1
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Uversky VN. Functional unfoldomics: Roles of intrinsic disorder in protein (multi)functionality. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:179-210. [PMID: 38220424 DOI: 10.1016/bs.apcsb.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Intrinsically disordered proteins (IDPs), which are functional proteins without stable tertiary structure, and hybrid proteins containing ordered domains and intrinsically disordered regions (IDRs) constitute prominent parts of all proteomes collectively known as unfoldomes. IDPs/IDRs exist as highly dynamic structural ensembles of rapidly interconverting conformations and are characterized by the exceptional structural heterogeneity, where their different parts are (dis)ordered to different degree, and their overall structure represents a complex mosaic of foldons, inducible foldons, inducible morphing foldons, non-foldons, semifoldons, and even unfoldons. Despite their lack of unique 3D structures, IDPs/IDRs play crucial roles in the control of various biological processes and the regulation of different cellular pathways and are commonly involved in recognition and signaling, indicating that the disorder-based functional repertoire is complementary to the functions of ordered proteins. Furthermore, IDPs/IDRs are frequently multifunctional, and this multifunctionality is defined by their structural flexibility and heterogeneity. Intrinsic disorder phenomenon is at the roots of the structure-function continuum model, where the structure continuum is defined by the presence of differently (dis)ordered regions, and the function continuum arises from the ability of all these differently (dis)ordered parts to have different functions. In their everyday life, IDPs/IDRs utilize a broad spectrum of interaction mechanisms thereby acting as interaction specialists. They are crucial for the biogenesis of numerous proteinaceous membrane-less organelles driven by the liquid-liquid phase separation. This review introduces functional unfoldomics by representing some aspects of the intrinsic disorder-based functionality.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
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2
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Camponeschi I, Damasco A, Uversky VN, Giuliani A, Bianchi MM. Phenotypic suppression caused by resonance with light-dark cycles indicates the presence of a 24-hours oscillator in yeast and suggests a new role of intrinsically disordered protein regions as internal mediators. J Biomol Struct Dyn 2020; 39:2490-2501. [PMID: 32223547 DOI: 10.1080/07391102.2020.1749133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The mutual interaction between environment and life is a main topic of biological sciences. An interesting aspect of this interaction is the existence of biological rhythms spanning all the levels of organisms from bacteria to humans. On the other hand, the existence of a coupling between external oscillatory stimuli and adaptation and evolution rate of biological systems is a still unexplored issue. Here we give the demonstration of a substantial increase of heritable phenotypic changes in yeast, an organism lacking a photoreception system, when growing at 12 h light/dark cycles, with respect to both stable dark (or light) or non-12 + 12 h cycling. The model system was a yeast strain lacking a gene whose product is at the crossroad of many different physiological regulations, so ruling out any simple explanation in terms of increase in reverse gene mutations. The abundance of intrinsically disordered protein regions (IDPRs) in both deleted gene product and in its vast ensemble of interactors supports the hypothesis that resonance with the environmental cycle might be mediated by intrinsic disorder-driven interactions of protein molecules. This result opens to the speculation of the effect of environment/biological resonance phenomena in evolution and of the role of protein intrinsically disordered regions as internal mediators.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ilaria Camponeschi
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza Università di Roma, Roma, Italy
| | - Achille Damasco
- Department of Physics 'Ettore Pancini', Università di Napoli Federico II, Napoli, Italy
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Russia
| | - Alessandro Giuliani
- Department of Environment and Health, Istituto Superiore di Sanità, Roma, Italy
| | - Michele M Bianchi
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza Università di Roma, Roma, Italy
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Fonin AV, Darling AL, Kuznetsova IM, Turoverov KK, Uversky VN. Multi-functionality of proteins involved in GPCR and G protein signaling: making sense of structure-function continuum with intrinsic disorder-based proteoforms. Cell Mol Life Sci 2019; 76:4461-4492. [PMID: 31428838 PMCID: PMC11105632 DOI: 10.1007/s00018-019-03276-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 12/21/2022]
Abstract
GPCR-G protein signaling system recognizes a multitude of extracellular ligands and triggers a variety of intracellular signaling cascades in response. In humans, this system includes more than 800 various GPCRs and a large set of heterotrimeric G proteins. Complexity of this system goes far beyond a multitude of pair-wise ligand-GPCR and GPCR-G protein interactions. In fact, one GPCR can recognize more than one extracellular signal and interact with more than one G protein. Furthermore, one ligand can activate more than one GPCR, and multiple GPCRs can couple to the same G protein. This defines an intricate multifunctionality of this important signaling system. Here, we show that the multifunctionality of GPCR-G protein system represents an illustrative example of the protein structure-function continuum, where structures of the involved proteins represent a complex mosaic of differently folded regions (foldons, non-foldons, unfoldons, semi-foldons, and inducible foldons). The functionality of resulting highly dynamic conformational ensembles is fine-tuned by various post-translational modifications and alternative splicing, and such ensembles can undergo dramatic changes at interaction with their specific partners. In other words, GPCRs and G proteins exist as sets of conformational/basic, inducible/modified, and functioning proteoforms characterized by a broad spectrum of structural features and possessing various functional potentials.
