1
|
Venati SR, Uversky VN. Exploring Intrinsic Disorder in Human Synucleins and Associated Proteins. Int J Mol Sci 2024; 25:8399. [PMID: 39125972 PMCID: PMC11313516 DOI: 10.3390/ijms25158399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/27/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
In this work, we explored the intrinsic disorder status of the three members of the synuclein family of proteins-α-, β-, and γ-synucleins-and showed that although all three human synucleins are highly disordered, the highest levels of disorder are observed in γ-synuclein. Our analysis of the peculiarities of the amino acid sequences and modeled 3D structures of the human synuclein family members revealed that the pathological mutations A30P, E46K, H50Q, A53T, and A53E associated with the early onset of Parkinson's disease caused some increase in the local disorder propensity of human α-synuclein. A comparative sequence-based analysis of the synuclein proteins from various evolutionary distant species and evaluation of their levels of intrinsic disorder using a set of commonly used bioinformatics tools revealed that, irrespective of their origin, all members of the synuclein family analyzed in this study were predicted to be highly disordered proteins, indicating that their intrinsically disordered nature represents an evolutionary conserved and therefore functionally important feature. A detailed functional disorder analysis of the proteins in the interactomes of the human synuclein family members utilizing a set of commonly used disorder analysis tools showed that the human α-synuclein interactome has relatively higher levels of intrinsic disorder as compared with the interactomes of human β- and γ- synucleins and revealed that, relative to the β- and γ-synuclein interactomes, α-synuclein interactors are involved in a much broader spectrum of highly diversified functional pathways. Although proteins interacting with three human synucleins were characterized by highly diversified functionalities, this analysis also revealed that the interactors of three human synucleins were involved in three common functional pathways, such as the synaptic vesicle cycle, serotonergic synapse, and retrograde endocannabinoid signaling. Taken together, these observations highlight the critical importance of the intrinsic disorder of human synucleins and their interactors in various neuronal processes.
Collapse
Affiliation(s)
- Sriya Reddy Venati
- 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
| |
Collapse
|
2
|
Sharma A, Shah OP, Sharma L, Gulati M, Behl T, Khalid A, Mohan S, Najmi A, Zoghebi K. Molecular Chaperones as Therapeutic Target: Hallmark of Neurodegenerative Disorders. Mol Neurobiol 2024; 61:4750-4767. [PMID: 38127187 DOI: 10.1007/s12035-023-03846-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023]
Abstract
Misfolded and aggregated proteins build up in neurodegenerative illnesses, which causes neuronal dysfunction and ultimately neuronal death. In the last few years, there has been a significant upsurge in the level of interest towards the function of molecular chaperones in the control of misfolding and aggregation. The crucial molecular chaperones implicated in neurodegenerative illnesses are covered in this review article, along with a variety of their different methods of action. By aiding in protein folding, avoiding misfolding, and enabling protein breakdown, molecular chaperones serve critical roles in preserving protein homeostasis. By aiding in protein folding, avoiding misfolding, and enabling protein breakdown, molecular chaperones have integral roles in preserving regulation of protein balance. It has been demonstrated that aging, a significant risk factor for neurological disorders, affects how molecular chaperones function. The aggregation of misfolded proteins and the development of neurodegeneration may be facilitated by the aging-related reduction in chaperone activity. Molecular chaperones have also been linked to the pathophysiology of several instances of neuron withering illnesses, enumerating as Parkinson's disease, Huntington's disease, and Alzheimer's disease. Molecular chaperones have become potential therapy targets concerning with the prevention and therapeutic approach for brain disorders due to their crucial function in protein homeostasis and their connection to neurodegenerative illnesses. Protein homeostasis can be restored, and illness progression can be slowed down by methods that increase chaperone function or modify their expression. This review emphasizes the importance of molecular chaperones in the context of neuron withering disorders and their potential as therapeutic targets for brain disorders.
Collapse
Affiliation(s)
- Aditi Sharma
- School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, India
| | - Om Prakash Shah
- School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, India
| | - Lalit Sharma
- School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, India
| | - Monica Gulati
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, 1444411, India
- ARCCIM, Faculty of Health, University of Technology Sydney, Ultimo, NSW, 20227, Australia
| | - Tapan Behl
- Amity School of Pharmaceutical Sciences, Amity University, Mohali, Punjab, India, Amity University, Mohali, India.
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Centre, Jazan University, Jazan, 45142, Saudi Arabia
- Medicinal and Aromatic Plants Research Institute, National Center for Research, P.O. Box 2424, 11111, Khartoum, Sudan
| | - Syam Mohan
- Substance Abuse and Toxicology Research Centre, Jazan University, Jazan, 45142, Saudi Arabia.
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, India.
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India.
| | - Asim Najmi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, P.O. Box 114, Jazan, Saudi Arabia
| | - Khalid Zoghebi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, P.O. Box 114, Jazan, Saudi Arabia
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Fantini J. Lipid rafts and human diseases: why we need to target gangliosides. FEBS Open Bio 2023; 13:1636-1650. [PMID: 37052878 PMCID: PMC10476576 DOI: 10.1002/2211-5463.13612] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/02/2023] [Accepted: 04/12/2023] [Indexed: 04/14/2023] Open
Abstract
Gangliosides are functional components of membrane lipid rafts that control critical functions in cell communication. Many pathologies involve raft gangliosides, which therefore represent an approach of choice for developing innovative therapeutic strategies. Beginning with a discussion of what a disease is (and is not), this review lists the major human pathologies that involve gangliosides, which includes cancer, diabetes, and infectious and neurodegenerative diseases. In most cases, the problem is due to a protein whose binding to gangliosides either creates a pathological condition or impairs a physiological function. Then, I draw up an inventory of the different molecular mechanisms of protein-ganglioside interactions. I propose to classify the ganglioside-binding domains of proteins into four categories, which I name GBD-1, GBD-2, GBD-3, and GBD-4. This structural and functional classification could help to rationalize the design of innovative molecules capable of disrupting the binding of selected proteins to gangliosides without generating undesirable effects. The biochemical specificities of gangliosides expressed in the human brain must also be taken into account to improve the reliability of animal models (or any animal-free alternative) of Alzheimer's and Parkinson's diseases.
Collapse
|
5
|
Gonçalves-Kulik M, Schmid F, Andrade-Navarro MA. One Step Closer to the Understanding of the Relationship IDR-LCR-Structure. Genes (Basel) 2023; 14:1711. [PMID: 37761851 PMCID: PMC10531472 DOI: 10.3390/genes14091711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Intrinsically disordered regions (IDRs) in protein sequences are emerging as functionally important elements for interaction and regulation. While being generally flexible, we previously showed, by observation of experimentally obtained structures, that they contain regions of reduced sequence complexity that have an increased propensity to form structure. Here we expand the universe of cases taking advantage of structural predictions by AlphaFold. Our studies focus on low complexity regions (LCRs) found within IDRs, where these LCRs have only one or two residue types (polyX and polyXY, respectively). In addition to confirming previous observations that polyE and polyEK have a tendency towards helical structure, we find a similar tendency for other LCRs such as polyQ and polyER, most of them including charged residues. We analyzed the position of polyXY containing IDRs within proteins, which allowed us to show that polyAG and polyAK accumulate at the N-terminal, with the latter showing increased helical propensity at that location. Functional enrichment analysis of polyXY with helical propensity indicated functions requiring interaction with RNA and DNA. Our work adds evidence of the function of LCRs in interaction-dependent structuring of disordered regions, encouraging the development of tools for the prediction of their dynamic structural properties.
Collapse
Affiliation(s)
- Mariane Gonçalves-Kulik
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Friederike Schmid
- Faculty of Physics, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Miguel A. Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| |
Collapse
|
6
|
Kolonko-Adamska M, Zawadzka-Kazimierczuk A, Bartosińska-Marzec P, Koźmiński W, Popowicz G, Krężel A, Ożyhar A, Greb-Markiewicz B. Interaction patterns of methoprene-tolerant and germ cell-expressed Drosophila JH receptors suggest significant differences in their functioning. Front Mol Biosci 2023; 10:1215550. [PMID: 37654797 PMCID: PMC10465699 DOI: 10.3389/fmolb.2023.1215550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/17/2023] [Indexed: 09/02/2023] Open
Abstract
Methoprene-tolerant (Met) and germ cell-expressed (Gce) proteins were shown to be juvenile hormone (JH) receptors of Drosophila melanogaster with partially redundant functions. We raised the question of where the functional differentiation of paralogs comes from. Therefore, we tested Met and Gce interaction patterns with selected partners. In this study, we showed the ability of Gce and its C-terminus (GceC) to interact with 14-3-3 in the absence of JH. In contrast, Met or Met C-terminus (MetC) interactions with 14-3-3 were not observed. We also performed a detailed structural analysis of Met/Gce interactions with the nuclear receptor fushi tarazu factor-1 (Ftz-F1) ligand-binding domain. We showed that GceC comprising an Ftz-F1-binding site and full-length protein interacts with Ftz-F1. In contrast to Gce, only MetC (not full-length Met) can interact with Ftz-F1 in the absence of JH. We propose that the described differences result from the distinct tertiary structure and accessibility of binding sites in the full-length Met/Gce. Moreover, we hypothesize that each interacting partner can force disordered MetC and GceC to change the structure in a partner-specific manner. The observed interactions seem to determine the subcellular localization of Met/Gce by forcing their translocation between the nucleus and the cytoplasm, which may affect the activity of the proteins. The presented differences between Met and Gce can be crucial for their functional differentiation during D. melanogaster development and indicate Gce as a more universal and more active paralog. It is consistent with the theory indicating gce as an ancestor gene.
Collapse
Affiliation(s)
- M. Kolonko-Adamska
- Department of Biochemistry, Molecular Biology and Biotechnology, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - A. Zawadzka-Kazimierczuk
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - P. Bartosińska-Marzec
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - W. Koźmiński
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - G. Popowicz
- Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, Germany
| | - A. Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - A. Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - B. Greb-Markiewicz
- Department of Biochemistry, Molecular Biology and Biotechnology, Wroclaw University of Science and Technology, Wroclaw, Poland
| |
Collapse
|
7
|
Russell BL, Ntwasa M. Expression, purification, and characterisation of the p53 binding domain of Retinoblastoma binding protein 6 (RBBP6). PLoS One 2023; 18:e0277478. [PMID: 36763571 PMCID: PMC9916574 DOI: 10.1371/journal.pone.0277478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 10/28/2022] [Indexed: 02/11/2023] Open
Abstract
RBBP6 is a 250 kDa eukaryotic protein known to be a negative regulator of p53 and essential for embryonic development. Furthermore, RBBP6 is a critical element in carcinogenesis and has been identified as a potential biomarker for certain cancers. RBBP6's ability to interact with p53 and cause its degradation makes it a potential drug target in cancer therapy. Therefore, a better understating of the p53 binding domain of RBBP6 is needed. This study presents a three-part purification protocol for the polyhistidine-tagged p53 binding domain of RBBP6, expressed in Escherichia coli bacterial cells. The purified recombinant domain was shown to have structure and is functional as it could bind endogenous p53. We characterized it using clear native PAGE and far-UV CD and found that it exists in a single form, most likely monomer. We predict that its secondary structure is predominantly random coil with 19% alpha-helices, 9% beta-strand and 14% turns. When we exposed the recombinant domain to increasing temperature or known denaturants, our investigation suggested that the domain undergoes relatively small structural changes, especially with increased temperature. Moreover, we notice a high percentage recovery after returning the domain close to starting conditions. The outcome of this study is a pure, stable, and functional recombinant RBBP6-p53BD that is primarily intrinsically disordered.
