201
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Deciphering RNA-Recognition Patterns of Intrinsically Disordered Proteins. Int J Mol Sci 2018; 19:ijms19061595. [PMID: 29843482 PMCID: PMC6032373 DOI: 10.3390/ijms19061595] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/10/2018] [Accepted: 05/16/2018] [Indexed: 02/06/2023] Open
Abstract
Intrinsically disordered regions (IDRs) and protein (IDPs) are highly flexible owing to their lack of well-defined structures. A subset of such proteins interacts with various substrates; including RNA; frequently adopting regular structures in the final complex. In this work; we have analysed a dataset of protein–RNA complexes undergoing disorder-to-order transition (DOT) upon binding. We found that DOT regions are generally small in size (less than 3 residues) for RNA binding proteins. Like structured proteins; positively charged residues are found to interact with RNA molecules; indicating the dominance of electrostatic and cation-π interactions. However, a comparison of binding frequency shows that interface hydrophobic and aromatic residues have more interactions in only DOT regions than in a protein. Further; DOT regions have significantly higher exposure to water than their structured counterparts. Interactions of DOT regions with RNA increase the sheet formation with minor changes in helix forming residues. We have computed the interaction energy for amino acids–nucleotide pairs; which showed the preference of His–G; Asn–U and Ser–U at for the interface of DOT regions. This study provides insights to understand protein–RNA interactions and the results could also be used for developing a tool for identifying DOT regions in RNA binding proteins.
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202
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Lindström I, Dogan J. Dynamics, Conformational Entropy, and Frustration in Protein-Protein Interactions Involving an Intrinsically Disordered Protein Domain. ACS Chem Biol 2018; 13:1218-1227. [PMID: 29614221 DOI: 10.1021/acschembio.7b01105] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Intrinsically disordered proteins (IDPs) are abundant in the eukaryotic proteome. However, little is known about the role of subnanosecond dynamics and the conformational entropy that it represents in protein-protein interactions involving IDPs. Using nuclear magnetic resonance side chain and backbone relaxation, stopped-flow kinetics, isothermal titration calorimetry, and computational studies, we have characterized the interaction between the globular TAZ1 domain of the CREB binding protein and the intrinsically disordered transactivation domain of STAT2 (TAD-STAT2). We show that the TAZ1/TAD-STAT2 complex retains considerable subnanosecond motions, with TAD-STAT2 undergoing only a partial disorder-to-order transition. We report here the first experimental determination of the conformational entropy change for both binding partners in an IDP binding interaction and find that the total change even exceeds in magnitude the binding enthalpy and is comparable to the contribution from the hydrophobic effect, demonstrating its importance in the binding energetics. Furthermore, we show that the conformational entropy change for TAZ1 is also instrumental in maintaining a biologically meaningful binding affinity. Strikingly, a spatial clustering of very high amplitude motions and a cluster of more rigid sites in the complex exist, which through computational studies we found to overlap with regions that experience energetic frustration and are less frustrated, respectively. Thus, the residual dynamics in the bound state could be necessary for faster dissociation, which is important for proteins that interact with multiple binding partners.
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Affiliation(s)
- Ida Lindström
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Jakob Dogan
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
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203
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Li XH, Chavali PL, Pancsa R, Chavali S, Babu MM. Function and Regulation of Phase-Separated Biological Condensates. Biochemistry 2018; 57:2452-2461. [PMID: 29392932 DOI: 10.1021/acs.biochem.7b01228] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Achieving functional specificity while minimizing cost to fitness is a key constraint during evolution. Formation of biological condensates by liquid-liquid phase separation (LLPS) appears to serve as an important regulatory mechanism to generate moderate specificity in molecular recognition while maintaining a reasonable cost for fitness in terms of design complexity. Formation of biological condensates serves as a unique mechanism of molecular recognition achieving some level of specificity without a huge cost to fitness. Rapid formation of biological condensates in vivo induced by specific cellular or environmental triggers has been shown to be an important mechanism for increasing cellular fitness. Here we discuss the functions and regulation of biological condensates, especially those formed by LLPS, involving interactions between proteins and nucleic acids. These condensates are spatially isolated within the cytosol or nucleus and can facilitate specific biochemical functions under conditions such as stress. The misregulation of biological condensates resulting in nondynamic aggregates has been implicated in a number of diseases. Understanding the functional importance of biological condensates and their regulation opens doors for development of therapies targeting dysfunctional biological condensates, as well as spatiotemporal engineering of functions in cells.
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Affiliation(s)
- Xiao-Han Li
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge , U.K
| | - Pavithra L Chavali
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge , U.K
| | - Rita Pancsa
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge , U.K
| | - Sreenivas Chavali
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge , U.K
| | - M Madan Babu
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge , U.K
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204
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Dzuricky M, Roberts S, Chilkoti A. Convergence of Artificial Protein Polymers and Intrinsically Disordered Proteins. Biochemistry 2018; 57:2405-2414. [PMID: 29683665 DOI: 10.1021/acs.biochem.8b00056] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A flurry of research in recent years has revealed the molecular origins of many membraneless organelles to be the liquid phase separation of intrinsically disordered proteins (IDPs). Consequently, protein disorder has emerged as an important driver of intracellular compartmentalization by providing specialized microenvironments chemically distinct from the surrounding medium. Though the importance of protein disorder and its relationship to intracellular phase behavior are clear, a detailed understanding of how such phase behavior can be predicted and controlled remains elusive. While research in IDPs has largely focused on the implications of structural disorder on cellular function and disease, another field, that of artificial protein polymers, has focused on the de novo design of protein polymers with controllable material properties. A subset of these polymers, specifically those derived from structural proteins such as elastin and resilin, are also disordered sequences that undergo liquid-liquid phase separation. This phase separation has been used in a variety of biomedical applications, and researchers studying these polymers have developed methods to precisely characterize and tune their phase behavior. Despite their disparate origins, both fields are complementary as they study the phase behavior of intrinsically disordered polypeptides. This Perspective hopes to stimulate collaborative efforts by highlighting the similarities between these two fields and by providing examples of how such collaboration could be mutually beneficial.
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Affiliation(s)
- Michael Dzuricky
- Department of Biomedical Engineering , Duke University , Durham , North Carolina 27708-0281 , United States
| | - Stefan Roberts
- Department of Biomedical Engineering , Duke University , Durham , North Carolina 27708-0281 , United States
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering , Duke University , Durham , North Carolina 27708-0281 , United States
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205
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Prates ET, Guan X, Li Y, Wang X, Chaffey PK, Skaf MS, Crowley MF, Tan Z, Beckham GT. The impact of O-glycan chemistry on the stability of intrinsically disordered proteins. Chem Sci 2018; 9:3710-3715. [PMID: 29780502 PMCID: PMC5939190 DOI: 10.1039/c7sc05016j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 03/19/2018] [Indexed: 01/14/2023] Open
Abstract
Protein glycosylation is a diverse post-translational modification that serves myriad biological functions. O-linked glycans in particular vary widely in extent and chemistry in eukaryotes, with secreted proteins from fungi and yeast commonly exhibiting O-mannosylation in intrinsically disordered regions of proteins, likely for proteolysis protection, among other functions. However, it is not well understood why mannose is often the preferred glycan, and more generally, if the neighboring protein sequence and glycan have coevolved to protect against proteolysis in glycosylated intrinsically disordered proteins (IDPs). Here, we synthesized variants of a model IDP, specifically a natively O-mannosylated linker from a fungal enzyme, with α-O-linked mannose, glucose, and galactose moieties, along with a non-glycosylated linker. Upon exposure to thermolysin, O-mannosylation, by far, provides the highest extent of proteolysis protection. To explain this observation, extensive molecular dynamics simulations were conducted, revealing that the axial configuration of the C2-hydroxyl group (2-OH) of α-mannose adjacent to the glycan-peptide bond strongly influences the conformational features of the linker. Specifically, α-mannose restricts the torsions of the IDP main chain more than other glycans whose equatorial 2-OH groups exhibit interactions that favor perpendicular glycan-protein backbone orientation. We suggest that IDP stiffening due to O-mannosylation impairs protease action, with contributions from protein-glycan interactions, protein flexibility, and protein stability. Our results further imply that resistance to proteolysis is an important driving force for evolutionary selection of α-mannose in eukaryotic IDPs, and more broadly, that glycan motifs for proteolysis protection likely coevolve with the protein sequence to which they attach.
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Affiliation(s)
- Erica T Prates
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80403 , USA .
- Institute of Chemistry , Center for Computational Engineering and Sciences , University of Campinas , 13084-862 , SP , Brazil
| | - Xiaoyang Guan
- Department of Chemistry and Biochemistry and BioFrontiers Institute , University of Colorado , Boulder , CO 80303 , USA .
| | - Yaohao Li
- Department of Chemistry and Biochemistry and BioFrontiers Institute , University of Colorado , Boulder , CO 80303 , USA .
| | - Xinfeng Wang
- Department of Chemistry and Biochemistry and BioFrontiers Institute , University of Colorado , Boulder , CO 80303 , USA .
| | - Patrick K Chaffey
- Department of Chemistry and Biochemistry and BioFrontiers Institute , University of Colorado , Boulder , CO 80303 , USA .
| | - Munir S Skaf
- Institute of Chemistry , Center for Computational Engineering and Sciences , University of Campinas , 13084-862 , SP , Brazil
| | - Michael F Crowley
- Biosciences Center , National Renewable Energy Laboratory , Golden , CO 80403 , USA .
| | - Zhongping Tan
- Department of Chemistry and Biochemistry and BioFrontiers Institute , University of Colorado , Boulder , CO 80303 , USA .
| | - Gregg T Beckham
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80403 , USA .
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206
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Perez-Pepe M, Fernández-Alvarez AJ, Boccaccio GL. Life and Work of Stress Granules and Processing Bodies: New Insights into Their Formation and Function. Biochemistry 2018; 57:2488-2498. [PMID: 29595960 DOI: 10.1021/acs.biochem.8b00025] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The dynamic formation of stress granules (SGs), processing bodies (PBs), and related RNA organelles regulates diverse cellular processes, including the coordination of functionally connected messengers, the translational regulation at the synapse, and the control of viruses and retrotransposons. Recent studies have shown that pyruvate kinase and other enzymes localize in SGs and PBs, where they become protected from stress insults. These observations may have implications for enzyme regulation and metabolic control exerted by RNA-based organelles. The formation of these cellular bodies is governed by liquid-liquid phase separation (LLPS) processes, and it needs to be strictly controlled to prevent pathogenic aggregation. The intracellular concentration of key metabolites, such as ATP and sterol derivatives, may influence protein solubility, thus affecting the dynamics of liquid organelles. LLPS in vitro depends on the thermal diffusion of macromolecules, which is limited inside cells, where the condensation and dissolution of membrane-less organelles are helped by energy-driven processes. The active transport by the retrograde motor dynein helps SG assembly, whereas the anterograde motor kinesin mediates SG dissolution; a tug of war between these two molecular motors allows transient SG formation. There is evidence that the efficiency of dynein-mediated transport increases with the number of motor molecules associated with the cargo. The dynein-dependent transport may be influenced by cargo size as larger cargos can load a larger number of motors. We propose a model based on this emergent property of dynein motors, which would be collectively stronger during SG condensation and weaker during SG breakdown, thus allowing kinesin-mediated dispersion.