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Affiliation(s)
- Alexander V Fonin
- Laboratory of structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russian Federation
| | - April L Darling
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Irina M Kuznetsova
- Laboratory of structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russian Federation
| | - Konstantin K Turoverov
- Laboratory of structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russian Federation
- Department of Biophysics, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya av. 29, St. Petersburg, 195251, Russian Federation
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow, Russian Federation.
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Oldfield CJ, Uversky VN, Dunker AK, Kurgan L. Introduction to intrinsically disordered proteins and regions. Proteins 2019. [DOI: 10.1016/b978-0-12-816348-1.00001-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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5
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Uversky VN. Protein intrinsic disorder and structure-function continuum. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 166:1-17. [DOI: 10.1016/bs.pmbts.2019.05.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Paraan M, Bhattacharya N, Uversky VN, Stagg SM. Flexibility of the Sec13/31 cage is influenced by the Sec31 C-terminal disordered domain. J Struct Biol 2018; 204:250-260. [PMID: 30172710 PMCID: PMC6188663 DOI: 10.1016/j.jsb.2018.08.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 08/23/2018] [Accepted: 08/29/2018] [Indexed: 01/30/2023]
Abstract
In COPII mediated vesicle formation, Sec13/Sec31 heterotetramers play a role in organizing the membranes into a spherical vesicle. There they oligomerize into a cage that interacts with the other COPII proteins to direct vesicle formation and concentrate cargo into a bud. In this role they must be flexible to accommodate different sizes and shapes of cargo, but also have elements that provide rigidity to help deform the membrane. Here we characterize the influence the C-terminal disordered region of Sec31 has on cage flexibility and rigidity. After deleting this region (residues 820-1220), we characterized Sec13/Sec31ΔC heterotetramers biophysically and structurally through cryo-EM. Our results show that Sec13/31ΔC self-assembles into canonical cuboctahedral cages in vitro at buffer conditions similar to wild type. The distribution of cage sizes indicated that unlike the wild type, Sec13/31ΔC cages have a more homogeneous geometry. However, the structure of cuboctahedrons exhibited more conformational heterogeneity than wild type. Through localized reconstruction of cage vertices and molecular dynamics flexible fitting we found a new hinge for the flexing of Sec31 β-propeller domain and more flexibility of the previously known hinge. Together, these results show that the C-terminal region of Sec31 regulates the flexing of other domains such that flexibility and rigidity are not compromised during transport of large and/or asymmetric cargo.
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Affiliation(s)
- Mohammadreza Paraan
- Institute of Molecular Biophysics, 91 Chieftan Way, Florida State University, Tallahassee, FL 32306, USA
| | - Nilakshee Bhattacharya
- Institute of Molecular Biophysics, 91 Chieftan Way, Florida State University, Tallahassee, FL 32306, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Scott M Stagg
- Institute of Molecular Biophysics, 91 Chieftan Way, Florida State University, Tallahassee, FL 32306, USA; Department of Chemistry and Biochemistry, 95 Chieftain Way, Florida State University, Tallahassee, FL 32306, USA.
