil stability, and water movement.

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Enhancing Binding Affinity of an Intrinsically Disordered Protein by α-Methylation of Key Amino Acid Residues

10.26434/chemrxiv.10113128 ◽

2019 ◽

Author(s):

Valentin Bauer ◽

Boris Schmidtgall ◽

Gergő Gógl ◽

Jozica Dolenc ◽

Judit Osz ◽

...

Keyword(s):

Amino Acids ◽

Protein Interactions ◽

Intrinsically Disordered Proteins ◽

Intrinsically Disordered Protein ◽

Selective Inhibition ◽

Disordered Proteins ◽

Creb Binding Protein ◽

Alpha Helices ◽

Intrinsically Disordered ◽

Order Of Magnitude

Intrinsically disordered proteins (IDPs), which undergo folding upon binding to their targets, are critical players in protein interaction networks. Here we demonstrate that incorporation of non-canonical alpha-methylated amino acids into the unstructured activation domain of the transcriptional coactivator ACTR can stabilize helical conformations and strengthen binding interactions with the nuclear coactivator binding domain (NCBD) of CREB-binding protein (CBP). A combinatorial alpha-methylation scan of the ACTR sequence converged on two substitutions at positions 1055 and 1076 that increase affinity for both NCBD and the full length 270 kDa CBP by one order of magnitude. The first X-ray structure of the modified ACTR domain bound to NCBD revealed that the key alpha-methylated amino acids were localized within alpha-helices. Biophysical studies showed that the observed changes in binding energy are the result of long-range interactions and redistribution of enthalpy and entropy. This proof-of-concept study establishes a potential strategy for selective inhibition of protein-protein interactions involving IDPs in cells.<br>

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An intrinsically disordered protein, CP12: jack of all trades and master of the Calvin cycle

Biochemical Society Transactions ◽

10.1042/bst20120097 ◽

2012 ◽

Vol 40 (5) ◽

pp. 995-999 ◽

Cited By ~ 41

Author(s):

Brigitte Gontero ◽

Stephen C. Maberly

Keyword(s):

Amino Acids ◽

Stress Responses ◽

Intrinsically Disordered Proteins ◽

Calvin Cycle ◽

Intrinsically Disordered Protein ◽

Disulfide Bridge ◽

Co2 Assimilation ◽

Disordered Proteins ◽

Dimensional Structure ◽

Intrinsically Disordered

Many proteins contain disordered regions under physiological conditions and lack specific three-dimensional structure. These are referred to as IDPs (intrinsically disordered proteins). CP12 is a chloroplast protein of approximately 80 amino acids and has a molecular mass of approximately 8.2–8.5 kDa. It is enriched in charged amino acids and has a small number of hydrophobic residues. It has a high proportion of disorder-promoting residues, but has at least two (often four) cysteine residues forming one (or two) disulfide bridge(s) under oxidizing conditions that confers some order. However, CP12 behaves like an IDP. It appears to be universally distributed in oxygenic photosynthetic organisms and has recently been detected in a cyanophage. The best studied role of CP12 is its regulation of the Calvin cycle responsible for CO2 assimilation. Oxidized CP12 forms a supramolecular complex with two key Calvin cycle enzymes, GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and PRK (phosphoribulokinase), down-regulating their activity. Association–dissociation of this complex, induced by the redox state of CP12, allows the Calvin cycle to be inactive in the dark and active in the light. CP12 is promiscuous and interacts with other enzymes such as aldolase and malate dehydrogenase. It also plays other roles in plant metabolism such as protecting GAPDH from inactivation and scavenging metal ions such as copper and nickel, and it is also linked to stress responses. Thus CP12 seems to be involved in many functions in photosynthetic cells and behaves like a jack of all trades as well as being a master of the Calvin cycle.

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A predictive coarse-grained model for position-specific effects of post-translational modifications on disordered protein phase separation

10.1101/2020.06.12.148650 ◽

2020 ◽

Cited By ~ 4

Author(s):

T. M. Perdikari ◽

N. Jovic ◽

G. L. Dignon ◽

Y. C. Kim ◽

N. L. Fawzi ◽

...

Keyword(s):

