Medicine and Health Sciences Commons^™

Actinidia Drm1 - An Intrinsically Disordered Protein Whose Mrna Expression Is Inversely Correlated With Spring Budbreak In Kiwifruit, Marion Wood, Georgina M. Rae, Rong-Mei Wu, Eric F. Walton, Bin Xue, Roger P. Hellens, Vladimir N. Uversky

Molecular Medicine Faculty Publications

Intrinsically disordered proteins (IDPs) are a relatively recently defined class of proteins which, under native conditions, lack a unique tertiary structure whilst maintaining essential biological functions. Functional classification of IDPs have implicated such proteins as being involved in various physiological processes including transcription and translation regulation, signal transduction and protein modification. Actinidia DRM1 (Ade DORMANCY ASSOCIATED GENE 1), represents a robust dormancy marker whose mRNA transcript expression exhibits a strong inverse correlation with the onset of growth following periods of physiological dormancy. Bioinformatic analyses suggest that DRM1 is plant specific and highly conserved at both the nucleotide and protein …

Ordered Disorder Of The Astrocytic Dystrophin-Associated Protein Complex In The Norm And Pathology, Insung Na, Derek Redmon, Markus Kopa, Yiru Qin, Bin Xue, Vladimir N. Uversky

Molecular Medicine Faculty Publications

The abundance and potential functional roles of intrinsically disordered regions in aquaporin-4, Kir4.1, a dystrophin isoforms Dp71, α-1 syntrophin, and α-dystrobrevin; i.e., proteins constituting the functional core of the astrocytic dystrophin-associated protein complex (DAPC), are analyzed by a wealth of computational tools. The correlation between protein intrinsic disorder, single nucleotide polymorphisms (SNPs) and protein function is also studied together with the peculiarities of structural and functional conservation of these proteins. Our study revealed that the DAPC members are typical hybrid proteins that contain both ordered and intrinsically disordered regions. Both ordered and disordered regions are important for the stabilization of …

The Alphabet Of Intrinsic Disorder: I. Act Like A Pro: On The Abundance And Roles Of Proline Residues In Intrinsically Disordered Proteins, Francois-Xavier Theillet, Lajos Kalmar, Peter Tompa, Kyou-Hoon Han, Philipp Selenko, A. Keith Dunker, Gary W. Daughdrill, Vladimir N. Uversky

Molecular Medicine Faculty Publications

A significant fraction of every proteome is occupied by biologically active proteins that do not form unique three-dimensional structures. These intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) have essential biological functions and are characterized by extensive structural plasticity. Such structural and functional behavior is encoded in the amino acid sequences of IDPs/IDPRs, which are enriched in disorder-promoting residues and depleted in order-promoting residues. In fact, amino acid residues can be arranged according to their disorder-promoting tendency to form an alphabet of intrinsic disorder that defines the structural complexity and diversity of IDPs/IDPRs. This review is the first in a …

What’S In A Name? Why These Proteins Are Intrinsically Disordered, A. Keith Dunker, M. Madan Babu, Elisar Barbar, Martin Blackledge, Sarah E. Bondos, Zsuzsanna Dosztányi, H. Jane Dyson, Julie D. Forman-Kay, Monika Fuxreiter, Joerg Gsponer, Kyou-Hoon Han, David T. Jones, Sonia Longhi, Steven J. Metallo, Ken Nishikawa, Ruth Nussinov, Zoran Obradovic, Rohit V. Pappu, ,Burkhard Rost, Philipp Selenko, Vinod Subramaniam, Joel Sussman, Peter Tompa, Vladimir N. Uversky

Molecular Medicine Faculty Publications

“What’s in a name? That which we call a rose By any other name would smell as sweet.” From “Romeo and Juliet”, William Shakespeare (1594)

This article opens a series of publications on disambiguation of the basic terms used in the field of intrinsically disordered proteins. We start from the beginning, namely from the explanation of what the expression “intrinsically disordered protein” actually means and why this particular term has been chosen as the common denominator for this class of proteins characterized by broad structural, dynamic and functional characteristics.

