1
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Anila MM, Rogowski P, Różycki B. Scrutinising the Conformational Ensemble of the Intrinsically Mixed-Folded Protein Galectin-3. Molecules 2024; 29:2768. [PMID: 38930833 PMCID: PMC11207097 DOI: 10.3390/molecules29122768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/24/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Galectin-3 is a protein involved in many intra- and extra-cellular processes. It has been identified as a diagnostic or prognostic biomarker for certain types of heart disease, kidney disease and cancer. Galectin-3 comprises a carbohydrate recognition domain (CRD) and an N-terminal domain (NTD), which is unstructured and contains eight collagen-like Pro-Gly-rich tandem repeats. While the structure of the CRD has been solved using protein crystallography, current knowledge about conformations of full-length galectin-3 is limited. To fill in this knowledge gap, we performed molecular dynamics (MD) simulations of full-length galectin-3. We systematically re-scaled the solute-solvent interactions in the Martini 3 force field to obtain the best possible agreement between available data from SAXS experiments and the ensemble of conformations generated in the MD simulations. The simulation conformations were found to be very diverse, as reflected, e.g., by (i) large fluctuations in the radius of gyration, ranging from about 2 to 5 nm, and (ii) multiple transient contacts made by amino acid residues in the NTD. Consistent with evidence from NMR experiments, contacts between the CRD and NTD were observed to not involve the carbohydrate-binding site on the CRD surface. Contacts within the NTD were found to be made most frequently by aromatic residues. Formation of fuzzy complexes with unspecific stoichiometry was observed to be mediated mostly by the NTD. Taken together, we offer a detailed picture of the conformational ensemble of full-length galectin-3, which will be important for explaining the biological functions of this protein at the molecular level.
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Affiliation(s)
| | | | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland; (M.M.A.); (P.R.)
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2
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Dudas EF, Tully MD, Foldes T, Kelly G, Tartaglia GG, Pastore A. The structural properties of full-length annexin A11. Front Mol Biosci 2024; 11:1347741. [PMID: 38516187 PMCID: PMC10955470 DOI: 10.3389/fmolb.2024.1347741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/17/2024] [Indexed: 03/23/2024] Open
Abstract
Annexin A11 (ANXA11) is a calcium-dependent phospholipid-binding protein belonging to the annexin protein family and implicated in the neurodegenerative amyotrophic lateral sclerosis. Structurally, ANXA11 contains a conserved calcium-binding C-terminal domain common to all annexins and a putative intrinsically unfolded N-terminus specific for ANXA11. Little is known about the structure and functions of this region of the protein. By analogy with annexin A1, it was suggested that residues 38 to 59 within the ANXA11 N-terminus could form a helical region that would be involved in interactions. Interestingly, this region contains residues that, when mutated, may lead to clinical manifestations. In the present study, we have studied the structural features of the full-length protein with special attention to the N-terminal region using a combination of biophysical techniques which include nuclear magnetic resonance and small angle X-ray scattering. We show that the N-terminus is intrinsically disordered and that the overall features of the protein are not markedly affected by the presence of calcium. We also analyzed the 38-59 helix hypothesis using synthetic peptides spanning both the wild-type sequence and clinically relevant mutations. We show that the peptides have a remarkable character typical of a native helix and that mutations do not alter the behaviour suggesting that they are required for interactions rather than being structurally important. Our work paves the way to a more thorough understanding of the ANXA11 functions.
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Affiliation(s)
- Erika F. Dudas
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
- European Synchrotron Radiation Facility, Grenoble, France
| | - Mark D. Tully
- European Synchrotron Radiation Facility, Grenoble, France
| | - Tamas Foldes
- University College London, Department of Physics and Astronomy, University College London, London, United Kingdom
- Institut de Biologie Structurale (IBS), Institut Laue-Langevin, University Grenoble Alpes, Grenoble, France
| | - Geoff Kelly
- MRC Biomedical NMR Centre, The Francis Crick Institute, London, United Kingdom
| | | | - Annalisa Pastore
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
- European Synchrotron Radiation Facility, Grenoble, France
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3
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Guillien M, Mouhand A, Sagar A, Fournet A, Allemand F, Pereira GAN, Thureau A, Bernadó P, Banères JL, Sibille N. Phosphorylation motif dictates GPCR C-terminal domain conformation and arrestin interaction. Structure 2023; 31:1394-1406.e7. [PMID: 37669668 DOI: 10.1016/j.str.2023.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 09/07/2023]
Abstract
Arrestin-dependent G protein-coupled receptor (GPCR) signaling pathway is regulated by the phosphorylation state of GPCR's C-terminal domain, but the molecular bases of arrestin:receptor interaction are to be further illuminated. Here we investigated the impact of phosphorylation on the conformational features of the C-terminal region from three rhodopsin-like GPCRs, the vasopressin V2 receptor (V2R), the growth hormone secretagogue or ghrelin receptor type 1a (GHSR), and the β2-adernergic receptor (β2AR). Using phosphomimetic variants, we identified pre-formed secondary structure elements, or short linear motifs (SLiMs), that undergo specific conformational transitions upon phosphorylation. Of importance, such conformational transitions appear to favor arrestin-2 binding. Hence, our results suggest a model in which the phosphorylation-dependent structuration of the GPCR C-terminal regions would modulate arrestin binding and therefore signaling outcomes in arrestin-dependent pathways.
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Affiliation(s)
- Myriam Guillien
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Assia Mouhand
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Amin Sagar
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Aurélie Fournet
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Frédéric Allemand
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Glaécia A N Pereira
- Institut des Biomolécules Max Mousseron (IBMM), UMR-5247, University Montpellier, CNRS, ENSCM, Montpellier, France
| | - Aurélien Thureau
- HélioBio Section, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin BP 48, 91190 Gif-sur-Yvette, France
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France
| | - Jean-Louis Banères
- Institut des Biomolécules Max Mousseron (IBMM), UMR-5247, University Montpellier, CNRS, ENSCM, Montpellier, France
| | - Nathalie Sibille
- Centre de Biologie Structurale (CBS), CNRS, University Montpellier, Inserm, Montpellier, France.
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4
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Paladino A, Vitagliano L, Graziano G. The Action of Chemical Denaturants: From Globular to Intrinsically Disordered Proteins. BIOLOGY 2023; 12:biology12050754. [PMID: 37237566 DOI: 10.3390/biology12050754] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023]
Abstract
Proteins perform their many functions by adopting either a minimal number of strictly similar conformations, the native state, or a vast ensemble of highly flexible conformations. In both cases, their structural features are highly influenced by the chemical environment. Even though a plethora of experimental studies have demonstrated the impact of chemical denaturants on protein structure, the molecular mechanism underlying their action is still debated. In the present review, after a brief recapitulation of the main experimental data on protein denaturants, we survey both classical and more recent interpretations of the molecular basis of their action. In particular, we highlight the differences and similarities of the impact that denaturants have on different structural classes of proteins, i.e., globular, intrinsically disordered (IDP), and amyloid-like assemblies. Particular attention has been given to the IDPs, as recent studies are unraveling their fundamental importance in many physiological processes. The role that computation techniques are expected to play in the near future is illustrated.
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Affiliation(s)
- Antonella Paladino
- Institute of Biostructures and Bioimaging, CNR, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giuseppe Graziano
- Department of Science and Technology, University of Sannio, via Francesco de Sanctis snc, 82100 Benevento, Italy
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5
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Szpotkowski K, Wójcik K, Kurzyńska-Kokorniak A. Structural studies of protein-nucleic acid complexes: A brief overview of the selected techniques. Comput Struct Biotechnol J 2023; 21:2858-2872. [PMID: 37216015 PMCID: PMC10195699 DOI: 10.1016/j.csbj.2023.04.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
Protein-nucleic acid complexes are involved in all vital processes, including replication, transcription, translation, regulation of gene expression and cell metabolism. Knowledge of the biological functions and molecular mechanisms beyond the activity of the macromolecular complexes can be determined from their tertiary structures. Undoubtably, performing structural studies of protein-nucleic acid complexes is challenging, mainly because these types of complexes are often unstable. In addition, their individual components may display extremely different surface charges, causing the complexes to precipitate at higher concentrations used in many structural studies. Due to the variety of protein-nucleic acid complexes and their different biophysical properties, no simple and universal guideline exists that helps scientists chose a method to successfully determine the structure of a specific protein-nucleic acid complex. In this review, we provide a summary of the following experimental methods, which can be applied to study the structures of protein-nucleic acid complexes: X-ray and neutron crystallography, nuclear magnetic resonance (NMR) spectroscopy, cryogenic electron microscopy (cryo-EM), atomic force microscopy (AFM), small angle scattering (SAS) methods, circular dichroism (CD) and infrared (IR) spectroscopy. Each method is discussed regarding its historical context, advancements over the past decades and recent years, and weaknesses and strengths. When a single method does not provide satisfactory data on the selected protein-nucleic acid complex, a combination of several methods should be considered as a hybrid approach; thus, specific structural problems can be solved when studying protein-nucleic acid complexes.
