1
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Martins G, Galamba N. Wild-Type α-Synuclein Structure and Aggregation: A Comprehensive Coarse-Grained and All-Atom Molecular Dynamics Study. J Chem Inf Model 2024; 64:6115-6131. [PMID: 39046235 PMCID: PMC11323248 DOI: 10.1021/acs.jcim.4c00965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/14/2024] [Accepted: 07/18/2024] [Indexed: 07/25/2024]
Abstract
α-Synuclein (α-syn) is a 140 amino acid intrinsically disordered protein (IDP) and the primary component of cytotoxic oligomers implicated in the etiology of Parkinson's disease (PD). While IDPs lack a stable three-dimensional structure, they sample a heterogeneous ensemble of conformations that can, in principle, be assessed through molecular dynamics simulations. However, describing the structure and aggregation of large IDPs is challenging due to force field (FF) accuracy and sampling limitations. To cope with the latter, coarse-grained (CG) FFs emerge as a potential alternative at the expense of atomic detail loss. Whereas CG models can accurately describe the structure of the monomer, less is known about aggregation. The latter is key for assessing aggregation pathways and designing aggregation inhibitor drugs. Herein, we investigate the structure and dynamics of α-syn using different resolution CG (Martini3 and Sirah2) and all-atom (Amber99sb and Charmm36m) FFs to gain insight into the differences and resemblances between these models. The dependence of the magnitude of protein-water interactions and the putative need for enhanced sampling (replica exchange) methods in CG simulations are analyzed to distinguish between force field accuracy and sampling limitations. The stability of the CG models of an α-syn fibril was also investigated. Additionally, α-syn aggregation was studied through umbrella sampling for the CG models and CG/all-atom models for an 11-mer peptide (NACore) from an amyloidogenic domain of α-syn. Our results show that despite the α-syn structures of Martini3 and Sirah2 with enhanced protein-water interactions being similar, major differences exist concerning aggregation. The Martini3 fibril is not stable, and the binding free energy of α-syn and NACore is positive, opposite to Sirah2. Sirah2 peptides in a zwitterionic form, in turn, display termini interactions that are too strong, resulting in end-to-end orientation. Sirah2, with enhanced protein-water interactions and neutral termini, provides, however, a peptide aggregation free energy profile similar to that found with all-atom models. Overall, we find that Sirah2 with enhanced protein-water interactions is suitable for studying protein-protein and protein-drug aggregation.
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Affiliation(s)
- Gabriel
F. Martins
- BioISI—Biosystems
and Integrative Sciences Institute, Faculty
of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal
| | - Nuno Galamba
- BioISI—Biosystems
and Integrative Sciences Institute, Faculty
of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal
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2
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McIvor JAP, Larsen DS, Mercadante D. Charge Relaying within a Phospho-Motif Rescue Binding Competency of a Disordered Transcription Factor. J Chem Inf Model 2024; 64:6041-6052. [PMID: 39074869 DOI: 10.1021/acs.jcim.4c00286] [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: 07/31/2024]
Abstract
Structural disorder in proteins is central to cellular signaling, where conformational plasticity equips molecules to promiscuously interact with different partners. By engaging with multiple binding partners via the rearrangement of its three helices, the nuclear coactivator binding domain (NCBD) of the CBP/p300 transcription factor is a paradigmatic example of promiscuity. Recently, molecular simulations and experiments revealed that, through the establishment of long-range electrostatic interactions, intended as salt-bridges formed between the post-translationally inserted phosphate and positively charged residues in helix H3 of NCBD, phosphorylation triggers NCBD compaction, lowering its affinity for binding partners. By means of extensive molecular simulations, we here investigated the effect of short-range electrostatics on the conformational ensemble of NCBD, by monitoring the interactions between a phosphorylated serine and conserved positively charged residues within the NCBD phospho-motif. We found that empowering proximal electrostatic interactions, as opposed to long-range electrostatics, can reshape the NCBD ensemble rescuing the binding competency of phosphorylated NCBD. Given the conservation of positive charges in phospho-motifs, proximal electrostatic interactions might dampen the effects of phosphorylation and act as a relay to regulate phosphorylated intrinsically disordered proteins, ultimately tuning the binding affinity for different cellular partners.
