1
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Yi X, Zhang L, Friesner RA, McDermott A. Predicted and Experimental NMR Chemical Shifts at Variable Temperatures: The Effect of Protein Conformational Dynamics. J Phys Chem Lett 2024; 15:2270-2278. [PMID: 38381862 DOI: 10.1021/acs.jpclett.3c02589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
NMR chemical shifts provide a sensitive probe of protein structure and dynamics but remain challenging to predict and interpret. We examine the effect of protein conformational distributions on 15N chemical shifts for dihydrofolate reductase (DHFR), comparing QM/MM predicted shifts with experimental shifts in solution as well as frozen distributions. Representative snapshots from MD trajectories exhibit variation in predicted 15N chemical shifts of up to 25 ppm. The average over the fluctuations is in significantly better agreement with room temperature solution experimental values than the prediction for any single optimal conformations. Meanwhile, solid-state NMR (SSNMR) measurements of frozen solutions at 105 K exhibit broad lines whose widths agree well with the widths of distributions of predicted shifts for samples from the trajectory. The backbone torsion angle ψi-1 varies over 60° on the picosecond time scale, compensated by φi. These fluctuations can explain much of the shift variation.
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Affiliation(s)
- Xu Yi
- Department of Chemistry, Columbia University, New York, New York 10025, United States
| | - Lichirui Zhang
- Department of Chemistry, Columbia University, New York, New York 10025, United States
| | - Richard A Friesner
- Department of Chemistry, Columbia University, New York, New York 10025, United States
| | - Ann McDermott
- Department of Chemistry, Columbia University, New York, New York 10025, United States
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2
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Elias RD, Zhu Y, Su Q, Ghirlando R, Zhang J, Deshmukh L. Reversible phase separation of ESCRT protein ALIX through tyrosine phosphorylation. SCIENCE ADVANCES 2023; 9:eadg3913. [PMID: 37450591 PMCID: PMC10348681 DOI: 10.1126/sciadv.adg3913] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
Cytokinetic abscission, the last step of cell division, is regulated by the ESCRT machinery. In response to mitotic errors, ESCRT proteins, namely, ALIX, CHMP4B, and CHMP4C, accumulate in the cytosolic compartments termed "abscission checkpoint bodies" (ACBs) to delay abscission and prevent tumorigenesis. ALIX contributes to the biogenesis and stability of ACBs via an unknown mechanism. We show that ALIX phase separates into nondynamic condensates in vitro and in vivo, mediated by the amyloidogenic portion of its proline-rich domain. ALIX condensates confined CHMP4 paralogs in vitro. These condensates dissolved and reformed upon reversible tyrosine phosphorylation of ALIX, mediated by Src kinase and PTP1B, and sequestration of CHMP4C altered their Src-mediated dissolution. NMR analysis revealed how ALIX triggers the activation of CHMP4 proteins, which is required for successful abscission. These results implicate ALIX's phase separation in the modulation of ACBs. This study also highlights how posttranslational modifications can control protein phase separation.
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Affiliation(s)
- Ruben D. Elias
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yingqi Zhu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Qi Su
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lalit Deshmukh
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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3
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Yi X, Zhang L, Friesner RA, McDermott A. Predicted and Experimental NMR Chemical Shifts at Variable Temperatures: The Effect of Protein Conformational Dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525502. [PMID: 36747635 PMCID: PMC9900828 DOI: 10.1101/2023.01.25.525502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
NMR chemical shifts provide a sensitive probe of protein structure and dynamics. Prediction of shifts, and therefore interpretation of shifts, particularly for the frequently measured amidic 15 N sites, remains a tall challenge. We demonstrate that protein 15 N chemical shift prediction from QM/MM predictions can be improved if conformational variation is included via MD sampling, focusing on the antibiotic target, E. coli Dihydrofolate reductase (DHFR). Variations of up to 25 ppm in predicted 15 N chemical shifts are observed over the trajectory. For solution shifts the average of fluctuations on the low picosecond timescale results in a superior prediction to a single optimal conformation. For low temperature solid state measurements, the histogram of predicted shifts for locally minimized snapshots with specific solvent arrangements sampled from the trajectory explains the heterogeneous linewidths; in other words, the conformations and associated solvent are 'frozen out' at low temperatures and result in inhomogeneously broadened NMR peaks. We identified conformational degrees of freedom that contribute to chemical shift variation. Backbone torsion angles show high amplitude fluctuations during the trajectory on the low picosecond timescale. For a number of residues, including I60, ψ varies by up to 60º within a conformational basin during the MD simulations, despite the fact that I60 (and other sites studied) are in a secondary structure element and remain well folded during the trajectory. Fluctuations in ψ appear to be compensated by other degrees of freedom in the protein, including φ of the succeeding residue, resulting in "rocking" of the amide plane with changes in hydrogen bonding interactions. Good agreement for both room temperature and low temperature NMR spectra provides strong support for the specific approach to conformational averaging of computed chemical shifts.