Collapse
Affiliation(s)
- Bonnie L. Russell
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Florida, Roodepoort, South Africa
- Innovation Hub, Buboo (Pty) Ltd, Pretoria, South Africa
| | - Monde Ntwasa
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Florida, Roodepoort, South Africa
- * E-mail:
| |
Collapse
|
8
|
AmyP53 Prevents the Formation of Neurotoxic β-Amyloid Oligomers through an Unprecedent Mechanism of Interaction with Gangliosides: Insights for Alzheimer's Disease Therapy. Int J Mol Sci 2023; 24:ijms24021760. [PMID: 36675271 PMCID: PMC9864847 DOI: 10.3390/ijms24021760] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
A broad range of data identify Ca2+-permeable amyloid pores as the most neurotoxic species of Alzheimer's β-amyloid peptide (Aβ1-42). Following the failures of clinical trials targeting amyloid plaques by immunotherapy, a consensus is gradually emerging to change the paradigm, the strategy, and the target to cure Alzheimer's disease. In this context, the therapeutic peptide AmyP53 was designed to prevent amyloid pore formation driven by lipid raft microdomains of the plasma membrane. Here, we show that AmyP53 outcompetes Aβ1-42 binding to lipid rafts through a unique mode of interaction with gangliosides. Using a combination of cellular, physicochemical, and in silico approaches, we unraveled the mechanism of action of AmyP53 at the atomic, molecular, and cellular levels. Molecular dynamics simulations (MDS) indicated that AmyP53 rapidly adapts its conformation to gangliosides for an optimal interaction at the periphery of a lipid raft, where amyloid pore formation occurs. Hence, we define it as an adaptive peptide. Our results describe for the first time the kinetics of AmyP53 interaction with lipid raft gangliosides at the atomic level. Physicochemical studies and in silico simulations indicated that Aβ1-42 cannot interact with lipid rafts in presence of AmyP53. These data demonstrated that AmyP53 prevents amyloid pore formation and cellular Ca2+ entry by competitive inhibition of Aβ1-42 binding to lipid raft gangliosides. The molecular details of AmyP53 action revealed an unprecedent mechanism of interaction with lipid rafts, offering innovative therapeutic opportunities for lipid raft and ganglioside-associated diseases, including Alzheimer's, Parkinson's, and related proteinopathies.
Collapse
|
9
|
Dayhoff GW, Uversky VN. Rapid prediction and analysis of protein intrinsic disorder. Protein Sci 2022; 31:e4496. [PMID: 36334049 PMCID: PMC9679974 DOI: 10.1002/pro.4496] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/07/2022]
Abstract
Protein intrinsic disorder is found in all kingdoms of life and is known to underpin numerous physiological and pathological processes. Computational methods play an important role in characterizing and identifying intrinsically disordered proteins and protein regions. Herein, we present a new high-efficiency web-based disorder predictor named Rapid Intrinsic Disorder Analysis Online (RIDAO) that is designed to facilitate the application of protein intrinsic disorder analysis in genome-scale structural bioinformatics and comparative genomics/proteomics. RIDAO integrates six established disorder predictors into a single, unified platform that reproduces the results of individual predictors with near-perfect fidelity. To demonstrate the potential applications, we construct a test set containing more than one million sequences from one hundred organisms comprising over 420 million residues. Using this test set, we compare the efficiency and accessibility (i.e., ease of use) of RIDAO to five well-known and popular disorder predictors, namely: AUCpreD, IUPred3, metapredict V2, flDPnn, and SPOT-Disorder2. We show that RIDAO yields per-residue predictions at a rate two to six orders of magnitude greater than the other predictors and completely processes the test set in under an hour. RIDAO can be accessed free of charge at https://ridao.app.
Collapse
Affiliation(s)
- Guy W. Dayhoff
- Department of ChemistryUniversity of South FloridaTampaFloridaUSA
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research InstituteUniversity of South FloridaTampaFloridaUSA
| |
Collapse
|
10
|
Intrinsically Disordered Proteins: An Overview. Int J Mol Sci 2022; 23:ijms232214050. [PMID: 36430530 PMCID: PMC9693201 DOI: 10.3390/ijms232214050] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Many proteins and protein segments cannot attain a single stable three-dimensional structure under physiological conditions; instead, they adopt multiple interconverting conformational states. Such intrinsically disordered proteins or protein segments are highly abundant across proteomes, and are involved in various effector functions. This review focuses on different aspects of disordered proteins and disordered protein regions, which form the basis of the so-called "Disorder-function paradigm" of proteins. Additionally, various experimental approaches and computational tools used for characterizing disordered regions in proteins are discussed. Finally, the role of disordered proteins in diseases and their utility as potential drug targets are explored.
Collapse
|
11
|
Polanco C, Uversky VN, Huberman A, Vargas-Alarcón G, Castañón González JA, Buhse T, Hernández Lemus E, Rios Castro M, López Oliva EJ, Solís Nájera SE. Bioinformatics-based Characterization of the Sequence Variability of
Zika Virus Polyprotein and Envelope Protein (E). Evol Bioinform Online 2022; 18:11769343221130730. [PMCID: PMC9623037 DOI: 10.1177/11769343221130730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Zika virus, which is widely spread and infects humans through the bites of
Aedes albopictus and Aedes aegypti
female mosquitoes, represents a serious global health issue. Objective: The objective of the present study is to computationally characterize Zika
virus polyproteins (UniProt Name: PRO_0000443018 [residues 1-3423],
PRO_0000445659 [residues 1-3423] and PRO_0000435828 [residues 1-3419]) and
their envelope proteins using their physico-chemical properties. Methods: To achieve this, the Polarity Index Method (PIM) profile and the Protein
Intrinsic Disorder Predisposition (PIDP) profile of 3 main groups of
proteins were evaluated: structural proteins extracted from specific
Databases, Zika virus polyproteins, and their envelope proteins (E)
extracted from UniProt Database. Once the PIM profile of the Zika virus
envelope proteins (E) was obtained and since the Zika virus polyproteins
were also identified with this profile, the proteins defined as “reviewed
proteins” extracted from the UniProt Database were searched
for the similar PIM profile. Finally, the difference between the PIM
profiles of the Zika virus polyproteins and their envelope proteins (E) was
tested using 2 non-parametric statistical tests. Results: It was found and tested that the PIM profile is an efficient discriminant
that allows obtaining a “computational fingerprint” of each Zika virus
polyprotein from its envelope protein (E). Conclusion: PIM profile represents a computational tool, which can be used to effectively
discover Zika virus polyproteins from Databases, from their envelope
proteins (E) sequences.
Collapse
Affiliation(s)
- Carlos Polanco
- Department of Electromechanical
Instrumentation, Instituto Nacional de Cardiología “Ignacio Chávez,” México City,
México,Department of Mathematics, Faculty of
Sciences, Universidad Nacional Autónoma de México, México City, México,Carlos Polanco, Department of
Electromechanical Instrumentation, Instituto Nacional de Cardiología “Ignacio
Chávez,” Juan Badiano 1 Tlalpan, México City 14800, México.
| | - 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,Protein Research Group, 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, Moscow Region, Russia
| | - Alberto Huberman
- Department of Biochemistry, Instituto
Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, México City,
México
| | | | | | - Thomas Buhse
- Chemical Research Center, Universidad
Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Enrique Hernández Lemus
- Department of Computational Genomics,
Instituto Nacional de Medicina Genómica, México City, México
| | - Martha Rios Castro
- Department of Electromechanical
Instrumentation, Instituto Nacional de Cardiología “Ignacio Chávez,” México City,
México
| | - Erika Jeannette López Oliva
- Department of Electromechanical
Instrumentation, Instituto Nacional de Cardiología “Ignacio Chávez,” México City,
México
| | | |
Collapse
|
12
|
Azzaz F, Yahi N, Chahinian H, Fantini J. The Epigenetic Dimension of Protein Structure Is an Intrinsic Weakness of the AlphaFold Program. Biomolecules 2022; 12:biom12101527. [PMID: 36291736 PMCID: PMC9599222 DOI: 10.3390/biom12101527] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/12/2022] [Accepted: 10/16/2022] [Indexed: 12/02/2022] Open
Abstract
One of the most important lessons we have learned from sequencing the human genome is that not all proteins have a 3D structure. In fact, a large part of the human proteome is made up of intrinsically disordered proteins (IDPs) which can adopt multiple structures, and therefore, multiple functions, depending on the ligands with which they interact. Under these conditions, one can wonder about the value of algorithms developed for predicting the structure of proteins, in particular AlphaFold, an AI which claims to have solved the problem of protein structure. In a recent study, we highlighted a particular weakness of AlphaFold for membrane proteins. Based on this observation, we have proposed a paradigm, referred to as “Epigenetic Dimension of Protein Structure” (EDPS), which takes into account all environmental parameters that control the structure of a protein beyond the amino acid sequence (hence “epigenetic”). In this new study, we compare the reliability of the AlphaFold and Robetta algorithms’ predictions for a new set of membrane proteins involved in human pathologies. We found that Robetta was generally more accurate than AlphaFold for ascribing a membrane-compatible topology. Raft lipids (e.g., gangliosides), which control the structural dynamics of membrane protein structure through chaperone effects, were identified as major actors of the EDPS paradigm. We conclude that the epigenetic dimension of a protein structure is an intrinsic weakness of AI-based protein structure prediction, especially AlphaFold, which warrants further development.
Collapse
|
13
|
Piersimoni L, Abd El Malek M, Bhatia T, Bender J, Brankatschk C, Calvo Sánchez J, Dayhoff GW, Di Ianni A, Figueroa Parra JO, Garcia-Martinez D, Hesselbarth J, Köppen J, Lauth LM, Lippik L, Machner L, Sachan S, Schmidt L, Selle R, Skalidis I, Sorokin O, Ubbiali D, Voigt B, Wedler A, Wei AAJ, Zorn P, Dunker AK, Köhn M, Sinz A, Uversky VN. Lighting up Nobel Prize-winning studies with protein intrinsic disorder. Cell Mol Life Sci 2022; 79:449. [PMID: 35882686 PMCID: PMC11072364 DOI: 10.1007/s00018-022-04468-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/18/2022] [Accepted: 07/04/2022] [Indexed: 11/03/2022]
Abstract
Intrinsically disordered proteins and regions (IDPs and IDRs) and their importance in biology are becoming increasingly recognized in biology, biochemistry, molecular biology and chemistry textbooks, as well as in current protein science and structural biology curricula. We argue that the sequence → dynamic conformational ensemble → function principle is of equal importance as the classical sequence → structure → function paradigm. To highlight this point, we describe the IDPs and/or IDRs behind the discoveries associated with 17 Nobel Prizes, 11 in Physiology or Medicine and 6 in Chemistry. The Nobel Laureates themselves did not always mention that the proteins underlying the phenomena investigated in their award-winning studies are in fact IDPs or contain IDRs. In several cases, IDP- or IDR-based molecular functions have been elucidated, while in other instances, it is recognized that the respective protein(s) contain IDRs, but the specific IDR-based molecular functions have yet to be determined. To highlight the importance of IDPs and IDRs as general principle in biology, we present here illustrative examples of IDPs/IDRs in Nobel Prize-winning mechanisms and processes.