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Abramov VM, Kosarev IV, Motin VL, Khlebnikov VS, Vasilenko RN, Sakulin VK, Machulin AV, Uversky VN, Karlyshev AV. Binding of LcrV protein from Yersinia pestis to human T-cells induces apoptosis, which is completely blocked by specific antibodies. Int J Biol Macromol 2018; 122:1062-1070. [PMID: 30218736 DOI: 10.1016/j.ijbiomac.2018.09.054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/11/2018] [Accepted: 09/11/2018] [Indexed: 11/29/2022]
Abstract
The V antigen (LcrV) of the plague bacterium Yersinia pestis is a potent protective protein that is considered as a vaccine component for humans. LcrV mediates the delivery of Yop toxins into host cells and upregulates TLR2-dependent IL-10 production. Although LcrV can interact with the receptor-bound human interferon-γ (hIFN-γ), the significance of these interactions in plague pathogenesis is not known. In this study, we determined the parameters of specific interactions of LcrV and LcrV68-326 with primary human thymocytes and Jurkat T-leukemia cells in the presence of receptor-bound hIFN-γ. Although the C-terminal region of hIFN-γ contains a GRRA138-141 site needed for high-affinity binding of LcrV and LcrV68-326, in the hIFN-γ homodimer, these GRRA138-141 target sites becomes accessible for targeting by LcrV or LcrV68-326 only after immobilization of the hIFN-γ homodimer on the hIFN-γ receptors of thymocytes or Jurkat T-cells. The interaction of LcrV or LcrV68-326 with receptor-bound hIFN-γ on the thymocytes or Jurkat T-cells caused apoptosis of both cell types, which can be completely blocked by the addition of monoclonal antibodies specific to the LEEL32-35 and DEEI203-206 sites of LcrV. The ability of LcrV to utilize hIFN-γ is insidious and may account in part for the severe symptoms of plague in humans.
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Affiliation(s)
- Vyacheslav M Abramov
- Department of Immunology and Biodefence, Institute of Immunological Engineering, 142380 Lyubuchany, Russia
| | - Igor V Kosarev
- Department of Immunology and Biodefence, Institute of Immunological Engineering, 142380 Lyubuchany, Russia
| | - Vladimir L Motin
- Department of Pathology/Microbiology & Immunology, University of Texas Medical Branch, Galverston, TX 77555, USA
| | - Valentin S Khlebnikov
- Department of Immunology and Biodefence, Institute of Immunological Engineering, 142380 Lyubuchany, Russia
| | - Raisa N Vasilenko
- Department of Immunology and Biodefence, Institute of Immunological Engineering, 142380 Lyubuchany, Russia
| | - Vadim K Sakulin
- Department of Immunology and Biodefence, Institute of Immunological Engineering, 142380 Lyubuchany, Russia
| | - Andrey V Machulin
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino 142290, Russia.
| | - Andrey V Karlyshev
- Department of Science, Engineering and Computing, Kingston University, Kingston, UK
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Prediction of Disordered Regions and Their Roles in the Anti-Pathogenic and Immunomodulatory Functions of Butyrophilins. Molecules 2018; 23:molecules23020328. [PMID: 29401697 PMCID: PMC6017450 DOI: 10.3390/molecules23020328] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 12/13/2022] Open
Abstract
Butyrophilins (BTNs) are a group of the moonlighting proteins, some members of which are secreted in milk. They constitute a large family of structurally similar type 1 transmembrane proteins from the immunoglobulin superfamily. Although the founding member of this family is related to lactation, participating in the secretion, formation and stabilization of milk fat globules, it may also have a cell surface receptor function. Generally, the BTN family members are known to modulate co-stimulatory responses, T cell selection, differentiation, and cell fate determination. Polymorphism of these genes was shown to be associated with the pathology of several human diseases. Despite their biological significance, structural information on human butyrophilins is rather limited. Based on their remarkable multifunctionality, butyrophilins seem to belong to the category of moonlighting proteins, which are known to contain intrinsically disordered protein regions (IDPRs). However, the disorder status of human BTNs was not systematically investigated as of yet. The goal of this study is to fill this gap and to evaluate peculiarities of intrinsic disorder predisposition of the members of human BTN family, and to find if they have IDPRs that can be attributed to the multifunctionality of these important proteins.