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4
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González-Delgado J, Bernadó P, Neuvial P, Cortés J. Statistical proofs of the interdependence between nearest neighbor effects on polypeptide backbone conformations. J Struct Biol 2022; 214:107907. [PMID: 36272694 DOI: 10.1016/j.jsb.2022.107907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 10/03/2022] [Accepted: 10/09/2022] [Indexed: 11/06/2022]
Abstract
Backbone dihedral angles ϕ and ψ are the main structural descriptors of proteins and peptides. The distribution of these angles has been investigated over decades as they are essential for the validation and refinement of experimental measurements, as well as for structure prediction and design methods. The dependence of these distributions, not only on the nature of each amino acid but also on that of the closest neighbors, has been the subject of numerous studies. Although neighbor-dependent distributions are nowadays generally accepted as a good model, there is still some controversy about the combined effects of left and right neighbors. We have investigated this question using rigorous methods based on recently-developed statistical techniques. Our results unambiguously demonstrate that the influence of left and right neighbors cannot be considered independently. Consequently, three-residue fragments should be considered as the minimal building blocks to investigate polypeptide sequence-structure relationships.
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Affiliation(s)
- Javier González-Delgado
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France; Institut de Mathématiques de Toulouse, Université de Toulouse, CNRS, France
| | - Pau Bernadó
- Centre de Biologie Structurale, Université de Montpellier, INSERM, CNRS, France
| | - Pierre Neuvial
- Institut de Mathématiques de Toulouse, Université de Toulouse, CNRS, France
| | - Juan Cortés
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France.
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5
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Teixeira JMC, Liu ZH, Namini A, Li J, Vernon RM, Krzeminski M, Shamandy AA, Zhang O, Haghighatlari M, Yu L, Head-Gordon T, Forman-Kay JD. IDPConformerGenerator: A Flexible Software Suite for Sampling the Conformational Space of Disordered Protein States. J Phys Chem A 2022; 126:5985-6003. [PMID: 36030416 PMCID: PMC9465686 DOI: 10.1021/acs.jpca.2c03726] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The power of structural information for informing biological
mechanisms
is clear for stable folded macromolecules, but similar structure–function
insight is more difficult to obtain for highly dynamic systems such
as intrinsically disordered proteins (IDPs) which must be described
as structural ensembles. Here, we present IDPConformerGenerator, a
flexible, modular open-source software platform for generating large
and diverse ensembles of disordered protein states that builds conformers
that obey geometric, steric, and other physical restraints on the
input sequence. IDPConformerGenerator samples backbone phi (φ),
psi (ψ), and omega (ω) torsion angles of relevant sequence
fragments from loops and secondary structure elements extracted from
folded protein structures in the RCSB Protein Data Bank and builds
side chains from robust Monte Carlo algorithms using expanded rotamer
libraries. IDPConformerGenerator has many user-defined options enabling
variable fractional sampling of secondary structures, supports Bayesian
models for assessing the agreement of IDP ensembles for consistency
with experimental data, and introduces a machine learning approach
to transform between internal and Cartesian coordinates with reduced
error. IDPConformerGenerator will facilitate the characterization
of disordered proteins to ultimately provide structural insights into
these states that have key biological functions.