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Affiliation(s)
- Marcelo Perez-Pepe
- Instituto Leloir and Instituto de Investigaciones Bioquı́micas de Buenos Aires (IIBBA)-CONICET , Buenos Aires , Argentina
| | - Ana J Fernández-Alvarez
- Instituto Leloir and Instituto de Investigaciones Bioquı́micas de Buenos Aires (IIBBA)-CONICET , Buenos Aires , Argentina
| | - Graciela L Boccaccio
- Instituto Leloir and Instituto de Investigaciones Bioquı́micas de Buenos Aires (IIBBA)-CONICET , Buenos Aires , Argentina
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207
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Lou F, Yang J, Wu S, Perrett S. A co-expression strategy to achieve labeling of individual subunits within a dimeric protein for single molecule analysis. Chem Commun (Camb) 2018. [PMID: 28650509 DOI: 10.1039/c7cc03032k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A generic co-expression strategy for site-specific incorporation of a single donor-acceptor dye pair into any position in a dimeric protein, allowing single molecule FRET study of proteins previously inaccessible to this technique, such as the intrinsically disordered prion N-domain of Ure2 in the context of its globular dimeric C-domain.
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Affiliation(s)
- Fei Lou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China. and University of the Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Jie Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China. and University of the Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Si Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China. and University of the Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Sarah Perrett
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China. and University of the Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
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208
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Niesteruk A, Hutchison M, Sreeramulu S, Jonker HRA, Richter C, Abele R, Bock C, Schwalbe H. Structural characterization of the intrinsically disordered domain of Mycobacterium tuberculosis protein tyrosine kinase A. FEBS Lett 2018; 592:1233-1245. [PMID: 29494752 DOI: 10.1002/1873-3468.13022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 02/22/2018] [Indexed: 11/10/2022]
Abstract
Although intrinsically disordered proteins or protein domains (IDPs or IDD) are less abundant in bacteria than in eukaryotes, their presence in pathogenic bacterial proteins is important for protein-protein interactions. The protein tyrosine kinase A (PtkA) from Mycobacterium tuberculosis possesses an 80-residue disordered region (IDDPtkA ) of unknown function, located N-terminally to the well-folded kinase core domain. Here, we characterize the conformation of IDDPtkA under varying biophysical conditions and phosphorylation using NMR-spectroscopy. Our results confirm that the N-terminal domain of PtkA exists as an IDD at physiological pH. Furthermore, phosphorylation of IDDPtkA increases the activity of PtkA. Our findings will complement future approaches in understanding molecular mechanisms of key proteins in pathogenic virulence.
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Affiliation(s)
- Anna Niesteruk
- Goethe-University Frankfurt am Main, Institute for Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Frankfurt am Main, Germany
| | - Marie Hutchison
- Goethe-University Frankfurt am Main, Institute for Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Frankfurt am Main, Germany
| | - Sridhar Sreeramulu
- Goethe-University Frankfurt am Main, Institute for Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Frankfurt am Main, Germany
| | - Hendrik R A Jonker
- Goethe-University Frankfurt am Main, Institute for Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Frankfurt am Main, Germany
| | - Christian Richter
- Goethe-University Frankfurt am Main, Institute for Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Frankfurt am Main, Germany
| | - Rupert Abele
- Goethe-University Frankfurt am Main, Institute of Biochemistry, Biocenter, Frankfurt am Main, Germany
| | - Christoph Bock
- Goethe-University Frankfurt am Main, Institute of Biochemistry, Biocenter, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Goethe-University Frankfurt am Main, Institute for Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Frankfurt am Main, Germany
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209
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Henriques J, Arleth L, Lindorff-Larsen K, Skepö M. On the Calculation of SAXS Profiles of Folded and Intrinsically Disordered Proteins from Computer Simulations. J Mol Biol 2018; 430:2521-2539. [PMID: 29548755 DOI: 10.1016/j.jmb.2018.03.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/02/2018] [Accepted: 03/02/2018] [Indexed: 11/15/2022]
Abstract
Solution techniques such as small-angle X-ray scattering (SAXS) play a central role in structural studies of intrinsically disordered proteins (IDPs); yet, due to low resolution, it is generally necessary to combine SAXS with additional experimental sources of data and to use molecular simulations. Computational methods for the calculation of theoretical SAXS intensity profiles can be separated into two groups, depending on whether the solvent is modeled implicitly as continuous electron density or considered explicitly. The former offers reduced computational cost but requires the definition of a number of free parameters to account for, for example, the excess density of the solvation layer. Overfitting can thus be an issue, particularly when the structural ensemble is unknown. Here, we investigate and show how small variations of the contrast of the hydration shell, δρ, severely affect the outcome, analysis and interpretation of computed SAXS profiles for folded and disordered proteins. For both the folded and disordered proteins studied here, using a default δρ may, in some cases, result in the calculation of non-representative SAXS profiles, leading to an overestimation of their size and a misinterpretation of their structural nature. The solvation layer of the different IDP simulations also impacts their size estimates differently, depending on the protein force field used. The same is not true for the folded protein simulations, suggesting differences in the solvation of the two classes of proteins, and indicating that different force fields optimized for IDPs may cause expansion of the polypeptide chain through different physical mechanisms.
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Affiliation(s)
- João Henriques
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, Kemicentrum, PO Box 124, S-221 00 Lund, Sweden; Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
| | - Lise Arleth
- Structural Biophysics, Section for Neutron and X-ray Science, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark.
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
| | - Marie Skepö
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, Kemicentrum, PO Box 124, S-221 00 Lund, Sweden.
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210
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Jana AK, Batkulwar KB, Kulkarni MJ, Sengupta N. Glycation induces conformational changes in the amyloid-β peptide and enhances its aggregation propensity: molecular insights. Phys Chem Chem Phys 2018; 18:31446-31458. [PMID: 27827482 DOI: 10.1039/c6cp05041g] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The cytotoxicity of the amyloid beta (Aβ) peptide, implicated in the pathogenesis of Alzheimer's disease (AD), can be enhanced by its post-translational glycation, a series of non-enzymatic reactions with reducing sugars and reactive dicarbonyls. However, little is known about the underlying mechanisms that potentially enhance the cytotoxicity of the advanced glycation modified Aβ. In this work, fully atomistic molecular dynamics (MD) simulations are exploited to obtain direct molecular insights into the process of early Aβ self-assembly in the presence and absence of glycated lysine residues. Analyses of data exceeding cumulative timescales of 1 microsecond for each system reveal that glycation results in a stronger enthalpy of association between Aβ monomers and lower conformational entropy, in addition to a sharp overall increase in the beta-sheet content. Further analyses reveal that the enhanced interactions originate, in large part, due to markedly stronger, as well as new, inter-monomer salt bridging propensities in the glycated variety. Interestingly, these conformational and energetic effects are broadly reflected in preformed protofibrillar forms of Aβ small oligomers modified with glycation. Our combined results imply that glycation consolidates Aβ self-assembly regardless of its point of occurrence in the pathway. They provide a basis for further mechanistic studies and therapeutic endeavors that could potentially result in novel ways of combating AGE related AD progression.
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Affiliation(s)
- Asis K Jana
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India and Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Kedar B Batkulwar
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India and Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India.
| | - Mahesh J Kulkarni
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India and Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India.
| | - Neelanjana Sengupta
- Dept. of Biological Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741 246, W. Bengal, India.
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211
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Mattapally S, Singh M, Murthy KS, Asthana S, Banerjee SK. Computational modeling suggests impaired interactions between NKX2.5 and GATA4 in individuals carrying a novel pathogenic D16N NKX2.5 mutation. Oncotarget 2018; 9:13713-13732. [PMID: 29568389 PMCID: PMC5862610 DOI: 10.18632/oncotarget.24459] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/24/2018] [Indexed: 12/31/2022] Open
Abstract
NKX2.5, a homeobox containing gene, plays an important role in embryonic heart development and associated mutations are linked with various cardiac abnormalities. We sequenced the NKX2.5 gene in 100 congenital heart disease (CHD) patients and 200 controls. Our analysis revealed a total of 7 mutations, 3 in intronic region, 3 in coding region and 1 in 3’ UTR. Of the above mutations, one mutation was found to be associated with tetralogy of fallot (TOF) and two (rs2277923 and a novel mutation, D16N) were strongly associated with VSD. A novel missense mutation, D16N (p-value =0.009744), located in the tinman (TN) region and associated with ventricular septal defect (VSD), is the most significant findings of this study. Computational analysis revealed that D16N mutation is pathogenic in nature. Through the molecular modeling, docking and molecular dynamics simulation studies, we have identified the location of mutant D16N in NKX2.5 and its interaction map with other partners at the atomic level. We found NKX2.5-GATA4 complex is stable, however, in case of mutant we observed significant conformational changes and loss of key polar interactions, which might be a cause of the pathogenic behavior. This study underscores the structural basis of D16N pathogenic mutation in the regulation of NKX2.5 and how this mutation renders the structural-functional divergence that possibly leading towards the diseased state.
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Affiliation(s)
- Saidulu Mattapally
- Division of Medicinal Chemistry and Pharmacology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India
| | - Mrityunjay Singh
- Drug Discovery Research Center (DDRC), Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana 121001, India
| | | | - Shailendra Asthana
- Drug Discovery Research Center (DDRC), Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana 121001, India
| | - Sanjay K Banerjee
- Division of Medicinal Chemistry and Pharmacology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India.,Drug Discovery Research Center (DDRC), Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana 121001, India
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212
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Tolchard J, Walpole SJ, Miles AJ, Maytum R, Eaglen LA, Hackstadt T, Wallace BA, Blumenschein TMA. The intrinsically disordered Tarp protein from chlamydia binds actin with a partially preformed helix. Sci Rep 2018; 8:1960. [PMID: 29386631 PMCID: PMC5792643 DOI: 10.1038/s41598-018-20290-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/16/2018] [Indexed: 12/02/2022] Open
Abstract
Tarp (translocated actin recruiting phosphoprotein) is an effector protein common to all chlamydial species that functions to remodel the host-actin cytoskeleton during the initial stage of infection. In C. trachomatis, direct binding to actin monomers has been broadly mapped to a 100-residue region (726-825) which is predicted to be predominantly disordered, with the exception of a ~10-residue α-helical patch homologous to other WH2 actin-binding motifs. Biophysical investigations demonstrate that a Tarp726-825 construct behaves as a typical intrinsically disordered protein; within it, NMR relaxation measurements and chemical shift analysis identify the ten residue WH2-homologous region to exhibit partial α-helix formation. Isothermal titration calorimetry experiments on the same construct in the presence of monomeric G-actin show a well defined binding event with a 1:1 stoichiometry and Kd of 102 nM, whilst synchrotron radiation circular dichroism spectroscopy suggests the binding is concomitant with an increase in helical secondary structure. Furthermore, NMR experiments in the presence of G-actin indicate this interaction affects the proposed WH2-like α-helical region, supporting results from in silico docking calculations which suggest that, when folded, this α-helix binds within the actin hydrophobic cleft as seen for other actin-associated proteins.