Collapse
Affiliation(s)
- Lolita Piersimoni
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Marina Abd El Malek
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Twinkle Bhatia
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Julian Bender
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Christin Brankatschk
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Jaime Calvo Sánchez
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Guy W Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, FL, 33620, USA
| | - Alessio Di Ianni
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | | | - Dailen Garcia-Martinez
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Julia Hesselbarth
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Janett Köppen
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Luca M Lauth
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Laurin Lippik
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Lisa Machner
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Shubhra Sachan
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Lisa Schmidt
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Robin Selle
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Ioannis Skalidis
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Oleksandr Sorokin
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Daniele Ubbiali
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Bruno Voigt
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alice Wedler
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alan An Jung Wei
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Peter Zorn
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alan Keith Dunker
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Marcel Köhn
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany.
| | - Andrea Sinz
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany.
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
| |
Collapse
|
14
|
Redwan EM, Aljadawi AA, Uversky VN. Hepatitis C Virus Infection and Intrinsic Disorder in the Signaling Pathways Induced by Toll-Like Receptors. BIOLOGY 2022; 11:1091. [PMID: 36101469 PMCID: PMC9312352 DOI: 10.3390/biology11071091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/07/2022] [Accepted: 07/19/2022] [Indexed: 11/23/2022]
Abstract
In this study, we examined the interplay between protein intrinsic disorder, hepatitis C virus (HCV) infection, and signaling pathways induced by Toll-like receptors (TLRs). To this end, 10 HCV proteins, 10 human TLRs, and 41 proteins from the TLR-induced downstream pathways were considered from the prevalence of intrinsic disorder. Mapping of the intrinsic disorder to the HCV-TLR interactome and to the TLR-based pathways of human innate immune response to the HCV infection demonstrates that substantial levels of intrinsic disorder are characteristic for proteins involved in the regulation and execution of these innate immunity pathways and in HCV-TLR interaction. Disordered regions, being commonly enriched in sites of various posttranslational modifications, may play important functional roles by promoting protein-protein interactions and support the binding of the analyzed proteins to other partners such as nucleic acids. It seems that this system represents an important illustration of the role of intrinsic disorder in virus-host warfare.
Collapse
Affiliation(s)
- Elrashdy M. Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (E.M.R.); (A.A.A.)
- Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg EL-Arab, Alexandria 21934, Egypt
| | - Abdullah A. Aljadawi
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (E.M.R.); (A.A.A.)
| | - Vladimir N. Uversky
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (E.M.R.); (A.A.A.)
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| |
Collapse
|
15
|
Corrigan AN, Lemkul JA. Electronic Polarization at the Interface between the p53 Transactivation Domain and Two Binding Partners. J Phys Chem B 2022; 126:4814-4827. [PMID: 35749260 PMCID: PMC9267131 DOI: 10.1021/acs.jpcb.2c02268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) are an abundant class of highly charged proteins that participate in numerous crucial biological processes, often in regulatory roles. IDPs do not have one major free energy minimum with a dominant structure, instead existing as conformational ensembles of multiple semistable conformations. p53 is a prototypical protein with disordered regions and binds to many structurally diverse partners, making it a useful model for exploring the role of electrostatic interactions at IDP binding interfaces. In this study, we used the Drude-2019 force field to simulate the p53 transactivation domain with two protein partners to probe the role of electrostatic interactions in IDP protein-protein interactions. We found that the Drude-2019 polarizable force field reasonably reproduced experimental chemical shifts of the p53 transactivation domain (TAD) in one complex for which these data are available. We also found that the proteins in these complexes displayed dipole response at specific residues of each protein and that residues primarily involved in binding showed a large percent change in dipole moment between the unbound and complexed states. Probing the role of electrostatic interactions in IDP binding can allow us greater fundamental understanding of these interactions and may help with targeting p53 or its partners for drug design.
Collapse
Affiliation(s)
| | - Justin A. Lemkul
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 20461, United States,Center for Drug Discovery, Virginia Tech, Blacksburg, VA 20461, United States,Corresponding Author: , Address: 111 Engel Hall, 340 West Campus Dr., Blacksburg, VA 24061, Phone: +1 (540) 231-3129
| |
Collapse
|
16
|
Bokor M, Házy E, Tantos Á. Wide-Line NMR Melting Diagrams, Their Thermodynamic Interpretation, and Secondary Structure Predictions for A30P and E46K α-Synuclein. ACS OMEGA 2022; 7:18323-18330. [PMID: 35694516 PMCID: PMC9178613 DOI: 10.1021/acsomega.2c00477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Parkinson's disease is thought to be caused by aggregation of the intrinsically disordered protein, α-synuclein. Two amyloidogenic variants, A30P, and E46K familial mutants were investigated by wide-line 1H NMR spectrometry as a completion of our earlier work on wild-type and A53T α-synuclein (Bokor M. et al. WT and A53T α-synuclein systems: melting diagram and its new interpretation. Int. J. Mol. Sci.2020, 21, 3997.). A monolayer of mobile water molecules hydrates A30P α-synuclein at the lowest potential barriers (temperatures), while E46K α-synuclein has here third as much mobile hydration, insufficient for functionality. According to wide-line 1H NMR results and secondary structure predictions, E46K α-synuclein is more compact than the A30P variant and they are more compact than the wild type (WT) and A53T variants. Linear hydration vs potential barrier sections of A30P α-synuclein shows one and E46K shows two slopes. The different slopes of the latter between potential barriers E a,1 and E a,2 reflect a change in water-protein interactions. The 31-32% homogeneous potential barrier distribution of the protein-water bonds refers to a non-negligible amount of secondary structures in all four α-synuclein variants. The secondary structures detected by wide-line 1H NMR are solvent-exposed α-helices, which are predicted by secondary structure models. β-sheets are only minor components of the protein structures as three- and eight-state predicted secondary structures are dominated by α-helices and coils.
Collapse
Affiliation(s)
- Mónika Bokor
- Institute
for Solid State Physics and Optics, Wigner
Research Centre for Physics, 1121 Budapest, Hungary
| | - Eszter Házy
- Institute
of Enzymology, Research Centre for Natural
Sciences, 1117 Budapest, Hungary
| | - Ágnes Tantos
- Institute
of Enzymology, Research Centre for Natural
Sciences, 1117 Budapest, Hungary
| |
Collapse
|
17
|
Kulkarni P, Bhattacharya S, Achuthan S, Behal A, Jolly MK, Kotnala S, Mohanty A, Rangarajan G, Salgia R, Uversky V. Intrinsically Disordered Proteins: Critical Components of the Wetware. Chem Rev 2022; 122:6614-6633. [PMID: 35170314 PMCID: PMC9250291 DOI: 10.1021/acs.chemrev.1c00848] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Despite the wealth of knowledge gained about intrinsically disordered proteins (IDPs) since their discovery, there are several aspects that remain unexplored and, hence, poorly understood. A living cell is a complex adaptive system that can be described as a wetware─a metaphor used to describe the cell as a computer comprising both hardware and software and attuned to logic gates─capable of "making" decisions. In this focused Review, we discuss how IDPs, as critical components of the wetware, influence cell-fate decisions by wiring protein interaction networks to keep them minimally frustrated. Because IDPs lie between order and chaos, we explore the possibility that they can be modeled as attractors. Further, we discuss how the conformational dynamics of IDPs manifests itself as conformational noise, which can potentially amplify transcriptional noise to stochastically switch cellular phenotypes. Finally, we explore the potential role of IDPs in prebiotic evolution, in forming proteinaceous membrane-less organelles, in the origin of multicellularity, and in protein conformation-based transgenerational inheritance of acquired characteristics. Together, these ideas provide a new conceptual framework to discern how IDPs may perform critical biological functions despite their lack of structure.
Collapse
Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
- Address for correspondence: Prakash Kulkarni, Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, , Vladimir N. Uversky, Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612,
| | - Supriyo Bhattacharya
- Integrative Genomics Core, City of Hope National Medical Center, Duarte, CA, USA
| | - Srisairam Achuthan
- Division of Research Informatics, Center for Informatics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Amita Behal
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Sourabh Kotnala
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore 560012, India
- Center for Neuroscience, Indian Institute of Science, Bangalore 560012, India
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Vladimir Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, Moscow region 141700, Russia
- Address for correspondence: Prakash Kulkarni, Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, , Vladimir N. Uversky, Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612,
| |
Collapse
|
18
|
Poboinev VV, Khrustalev VV, Khrustaleva TA, Kasko TE, Popkov VD. The PentUnFOLD algorithm as a tool to distinguish the dark and the light sides of the structural instability of proteins. Amino Acids 2022; 54:1155-1171. [PMID: 35294674 PMCID: PMC8924573 DOI: 10.1007/s00726-022-03153-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 02/14/2022] [Indexed: 12/12/2022]
Abstract
Intrinsically disordered proteins are frequently involved in important regulatory processes in the cell thanks to their ability to bind several different targets performing sometimes even opposite functions. The PentUnFOLD algorithm is a physicochemical method that is based on new propensity scales for disordered, nonstable and stable elements of secondary structure and on the counting of stabilizing and destabilizing intraprotein contacts. Unlike other methods, it works with a PDB file, and it can determine not only those fragments of alpha helices, beta strands, and random coils that can turn into disordered state (the “dark” side of the disorder), but also nonstable regions of alpha helices and beta strands which are able to turn into random coils (the “light” side), and vice versa (H ↔ C, E ↔ C). The scales have been obtained from structural data on disordered regions from the middle parts of amino acid sequences only, and not on their expectedly disordered N- and C-termini. Among other tendencies we have found that regions of both alpha helices and beta strands that can turn into the disordered state are relatively enriched in residues of Ala, Met, Asp, and Lys, while regions of both alpha helices and beta strands that can turn into random coil are relatively enriched in hydrophilic residues, and Cys, Pro, and Gly. Moreover, PentUnFOLD has the option to determine the effect of secondary structure transitions on the stability of a given region of a protein. The PentUnFOLD algorithm is freely available at http://3.17.12.213/pent-un-fold and http://chemres.bsmu.by/PentUnFOLD.htm.
Collapse
Affiliation(s)
| | | | - Tatyana Aleksandrovna Khrustaleva
- Biochemical Group of the Multidisciplinary Diagnostic Laboratory, Institute of Physiology of the National Academy of Sciences of Belarus, Minsk, Belarus
| | - Tihon Evgenyevich Kasko
- Department of General Chemistry, Belarusian State Medical University, Dzerzinskogo 83, Minsk, Belarus
| | - Vadim Dmitrievich Popkov
- Department of General Chemistry, Belarusian State Medical University, Dzerzinskogo 83, Minsk, Belarus
| |
Collapse
|
19
|
Park H, Yamanaka T, Nukina N. Proteomic analysis of heat-stable proteins revealed an increased proportion of proteins with compositionally biased regions. Sci Rep 2022; 12:4347. [PMID: 35289333 PMCID: PMC8921518 DOI: 10.1038/s41598-022-08044-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/17/2022] [Indexed: 11/09/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) have been in the spotlight for their unique properties, such as their lack of secondary structures and low sequence complexity. Alpha-synuclein and tau are representative disease-related IDPs with low complexity regions in their sequences, accumulating in the brains of patients with Parkinson disease and Alzheimer disease, respectively. Their heat resistance in particular was what attracted our attention. We assumed that there exist many other unidentified proteins that are resistant to heat-treatment, referred to as heat-stable proteins, which would also have low sequence complexity. In this study, we performed proteomic analysis of heat-stable proteins of mouse brains and found that proteins with compositionally biased regions are abundant in the heat-stable proteins. The proteins related to neurodegeneration are known to undergo different types of post-translational modifications (PTMs) such as phosphorylation and ubiquitination. We then investigated the heat-stability and aggregation properties of phosphorylated synuclein and tau with different phosphorylation sites. We suggest that PTMs can be important factors that determine the heat-stability and aggregation properties of a protein. IDPs identified in the heat-stable proteins of mouse brains would be candidates for the pathogenic proteins for neurodegeneration.
