(Intrinsically disordered) splice variants in the proteome: implications for novel drug discovery

Vladimir N. Uversky 한국유전학회 2016 Genes & Genomics Vol.38 No.7

In higher eukaryotes, proteomes are typically larger than corresponding genomes mostly due to alternative spicing (AS) which is affecting more than 86 % of human genes. Tissue specificity of many proteins is often determined by the AS of pre-mRNAs that generates multiple proteins from a single gene. Aberrations in AS are found in numerous human diseases. This article shows that AS expanded the classic ‘‘one-gene–one-protein’’ paradigm to the ‘‘one-gene–many-proteins’’ concept. AS is intimately associated with protein intrinsic disorder. There is a tight connection between the altered AS of some key intrinsically disordered proteins and pathogenesis of neurodegenerative diseases, cardiovascular disease, cancer, and diabetes. The development of drugs for splice variants is a challenging endeavor. AS has tremendous influence on the applicability of several drugs developed to affect functions typically attributed to the ordered parts of disease- related proteins. Although there are several means for the differential targeting of splice variants, new approaches are obviously needed. It is expected that better understanding of the molecular mechanisms underlying modulation of biological activities of numerous spliced variants will be achieved and new drug design approaches for proteins with multiple splice variants will be developed.

How Do We Study the Dynamic Structure of Unstructured Proteins: A Case Study on Nopp140 as an Example of a Large, Intrinsically Disordered Protein

Na, Jung-Hyun,Lee, Won-Kyu,Yu, Yeon Gyu MDPI AG 2018 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.19 No.2

<P>Intrinsically disordered proteins (IDPs) represent approximately 30% of the human genome and play key roles in cell proliferation and cellular signaling by modulating the function of target proteins via protein–protein interactions. In addition, IDPs are involved in various human disorders, such as cancer, neurodegenerative diseases, and amyloidosis. To understand the underlying molecular mechanism of IDPs, it is important to study their structural features during their interactions with target proteins. However, conventional biochemical and biophysical methods for analyzing proteins, such as X-ray crystallography, have difficulty in characterizing the features of IDPs because they lack an ordered three-dimensional structure. Here, we present biochemical and biophysical studies on nucleolar phosphoprotein 140 (Nopp140), which mostly consists of disordered regions, during its interaction with casein kinase 2 (CK2), which plays a central role in cell growth. Surface plasmon resonance and electron paramagnetic resonance studies were performed to characterize the interaction between Nopp140 and CK2. A single-molecule fluorescence resonance energy transfer study revealed conformational change in Nopp140 during its interaction with CK2. These studies on Nopp140 can provide a good model system for understanding the molecular function of IDPs.</P>

Backbone assignment of the intrinsically disordered N-terminal region of Bloom syndrome protein

양민준,박진주 한국자기공명학회 2023 Journal of the Korean Magnetic Resonance Society Vol.27 No.3

Bloom syndrome protein (BLM) is a pivotal RecQ helicase necessary for genetic stability through DNA repair processes. Our investigation focuses on the N-terminal region of BLM, which has been considered as an intrinsically disordered region (IDR). This IDR plays a critical role in DNA metabolism by interacting with other proteins. In this study, we performed triple resonance experiments of BLM220-300 and presented the backbone chemical shifts. The secondary structure prediction based on chemical shifts of the backbone atoms shows the region is disordered. Our data could help further interaction studies between BLM220-300 and its binding partners using NMR.

An NMR study on the intrinsically disordered core transactivation domain of human glucocorticoid receptor

( Do-hyoung Kim ),( Anthony Wright ),( Kyou-hoon Han ) 생화학분자생물학회 2017 BMB Reports Vol.50 No.10

A large number of transcriptional activation domains (TADs) are intrinsically unstructured, meaning they are devoid of a three-dimensional structure. The fact that these TADs are transcriptionally active without forming a 3-D structure raises the question of what features in these domains enable them to function. One of two TADs in human glucocorticoid receptor (hGR) is located at its N-terminus and is responsible for ∼70% of the transcriptional activity of hGR. This 58-residue intrinsically-disordered TAD, named tau1c in an earlier study, was shown to form three helices under trifluoroethanol, which might be important for its activity. We carried out heteronuclear multi-dimensional NMR experiments on hGR tau1c in a more physiological aqueous buffer solution and found that it forms three helices that are ∼30% pre-populated. Since pre-populated helices in several TADs were shown to be key elements for transcriptional activity, the three pre-formed helices in hGR tau1c delineated in this study should be critical determinants of the transcriptional activity of hGR. The presence of prestructured helices in hGR tau1c strongly suggests that the existence of pre-structured motifs in target-unbound TADs is a very broad phenomenon. [BMB Reports 2017; 50(10): 522-527]