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Uversky VN, El-Baky NA, El-Fakharany EM, Sabry A, Mattar EH, Uversky AV, Redwan EM. Functionality of intrinsic disorder in tumor necrosis factor-α and its receptors. FEBS J 2017; 284:3589-3618. [PMID: 28746777 DOI: 10.1111/febs.14182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/15/2017] [Accepted: 07/20/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Vladimir N. Uversky
- Department of Biological Sciences; Faculty of Sciences; King Abdulaziz University; Jeddah Saudi Arabia
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; Morsani College of Medicine; University of South Florida; Tampa FL USA
- Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region Russia
| | - Nawal Abd El-Baky
- Protective Proteins Laboratory; Protein Research Department; Genetic Engineering and Biotechnology Research Institute; City for Scientific Research and Technology Applications; New Borg EL-Arab, Alexandria Egypt
| | - Esmail M. El-Fakharany
- Protective Proteins Laboratory; Protein Research Department; Genetic Engineering and Biotechnology Research Institute; City for Scientific Research and Technology Applications; New Borg EL-Arab, Alexandria Egypt
| | - Amira Sabry
- Protective Proteins Laboratory; Protein Research Department; Genetic Engineering and Biotechnology Research Institute; City for Scientific Research and Technology Applications; New Borg EL-Arab, Alexandria Egypt
| | - Ehab H. Mattar
- Department of Biological Sciences; Faculty of Sciences; King Abdulaziz University; Jeddah Saudi Arabia
| | - Alexey V. Uversky
- Center for Data Analytics and Biomedical Informatics; Department of Computer and Information Sciences; College of Science and Technology; Temple University; Philadelphia PA USA
| | - Elrashdy M. Redwan
- Department of Biological Sciences; Faculty of Sciences; King Abdulaziz University; Jeddah Saudi Arabia
- Protective Proteins Laboratory; Protein Research Department; Genetic Engineering and Biotechnology Research Institute; City for Scientific Research and Technology Applications; New Borg EL-Arab, Alexandria Egypt
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Two Isoforms of Yersinia pestis Plasminogen Activator Pla: Intraspecies Distribution, Intrinsic Disorder Propensity, and Contribution to Virulence. PLoS One 2016; 11:e0168089. [PMID: 27936190 PMCID: PMC5148098 DOI: 10.1371/journal.pone.0168089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 11/25/2016] [Indexed: 12/12/2022] Open
Abstract
It has been shown previously that several endemic Y. pestis isolates with limited virulence contained the I259 isoform of the outer membrane protease Pla, while the epidemic highly virulent strains possessed only the T259 Pla isoform. Our sequence analysis of the pla gene from 118 Y. pestis subsp. microtus strains revealed that the I259 isoform was present exclusively in the endemic strains providing a convictive evidence of more ancestral origin of this isoform. Analysis of the effects of the I259T polymorphism on the intrinsic disorder propensity of Pla revealed that the I259T mutation slightly increases the intrinsic disorder propensity of the C-terminal tail of Pla and makes this protein slightly more prone for disorder-based protein-protein interactions, suggesting that the T259 Pla could be functionally more active than the I259 Pla. This assumption was proven experimentally by assessing the coagulase and fibrinolytic activities of the two Pla isoforms in human plasma, as well as in a direct fluorometric assay with the Pla peptide substrate. The virulence testing of Pla-negative or expressing the I259 and T259 Pla isoforms Y. pestis subsp. microtus and subsp. pestis strains did not reveal any significant difference in LD50 values and dose-dependent survival assays between them by using a subcutaneous route of challenge of mice and guinea pigs or intradermal challenge of mice. However, a significant decrease in time-to-death was observed in animals infected with the epidemic T259 Pla-producing strains as compared to the parent Pla-negative variants. Survival curves of the endemic I259 Pla+ strains fit between them, but significant difference in mean time to death post infection between the Pla−strains and their I259 Pla+ variants could be seen only in the isogenic set of subsp. pestis strains. These findings suggest an essential role for the outer membrane protease Pla evolution in Y. pestis bubonic infection exacerbation that is necessary for intensification of epidemic process from endemic natural focality with sporadic cases in men to rapidly expanding epizootics followed by human epidemic outbreaks, local epidemics or even pandemics.
