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Bosko M Stojanovski, Leonid Breydo, Vladimir N Uversky, Gloria C Ferreira
In this communication, we report the equilibrium and kinetic properties of the unfolding pathways of the native (pH 7.5) and alkaline molten globule (pH 10.5) states of the pyridoxal 5'-phosphate (PLP)-dependent enzyme 5-aminolevulinate synthase (ALAS). The stability of the molten globule state is adversely affected by thermal- and guanidine hydrochloride (GuHCl)-induced denaturation, and the equilibrium unfolding pathways, irrespective of pH, cannot be described with simple two-state models. Rapid kinetic measurements, in the presence of denaturing GuHCl concentrations, reveal that at pH 10...
October 14, 2016: Biochemical and Biophysical Research Communications
Jaymin J Kathiriya, Ravi Ramesh Pathak, Alexandr Bezginov, Bin Xue, Vladimir N Uversky, Elisabeth R M Tillier, Vrushank Davé
Therapeutic protein kinase inhibitors are designed on the basis of kinase structures. Here, we define intrinsically disordered regions (IDRs) in structurally hybrid kinases. We reveal that 65% of kinases have an IDR adjacent to their kinase domain (KD). These IDRs are evolutionarily more conserved than IDRs distant to KDs. Strikingly, 36 kinases have adjacent IDRs extending into their KDs, defining a unique structural and functional subset of the kinome. Functional network analysis of this subset of the kinome uncovered FAK1 as topologically the most connected hub kinase...
October 5, 2016: Biochimica et Biophysica Acta
Michelle A Carmell, Gregoriy A Dokshin, Helen Skaletsky, Yueh-Chiang Hu, Josien C van Wolfswinkel, Kyomi J Igarashi, Daniel W Bellott, Michael Nefedov, Peter W Reddien, George C Enders, Vladimir N Uversky, Craig C Mello, David C Page
The advent of sexual reproduction and the evolution of a dedicated germline in multicellular organisms are critical landmarks in eukaryotic evolution. We report an ancient family of GCNA (germ cell nuclear antigen) proteins that arose in the earliest eukaryotes, and feature a rapidly evolving intrinsically disordered region (IDR). Phylogenetic analysis reveals that GCNA proteins emerged before the major eukaryotic lineages diverged; GCNA predates the origin of a dedicated germline by a billion years. Gcna gene expression is enriched in reproductive cells across eukarya - either just prior to or during meiosis in single-celled eukaryotes, and in stem cells and germ cells of diverse multicellular animals...
October 8, 2016: ELife
Luisa A Ferreira, Vladimir N Uversky, Boris Y Zaslavsky
Partition coefficients of non-ionic essentially nonpolar compounds between air and rat biological tissues and between blood and other tissues were examined and found to be linearly interrelated according to the previously established equation for partition coefficients of solutes in aqueous two-phase systems: log Kblood-tissue-1 = k0 + k1 log Kblood-tissue-2 + k2 log Kblood-tissue-3, where k0, k1, and k2 are constants. Analysis of partition coefficients of amphiphilic and ionizable drugs between blood and different tissues in rats in vivo showed that the above relationship holds for the blood-tissue partition coefficients of these compounds as well...
September 28, 2016: Molecular BioSystems
Tibor Szénási, Judit Oláh, Adél Szabó, Sándor Szunyogh, András Láng, András Perczel, Attila Lehotzky, Vladimir N Uversky, Judit Ovádi
The hallmarks of Parkinson's disease and other synucleinopathies, Tubulin Polymerization Promoting Protein (TPPP/p25) and α-synuclein (SYN) have two key features: they are disordered and co-enriched/co-localized in brain inclusions. These Neomorphic Moonlighting Proteins display both physiological and pathological functions due to their interactions with distinct partners. To achieve the selective targeting of the pathological TPPP/p25-SYN but not the physiological TPPP/p25-tubulin complex, their interfaces were identified as a specific innovative strategy for the development of anti-Parkinson drugs...
September 23, 2016: Biochimica et Biophysica Acta
Zhonghua Wu, Gang Hu, Kui Wang, Boris Yu Zaslavsky, Lukasz Kurgan, Vladimir N Uversky
Protein partitioning in aqueous two-phase systems (ATPSs) represents a convenient, inexpensive, and easy to scale-up protein separation technique. Since partition behavior of a protein dramatically depends on an ATPS composition, it would be highly beneficial to have reliable means for (even qualitative) prediction of partitioning of a target protein under different conditions. Our aim was to understand which structural features of proteins contribute to partitioning of a query protein in a given ATPS. We undertook a systematic empirical analysis of relations between 57 numerical structural descriptors derived from the corresponding amino acid sequences and crystal structures of 10 well-characterized proteins and the partition behavior of these proteins in 29 different ATPSs...