Ferritin nanocage with intrinsically disordered proteins and affibody: A platform for tumor targeting with extended pharmacokinetics

Lee, Na Kyeong,Lee, Eun Jung,Kim, Soyoun,Nam, Gi-hoon,Kih, Minwoo,Hong, Yeonsun,Jeong, Cherlhyun,Yang, Yoosoo,Byun, Youngro,Kim, In-San Elsevier 2017 Journal of controlled release Vol.267 No.-

<P><B>Abstract</B></P> <P>Ferritin nanocages are of particular interest as a novel platform for drug and vaccine delivery, diagnosis, biomineralization scaffold and more, due to their perfect and complex symmetry, ideal physical properties, high biocompatibility, low toxicity profiles as well as easy manipulation by genetic or chemical strategies. However, a short half-life is still a hurdle for the translation of ferritin-based nanomedicines into the clinic. Here, we developed a series of rationally designed long circulating ferritin nanocages (LCFNs) with ‘Intrinsically Disordered Proteins (IDP)’ as a stealth layer for extending the half-life of ferritin nanocages. Through predictions with 3D modelling, the LCFNs were designed, generated and their pharmacokinetic parameters including half-life, clearance rate, mean residence time, and more, were evaluated by qualitative and quantitative analysis. LCFNs have a tenfold increased half-life and overall improved pharmacokinetic parameters compared to wild-type ferritin nanocages (wtFN), corresponding to the low binding against bone marrow-derived macrophages (BMDMs) and endothelial cells. Subsequently, a tumor targeting moiety, epidermal growth factor receptor (EGFR)-targeting affibody peptide, was fused to LCFNs for evaluating their potential as a theragnostic platform. The tumor targeting-LCFNs successfully accumulated to the tumor tissue, by efficient targeting <I>via</I> active and passive properties, and also the shielding effect of IDP <I>in vivo</I>. This strategy can be applied to other protein-based nanocages for further progressing their use in the field of nanomedicine.</P> <P><B>Graphical abstract</B></P> <P>Long circulating ferritin nanocages are designed by 3D modelling. Modified by intrinsically disordered protein (IDP) clouds, this novel biocompatible nanocage platform can be applied in the field of nanomedicine.</P> <P>[DISPLAY OMISSION]</P>

Designed Protein-based Hydrogel using Intrinsically Disordered Protein with PEG Cross-linkers.

Eunjung LEE,HyeonWoo JE,WonKyung AHN,WonJun KIM,Dayeon KANG 한국생물공학회 2019 한국생물공학회 학술대회 Vol.2019 No.4

Direct force measurements reveal that protein Tau confers short-range attractions and isoform-dependent steric stabilization to microtubules

Chung, Peter J.,Choi, Myung Chul,Miller, Herbert P.,Feinstein, H. Eric,Raviv, Uri,Li, Youli,Wilson, Leslie,Feinstein, Stuart C.,Safinya, Cyrus R. National Academy of Sciences 2015 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.112 No.47