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Affiliation(s)
- James Tolchard
- Center for Molecular and Structural Biology, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Samuel J Walpole
- Center for Molecular and Structural Biology, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Andrew J Miles
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1E 7HX, UK
| | - Robin Maytum
- School of Life Sciences, University of Bedfordshire, Park Square, Luton, LU1 3JU, UK
| | - Lawrence A Eaglen
- Center for Molecular and Structural Biology, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Ted Hackstadt
- Host-parasite Interactions Section, Laboratory of Intracellular Parasites, NIAID, NIH, Rocky Mountain Laboratories, Hamilton, MT, 59840, USA
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1E 7HX, UK
| | - Tharin M A Blumenschein
- Center for Molecular and Structural Biology, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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213
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Shigemitsu Y, Hiroaki H. Common molecular pathogenesis of disease-related intrinsically disordered proteins revealed by NMR analysis. J Biochem 2018; 163:11-18. [PMID: 28992347 DOI: 10.1093/jb/mvx056] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 06/17/2017] [Indexed: 01/23/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) are either completely unstructured or contain large disordered regions in their native state; they have drawn much attention in the field of molecular pathology. Some of them substantially tend to form protein self-assemblies, such as toxic or non-toxic aggregates and fibrils, and have been postulated to relate to diseases. These disease-related IDPs include Aβ(1-42) [Alzheimer's disease (AD)], Tau (AD and tauopathy), α-synuclein (Parkinson's disease) and p53 (cancer). Several studies suggest that these aggregation and/or fibril formation processes are often initiated by transient conformational changes of the IDPs prior to protein self-assembly. Interestingly, the pathological molecular processes of these IDPs share multiple common features with those of protein misfolding diseases, such as transmissible spongiform encephalopathy (PrPsc) and AL-amyloidosis (VL-domain of γ-immunoglobulin). This review provides an overview of solution NMR techniques that can help analyse the early and transient events of conformational equilibrium of IDPs and folded proteins.
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Affiliation(s)
- Yoshiki Shigemitsu
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Aichi 464-8601, Japan
| | - Hidekazu Hiroaki
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Aichi 464-8601, Japan
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214
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Zhou HX, Pang X. Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation. Chem Rev 2018; 118:1691-1741. [PMID: 29319301 DOI: 10.1021/acs.chemrev.7b00305] [Citation(s) in RCA: 454] [Impact Index Per Article: 75.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less specific electrostatic interactions, impart important properties to proteins. Modulation of the charges on the amino acids, e.g., by pH and by phosphorylation and dephosphorylation, have significant effects such as protein denaturation and switch-like response of signal transduction networks. This review aims to present a unifying theme among the various effects of protein charges and polar groups. Simple models will be used to illustrate basic ideas about electrostatic interactions in proteins, and these ideas in turn will be used to elucidate the roles of electrostatic interactions in protein structure, folding, binding, condensation, and related biological functions. In particular, we will examine how charged side chains are spatially distributed in various types of proteins and how electrostatic interactions affect thermodynamic and kinetic properties of proteins. Our hope is to capture both important historical developments and recent experimental and theoretical advances in quantifying electrostatic contributions of proteins.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Chemistry and Department of Physics, University of Illinois at Chicago , Chicago, Illinois 60607, United States.,Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
| | - Xiaodong Pang
- Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
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215
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IDPs in macromolecular complexes: the roles of multivalent interactions in diverse assemblies. Curr Opin Struct Biol 2018; 49:36-43. [PMID: 29306779 DOI: 10.1016/j.sbi.2017.12.007] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/18/2017] [Accepted: 12/19/2017] [Indexed: 01/21/2023]
Abstract
Intrinsically disordered proteins (IDPs) have critical roles in a diverse array of cellular functions. Of relevance here is that they are components of macromolecular complexes, where their conformational flexibility helps mediate interactions with binding partners. IDPs often interact with their binding partners through short sequence motifs, commonly repeated within the disordered regions. As such, multivalent interactions are common for IDPs and their binding partners within macromolecular complexes. Here we discuss the importance of IDP multivalency in three very different macromolecular assemblies: biomolecular condensates, the nuclear pore, and the cytoskeleton.
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216
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Jaraíz-Rodríguez M, González-Sánchez A, García-Vicente L, Medina JM, Tabernero A. Biotinylated Cell-penetrating Peptides to Study Intracellular Protein-protein Interactions. J Vis Exp 2017:56457. [PMID: 29286477 PMCID: PMC5755618 DOI: 10.3791/56457] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Here we present a protocol to study intracellular protein-protein interactions that is based on the widely used biotin-avidin pull-down system. The modification presented includes the combination of this technique with cell-penetrating sequences. We propose to design cell-penetrating baits that can be incubated with living cells instead of cell lysates and therefore the interactions found will reflect those that occur within the intracellular context. Connexin43 (Cx43), a protein that forms gap junction channels and hemichannels is down-regulated in high-grade gliomas. The Cx43 region comprising amino acids 266-283 is responsible for the inhibition of the oncogenic activity of c-Src in glioma cells. Here we use TAT as the cell-penetrating sequence, biotin as the pull-down tag and the region of Cx43 comprised between amino acids 266-283 as the target to find intracellular interactions in the hard-to-transfect human glioma stem cells. One of the limitations of the proposed method is that the molecule used as bait could fail to fold properly and, consequently, the interactions found could not be associated with the effect. However, this method can be especially interesting for the interactions involved in signal transduction pathways because they are usually carried out by intrinsically disordered regions and, therefore, they do not require an ordered folding. In addition, one of the advantages of the proposed method is that the relevance of each residue on the interaction can be easily studied. This is a modular system; therefore, other cell-penetrating sequences, other tags, and other intracellular targets can be employed. Finally, the scope of this protocol is far beyond protein-protein interaction because this system can be applied to other bioactive cargoes such as RNA sequences, nanoparticles, viruses or any molecule that can be transduced with cell-penetrating sequences and fused to pull-down tags to study their intracellular mechanism of action.
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Affiliation(s)
- Myriam Jaraíz-Rodríguez
- Instituto de Neurociencias de Castilla y León (INCYL), Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca
| | - Ana González-Sánchez
- Instituto de Neurociencias de Castilla y León (INCYL), Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca; Centre for Cancer Research & Cell Biology (CCRCB), School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast
| | - Laura García-Vicente
- Instituto de Neurociencias de Castilla y León (INCYL), Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca
| | - Jose M Medina
- Instituto de Neurociencias de Castilla y León (INCYL), Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca
| | - Arantxa Tabernero
- Instituto de Neurociencias de Castilla y León (INCYL), Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca;
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217
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Liu X, Chen J. HyRes: a coarse-grained model for multi-scale enhanced sampling of disordered protein conformations. Phys Chem Chem Phys 2017; 19:32421-32432. [PMID: 29186229 PMCID: PMC5729119 DOI: 10.1039/c7cp06736d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Efficient coarse-grained (CG) models can be coupled with atomistic force fields to accelerate the sampling of atomistic energy landscapes in the multi-scale enhanced sampling (MSES) framework. This approach may be particularly suitable for generating atomistic conformational ensembles of intrinsically disordered proteins (IDPs). While MSES is relatively robust to inherent CG artifacts, achieving optimal sampling efficiency requires CG modeling to generate the local and long-range fluctuations that are largely consistent with those at the atomistic level. Here, we describe a new hybrid resolution CG model (HyRes) for MSES simulations of disordered protein states, which is specifically designed to provide semi-quantitative secondary structure propensities together with a qualitative description of long-range nonspecific interactions. The HyRes model contains an atomistic description of the backbone with intermediate resolution side chains. The secondary structure propensities are tuned by adjusting the backbone hydrogen-bonding strength and the ϕ/ψ torsion profile. The sizes and covalent geometries of the side chains are parameterized to reproduce distributions derived from atomistic simulations. Lennard-Jones parameters for sidechain beads are assigned to reproduce statistical potentials derived from the protein structural database, and then globally parameterized with nonspecific electrostatic interactions to reproduce the free energy profiles of pair wise interactions and the key conformational properties of model peptides. Application of HyRes to MSES simulations of small IDPs suggests that it is capable of driving faster structural transitions at the atomistic level and increasing the convergence rate compared to the Cα-only Gō-like models previously utilized. With further optimization, we believe that the new CG model could greatly improve the efficiency of MSES simulations of the larger and more complex IDPs frequently involved in cellular signalling and regulation.
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Affiliation(s)
- Xiaorong Liu
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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218
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Cheong HSJ, VanBerkum MFA. Long disordered regions of the C-terminal domain of Abelson tyrosine kinase have specific and additive functions in regulation and axon localization. PLoS One 2017; 12:e0189338. [PMID: 29232713 PMCID: PMC5726718 DOI: 10.1371/journal.pone.0189338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/22/2017] [Indexed: 01/28/2023] Open
Abstract
Abelson tyrosine kinase (Abl) is a key regulator of actin-related morphogenetic processes including axon guidance, where it functions downstream of several guidance receptors. While the long C-terminal domain (CTD) of Abl is required for function, its role is poorly understood. Here, a battery of mutants of Drosophila Abl was created that systematically deleted large segments of the CTD from Abl or added them back to the N-terminus alone. The functionality of these Abl transgenes was assessed through rescue of axon guidance defects and adult lethality in Abl loss-of-function, as well as through gain-of-function effects in sensitized slit or frazzled backgrounds that perturb midline guidance in the Drosophila embryonic nerve cord. Two regions of the CTD play important and distinct roles, but additive effects for other regions were also detected. The first quarter of the CTD, including a conserved PxxP motif and its surrounding sequence, regulates Abl function while the third quarter localizes Abl to axons. These regions feature long stretches of intrinsically disordered sequence typically found in hub proteins and are associated with diverse protein-protein interactions. Thus, the CTD of Abl appears to use these disordered regions to establish a variety of different signaling complexes required during formation of axon tracts.
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Affiliation(s)
- Han S J Cheong
- Department of Biological Sciences, Wayne State University, Detroit, United States of America
| | - Mark F A VanBerkum
- Department of Biological Sciences, Wayne State University, Detroit, United States of America
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219
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Banerjee S, Feyertag F, Alvarez-Ponce D. Intrinsic protein disorder reduces small-scale gene duplicability. DNA Res 2017; 24:435-444. [PMID: 28430886 PMCID: PMC5737077 DOI: 10.1093/dnares/dsx015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/28/2017] [Indexed: 01/23/2023] Open
Abstract
Whereas the rate of gene duplication is relatively high, only certain duplications survive the filter of natural selection and can contribute to genome evolution. However, the reasons why certain genes can be retained after duplication whereas others cannot remain largely unknown. Many proteins contain intrinsically disordered regions (IDRs), whose structures fluctuate between alternative conformational states. Due to their high flexibility, IDRs often enable protein–protein interactions and are the target of post-translational modifications. Intrinsically disordered proteins (IDPs) have characteristics that might either stimulate or hamper the retention of their encoding genes after duplication. On the one hand, IDRs may enable functional diversification, thus promoting duplicate retention. On the other hand, increased IDP availability is expected to result in deleterious unspecific interactions. Here, we interrogate the proteomes of human, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Arabidopsis thaliana and Escherichia coli, in order to ascertain the impact of protein intrinsic disorder on gene duplicability. We show that, in general, proteins encoded by duplicated genes tend to be less disordered than those encoded by singletons. The only exception is proteins encoded by ohnologs, which tend to be more disordered than those encoded by singletons or genes resulting from small-scale duplications. Our results indicate that duplication of genes encoding IDPs outside the context of whole-genome duplication (WGD) is often deleterious, but that IDRs facilitate retention of duplicates in the context of WGD. We discuss the potential evolutionary implications of our results.