Modulating The Intrinsic Disorder In The Cytoplasmic Domain Alters The Biological Activity Of The N-Methyl-D-Spartate-Sensitive Glutamate Receptor, Ucheor B. Choi, Rashek Kazi, Natalie Stenzoski, Lonnie P. Wollmuth, Vladimir N. Uversky, Mark E. Bowen

Molecular Medicine Faculty Publications

The NMDA-sensitive glutamate receptor is a ligand-gated ion channel that mediates excitatory synaptic transmission in the nervous system. Extracellular zinc allosterically regulates the NMDA receptor by binding to the extracellular N-terminal domain, which inhibits channel gating. Phosphorylation of the intrinsically disordered intracellular C-terminal domain alleviates inhibition by extracellular zinc. The mechanism for this functional effect is largely unknown. Proline is a hallmark of intrinsic disorder, so we used proline mutagenesis to modulate disorder in the cytoplasmic domain. Proline depletion selectively uncoupled zinc inhibition with little effect on receptor biogenesis, surface trafficking, or ligand-activated gating. Proline depletion also reduced the affinity …

Alpha 1-Antichymotrypsin, An Inflammatory Protein Overexpressed In The Brains Of Patients With Alzheimer’S Disease, Induces Tau Hyperphosphorylation Through C-Jun N-Terminal Kinase Activation, Ethika Tyagi, Tina Fiorelli, Michelle Norden, Jaya Padmanabhan

Molecular Medicine Faculty Publications

The association of inflammatory proteins with neuritic plaques in the brains of Alzheimer’s disease (AD) patients has led to the hypothesis that inflammation plays a pivotal role in the development of pathology in AD. Earlier studies have shown that alpha 1-antichymotrypsin (ACT) enhances amyloid beta fibrillization and accelerated plaque formation in APP transgenic mice. Later studies from our laboratory have shown that purified ACT induces tau hyperphosphorylation and degeneration in neurons. In order to understand the mechanisms by which inflammatory proteins enhance tau hyperphosphorylation, we injected interleukin-1β (IL-1β) intracerebroventricularly into mice expressing human ACT, human tau, or …

Dysregulated Alternative Splicing Pattern Of Pkc During Differentiation Of Human Preadipocytes Represents Distinct Differences Between Lean And Obese Adipocytes, Gay Carter, André Apostolatos, Rekha Patel, Abhishek Mathur, Denise Cooper, Michel Murr, Niketa A. Patel

Molecular Medicine Faculty Publications

Obesity and its comorbidities affect millions of people. Here, we demonstrate that human preadipocytes are susceptible to programmed cell death (apoptosis) while mature adipocytes are resistant to apoptosis. The molecular mechanisms underlying the phenotype of apoptosis-resistant adipocytes are lesser known. To study the role of apoptosis and define molecular differences in the developmental process of adipogenesis, human preadipocytes were differentiated in vitro to mature adipocytes. Many genes in the apoptosis pathway are alternatively spliced. Our data demonstrates that during differentiation PKCδ, Bclx, and Caspase9 switch to their prosurvival splice variants along with an increase in Bcl2 expression when …

Persistent Human Herpesvirus-6 Infection In Patients With An Inherited Form Of The Virus, Shara N. Pantry, Maria M. Medveczky, Jesse H. Arbuckle, Janos Luka, Jose G. Montoya, Jianhong Hu, Rolf Renne, Daniel Peterson, Joshua C. Pritchett, Dharam V. Ablashi, Peter G. Medveczky