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Affiliation(s)
- Kamil Szpotkowski
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Klaudia Wójcik
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Anna Kurzyńska-Kokorniak
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Poland
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6
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Chowdhury UD, Paul A, Bhargava BL. Interaction of the tau fibrils with the neuronal membrane. Biophys Chem 2023; 298:107024. [PMID: 37104971 DOI: 10.1016/j.bpc.2023.107024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/17/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023]
Abstract
Tau proteins are recently gaining a lot of interest due to their active role in causing a range of tauopathies. Molecular mechanisms underlying the tau interaction with the neuronal membrane are hitherto unknown and difficult to characterize using experimental methods. Using the cryo-EM structure of the tau-fibrils we have used atomistic molecular dynamics simulation to model the tau fibril and neuronal membrane interaction using explicit solvation. The dynamics and structural characteristics of the tau fibril with the neuronal membrane are compared to the tau fibril in the aqueous phase to corroborate the effect of the neuronal membrane in the tau structure. Tau fibrils have been modelled using CHARMM-36m force field and the six component neuronal membrane composition is taken from the earlier simulation results. The timescale conceivable in our molecular dynamics simulations is of the order of microseconds which captures the onset of the interaction of the tau fibrils with the neuronal membrane. This interaction is found to impact the tau pathogenesis that finally causes neuronal toxicity. Our study initiates the understanding of tau conformational ensemble in the presence of neuronal membrane and sheds the light on the significant tau-membrane interactions.
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Affiliation(s)
- Unmesh D Chowdhury
- School of Chemical Sciences, National Institute of Science Education & Research-Bhubaneswar, An OCC of Homi Bhabha National Institute, P.O. Jatni, Khurda, Odisha 752050, India
| | - Arnav Paul
- School of Chemical Sciences, National Institute of Science Education & Research-Bhubaneswar, An OCC of Homi Bhabha National Institute, P.O. Jatni, Khurda, Odisha 752050, India
| | - B L Bhargava
- School of Chemical Sciences, National Institute of Science Education & Research-Bhubaneswar, An OCC of Homi Bhabha National Institute, P.O. Jatni, Khurda, Odisha 752050, India.
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7
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Barclay A, Kragelund BB, Arleth L, Pedersen MC. Modeling of flexible membrane-bound biomolecular complexes for solution small-angle scattering. J Colloid Interface Sci 2023; 635:611-621. [PMID: 36634513 DOI: 10.1016/j.jcis.2022.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/18/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
Recent advances in protein expression protocols, sample handling, and experimental set up of small-angle scattering experiments have allowed users of the technique to structurally investigate biomolecules of growing complexity and structural disorder. Notable examples include intrinsically disordered proteins, multi-domain proteins and membrane proteins in suitable carrier systems. Here, we outline a modeling scheme for calculating the scattering profiles from such complex samples. This kind of modeling is necessary for structural information to be refined from the corresponding data. The scheme bases itself on a hybrid of classical form factor based modeling and the well-known spherical harmonics-based formulation of small-angle scattering amplitudes. Our framework can account for flexible domains alongside other structurally elaborate components of the molecular system in question. We demonstrate the utility of this modeling scheme through a recent example of a structural model of the growth hormone receptor membrane protein in a phospholipid bilayer nanodisc which is refined against experimental SAXS data. Additionally we investigate how the scattering profiles from the complex would appear under different scattering contrasts. For each contrast situation we discuss what structural information is contained and the related consequences for modeling of the data.
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Affiliation(s)
- Abigail Barclay
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen 2200, Denmark.
| | - Lise Arleth
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark.
| | - Martin Cramer Pedersen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark.
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8
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Pradhan R, Panigrahi S, Sahu PK. Conformational Search for the Building Block of Proteins Based on the Gradient Gravitational Search Algorithm (ConfGGS) Using Force Fields: CHARMM, AMBER, and OPLS-AA. J Chem Inf Model 2023; 63:670-690. [PMID: 36625780 DOI: 10.1021/acs.jcim.2c01398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Proteins are linear polymers built from a repertoire of 20 different amino acids, which are considered building blocks of proteins. The diversity and versatility of these 20 building blocks with regard to their conformations are key to adopting three-dimensional structures that facilitate proteins to undergo important mechanistic biological processes in living systems. The present investigation reports a conformational search of 20 different amino acids, building blocks of proteins, using three different force fields, CHARMM, AMBER, and OPLS-AA, implemented in the gradient gravitational search algorithm. The search technique (ConfGGS) includes the contribution from both bonded and nonbonded terms using Cartesian coordinates. The efficiency of such conformational searches has also been compared with other optimization algorithms: DE/Best, DE/Rand, and PSO algorithms with respect to computational time and accuracy based on the minimum number of iteration steps and computed lowest mean absolute error (MAE) and mean standard deviation (MSD) values for dihedral angles of respective near-optimal structures. Moreover, the ConfGGS technique has also been extended to an ordered protein fragment (PQITL) extracted from HIV-1 protease (PDB ID: 1YTH), an intrinsically disordered protein fragment, i.e., an amyloid-forming segment (AVVTGVTAV), from the NAC domain of Parkinson's disease protein α-synuclein, residues 69-77 (PDB ID: 4RIK), the experimental NMR atomic-resolution structure of α-synuclein fibrils (PDB ID: 2N0A), and a disulfide bond-containing protein fragment sequence (PCYGWPVCY), residues 59-67 (PDB ID: 6Y4F) toward structure prediction as a close homologue compared with experimental accuracy, using the CHARMM force field. The MolProbity validation results for the protein fragment (PQITL) obtained by ConfGGS/CHARMM are in better agreement with the native protein fragment structure of HIV-1 protease (PDB ID: 1YTH). Furthermore, the computed results have also been compared with the coordinates obtained from the AlphaFold network.
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Affiliation(s)
- Rojalin Pradhan
- Computational Modeling Research Laboratory, School of Chemistry (Autonomous), Sambalpur University, Jyoti Vihar, Burla768019, India
| | - Sibarama Panigrahi
- Computational Modeling Research Laboratory, School of Chemistry (Autonomous), Sambalpur University, Jyoti Vihar, Burla768019, India
- Department of Computer Science and Engineering, Sambalpur University Institute of Information Technology, Jyoti Vihar, Burla768019, India
| | - Prabhat K Sahu
- Computational Modeling Research Laboratory, School of Chemistry (Autonomous), Sambalpur University, Jyoti Vihar, Burla768019, India
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9
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Newcombe EA, Delaforge E, Hartmann-Petersen R, Skriver K, Kragelund BB. How phosphorylation impacts intrinsically disordered proteins and their function. Essays Biochem 2022; 66:901-913. [PMID: 36350035 PMCID: PMC9760426 DOI: 10.1042/ebc20220060] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/10/2022]
Abstract
Phosphorylation is the most common post-translational modification (PTM) in eukaryotes, occurring particularly frequently in intrinsically disordered proteins (IDPs). These proteins are highly flexible and dynamic by nature. Thus, it is intriguing that the addition of a single phosphoryl group to a disordered chain can impact its function so dramatically. Furthermore, as many IDPs carry multiple phosphorylation sites, the number of possible states increases, enabling larger complexities and novel mechanisms. Although a chemically simple and well-understood process, the impact of phosphorylation on the conformational ensemble and molecular function of IDPs, not to mention biological output, is highly complex and diverse. Since the discovery of the first phosphorylation site in proteins 75 years ago, we have come to a much better understanding of how this PTM works, but with the diversity of IDPs and their capacity for carrying multiple phosphoryl groups, the complexity grows. In this Essay, we highlight some of the basic effects of IDP phosphorylation, allowing it to serve as starting point when embarking on studies into this topic. We further describe how recent complex cases of multisite phosphorylation of IDPs have been instrumental in widening our view on the effect of protein phosphorylation. Finally, we put forward perspectives on the phosphorylation of IDPs, both in relation to disease and in context of other PTMs; areas where deep insight remains to be uncovered.
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Affiliation(s)
- Estella A Newcombe
- REPIN, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, DK-2200 Copenhagen N, Denmark
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes vej 5, DK-2200 Copenhagen N, Denmark
- The Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, DK-2200 Copenhagen N, Denmark
| | - Elise Delaforge
- REPIN, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, DK-2200 Copenhagen N, Denmark
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes vej 5, DK-2200 Copenhagen N, Denmark
- The Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, DK-2200 Copenhagen N, Denmark
| | - Rasmus Hartmann-Petersen
- REPIN, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, DK-2200 Copenhagen N, Denmark
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes vej 5, DK-2200 Copenhagen N, Denmark
| | - Karen Skriver
- REPIN, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, DK-2200 Copenhagen N, Denmark
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes vej 5, DK-2200 Copenhagen N, Denmark
| | - Birthe B Kragelund
- REPIN, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, DK-2200 Copenhagen N, Denmark
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Ole Maaløes vej 5, DK-2200 Copenhagen N, Denmark
- The Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, DK-2200 Copenhagen N, Denmark
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10
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Momin AA, Mendes T, Barthe P, Faure C, Hong S, Yu P, Kadaré G, Jaremko M, Girault JA, Jaremko Ł, Arold ST. PYK2 senses calcium through a disordered dimerization and calmodulin-binding element. Commun Biol 2022; 5:800. [PMID: 35945264 PMCID: PMC9363500 DOI: 10.1038/s42003-022-03760-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 07/22/2022] [Indexed: 11/25/2022] Open
Abstract
Multidomain kinases use many ways to integrate and process diverse stimuli. Here, we investigated the mechanism by which the protein tyrosine kinase 2-beta (PYK2) functions as a sensor and effector of cellular calcium influx. We show that the linker between the PYK2 kinase and FAT domains (KFL) encompasses an unusual calmodulin (CaM) binding element. PYK2 KFL is disordered and engages CaM through an ensemble of transient binding events. Calcium increases the association by promoting structural changes in CaM that expose auxiliary interaction opportunities. KFL also forms fuzzy dimers, and dimerization is enhanced by CaM binding. As a monomer, however, KFL associates with the PYK2 FERM-kinase fragment. Thus, we identify a mechanism whereby calcium influx can promote PYK2 self-association, and hence kinase-activating trans-autophosphorylation. Collectively, our findings describe a flexible protein module that expands the paradigms for CaM binding and self-association, and their use for controlling kinase activity. Protein tyrosine kinase 2-beta is shown to function as a sensor and effector of cellular calcium influx through self-association.