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Affiliation(s)
- Jordan A P McIvor
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
| | - Danaé S Larsen
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
| | - Davide Mercadante
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
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3
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An Y, Gao T, Wang T, Zhang D, Bharti B. Effects of charge asymmetry on the liquid-liquid phase separation of polyampholytes and their condensate properties. SOFT MATTER 2024; 20:6150-6159. [PMID: 39044475 DOI: 10.1039/d4sm00532e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Liquid-liquid phase separation (LLPS) is the mechanism underlying the formation of bio-molecular condensates which are important compartments regulating intra- and extra-cellular functions. Electrostatic interactions are some of the important driving forces of the LLPS behaviors of biomolecules. However, the understanding of the electrostatic interactions is still limited, especially in the mixtures of biomolecules with different charge patterns. Here, we focus on the electrostatic interactions in mixtures of charge-asymmetric and charge-symmetric polyampholytes and their roles in the phase separation behaviors. We build charge-asymmetric and charge-symmetric model proteins consisting of both glutamic acid (E, negatively charged) and lysine (K, positively charged), i.e. polyampholytes of E35K15 (charge asymmetric) and E25K25 (charge symmetric). Pure E25K25 can undergo LLPS. To investigate the effects of charge-asymmetric polyampholytes on the mixtures of E25K25/E35K15, we perform coarse-grained simulations to determine their phase separation. The charge-asymmetric polyampholyte E35K15 is resistant to the LLPS of the mixtures of E25K25/E35K15. The condensate density decreases with the molar fraction of E35K15 increasing to 0.4, and no LLPS occurs at the molar fraction of 0.5 and above. This can be attributed to the electrostatic repulsion between the negatively charged E35K15 polymers. We further investigate the effects of charge asymmetry on the conformations and properties of the condensates. The E35K15 polymers in the condensates exhibit a more collapsed state as the molar fraction of E35K15 increases. However, the conformation of E25K25 polymers changes slightly across different condensates. The surface tensions of condensates decline with the increase of the molar fraction of E35K15 polymers, while the diffusivity of polymers in the condensed phases is enhanced. This work elucidates the role of charge-asymmetric polyampholytes in determining the LLPS behaviours of binary mixtures of charge-symmetric and charge-asymmetric proteins as well as the properties of condensed phases.
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Affiliation(s)
- Yaxin An
- Department of Chemical Engineering, Louisiana State University, USA.
| | - Tong Gao
- Department of Chemical Engineering, Louisiana State University, USA.
| | - Tianyi Wang
- Department of Chemical Engineering, Louisiana State University, USA.
| | - Donghui Zhang
- Department of Chemistry, Louisiana State University, USA
| | - Bhuvnesh Bharti
- Department of Chemical Engineering, Louisiana State University, USA.
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4
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Coskuner-Weber O. Structures prediction and replica exchange molecular dynamics simulations of α-synuclein: A case study for intrinsically disordered proteins. Int J Biol Macromol 2024; 276:133813. [PMID: 38996889 DOI: 10.1016/j.ijbiomac.2024.133813] [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: 06/10/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/14/2024]
Abstract
In recent years, a variety of three-dimensional structure prediction tools, including AlphaFold2, AlphaFold3, I-TASSER, C-I-TASSER, Phyre2, ESMFold, and RoseTTAFold, have been employed in the investigation of intrinsically disordered proteins. However, a comprehensive validation of these tools specifically for intrinsically disordered proteins has yet to be conducted. In this study, we utilize AlphaFold2, AlphaFold3, I-TASSER, C-I-TASSER, Phyre2, ESMFold, and RoseTTAFold to predict the structure of a model intrinsically disordered α-synuclein protein. Additionally, extensive replica exchange molecular dynamics simulations of the intrinsically disordered protein are conducted. The resulting structures from both structure prediction tools and replica exchange molecular dynamics simulations are analyzed for radius of gyration, secondary and tertiary structure properties, as well as Cα and Hα chemical shift values. A comparison of the obtained results with experimental data reveals that replica exchange molecular dynamics simulations provide results in excellent agreement with experimental observations. However, none of the structure prediction tools utilized in this study can fully capture the structural characteristics of the model intrinsically disordered protein. This study shows that a cluster of ensembles are required for intrinsically disordered proteins. Artificial-intelligence based structure prediction tools such as AlphaFold3 and C-I-TASSER could benefit from stochastic sampling or Monte Carlo simulations for generating an ensemble of structures for intrinsically disordered proteins.