Collapse
Affiliation(s)
- Hongsun Park
- Laboratory of Structural Neuropathology, Doshisha University Graduate School of Brain Science, 1-3 Miyakodanitatara, Kyotanabe-shi, Kyoto, 610-0394, Japan
| | - Tomoyuki Yamanaka
- Laboratory of Structural Neuropathology, Doshisha University Graduate School of Brain Science, 1-3 Miyakodanitatara, Kyotanabe-shi, Kyoto, 610-0394, Japan.,Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, Japan
| | - Nobuyuki Nukina
- Laboratory of Structural Neuropathology, Doshisha University Graduate School of Brain Science, 1-3 Miyakodanitatara, Kyotanabe-shi, Kyoto, 610-0394, Japan.
| |
Collapse
|
20
|
Bondos SE, Dunker AK, Uversky VN. Intrinsically disordered proteins play diverse roles in cell signaling. Cell Commun Signal 2022; 20:20. [PMID: 35177069 PMCID: PMC8851865 DOI: 10.1186/s12964-022-00821-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/11/2021] [Indexed: 11/29/2022] Open
Abstract
Signaling pathways allow cells to detect and respond to a wide variety of chemical (e.g. Ca2+ or chemokine proteins) and physical stimuli (e.g., sheer stress, light). Together, these pathways form an extensive communication network that regulates basic cell activities and coordinates the function of multiple cells or tissues. The process of cell signaling imposes many demands on the proteins that comprise these pathways, including the abilities to form active and inactive states, and to engage in multiple protein interactions. Furthermore, successful signaling often requires amplifying the signal, regulating or tuning the response to the signal, combining information sourced from multiple pathways, all while ensuring fidelity of the process. This sensitivity, adaptability, and tunability are possible, in part, due to the inclusion of intrinsically disordered regions in many proteins involved in cell signaling. The goal of this collection is to highlight the many roles of intrinsic disorder in cell signaling. Following an overview of resources that can be used to study intrinsically disordered proteins, this review highlights the critical role of intrinsically disordered proteins for signaling in widely diverse organisms (animals, plants, bacteria, fungi), in every category of cell signaling pathway (autocrine, juxtacrine, intracrine, paracrine, and endocrine) and at each stage (ligand, receptor, transducer, effector, terminator) in the cell signaling process. Thus, a cell signaling pathway cannot be fully described without understanding how intrinsically disordered protein regions contribute to its function. The ubiquitous presence of intrinsic disorder in different stages of diverse cell signaling pathways suggest that more mechanisms by which disorder modulates intra- and inter-cell signals remain to be discovered.
Collapse
Affiliation(s)
- Sarah E. Bondos
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843 USA
| | - A. Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202 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, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, Moscow Region, Russia 142290
| |
Collapse
|
21
|
Reid LM, Guzzetti I, Svensson T, Carlsson AC, Su W, Leek T, von Sydow L, Czechtizky W, Miljak M, Verma C, De Maria L, Essex JW. How well does molecular simulation reproduce environment-specific conformations of the intrinsically disordered peptides PLP, TP2 and ONEG? Chem Sci 2022; 13:1957-1971. [PMID: 35308859 PMCID: PMC8848758 DOI: 10.1039/d1sc03496k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 01/03/2022] [Indexed: 12/31/2022] Open
Abstract
Understanding the conformational ensembles of intrinsically disordered proteins and peptides (IDPs) in their various biological environments is essential for understanding their mechanisms and functional roles in the proteome, leading to a greater knowledge of, and potential treatments for, a broad range of diseases. To determine whether molecular simulation is able to generate accurate conformational ensembles of IDPs, we explore the structural landscape of the PLP peptide (an intrinsically disordered region of the proteolipid membrane protein) in aqueous and membrane-mimicking solvents, using replica exchange with solute scaling (REST2), and examine the ability of four force fields (ff14SB, ff14IDPSFF, CHARMM36 and CHARMM36m) to reproduce literature circular dichroism (CD) data. Results from variable temperature (VT) 1H and Rotating frame Overhauser Effect SpectroscopY (ROESY) nuclear magnetic resonance (NMR) experiments are also presented and are consistent with the structural observations obtained from the simulations and CD. We also apply the optimum simulation protocol to TP2 and ONEG (a cell-penetrating peptide (CPP) and a negative control peptide, respectively) to gain insight into the structural differences that may account for the observed difference in their membrane-penetrating abilities. Of the tested force fields, we find that CHARMM36 and CHARMM36m are best suited to the study of IDPs, and accurately predict a disordered to helical conformational transition of the PLP peptide accompanying the change from aqueous to membrane-mimicking solvents. We also identify an α-helical structure of TP2 in the membrane-mimicking solvents and provide a discussion of the mechanistic implications of this observation with reference to the previous literature on the peptide. From these results, we recommend the use of CHARMM36m with the REST2 protocol for the study of environment-specific IDP conformations. We believe that the simulation protocol will allow the study of a broad range of IDPs that undergo conformational transitions in different biological environments.
Collapse
Affiliation(s)
- Lauren M Reid
- School of Chemistry, University of Southampton Highfield Southampton SO17 1BJ UK
- Bioinformatics Institute (ASTAR) 30 Biolpolis Street Matrix 138671 Singapore
- MedChemica Ltd Alderley Park Macclesfield Cheshire SK10 4TG UK
| | - Ileana Guzzetti
- Medical Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Tor Svensson
- Medical Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Anna-Carin Carlsson
- Early Chemical Development, Pharmaceutical Sciences, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Wu Su
- Medical Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Tomas Leek
- Medical Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Lena von Sydow
- Medical Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Werngard Czechtizky
- Medical Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Marija Miljak
- School of Chemistry, University of Southampton Highfield Southampton SO17 1BJ UK
| | - Chandra Verma
- Bioinformatics Institute (ASTAR) 30 Biolpolis Street Matrix 138671 Singapore
- Department of Biological Sciences, National University of Singapore 16 Science Drive 4 117558 Singapore
- School of Biological Sciences, Nanyang Technological University 60 Nanyang Dr 637551 Singapore
| | - Leonardo De Maria
- Medical Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Jonathan W Essex
- School of Chemistry, University of Southampton Highfield Southampton SO17 1BJ UK
| |
Collapse
|
22
|
Kulkarni P, Behal A, Mohanty A, Salgia R, Nedelcu AM, Uversky VN. Co-opting disorder into order: Intrinsically disordered proteins and the early evolution of complex multicellularity. Int J Biol Macromol 2022; 201:29-36. [PMID: 34998872 DOI: 10.1016/j.ijbiomac.2021.12.182] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/18/2021] [Accepted: 12/28/2021] [Indexed: 02/07/2023]
Abstract
Intrinsically disordered proteins (IDPs) are proteins that lack rigid structures yet play important roles in myriad biological phenomena. A distinguishing feature of IDPs is that they often mediate specific biological outcomes via multivalent weak cooperative interactions with multiple partners. Here, we show that several proteins specifically associated with processes that were key in the evolution of complex multicellularity in the lineage leading to the multicellular green alga Volvox carteri are IDPs. We suggest that, by rewiring cellular protein interaction networks, IDPs facilitated the co-option of ancestral pathways for specialized multicellular functions, underscoring the importance of IDPs in the early evolution of complex multicellularity.
Collapse
Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA, USA.
| | - Amita Behal
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA, USA
| | - Atish Mohanty
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA, USA
| | - Ravi Salgia
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA, USA
| | - Aurora M Nedelcu
- Department of Biology, University of New Brunswick, Fredericton, Canada.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, Moscow region 141700, Russia.
| |
Collapse
|
23
|
Alghamdi M, Alamry SA, Bahlas SM, Uversky VN, Redwan EM. Circulating extracellular vesicles and rheumatoid arthritis: a proteomic analysis. Cell Mol Life Sci 2021; 79:25. [PMID: 34971426 PMCID: PMC11072894 DOI: 10.1007/s00018-021-04020-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 12/14/2022]
Abstract
Circulating extracellular vesicles (EVs) are membrane-bound nanoparticles secreted by most cells for intracellular communication and transportation of biomolecules. EVs carry proteins, lipids, nucleic acids, and receptors that are involved in human physiology and pathology. EV cargo is variable and highly related to the type and state of the cellular origin. Three subtypes of EVs have been identified: exosomes, microvesicles, and apoptotic bodies. Exosomes are the smallest and the most well-studied class of EVs that regulate different biological processes and participate in several diseases, such as cancers and autoimmune diseases. Proteomic analysis of exosomes succeeded in profiling numerous types of proteins involved in disease development and prognosis. In rheumatoid arthritis (RA), exosomes revealed a potential function in joint inflammation. These EVs possess a unique function, as they can transfer specific autoantigens and mediators between distant cells. Current proteomic data demonstrated that exosomes could provide beneficial effects against autoimmunity and exert an immunosuppressive action, particularly in RA. Based on these observations, effective therapeutic strategies have been developed for arthritis and other inflammatory disorders.
Collapse
Affiliation(s)
- Mohammed Alghamdi
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia
- Laboratory Department, University Medical Services Center, King Abdulaziz University, P.O. Box 80200, Jeddah, 21589, Saudi Arabia
| | - Sultan Abdulmughni Alamry
- Immunology Diagnostic Laboratory Department, King Abdulaziz University Hospital, P.O Box 80215, Jeddah, 21589, Saudi Arabia
| | - Sami M Bahlas
- Department of Internal Medicine, Faculty of Medicine, King Abdulaziz University, P.O. Box 80215, Jeddah, 21589, Saudi Arabia
| | - Vladimir N Uversky
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, 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
| | - Elrashdy M Redwan
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia.
- Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg EL-Arab, 21934, Alexandria, Egypt.
| |
Collapse
|
24
|
Sacquin-Mora S, Prévost C. When Order Meets Disorder: Modeling and Function of the Protein Interface in Fuzzy Complexes. Biomolecules 2021; 11:1529. [PMID: 34680162 PMCID: PMC8533853 DOI: 10.3390/biom11101529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 11/30/2022] Open
Abstract
The degree of proteins structural organization ranges from highly structured, compact folding to intrinsic disorder, where each degree of self-organization corresponds to specific functions: well-organized structural motifs in enzymes offer a proper environment for precisely positioned functional groups to participate in catalytic reactions; at the other end of the self-organization spectrum, intrinsically disordered proteins act as binding hubs via the formation of multiple, transient and often non-specific interactions. This review focusses on cases where structurally organized proteins or domains associate with highly disordered protein chains, leading to the formation of interfaces with varying degrees of fuzziness. We present a review of the computational methods developed to provide us with information on such fuzzy interfaces, and how they integrate experimental information. The discussion focusses on two specific cases, microtubules and homologous recombination nucleoprotein filaments, where a network of intrinsically disordered tails exerts regulatory function in recruiting partner macromolecules, proteins or DNA and tuning the atomic level association. Notably, we show how computational approaches such as molecular dynamics simulations can bring new knowledge to help bridging the gap between experimental analysis, that mostly concerns ensemble properties, and the behavior of individual disordered protein chains that contribute to regulation functions.