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Affiliation(s)
- Sanghita Banerjee
- Department of Biology, University of Nevada, Reno, NV 89557, USA.,Machine Intelligence Unit, Indian Statistical Institute, Kolkata 700108, India
| | - Felix Feyertag
- Department of Biology, University of Nevada, Reno, NV 89557, USA
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220
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Weber OC, Uversky VN. How accurate are your simulations? Effects of confined aqueous volume and AMBER FF99SB and CHARMM22/CMAP force field parameters on structural ensembles of intrinsically disordered proteins: Amyloid-β 42 in water. INTRINSICALLY DISORDERED PROTEINS 2017; 5:e1377813. [PMID: 30250773 DOI: 10.1080/21690707.2017.1377813] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/04/2017] [Accepted: 09/06/2017] [Indexed: 12/14/2022]
Abstract
Amyloid-β42 (Aβ42) is an intrinsically disordered peptide intimately related to the pathogenesis of several neurodegenerative diseases. Molecular dynamics (MD) simulations are extensively utilized in the characterization of the structures and conformational dynamics of intrinsically disordered proteins (IDPs) including Aβ42, with AMBER and CHARMM parameters being commonly used in these studies. Recently, comparison of the effects of force field parameters on the Aβ42 structures has started to gain significant attention. In this study, the structures of Aβ42 are simulated using AMBER FF99SB and CHARMM22/CMAP parameters via replica exchange MD simulations utilizing a widely used clustering algorithm. These analyses show that the structural properties (extent and positioning of the elements of secondary and tertiary structure), radius of gyration values, number and position of salt bridges are extremely dependent on the chosen force field parameters notably with the usage of clustering algorithms. For example, predicted secondary structure elements, which are of the great importance for better understanding of the molecular mechanisms of neurodegenerative diseases, deviate enormously in models generated using currently available force field parameters for proteins. Based on the derived models, chemical shift values are calculated and compared to the experimentally determined data. This comparison revealed that although both force field parameters yield results in agreement with experiments, the obtained structural properties were rather different using a clustering algorithm. In other words, these results show that the predicted structures depend heavily on the force field parameters. Importantly, since none of the force field parameters currently utilized in MD studies were developed specifically taking into account the disordered nature of IDPs, these findings clearly indicate that new force field parameters have to be developed for IDPs considering their rapid flexibility and dynamics with high amplitude. Furthermore, molecular simulations of IDPs are typically conducted using one water volume. We show that the confined aqueous volume impacts the predicted structural properties of Aβ42 in water. Although up to date, confined aqueous volume effects have been ignored in the MD simulations of IDPs in water, our data indicate that these effects have to be taken into account in predicting the structural and thermodynamic properties of disordered proteins in solution.
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Affiliation(s)
- Orkid Coskuner Weber
- Department of Chemistry and Neurosciences Institute, The University of Texas at San Antonio, San Antonio, TX, USA.,Institut für Physikalische Chemie, Universität zu Köln, Köln, Germany.,Molecular Biotechnology Division, Turkisch-Deutsche Universität, Istanbul Turkey
| | - Vladimir N Uversky
- Department of Molecular Medicine, 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, Russia
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221
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Barker CS, Meshcheryakova IV, Kostyukova AS, Freddolino PL, Samatey FA. An intrinsically disordered linker controlling the formation and the stability of the bacterial flagellar hook. BMC Biol 2017; 15:97. [PMID: 29078764 PMCID: PMC5660449 DOI: 10.1186/s12915-017-0438-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/10/2017] [Indexed: 12/15/2022] Open
Abstract
Background In a macro-molecular complex, any minor change may prove detrimental. For a supra-molecular nano-machine like the bacterial flagellum, which consists of several distinct parts with specific characteristics, stability is important. During the rotation of the bacterial flagellar motor, which is located in the membrane, the flagella rotate at speeds between 200 and 2000 rpm, depending on the bacterial species. The hook substructure of the bacterial flagellum acts as a universal joint connecting the motor to the flagellar filament. We investigated the formation of the bacterial flagellar hook and its overall stability between the FlgE subunits that make up the hook and attempted to understand how this stability differs between bacteria. Results An intrinsically disordered segment plays an important role for overall hook stability and for its structural cohesion during motor rotation. The length of this linker segment depends on the species of bacteria; for Salmonella enterica and Campylobacter jejuni it is approximately 37 and 54 residues, respectively. Few residues of the linker are conserved and mutating the conserved residues of the linker yields non-flagellated cells. In the case of Campylobacter, which rotates its flagella at a speed much higher than that of Salmonella, shortening the linker leads to a rupture of the hook at its base, decreasing cell motility. Our experiments show that this segment is required for polymerization and stability of the hook, demonstrating a surprising role for a disordered region in one of the most finely tuned and closely studied macromolecular machines. Conclusions This study reveals a detailed functional characteristic of an intrinsically disordered segment in the hook protein. This segment evolved to fulfill a specific role in the formation of the hook, and it is at the core of the stability and flexibility of the hook. Its length is important in the case of bacteria with high-speed rotating flagella. Finding a way of disrupting this linker in Campylobacter might help in preventing infections. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0438-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Clive S Barker
- Trans-membrane Trafficking Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami, Okinawa, 904-0495, Japan
| | - Irina V Meshcheryakova
- Trans-membrane Trafficking Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami, Okinawa, 904-0495, Japan
| | - Alla S Kostyukova
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, USA
| | - Peter L Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Fadel A Samatey
- Trans-membrane Trafficking Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami, Okinawa, 904-0495, Japan.
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222
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Liu X, Jia Z, Chen J. Enhanced Sampling of Intrinsic Structural Heterogeneity of the BH3-Only Protein Binding Interface of Bcl-xL. J Phys Chem B 2017; 121:9160-9168. [PMID: 28903561 DOI: 10.1021/acs.jpcb.7b06768] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Antiapoptotic Bcl-xL plays central roles in regulating programed cell death. Partial unfolding of Bcl-xL has been observed at the interface upon specific binding to the pro-apoptotic BH3-only protein PUMA, which in turn disrupts the interaction of Bcl-xL with tumor suppressor p53 and promotes apoptosis. Previous analysis of existing Bcl-xL structures and atomistic molecular dynamics (MD) simulations have suggested that substantial intrinsic structure heterogeneity exists at the BH3-only protein binding interface of Bcl-xL to facilitate its conformational transitions upon binding. In this study, enhanced sampling is applied to further characterize the interfacial conformations of unbound Bcl-xL in explicit solvent. Extensive replica exchange with solute tempering (REST) simulations, with a total accumulated time of 16 μs, were able to cover much wider conformational spaces for the interfacial region of Bcl-xL. The resulting structural ensembles are much better converged, with local and long-range structural features that are highly consistent with existing NMR data. These simulations further demonstrate that the BH3-only protein binding interface of Bcl-xL is intrinsically disordered and samples many rapidly interconverting conformations. Intriguingly, all previously observed conformers are well represented in the unbound structure ensemble. Such intrinsic structural heterogeneity and flexibility may be critical for Bcl-xL to undergo partial unfolding induced by PUMA binding, and likely provide a robust basis that allows Bcl-xL to respond sensitively to binding of various ligands in cellular signaling and regulation.
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Affiliation(s)
- Xiaorong Liu
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst , Amherst, Massachusetts 01003, United States
| | - Zhiguang Jia
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst , Amherst, Massachusetts 01003, United States
| | - Jianhan Chen
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst , Amherst, Massachusetts 01003, United States
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223
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Kizilsavas G, Ledolter K, Kurzbach D. Hydrophobic Collapse of the Intrinsically Disordered Transcription Factor Myc Associated Factor X. Biochemistry 2017; 56:5365-5372. [DOI: 10.1021/acs.biochem.7b00679] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gönül Kizilsavas
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Karin Ledolter
- Department
for Structural and Computational Biology, Max F. Perutz Laboratories, University Vienna, Campus Vienna BioCenter 5, 1030 Vienna, Austria
| | - Dennis Kurzbach
- Département
de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules (LBM), Paris, France
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224
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Martini C, Bédard M, Lavigne P, Denault JB. Characterization of Hsp90 Co-Chaperone p23 Cleavage by Caspase-7 Uncovers a Peptidase–Substrate Interaction Involving Intrinsically Disordered Regions. Biochemistry 2017; 56:5099-5111. [DOI: 10.1021/acs.biochem.7b00298] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Cyrielle Martini
- Department
of Pharmacology-Physiology and ‡Department of Biochemistry, Institut
de Pharmacologie de Sherbrooke, Université de Sherbrooke, Faculty of Medicine and Health Sciences, 3001, 12th Avenue North, Sherbrooke, QC J1H 5N4, Canada
| | - Mikaël Bédard
- Department
of Pharmacology-Physiology and ‡Department of Biochemistry, Institut
de Pharmacologie de Sherbrooke, Université de Sherbrooke, Faculty of Medicine and Health Sciences, 3001, 12th Avenue North, Sherbrooke, QC J1H 5N4, Canada
| | - Pierre Lavigne
- Department
of Pharmacology-Physiology and ‡Department of Biochemistry, Institut
de Pharmacologie de Sherbrooke, Université de Sherbrooke, Faculty of Medicine and Health Sciences, 3001, 12th Avenue North, Sherbrooke, QC J1H 5N4, Canada
| | - Jean-Bernard Denault
- Department
of Pharmacology-Physiology and ‡Department of Biochemistry, Institut
de Pharmacologie de Sherbrooke, Université de Sherbrooke, Faculty of Medicine and Health Sciences, 3001, 12th Avenue North, Sherbrooke, QC J1H 5N4, Canada
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225
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Jones CL, Njomen E, Sjögren B, Dexheimer TS, Tepe JJ. Small Molecule Enhancement of 20S Proteasome Activity Targets Intrinsically Disordered Proteins. ACS Chem Biol 2017; 12:2240-2247. [PMID: 28719185 DOI: 10.1021/acschembio.7b00489] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 20S proteasome is the main protease for the degradation of oxidatively damaged and intrinsically disordered proteins. When accumulation of disordered or oxidatively damaged proteins exceeds proper clearance in neurons, imbalanced pathway signaling or aggregation occurs, which have been implicated in the pathogenesis of several neurological disorders. Screening of the NIH Clinical Collection and Prestwick libraries identified the neuroleptic agent chlorpromazine as a lead agent capable of enhancing 20S proteasome activity. Chemical manipulation of chlorpromazine abrogated its D2R receptor binding affinity while retaining its ability to enhance 20S mediated proteolysis at low micromolar concentrations. The resulting small molecule enhancers of 20S proteasome activity induced the degradation of intrinsically disordered proteins, α-synuclein, and tau but not structured proteins. These small molecule 20S agonists can serve as leads to explore the therapeutic potential of 20S activation or as new tools to provide insight into the yet unclear mechanics of 20S-gate regulation.