Amino Acids ◽

Phase Separation ◽

Phase Behavior ◽

Intrinsically Disordered Proteins ◽

Coarse Grained ◽

Disordered Proteins ◽

Post Translational Modifications ◽

Coarse Grained Model ◽

Intrinsically Disordered ◽

Liquid Liquid Phase Separation

AbstractBiomolecules undergo liquid-liquid phase separation (LLPS) resulting in the formation of multicomponent protein-RNA membraneless organelles in cells. However, the physiological and pathological role of post translational modifications (PTMs) on the biophysics of phase behavior is only beginning to be probed. To study the effect of PTMs on LLPS in silico, we extend our transferable coarse-grained model of intrinsically disordered proteins to include phosphorylated and acetylated amino acids. Using the parameters for modified amino acids available for fixed charge atomistic forcefields, we parameterize the size and atomistic hydropathy of the coarse-grained modified amino acid beads, and hence the interactions between the modified and natural amino acids. We then elucidate how the number and position of phosphorylated and acetylated residues alter the protein’s single chain compactness and its propensity to phase separate. We show that both the number and the position of phosphorylated threonines/serines or acetylated lysines can serve as a molecular on/off switch for phase separation in the well-studied disordered regions of FUS and DDX3X, respectively. We also compare modified residues to their commonly used PTM mimics for their impact on chain properties. Importantly, we show that the model can predict and capture experimentally measured differences in the phase behavior for position-specific modifications, showing that the position of modifications can dictate phase separation. In sum, this model will be useful for studying LLPS of post-translationally modified intrinsically disordered proteins and predicting how modifications control phase behavior with position-specific resolution.Statement of SignificancePost-translational modifications are important regulators of liquid-liquid phase separation (LLPS) which drives the formation of biomolecular condensates. Theoretical methods can be used to characterize the biophysical properties of intrinsically disordered proteins (IDPs). Our recent framework for molecular simulations using a Cα-centered coarse-grained model can predict the effect of various perturbations such as mutations (Dignon et al. PloS Comput. Biol, 2018) and temperature (Dignon et al, ACS Cent. Sci., 2019) on LLPS. Here, we expand this framework to incorporate modified residues like phosphothreonine, phosphoserine and acetylysine. This model will prove useful for simulating the phase separation of post-translationally modified IDPs and predicting how position-specific modifications can control phase behavior across the large family of proteins known to be phosphorylated and acetylated.

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Beyond Microsatellite Instability: Intrinsic Disorder as a Potential Link Between Protein Short Tandem Repeats and Cancer

Frontiers in Bioinformatics ◽

10.3389/fbinf.2021.685844 ◽

2021 ◽

Vol 1 ◽

Author(s):

Max A. Verbiest ◽

Matteo Delucchi ◽

Tugce Bilgin Sonay ◽

Maria Anisimova

Keyword(s):

Amino Acids ◽

Microsatellite Instability ◽

Short Tandem Repeats ◽

Tandem Repeats ◽

Disordered Proteins ◽

Future Research ◽

Protein Coding ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Short Tandem

Short tandem repeats (STRs) are abundant in genomic sequences and are known for comparatively high mutation rates; STRs therefore are thought to be a potent source of genetic diversity. In protein-coding sequences STRs primarily encode disorder-promoting amino acids and are often located in intrinsically disordered regions (IDRs). STRs are frequently studied in the scope of microsatellite instability (MSI) in cancer, with little focus on the connection between protein STRs and IDRs. We believe, however, that this relationship should be explicitly included when ascertaining STR functionality in cancer. Here we explore this notion using all canonical human proteins from SwissProt, wherein we detected 3,699 STRs. Over 80% of these consisted completely of disorder promoting amino acids. 62.1% of amino acids in STR sequences were predicted to also be in an IDR, compared to 14.2% for non-repeat sequences. Over-representation analysis showed STR-containing proteins to be primarily located in the nucleus where they perform protein- and nucleotide-binding functions and regulate gene expression. They were also enriched in cancer-related signaling pathways. Furthermore, we found enrichments of STR-containing proteins among those correlated with patient survival for cancers derived from eight different anatomical sites. Intriguingly, several of these cancer types are not known to have a MSI-high (MSI-H) phenotype, suggesting that protein STRs play a role in cancer pathology in non MSI-H settings. Their intrinsic link with IDRs could therefore be an attractive topic of future research to further explore the role of STRs and IDRs in cancer. We speculate that our observations may be linked to the known dosage-sensitivity of disordered proteins, which could hint at a concentration-dependent gain-of-function mechanism in cancer for proteins containing STRs and IDRs.

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Folding of poly-amino acids and intrinsically disordered proteins in overcrowded milieu induced by pH change

International Journal of Biological Macromolecules ◽

10.1016/j.ijbiomac.2018.12.038 ◽

2019 ◽

Vol 125 ◽

pp. 244-255 ◽

Cited By ~ 3

Author(s):

Alexander V. Fonin ◽

Olga V. Stepanenko ◽

Asiia K. Sitdikova ◽

Iuliia A. Antifeeva ◽

Elena I. Kostyleva ◽

...

Keyword(s):

Amino Acids ◽

Intrinsically Disordered Proteins ◽

Disordered Proteins ◽

Ph Change ◽

Intrinsically Disordered

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Enhancing Binding Affinity of an Intrinsically Disordered Protein by α-Methylation of Key Amino Acid Residues

10.26434/chemrxiv.10113128.v1 ◽

2019 ◽

Author(s):

Valentin Bauer ◽

Boris Schmidtgall ◽

Gergő Gógl ◽

Jozica Dolenc ◽

Judit Osz ◽

...