Collapse
Affiliation(s)
- Sophie Sacquin-Mora
- CNRS, Laboratoire de Biochimie Théorique, UPR9080, Université de Paris, 13 Rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75006 Paris, France
| | - Chantal Prévost
- CNRS, Laboratoire de Biochimie Théorique, UPR9080, Université de Paris, 13 Rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75006 Paris, France
| |
Collapse
|
25
|
Thapa C, Roivas P, Haataja T, Permi P, Pentikäinen U. Interaction mechanism of endogenous PP2A inhibitor protein ENSA with PP2A. FEBS J 2021; 289:519-534. [PMID: 34346186 DOI: 10.1111/febs.16150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/06/2021] [Accepted: 08/03/2021] [Indexed: 01/09/2023]
Abstract
The vast diversity of protein phosphatase 2A (PP2A) holoenzyme composition ensures its multifaceted role in the regulation of cellular growth and signal transduction. In several pathological conditions, such as cancer, PP2A is inhibited by endogenous inhibitor proteins. Several PP2A inhibitor proteins have been identified, one of which is α-endosulfine (ENSA). ENSA inhibits PP2A activity when it is phosphorylated at Ser67 by Greatwall (Gwl) kinase. The role of ENSA in PP2A inhibition is rather well characterized, but knowledge of the mechanism of inhibition is scarce. In this study, we have performed comprehensive structural characterization of ENSA, and its interaction with PP2A A- and various B56-subunit isoforms by combining NMR spectroscopy, small-angle X-ray scattering (SAXS) and interaction assays. The results clearly indicate that ENSA is an intrinsically disordered protein containing three transient α-helical structures. ENSA was observed to interact PP2A mainly via A-subunit, as the affinity with the A-subunit is significantly stronger than with any of the B56 subunits. Based on our results, it seems that ENSA follows the dock-and-coalesce mechanism in associating with PP2A A-subunit. Taken together, our results provide an essential structural and molecular framework to understanding molecular bases of ENSA-mediated PP2A inhibition, which is crucial for the development of new therapies for diseases linked to PP2A inhibition.
Collapse
Affiliation(s)
- Chandan Thapa
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Finland.,Institute of Biomedicine, University of Turku, Finland.,Turku BioScience, University of Turku, Finland
| | - Pekka Roivas
- Institute of Biomedicine, University of Turku, Finland.,Turku BioScience, University of Turku, Finland
| | - Tatu Haataja
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Finland
| | - Perttu Permi
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Finland.,Department of Chemistry and Nanoscience Center, University of Jyvaskyla, Finland
| | - Ulla Pentikäinen
- Institute of Biomedicine, University of Turku, Finland.,Turku BioScience, University of Turku, Finland
| |
Collapse
|
26
|
Jacoby G, Segal Asher M, Ehm T, Abutbul Ionita I, Shinar H, Azoulay-Ginsburg S, Zemach I, Koren G, Danino D, Kozlov MM, Amir RJ, Beck R. Order from Disorder with Intrinsically Disordered Peptide Amphiphiles. J Am Chem Soc 2021; 143:11879-11888. [PMID: 34310121 PMCID: PMC8397319 DOI: 10.1021/jacs.1c06133] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Indexed: 01/02/2023]
Abstract
Amphiphilic molecules and their self-assembled structures have long been the target of extensive research due to their potential applications in fields ranging from materials design to biomedical and cosmetic applications. Increasing demands for functional complexity have been met with challenges in biochemical engineering, driving researchers to innovate in the design of new amphiphiles. An emerging class of molecules, namely, peptide amphiphiles, combines key advantages and circumvents some of the disadvantages of conventional phospholipids and block copolymers. Herein, we present new peptide amphiphiles composed of an intrinsically disordered peptide conjugated to two variants of hydrophobic dendritic domains. These molecules, termed intrinsically disordered peptide amphiphiles (IDPA), exhibit a sharp pH-induced micellar phase-transition from low-dispersity spheres to extremely elongated worm-like micelles. We present an experimental characterization of the transition and propose a theoretical model to describe the pH-response. We also present the potential of the shape transition to serve as a mechanism for the design of a cargo hold-and-release application. Such amphiphilic systems demonstrate the power of tailoring the interactions between disordered peptides for various stimuli-responsive biomedical applications.
Collapse
Affiliation(s)
- Guy Jacoby
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for NanoTechnology & NanoScience, Tel Aviv Univeristy, Tel Aviv 6997801, Israel
| | - Merav Segal Asher
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for NanoTechnology & NanoScience, Tel Aviv Univeristy, Tel Aviv 6997801, Israel
- Raymond
& Beverly Sackler School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tamara Ehm
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for NanoTechnology & NanoScience, Tel Aviv Univeristy, Tel Aviv 6997801, Israel
- Faculty
of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, München D-80539, Germany
| | - Inbal Abutbul Ionita
- CryoEM
Laboratory of Soft Matter, Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Hila Shinar
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for NanoTechnology & NanoScience, Tel Aviv Univeristy, Tel Aviv 6997801, Israel
| | - Salome Azoulay-Ginsburg
- Raymond
& Beverly Sackler School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ido Zemach
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for NanoTechnology & NanoScience, Tel Aviv Univeristy, Tel Aviv 6997801, Israel
| | - Gil Koren
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for NanoTechnology & NanoScience, Tel Aviv Univeristy, Tel Aviv 6997801, Israel
| | - Dganit Danino
- CryoEM
Laboratory of Soft Matter, Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 3200003, Israel
- Guangdong-Technion
Israel Institute of Technology, Shantou, Guangdong Province 515063, China
| | - Michael M. Kozlov
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- Sackler School
of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Roey J. Amir
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for NanoTechnology & NanoScience, Tel Aviv Univeristy, Tel Aviv 6997801, Israel
- Raymond
& Beverly Sackler School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Roy Beck
- Raymond
& Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for Physics & Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for NanoTechnology & NanoScience, Tel Aviv Univeristy, Tel Aviv 6997801, Israel
| |
Collapse
|
27
|
Marzullo L, Turco MC, Uversky VN. What's in the BAGs? Intrinsic disorder angle of the multifunctionality of the members of a family of chaperone regulators. J Cell Biochem 2021; 123:22-42. [PMID: 34339540 DOI: 10.1002/jcb.30123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/28/2021] [Accepted: 07/22/2021] [Indexed: 01/22/2023]
Abstract
In humans, the family of Bcl-2 associated athanogene (BAG) proteins includes six members characterized by exceptional multifunctionality and engagement in the pathogenesis of various diseases. All of them are capable of interacting with a multitude of often unrelated binding partners. Such binding promiscuity and related functional and pathological multifacetedness cannot be explained or understood within the frames of the classical "one protein-one structure-one function" model, which also fails to explain the presence of multiple isoforms generated for BAG proteins by alternative splicing or alternative translation initiation and their extensive posttranslational modifications. However, all these mysteries can be solved by taking into account the intrinsic disorder phenomenon. In fact, high binding promiscuity and potential to participate in a broad spectrum of interactions with multiple binding partners, as well as a capability to be multifunctional and multipathogenic, are some of the characteristic features of intrinsically disordered proteins and intrinsically disordered protein regions. Such functional proteins or protein regions lacking unique tertiary structures constitute a cornerstone of the protein structure-function continuum concept. The aim of this paper is to provide an overview of the functional roles of human BAG proteins from the perspective of protein intrinsic disorder which will provide a means for understanding their binding promiscuity, multifunctionality, and relation to the pathogenesis of various diseases.
Collapse
Affiliation(s)
- Liberato Marzullo
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Italy.,Research and Development Division, BIOUNIVERSA s.r.l., Baronissi, Italy
| | - Maria C Turco
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Italy.,Research and Development Division, BIOUNIVERSA s.r.l., Baronissi, Italy
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| |
Collapse
|
28
|
Uversky VN, Giuliani A. Networks of Networks: An Essay on Multi-Level Biological Organization. Front Genet 2021; 12:706260. [PMID: 34234818 PMCID: PMC8255927 DOI: 10.3389/fgene.2021.706260] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 05/31/2021] [Indexed: 01/01/2023] Open
Abstract
The multi-level organization of nature is self-evident: proteins do interact among them to give rise to an organized metabolism, while in the same time each protein (a single node of such interaction network) is itself a network of interacting amino-acid residues allowing coordinated motion of the macromolecule and systemic effect as allosteric behavior. Similar pictures can be drawn for structure and function of cells, organs, tissues, and ecological systems. The majority of biologists are used to think that causally relevant events originate from the lower level (the molecular one) in the form of perturbations, that “climb up” the hierarchy reaching the ultimate layer of macroscopic behavior (e.g., causing a specific disease). Such causative model, stemming from the usual genotype-phenotype distinction, is not the only one. As a matter of fact, one can observe top-down, bottom-up, as well as middle-out perturbation/control trajectories. The recent complex network studies allow to go further the pure qualitative observation of the existence of both non-linear and non-bottom-up processes and to uncover the deep nature of multi-level organization. Here, taking as paradigm protein structural and interaction networks, we review some of the most relevant results dealing with between networks communication shedding light on the basic principles of complex system control and dynamics and offering a more realistic frame of causation in biology.
Collapse
Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Alessandro Giuliani
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| |
Collapse
|
29
|
Koshkin SA, Anatskaya OV, Vinogradov AE, Uversky VN, Dayhoff GW, Bystriakova MA, Pospelov VA, Tolkunova EN. Isolation and Characterization of Human Colon Adenocarcinoma Stem-Like Cells Based on the Endogenous Expression of the Stem Markers. Int J Mol Sci 2021; 22:4682. [PMID: 33925224 PMCID: PMC8124683 DOI: 10.3390/ijms22094682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/26/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Cancer stem cells' (CSCs) self-maintenance is regulated via the pluripotency pathways promoting the most aggressive tumor phenotype. This study aimed to use the activity of these pathways for the CSCs' subpopulation enrichment and separating cells characterized by the OCT4 and SOX2 expression. METHODS To select and analyze CSCs, we used the SORE6x lentiviral reporter plasmid for viral transduction of colon adenocarcinoma cells. Additionally, we assessed cell chemoresistance, clonogenic, invasive and migratory activity and the data of mRNA-seq and intrinsic disorder predisposition protein analysis (IDPPA). RESULTS We obtained the line of CSC-like cells selected on the basis of the expression of the OCT4 and SOX2 stem cell factors. The enriched CSC-like subpopulation had increased chemoresistance as well as clonogenic and migration activities. The bioinformatic analysis of mRNA seq data identified the up-regulation of pluripotency, development, drug resistance and phototransduction pathways, and the downregulation of pathways related to proliferation, cell cycle, aging, and differentiation. IDPPA indicated that CSC-like cells are predisposed to increased intrinsic protein disorder. CONCLUSION The use of the SORE6x reporter construct for CSCs enrichment allows us to obtain CSC-like population that can be used as a model to search for the new prognostic factors and potential therapeutic targets for colon cancer treatment.
Collapse
Affiliation(s)
- Sergei A. Koshkin
- Institute of Cytology of the Russian Academy of Science, 194064 St-Petersburg, Russia; (M.A.B.); (V.A.P.)