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Affiliation(s)
- Corey L. Jones
- Department
of Chemistry and ‡Department of Pharmacology and Toxicology, Michigan State University, East
Lansing, Michigan 48824, United States
| | - Evert Njomen
- Department
of Chemistry and ‡Department of Pharmacology and Toxicology, Michigan State University, East
Lansing, Michigan 48824, United States
| | - Benita Sjögren
- Department
of Chemistry and ‡Department of Pharmacology and Toxicology, Michigan State University, East
Lansing, Michigan 48824, United States
| | - Thomas S. Dexheimer
- Department
of Chemistry and ‡Department of Pharmacology and Toxicology, Michigan State University, East
Lansing, Michigan 48824, United States
| | - Jetze J. Tepe
- Department
of Chemistry and ‡Department of Pharmacology and Toxicology, Michigan State University, East
Lansing, Michigan 48824, United States
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226
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Sequence Specificity in the Entropy-Driven Binding of a Small Molecule and a Disordered Peptide. J Mol Biol 2017; 429:2772-2779. [DOI: 10.1016/j.jmb.2017.07.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 07/16/2017] [Accepted: 07/20/2017] [Indexed: 11/20/2022]
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227
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Heller GT, Aprile FA, Vendruscolo M. Methods of probing the interactions between small molecules and disordered proteins. Cell Mol Life Sci 2017; 74:3225-3243. [PMID: 28631009 PMCID: PMC5533867 DOI: 10.1007/s00018-017-2563-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/01/2017] [Indexed: 12/15/2022]
Abstract
It is generally recognized that a large fraction of the human proteome is made up of proteins that remain disordered in their native states. Despite the fact that such proteins play key biological roles and are involved in many major human diseases, they still represent challenging targets for drug discovery. A major bottleneck for the identification of compounds capable of interacting with these proteins and modulating their disease-promoting behaviour is the development of effective techniques to probe such interactions. The difficulties in carrying out binding measurements have resulted in a poor understanding of the mechanisms underlying these interactions. In order to facilitate further methodological advances, here we review the most commonly used techniques to probe three types of interactions involving small molecules: (1) those that disrupt functional interactions between disordered proteins; (2) those that inhibit the aberrant aggregation of disordered proteins, and (3) those that lead to binding disordered proteins in their monomeric states. In discussing these techniques, we also point out directions for future developments.
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Affiliation(s)
- Gabriella T Heller
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Francesco A Aprile
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
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228
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Pauwels K, Lebrun P, Tompa P. To be disordered or not to be disordered: is that still a question for proteins in the cell? Cell Mol Life Sci 2017; 74:3185-3204. [PMID: 28612216 PMCID: PMC11107661 DOI: 10.1007/s00018-017-2561-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 06/01/2017] [Indexed: 12/26/2022]
Abstract
There is ample evidence that many proteins or regions of proteins lack a well-defined folded structure under native-like conditions. These are called intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). Whether this intrinsic disorder is also their main structural characteristic in living cells has been a matter of intense debate. The structural analysis of IDPs became an important challenge also because of their involvement in a plethora of human diseases, which made IDPs attractive targets for therapeutic development. Therefore, biophysical approaches are increasingly being employed to probe the structural and dynamical state of proteins, not only in isolation in a test tube, but also in a complex biological environment and even within intact cells. Here, we survey direct and indirect evidence that structural disorder is in fact the physiological state of many proteins in the proteome. The paradigmatic case of α-synuclein is used to illustrate the controversial nature of this topic.
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Affiliation(s)
- Kris Pauwels
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Pierre Lebrun
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Peter Tompa
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium.
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium.
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.
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229
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Mercadante D, Wagner JA, Aramburu IV, Lemke EA, Gräter F. Sampling Long- versus Short-Range Interactions Defines the Ability of Force Fields To Reproduce the Dynamics of Intrinsically Disordered Proteins. J Chem Theory Comput 2017; 13:3964-3974. [DOI: 10.1021/acs.jctc.7b00143] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Davide Mercadante
- HITS—Heidelberg Institute for Theoretical Studies, 35 Schloß Wolfsbrunnenweg, 69118 Heidelberg, Germany
- IWR—Interdisciplinary
Center for Scientific Computing, Heidelberg University, Mathematikon,
Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Johannes A. Wagner
- HITS—Heidelberg Institute for Theoretical Studies, 35 Schloß Wolfsbrunnenweg, 69118 Heidelberg, Germany
| | - Iker V. Aramburu
- Structural
and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Edward A. Lemke
- Structural
and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Frauke Gräter
- HITS—Heidelberg Institute for Theoretical Studies, 35 Schloß Wolfsbrunnenweg, 69118 Heidelberg, Germany
- IWR—Interdisciplinary
Center for Scientific Computing, Heidelberg University, Mathematikon,
Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
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230
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Kosciolek T, Buchan DWA, Jones DT. Predictions of Backbone Dynamics in Intrinsically Disordered Proteins Using De Novo Fragment-Based Protein Structure Predictions. Sci Rep 2017; 7:6999. [PMID: 28765603 PMCID: PMC5539115 DOI: 10.1038/s41598-017-07156-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/23/2017] [Indexed: 11/08/2022] Open
Abstract
Intrinsically disordaered proteins (IDPs) are a prevalent phenomenon with over 30% of human proteins estimated to have long disordered regions. Computational methods are widely used to study IDPs, however, nearly all treat disorder in a binary fashion, not accounting for the structural heterogeneity present in disordered regions. Here, we present a new de novo method, FRAGFOLD-IDP, which addresses this problem. Using 200 protein structural ensembles derived from NMR, we show that FRAGFOLD-IDP achieves superior results compared to methods which can predict related data (NMR order parameter, or crystallographic B-factor). FRAGFOLD-IDP produces very good predictions for 33.5% of cases and helps to get a better insight into the dynamics of the disordered ensembles. The results also show it is not necessary to predict the correct fold of the protein to reliably predict per-residue fluctuations. It implies that disorder is a local property and it does not depend on the fold. Our results are orthogonal to DynaMine, the only other method significantly better than the naïve prediction. We therefore combine these two using a neural network. FRAGFOLD-IDP enables better insight into backbone dynamics in IDPs and opens exciting possibilities for the design of disordered ensembles, disorder-to-order transitions, or design for protein dynamics.
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Affiliation(s)
- Tomasz Kosciolek
- Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, United Kingdom
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Daniel W A Buchan
- Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - David T Jones
- Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, United Kingdom.
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231
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Bhowmik D, Bhardwaj N, Chatterji D. Influence of Flexible "ω" on the Activity of E. coli RNA Polymerase: A Thermodynamic Analysis. Biophys J 2017; 112:901-910. [PMID: 28297649 DOI: 10.1016/j.bpj.2017.01.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 01/12/2017] [Accepted: 01/23/2017] [Indexed: 12/15/2022] Open
Abstract
The Escherichia coli RNA polymerase (RNAP) is a multisubunit protein complex containing the smallest subunit, ω. Despite the evolutionary conservation of ω and its role in assembly of RNAP, E. coli mutants lacking rpoZ (codes for ω) are viable due to the association of RNAP with the global chaperone protein GroEL. With an aim to get better insight into the structure and functional role of ω, we isolated a dominant negative mutant of ω (ω6), which is predominantly α-helical, in contrast to largely unstructured native ω, and then studied its assembly with reconstituted core1 (α2ββ') by a biophysical approach. The mutant showed higher binding affinity compared to native ω. We observed that the interaction between core1 and ω6 is driven by highly negative enthalpy and a small but unfavorable negative entropy term. Extensive structural alteration in ω6 makes it more rigid, the plasticity of the interacting domain formed by ω6 and core1 is compromised, which may be responsible for the entropic cost. Such tight binding of the structured mutant (ω6) affects initiation of transcription. However, once preinitiated, the complex elongates the RNA chain efficiently. The initiation of transcription requires recognition of appropriate σ-factors by the core enzyme (core2: α2ββ'ω). We found that the altered core enzyme (α2ββ'ω6) with mutant ω showed a decrease in binding affinity to the σ-factors (σ70, σ32 and σ38) compared to that of the core enzyme containing native ω. In the absence of unstructured ω, the association of σ-factors to the core is less efficient, suggesting that the flexible native ω plays a direct role in σ-factor recruitment.
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Affiliation(s)
- Debipreeta Bhowmik
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Neerupma Bhardwaj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
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232
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The contribution of intrinsically disordered regions to protein function, cellular complexity, and human disease. Biochem Soc Trans 2017; 44:1185-1200. [PMID: 27911701 PMCID: PMC5095923 DOI: 10.1042/bst20160172] [Citation(s) in RCA: 259] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 12/23/2022]
Abstract
In the 1960s, Christian Anfinsen postulated that the unique three-dimensional structure of a protein is determined by its amino acid sequence. This work laid the foundation for the sequence–structure–function paradigm, which states that the sequence of a protein determines its structure, and structure determines function. However, a class of polypeptide segments called intrinsically disordered regions does not conform to this postulate. In this review, I will first describe established and emerging ideas about how disordered regions contribute to protein function. I will then discuss molecular principles by which regulatory mechanisms, such as alternative splicing and asymmetric localization of transcripts that encode disordered regions, can increase the functional versatility of proteins. Finally, I will discuss how disordered regions contribute to human disease and the emergence of cellular complexity during organismal evolution.
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233
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Moriarty GM, Olson MP, Atieh TB, Janowska MK, Khare SD, Baum J. A pH-dependent switch promotes β-synuclein fibril formation via glutamate residues. J Biol Chem 2017; 292:16368-16379. [PMID: 28710275 DOI: 10.1074/jbc.m117.780528] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 07/11/2017] [Indexed: 01/10/2023] Open
Abstract
α-Synuclein (αS) is the primary protein associated with Parkinson's disease, and it undergoes aggregation from its intrinsically disordered monomeric form to a cross-β fibrillar form. The closely related homolog β-synuclein (βS) is essentially fibril-resistant under cytoplasmic physiological conditions. Toxic gain-of-function by βS has been linked to dysfunction, but the aggregation behavior of βS under altered pH is not well-understood. In this work, we compare fibril formation of αS and βS at pH 7.3 and mildly acidic pH 5.8, and we demonstrate that pH serves as an on/off switch for βS fibrillation. Using αS/βS domain-swapped chimera constructs and single residue substitutions in βS, we localized the switch to acidic residues in the N-terminal and non-amyloid component domains of βS. Computational models of βS fibril structures indicate that key glutamate residues (Glu-31 and Glu-61) in these domains may be sites of pH-sensitive interactions, and variants E31A and E61A show dramatically altered pH sensitivity for fibril formation supporting the importance of these charged side chains in fibril formation of βS. Our results demonstrate that relatively small changes in pH, which occur frequently in the cytoplasm and in secretory pathways, may induce the formation of βS fibrils and suggest a complex role for βS in synuclein cellular homeostasis and Parkinson's disease.