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p53 Proteoforms and Intrinsic Disorder: An Illustration of the Protein Structure-Function Continuum Concept. Int J Mol Sci 2016; 17:ijms17111874. [PMID: 27834926 PMCID: PMC5133874 DOI: 10.3390/ijms17111874] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/27/2016] [Accepted: 11/03/2016] [Indexed: 01/10/2023] Open
Abstract
Although it is one of the most studied proteins, p53 continues to be an enigma. This protein has numerous biological functions, possesses intrinsically disordered regions crucial for its functionality, can form both homo-tetramers and isoform-based hetero-tetramers, and is able to interact with many binding partners. It contains numerous posttranslational modifications, has several isoforms generated by alternative splicing, alternative promoter usage or alternative initiation of translation, and is commonly mutated in different cancers. Therefore, p53 serves as an important illustration of the protein structure–function continuum concept, where the generation of multiple proteoforms by various mechanisms defines the ability of this protein to have a multitude of structurally and functionally different states. Considering p53 in the light of a proteoform-based structure–function continuum represents a non-canonical and conceptually new contemplation of structure, regulation, and functionality of this important protein.
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Kopylov PK, Platonov ME, Ablamunits VG, Kombarova TI, Ivanov SA, Kadnikova LA, Somov AN, Dentovskaya SV, Uversky VN, Anisimov AP. Yersinia pestis Caf1 Protein: Effect of Sequence Polymorphism on Intrinsic Disorder Propensity, Serological Cross-Reactivity and Cross-Protectivity of Isoforms. PLoS One 2016; 11:e0162308. [PMID: 27606595 PMCID: PMC5015843 DOI: 10.1371/journal.pone.0162308] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/19/2016] [Indexed: 12/11/2022] Open
Abstract
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. Sequencing of caf1 genes from 119 Y. pestis strains belonging to different biovars within subsp. microtus showed that the Caf1 proteins exist in three isoforms, the global type Caf1NT1 (Ala48 Phe117), type Caf1NT2 (Ser48 Phe117) found in Transcaucasian-highland and Pre-Araks natural plague foci #4-7, and a novel Caf1NT3 type (Ala48 Val117) endemic in Dagestan-highland natural plague focus #39. Both minor types are the progenies of the global isoform. In this report, Caf1 polymorphism was analyzed by comparing predicted intrinsic disorder propensities and potential protein-protein interactivities of the three Caf1 isoforms. The analysis revealed that these properties of Caf1 protein are minimally affected by its polymorphism. All protein isoforms could be equally detected by an immunochromatography test for plague at the lowest protein concentration tested (1.0 ng/mL), which is the detection limit. When compared to the classic Caf1NT1 isoform, the endemic Caf1NT2 or Caf1NT3 had lower immunoreactivity in ELISA and lower indices of self- and cross-protection. Despite a visible reduction in cross-protection between all Caf1 isoforms, our data suggest that polymorphism in the caf1 gene may not allow the carriers of Caf1NT2 or Caf1NT3 variants escaping from the Caf1NT1-mediated immunity to plague in the case of a low-dose flea-borne infection.
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Affiliation(s)
- Pavel Kh. Kopylov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Mikhail E. Platonov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | | | - Tat’yana I. Kombarova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Sergey A. Ivanov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Lidiya A. Kadnikova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Aleksey N. Somov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Svetlana V. Dentovskaya
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Andrey P. Anisimov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
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Smeller L. Folding superfunnel to describe cooperative folding of interacting proteins. Proteins 2016; 84:1009-16. [DOI: 10.1002/prot.25051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/06/2016] [Accepted: 04/08/2016] [Indexed: 12/18/2022]
Affiliation(s)
- László Smeller
- Department of Biophysics and Radiation Biology; Semmelweis University; Budapest Hungary
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Yacoub HA, Al-Maghrabi OA, Ahmed ES, Uversky VN. Abundance and functional roles of intrinsic disorder in the antimicrobial peptides of the NK-lysin family. J Biomol Struct Dyn 2016; 35:836-856. [DOI: 10.1080/07391102.2016.1164077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Haitham A. Yacoub
- Faculty of Science, Department of Biological Sciences, University of Jeddah, Jeddah, Saudi Arabia
- Department of Cell Biology, Genetic Engineering and Biotechnology Division, National Research Centre, P.O. Box 12622, Gizza, Egypt
| | - Omar A. Al-Maghrabi
- Faculty of Science, Department of Biological Sciences, University of Jeddah, Jeddah, Saudi Arabia