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, 1015 Walnut Street, Ste. 1024, Philadelphia, PA 19107, USA
| | - Olga V. Anatskaya
- Institute of Cytology of the Russian Academy of Science, 194064 St-Petersburg, Russia; (M.A.B.); (V.A.P.)
| | - Alexander E. Vinogradov
- Institute of Cytology of the Russian Academy of Science, 194064 St-Petersburg, Russia; (M.A.B.); (V.A.P.)
| | - 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
| | - Guy W. Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, FL 33620, USA;
| | - Margarita A. Bystriakova
- Institute of Cytology of the Russian Academy of Science, 194064 St-Petersburg, Russia; (M.A.B.); (V.A.P.)
| | - Valery A. Pospelov
- Institute of Cytology of the Russian Academy of Science, 194064 St-Petersburg, Russia; (M.A.B.); (V.A.P.)
| | - Elena N. Tolkunova
- Institute of Cytology of the Russian Academy of Science, 194064 St-Petersburg, Russia; (M.A.B.); (V.A.P.)
| |
Collapse
|
30
|
Kumar N, Kaushik R, Tennakoon C, Uversky VN, Longhi S, Zhang KYJ, Bhatia S. Insights into the evolutionary forces that shape the codon usage in the viral genome segments encoding intrinsically disordered protein regions. Brief Bioinform 2021; 22:6231751. [PMID: 33866372 DOI: 10.1093/bib/bbab145] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/17/2021] [Accepted: 03/26/2021] [Indexed: 12/22/2022] Open
Abstract
Intrinsically disordered regions/proteins (IDRs) are abundant across all the domains of life, where they perform important regulatory roles and supplement the biological functions of structured proteins/regions (SRs). Despite the multifunctionality features of IDRs, several interrogations on the evolution of viral genomic regions encoding IDRs in diverse viral proteins remain unreciprocated. To fill this gap, we benchmarked the findings of two most widely used and reliable intrinsic disorder prediction algorithms (IUPred2A and ESpritz) to a dataset of 6108 reference viral proteomes to unravel the multifaceted evolutionary forces that shape the codon usage in the viral genomic regions encoding for IDRs and SRs. We found persuasive evidence that the natural selection predominantly governs the evolution of codon usage in regions encoding IDRs by most of the viruses. In addition, we confirm not only that codon usage in regions encoding IDRs is less optimized for the protein synthesis machinery (transfer RNAs pool) of their host than for those encoding SRs, but also that the selective constraints imposed by codon bias sustain this reduced optimization in IDRs. Our analysis also establishes that IDRs in viruses are likely to tolerate more translational errors than SRs. All these findings hold true, irrespective of the disorder prediction algorithms used to classify IDRs. In conclusion, our study offers a novel perspective on the evolution of viral IDRs and the evolutionary adaptability to multiple taxonomically divergent hosts.
Collapse
Affiliation(s)
- Naveen Kumar
- Diagnostic & Vaccine Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India
| | - Rahul Kaushik
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | | | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.,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', Moscow region, Pushchino 142290, Russia
| | - Sonia Longhi
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Sandeep Bhatia
- Diagnostic & Vaccine Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India
| |
Collapse
|
31
|
Identification of Intrinsically Disordered Protein Regions Based on Deep Neural Network-VGG16. ALGORITHMS 2021. [DOI: 10.3390/a14040107] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The accurate of i identificationntrinsically disordered proteins or protein regions is of great importance, as they are involved in critical biological process and related to various human diseases. In this paper, we develop a deep neural network that is based on the well-known VGG16. Our deep neural network is then trained through using 1450 proteins from the dataset DIS1616 and the trained neural network is tested on the remaining 166 proteins. Our trained neural network is also tested on the blind test set R80 and MXD494 to further demonstrate the performance of our model. The MCC value of our trained deep neural network is 0.5132 on the test set DIS166, 0.5270 on the blind test set R80 and 0.4577 on the blind test set MXD494. All of these MCC values of our trained deep neural network exceed the corresponding values of existing prediction methods.
Collapse
|
32
|
Thapa C, Roivas P, Haataja T, Permi P, Pentikäinen U. The Interaction Mechanism of Intrinsically Disordered PP2A Inhibitor Proteins ARPP-16 and ARPP-19 With PP2A. Front Mol Biosci 2021; 8:650881. [PMID: 33842550 PMCID: PMC8032985 DOI: 10.3389/fmolb.2021.650881] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/03/2021] [Indexed: 12/01/2022] Open
Abstract
Protein phosphatase 2A (PP2A) activity is critical for maintaining normal physiological cellular functions. PP2A is inhibited by endogenous inhibitor proteins in several pathological conditions including cancer. A PP2A inhibitor protein, ARPP-19, has recently been connected to several human cancer types. Accordingly, the knowledge about ARPP-19—PP2A inhibition mechanism is crucial for the understanding the disease development and the therapeutic targeting of ARPP-19—PP2A. Here, we show the first structural characterization of ARPP-19, and its splice variant ARPP-16 using NMR spectroscopy, and SAXS. The results reveal that both ARPP proteins are intrinsically disordered but contain transient secondary structure elements. The interaction mechanism of ARPP-16/19 with PP2A was investigated using microscale thermophoresis and NMR spectroscopy. Our results suggest that ARPP—PP2A A-subunit interaction is mediated by linear motif and has modest affinity whereas, the interaction of ARPPs with B56-subunit is weak and transient. Like many IDPs, ARPPs are promiscuous binders that transiently interact with PP2A A- and B56 subunits using multiple interaction motifs. In summary, our results provide a good starting point for future studies and development of therapeutics that block ARPP-PP2A interactions.
Collapse
Affiliation(s)
- Chandan Thapa
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.,Institute of Biomedicine, University of Turku, Turku, Finland.,Turku BioScience Centre, University of Turku, Turku, Finland
| | - Pekka Roivas
- Institute of Biomedicine, University of Turku, Turku, Finland.,Turku BioScience Centre, University of Turku, Turku, Finland
| | - Tatu Haataja
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.,Institute of Biomedicine, University of Turku, Turku, Finland.,Turku BioScience Centre, University of Turku, Turku, Finland
| | - Perttu Permi
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.,Department of Chemistry and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Ulla Pentikäinen
- Institute of Biomedicine, University of Turku, Turku, Finland.,Turku BioScience Centre, University of Turku, Turku, Finland
| |
Collapse
|
33
|
The Participation of the Intrinsically Disordered Regions of the bHLH-PAS Transcription Factors in Disease Development. Int J Mol Sci 2021; 22:ijms22062868. [PMID: 33799876 PMCID: PMC8001110 DOI: 10.3390/ijms22062868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/05/2021] [Accepted: 03/07/2021] [Indexed: 12/14/2022] Open
Abstract
The basic helix–loop–helix/Per-ARNT-SIM (bHLH-PAS) proteins are a family of transcription factors regulating expression of a wide range of genes involved in different functions, ranging from differentiation and development control by oxygen and toxins sensing to circadian clock setting. In addition to the well-preserved DNA-binding bHLH and PAS domains, bHLH-PAS proteins contain long intrinsically disordered C-terminal regions, responsible for regulation of their activity. Our aim was to analyze the potential connection between disordered regions of the bHLH-PAS transcription factors, post-transcriptional modifications and liquid-liquid phase separation, in the context of disease-associated missense mutations. Highly flexible disordered regions, enriched in short motives which are more ordered, are responsible for a wide spectrum of interactions with transcriptional co-regulators. Based on our in silico analysis and taking into account the fact that the functions of transcription factors can be modulated by posttranslational modifications and spontaneous phase separation, we assume that the locations of missense mutations inducing disease states are clearly related to sequences directly undergoing these processes or to sequences responsible for their regulation.
Collapse
|
34
|
Zhao B, Katuwawala A, Uversky VN, Kurgan L. IDPology of the living cell: intrinsic disorder in the subcellular compartments of the human cell. Cell Mol Life Sci 2021; 78:2371-2385. [PMID: 32997198 PMCID: PMC11071772 DOI: 10.1007/s00018-020-03654-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/09/2020] [Accepted: 09/22/2020] [Indexed: 12/11/2022]
Abstract
Intrinsic disorder can be found in all proteomes of all kingdoms of life and in viruses, being particularly prevalent in the eukaryotes. We conduct a comprehensive analysis of the intrinsic disorder in the human proteins while mapping them into 24 compartments of the human cell. In agreement with previous studies, we show that human proteins are significantly enriched in disorder relative to a generic protein set that represents the protein universe. In fact, the fraction of proteins with long disordered regions and the average protein-level disorder content in the human proteome are about 3 times higher than in the protein universe. Furthermore, levels of intrinsic disorder in the majority of human subcellular compartments significantly exceed the average disorder content in the protein universe. Relative to the overall amount of disorder in the human proteome, proteins localized in the nucleus and cytoskeleton have significantly increased amounts of disorder, measured by both high disorder content and presence of multiple long intrinsically disordered regions. We empirically demonstrate that, on average, human proteins are assigned to 2.3 subcellular compartments, with proteins localized to few subcellular compartments being more disordered than the proteins that are localized to many compartments. Functionally, the disordered proteins localized in the most disorder-enriched subcellular compartments are primarily responsible for interactions with nucleic acids and protein partners. This is the first-time disorder is comprehensively mapped into the human cell. Our observations add a missing piece to the puzzle of functional disorder and its organization inside the cell.
Collapse
Affiliation(s)
- Bi Zhao
- Department of Computer Science, Virginia Commonwealth University, 401 West Main Street, Room E4225, Richmond, VA, 23284, USA
| | - Akila Katuwawala
- Department of Computer Science, Virginia Commonwealth University, 401 West Main Street, Room E4225, Richmond, VA, 23284, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL, 33612, 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.
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, 401 West Main Street, Room E4225, Richmond, VA, 23284, USA.
| |
Collapse
|
35
|
Polanco C, Uversky VN, Huberman A, Andrés L, Buhse T, Castañón-González JA, Sánchez-Guerrero AF. Bioinformatics-based Identification of Proteins Expressed by Arthropod- borne Viruses Transmitted by Aedes Aegypti Mosquito. CURR PROTEOMICS 2021. [DOI: 10.2174/1570164617999200422123618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The female Aedes aegypti mosquito is a vector of several arthropod-borne
viruses, such as Mayaro, Dengue, Chikungunya, Yellow Fever, and Zika. These viruses cause the
death of at least 600000 people a year and temporarily disable several million more around the
world. Up to date, there are no effective prophylactic measures that would prevent the contact and
bite of this arthropod and, therefore, its consequential contagion.
Objective:
The objective of the present study was to search for the regularities of the proteins expressed
by these five viruses, at residues level, and obtain a “bioinformatic fingerprint” to select
them.
Methods:
We used two bioinformatic systems, our in-house bioinformatic system named Polarity
Index Method® (PIM®) supported at residues level, and the commonly used algorithm for the prediction
of intrinsic disorder predisposition, PONDR® FIT. We applied both programs to the 29 proteins
that express the five groups of arboviruses studied, and we calculated for each of them their
Polarity Index Method® profile and their intrinsic disorder predisposition. This information was
then compared with analogous information for other protein groups, such as proteins from bacteria,
fungi, viruses, and cell-penetrating peptides from the UniProt database, and a set of intrinsically disordered
proteins. Once the “fingerprint” of each group of arboviruses was obtained, these “fingerprints”
were searched among the 559228 “reviewed” proteins from the UniProt database.
Results:
In total, 1736 proteins were identified from the 559228 “reviewed” proteins from the
UniProt database, with similar “PIM® profile” to the 29 mutated proteins that express the five
groups of arboviruses.
Conclusion:
We propose that the “PIM® profile” of characterization of proteins might be useful for
the identification of proteins expressed by arthropod-borne viruses transmitted by Aedes aegypti
mosquito.