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Affiliation(s)
- Afaque A Momin
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Tiago Mendes
- Inserm UMR-S 1270, Sorbonne Université, Faculty of Sciences and Engineering, Institut du Fer à Moulin, 75005, Paris, France
| | - Philippe Barthe
- Centre de Biologie Structurale (CBS), University Montpellier, INSERM U1054, CNRS UMR 5048, 34090, Montpellier, France
| | - Camille Faure
- Inserm UMR-S 1270, Sorbonne Université, Faculty of Sciences and Engineering, Institut du Fer à Moulin, 75005, Paris, France
| | - SeungBeom Hong
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Piao Yu
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Gress Kadaré
- Inserm UMR-S 1270, Sorbonne Université, Faculty of Sciences and Engineering, Institut du Fer à Moulin, 75005, Paris, France
| | - Mariusz Jaremko
- Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Jean-Antoine Girault
- Inserm UMR-S 1270, Sorbonne Université, Faculty of Sciences and Engineering, Institut du Fer à Moulin, 75005, Paris, France
| | - Łukasz Jaremko
- Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Stefan T Arold
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia. .,Bioscience Program, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia. .,Centre de Biologie Structurale (CBS), University Montpellier, INSERM U1054, CNRS UMR 5048, 34090, Montpellier, France.
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11
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Chowdhury UD, Paul A, Bhargava BL. The effect of lipid composition on the dynamics of tau fibrils. Proteins 2022; 90:2103-2115. [DOI: 10.1002/prot.26401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/01/2022] [Accepted: 07/15/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Unmesh Dutta Chowdhury
- School of Chemical Sciences National Institute of Science Education & Research‐Bhubaneswar, OCC of Homi Bhabha National Institute Khurda Odisha India
| | - Arnav Paul
- School of Chemical Sciences National Institute of Science Education & Research‐Bhubaneswar, OCC of Homi Bhabha National Institute Khurda Odisha India
| | - B. L. Bhargava
- School of Chemical Sciences National Institute of Science Education & Research‐Bhubaneswar, OCC of Homi Bhabha National Institute Khurda Odisha India
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12
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Pahari S, Liu S, Lee CH, Akbulut M, Kwon JSI. SAXS-guided unbiased coarse-grained Monte Carlo simulation for identification of self-assembly nanostructures and dimensions. SOFT MATTER 2022; 18:5282-5292. [PMID: 35789362 DOI: 10.1039/d2sm00601d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recent studies have shown that solvated amphiphiles can form nanostructured self-assemblies called dynamic binary complexes (DBCs) in the presence of ions. Since the nanostructures of DBCs are directly related to their viscoelastic properties, it is important to understand how the nanostructures change under different solution conditions. However, it is challenging to obtain a three-dimensional molecular description of these nanostructures by utilizing conventional experimental characterization techniques or thermodynamic models. To this end, we combined the structural data from small angle X-ray scattering (SAXS) experiments and thermodynamic knowledge from coarse-grained Monte Carlo (CGMC) simulations to identify the detailed three-dimensional nanostructure of DBCs. Specifically, unbiased CGMC simulations are performed with SAXS-guided initial conditions, which aids us to sample accurate nanostructures in a computationally efficient fashion. As a result, an elliptical bilayer nanostructure is obtained as the most probable nanostructure of DBCs whose dimensions are validated by scanning electron microscope (SEM) images. Then, utilizing the obtained molecular model of DBCs, we could also explain the pH tunability of the system. Overall, our results from SAXS-guided unbiased CGMC simulations highlight that using potential energy combined with SAXS data, we can distinguish otherwise degenerate nanostructures resulting from the inherent ambiguity of SAXS patterns.
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Affiliation(s)
- Silabrata Pahari
- Texas A&M University, Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA.
- Texas A&M Energy Institute, Texas A&M Energy Institute, 1617 Research Pkwy, College Station, TX 77843, USA
| | - Shuhao Liu
- Texas A&M University, Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA.
| | - Chi Ho Lee
- Texas A&M University, Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA.
- Texas A&M Energy Institute, Texas A&M Energy Institute, 1617 Research Pkwy, College Station, TX 77843, USA
| | - Mustafa Akbulut
- Texas A&M University, Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA.
- Texas A&M Energy Institute, Texas A&M Energy Institute, 1617 Research Pkwy, College Station, TX 77843, USA
| | - Joseph Sang-Il Kwon
- Texas A&M University, Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA.
- Texas A&M Energy Institute, Texas A&M Energy Institute, 1617 Research Pkwy, College Station, TX 77843, USA
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13
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Conformational ensemble of the full-length SARS-CoV-2 nucleocapsid (N) protein based on molecular simulations and SAXS data. Biophys Chem 2022; 288:106843. [PMID: 35696898 PMCID: PMC9172258 DOI: 10.1016/j.bpc.2022.106843] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/10/2022] [Accepted: 06/02/2022] [Indexed: 11/02/2022]
Abstract
The nucleocapsid protein of the SARS-CoV-2 virus comprises two RNA-binding domains and three regions that are intrinsically disordered. While the structures of the RNA-binding domains have been solved using protein crystallography and NMR, current knowledge of the conformations of the full-length nucleocapsid protein is rather limited. To fill in this knowledge gap, we combined coarse-grained molecular simulations with data from small-angle X-ray scattering (SAXS) experiments using the ensemble refinement of SAXS (EROS) method. Our results show that the dimer of the full-length nucleocapsid protein exhibits large conformational fluctuations with its radius of gyration ranging from about 4 to 8 nm. The RNA-binding domains do not make direct contacts. The disordered region that links these two domains comprises a hydrophobic α-helix which makes frequent and nonspecific contacts with the RNA-binding domains. Each of the intrinsically disordered regions adopts conformations that are locally compact, yet on average, much more extended than Gaussian chains of equivalent lengths. We offer a detailed picture of the conformational ensemble of the nucleocapsid protein dimer under near-physiological conditions, which will be important for understanding the nucleocapsid assembly process.
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14
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Han ZZ, Kang SG, Arce L, Westaway D. Prion-like strain effects in tauopathies. Cell Tissue Res 2022; 392:179-199. [PMID: 35460367 PMCID: PMC9034081 DOI: 10.1007/s00441-022-03620-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/25/2022] [Indexed: 12/30/2022]
Abstract
Tau is a microtubule-associated protein that plays crucial roles in physiology and pathophysiology. In the realm of dementia, tau protein misfolding is associated with a wide spectrum of clinicopathologically diverse neurodegenerative diseases, collectively known as tauopathies. As proposed by the tau strain hypothesis, the intrinsic heterogeneity of tauopathies may be explained by the existence of structurally distinct tau conformers, “strains”. Tau strains can differ in their associated clinical features, neuropathological profiles, and biochemical signatures. Although prior research into infectious prion proteins offers valuable lessons for studying how a protein-only pathogen can encompass strain diversity, the underlying mechanism by which tau subtypes are generated remains poorly understood. Here we summarize recent advances in understanding different tau conformers through in vivo and in vitro experimental paradigms, and the implications of heterogeneity of pathological tau species for drug development.
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Affiliation(s)
- Zhuang Zhuang Han
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2M8, Canada.,Department of Medicine, University of Alberta, Edmonton, AB, Canada.,Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Sang-Gyun Kang
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2M8, Canada.,Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Luis Arce
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2M8, Canada.,Department of Medicine, University of Alberta, Edmonton, AB, Canada.,Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - David Westaway
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2M8, Canada. .,Department of Medicine, University of Alberta, Edmonton, AB, Canada. .,Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
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15
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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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16
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Shukla S, Agarwal P, Kumar A. Disordered regions tune order in chromatin organization and function. Biophys Chem 2022; 281:106716. [PMID: 34844028 DOI: 10.1016/j.bpc.2021.106716] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/10/2021] [Accepted: 11/10/2021] [Indexed: 12/29/2022]
Abstract
Intrinsically disordered proteins or hybrid proteins with ordered domains and disordered regions (both collectively designated as IDP(R)s) defy the well-established structure-function paradigm due to their ability to perform multiple biological functions even in the absence of a well-defined 3D structure. IDP(R)s have a unique ability to exist as a functional heterogeneous ensemble, where they adopt multiple thermodynamically stable conformations with low energy barriers between states. The resultant structural plasticity or conformational adaptability provides them with a high functional diversity and ease of regulation. Hence, IDP(R)s are highly efficient biological machinery to mediate intricate cellular functions such as signaling, gene expression, and assembly of complex structures. One such structure is the nucleoprotein complex known as Chromatin. Interestingly, the proteins involved in shaping up the structure and function of chromatin are abundant in disordered regions, which serve more than just as mere flexible linkers. The disordered regions are involved in crucial processes such as gene expression regulation, chromatin architecture maintenance, and liquid-liquid phase separation initiation. This review is an attempt to explore the advantages and the functional and regulatory roles of intrinsic disorder in several Chromatin Associated Proteins from a mechanistic standpoint.