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Affiliation(s)
- João M. C. Teixeira
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Zi Hao Liu
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Ashley Namini
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | | | - Robert M. Vernon
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Mickaël Krzeminski
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Alaa A. Shamandy
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario M5S 2E4, Canada
| | | | | | | | | | - Julie D. Forman-Kay
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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6
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Structural Insights into the Intrinsically Disordered GPCR C-Terminal Region, Major Actor in Arrestin-GPCR Interaction. Biomolecules 2022; 12:biom12050617. [PMID: 35625550 PMCID: PMC9138321 DOI: 10.3390/biom12050617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 02/04/2023] Open
Abstract
Arrestin-dependent pathways are a central component of G protein-coupled receptor (GPCRs) signaling. However, the molecular processes regulating arrestin binding are to be further illuminated, in particular with regard to the structural impact of GPCR C-terminal disordered regions. Here, we used an integrated biophysical strategy to describe the basal conformations of the C-terminal domains of three class A GPCRs, the vasopressin V2 receptor (V2R), the growth hormone secretagogue or ghrelin receptor type 1a (GHSR) and the β2-adernergic receptor (β2AR). By doing so, we revealed the presence of transient secondary structures in these regions that are potentially involved in the interaction with arrestin. These secondary structure elements differ from those described in the literature in interaction with arrestin. This suggests a mechanism where the secondary structure conformational preferences in the C-terminal regions of GPCRs could be a central feature for optimizing arrestins recognition.
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7
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Xue K, Nimerovsky E, Tekwani Movellan KA, Becker S, Andreas LB. Backbone Torsion Angle Determination Using Proton Detected Magic-Angle Spinning Nuclear Magnetic Resonance. J Phys Chem Lett 2022; 13:18-24. [PMID: 34957837 PMCID: PMC8762656 DOI: 10.1021/acs.jpclett.1c03267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
Protein torsion angles define the backbone secondary structure of proteins. Magic-angle spinning (MAS) NMR methods using carbon detection have been developed to measure torsion angles by determining the relative orientation between two anisotropic interactions─dipolar coupling or chemical shift anisotropy. Here we report a new proton-detection based method to determine the backbone torsion angle by recoupling NH and CH dipolar couplings within the HCANH pulse sequence, for protonated or partly deuterated samples. We demonstrate the efficiency and precision of the method with microcrystalline chicken α spectrin SH3 protein and the influenza A matrix 2 (M2) membrane protein, using 55 or 90 kHz MAS. For M2, pseudo-4D data detect a turn between transmembrane and amphipathic helices.
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8
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Chatterjee P, Le T, Bui HTD, Cho MK, Ham S. Atomic Level Investigations of Early Aggregation of Tau43 in Water I. Conformational Propensity of Monomeric Tau43. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Prathit Chatterjee
- Department of Chemistry The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa‐ro 47‐Gil 100, Yongsan‐Ku Seoul 04310 Korea
| | - Thi‐Diem Le
- Department of Chemistry The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa‐ro 47‐Gil 100, Yongsan‐Ku Seoul 04310 Korea
| | - Huong T. D. Bui
- Department of Chemistry The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa‐ro 47‐Gil 100, Yongsan‐Ku Seoul 04310 Korea
| | - Myung Keun Cho
- Department of Chemistry The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa‐ro 47‐Gil 100, Yongsan‐Ku Seoul 04310 Korea
- Department of Chemistry College of Natural Sciences, Seoul National University, Gwanak‐ro 1, Gwanak‐ku Seoul 08826 Korea
| | - Sihyun Ham
- Department of Chemistry The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa‐ro 47‐Gil 100, Yongsan‐Ku Seoul 04310 Korea
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9
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Pinet L, Wang YH, Deville C, Lescop E, Guerlesquin F, Badache A, Bontems F, Morellet N, Durand D, Assrir N, van Heijenoort C. Structural and dynamic characterization of the C-terminal tail of ErbB2: Disordered but not random. Biophys J 2021; 120:1869-1882. [PMID: 33741354 DOI: 10.1016/j.bpj.2021.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 01/23/2023] Open
Abstract
ErbB2 (or HER2) is a receptor tyrosine kinase overexpressed in some breast cancers and associated with poor prognosis. Treatments targeting the receptor extracellular and kinase domains have greatly improved disease outcome in the last 20 years. In parallel, the structures of these domains have been described, enabling better mechanistic understanding of the receptor function and targeted inhibition. However, the ErbB2 disordered C-terminal cytoplasmic tail (CtErbB2) remains very poorly characterized in terms of structure, dynamics, and detailed functional mechanism. Yet, it is where signal transduction is triggered via phosphorylation of tyrosine residues and carried out via interaction with adaptor proteins. Here, we report the first description, to our knowledge, of the ErbB2 disordered tail at atomic resolution using NMR, complemented by small-angle x-ray scattering. We show that although no part of CtErbB2 has any fully populated secondary or tertiary structure, it contains several transient α-helices and numerous transient polyproline II helices, populated up to 20 and 40%, respectively, and low but significant compaction. The presence of some structural elements suggests, along the lines of the results obtained for EGFR (ErbB1), that they may have a functional role in ErbB2's autoregulation processes. In addition, the transient formation of polyproline II helices is compliant with previously suggested interactions with SH3 domains. All in all, our in-depth structural study opens perspectives in the mechanistic understanding of ErbB2.