| | - Ekram S. Ahmed
- Department of Cell Biology, Genetic Engineering and Biotechnology Division, National Research Centre, P.O. Box 12622, Gizza, Egypt
| | - Vladimir N. Uversky
- Faculty of Sciences, Department of Biological Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
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15
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Permyakov SE, Permyakov EA, Uversky VN. Intrinsically disordered caldesmon binds calmodulin via the "buttons on a string" mechanism. PeerJ 2015; 3:e1265. [PMID: 26417545 PMCID: PMC4582948 DOI: 10.7717/peerj.1265] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/03/2015] [Indexed: 01/27/2023] Open
Abstract
We show here that chicken gizzard caldesmon (CaD) and its C-terminal domain (residues 636–771, CaD136) are intrinsically disordered proteins. The computational and experimental analyses of the wild type CaD136 and series of its single tryptophan mutants (W674A, W707A, and W737A) and a double tryptophan mutant (W674A/W707A) suggested that although the interaction of CaD136 with calmodulin (CaM) can be driven by the non-specific electrostatic attraction between these oppositely charged molecules, the specificity of CaD136-CaM binding is likely to be determined by the specific packing of important CaD136 tryptophan residues at the CaD136-CaM interface. It is suggested that this interaction can be described as the “buttons on a charged string” model, where the electrostatic attraction between the intrinsically disordered CaD136 and the CaM is solidified in a “snapping buttons” manner by specific packing of the CaD136 “pliable buttons” (which are the short segments of fluctuating local structure condensed around the tryptophan residues) at the CaD136-CaM interface. Our data also show that all three “buttons” are important for binding, since mutation of any of the tryptophans affects CaD136-CaM binding and since CaD136 remains CaM-buttoned even when two of the three tryptophans are mutated to alanines.
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Affiliation(s)
- Sergei E Permyakov
- Protein Research Group, Institute for Biological Instrumentation, Russian Academy of Sciences , Pushchino, Moscow Region , Russia
| | - Eugene A Permyakov
- Protein Research Group, Institute for Biological Instrumentation, Russian Academy of Sciences , Pushchino, Moscow Region , Russia
| | - Vladimir N Uversky
- Protein Research Group, Institute for Biological Instrumentation, Russian Academy of Sciences , Pushchino, Moscow Region , Russia ; Department of Molecular Medicine, University of South Florida , Tampa, FL , USA
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Wu CF, Li ZM, Xu XN, Zhao ZX, Zhao X, Wang RX, Li ZT. Folding-Induced Folding: The Assembly of Aromatic Amide and 1,2,3-Triazole Hybrid Helices. Chemistry 2014; 20:1418-26. [DOI: 10.1002/chem.201304161] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Indexed: 12/15/2022]
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Xue B, Uversky VN. Intrinsic disorder in proteins involved in the innate antiviral immunity: another flexible side of a molecular arms race. J Mol Biol 2013; 426:1322-50. [PMID: 24184279 DOI: 10.1016/j.jmb.2013.10.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/25/2013] [Accepted: 10/23/2013] [Indexed: 02/08/2023]
Abstract
We present a comprehensive bioinformatics analysis of the abundance and roles of intrinsic disorder in human proteins involved in the antiviral innate immune response. The commonness of intrinsic disorder and disorder-based binding sites is evaluated in 840 human antiviral proteins and proteins associated with innate immune response and defense response to virus. Among the mechanisms engaged in the innate immunity to viral infection are three receptor-based pathways activated by the specific recognition of various virus-associated patterns by several retinoic acid-inducible gene I-like receptors, toll-like receptors, and nucleotide oligomerization domain-like receptors. These modules are tightly regulated and intimately interconnected being jointly controlled via a complex set of protein-protein interactions. Focused analysis of the major players involved in these three pathways is performed to illustrate the roles of protein intrinsic disorder in controlling and regulating the innate antiviral immunity. We mapped the disorder into an integrated network of receptor-based pathways of human innate immunity to virus infection and demonstrate that proteins involved in regulation and execution of these innate immunity pathways possess substantial amount of intrinsic disorder. Disordered regions are engaged in a number of crucial functions, such as protein-protein interactions and interactions with other partners including nucleic acids and other ligands, and are enriched in posttranslational modification sites. Therefore, host cells use numerous advantages of intrinsically disordered proteins and regions to fight flexible invaders and viruses and to successfully overcome the viral invasion.