<P><B>Significance</B></P><P>The microtubule-associated protein Tau is known to stabilize microtubules against depolymerization in neuronal axons, ensuring proper trafficking of organelles along microtubules in long axons. Abnormal interactions between Tau and microtubules are implicated in Alzheimer’s disease and other neurodegenerative disorders. We directly measured forces between microtubules coated with Tau isoforms by synchrotron small-angle X-ray scattering of reconstituted Tau–microtubule mixtures under osmotic pressure (mimicking molecular crowding in cells). We found that select Tau isoforms fundamentally alter forces between microtubules by undergoing a conformational change on microtubule surfaces at a coverage indicative of an unusually extended Tau state. This gain of function by longer isoforms in imparting steric stabilization to microtubules is essential in preventing microtubule aggregation and loss of function in organelle trafficking.</P><P>Microtubules (MTs) are hollow cytoskeletal filaments assembled from αβ-tubulin heterodimers. Tau, an unstructured protein found in neuronal axons, binds to MTs and regulates their dynamics. Aberrant Tau behavior is associated with neurodegenerative dementias, including Alzheimer’s. Here, we report on a direct force measurement between paclitaxel-stabilized MTs coated with distinct Tau isoforms by synchrotron small-angle X-ray scattering (SAXS) of MT-Tau mixtures under osmotic pressure (<I>P</I>). In going from bare MTs to MTs with Tau coverage near the physiological submonolayer regime (Tau/tubulin-dimer molar ratio; Φ<SUB>Tau</SUB> = 1/10), isoforms with longer N-terminal tails (NTTs) sterically stabilized MTs, preventing bundling up to <I>P</I><SUB>B</SUB> ∼ 10,000–20,000 Pa, an order of magnitude larger than bare MTs. Tau with short NTTs showed little additional effect in suppressing the bundling pressure (<I>P</I><SUB>B</SUB> ∼ 1,000–2,000 Pa) over the same range. Remarkably, the abrupt increase in <I>P</I><SUB>B</SUB> observed for longer isoforms suggests a mushroom to brush transition occurring at 1/13 < Φ<SUB>Tau</SUB> < 1/10, which corresponds to MT-bound Tau with NTTs that are considerably more extended than SAXS data for Tau in solution indicate. Modeling of Tau-mediated MT–MT interactions supports the hypothesis that longer NTTs transition to a polyelectrolyte brush at higher coverages. Higher pressures resulted in isoform-independent irreversible bundling because the polyampholytic nature of Tau leads to short-range attractions. These findings suggest an isoform-dependent biological role for regulation by Tau, with longer isoforms conferring MT steric stabilization against aggregation either with other biomacromolecules or into tight bundles, preventing loss of function in the crowded axon environment.</P>

Ferritin Conjugated with Intrinsically Disordered Protein to Form Protein-based Hydrogels

Nayeon KIM,Yeram LEE,Yeju KO,Eunjung LEE 한국생물공학회 2022 한국생물공학회 학술대회 Vol.2022 No.4

Structure-dynamic basis of splicing-dependent regulation in tissue-specific variants of the sodium-calcium exchanger

Lee, Su Youn,Giladi, Moshe,Bohbot, Hilla,Hiller, Reuben,Chung, Ka Young,Khananshvili, Daniel The Federation of American Societies for Experimen 2016 The FASEB Journal Vol.30 No.3

<P>Tissue-specific splice variants of Na+/Ca2+ exchangers contain 2 Ca2+-binding regulatory domains (CBDs), CBD1 and CBD2. Ca2+ interaction with CBD1 activates sodium-calcium exchangers (NCXs), and Ca2+ binding to CBD2 alleviates Na+-dependent inactivation. A combination of mutually exclusive (A, B) and cassette (C-F) exons in CBD2 raises functionally diverse splice variants through unknown mechanisms. Here, the effect of exons on CBDs backbone dynamics were investigated in the 2-domain tandem (CBD12) of the brain, kidney, and cardiac splice variants by using hydrogen-deuterium exchange mass spectrometry and stopped-flow techniques. Mutually exclusive exons stabilize interdomain interactions in the apoprotein, which primarily predefines the extent of responses to Ca2+ binding. Deuterium uptake levels were up to 20% lower in the cardiac vs. the brain CBD12, reveling that elongation of the CBD2 FG loop by cassette exons rigidifies the interdomain Ca2+ salt bridge at the 2-domain interface, which secondarily modulates the Ca2+-bound states. In matching splice variants, the extent of Ca2+-induced rigidification correlates with decreased (up to 10-fold) Ca2+ off rates, where the cardiac CBD12 exhibits the slowest Ca2+ off rates. Collectively, structurally disordered/dynamic segments at mutually exclusive and cassette exons have local and distant effects on the folded structures nearby the Ca2+ binding sites, which may serve as a structure-dynamic basis for splicing-dependent regulation of NCX.</P>

Complex Coacervate Formation of Human Bone Morphogenetic Protein-2 through Introducing Intrinsically Disordered Regions

Hyunsuk CHOI,Dawoon JEONG,Yoo Seong CHOI 한국생물공학회 2024 한국생물공학회 학술대회 Vol.2024 No.4