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Affiliation(s)
- Louise Pinet
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France; Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Ying-Hui Wang
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France; SGS Taiwan LTD, New Taipei City, Taiwan
| | - Célia Deville
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France; IGBMC, University of Strasbourg, CNRS UMR, Illkirch, France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Françoise Guerlesquin
- LISM, Institut de Microbiologie de la Méditerranée, CNRS and Aix-Marseille University, Marseille, France
| | - Ali Badache
- Centre de Recherche en Cancérologie de Marseille, Aix-Marseille Univ, INSERM, Institut Paoli-Calmettes, CNRS, Marseille, France
| | - François Bontems
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France; Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France
| | - Nelly Morellet
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Dominique Durand
- I2BC, Université Paris-Saclay, CNRS UMR 9198, Gif-sur-Yvette, France
| | - Nadine Assrir
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Carine van Heijenoort
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France.
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10
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Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins. Molecules 2021; 26:molecules26030634. [PMID: 33530506 PMCID: PMC7865441 DOI: 10.3390/molecules26030634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/18/2021] [Accepted: 01/23/2021] [Indexed: 01/10/2023] Open
Abstract
The α and polyproline II (PPII) basins are the two most populated regions of the Ramachandran map when constructed from the protein coil library, a widely used denatured state model built from the segments of irregular structure found in the Protein Data Bank. This indicates the α and PPII conformations are dominant components of the ensembles of denatured structures that exist in solution for biological proteins, an observation supported in part by structural studies of short, and thus unfolded, peptides. Although intrinsic conformational propensities have been determined experimentally for the common amino acids in short peptides, and estimated from surveys of the protein coil library, the ability of these intrinsic conformational propensities to quantitatively reproduce structural behavior in intrinsically disordered proteins (IDPs), an increasingly important class of proteins in cell function, has thus far proven elusive to establish. Recently, we demonstrated that the sequence dependence of the mean hydrodynamic size of IDPs in water and the impact of heat on the coil dimensions, provide access to both the sequence dependence and thermodynamic energies that are associated with biases for the α and PPII backbone conformations. Here, we compare results from peptide-based studies of intrinsic conformational propensities and surveys of the protein coil library to those of the sequence-based analysis of heat effects on IDP hydrodynamic size, showing that a common structural and thermodynamic description of the protein denatured state is obtained.
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11
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Kanapeckaitė A, Beaurivage C, Hancock M, Verschueren E. Fi-score: a novel approach to characterise protein topology and aid in drug discovery studies. J Biomol Struct Dyn 2020; 40:4197-4207. [DOI: 10.1080/07391102.2020.1854859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | - Claudia Beaurivage
- Galapagos BV, Leiden, The Netherlands
- Department of Biomedical Science, Faculty of Science, University of Sheffield, Sheffield, UK
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12
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Elias RD, Ma W, Ghirlando R, Schwieters CD, Reddy VS, Deshmukh L. Proline-rich domain of human ALIX contains multiple TSG101-UEV interaction sites and forms phosphorylation-mediated reversible amyloids. Proc Natl Acad Sci U S A 2020; 117:24274-24284. [PMID: 32917811 PMCID: PMC7533887 DOI: 10.1073/pnas.2010635117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Proline-rich domains (PRDs) are among the most prevalent signaling modules of eukaryotes but often unexplored by biophysical techniques as their heterologous recombinant expression poses significant difficulties. Using a "divide-and-conquer" approach, we present a detailed investigation of a PRD (166 residues; ∼30% prolines) belonging to a human protein ALIX, a versatile adaptor protein involved in essential cellular processes including ESCRT-mediated membrane remodeling, cell adhesion, and apoptosis. In solution, the N-terminal fragment of ALIX-PRD is dynamically disordered. It contains three tandem sequentially similar proline-rich motifs that compete for a single binding site on its signaling partner, TSG101-UEV, as evidenced by heteronuclear NMR spectroscopy. Global fitting of relaxation dispersion data, measured as a function of TSG101-UEV concentration, allowed precise quantitation of these interactions. In contrast to the soluble N-terminal portion, the C-terminal tyrosine-rich fragment of ALIX-PRD forms amyloid fibrils and viscous gels validated using dye-binding assays with amyloid-specific probes, congo red and thioflavin T (ThT), and visualized by transmission electron microscopy. Remarkably, fibrils dissolve at low temperatures (2 to 6 °C) or upon hyperphosphorylation with Src kinase. Aggregation kinetics monitored by ThT fluorescence shows that charge repulsion dictates phosphorylation-mediated fibril dissolution and that the hydrophobic effect drives fibril formation. These data illuminate the mechanistic interplay between interactions of ALIX-PRD with TSG101-UEV and polymerization of ALIX-PRD and its central role in regulating ALIX function. This study also demonstrates the broad functional repertoires of PRDs and uncovers the impact of posttranslational modifications in the modulation of reversible amyloids.