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Affiliation(s)
- Shivangi Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Prakhar Agarwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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17
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Trewhella J. Recent advances in small-angle scattering and its expanding impact in structural biology. Structure 2022; 30:15-23. [PMID: 34995477 DOI: 10.1016/j.str.2021.09.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/23/2021] [Accepted: 09/20/2021] [Indexed: 10/19/2022]
Abstract
Applications of small-angle scattering (SAS) in structural biology have benefited from continuing developments in instrumentation, tools for data analysis, modeling capabilities, standards for data and model presentation, and data archiving. The interplay of these capabilities has enabled SAS to contribute to advances in structural biology as the field pushes the boundaries in studies of biomolecular complexes and assemblies as large as whole cells, membrane proteins in lipid environments, and dynamic systems on time scales ranging from femtoseconds to hours. This review covers some of the important advances in biomolecular SAS capabilities for structural biology focused on over the last 5 years and presents highlights of recent applications that demonstrate how the technique is exploring new territories.
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Affiliation(s)
- Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW 2006, Australia.
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18
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Tsegaye S, Dedefo G, Mehdi M. Biophysical applications in structural and molecular biology. Biol Chem 2021; 402:1155-1177. [PMID: 34218543 DOI: 10.1515/hsz-2021-0232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 05/27/2021] [Indexed: 11/15/2022]
Abstract
The main objective of structural biology is to model proteins and other biological macromolecules and link the structural information to function and dynamics. The biological functions of protein molecules and nucleic acids are inherently dependent on their conformational dynamics. Imaging of individual molecules and their dynamic characteristics is an ample source of knowledge that brings new insights about mechanisms of action. The atomic-resolution structural information on most of the biomolecules has been solved by biophysical techniques; either by X-ray diffraction in single crystals or by nuclear magnetic resonance (NMR) spectroscopy in solution. Cryo-electron microscopy (cryo-EM) is emerging as a new tool for analysis of a larger macromolecule that couldn't be solved by X-ray crystallography or NMR. Now a day's low-resolution Cryo-EM is used in combination with either X-ray crystallography or NMR. The present review intends to provide updated information on applications like X-ray crystallography, cryo-EM and NMR which can be used independently and/or together in solving structures of biological macromolecules for our full comprehension of their biological mechanisms.
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Affiliation(s)
- Solomon Tsegaye
- Department of Biochemistry, College of Health Sciences, Arsi University, Oromia, Ethiopia
| | - Gobena Dedefo
- Department of Medical Laboratory Technology, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Mohammed Mehdi
- Department of Biochemistry, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
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19
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Das M, Chen N, LiWang A, Wang LP. Identification and characterization of metamorphic proteins: Current and future perspectives. Biopolymers 2021; 112:e23473. [PMID: 34528703 DOI: 10.1002/bip.23473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 11/06/2022]
Abstract
Proteins that can reversibly alternate between distinctly different folds under native conditions are described as being metamorphic. The "metamorphome" is the collection of all metamorphic proteins in the proteome, but it remains unknown the extent to which the proteome is populated by this class of proteins. We propose that uncovering the metamorphome will require a synergy of computational screening of protein sequences to identify potential metamorphic behavior and validation through experimental techniques. This perspective discusses computational and experimental approaches that are currently used to predict and characterize metamorphic proteins as well as the need for developing improved methodologies. Since metamorphic proteins act as molecular switches, understanding their properties and behavior could lead to novel applications of these proteins as sensors in biological or environmental contexts.
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Affiliation(s)
- Madhurima Das
- School of Natural Sciences, University of California, Merced, California, USA
| | - Nanhao Chen
- Department of Chemistry, University of California, Davis, California, USA
| | - Andy LiWang
- School of Natural Sciences, University of California, Merced, California, USA.,Department of Chemistry and Biochemistry, University of California, Merced, California, USA.,Center for Cellular and Biomolecular Machines, University of California, Merced, California, USA.,Health Sciences Research Institute, University of California, Merced, California, USA.,Center for Circadian Biology, University of California, San Diego, California, USA
| | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, California, USA
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20
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Gomes T, Martin-Malpartida P, Ruiz L, Aragón E, Cordeiro TN, Macias MJ. Conformational landscape of multidomain SMAD proteins. Comput Struct Biotechnol J 2021; 19:5210-5224. [PMID: 34630939 PMCID: PMC8479633 DOI: 10.1016/j.csbj.2021.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/21/2022] Open
Abstract
SMAD transcription factors, the main effectors of the TGFβ (transforming growth factor β) network, have a mixed architecture of globular domains and flexible linkers. Such a complicated architecture precluded the description of their full-length (FL) structure for many years. In this study, we unravel the structures of SMAD4 and SMAD2 proteins through an integrative approach combining Small-angle X-ray scattering, Nuclear Magnetic Resonance spectroscopy, X-ray, and computational modeling. We show that both proteins populate ensembles of conformations, with the globular domains tethered by disordered and flexible linkers, which defines a new dimension of regulation. The flexibility of the linkers facilitates DNA and protein binding and modulates the protein structure. Yet, SMAD4FL is monomeric, whereas SMAD2FL is in different monomer-dimer-trimer states, driven by interactions of the MH2 domains. Dimers are present regardless of the SMAD2FL activation state and concentration. Finally, we propose that SMAD2FL dimers are key building blocks for the quaternary structures of SMAD complexes.
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Affiliation(s)
- Tiago Gomes
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Pau Martin-Malpartida
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Lidia Ruiz
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Eric Aragón
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Tiago N. Cordeiro
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Maria J. Macias
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
- ICREA, Passeig Lluís Companys 23, Barcelona 08010, Spain
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21
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Clerc I, Sagar A, Barducci A, Sibille N, Bernadó P, Cortés J. The diversity of molecular interactions involving intrinsically disordered proteins: A molecular modeling perspective. Comput Struct Biotechnol J 2021; 19:3817-3828. [PMID: 34285781 PMCID: PMC8273358 DOI: 10.1016/j.csbj.2021.06.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 01/15/2023] Open
Abstract
Intrinsically Disordered Proteins and Regions (IDPs/IDRs) are key components of a multitude of biological processes. Conformational malleability enables IDPs/IDRs to perform very specialized functions that cannot be accomplished by globular proteins. The functional role for most of these proteins is related to the recognition of other biomolecules to regulate biological processes or as a part of signaling pathways. Depending on the extent of disorder, the number of interacting sites and the type of partner, very different architectures for the resulting assemblies are possible. More recently, molecular condensates with liquid-like properties composed of multiple copies of IDPs and nucleic acids have been proven to regulate key processes in eukaryotic cells. The structural and kinetic details of disordered biomolecular complexes are difficult to unveil experimentally due to their inherent conformational heterogeneity. Computational approaches, alone or in combination with experimental data, have emerged as unavoidable tools to understand the functional mechanisms of this elusive type of assemblies. The level of description used, all-atom or coarse-grained, strongly depends on the size of the molecular systems and on the timescale of the investigated mechanism. In this mini-review, we describe the most relevant architectures found for molecular interactions involving IDPs/IDRs and the computational strategies applied for their investigation.
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Affiliation(s)
- Ilinka Clerc
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
| | - Amin Sagar
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Alessandro Barducci
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Nathalie Sibille
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Juan Cortés
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
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22
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Sagar A, Jeffries CM, Petoukhov MV, Svergun DI, Bernadó P. Comment on the Optimal Parameters to Derive Intrinsically Disordered Protein Conformational Ensembles from Small-Angle X-ray Scattering Data Using the Ensemble Optimization Method. J Chem Theory Comput 2021; 17:2014-2021. [PMID: 33725442 DOI: 10.1021/acs.jctc.1c00014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Ensemble Optimization Method (EOM) is a popular approach to describe small-angle X-ray scattering (SAXS) data from highly disordered proteins. The EOM algorithm selects subensembles of coexisting states from large pools of randomized conformations to fit the SAXS data. Based on the unphysical bimodal radius of gyration (Rg) distribution of conformations resulting from the EOM analysis, a recent article (Fagerberg et al. J. Chem. Theory Comput. 2019, 15 (12), 6968-6983) concluded that this approach inadequately described the SAXS data measured for human Histatin 5 (Hst5), a peptide with antifungal properties. Using extensive experimental and synthetic data, we explored the origin of this observation. We found that the one-bead-per-residue coarse-grained representation with averaged scattering form factors (provided in the EOM as an add-on to represent disordered missing loops or domains) may not be appropriate for EOM analyses of scattering data from short (below 50 residues) proteins/peptides. The method of choice for these proteins is to employ atomistic models (e.g., from molecular dynamics simulations) to sample the protein conformational landscape. As a convenient alternative, we have also improved the coarse-grained approach by introducing amino acid specific form factors in the calculations. We also found that, for small proteins, the search for relatively large subensembles of 20-50 conformers (as implemented in the original EOM version) more adequately describes the conformational space sampled in solution than the procedures optimizing the ensemble size. Our observations have been added as recommendations into the information for EOM users to promote the proper utilization of the program for ensemble-based modeling of SAXS data for all types of disordered systems.