Keyword(s):

Amino Acids ◽

Protein Interactions ◽

Intrinsically Disordered Proteins ◽

Intrinsically Disordered Protein ◽

Selective Inhibition ◽

Disordered Proteins ◽

Creb Binding Protein ◽

Alpha Helices ◽

Intrinsically Disordered ◽

Order Of Magnitude

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Variants of intrinsic disorder: structural characterization

10.1101/721308 ◽

2019 ◽

Author(s):

Sergio Forcelloni ◽

Antonio Deiana ◽

Andrea Giansanti

Keyword(s):

Amino Acids ◽

Structural Model ◽

Intrinsically Disordered Proteins ◽

Scaling Law ◽

Intrinsically Disordered Protein ◽

Accessible Surface Area ◽

Human Proteome ◽

Disordered Proteins ◽

Radius Of Gyration ◽

Intrinsically Disordered

AbstractIn a recent study, we have introduced an operational classification of the human proteome in three variants of disorder: ordered proteins (ORDPs), structured proteins with intrinsically disordered protein regions (IDPRs), intrinsically disordered proteins (IDPs). That classification was useful in functionally separating IDPRs from IDPs, which up until now have been generally considered as a whole. In this study, we corroborate this distinction by considering different physical-chemical and structural properties. Both ORDPs and IDPRs are enriched in order-promoting amino acids, whereas only IDPs show an enrichment in disordered-promoting amino acids. Consistently, ORDPs and IDPRs are preferentially located in the ordered phase of the charge-hydropathy plot, whereas IDPs are widespread over the disordered phase. We introduce the mean packing - mean pairwise energy (MP-MPE) plane to structurally characterize these variants even in the absence of a structural model. As expected for well-packed proteins, a negative linear correlation is observed between MP and MPE for ORDPs and IDPRs, whereas IDPs break this linear dependence. Finally, we find that IDPs have a more extended conformation as measured by the scaling law between the radius of gyration and the length of these proteins, and accordingly they have higher solubility and accessible surface area than ORDPs and IDPRs. Overall, our results confirm the relevance of our operational separation of IDPRs from IDPs and provide further validation of our criteria to separate IDPs from the rest of human proteome.

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Intrinsically disordered proteins share a common molecular mechanism in membranes damages: Lipid-chaperone hypothesis

10.1021/scimeetings.0c02079 ◽

2020 ◽

Author(s):

Carmelo La Rosa

Keyword(s):

Molecular Mechanism ◽

Intrinsically Disordered Proteins ◽

Disordered Proteins ◽

Intrinsically Disordered

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Intrinsically Disordered Proteins

10.1016/s0076-6879(18)x0012-3 ◽

2018 ◽

Keyword(s):

Intrinsically Disordered Proteins ◽

Disordered Proteins ◽

Intrinsically Disordered

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Sequence Specificity Despite Intrinsic Disorder: How a Disease-Associated Val/Met Polymorphism Shifts Tertiary Interactions in a Long Disordered Protein

10.26434/chemrxiv.8135777.v1 ◽

2019 ◽

Author(s):

Ruchi Lohia ◽

Reza Salari ◽

Grace Brannigan

Keyword(s):

Secondary Structure ◽

Electrostatic Interactions ◽

Intrinsically Disordered Proteins ◽

Disordered Proteins ◽

Sequence Specificity ◽

Intrinsically Disordered ◽

Specific Effects ◽

Heterogeneous Polymer ◽

Non Local ◽

Dynamics Simulations

<div>The role of electrostatic interactions and mutations that change charge states in intrinsically disordered proteins (IDPs) is well-established, but many disease-associated mutations in IDPs are charge-neutral. The Val66Met single nucleotide polymorphism (SNP) encodes a hydrophobic-to-hydrophobic mutation at the midpoint of the prodomain of precursor brain-derived neurotrophic factor (BDNF), one of the earliest SNPs to be associated with neuropsychiatric disorders, for which the underlying molecular mechanism is unknown. Here we report on over 250 μs of fully-atomistic, explicit solvent, temperature replica exchange molecular dynamics simulations of the 91 residue BDNF prodomain, for both the V66 and M66 sequence.</div><div>The simulations were able to correctly reproduce the location of both local and non-local secondary changes due to the Val66Met mutation when compared with NMR spectroscopy. We find that the local structure change is mediated via entropic and sequence specific effects. We show that the highly disordered prodomain can be meaningfully divided into domains based on sequence alone. Monte Carlo simulations of a self-excluding heterogeneous polymer, with monomers representing each domain, suggest the sequence would be effectively segmented by the long, highly disordered polyampholyte near the sequence midpoint. This is qualitatively consistent with observed interdomain contacts within the BDNF prodomain, although contacts between the two segments are enriched relative to the self-excluding polymer. The Val66Met mutation increases interactions across the boundary between the two segments, due in part to a specific Met-Met interaction with a Methionine in the other segment. This effect propagates to cause the non-local change in secondary structure around the second methionine, previously observed in NMR. The effect is not mediated simply via changes in inter-domain contacts but is also dependent on secondary structure formation around residue 66, indicating a mechanism for secondary structure coupling in disordered proteins. </div>

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