Collapse
Affiliation(s)
- Carlos Polanco
- Department of Mathematics, Faculty of Sciences, Universidad Nacional Autonoma de Mexico, Mexico City 04510, Mexico
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL33647, United States
| | - Alberto Huberman
- Department of Biochemistry, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, 14080 Mexico City, Mexico
| | - Leire Andrés
- Department of Pathology, Hospital de Cruces, 48903, Barakaldo, Spain
| | - Thomas Buhse
- Centro de Investigaciones Quimicas, Universidad Autonoma del Estado de Morelos, Cuernavaca Morelos 62209, Mexico
| | | | | |
Collapse
|
36
|
Blanco PM, Madurga S, Garcés JL, Mas F, Dias RS. Influence of macromolecular crowding on the charge regulation of intrinsically disordered proteins. SOFT MATTER 2021; 17:655-669. [PMID: 33215185 DOI: 10.1039/d0sm01475c] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this work we study the coupling between ionization and conformational properties of two IDPs, histatin-5 and β-amyloid 42, in the presence of neutral and charged crowders. The latter is modeled to resemble bovine serum albumin (BSA). With this aim, semi-grand canonical Monte Carlo simulations are performed, so that the IDP charge is a dynamic property, undergoing protonation/deprotonation processes. Both ionization properties (global and specific amino acid charge and binding capacitance) and radius of gyration are analyzed in a large range of pH values and salt concentrations. Without crowder agents, the titration curve of histatin-5, a polycation, is salt-dependent while that of β-amyloid 42, a polyampholyte, is almost unaffected. The salt concentration is found to be particularly relevant at pH values where the protein binding capacitance (directly linked with charge fluctuation) is larger. Upon addition of neutral crowders, charge regulation is observed in histatin-5, while for β-amyloid 42 this effect is very small. The main mechanism for charge regulation is found to be the effective increase in the ionic strength due to the excluded volume. In the presence of charged crowders, a significant increase in the charge of both IDPs is observed in almost all the pH range. In this case, the IDP charge is altered not only by the increase in the effective ionic strength but also by its direct electrostatic interaction with the charged crowders.
Collapse
Affiliation(s)
- Pablo M Blanco
- Physical Chemistry Unit, Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB) of Barcelona University (UB), Barcelona, Catalonia, Spain.
| | - Sergio Madurga
- Physical Chemistry Unit, Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB) of Barcelona University (UB), Barcelona, Catalonia, Spain.
| | - Josep L Garcés
- Chemistry Department, Technical School of Agricultural Engineering & AGROTECNIO of Lleida University (UdL), Lleida, Catalonia, Spain
| | - Francesc Mas
- Physical Chemistry Unit, Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB) of Barcelona University (UB), Barcelona, Catalonia, Spain.
| | - Rita S Dias
- Department of Physics, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
| |
Collapse
|
37
|
Uversky VN. Functions of short lifetime biological structures at large: the case of intrinsically disordered proteins. Brief Funct Genomics 2020; 19:60-68. [PMID: 29982297 DOI: 10.1093/bfgp/ely023] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Although for more than a century a protein function was intimately associated with the presence of unique structure in a protein molecule, recent years witnessed a skyrocket rise of the appreciation of protein intrinsic disorder concept that emphasizes the importance of the biologically active proteins without ordered structures. In different proteins, the depth and breadth of disorder penetrance are different, generating an amusing spatiotemporal heterogeneity of intrinsically disordered proteins (IDPs) and intrinsically disordered protein region regions (IDPRs), which are typically described as highly dynamic ensembles of rapidly interconverting conformations (or a multitude of short lifetime structures). IDPs/IDPRs constitute a substantial part of protein kingdom and have unique functions complementary to functional repertoires of ordered proteins. They are recognized as interaction specialists and global controllers that play crucial roles in regulation of functions of their binding partners and in controlling large biological networks. IDPs/IDPRs are characterized by immense binding promiscuity and are able to use a broad spectrum of binding modes, often resulting in the formation of short lifetime complexes. In their turn, functions of IDPs and IDPRs are controlled by various means, such as numerous posttranslational modifications and alternative splicing. Some of the functions of IDPs/IDPRs are briefly considered in this review to shed some light on the biological roles of short-lived structures at large.
Collapse
Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA and Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| |
Collapse
|
38
|
Hameduh T, Haddad Y, Adam V, Heger Z. Homology modeling in the time of collective and artificial intelligence. Comput Struct Biotechnol J 2020; 18:3494-3506. [PMID: 33304450 PMCID: PMC7695898 DOI: 10.1016/j.csbj.2020.11.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 12/12/2022] Open
Abstract
Homology modeling is a method for building protein 3D structures using protein primary sequence and utilizing prior knowledge gained from structural similarities with other proteins. The homology modeling process is done in sequential steps where sequence/structure alignment is optimized, then a backbone is built and later, side-chains are added. Once the low-homology loops are modeled, the whole 3D structure is optimized and validated. In the past three decades, a few collective and collaborative initiatives allowed for continuous progress in both homology and ab initio modeling. Critical Assessment of protein Structure Prediction (CASP) is a worldwide community experiment that has historically recorded the progress in this field. Folding@Home and Rosetta@Home are examples of crowd-sourcing initiatives where the community is sharing computational resources, whereas RosettaCommons is an example of an initiative where a community is sharing a codebase for the development of computational algorithms. Foldit is another initiative where participants compete with each other in a protein folding video game to predict 3D structure. In the past few years, contact maps deep machine learning was introduced to the 3D structure prediction process, adding more information and increasing the accuracy of models significantly. In this review, we will take the reader in a journey of exploration from the beginnings to the most recent turnabouts, which have revolutionized the field of homology modeling. Moreover, we discuss the new trends emerging in this rapidly growing field.
Collapse
Affiliation(s)
- Tareq Hameduh
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
| | - Yazan Haddad
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00 Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00 Brno, Czech Republic
| | - Zbynek Heger
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00 Brno, Czech Republic
| |
Collapse
|
39
|
Thapa CJ, Haataja T, Pentikäinen U, Permi P. 1H, 13C and 15N NMR chemical shift assignments of cAMP-regulated phosphoprotein-19 and -16 (ARPP-19 and ARPP-16). BIOMOLECULAR NMR ASSIGNMENTS 2020; 14:227-231. [PMID: 32468417 PMCID: PMC7462833 DOI: 10.1007/s12104-020-09951-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/21/2020] [Indexed: 05/09/2023]
Abstract
Protein Phosphatase 2A, PP2A, the principal Serine/threonine phosphatase, has major roles in broad range of signaling pathways that include regulation of cell cycle, cell proliferation and neuronal signaling. The loss of function of PP2A is linked with many human diseases, like cancer and neurodegenerative disorders. Protein phosphatase 2A (PP2A) functions as tumor suppressor and its tumor suppressor activity is inhibited by the overexpression of PP2A inhibitor proteins in most of the cancers. ARPP-19/ARPP-16 has been identified as one of the potential PP2A inhibitor proteins. Here, we report the resonance assignment of backbone 1H, 13C and 15N atoms of human ARPP-19 and ARPP-16 proteins. These chemical shift values can provide valuable information for the further study of the dynamics and interaction of ARPP-proteins to PP2A using NMR spectroscopy.
Collapse
Affiliation(s)
- Chandan J Thapa
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi, Turku, Finland
| | - Tatu Haataja
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
| | - Ulla Pentikäinen
- Institute of Biomedicine, University of Turku, Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi, Turku, Finland
| | - Perttu Permi
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland.
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.
| |
Collapse
|
40
|
Gadhave K, Gehi BR, Kumar P, Xue B, Uversky VN, Giri R. The dark side of Alzheimer's disease: unstructured biology of proteins from the amyloid cascade signaling pathway. Cell Mol Life Sci 2020; 77:4163-4208. [PMID: 31894361 PMCID: PMC11104979 DOI: 10.1007/s00018-019-03414-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/17/2019] [Accepted: 12/04/2019] [Indexed: 12/21/2022]
Abstract
Alzheimer's disease (AD) is a leading cause of age-related dementia worldwide. Despite more than a century of intensive research, we are not anywhere near the discovery of a cure for this disease or a way to prevent its progression. Among the various molecular mechanisms proposed for the description of the pathogenesis and progression of AD, the amyloid cascade hypothesis, according to which accumulation of a product of amyloid precursor protein (APP) cleavage, amyloid β (Aβ) peptide, induces pathological changes in the brain observed in AD, occupies a unique niche. Although multiple proteins have been implicated in this amyloid cascade signaling pathway, their structure-function relationships are mostly unexplored. However, it is known that two major proteins related to AD pathology, Aβ peptide, and microtubule-associated protein tau belong to the category of intrinsically disordered proteins (IDPs), which are the functionally important proteins characterized by a lack of fixed, ordered three-dimensional structure. IDPs and intrinsically disordered protein regions (IDPRs) play numerous vital roles in various cellular processes, such as signaling, cell cycle regulation, macromolecular recognition, and promiscuous binding. However, the deregulation and misfolding of IDPs may lead to disturbed signaling, interactions, and disease pathogenesis. Often, molecular recognition-related IDPs/IDPRs undergo disorder-to-order transition upon binding to their biological partners and contain specific disorder-based binding motifs, known as molecular recognition features (MoRFs). Knowing the intrinsic disorder status and disorder-based functionality of proteins associated with amyloid cascade signaling pathway may help to untangle the mechanisms of AD pathogenesis and help identify therapeutic targets. In this paper, we have used multiple computational tools to evaluate the presence of intrinsic disorder and MoRFs in 27 proteins potentially relevant to the amyloid cascade signaling pathway. Among these, BIN1, APP, APOE, PICALM, PSEN1 and CD33 were found to be highly disordered. Furthermore, their disorder-based binding regions and associated short linear motifs have also been identified. These findings represent important foundation for the future research, and experimental characterization of disordered regions in these proteins is required to better understand their roles in AD pathogenesis.
Collapse
Affiliation(s)
- Kundlik Gadhave
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | | | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Bin Xue
- Department of Cell Biology, Microbiology and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, Tampa, FL, 33620, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33620, USA.
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia.
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India.
| |
Collapse
|
41
|
Van Bibber NW, Haerle C, Khalife R, Dayhoff GW, Uversky VN. Intrinsic Disorder in Human Proteins Encoded by Core Duplicon Gene Families. J Phys Chem B 2020; 124:8050-8070. [PMID: 32880174 DOI: 10.1021/acs.jpcb.0c07676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Segmental duplications (i.e., highly homologous DNA fragments greater than 1 kb in length that are present within a genome at more than one site) are typically found in genome regions that are prone to rearrangements. A noticeable fraction of the human genome (∼5%) includes segmental duplications (or duplicons) that are assumed to play a number of vital roles in human evolution, human-specific adaptation, and genomic instability. Despite their importance for crucial events such as synaptogenesis, neuronal migration, and neocortical expansion, these segmental duplications continue to be rather poorly characterized. Of particular interest are the core duplicon gene (CDG) families, which are replicates sharing common "core" DNA among the randomly attached pieces and which expand along single chromosomes and might harbor newly acquired protein domains. Another important feature of proteins encoded by CDG families is their multifunctionality. Although it seems that these proteins might possess many characteristic features of intrinsically disordered proteins, to the best of our knowledge, a systematic investigation of the intrinsic disorder predisposition of the proteins encoded by core duplicon gene families has not been conducted yet. To fill this gap and to determine the degree to which these proteins might be affected by intrinsic disorder, we analyzed a set of human proteins encoded by the members of 10 core duplicon gene families, such as NBPF, RGPD, GUSBP, PMS2P, SPATA31, TRIM51, GOLGA8, NPIP, TBC1D3, and LRRC37. Our analysis revealed that the vast majority of these proteins are highly disordered, with their disordered regions often being utilized as means for the protein-protein interactions and/or targeted for numerous posttranslational modifications of different nature.