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Affiliation(s)
- Amin Sagar
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France
| | - Cy M Jeffries
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Maxim V Petoukhov
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, 119333 Moscow, Russia
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France
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23
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Shrestha UR, Smith JC, Petridis L. Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations. Commun Biol 2021; 4:243. [PMID: 33623120 PMCID: PMC7902620 DOI: 10.1038/s42003-021-01759-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 01/07/2021] [Indexed: 12/13/2022] Open
Abstract
Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.
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Affiliation(s)
- Utsab R Shrestha
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, USA
| | - Jeremy C Smith
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Loukas Petridis
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, USA.
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA.
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24
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Lazar T, Martínez-Pérez E, Quaglia F, Hatos A, Chemes L, Iserte JA, Méndez NA, Garrone NA, Saldaño T, Marchetti J, Rueda A, Bernadó P, Blackledge M, Cordeiro TN, Fagerberg E, Forman-Kay JD, Fornasari M, Gibson TJ, Gomes GNW, Gradinaru C, Head-Gordon T, Jensen MR, Lemke E, Longhi S, Marino-Buslje C, Minervini G, Mittag T, Monzon A, Pappu RV, Parisi G, Ricard-Blum S, Ruff KM, Salladini E, Skepö M, Svergun D, Vallet S, Varadi M, Tompa P, Tosatto SCE, Piovesan D. PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins. Nucleic Acids Res 2021; 49:D404-D411. [PMID: 33305318 PMCID: PMC7778965 DOI: 10.1093/nar/gkaa1021] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/13/2020] [Accepted: 12/08/2020] [Indexed: 12/21/2022] Open
Abstract
The Protein Ensemble Database (PED) (https://proteinensemble.org), which holds structural ensembles of intrinsically disordered proteins (IDPs), has been significantly updated and upgraded since its last release in 2016. The new version, PED 4.0, has been completely redesigned and reimplemented with cutting-edge technology and now holds about six times more data (162 versus 24 entries and 242 versus 60 structural ensembles) and a broader representation of state of the art ensemble generation methods than the previous version. The database has a completely renewed graphical interface with an interactive feature viewer for region-based annotations, and provides a series of descriptors of the qualitative and quantitative properties of the ensembles. High quality of the data is guaranteed by a new submission process, which combines both automatic and manual evaluation steps. A team of biocurators integrate structured metadata describing the ensemble generation methodology, experimental constraints and conditions. A new search engine allows the user to build advanced queries and search all entry fields including cross-references to IDP-related resources such as DisProt, MobiDB, BMRB and SASBDB. We expect that the renewed PED will be useful for researchers interested in the atomic-level understanding of IDP function, and promote the rational, structure-based design of IDP-targeting drugs.
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Affiliation(s)
- Tamas Lazar
- VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology, Brussels 1050, Belgium
- Structural Biology Brussels, Bioengineering Sciences Department, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | - Elizabeth Martínez-Pérez
- Bioinformatics Unit, Fundación Instituto Leloir, Buenos Aires, C1405BWE, Argentina
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Federica Quaglia
- Dept. of Biomedical Sciences, University of Padua, Padova 35131, Italy
| | - András Hatos
- Dept. of Biomedical Sciences, University of Padua, Padova 35131, Italy
| | - Lucía B Chemes
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde’’, IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de SanMartín, CP1650 San Martín, Buenos Aires, Argentina
| | - Javier A Iserte
- Bioinformatics Unit, Fundación Instituto Leloir, Buenos Aires, C1405BWE, Argentina
| | - Nicolás A Méndez
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde’’, IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de SanMartín, CP1650 San Martín, Buenos Aires, Argentina
| | - Nicolás A Garrone
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde’’, IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de SanMartín, CP1650 San Martín, Buenos Aires, Argentina
| | - Tadeo E Saldaño
- Laboratorio de Química y Biología Computacional, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal B1876BXD, Buenos Aires, Argentina
| | - Julia Marchetti
- Laboratorio de Química y Biología Computacional, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal B1876BXD, Buenos Aires, Argentina
| | - Ana Julia Velez Rueda
- Laboratorio de Química y Biología Computacional, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal B1876BXD, Buenos Aires, Argentina
| | - Pau Bernadó
- Centre de Biochimie Structurale (CBS), CNRS, INSERM, University of Montpellier, Montpellier 34090, France
| | | | - Tiago N Cordeiro
- Centre de Biochimie Structurale (CBS), CNRS, INSERM, University of Montpellier, Montpellier 34090, France
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras 2780-157, Portugal
| | - Eric Fagerberg
- Theoretical Chemistry, Lund University, Lund, POB 124, SE-221 00, Sweden
| | - Julie D Forman-Kay
- Molecular Medicine Program, Hospital for Sick Children, Toronto, M5G 1X8, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, Ontario, Canada
| | - Maria S Fornasari
- Laboratorio de Química y Biología Computacional, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal B1876BXD, Buenos Aires, Argentina
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Gregory-Neal W Gomes
- Department of Physics, University of Toronto, Toronto, M5S 1A7, Ontario, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, L5L 1C6, Ontario, Canada
| | - Claudiu C Gradinaru
- Department of Physics, University of Toronto, Toronto, M5S 1A7, Ontario, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, L5L 1C6, Ontario, Canada
| | - Teresa Head-Gordon
- Departments of Chemistry, Bioengineering, Chemical and Biomolecular Engineering University of California, Berkeley, CA 94720, USA
| | | | - Edward A Lemke
- Biocentre, Johannes Gutenberg-University Mainz, Mainz 55128, Germany
- Institute of Molecular Biology, Mainz 55128, Germany
| | - Sonia Longhi
- Aix-Marseille University, CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille 13288, France
| | | | | | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | | | - Rohit V Pappu
- Department of Biomedical Engineering, Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, MO 63130, USA
| | - Gustavo Parisi
- Laboratorio de Química y Biología Computacional, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal B1876BXD, Buenos Aires, Argentina
| | - Sylvie Ricard-Blum
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, Villeurbanne, 69629 Lyon Cedex 07, France
| | - Kiersten M Ruff
- Department of Biomedical Engineering, Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, MO 63130, USA
| | - Edoardo Salladini
- Aix-Marseille University, CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille 13288, France
| | - Marie Skepö
- Theoretical Chemistry, Lund University, Lund, POB 124, SE-221 00, Sweden
- LINXS - Lund Institute of Advanced Neutron and X-ray Science, Lund 223 70, Sweden
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg 22607, Germany
| | - Sylvain D Vallet
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, Villeurbanne, 69629 Lyon Cedex 07, France
| | - Mihaly Varadi
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Peter Tompa
- To whom correspondence should be addressed. Tel +32 473 785386;
| | - Silvio C E Tosatto
- Correspondence may also be addressed to Silvio C. E. Tosatto. Tel: +39 049 827 6269;
| | - Damiano Piovesan
- Dept. of Biomedical Sciences, University of Padua, Padova 35131, Italy
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25
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Fatafta H, Samantray S, Sayyed-Ahmad A, Coskuner-Weber O, Strodel B. Molecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 183:135-185. [PMID: 34656328 DOI: 10.1016/bs.pmbts.2021.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Intrinsically disordered proteins (IDPs) lack a well-defined three-dimensional structure but do exhibit some dynamical and structural ordering. The structural plasticity of IDPs indicates that entropy-driven motions are crucial for their function. Many IDPs undergo function-related disorder-to-order transitions upon by their interaction with specific binding partners. Approaches that are based on both experimental and theoretical tools enable the biophysical characterization of IDPs. Molecular simulations provide insights into IDP structural ensembles and disorder-to-order transition mechanisms. However, such studies depend strongly on the chosen force field parameters and simulation techniques. In this chapter, we provide an overview of IDP characteristics, review all-atom force fields recently developed for IDPs, and present molecular dynamics-based simulation methods that allow IDP ensemble generation as well as the characterization of disorder-to-order transitions. In particular, we introduce metadynamics, replica exchange molecular dynamics simulations, and also kinetic models resulting from Markov State modeling, and provide various examples for the successful application of these simulation methods to IDPs.