Molecular Medicine Faculty Publications

Human herpesvirus-6 (HHV-6)A and 6B are ubiquitous betaherpesviruses viruses with lymphotropic and neurotropic potential. As reported earlier, these viruses establish latency by integration into the telomeres of host chromosomes. Chromosomally integrated HHV-6 (CIHHV-6) can be transmitted vertically from parent to child. Some CIHHV-6 patients are suffering from neurological symptoms, while others remain asymptomatic. Four patients with CIHHV-6 and CNS dysfunction were treated with valganciclovir or foscarnet. HHV-6 replication was detected by reverse transcriptase polymerase chain reaction amplification of a late envelope glycoprotein. In this study we also compared the inherited and persistent HHV-6 viruses by DNA sequencing. The prevalence of …

Understanding The Molecular Mechanisms Underlying Complex Cancer Genome Rearrangements, Robert Hedlund, Vladimir N. Uversky

Molecular Medicine Faculty Publications

In their recent paper, Malhotra et al. performed a comprehensive analysis of the structural variation breakpoints in 64 cancer genomes from 7 tumor types to find the prevalence and origins of complex genomic rearrangements.1 Since this work represents a breakthrough in understanding of the molecular mechanisms underlying complex cancer genome rearrangements, we provide a brief overview of this outstanding study.

Interplay Between Estrogen Receptor And Akt In Estradiol-Induced Alternative Splicing, Poornima Bhat-Nakshatri, Eun-Kyung Song, Nikail R. Collins, Vladimir N. Uversky, A. Keith Dunker, Bert W. O'Malley, Tim R. Geistlinger, Jason S. Carroll, Myles Brown, Harikrishna Nakshatri

Molecular Medicine Faculty Publications

Background: Alternative splicing is critical for generating complex proteomes in response to extracellular signals. Nuclear receptors including estrogen receptor alpha (ERα) and their ligands promote alternative splicing. The endogenous targets of ERα:estradiol (E2)-mediated alternative splicing and the influence of extracellular kinases that phosphorylate ERα on E2-induced splicing are unknown.
Methods: MCF-7 and its anti-estrogen derivatives were used for the majority of the assays. CD44 mini gene was used to measure the effect of E2 and AKT on alternative splicing. ExonHit array analysis was performed to identify E2 and AKT-regulated endogenous alternatively spliced apoptosis-related genes. Quantitative reverse transcription polymerase chain reaction …

The Ube2e Proteins As Conjugating Dispersers: Extending Function With Extended Extensions, Vladimir N. Uversky

Molecular Medicine Faculty Publications

No abstract provided.

Malleable Ribonucleoprotein Machine: Protein Intrinsic Disorder In The Saccharomyces Cerevisiae Spliceosome, Maria De Lourdes Coelho Ribeiro, Julio Espinosa, Sameen Islam, Osvaldo Martinez, Jayesh Jamnadas Thanki, Stephanie Mazariegos, Tam Nguyen, Maya Larina, Bin Xue, Vladimir N. Uversky

Molecular Medicine Faculty Publications

Recent studies revealed that a significant fraction of any given proteome is presented by proteins that do not have unique 3D structures as a whole or in significant parts. These intrinsically disordered proteins possess dramatic structural and functional variability, being especially enriched in signaling and regulatory functions since their lack of fixed structure defines their ability to be involved in interaction with several proteins and allows them to be re-used in multiple pathways. Among recognized disorder-based protein functions are interactions with nucleic acids and multi-target binding; i.e., the functions ascribed to many spliceosomal proteins. Therefore, the spliceosome, a multimegadalton ribonucleoprotein …

Structural Characterizations Of Phosphorylatable Residues In Transmembrane Proteins From Arabidopsis Thaliana, Bin Xue, Vladimir N. Uversky

Molecular Medicine Faculty Publications

Phosphorylation is a common post-translational modification that plays important roles in a wide range of biochemical and cellular processes. Many enzymes and receptors can be switched “on” or “off” by conformational changes induced by phosphorylation. The phosphorylation process is mediated by a family of enzymes called kinase. Currently, more than 1,000 different kinases have been identified in Arabidopsis thaliana proteome. Kinases interact with each other and with many regulatory proteins forming phosphorylation networks. These phosphorylation networks modulate the signaling processes and control the functions of cells. Normally, kinases phosphorylate serines, threonines, and tyrosines. However, in many proteins, not all of …

