Medicine and Health Sciences Commons^™

Understanding Viral Transmission Behavior Via Protein Intrinsic Disorder Prediction: Coronaviruses, Gerard Kian-Meng Goh, A. Keith Dunker, Vladimir N. Uversky

Molecular Medicine Faculty Publications

Besides being a common threat to farm animals and poultry, coronavirus (CoV) was responsible for the human severe acute respiratory syndrome (SARS) epidemic in 2002–4. However, many aspects of CoV behavior, including modes of its transmission, are yet to be fully understood. We show that the amount and the peculiarities of distribution of the protein intrinsic disorder in the viral shell can be used for the efficient analysis of the behavior and transmission modes of CoV. The proposed model allows categorization of the various CoVs by the peculiarities of disorder distribution in their membrane (M) and nucleocapsid (N). This categorization …

Apolipoprotein E: Essential Catalyst Of The Alzheimer Amyloid Cascade, Huntington Potter, Thomas Wisniewski

Molecular Medicine Faculty Publications

The amyloid cascade hypothesis remains a robust model of AD neurodegeneration. However, amyloid deposits contain proteins besides Aβ, such as apolipoprotein E (apoE). Inheritance of the apoE4 allele is the strongest genetic risk factor for late-onset AD. However, there is no consensus on how different apoE isotypes contribute to AD pathogenesis. It has been hypothesized that apoE and apoE4 in particular is an amyloid catalyst or “pathological chaperone”. Alternatively it has been posited that apoE regulates Aβ clearance, with apoE4 been worse at this function compared to apoE3. These views seem fundamentally opposed. The former would indicate …

An Intrinsically Disordered Region Of The Acetyltransferase P300 With Similarity To Prion-Like Domains Plays A Role In Aggregation, Alexander Kirilyuk, Mika Shimoji, Jason Catania, Geetaram Sahu, Nagarajan Pattabiraman, Antonio Giordano, Christopher Albanese, Italo Mocchetti, Jeffrey A. Toretsky, Vladimir N. Uversky, Maria Laura Avantaggiati

Molecular Medicine Faculty Publications

Several human diseases including neurodegenerative disorders and cancer are associated with abnormal accumulation and aggregation of misfolded proteins. Proteins with high tendency to aggregate include the p53 gene product, TAU and alpha synuclein. The potential toxicity of aberrantly folded proteins is limited via their transport into intracellular sub-compartments, the aggresomes, where misfolded proteins are stored or cleared via autophagy. We have identified a region of the acetyltransferase p300 that is highly disordered and displays similarities with prion-like domains. We show that this region is encoded as an alternative spliced variant independently of the acetyltransferase domain, and provides an interaction interface …

Common Features At The Start Of The Neurodegeneration Cascade, Rubén Hervás, Javier Oroz, Albert Galera-Prat, Oscar Goñi, Alejandro Valbuena, Andrés M. Vera, Àngel Gómez-Sicilia, Fernando Losada-Urzáiz, Vladimir N. Uversky, Margarita Menéndez, Douglas V. Laurents, Marta Bruix, Mariano Carrión-Vázquez

Molecular Medicine Faculty Publications

Amyloidogenic neurodegenerative diseases are incurable conditions with high social impact that are typically caused by specific, largely disordered proteins. However, the underlying molecular mechanism remains elusive to established techniques. A favored hypothesis postulates that a critical conformational change in the monomer (an ideal therapeutic target) in these “neurotoxic proteins” triggers the pathogenic cascade. We use force spectroscopy and a novel methodology for unequivocal single-molecule identification to demonstrate a rich conformational polymorphism in the monomer of four representative neurotoxic proteins. This polymorphism strongly correlates with amyloidogenesis and neurotoxicity: it is absent in a fibrillization-incompetent mutant, favored by familial-disease mutations and diminished …

Morfpred, A Computational Tool For Sequence-Based Prediction And Characterization Of Short Disorder-To-Order Transitioning Binding Regions In Proteins, Fatemeh Miri Disfani, Wei-Lun Hsu, Marcin J. Mizianty, Christopher J. Oldfield, Bin Xue, A. Keith Dunker, Vladimir N. Uversky, Lukasz Kurgan

Molecular Medicine Faculty Publications

Motivation: Molecular recognition features (MoRFs) are short binding regions located within longer intrinsically disordered regions that bind to protein partners via disorder-to-order transitions. MoRFs are implicated in important processes including signaling and regulation. However, only a limited number of experimentally validated MoRFs is known, which motivates development of computational methods that predict MoRFs from protein chains.