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Affiliation(s)
- Hebah Fatafta
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Suman Samantray
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany; AICES Graduate School, RWTH Aachen University, Aachen, Germany
| | | | - Orkid Coskuner-Weber
- Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi, Istanbul, Turkey
| | - Birgit Strodel
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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26
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Borges PT, Brissos V, Hernandez G, Masgrau L, Lucas MF, Monza E, Frazão C, Cordeiro TN, Martins LO. Methionine-Rich Loop of Multicopper Oxidase McoA Follows Open-to-Close Transitions with a Role in Enzyme Catalysis. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01623] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Patrícia T. Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Vânia Brissos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Guillem Hernandez
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Laura Masgrau
- Zymvol Biomodeling, Carrer Roc Boronat, 117, 08018 Barcelona, Spain
- Department of Chemistry, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | | | - Emanuele Monza
- Zymvol Biomodeling, Carrer Roc Boronat, 117, 08018 Barcelona, Spain
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Tiago N. Cordeiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Lígia O. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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27
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Munari F, D'Onofrio M, Assfalg M. Solution NMR insights into dynamic supramolecular assemblies of disordered amyloidogenic proteins. Arch Biochem Biophys 2020; 683:108304. [PMID: 32097611 DOI: 10.1016/j.abb.2020.108304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/12/2020] [Accepted: 02/14/2020] [Indexed: 12/29/2022]
Abstract
The extraordinary flexibility and structural heterogeneity of intrinsically disordered proteins (IDP) make them functionally versatile molecules. We have now begun to better understand their fundamental role in biology, however many aspects of their behaviour remain difficult to grasp experimentally. This is especially true for the intermolecular interactions which lead to the formation of transient or highly dynamic supramolecular self-assemblies, such as oligomers, aggregation intermediates and biomolecular condensates. Both the emerging functions and pathogenicity of these structures have stimulated great efforts to develop methodologies capable of providing useful insights. Significant progress in solution NMR spectroscopy has made this technique one of the most powerful to describe structural and dynamic features of IDPs within such assemblies at atomic resolution. Here, we review the most recent works that have illuminated key aspects of IDP assemblies and contributed significant advancements towards our understanding of the complex conformational landscape of prototypical disease-associated proteins. We also include a primer on some of the fundamental and innovative NMR methods being used in the discussed studies.
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Affiliation(s)
- Francesca Munari
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Mariapina D'Onofrio
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
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28
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Neira JL, Ortore MG, Florencio FJ, Muro-Pastor MI, Rizzuti B. Dynamics of the intrinsically disordered inhibitor IF7 of glutamine synthetase in isolation and in complex with its partner. Arch Biochem Biophys 2020; 683:108303. [PMID: 32074499 DOI: 10.1016/j.abb.2020.108303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 02/09/2020] [Accepted: 02/11/2020] [Indexed: 11/26/2022]
Abstract
Glutamine synthetase (GS) catalyzes the ATP-dependent formation of glutamine from glutamate and ammonia. The activity of Synechocystis sp. PCC 6803 GS is regulated, among other mechanisms, by protein-protein interactions with a 65-residue-long, intrinsically disordered protein (IDP), named IF7. IDPs explore diverse conformations in their free states and, in some cases, in their molecular complexes. We used both nuclear magnetic resonance (NMR) at 11.7 T and small angle X-ray scattering (SAXS) to study the size and the dynamics in the picoseconds-to-nanosecond (ps-ns) timescale of: (i) isolated IF7; and (ii) the IF7/GS complex. Our SAXS findings, together with MD results, show: (i) some of the possible IF7 structures in solution; and, (ii) that the presence of IF7 affected the structure of GS in solution. The joint use of SAXS and NMR shows that movements of each amino acid of IF7 were uncorrelated with those of its neighbors. Residues of IF7 with the largest values of the relaxation rates (R1, R2 and ηxy), in the free and bound species, were mainly clustered around: (i) the C terminus of the protein; and (ii) Ala30. These residues, together with Arg8 (which is a hot-spot residue in the interaction with GS), had a restricted mobility in the presence of GS. The C-terminal region, which appeared more compact in our MD simulations of isolated IF7, seemed to be involved in non-native contacts with GS that help in the binding between the two macromolecules.
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Affiliation(s)
- José L Neira
- IDIBE, Universidad Miguel Hernández, Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain.
| | - Maria Grazia Ortore
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy.
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Seville, Spain
| | - M Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Seville, Spain
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, Via P. Bucci, Cubo 31 C, 87036, Arcavacata di Rende, Cosenza, Italy
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29
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Abstract
Functions of intrinsically disordered proteins do not require structure. Such structure-independent functionality has melted away the classic rigid "lock and key" representation of structure-function relationships in proteins, opening a new page in protein science, where molten keys operate on melted locks and where conformational flexibility and intrinsic disorder, structural plasticity and extreme malleability, multifunctionality and binding promiscuity represent a new-fangled reality. Analysis and understanding of this new reality require novel tools, and some of the techniques elaborated for the examination of intrinsically disordered protein functions are outlined in this review.
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Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33620, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Russian Federation
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30
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Gräwert TW, Svergun DI. Structural Modeling Using Solution Small-Angle X-ray Scattering (SAXS). J Mol Biol 2020; 432:3078-3092. [PMID: 32035901 DOI: 10.1016/j.jmb.2020.01.030] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 01/21/2020] [Accepted: 01/21/2020] [Indexed: 01/01/2023]
Abstract
Small-angle X-ray scattering (SAXS) offers a way to examine the overall shape and oligomerization state of biological macromolecules under quasi native conditions in solution. In the past decades, SAXS has become a standard tool for structure biologists due to the availability of high brilliance X-ray sources and the development of data analysis/interpretation methods. Sample handling robots and software pipelines have significantly reduced the time necessary to conduct SAXS experiments. Presently, most synchrotrons feature beamlines dedicated to biological SAXS, and the SAXS-derived models are deposited into dedicated and accessible databases. The size of macromolecules that may be analyzed ranges from small peptides or snippets of nucleic acids to gigadalton large complexes or even entire viruses. Compared to other structural methods, sample preparation is straightforward, and the risk of inducing preparation artefacts is minimal. Very importantly, SAXS is a method of choice to study flexible systems like unfolded or disordered proteins, providing the structural ensembles compatible with the data. Although it may be utilized stand-alone, SAXS profits a lot from available experimental or predicted high-resolution data and information from complementary biophysical methods. Here, we show the basic principles of SAXS and review latest developments in the fields of hybrid modeling and flexible systems.
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Affiliation(s)
- Tobias W Gräwert
- Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany.
| | - Dmitri I Svergun
- Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany.
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31
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Sagar A, Svergun D, Bernadó P. Structural Analyses of Intrinsically Disordered Proteins by Small-Angle X-Ray Scattering. Methods Mol Biol 2020; 2141:249-269. [PMID: 32696361 DOI: 10.1007/978-1-0716-0524-0_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Small-angle X-ray scattering (SAXS) is a low-resolution method for the structural characterization of biological macromolecules in solution. Information about the overall structural features provided by SAXS is highly complementary to X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy, which are high-resolution methods. SAXS not only provides the shape, oligomeric state, and quaternary structure of folded proteins and protein complexes but also allows for quantitative analysis of flexible biomolecules. In this chapter, the most relevant SAXS procedures for structural characterization of flexible macromolecules, including intrinsically disordered proteins (IDPs), are presented. The sample requirements for SAXS experiments on protein solutions and the sequence of steps in data collection and processing are described. The use of the advanced data analysis tools to quantitatively characterize flexible proteins is presented in detail. Typical experimental issues and potential problems encountered during SAXS data measurements and analyses are discussed.
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Affiliation(s)
- Amin Sagar
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, France.
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Hamburg, Germany
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, France.
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32
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Jiménez-García B, Bernadó P, Fernández-Recio J. Structural Characterization of Protein-Protein Interactions with pyDockSAXS. Methods Mol Biol 2020; 2112:131-144. [PMID: 32006283 DOI: 10.1007/978-1-0716-0270-6_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Structural characterization of protein-protein interactions can provide essential details to understand biological functions at the molecular level and to facilitate their manipulation for biotechnological and biomedical purposes. Unfortunately, the 3D structure is available for only a small fraction of all possible protein-protein interactions, due to the technical limitations of high-resolution structural determination methods. In this context, low-resolution structural techniques, such as small-angle X-ray scattering (SAXS), can be combined with computational docking to provide structural models of protein-protein interactions at large scale. In this chapter, we describe the pyDockSAXS web server ( https://life.bsc.es/pid/pydocksaxs ), which uses pyDock docking and scoring to provide structural models that optimally satisfy the input SAXS data. This server, which is freely available to the scientific community, provides an automatic pipeline to model the structure of a protein-protein complex from SAXS data.
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Affiliation(s)
- Brian Jiménez-García
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Pau Bernadó
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Juan Fernández-Recio
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.
- Institut de Biologia Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain.
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas (CSIC), Logroño, Spain.