September 21, 2016: Biochimica et Biophysica Acta
Barbara Zambelli, Vladimir N Uversky, Stefano Ciurli
The interplay of the presence of nickel and protein disorder in processes affecting human health is the focus of the present review. Many systems involving nickel as either a cofactor or as a toxic contaminant are characterized by large disorder. The role of nickel in the biochemistry of bacterial enzymes is discussed here, covering both the beneficial effects of nickel in the human microbiota as well as the role of nickel-depending bacteria in human pathogenesis. In addition, the hazardous health effects caused by nickel exposure to humans, namely nickel-induced carcinogenesis and allergy, are triggered by non-specific interactions of nickel with macromolecules and formation of reactive compounds that mediate cellular damage...
September 17, 2016: Biochimica et Biophysica Acta
Bogdan S Melnik, Galina S Nagibina, Anatoly S Glukhov, Tatiana N Melnik, Vladimir N Uversky
Various effects of amino acid substitutions on properties of globular proteins have been described in a large number of research papers. Nevertheless, no definite "rule" has been formulated as of yet that could be used by experimentalists to introduce desirable changes in the properties of proteins. Herein we attempt to establish such a "rule". To this end, a hypothesis is proposed on the effects of substitutions of hydrophobic residues with large number of contacts on free energies of different states of a globular protein...
September 14, 2016: Biochimica et Biophysica Acta
Pavel Kh Kopylov, Mikhail E Platonov, Vitaly G Ablamunits, Tat'yana I Kombarova, Sergey A Ivanov, Lidiya A Kadnikova, Aleksey N Somov, Svetlana V Dentovskaya, Vladimir N Uversky, Andrey P Anisimov
Yersinia pestis Caf1 is a multifunctional protein responsible for antiphagocytic activity and is a key protective antigen. It is generally conserved between globally distributed Y. pestis strains, but Y. pestis subsp. microtus biovar caucasica strains circulating within populations of common voles in Georgia and Armenia were reported to carry a single substitution of alanine to serine. We investigated polymorphism of the Caf1 sequences among other Y. pestis subsp. microtus strains, which have a limited virulence in guinea pigs and in humans...
2016: PloS One
Hiba Shaban, Insing Na, Angelina A Kislichkina, Svetlana V Dentovskaya, Andrey P Anisimov, Vladimir N Uversky
The Yersinia pestis outer membrane porin F (OmpF) is a transmembrane protein located in the outer membrane of this Gram-negative bacterium which is the causative agent of plague, where it plays a significant role in controlling the selective permeability of the membrane. The amino acid sequences of OmpF proteins from 48 Y. pestis strains representing all currently available phylogenetic groups of this Gram-negative bacterium were recently deduced. Comparison of these amino acid sequences revealed that the OmpF can be present in four isoforms, the pestis-pestis type, and the pestis-microtus types I, II, and III...
September 3, 2016: Journal of Biomolecular Structure & Dynamics
Shelly DeForte, Vladimir N Uversky
In addition to the "traditional" proteins characterized by the unique crystal-like structures needed for unique functions, it is increasingly recognized that many proteins or protein regions (collectively known as intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs)), being biologically active, do not have a specific 3D-structure in their unbound states under physiological conditions. There are also subtler categories of disorder, such as conditional (or dormant) disorder and partial disorder...
2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Krishna D Reddy, Jashwanth Malipeddi, Shelly DeForte, Vikas Pejaver, Predrag Radivojac, Vladimir N Uversky, Robert J Deschenes
Over the past 30 years, several hundred eukaryotic proteins spanning from yeast to man have been shown to be S-palmitoylated. This post-translational modification involves the reversible addition of a 16-carbon saturated fatty acyl chain onto the cysteine residue of a protein where it regulates protein membrane association and distribution, conformation, and stability. However, the large-scale proteome-wide discovery of new palmitoylated proteins has been hindered by the difficulty of identifying a palmitoylation consensus sequence...
August 7, 2016: Journal of Biomolecular Structure & Dynamics
Sajjad Javadi, Reza Yousefi, Saman Hosseinkhani, Ali-Mohammad Tamaddon, Vladimir N Uversky
The high level of dehydroascorbic acid (DHA) in the lenticular tissue is an important risk factor for the development of age-related cataracts. In this study, the effects of DHA on structure and function of lens crystallins were studied in the presence of carnosine using gel mobility shift assay, different spectroscopic techniques, and lens culture analysis. The DHA-induced unfolding and aggregation of lens proteins were largely prevented by this endogenous dipeptide. The ability of carnosine to preserve native protein structure upon exposure to DHA suggests the essential role of this dipeptide in prevention of the senile cataract development...