Distribution And Cluster Analysis Of Predicted Intrinsically Disordered Protein Pfam Domains, Robert W. Williams, Bin Xue, Vladimir N. Uversky, A. Keith Dunker

Molecular Medicine Faculty Publications

The Pfam database groups regions of proteins by how well hidden Markov models (HMMs) can be trained to recognize similarities among them. Conservation pressure is probably in play here. The Pfam seed training set includes sequence and structure information, being drawn largely from the PDB. A long standing hypothesis among intrinsically disordered protein (IDP) investigators has held that conservation pressures are also at play in the evolution of different kinds of intrinsic disorder, but we find that predicted intrinsic disorder (PID) is not always conserved across Pfam domains. Here we analyze distributions and clusters of PID regions in 193024 members …

Intrinsic Disorder In Pten And Its Interactome Confers Structural Plasticity And Functional Versatility, Prerna Malaney, Ravi Ramesh Pathak, Bin Xue, Vladimir N. Uversky, Vrushank Davé

Molecular Medicine Faculty Publications

IDPs, while structurally poor, are functionally rich by virtue of their flexibility and modularity. However, how mutations in IDPs elicit diseases, remain elusive. Herein, we have identified tumor suppressor PTEN as an intrinsically disordered protein (IDP) and elucidated the molecular principles by which its intrinsically disordered region (IDR) at the carboxyl-terminus (C-tail) executes its functions. Post-translational modifications, conserved eukaryotic linear motifs and molecular recognition features present in the C-tail IDR enhance PTEN's protein-protein interactions that are required for its myriad cellular functions. PTEN primary and secondary interactomes are also enriched in IDPs, most being cancer related, revealing that PTEN functions …

D2P2: Database Of Disordered Protein Predictions, Matt E. Oates, Pedro R. Romero, Takashi Ishida, Mohamed Ghalwash, Marcin J. Mizianty, Bin Xue, Zsuzsanna Dosztányi, Vladimir N. Uversky, Zoran Obradovic, Lukasz Kurgan, A. Keith Dunker, Julian Gough

Molecular Medicine Faculty Publications

We present the Database of Disordered Protein Prediction (D2P2), available at http://d2p2.pro (including website source code). A battery of disorder predictors and their variants, VL-XT, VSL2b, PrDOS, PV2, Espritz and IUPred, were run on all protein sequences from 1765 complete proteomes (to be updated as more genomes are completed). Integrated with these results are all of the predicted (mostly structured) SCOP domains using the SUPERFAMILY predictor. These disorder/structure annotations together enable comparison of the disorder predictors with each other and examination of the overlap between disordered predictions and SCOP domains on a large scale. D2P2 will increase our understanding of …

Extracting Structural Information From Charge-State Distributions Of Intrinsically Disordered Proteins By Non-Denaturing Electrospray-Ionization Mass Spectrometry, Lorenzo Testa, Stefania Brocca, Carlo Santambrogio, Annalisa D'Urzo, Johnny Habchi, Sonia Longhi, Vladimir N. Uversky, Rita Grandori

Molecular Medicine Faculty Publications

Intrinsically disordered proteins (IDPs) exert key biological functions but tend to escape identification and characterization due to their high structural dynamics and heterogeneity. The possibility to dissect conformational ensembles by electrospray-ionization mass spectrometry (ESI-MS) offers an attracting possibility to develop a signature for this class of proteins based on their peculiar ionization behavior. This review summarizes available data on charge-state distributions (CSDs) obtained for IDPs by non-denaturing ESI-MS, with reference to globular or chemically denatured proteins. The results illustrate the contributions that direct ESI-MS analysis can give to the identification of new putative IDPs and to their conformational investigation.