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Affiliation(s)
- Ruben D Elias
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Wen Ma
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Charles D Schwieters
- Division of Computational Biosciences, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892
| | - Vijay S Reddy
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Lalit Deshmukh
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093;
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13
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Ferrie JJ, Petersson EJ. A Unified De Novo Approach for Predicting the Structures of Ordered and Disordered Proteins. J Phys Chem B 2020; 124:5538-5548. [PMID: 32525675 DOI: 10.1021/acs.jpcb.0c02924] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
As recognition of the abundance and relevance of intrinsically disordered proteins (IDPs) continues to grow, demand increases for methods that can rapidly predict the conformational ensembles populated by these proteins. To date, IDP simulations have largely been dominated by molecular dynamics (MD) simulations, which require significant compute times and/or complex hardware. Recent developments in MD have afforded methods capable of simulating both ordered and disordered proteins, yet to date, accurate fold prediction from a sequence has been dominated by Monte Carlo (MC)-based methods such as Rosetta. To overcome the limitations of current approaches in IDP simulation using Rosetta while maintaining its utility for modeling folded domains, we developed PyRosetta-based algorithms that allow for the accurate de novo prediction of proteins across all degrees of foldedness along with structural ensembles of disordered proteins. Our simulations have accuracy comparable to state-of-the-art MD with vastly reduced computational demands.
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Affiliation(s)
- John J Ferrie
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
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14
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Mariño L, Ramis R, Casasnovas R, Ortega-Castro J, Vilanova B, Frau J, Adrover M. Unravelling the effect of N(ε)-(carboxyethyl)lysine on the conformation, dynamics and aggregation propensity of α-synuclein. Chem Sci 2020; 11:3332-3344. [PMID: 34122841 PMCID: PMC8157327 DOI: 10.1039/d0sc00906g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
α-Synuclein (αS) aggregation is a hallmark in several neurodegenerative diseases. Among them, Parkinson's disease is highlighted, characterized by the intraneuronal deposition of Lewy bodies (LBs) which causes the loss of dopaminergic neurons. αS is the main component of LBs and in them, it usually contains post-translational modifications. One of them is the formation of advanced glycation end-products (mainly CEL and MOLD) arising from its reaction with methylglyoxal. Despite its biological relevance, there are no data available proving the effect of glycation on the conformation of αS, nor on its aggregation mechanism. This has been hampered by the formation of a heterogeneous set of compounds that precluded conformational studies. To overcome this issue, we have here produced αS homogeneously glycated with CEL. Its use, together with different biophysical techniques and molecular dynamics simulations, allowed us to study for the first time the effect of glycation on the conformation of a protein. CEL extended the conformation of the N-terminal domain as a result of the loss of transient N-/C-terminal long-range contacts while increasing the heterogeneity of the conformational population. CEL also inhibited the αS aggregation, but it was not able to disassemble preexisting amyloid fibrils, thus proving that CEL found on LBs must be formed in a later event after aggregation. We study the effect of an advanced glycation end product (N(ε)-(carboxyethyl)lysine), found on the Lewy bodies of people suffering from Parkinson’s disease, on the conformational and aggregation features of alpha-synuclein.![]()