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Affiliation(s)
- Gina M Moriarty
- From the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854
| | - Michael P Olson
- From the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854
| | - Tamr B Atieh
- From the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854
| | - Maria K Janowska
- From the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854
| | - Sagar D Khare
- From the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854
| | - Jean Baum
- From the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854
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234
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Eukaryotic transcription factors: paradigms of protein intrinsic disorder. Biochem J 2017; 474:2509-2532. [DOI: 10.1042/bcj20160631] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/19/2017] [Accepted: 05/05/2017] [Indexed: 12/17/2022]
Abstract
Gene-specific transcription factors (TFs) are key regulatory components of signaling pathways, controlling, for example, cell growth, development, and stress responses. Their biological functions are determined by their molecular structures, as exemplified by their structured DNA-binding domains targeting specific cis-acting elements in genes, and by the significant lack of fixed tertiary structure in their extensive intrinsically disordered regions. Recent research in protein intrinsic disorder (ID) has changed our understanding of transcriptional activation domains from ‘negative noodles’ to ID regions with function-related, short sequence motifs and molecular recognition features with structural propensities. This review focuses on molecular aspects of TFs, which represent paradigms of ID-related features. Through specific examples, we review how the ID-associated flexibility of TFs enables them to participate in large interactomes, how they use only a few hydrophobic residues, short sequence motifs, prestructured motifs, and coupled folding and binding for their interactions with co-activators, and how their accessibility to post-translational modification affects their interactions. It is furthermore emphasized how classic biochemical concepts like allostery, conformational selection, induced fit, and feedback regulation are undergoing a revival with the appreciation of ID. The review also describes the most recent advances based on computational simulations of ID-based interaction mechanisms and structural analysis of ID in the context of full-length TFs and suggests future directions for research in TF ID.
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235
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Abstract
Vertebrate CtIP, and its fission yeast (Ctp1), budding yeast (Sae2) and plant (Com1) orthologs have emerged as key regulatory molecules in cellular responses to DNA double strand breaks (DSBs). By modulating the nucleolytic 5'-3' resection activity of the Mre11/Rad50/Nbs1 (MRN) DSB repair processing and signaling complex, CtIP/Ctp1/Sae2/Com1 is integral to the channeling of DNA double strand breaks through DSB repair by homologous recombination (HR). Nearly two decades since its discovery, emerging new data are defining the molecular underpinnings for CtIP DSB repair regulatory activities. CtIP homologs are largely intrinsically unstructured proteins comprised of expanded regions of low complexity sequence, rather than defined folded domains typical of DNA damage metabolizing enzymes and nucleases. A compact structurally conserved N-terminus forms a functionally critical tetrameric helical dimer of dimers (THDD) region that bridges CtIP oligomers, and is flexibly appended to a conserved C-terminal Sae2-homology DNA binding and DSB repair pathway choice regulatory hub which influences nucleolytic activities of the MRN core nuclease complex. The emerging evidence from structural, biophysical, and biological studies converges on CtIP having functional roles in DSB repair that include: 1) dynamic DNA strand coordination through direct DNA binding and DNA bridging activities, 2) MRN nuclease complex cofactor functions that direct MRN endonucleolytic cleavage of protein-blocked DSB ends and 3) acting as a protein binding hub targeted by the cell cycle regulatory apparatus, which influences CtIP expression and activity via layers of post-translational modifications, protein-protein interactions and DNA binding.
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Affiliation(s)
- Sara N Andres
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, United States
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, United States.
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236
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Willows R, Navaratnam N, Lima A, Read J, Carling D. Effect of different γ-subunit isoforms on the regulation of AMPK. Biochem J 2017; 474:1741-1754. [PMID: 28302767 PMCID: PMC5423082 DOI: 10.1042/bcj20170046] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 12/04/2022]
Abstract
AMP-activated protein kinase (AMPK) plays a key role in integrating metabolic pathways in response to energy demand. AMPK activation results in a wide range of downstream responses, many of which are associated with improved metabolic outcome, making AMPK an attractive target for the treatment of metabolic diseases. AMPK is a heterotrimeric complex consisting of a catalytic subunit (α) and two regulatory subunits (β and γ). The γ-subunit harbours the nucleotide-binding sites and plays an important role in AMPK regulation in response to cellular energy levels. In mammals, there are three isoforms of the γ-subunit and these respond differently to regulation by nucleotides, but there is limited information regarding their role in activation by small molecules. Here, we determined the effect of different γ-isoforms on AMPK by a direct activator, 991. In cells, 991 led to a greater activation of γ2-containing AMPK complexes compared with either γ1 or γ3. This effect was dependent on the long N-terminal region of the γ2-isoform. We were able to rule out an effect of Ser108 phosphorylation, since mutation of Ser108 to alanine in the β2-isoform had no effect on activation of AMPK by 991 in either γ1- or γ2-complexes. The rate of dephosphorylation of Thr172 was slower for γ2- compared with γ1-complexes, both in the absence and presence of 991. Our studies show that activation of AMPK by 991 depends on the nature of the γ-isoform. This finding may have implications for the design of isoform-selective AMPK activators.
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Affiliation(s)
- Robin Willows
- Cellular Stress Group, Medical Research Council London Institute of Medical Sciences, Hammersmith Hospital, Imperial College, London W12 0NN, U.K
| | - Naveenan Navaratnam
- Cellular Stress Group, Medical Research Council London Institute of Medical Sciences, Hammersmith Hospital, Imperial College, London W12 0NN, U.K
| | - Ana Lima
- Cellular Stress Group, Medical Research Council London Institute of Medical Sciences, Hammersmith Hospital, Imperial College, London W12 0NN, U.K
| | - Jon Read
- AstraZeneca R&D, Discovery Sciences, Darwin Building, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K
| | - David Carling
- Cellular Stress Group, Medical Research Council London Institute of Medical Sciences, Hammersmith Hospital, Imperial College, London W12 0NN, U.K
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, U.K
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237
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Yruela I, Contreras-Moreira B, Magalhães C, Osório NS, Gonzalo-Asensio J. Mycobacterium tuberculosis Complex Exhibits Lineage-Specific Variations Affecting Protein Ductility and Epitope Recognition. Genome Biol Evol 2017; 8:3751-3764. [PMID: 28062754 PMCID: PMC5521731 DOI: 10.1093/gbe/evw279] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2016] [Indexed: 12/19/2022] Open
Abstract
The advent of whole-genome sequencing has provided an unprecedented detail about the evolution and genetic significance of species-specific variations across the whole Mycobacterium tuberculosis Complex. However, little attention has been focused on understanding the functional roles of these variations in the protein coding sequences. In this work, we compare the coding sequences from 74 sequenced mycobacterial species including M. africanum, M. bovis, M. canettii, M. caprae, M. orygis, and M. tuberculosis. Results show that albeit protein variations affect all functional classes, those proteins involved in lipid and intermediary metabolism and respiration have accumulated mutations during evolution. To understand the impact of these mutations on protein functionality, we explored their implications on protein ductility/disorder, a yet unexplored feature of mycobacterial proteomes. In agreement with previous studies, we found that a Gly71Ile substitution in the PhoPR virulence system severely affects the ductility of its nearby region in M. africanum and animal-adapted species. In the same line of evidence, the SmtB transcriptional regulator shows amino acid variations specific to the Beijing lineage, which affects the flexibility of the N-terminal trans-activation domain. Furthermore, despite the fact that MTBC epitopes are evolutionary hyperconserved, we identify strain- and lineage-specific amino acid mutations affecting previously known T-cell epitopes such as EsxH and FbpA (Ag85A). Interestingly, in silico studies reveal that these variations result in differential interaction of epitopes with the main HLA haplogroups.
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Affiliation(s)
- Inmaculada Yruela
- Estación Experimental de Aula Dei-Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Zaragoza, Spain.,Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada I+D+i al CSIC, Zaragoza, Spain
| | - Bruno Contreras-Moreira
- Estación Experimental de Aula Dei-Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Zaragoza, Spain.,Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada I+D+i al CSIC, Zaragoza, Spain.,Fundación ARAID, Aragón, Spain
| | - Carlos Magalhães
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Nuno S Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Jesús Gonzalo-Asensio
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain.,CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI-UNIZAR), Zaragoza, Spain.,Servicio de Microbiología Hospital Universitario Miguel Servet, ISS Aragón, Zaragoza, Spain
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238
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Signorelli S, Cannistraro S, Bizzarri AR. Structural Characterization of the Intrinsically Disordered Protein p53 Using Raman Spectroscopy. APPLIED SPECTROSCOPY 2017; 71:823-832. [PMID: 27340212 DOI: 10.1177/0003702816651891] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The intrinsically disordered protein p53 has attracted a strong interest for its important role in genome safeguarding and potential therapeutic applications. However, its disordered character makes difficult a full characterization of p53 structural architecture. A deep knowledge of p53 structural motifs could significantly help the understanding of its functional properties, in connection with its complex binding network. We have applied Raman spectroscopy to investigate the structural composition and the conformational heterogeneity of both full-length p53 and its DNA binding domain (DBD), in different solvent environments. In particular, a careful analysis of the Amide I Raman band, which is highly sensitive to protein secondary structure elements such as α-helices, β-sheets and random coils, has revealed the presence of extended random coils in p53 and predominant β-sheet regions in its DBD. In addition, this analysis has allowed us to explore the ensemble of interchanging conformations in both p53 and its DBD, highlighting a higher conformational heterogeneity in p53 than in its DBD. Furthermore, by applying a principal components analysis, we have identified the principal spectral markers in both p53 and DBD samples. The combination of the two approaches could be insightful for the study of intrinsically disordered proteins, by offering increased versatility and wide application as a label-free, real-time and non-invasive detection method.
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Affiliation(s)
- Sara Signorelli
- 1 Biophysics and Nanoscience Centre, Università della Tuscia, Italy
- 2 Department of Science, University Roma Tre, Italy
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239
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Moldogazieva NT, Shaitan KV, Antonov MY, Mokhosoev IM, Levtsova OV, Terentiev AA. Human EGF-derived direct and reverse short linear motifs: conformational dynamics insight into the receptor-binding residues. J Biomol Struct Dyn 2017; 36:1286-1305. [PMID: 28447543 DOI: 10.1080/07391102.2017.1321502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Short linear motifs (SLiMs) have been recognized to perform diverse functions in a variety of regulatory proteins through the involvement in protein-protein interactions, signal transduction, cell cycle regulation, protein secretion, etc. However, detailed molecular mechanisms underlying their functions including roles of definite amino acid residues remain obscure. In our previous studies, we demonstrated that conformational dynamics of amino acid residues in oligopeptides derived from regulatory proteins such as alpha-fetoprotein (AFP), carcino-embryonic antigen (CEA), and pregnancy specific β1-glycoproteins (PSGs) contributes greatly to their biological activities. In the present work, we revealed the 22-member linear modules composed of direct and reverse AFP14-20-like heptapeptide motifs linked by CxxGY/FxGx consensus motif within epidermal growth factor (EGF), growth factors of EGF family and numerous regulatory proteins containing EGF-like modules. We showed, first, the existence of similarity in amino acid signatures of both direct and reverse motifs in terms of their physicochemical properties. Second, molecular dynamics (MD) simulation study demonstrated that key receptor-binding residues in human EGF in the aligned positions of the direct and reverse motifs may have similar distribution of conformational probability densities and dynamic behavior despite their distinct physicochemical properties. Third, we found that the length of a polypeptide chain (from 7 to 53 residues) has no effect, while disulfide bridging and backbone direction significantly influence the conformational distribution and dynamics of the residues. Our data may contribute to the atomic level structure-function analysis and protein structure decoding; additionally, they may provide a basis for novel protein/peptide engineering and peptide-mimetic drug design.