Looking At Microbial Metabolism By High-Resolution (2)H-Nmr Spectroscopy, Victor P. Kutyshenko, Peter M. Beskaravayny, Maxim V. Molchanov, Svetlana I. Paskevich, Dmitry A. Prokhorov, Vladimir N. Uversky

Molecular Medicine Faculty Publications

We analyzed the applicability of high-resolution (2)H-HMR spectroscopy for the analysis of microbe metabolism in samples of mitochondrion isolated from rat liver and from aqueous extracts of homogenates of rat liver and other organs and tissues in the presence of high D2O contents. Such analysis is possible due to the fast microbe adaptation to life in the heavy water. It is also shown that some enzymatic processes typical for the intact cells are preserved in the homogenized tissue preparations. The microbial and cellular metabolic processes can be differentiated via the strategic use of cell poisons and antibiotics.

The Alphabet Of Intrinsic Disorder: Ii. Various Roles Of Glutamic Acid In Ordered And Intrinsically Disordered Proteins, Vladimir N. Uversky

Molecular Medicine Faculty Publications

The ability of a protein to fold into unique functional state or to stay intrinsically disordered is encoded in its amino acid sequence. Both ordered and intrinsically disordered proteins (IDPs) are natural polypeptides that use the same arsenal of 20 proteinogenic amino acid residues as their major building blocks. The exceptional structural plasticity of IDPs, their capability to exist as heterogeneous structural ensembles and their wide array of important disorder-based biological functions that complements functional repertoire of ordered proteins are all rooted within the peculiar differential usage of these building blocks by ordered proteins and IDPs. In fact, some residues …

Digested Disorder: Quarterly Intrinsic Disorder Digest (January/February/March, 2013), Vladimir N. Uversky

Molecular Medicine Faculty Publications

The current literature on intrinsically disordered proteins is blooming. A simple PubMed search for "intrinsically disordered protein OR natively unfolded protein" returns about 1,800 hits (as of June 17, 2013), with many papers published quite recently. To keep interested readers up to speed with this literature, we are starting a "Digested Disorder" project, which will encompass a series of reader's digest type of publications aiming at the objective representation of the research papers and reviews on intrinsically disordered proteins. The only two criteria for inclusion in this digest are the publication date (a paper should be published within the covered …

Biophysical Characterization Of Α-Synuclein And Rotenone Interaction, Blanca A. Silva, Olöf Einarsdóttir, Anthony L. Fink, Vladimir N. Uversky

Molecular Medicine Faculty Publications

Previous studies revealed that pesticides interact with α-synuclein and accelerate the rate of fibrillation. These results are consistent with the prevailing hypothesis that the direct interaction of α-synuclein with pesticides is one of many suspected factors leading to α-synuclein fibrillation and ultimately to Parkinson's disease. In this study, the biophysical properties and fibrillation kinetics of α-synuclein in the presence of rotenone were investigated and, more specifically, the effects of rotenone on the early-stage misfolded forms of α-synuclein were considered. The thioflavine T (ThT) fluorescence assay studies provide evidence that early-phase misfolded α-synuclein forms are affected by rotenone and that the …

The Case For Intrinsically Disordered Proteins Playing Contributory Roles In Molecular Recognition Without A Stable 3d Structure, Vladimir N. Uversky, A. Keith Dunker

Molecular Medicine Faculty Publications

The classical ‘lock-and-key’ and ‘induced-fit’ mechanisms for binding both originated in attempts to explain features of enzyme catalysis. For both of these mechanisms and for their recent refinements, enzyme catalysis requires exquisite spatial and electronic complementarity between the substrate and the catalyst. Thus, binding models derived from models originally based on catalysis will be highly biased towards mechanisms that utilize structural complementarity. If mere binding without catalysis is the endpoint, then the structural requirements for the interaction become much more relaxed. Recent observations on specific examples suggest that this relaxation can reach an extreme lack of specific 3D structure, leading …