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Affiliation(s)
- Laura Mariño
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut d'Investigació Sanitària Illes Balears (IdISBa), Departament de Química, Universitat de les Illes Balears Ctra. Valldemossa km 7.5 E-07122 Palma de Mallorca Spain +34 971 173426 +34 971 173491
| | - Rafael Ramis
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut d'Investigació Sanitària Illes Balears (IdISBa), Departament de Química, Universitat de les Illes Balears Ctra. Valldemossa km 7.5 E-07122 Palma de Mallorca Spain +34 971 173426 +34 971 173491
| | - Rodrigo Casasnovas
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut d'Investigació Sanitària Illes Balears (IdISBa), Departament de Química, Universitat de les Illes Balears Ctra. Valldemossa km 7.5 E-07122 Palma de Mallorca Spain +34 971 173426 +34 971 173491
| | - Joaquín Ortega-Castro
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut d'Investigació Sanitària Illes Balears (IdISBa), Departament de Química, Universitat de les Illes Balears Ctra. Valldemossa km 7.5 E-07122 Palma de Mallorca Spain +34 971 173426 +34 971 173491
| | - Bartolomé Vilanova
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut d'Investigació Sanitària Illes Balears (IdISBa), Departament de Química, Universitat de les Illes Balears Ctra. Valldemossa km 7.5 E-07122 Palma de Mallorca Spain +34 971 173426 +34 971 173491
| | - Juan Frau
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut d'Investigació Sanitària Illes Balears (IdISBa), Departament de Química, Universitat de les Illes Balears Ctra. Valldemossa km 7.5 E-07122 Palma de Mallorca Spain +34 971 173426 +34 971 173491
| | - Miquel Adrover
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut d'Investigació Sanitària Illes Balears (IdISBa), Departament de Química, Universitat de les Illes Balears Ctra. Valldemossa km 7.5 E-07122 Palma de Mallorca Spain +34 971 173426 +34 971 173491
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15
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Hendus-Altenburger R, Fernandes CB, Bugge K, Kunze MBA, Boomsma W, Kragelund BB. Random coil chemical shifts for serine, threonine and tyrosine phosphorylation over a broad pH range. JOURNAL OF BIOMOLECULAR NMR 2019; 73:713-725. [PMID: 31598803 PMCID: PMC6875518 DOI: 10.1007/s10858-019-00283-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/30/2019] [Indexed: 05/26/2023]
Abstract
Phosphorylation is one of the main regulators of cellular signaling typically occurring in flexible parts of folded proteins and in intrinsically disordered regions. It can have distinct effects on the chemical environment as well as on the structural properties near the modification site. Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins (IDPs) and the reliability of the analysis depends on an appropriate choice of random coil model. Random coil chemical shifts and sequence correction factors were previously determined for an Ac-QQXQQ-NH2-peptide series with X being any of the 20 common amino acids. However, a matching dataset on the phosphorylated states has so far only been incompletely determined or determined only at a single pH value. Here we extend the database by the addition of the random coil chemical shifts of the phosphorylated states of serine, threonine and tyrosine measured over a range of pH values covering the pKas of the phosphates and at several temperatures (www.bio.ku.dk/sbinlab/randomcoil). The combined results allow for accurate random coil chemical shift determination of phosphorylated regions at any pH and temperature, minimizing systematic biases of the secondary chemical shifts. Comparison of chemical shifts using random coil sets with and without inclusion of the phosphoryl group, revealed under/over estimations of helicity of up to 33%. The expanded set of random coil values will improve the reliability in detection and quantification of transient secondary structure in phosphorylation-modified IDPs.