Collapse
Affiliation(s)
- Nathan W Van Bibber
- Department of Molecular Medicine Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - Cornelia Haerle
- Department of Molecular Medicine Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - Roy Khalife
- Department of Molecular Medicine Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - Guy W Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, Florida 33620, United States
| | - Vladimir N Uversky
- Department of Molecular Medicine Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States.,USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States.,Institute for Biological Instrumentation, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 4 Institutskaya St., Pushchino, 142290, Moscow Region, Russia
| |
Collapse
|
42
|
Sabharwal P, Savithri HS. Functional Characterization of Pepper Vein Banding Virus-Encoded Proteins and Their Interactions: Implications in Potyvirus Infection. Viruses 2020; 12:v12091037. [PMID: 32957699 PMCID: PMC7551749 DOI: 10.3390/v12091037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 11/16/2022] Open
Abstract
Pepper vein banding virus (PVBV) is a distinct species in the Potyvirus genus which infects economically important plants in several parts of India. Like other potyviruses, PVBV encodes multifunctional proteins, with several interaction partners, having implications at different stages of the potyviral infection. In this review, we summarize the functional characterization of different PVBV-encoded proteins with an emphasis on their interaction partners governing the multifunctionality of potyviral proteins. Intrinsically disordered domains/regions of these proteins play an important role in their interactions with other proteins. Deciphering the function of PVBV-encoded proteins and their interactions with cognitive partners will help in understanding the putative mechanisms by which the potyviral proteins are regulated at different stages of the viral life-cycle. This review also discusses PVBV virus-like particles (VLPs) and their potential applications in nanotechnology. Further, virus-like nanoparticle-cell interactions and intracellular fate of PVBV VLPs are also discussed.
Collapse
|
43
|
Intrinsic Disorder in Tetratricopeptide Repeat Proteins. Int J Mol Sci 2020; 21:ijms21103709. [PMID: 32466138 PMCID: PMC7279152 DOI: 10.3390/ijms21103709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/12/2020] [Accepted: 05/22/2020] [Indexed: 12/27/2022] Open
Abstract
Among the realm of repeat containing proteins that commonly serve as “scaffolds” promoting protein-protein interactions, there is a family of proteins containing between 2 and 20 tetratricopeptide repeats (TPRs), which are functional motifs consisting of 34 amino acids. The most distinguishing feature of TPR domains is their ability to stack continuously one upon the other, with these stacked repeats being able to affect interaction with binding partners either sequentially or in combination. It is known that many repeat-containing proteins are characterized by high levels of intrinsic disorder, and that many protein tandem repeats can be intrinsically disordered. Furthermore, it seems that TPR-containing proteins share many characteristics with hybrid proteins containing ordered domains and intrinsically disordered protein regions. However, there has not been a systematic analysis of the intrinsic disorder status of TPR proteins. To fill this gap, we analyzed 166 human TPR proteins to determine the degree to which proteins containing TPR motifs are affected by intrinsic disorder. Our analysis revealed that these proteins are characterized by different levels of intrinsic disorder and contain functional disordered regions that are utilized for protein-protein interactions and often serve as targets of various posttranslational modifications.
Collapse
|
44
|
Badierah RA, Uversky VN, Redwan EM. Dancing with Trojan horses: an interplay between the extracellular vesicles and viruses. J Biomol Struct Dyn 2020; 39:3034-3060. [DOI: 10.1080/07391102.2020.1756409] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Raied A. Badierah
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Molecular Diagnostic Laboratory, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vladimir N. Uversky
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Federal Research Center ‘Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences’, Pushchino, Moscow Region, Russia
| | - Elrashdy M. Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
45
|
Probing Surfaces in Dynamic Protein Interactions. J Mol Biol 2020; 432:2949-2972. [DOI: 10.1016/j.jmb.2020.02.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 02/22/2020] [Accepted: 02/24/2020] [Indexed: 01/09/2023]
|
46
|
Porębska A, Różycka M, Hołubowicz R, Szewczuk Z, Ożyhar A, Dobryszycki P. Functional derivatives of human dentin matrix protein 1 modulate morphology of calcium carbonate crystals. FASEB J 2020; 34:6147-6165. [PMID: 32190922 DOI: 10.1096/fj.201901999r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 02/07/2020] [Accepted: 02/21/2020] [Indexed: 12/23/2022]
Abstract
Dentin matrix protein 1 (DMP1) is an acidic, extracellular matrix protein essential for biomineralization of calcium phosphate, in bone and dentin. It is proteolytically processed into two fragments, 44K and 56K. Recently, the presence of DMP1 was noticed in inner ear, specifically in otoconia, which are calcium carbonate biominerals involved in sensing of balance. In this study, the solution structure and biomineralization activity of otoconial 44K and 56K fragments toward calcium carbonate were investigated. The results of analytical ultracentrifugation, circular dichroism, and gel filtration indicated that DMP1 fragments are disordered in solution. Notably, 56K formed oligomers in the presence of calcium ions. It was also observed that both fragments influenced the crystal growth by in vitro biomineralization assay and scanning electron microscopy. In addition, they sequester the calcium ions during the calcite formation. Calcium carbonate crystals precipitated in vitro changed their size and shape in the presence of DMP1 fragments. Oligomerization propensity of 56K may significantly enhance this function. Our study indicates that intrinsically disordered DMP1 has a previously unknown regulatory function for biomineralization of otoconia.
Collapse
Affiliation(s)
- Aleksandra Porębska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Mirosława Różycka
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Rafał Hołubowicz
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | | | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Piotr Dobryszycki
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| |
Collapse
|
47
|
Abstract
Functions of intrinsically disordered proteins do not require structure. Such structure-independent functionality has melted away the classic rigid "lock and key" representation of structure-function relationships in proteins, opening a new page in protein science, where molten keys operate on melted locks and where conformational flexibility and intrinsic disorder, structural plasticity and extreme malleability, multifunctionality and binding promiscuity represent a new-fangled reality. Analysis and understanding of this new reality require novel tools, and some of the techniques elaborated for the examination of intrinsically disordered protein functions are outlined in this review.
Collapse
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, 33620, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Russian Federation
| |
Collapse
|
48
|
Abstract
Intrinsically disordered proteins (IDPs) and regions (IDRs) are commonly found in all proteomes analyzed so far. These proteins/regions are subject to numerous posttranslational modifications (PTMs) and alternative splicing, are involved in a wide range of cellular functions, and often facilitate protein-protein interactions (PPIs). Some of these proteins contain molecular recognition features (MoRFs), which are IDRs that bind to partner proteins and undergo disorder-to-order transitions. Although many IDPs/IDRs can fold upon binding, a large fraction of these proteins are known to maintain significant amounts of disorder in their bound states. Being well-recognized interaction specialists, IDPs/IDRs can participate in one-to-many and many-to-one interactions, where one IDP/IDR binds to multiple partners potentially gaining very different structures in the bound state, or where multiple unrelated IDPs/IDRs bind to one partner. As a result, IDPs frequently serve as hubs (i.e., proteins with many links) in complex PPI networks. The goal of this chapter is to describe computational and bioinformatics tools that can be used to look at the disorder status of proteins within a given PPI network and also to gain some knowledge on the disorder-based functionality of the members of this network. To this end, description is provided for some of the use of UniProt and DisProt databases, several databases generating PPI networks (BioGRID, IntAct, DIP, MINT, HPRD, APID, KEGG, and STRING), Composition profiler, some tools for the per-residue disorder predictions (PONDR® VLXT, PONDR® VL3, PONDR® VSL2, PONDR-FIT, and IUPred), binary disorder classifiers CH-plot and CDF-plot and their combined CH-CDF analysis, web-based tools for the visualization of disorder distribution in a query protein (D2P2 and MobiDB), as well as some tools for evaluation disorder-based functionality of proteins (ANCHOR, MoRFpred, DEPP, and ModPred).
Collapse
Affiliation(s)
- 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. .,Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation.
| |
Collapse
|
49
|
Katuwawala A, Oldfield CJ, Kurgan L. DISOselect: Disorder predictor selection at the protein level. Protein Sci 2020; 29:184-200. [PMID: 31642118 PMCID: PMC6933862 DOI: 10.1002/pro.3756] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 12/27/2022]
Abstract
The intense interest in the intrinsically disordered proteins in the life science community, together with the remarkable advancements in predictive technologies, have given rise to the development of a large number of computational predictors of intrinsic disorder from protein sequence. While the growing number of predictors is a positive trend, we have observed a considerable difference in predictive quality among predictors for individual proteins. Furthermore, variable predictor performance is often inconsistent between predictors for different proteins, and the predictor that shows the best predictive performance depends on the unique properties of each protein sequence. We propose a computational approach, DISOselect, to estimate the predictive performance of 12 selected predictors for individual proteins based on their unique sequence-derived properties. This estimation informs the users about the expected predictive quality for a selected disorder predictor and can be used to recommend methods that are likely to provide the best quality predictions. Our solution does not depend on the results of any disorder predictor; the estimations are made based solely on the protein sequence. Our solution significantly improves predictive performance, as judged with a test set of 1,000 proteins, when compared to other alternatives. We have empirically shown that by using the recommended methods the overall predictive performance for a given set of proteins can be improved by a statistically significant margin. DISOselect is freely available for non-commercial users through the webserver at http://biomine.cs.vcu.edu/servers/DISOselect/.
Collapse
Affiliation(s)
- Akila Katuwawala
- Department of Computer ScienceVirginia Commonwealth UniversityRichmondVirginia
| | | | - Lukasz Kurgan
- Department of Computer ScienceVirginia Commonwealth UniversityRichmondVirginia
| |
Collapse
|
50
|
Sun X, Malhis N, Zhao B, Xue B, Gsponer J, Rikkerink EHA. Computational Disorder Analysis in Ethylene Response Factors Uncovers Binding Motifs Critical to Their Diverse Functions. Int J Mol Sci 2019; 21:ijms21010074. [PMID: 31861935 PMCID: PMC6981732 DOI: 10.3390/ijms21010074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/15/2019] [Accepted: 12/18/2019] [Indexed: 01/01/2023] Open
Abstract
APETALA2/ETHYLENE RESPONSE FACTOR transcription factors (AP2/ERFs) play crucial roles in adaptation to stresses such as those caused by pathogens, wounding and cold. Although their name suggests a specific role in ethylene signalling, some ERF members also co-ordinate signals regulated by other key plant stress hormones such as jasmonate, abscisic acid and salicylate. We analysed a set of ERF proteins from three divergent plant species for intrinsically disorder regions containing conserved segments involved in protein–protein interaction known as Molecular Recognition Features (MoRFs). Then we correlated the MoRFs identified with a number of known functional features where these could be identified. Our analyses suggest that MoRFs, with plasticity in their disordered surroundings, are highly functional and may have been shuffled between related protein families driven by selection. A particularly important role may be played by the alpha helical component of the structured DNA binding domain to permit specificity. We also present examples of computationally identified MoRFs that have no known function and provide a valuable conceptual framework to link both disordered and ordered structural features within this family to diverse function.
Collapse
Affiliation(s)
- Xiaolin Sun
- The New Zealand Institute for Plant & Food Research Ltd., 120 Mt. Albert Rd, Private Bag 92169, 1025 Auckland, New Zealand;
| | - Nawar Malhis
- Michael Smith Laboratories—Centre for High-Throughput Biology, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (N.M.); (J.G.)
| | - Bi Zhao
- Department of Cell Biology, Microbiology and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, 4202 East Fowler Avenue, ISA 2015, Tampa, FL 33620-5150, USA; (B.Z.); (B.X.)
| | - Bin Xue
- Department of Cell Biology, Microbiology and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, 4202 East Fowler Avenue, ISA 2015, Tampa, FL 33620-5150, USA; (B.Z.); (B.X.)
| | - Joerg Gsponer
- Michael Smith Laboratories—Centre for High-Throughput Biology, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (N.M.); (J.G.)
| | - Erik H. A. Rikkerink
- The New Zealand Institute for Plant & Food Research Ltd., 120 Mt. Albert Rd, Private Bag 92169, 1025 Auckland, New Zealand;
- Correspondence: ; Tel.: +64-9-925-7157
| |
Collapse
|