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Affiliation(s)
- Bin Xue
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.
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Uversky AV, Xue B, Peng Z, Kurgan L, Uversky VN. On the intrinsic disorder status of the major players in programmed cell death pathways. F1000Res 2013; 2:190. [PMID: 24358900 PMCID: PMC3829196 DOI: 10.12688/f1000research.2-190.v1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/05/2013] [Indexed: 12/19/2022] Open
Abstract
Earlier computational and bioinformatics analysis of several large protein datasets across 28 species showed that proteins involved in regulation and execution of programmed cell death (PCD) possess substantial amounts of intrinsic disorder. Based on the comprehensive analysis of these datasets by a wide array of modern bioinformatics tools it was concluded that disordered regions of PCD-related proteins are involved in a multitude of biological functions and interactions with various partners, possess numerous posttranslational modification sites, and have specific evolutionary patterns (Peng
et al. 2013). This study extends our previous work by providing information on the intrinsic disorder status of some of the major players of the three major PCD pathways: apoptosis, autophagy, and necroptosis. We also present a detailed description of the disorder status and interactomes of selected proteins that are involved in the p53-mediated apoptotic signaling pathways.
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Affiliation(s)
- Alexey V Uversky
- Center for Data Analytics and Biomedical Informatics, Department of Computer and Information Sciences, College of Science and Technology, Temple University, Philadelphia, PA, 19122, USA
| | - Bin Xue
- Department of Molecular Medicine, College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Zhenling Peng
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Lukasz Kurgan
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Vladimir N Uversky
- Department of Molecular Medicine, College of Medicine, University of South Florida, Tampa, FL, 33612, USA ; Byrd Alzheimer's Research Institute, College of Medicine, University of South Florida, Tampa, FL, 33612, USA ; Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Russian Federation
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Coelho Ribeiro MDL, Espinosa J, Islam S, Martinez O, Thanki JJ, Mazariegos S, Nguyen T, Larina M, Xue B, Uversky VN. Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome. PeerJ 2013; 1:e2. [PMID: 23638354 PMCID: PMC3628832 DOI: 10.7717/peerj.2] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 12/01/2012] [Indexed: 12/29/2022] Open
Abstract
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 machine catalyzing the excision of introns from eukaryotic pre-mRNAs, represents an attractive target for the focused analysis of the abundance and functionality of intrinsic disorder in its proteinaceous components. In yeast cells, spliceosome consists of five small nuclear RNAs (U1, U2, U4, U5, and U6) and a range of associated proteins. Some of these proteins constitute cores of the corresponding snRNA-protein complexes known as small nuclear ribonucleoproteins (snRNPs). Other spliceosomal proteins have various auxiliary functions. To gain better understanding of the functional roles of intrinsic disorder, we have studied the prevalence of intrinsically disordered proteins in the yeast spliceosome using a wide array of bioinformatics methods. Our study revealed that similar to the proteins associated with human spliceosomes (Korneta & Bujnicki, 2012), proteins found in the yeast spliceosome are enriched in intrinsic disorder.
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Affiliation(s)
- Maria de Lourdes Coelho Ribeiro
- Cancer Imaging Metabolism, H. Lee Moffitt Cancer Center & Research Institute , United States ; Department of Molecular Medicine, University of South Florida , Tampa, Florida , United States
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DeForte S, Reddy KD, Uversky VN. Digested disorder: Quarterly intrinsic disorder digest (April-May-June, 2013). INTRINSICALLY DISORDERED PROTEINS 2013; 1:e27454. [PMID: 28516028 PMCID: PMC5424790 DOI: 10.4161/idp.27454] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 12/06/2013] [Indexed: 01/18/2023]
Abstract
The current literature on intrinsically disordered proteins is overwhelming. To keep interested readers up to speed with this literature, we continue a "Digested Disorder" project and represent a series of reader's digest type articles objectively representing the research papers and reviews on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the period of April, May, and June of 2013. The papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.
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Affiliation(s)
- Shelly DeForte
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA
| | - Krishna D Reddy
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA
| | - Vladimir N Uversky
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA.,USF Health Byrd Alzheimer's Research Institute; Morsani College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region, Russia
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