Results: We introduce a new MoRF predictor, MoRFpred, which identifies all MoRF types (α, β, coil and complex). We develop a comprehensive dataset of annotated MoRFs to build and empirically compare our method. MoRFpred utilizes a novel design in which annotations generated by sequence …

Free Cysteine Modulates The Conformation Of Human C/Ebp Homologous Protein, Vinay K. Singh, Mona M. Rahman, Kim Munro, Vladimir N. Uversky, Steven P. Smith, Zongchao Jia

Molecular Medicine Faculty Publications

The C/EBP Homologous Protein (CHOP) is a nuclear protein that is integral to the unfolded protein response culminating from endoplasmic reticulum stress. Previously, CHOP was shown to comprise extensive disordered regions and to self-associate in solution. In the current study, the intrinsically disordered nature of this protein was characterized further by comprehensive in silico analyses. Using circular dichroism, differential scanning calorimetry and nuclear magnetic resonance, we investigated the global conformation and secondary structure of CHOP and demonstrated, for the first time, that conformational changes in this protein can be induced by the free amino acid l-cysteine. Addition of l-cysteine caused …

Disease-Associated Mutations Disrupt Functionally Important Regions Of Intrinsic Protein Disorder, Vladimir Vacic, Phineus R. L. Markwick, Christopher J. Oldfield, Xiaoyue Zhao, Chad Haynes, Vladimir N. Uversky, Lilia M. Iakoucheva

Molecular Medicine Faculty Publications

The effects of disease mutations on protein structure and function have been extensively investigated, and many predictors of the functional impact of single amino acid substitutions are publicly available. The majority of these predictors are based on protein structure and evolutionary conservation, following the assumption that disease mutations predominantly affect folded and conserved protein regions. However, the prevalence of the intrinsically disordered proteins (IDPs) and regions (IDRs) in the human proteome together with their lack of fixed structure and low sequence conservation raise a question about the impact of disease mutations in IDRs. Here, we investigate annotated missense disease mutations …

Understanding Viral Transmission Behavior Via Protein Intrinsic Disorder Prediction: Coronaviruses, Gerard Kian-Meng Goh, A. Keith Dunker, Vladimir N. Uversky

Molecular Medicine Faculty Publications

Besides being a common threat to farm animals and poultry, coronavirus (CoV) was responsible for the human severe acute respiratory syndrome (SARS) epidemic in 2002–4. However, many aspects of CoV behavior, including modes of its transmission, are yet to be fully understood. We show that the amount and the peculiarities of distribution of the protein intrinsic disorder in the viral shell can be used for the efficient analysis of the behavior and transmission modes of CoV. The proposed model allows categorization of the various CoVs by the peculiarities of disorder distribution in their membrane (M) and nucleocapsid (N). This categorization …

Analyzing Thioflavin T Binding To Amyloid Fibrils By An Equilibrium Microdialysis-Based Technique, Irina M. Kuznetsova, Anna I. Sulatskaya, Vladimir N. Uversky, Konstantin K. Turoverov

Molecular Medicine Faculty Publications

A new approach for the determination of the amyloid fibril - thioflavin T (ThT) binding parameters (the number of binding modes, stoichiometry, and binding constants of each mode) is proposed. This approach is based on the absorption spectroscopy determination of the concentration of free and bound to fibril dye in solutions, which are prepared by equilibrium microdialysis. Furthermore, the proposed approach allowed us, for the first time, to determine the absorption spectrum, molar extinction coefficient, and fluorescence quantum yield of the ThT bound to fibril by each binding modes. This approach is universal and can be used for determining the …

Disordered Competitive Recruiter: Fast And Foldable, Vladimir N. Uversky

Molecular Medicine Faculty Publications

We report the crystal structure of the Escherichia coli TolB-Pal complex, a protein−protein complex involved in maintaining the integrity of the outer membrane (OM) in all Gram-negative bacteria that is parasitized by colicins (protein antibiotics) to expedite their entry into cells. Nuclease colicins competitively recruit TolB using their natively disordered regions (NDRs) to disrupt its complex with Pal, which is thought to trigger translocation of the toxin across a locally destabilized OM. The structure shows induced-fit binding of peptidoglycan-associated lipoprotein (Pal) to the β-propeller domain of TolB causing the N-terminus of one of its α-helices to unwind and several residues …