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33
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Guillien M, le Maire A, Mouhand A, Bernadó P, Bourguet W, Banères JL, Sibille N. IDPs and their complexes in GPCR and nuclear receptor signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:105-155. [DOI: 10.1016/bs.pmbts.2020.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Liu H, Song D, Zhang Y, Yang S, Luo R, Chen HF. Extensive tests and evaluation of the CHARMM36IDPSFF force field for intrinsically disordered proteins and folded proteins. Phys Chem Chem Phys 2019; 21:21918-21931. [PMID: 31552948 DOI: 10.1039/c9cp03434j] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Intrinsically disordered proteins (IDPs) have received increasing attention in recent studies due to their structural heterogeneity and critical biological functions. To fully understand the structural properties and determine accurate ensembles of IDPs, molecular dynamics (MD) simulation was widely used to sample diverse conformations and reveal the structural dynamics. However, the classical state-of-the-art force fields perform well for folded proteins while being unsatisfactory for the simulations of disordered proteins reported in many previous studies. Thus, improved force fields were developed to precisely describe both folded proteins and disordered proteins. Preliminary tests show that our newly developed CHARMM36IDPSFF (C36IDPSFF) force field can well reproduce the experimental observables of several disordered proteins, but more tests on different types of proteins are needed to further evaluate the performance of C36IDPSFF. Here, we extensively simulate short peptides, disordered proteins, and fast-folding proteins as well as folded proteins, and compare the simulated results with the experimental observables. The simulation results show that C36IDPSFF could substantially reproduce the experimental observables for most of the tested proteins but some limitations are also found in the radius of gyration of large disordered proteins and the stability of fast-folding proteins. This force field will facilitate large scale studies of protein structural dynamics and functions using MD simulations.
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Affiliation(s)
- Hao Liu
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
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35
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Han JY, Choi TS, Heo CE, Son MK, Kim HI. Gas-phase conformations of intrinsically disordered proteins and their complexes with ligands: Kinetically trapped states during transfer from solution to the gas phase. MASS SPECTROMETRY REVIEWS 2019; 38:483-500. [PMID: 31021441 DOI: 10.1002/mas.21596] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
Flexible structures of intrinsically disordered proteins (IDPs) are crucial for versatile functions in living organisms, which involve interaction with diverse partners. Electrospray ionization ion mobility mass spectrometry (ESI-IM-MS) has been widely applied for structural characterization of apo-state and ligand-associated IDPs via two-dimensional separation in the gas phase. Gas-phase IDP structures have been regarded as kinetically trapped states originated from conformational features in solution. However, an implication of the states remains elusive in the structural characterization of IDPs, because it is unclear what structural property of IDPs is preserved. Recent studies have indicated that the conformational features of IDPs in solution are not fully reproduced in the gas phase. Nevertheless, the molecular interactions captured in the gas phase amplify the structural differences between IDP conformers. Therefore, an IDP conformational change that is not observed in solution is observable in the gas-phase structures obtained by ESI-IM-MS. Herein, we have presented up-to-date researches on the key implications of kinetically trapped states in the gas phase with a brief summary of the structural dynamics of IDPs in ESI-IM-MS.
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Affiliation(s)
- Jong Yoon Han
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Tae Su Choi
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093
| | - Chae Eun Heo
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Myung Kook Son
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Hugh I Kim
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
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36
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Shou K, Bremer A, Rindfleisch T, Knox-Brown P, Hirai M, Rekas A, Garvey CJ, Hincha DK, Stadler AM, Thalhammer A. Conformational selection of the intrinsically disordered plant stress protein COR15A in response to solution osmolarity - an X-ray and light scattering study. Phys Chem Chem Phys 2019; 21:18727-18740. [PMID: 31424463 DOI: 10.1039/c9cp01768b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The plant stress protein COR15A stabilizes chloroplast membranes during freezing. COR15A is an intrinsically disordered protein (IDP) in aqueous solution, but acquires an α-helical structure during dehydration or the increase of solution osmolarity. We have used small- and wide-angle X-ray scattering (SAXS/WAXS) combined with static and dynamic light scattering (SLS/DLS) to investigate the structural and hydrodynamic properties of COR15A in response to increasing solution osmolarity. Coarse-grained ensemble modelling allowed a structure-based interpretation of the SAXS data. Our results demonstrate that COR15A behaves as a biomacromolecule with polymer-like properties which strongly depend on solution osmolarity. Biomacromolecular self-assembly occurring at high solvent osmolarity is initiated by the occurrence of two specific structural subpopulations of the COR15A monomer. The osmolarity dependent structural selection mechanism is an elegant way for conformational regulation and assembly of COR15A. It highlights the importance of the polymer-like properties of IDPs for their associated biological function.
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Affiliation(s)
- Keyun Shou
- Jülich Centre for Neutron Science (JCNS-1) and Institute for Complex Systems (ICS-1), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.
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37
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González-Magaña A, de Opakua AI, Merino N, Monteiro H, Diercks T, Murciano-Calles J, Luque I, Bernadó P, Cordeiro TN, Biasio AD, Blanco FJ. Double Monoubiquitination Modifies the Molecular Recognition Properties of p15 PAF Promoting Binding to the Reader Module of Dnmt1. ACS Chem Biol 2019; 14:2315-2326. [PMID: 31479228 DOI: 10.1021/acschembio.9b00679] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The proliferating cell nuclear antigen (PCNA)-associated factor p15PAF is a nuclear protein that acts as a regulator of DNA repair during DNA replication. The p15PAF gene is overexpressed in several types of human cancer, and its function is regulated by monoubiquitination of two lysines (K15 and K24) at the protein N-terminal region. We have previously shown that p15PAF is an intrinsically disordered protein which partially folds upon binding to PCNA and independently contacts DNA through its N-terminal tail. Here we present an NMR conformational characterization of p15PAF monoubiquitinated at both K15 and K24 via a disulfide bridge mimicking the isopeptide bond. We show that doubly monoubiquitinated p15PAF is monomeric, intrinsically disordered, and binds to PCNA as nonubiquitinated p15PAF does but interacts with DNA with reduced affinity. Our SAXS-derived conformational ensemble of doubly monoubiquitinated p15PAF shows that the ubiquitin moieties, separated by eight disordered residues, form transient dimers because of the high local effective ubiquitin concentration. This observation and the sequence similarity with histone H3 N-terminal tail suggest that doubly monoubiquitinated p15PAF is a binding target of DNA methyl transferase Dnmt1, as confirmed by calorimetry. Therefore, doubly monoubiquitinated p15PAF directly interacts with PCNA and recruits Dnmt1 for maintenance of DNA methylation during replication.
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Affiliation(s)
| | | | | | - Hugo Monteiro
- Instituto de Tecnologia Química e Biológica António Xabier, ITQB NOVA, 2780-157 Oeiras, Portugal
| | | | - Javier Murciano-Calles
- Department of Physical Chemistry and Institute of Biotechnology, Universidad de Granada, Granada 18071, Spain
| | - Irene Luque
- Department of Physical Chemistry and Institute of Biotechnology, Universidad de Granada, Granada 18071, Spain
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM, CNRS, and Université Montpellier, 34090 Montpellier, France
| | - Tiago N. Cordeiro
- Instituto de Tecnologia Química e Biológica António Xabier, ITQB NOVA, 2780-157 Oeiras, Portugal
| | - Alfredo De Biasio
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Leicester LE1 7RH, U.K
| | - Francisco J. Blanco
- CIC bioGUNE, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
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Cordeiro TN, Sibille N, Germain P, Barthe P, Boulahtouf A, Allemand F, Bailly R, Vivat V, Ebel C, Barducci A, Bourguet W, le Maire A, Bernadó P. Interplay of Protein Disorder in Retinoic Acid Receptor Heterodimer and Its Corepressor Regulates Gene Expression. Structure 2019; 27:1270-1285.e6. [DOI: 10.1016/j.str.2019.05.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 03/30/2019] [Accepted: 05/04/2019] [Indexed: 11/30/2022]
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Kumar S, Ray D, Abbas S, Saha D, Aswal VK, Kohlbrecher J. Reentrant phase behavior of nanoparticle solutions probed by small-angle scattering. Curr Opin Colloid Interface Sci 2019. [DOI: 10.1016/j.cocis.2019.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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40
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Ainis WN, Boire A, Solé-Jamault V, Nicolas A, Bouhallab S, Ipsen R. Contrasting Assemblies of Oppositely Charged Proteins. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:9923-9933. [PMID: 31264885 DOI: 10.1021/acs.langmuir.9b01046] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Oppositely charged proteins can form soluble assemblies that under specific physical chemical conditions lead to liquid-liquid phase separation, also called heteroprotein coacervation. Increasing evidence suggests that surface charge anisotropy plays a key role in heteroprotein complexation, and coacervation. Here, we investigated complexation of an acidic protein, β-lactoglobulin (BLG), with two basic proteins, rapeseed napin (NAP) and lysozyme (LYS), of similar net charge and size but differing in surface charge distribution. Using turbidity measurements and isothermal titration calorimetry, we confirmed that LYS binds BLG as expected from previous studies. This interaction leads to two types of phase separation phenomena, depending on pH: liquid-solid phase separation in the case of strong electrostatic attraction and liquid-liquid phase separation for weaker attraction. More interestingly, we showed using dynamic light scattering that NAP interacts with BLG, resulting in formation of assemblies in the nanometer size range. The formation of assemblies was also evident when modeling the interactions using Brownian dynamics for both BLG + NAP and BLG + LYS. Similarly, to DLS, BLG and NAP formed smaller assemblies than BLG with LYS. The molecular details rather than the net charge of BLG and NAP may therefore play a role in their assembly. Furthermore, simulated BLG + NAP assemblies were larger than those experimentally detected by DLS. We discuss the discrepancy between experiments and simulations in relation to the limitations of modelling precisely the molecular characteristics of proteins.