July 29, 2016: Journal of Biomolecular Structure & Dynamics
Haitham A Yacoub, Salem M El-Hamidy, Maged M Mahmoud, Mohamed Nabih Baeshen, Hussein A Almehdar, Vladimir N Uversky, Elrashdy M Redwan, Omar A Al-Maghrabi, Ahmed M Elazzazy
No abstract text is available yet for this article.
August 2016: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
Kevin S Landau, Insung Na, Ryan O Schenck, Vladimir N Uversky
Prostatic diseases such as prostate cancer and benign prostatic hyperplasia are highly prevalent among men. The number of studies focused on the abundance and roles of intrinsically disordered proteins in prostate cancer is rather limited. The goal of this study is to analyze the prevalence and degree of disorder in proteins that were previously associated with the prostate cancer pathogenesis and to compare these proteins to the entire human proteome. The analysis of these datasets provides means for drawing conclusions on the roles of disordered proteins in this common male disease...
September 2016: Asian Journal of Andrology
Qi Hu, Vladimir N Uversky, Mengyang Huang, Huicong Kang, Feng Xu, Xiaoyan Liu, Lifei Lian, Qiming Liang, Hong Jiang, Anding Liu, Cuntai Zhang, Francisco Pan-Montojo, Suiqiang Zhu
Parkinson's disease (PD) is a progressive neurodegenerative disease. α-Synuclein (α-syn) oligomers play a critical role in the progression of PD. Baicalein, a typical flavonoid compound, can inhibit the formation of the α-syn oligomers, and disaggregate existing α-syn oligomers in vitro. However, whether baicalein could inhibit or disaggregate α-syn oligomers in vivo has not been investigated. Therefore, this study was designed to investigate the inhibitory effects of baicalein on α-syn oligomers in vivo and to explore the possible mechanisms of such inhibition...
October 2016: Biochimica et Biophysica Acta
Jérôme Bürgi, Bin Xue, Vladimir N Uversky, F Gisou van der Goot
Intrinsically disordered regions (IDRs) are peculiar stretches of amino acids that lack stable conformations in solution. Intrinsic Disorder containing Proteins (IDP) are defined by the presence of at least one large IDR and have been linked to multiple cellular processes including cell signaling, DNA binding and cancer. Here we used computational analyses and publicly available databases to deepen insight into the prevalence and function of IDRs specifically in transmembrane proteins, which are somewhat neglected in most studies...
2016: PloS One
Insung Na, Fanchi Meng, Lukasz Kurgan, Vladimir N Uversky
Recent analyses indicated that autophagy can be regulated via some nuclear transcriptional networks and many important players in the autophagy and other forms of programmed cell death are known to be intrinsically disordered. To this end, we analyzed similarities and differences in the intrinsic disorder distribution of nuclear and non-nuclear proteins related to autophagy. We also looked at the peculiarities of the distribution of the intrinsically disordered autophagy-related proteins in various intra-nuclear organelles, such as the nucleolus, chromatin, Cajal bodies, nuclear speckles, promyelocytic leukemia (PML) nuclear bodies, nuclear lamina, nuclear pores, and perinucleolar compartment...
August 16, 2016: Molecular BioSystems
Victor P Kutyshenko, Galina V Mikoulinskaia, Nikolai V Molochkov, Dmitry A Prokhorov, Sergei A Taran, Vladimir N Uversky
Using high-resolution NMR spectroscopy we conducted a comparative analysis of the structural and dynamic properties of the bacteriophage T5 endolysin (EndoT5) and its retro-form; i.e., a protein with the reversed direction of the polypeptide chain (R-EndoT5). We show that structurally, retro-form can be described as the molten globule-like polypeptide that is easily able to form large oligomers and aggregates. To avoid complications associated with this high aggregation propensity of the retro protein, we compared EndoT5 and R-EndoT5 in the presence of strong denaturants...
October 2016: Biochimica et Biophysica Acta
Oscar D Luna-Martínez, Abraham Vidal-Limón, Miryam I Villalba-Velázquez, Rosalba Sánchez-Alcalá, Ramón Garduño-Juárez, Vladimir N Uversky, Baltazar Becerril
Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the stability of global structure, regardless of the protein topology. This method evaluates all of the residues in a 3D structure of a given globular protein by ranking them according to their connectivity and movement restrictions without topology constraints...
2016: PeerJ
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