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Affiliation(s)
- Nurbubu T Moldogazieva
- a Department of Biochemistry and Molecular Biology , N.I. Pirogov Russian National Research Medical University , 1 Ostrovityanov str., Moscow 117997 , Russian Federation
| | - Konstantin V Shaitan
- b Faculty of Biology, Department of Bioengineering , M.V. Lomonosov Moscow State University , 1 Vorobyevy Gory, Moscow 119991 , Russian Federation
| | - Mikhail Yu Antonov
- c M.K. Ammosov North-Eastern Federal University , 58 Belinskiy str., Yakutsk 677980 , Republic of Sakha (Yakutia) , Russian Federation
| | - Innokenty M Mokhosoev
- a Department of Biochemistry and Molecular Biology , N.I. Pirogov Russian National Research Medical University , 1 Ostrovityanov str., Moscow 117997 , Russian Federation
| | - Olga V Levtsova
- b Faculty of Biology, Department of Bioengineering , M.V. Lomonosov Moscow State University , 1 Vorobyevy Gory, Moscow 119991 , Russian Federation
| | - Alexander A Terentiev
- a Department of Biochemistry and Molecular Biology , N.I. Pirogov Russian National Research Medical University , 1 Ostrovityanov str., Moscow 117997 , Russian Federation
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240
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Guan FHX, Bailey CG, Metierre C, O'Young P, Gao D, Khoo TL, Holst J, Rasko JEJ. The antiproliferative ELF2 isoform, ELF2B, induces apoptosis in vitro and perturbs early lymphocytic development in vivo. J Hematol Oncol 2017; 10:75. [PMID: 28351373 PMCID: PMC5371273 DOI: 10.1186/s13045-017-0446-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/20/2017] [Indexed: 01/08/2023] Open
Abstract
Background ELF2 (E74-like factor 2) also known as NERF (new Ets-related factor), a member of the Ets family of transcription factors, regulates genes important in B and T cell development, cell cycle progression, and angiogenesis. Conserved ELF2 isoforms, ELF2A, and ELF2B, arising from alternative promoter usage can exert opposing effects on target gene expression. ELF2A activates, whilst ELF2B represses, gene expression, and the balance of expression between these isoforms may be important in maintaining normal cellular function. Methods We compared the function of ELF2 isoforms ELF2A and ELF2B with other ELF subfamily proteins ELF1 and ELF4 in primary and cancer cell lines using proliferation, colony-forming, cell cycle, and apoptosis assays. We further examined the role of ELF2 isoforms in haemopoietic development using a Rag1-/-murine bone marrow reconstitution model. Results ELF2B overexpression significantly reduced cell proliferation and clonogenic capacity, minimally disrupted cell cycle kinetics, and induced apoptosis. In contrast, ELF2A overexpression only marginally reduced clonogenic capacity with little effect on proliferation, cell cycle progression, or apoptosis. Deletion of the N-terminal 19 amino acids unique to ELF2B abrogated the antiproliferative and proapoptotic functions of ELF2B thereby confirming its crucial role. Mice expressing Elf2a or Elf2b in haemopoietic cells variously displayed perturbations in the pre-B cell stage and multiple stages of T cell development. Mature B cells, T cells, and myeloid cells in steady state were unaffected, suggesting that the main role of ELF2 is restricted to the early development of B and T cells and that compensatory mechanisms exist. No differences in B and T cell development were observed between ELF2 isoforms. Conclusions We conclude that ELF2 isoforms are important regulators of cellular proliferation, cell cycle progression, and apoptosis. In respect to this, ELF2B acts in a dominant negative fashion compared to ELF2A and as a putative tumour suppressor gene. Given that these cellular processes are critical during haemopoiesis, we propose that the regulatory interplay between ELF2 isoforms contributes substantially to early B and T cell development. Electronic supplementary material The online version of this article (doi:10.1186/s13045-017-0446-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fiona H X Guan
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Charles G Bailey
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Cynthia Metierre
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Patrick O'Young
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Dadi Gao
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Teh Liane Khoo
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Jeff Holst
- Sydney Medical School, University of Sydney, Camperdown, NSW, 2006, Australia.,Origins of Cancer Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia. .,Sydney Medical School, University of Sydney, Camperdown, NSW, 2006, Australia. .,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW, 2050, Australia.
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241
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Bakota L, Ussif A, Jeserich G, Brandt R. Systemic and network functions of the microtubule-associated protein tau: Implications for tau-based therapies. Mol Cell Neurosci 2017; 84:132-141. [PMID: 28318914 DOI: 10.1016/j.mcn.2017.03.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/23/2017] [Accepted: 03/05/2017] [Indexed: 01/04/2023] Open
Abstract
Tau is a microtubule-associated neuronal protein, whose primary role was long thought to regulate axonal microtubule assembly. Tau is subject to many posttranslational modifications and can aggregate into neurofibrillary tangles, which are considered to be a hallmark of several neurodegenerative diseases collectively called "tauopathies". The most common tauopathy is Alzheimer's disease, where tau pathology correlates with sites of neurodegeneration. Tau belongs to the class of intrinsically disordered proteins, which are known to interact with many partners and are considered to be involved in various signaling, regulation and recognition processes. Thus more recent evidence indicates that tau functionally interacts with many proteins and different cellular structures, which may have an important physiological role and may be involved in neurodegenerative processes. Furthermore, tau can be released from neurons and exert functional effects on other cells. This review article weighs the evidence that tau has subtle but important systemic effects on neuronal network function by maintaining physiological neuronal transmission and synaptic plasticity, which are possibly independent from tau's microtubule modulating activities. Implications for tau-based therapeutic approaches are discussed.
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Affiliation(s)
- Lidia Bakota
- Department of Neurobiology, University of Osnabrück, Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Abdala Ussif
- Department of Neurobiology, University of Osnabrück, Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Gunnar Jeserich
- Department of Neurobiology, University of Osnabrück, Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Roland Brandt
- Department of Neurobiology, University of Osnabrück, Barbarastrasse 11, 49076 Osnabrück, Germany.
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242
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DeRamus ML, Stacks DA, Zhang Y, Huisingh CE, McGwin G, Pittler SJ. GARP2 accelerates retinal degeneration in rod cGMP-gated cation channel β-subunit knockout mice. Sci Rep 2017; 7:42545. [PMID: 28198469 PMCID: PMC5309851 DOI: 10.1038/srep42545] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 01/09/2017] [Indexed: 12/20/2022] Open
Abstract
The Cngb1 locus-encoded β-subunit of rod cGMP-gated cation channel and associated glutamic acid rich proteins (GARPs) are required for phototransduction, disk morphogenesis, and rod structural integrity. To probe individual protein structure/function of the GARPs, we have characterized several transgenic mouse lines selectively restoring GARPs on a Cngb1 knockout (X1−/−) mouse background. Optical coherence tomography (OCT), light and transmission electron microscopy (TEM), and electroretinography (ERG) were used to analyze 6 genotypes including WT at three and ten weeks postnatal. Comparison of aligned histology/OCT images demonstrated that GARP2 accelerates the rate of degeneration. ERG results are consistent with the structural analyses showing the greatest attenuation of function when GARP2 is present. Even 100-fold or more overexpression of GARP1 could not accelerate degeneration as rapidly as GARP2, and when co-expressed GARP1 attenuated the structural and functional deficits elicited by GARP2. These results indicate that the GARPs are not fully interchangeable and thus, likely have separate and distinct functions in the photoreceptor. We also present a uniform murine OCT layer naming nomenclature system that is consistent with human retina layer designations to standardize murine OCT, which will facilitate data evaluation across different laboratories.
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Affiliation(s)
- Marci L DeRamus
- Departments of Optometry and Vision Science, University of Alabama at Birmingham, 1670 University Blvd, VH 375, Birmingham, AL 35294-0019, USA
| | - Delores A Stacks
- Departments of Optometry and Vision Science, University of Alabama at Birmingham, 1670 University Blvd, VH 375, Birmingham, AL 35294-0019, USA
| | - Youwen Zhang
- Departments of Optometry and Vision Science, University of Alabama at Birmingham, 1670 University Blvd, VH 375, Birmingham, AL 35294-0019, USA
| | - Carrie E Huisingh
- Department of Ophthalmology, University of Alabama at Birmingham, 700 18th Street South, Suite 609, Birmingham, AL 35294, USA
| | - Gerald McGwin
- Department of Epidemiology, University of Alabama at Birmingham, Ryals Public Health Building, 1665 University Boulevard, Birmingham, AL 35294, USA
| | - Steven J Pittler
- Departments of Optometry and Vision Science, University of Alabama at Birmingham, 1670 University Blvd, VH 375, Birmingham, AL 35294-0019, USA
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243
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Ginn BR. The thermodynamics of protein aggregation reactions may underpin the enhanced metabolic efficiency associated with heterosis, some balancing selection, and the evolution of ploidy levels. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 126:1-21. [PMID: 28185903 DOI: 10.1016/j.pbiomolbio.2017.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 01/24/2017] [Indexed: 01/04/2023]
Abstract
Identifying the physical basis of heterosis (or "hybrid vigor") has remained elusive despite over a hundred years of research on the subject. The three main theories of heterosis are dominance theory, overdominance theory, and epistasis theory. Kacser and Burns (1981) identified the molecular basis of dominance, which has greatly enhanced our understanding of its importance to heterosis. This paper aims to explain how overdominance, and some features of epistasis, can similarly emerge from the molecular dynamics of proteins. Possessing multiple alleles at a gene locus results in the synthesis of different allozymes at reduced concentrations. This in turn reduces the rate at which each allozyme forms soluble oligomers, which are toxic and must be degraded, because allozymes co-aggregate at low efficiencies. The model developed in this paper can explain how heterozygosity impacts the metabolic efficiency of an organism. It can also explain why the viabilities of some inbred lines seem to decline rapidly at high inbreeding coefficients (F > 0.5), which may provide a physical basis for truncation selection for heterozygosity. Finally, the model has implications for the ploidy level of organisms. It can explain why polyploids are frequently found in environments where severe physical stresses promote the formation of soluble oligomers. The model can also explain why complex organisms, which need to synthesize aggregation-prone proteins that contain intrinsically unstructured regions (IURs) and multiple domains because they facilitate complex protein interaction networks (PINs), tend to be diploid while haploidy tends to be restricted to relatively simple organisms.
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Affiliation(s)
- B R Ginn
- University of Georgia, GA 30602, United States.