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Affiliation(s)
- William Nicholas Ainis
- Section of Ingredient and Dairy Technology, Department of Food Science, Faculty of Science , University of Copenhagen , DK-1958 Frederiksberg , Denmark
| | - Adeline Boire
- INRA, Biopolymères Interactions Assemblages , F-44300 Nantes , France
| | | | - Aurélie Nicolas
- UMR1253, STLO, INRA, Agrocampus Ouest , F-35042 Rennes , France
| | - Said Bouhallab
- UMR1253, STLO, INRA, Agrocampus Ouest , F-35042 Rennes , France
| | - Richard Ipsen
- Section of Ingredient and Dairy Technology, Department of Food Science, Faculty of Science , University of Copenhagen , DK-1958 Frederiksberg , Denmark
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41
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Schramm A, Bignon C, Brocca S, Grandori R, Santambrogio C, Longhi S. An arsenal of methods for the experimental characterization of intrinsically disordered proteins - How to choose and combine them? Arch Biochem Biophys 2019; 676:108055. [PMID: 31356778 DOI: 10.1016/j.abb.2019.07.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/16/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022]
Abstract
In this review, we detail the most common experimental approaches to assess and characterize protein intrinsic structural disorder, with the notable exception of NMR and EPR spectroscopy, two ideally suited approaches that will be described in depth in two other reviews within this special issue. We discuss the advantages, the limitations, as well as the caveats of the various methods. We also describe less common and more demanding approaches that enable achieving further insights into the conformational properties of IDPs. Finally, we present recent developments that have enabled assessment of structural disorder in living cells, and discuss the currently available methods to model IDPs as conformational ensembles.
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Affiliation(s)
- Antoine Schramm
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Christophe Bignon
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Sonia Longhi
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France.
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42
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Gondelaud F, Ricard‐Blum S. Structures and interactions of syndecans. FEBS J 2019; 286:2994-3007. [DOI: 10.1111/febs.14828] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 02/04/2019] [Accepted: 03/29/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Frank Gondelaud
- ICBMS UMR 5246 CNRS – University Lyon 1 Univ Lyon Villeurbanne France
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43
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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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Chalupska D, Różycki B, Humpolickova J, Faltova L, Klima M, Boura E. Phosphatidylinositol 4-kinase IIIβ (PI4KB) forms highly flexible heterocomplexes that include ACBD3, 14-3-3, and Rab11 proteins. Sci Rep 2019; 9:567. [PMID: 30679637 PMCID: PMC6345845 DOI: 10.1038/s41598-018-37158-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/29/2018] [Indexed: 12/18/2022] Open
Abstract
Phosphatidylinositol 4-kinase IIIβ (PI4KB) is a key enzyme of the Golgi system because it produces its lipid hallmark - the phosphatidylinositol 4-phosphate (PI4P). It is recruited to Golgi by the Golgi resident ACBD3 protein, regulated by 14-3-3 proteins and it also serves as an adaptor because it recruits the small GTPase Rab11. Here, we analyzed the protein complexes formed by PI4KB in vitro using small angle x-ray scattering (SAXS) and we discovered that these protein complexes are highly flexible. The 14-3-3:PI4KB:Rab11 protein complex has 2:1:1 stoichiometry and its different conformations are rather compact, however, the ACBD3:PI4KB protein complex has both, very compact and very extended conformations. Furthermore, in vitro reconstitution revealed that the membrane is necessary for the formation of ACBD3:PI4KB:Rab11 protein complex at physiological (nanomolar) concentrations.
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Affiliation(s)
- Dominika Chalupska
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2., Prague, Czech Republic
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668, Warsaw, Poland
| | - Jana Humpolickova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2., Prague, Czech Republic
| | - Lenka Faltova
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen, PSI, Switzerland
| | - Martin Klima
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2., Prague, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2., Prague, Czech Republic.
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SAXS-guided Enhanced Unbiased Sampling for Structure Determination of Proteins and Complexes. Sci Rep 2018; 8:17748. [PMID: 30531946 PMCID: PMC6288155 DOI: 10.1038/s41598-018-36090-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 11/12/2018] [Indexed: 02/08/2023] Open
Abstract
Molecular simulations can be utilized to predict protein structure ensembles and dynamics, though sufficient sampling of molecular ensembles and identification of key biologically relevant conformations remains challenging. Low-resolution experimental techniques provide valuable structural information on biomolecule at near-native conditions, which are often combined with molecular simulations to determine and refine protein structural ensembles. In this study, we demonstrate how small angle x-ray scattering (SAXS) information can be incorporated in Markov state model-based adaptive sampling strategy to enhance time efficiency of unbiased MD simulations and identify functionally relevant conformations of proteins and complexes. Our results show that using SAXS data combined with additional information, such as thermodynamics and distance restraints, we are able to distinguish otherwise degenerate structures due to the inherent ambiguity of SAXS pattern. We further demonstrate that adaptive sampling guided by SAXS and hybrid information can significantly reduce the computation time required to discover target structures. Overall, our findings demonstrate the potential of this hybrid approach in predicting near-native structures of proteins and complexes. Other low-resolution experimental information can be incorporated in a similar manner to collectively enhance unbiased sampling and improve the accuracy of structure prediction from simulation.
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46
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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: 56] [Impact Index Per Article: 9.3] [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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47
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Intrinsic disorder in the regulatory N-terminal domain of diacylglycerol acyltransferase 1 from Brassica napus. Sci Rep 2018; 8:16665. [PMID: 30420764 PMCID: PMC6232145 DOI: 10.1038/s41598-018-34339-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 10/12/2018] [Indexed: 12/17/2022] Open
Abstract
Proteins with multifunctional regulatory domains often demonstrate structural plasticity or protein disorder, allowing the binding of multiple regulatory factors and post-translational modifications. While the importance of protein disorder is clear, it also poses a challenge for in vitro characterization. Here, we report protein intrinsic disorder in a plant molecular system, which despite its prevalence is less studied. We present a detailed biophysical characterization of the entire cytoplasmic N-terminal domain of Brassica napus diacylglycerol acyltransferase, (DGAT1), which includes an inhibitory module and allosteric binding sites. Our results demonstrate that the monomeric N-terminal domain can be stabilized for biophysical characterization and is largely intrinsically disordered in solution. This domain interacts with allosteric modulators of DGAT1, CoA and oleoyl-CoA, at micromolar concentrations. While solution scattering studies indicate conformational heterogeneity in the N-terminal domain of DGAT1, there is a small gain of secondary structure induced by ligand binding.
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48
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Srivastava A, Nagai T, Srivastava A, Miyashita O, Tama F. Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics. Int J Mol Sci 2018; 19:E3401. [PMID: 30380757 PMCID: PMC6274748 DOI: 10.3390/ijms19113401] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/20/2018] [Accepted: 10/27/2018] [Indexed: 12/13/2022] Open
Abstract
Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.
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Affiliation(s)
- Ashutosh Srivastava
- Institute of Transformative Bio-Molecules (WPI), Nagoya University, Nagoya, Aichi 464-8601, Japan.
| | - Tetsuro Nagai
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.
| | - Arpita Srivastava
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.
| | - Osamu Miyashita
- RIKEN-Center for Computational Science, Kobe, Hyogo 650-0047, Japan.
| | - Florence Tama
- Institute of Transformative Bio-Molecules (WPI), Nagoya University, Nagoya, Aichi 464-8601, Japan.
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.
- RIKEN-Center for Computational Science, Kobe, Hyogo 650-0047, Japan.
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49
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Schneider R, Blackledge M, Jensen MR. Elucidating binding mechanisms and dynamics of intrinsically disordered protein complexes using NMR spectroscopy. Curr Opin Struct Biol 2018; 54:10-18. [PMID: 30316104 DOI: 10.1016/j.sbi.2018.09.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/20/2018] [Accepted: 09/21/2018] [Indexed: 01/10/2023]
Abstract
Advances in characterizing complexes of intrinsically disordered proteins (IDPs) have led to the discovery of a remarkably diverse interaction landscape that includes folding-upon-binding, highly dynamic complexes, multivalent interactions as well as regulatory switches controlled by post-translational modifications. Nuclear magnetic resonance (NMR) spectroscopy has in recent years made significant contributions to this field by describing the binding mechanisms and mapping conformational dynamics on multiple time scales. Importantly, this progress has been associated with specific methodological developments in NMR, for example in exchange techniques, allowing challenging biological systems to be studied at atomic resolution. In general, the level of dynamics observed in IDP complexes does not correlate with binding affinities, demonstrating the intricate relationship between conformational dynamics and IDP regulatory function.
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Affiliation(s)
- Robert Schneider
- Univ. Lille, CNRS, UMR 8576 - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
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50
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Cukier RI. Generating Intrinsically Disordered Protein Conformational Ensembles from a Database of Ramachandran Space Pair Residue Probabilities Using a Markov Chain. J Phys Chem B 2018; 122:9087-9101. [DOI: 10.1021/acs.jpcb.8b05797] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Robert I. Cukier
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
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