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Affiliation(s)
- Ruth Hendus-Altenburger
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Catarina B Fernandes
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Katrine Bugge
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Micha B A Kunze
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen Ø, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
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16
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English LR, Voss SM, Tilton EC, Paiz EA, So S, Parra GL, Whitten ST. Impact of Heat on Coil Hydrodynamic Size Yields the Energetics of Denatured State Conformational Bias. J Phys Chem B 2019; 123:10014-10024. [PMID: 31679343 DOI: 10.1021/acs.jpcb.9b09088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conformational equilibria in the protein denatured state have key roles regulating folding, stability, and function. The extent of conformational bias in the protein denatured state under folding conditions, however, has thus far proven elusive to quantify, particularly with regard to its sequence dependence and energetic character. To better understand the structural preferences of the denatured state, we analyzed both the sequence dependence to the mean hydrodynamic size of disordered proteins in water and the impact of heat on the coil dimensions, showing that the sequence dependence and thermodynamic energies associated with intrinsic biases for the α and polyproline II (PPII) backbone conformations can be obtained. Experiments that evaluate how the hydrodynamic size changes with compositional changes in the protein reveal amino acid specific preferences for PPII that are in good quantitative agreement with calorimetry-measured values from unfolded peptides and those inferred by survey of the protein coil library. At temperatures above 25 °C, the denatured state follows the predictions of a PPII-dominant ensemble. Heat effects on coil hydrodynamic size indicate the α bias is comparable to the PPII bias at cold temperatures. Though historically thought to give poor resolution to structural details, the hydrodynamic size of the unfolded state is found to be an effective reporter on the extent of the biases for the α and PPII backbone conformations.
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17
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Choi JM, Pappu RV. Experimentally Derived and Computationally Optimized Backbone Conformational Statistics for Blocked Amino Acids. J Chem Theory Comput 2019; 15:1355-1366. [PMID: 30516982 PMCID: PMC10846683 DOI: 10.1021/acs.jctc.8b00572] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Experimentally derived, amino acid specific backbone dihedral angle distributions are invaluable for modeling data-driven conformational equilibria of proteins and for enabling quantitative assessments of the accuracies of molecular mechanics force fields. The protein coil library that is extracted from analysis of high-resolution structures of proteins has served as a useful proxy for quantifying intrinsic and context-dependent conformational distributions of amino acids. However, data that go into coil libraries will have hidden biases, and ad hoc procedures must be used to remove these biases. Here, we combine high-resolution biased information from protein structural databases with unbiased low-resolution information from spectroscopic measurements of blocked amino acids to obtain experimentally derived and computationally optimized coil-library landscapes for each of the 20 naturally occurring amino acids. Quantitative descriptions of conformational distributions require parsing of data into conformational basins with defined envelopes, centers, and statistical weights. We develop and deploy a numerical method to extract conformational basins. The weights of conformational basins are optimized to reproduce quantitative inferences drawn from spectroscopic experiments for blocked amino acids. The optimized distributions serve as touchstones for assessments of intrinsic conformational preferences and for quantitative comparisons of molecular mechanics force fields.
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Affiliation(s)
- Jeong-Mo Choi
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, Missouri 63130
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, Missouri 63130
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18
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Estaña A, Sibille N, Delaforge E, Vaisset M, Cortés J, Bernadó P. Realistic Ensemble Models of Intrinsically Disordered Proteins Using a Structure-Encoding Coil Database. Structure 2019; 27:381-391.e2. [DOI: 10.1016/j.str.2018.10.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/13/2018] [Accepted: 10/19/2018] [Indexed: 11/27/2022]
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19
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Milles S, Salvi N, Blackledge M, Jensen MR. Characterization of intrinsically disordered proteins and their dynamic complexes: From in vitro to cell-like environments. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 109:79-100. [PMID: 30527137 DOI: 10.1016/j.pnmrs.2018.07.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 07/16/2018] [Accepted: 07/16/2018] [Indexed: 05/08/2023]
Abstract
Over the last two decades, it has become increasingly clear that a large fraction of the human proteome is intrinsically disordered or contains disordered segments of significant length. These intrinsically disordered proteins (IDPs) play important regulatory roles throughout biology, underlining the importance of understanding their conformational behavior and interaction mechanisms at the molecular level. Here we review recent progress in the NMR characterization of the structure and dynamics of IDPs in various functional states and environments. We describe the complementarity of different NMR parameters for quantifying the conformational propensities of IDPs in their isolated and phosphorylated states, and we discuss the challenges associated with obtaining structural models of dynamic protein-protein complexes involving IDPs. In addition, we review recent progress in understanding the conformational behavior of IDPs in cell-like environments such as in the presence of crowding agents, in membrane-less organelles and in the complex environment of the human cell.
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Affiliation(s)
- Sigrid Milles
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
| | - Nicola Salvi
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
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