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244
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Abstract
The investigation of intrinsically disordered proteins (IDPs) is a new frontier in structural and molecular biology that requires a new paradigm to connect structural disorder to function. Molecular dynamics simulations and statistical thermodynamics potentially offer ideal tools for atomic-level characterizations and thermodynamic descriptions of this fascinating class of proteins that will complement experimental studies. However, IDPs display sensitivity to inaccuracies in the underlying molecular mechanics force fields. Thus, achieving an accurate structural characterization of IDPs via simulations is a challenge. It is also daunting to perform a configuration-space integration over heterogeneous structural ensembles sampled by IDPs to extract, in particular, protein configurational entropy. In this review, we summarize recent efforts devoted to the development of force fields and the critical evaluations of their performance when applied to IDPs. We also survey recent advances in computational methods for protein configurational entropy that aim to provide a thermodynamic link between structural disorder and protein activity.
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Affiliation(s)
- Song-Ho Chong
- Department of Chemistry, Sookmyung Women's University, Yongsan-Ku, Seoul 04310, Korea;
| | - Prathit Chatterjee
- Department of Chemistry, Sookmyung Women's University, Yongsan-Ku, Seoul 04310, Korea;
| | - Sihyun Ham
- Department of Chemistry, Sookmyung Women's University, Yongsan-Ku, Seoul 04310, Korea;
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245
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Carballo‐Pacheco M, Strodel B. Comparison of force fields for Alzheimer's A β42: A case study for intrinsically disordered proteins. Protein Sci 2017; 26:174-185. [PMID: 27727496 PMCID: PMC5275744 DOI: 10.1002/pro.3064] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 10/02/2016] [Accepted: 10/09/2016] [Indexed: 01/06/2023]
Abstract
Intrinsically disordered proteins are essential for biological processes such as cell signalling, but are also associated to devastating diseases including Alzheimer's disease, Parkinson's disease or type II diabetes. Because of their lack of a stable three-dimensional structure, molecular dynamics simulations are often used to obtain atomistic details that cannot be observed experimentally. The applicability of molecular dynamics simulations depends on the accuracy of the force field chosen to represent the underlying free energy surface of the system. Here, we use replica exchange molecular dynamics simulations to test five modern force fields, OPLS, AMBER99SB, AMBER99SB*ILDN, AMBER99SBILDN-NMR and CHARMM22*, in their ability to model Aβ42 , an intrinsically disordered peptide associated with Alzheimer's disease, and compare our results to nuclear magnetic resonance (NMR) experimental data. We observe that all force fields except AMBER99SBILDN-NMR successfully reproduce local NMR observables, with CHARMM22* being slightly better than the other force fields.
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Affiliation(s)
- Martín Carballo‐Pacheco
- Institute of Complex Systems, Structural Biochemistry (ICS‐6), Forschungszentrum Jülich GmbHJülich52425Germany
- AICES Graduate School, RWTH Aachen UniversitySchinkelstraße 2Aachen52062Germany
| | - Birgit Strodel
- Institute of Complex Systems, Structural Biochemistry (ICS‐6), Forschungszentrum Jülich GmbHJülich52425Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University DüsseldorfUniversitätstraße 1Düsseldorf40225Germany
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246
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Signorelli S, Santini S, Yamada T, Bizzarri AR, Beattie CW, Cannistraro S. Binding of Amphipathic Cell Penetrating Peptide p28 to Wild Type and Mutated p53 as studied by Raman, Atomic Force and Surface Plasmon Resonance spectroscopies. Biochim Biophys Acta Gen Subj 2017; 1861:910-921. [PMID: 28126403 DOI: 10.1016/j.bbagen.2017.01.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 12/21/2016] [Accepted: 01/20/2017] [Indexed: 10/20/2022]
Abstract
BACKGROUND Mutations within the DNA binding domain (DBD) of the tumor suppressor p53 are found in >50% of human cancers and may significantly modify p53 secondary structure impairing its function. p28, an amphipathic cell-penetrating peptide, binds to the DBD through hydrophobic interaction and induces a posttranslational increase in wildtype and mutant p53 restoring functionality. We use mutation analyses to explore which elements of secondary structure may be critical to p28 binding. METHODS Molecular modeling, Raman spectroscopy, Atomic Force Spectroscopy (AFS) and Surface Plasmon Resonance (SPR) were used to identify which secondary structure of site-directed and naturally occurring mutant DBDs are potentially altered by discrete changes in hydrophobicity and the molecular interaction with p28. RESULTS We show that specific point mutations that alter hydrophobicity within non-mutable and mutable regions of the p53 DBD alter specific secondary structures. The affinity of p28 was positively correlated with the β-sheet content of a mutant DBD, and reduced by an increase in unstructured or random coil that resulted from a loss in hydrophobicity and redistribution of surface charge. CONCLUSIONS These results help refine our knowledge of how mutations within p53-DBD alter secondary structure and provide insight on how potential structural alterations in p28 or similar molecules improve their ability to restore p53 function. GENERAL SIGNIFICANCE Raman spectroscopy, AFS, SPR and computational modeling are useful approaches to characterize how mutations within the p53DBD potentially affect secondary structure and identify those structural elements prone to influence the binding affinity of agents designed to increase the functionality of p53.
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Affiliation(s)
- Sara Signorelli
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Viterbo, Italy; Department of Science, University Roma Tre, Rome, Italy
| | - Simona Santini
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Viterbo, Italy
| | - Tohru Yamada
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, USA
| | - Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Viterbo, Italy.
| | - Craig W Beattie
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, USA
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247
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Kurzbach D, Vanas A, Flamm AG, Tarnoczi N, Kontaxis G, Maltar-Strmečki N, Widder K, Hinderberger D, Konrat R. Detection of correlated conformational fluctuations in intrinsically disordered proteins through paramagnetic relaxation interference. Phys Chem Chem Phys 2017; 18:5753-8. [PMID: 26411860 DOI: 10.1039/c5cp04858c] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Functionally relevant conformational states of intrinsically disordered proteins (IDPs) are typically concealed in a vast space of fast interconverting structures. Here we present a novel methodology, NMR-based paramagnetic relaxation interference (PRI), that allows for direct observation of concerted motions and cooperatively folded sub-states in IDPs. The proposed NMR technique is based on the exploitation of cross correlated electron-nuclear dipolar relaxation interferences in doubly spin-labeled proteins and probes the transient spatial encounter of electron-nucleus spin pairs.
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Affiliation(s)
- D Kurzbach
- Department for Structural and Computational Biology Max F. Perutz Laboratories, University of Vienna Vienna Biocenter Campus 5, 1030 Vienna, Austria.
| | - A Vanas
- Department for Structural and Computational Biology Max F. Perutz Laboratories, University of Vienna Vienna Biocenter Campus 5, 1030 Vienna, Austria.
| | - A G Flamm
- Department for Structural and Computational Biology Max F. Perutz Laboratories, University of Vienna Vienna Biocenter Campus 5, 1030 Vienna, Austria.
| | - N Tarnoczi
- Department for Structural and Computational Biology Max F. Perutz Laboratories, University of Vienna Vienna Biocenter Campus 5, 1030 Vienna, Austria.
| | - G Kontaxis
- Department for Structural and Computational Biology Max F. Perutz Laboratories, University of Vienna Vienna Biocenter Campus 5, 1030 Vienna, Austria.
| | - N Maltar-Strmečki
- Institute for Physical Chemistry Martin-Luther-Universität Halle-Wittenberg von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - K Widder
- Institute for Physical Chemistry Martin-Luther-Universität Halle-Wittenberg von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - D Hinderberger
- Institute for Physical Chemistry Martin-Luther-Universität Halle-Wittenberg von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - R Konrat
- Department for Structural and Computational Biology Max F. Perutz Laboratories, University of Vienna Vienna Biocenter Campus 5, 1030 Vienna, Austria.
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248
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English LR, Tilton EC, Ricard BJ, Whitten ST. Intrinsic α helix propensities compact hydrodynamic radii in intrinsically disordered proteins. Proteins 2017; 85:296-311. [PMID: 27936491 DOI: 10.1002/prot.25222] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/31/2016] [Accepted: 11/21/2016] [Indexed: 12/27/2022]
Abstract
Proteins that lack tertiary stability under normal conditions, known as intrinsically disordered, exhibit a wide range of biological activities. Molecular descriptions for the biology of intrinsically disordered proteins (IDPs) consequently rely on disordered structural models, which in turn require experiments that assess the origins to structural features observed. For example, while hydrodynamic size is mostly insensitive to sequence composition in chemically denatured proteins, IDPs show strong sequence-specific effects in the hydrodynamic radius (Rh ) when measured under normal conditions. To investigate sequence-modulation of IDP Rh , disordered ensembles generated by a hard sphere collision model modified with a structure-based parameterization of the solution energetics were used to parse the contributions of net charge, main chain dihedral angle bias, and excluded volume on hydrodynamic size. Ensembles for polypeptides 10-35 residues in length were then used to establish power-law scaling relationships for comparison to experimental Rh from 26 IDPs. Results showed the expected outcomes of increased hydrodynamic size from increases in excluded volume and net charge, and compaction from chain-solvent interactions. Chain bias representing intrinsic preferences for α helix and polyproline II (PPII ), however, modulated Rh with intricate dependence on the simulated propensities. PPII propensities at levels expected in IDPs correlated with heightened Rh sensitivity to even weak α helix propensities, indicating bias for common (φ, ψ) are important determinants of hydrodynamic size. Moreover, data show that IDP Rh can be predicted from sequence with good accuracy from a small set of physicochemical properties, namely intrinsic conformational propensities and net charge. Proteins 2017; 85:296-311. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Lance R English
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Erin C Tilton
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Benjamin J Ricard
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Steven T Whitten
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
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249
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Wang Y, Guo Y, Pu X, Li M. A sequence-based computational method for prediction of MoRFs. RSC Adv 2017. [DOI: 10.1039/c6ra27161h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Molecular recognition features (MoRFs) are relatively short segments (10–70 residues) within intrinsically disordered regions (IDRs) that can undergo disorder-to-order transitions during binding to partner proteins.
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Affiliation(s)
- Yu Wang
- College of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Yanzhi Guo
- College of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Xuemei Pu
- College of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Menglong Li
- College of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
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250
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Fadda E, Nixon MG. The transient manifold structure of the p53 extreme C-terminal domain: insight into disorder, recognition, and binding promiscuity by molecular dynamics simulations. Phys Chem Chem Phys 2017; 19:21287-21296. [DOI: 10.1039/c7cp02485a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The extreme C-terminus of the p53 tumour suppressor (p53-CTD) is a 30 residue long intrinsically disordered region, responsible for regulating the p53 DNA binding activity. Extensive conformational sampling through MD simulations of a p53-CTD derived peptide in solution highlights its propensity to form short and stable secondary structure motifs, specifically localized within the sequence.
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Affiliation(s)
- E. Fadda
- Department of Chemistry
- Maynooth University, and Hamilton Institute
- Maynooth University
- Maynooth
- Ireland
| | - M. G. Nixon
- Department of Chemistry
- Maynooth University, and Hamilton Institute
- Maynooth University
- Maynooth
- Ireland
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