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Affiliation(s)
- Orkid Coskuner-Weber
- Turkish-German University, Molecular Biotechnology, Sahinkaya Caddesi, No. 106, Beykoz, Istanbul 34820, Turkey.
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5
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He P, Wang H, Zhu A, Zhang Z, Sha J, Ni Z, Chen Y. Detection of Intrinsically Disordered Peptides by Biological Nanopore. Chem Asian J 2024:e202400389. [PMID: 38865098 DOI: 10.1002/asia.202400389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/03/2024] [Accepted: 06/11/2024] [Indexed: 06/13/2024]
Abstract
Intrinsically disordered protein regions (IDPRs) are pivotal in regulation of transcription and facilitation of signal transduction. Because of their multiple conformational states of structure, characterizing the highly flexible structures of IDPRs becomes challenging. Herein, we employed the wild-type (WT) aerolysin nanopore as a real-time biosensor for identification and monitoring of long peptides containing IDPRs. This sensor successfully identified three intrinsically disordered peptides, with the lengths up to 43 amino acids, by distinguishing the unique signatures of blockade current and duration time. The analysis of the binding constant revealed that interactions between the nanopore and peptides are critical for peptide translocation, which suggests that mechanisms beyond mere volume exclusion. Furthermore, we were able to compare the conformational stabilities of various IDPRs by examining the detailed current traces of blockade events. Our approach can detect the conformational changes of IDPR in a confined nanopore space. These insights broaden the understanding of peptide structural changes. The nanopore biosensor showed the potential to study the conformations change of IDPRs, IDPRs transmembrane interactions, and protein drug discovery.
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Affiliation(s)
- Pinyao He
- School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Haiyan Wang
- School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
- Engineering Research Center of New Light Sources Technology and Equipment, Ministry of Education, Southeast University, Nanjing, 211189, China
| | - Anqi Zhu
- School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Zhenyu Zhang
- School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Jingjie Sha
- School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Zhonghua Ni
- School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Yunfei Chen
- School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
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6
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Miller JJ, Mallimadugula UL, Zimmerman MI, Stuchell-Brereton MD, Soranno A, Bowman GR. Accounting for fast vs slow exchange in single molecule FRET experiments reveals hidden conformational states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597137. [PMID: 38895430 PMCID: PMC11185552 DOI: 10.1101/2024.06.03.597137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Proteins are dynamic systems whose structural preferences determine their function. Unfortunately, building atomically detailed models of protein structural ensembles remains challenging, limiting our understanding of the relationships between sequence, structure, and function. Combining single molecule Förster resonance energy transfer (smFRET) experiments with molecular dynamics simulations could provide experimentally grounded, all-atom models of a protein's structural ensemble. However, agreement between the two techniques is often insufficient to achieve this goal. Here, we explore whether accounting for important experimental details like averaging across structures sampled during a given smFRET measurement is responsible for this apparent discrepancy. We present an approach to account for this time-averaging by leveraging the kinetic information available from Markov state models of a protein's dynamics. This allows us to accurately assess which timescales are averaged during an experiment. We find this approach significantly improves agreement between simulations and experiments in proteins with varying degrees of dynamics, including the well-ordered protein T4 lysozyme, the partially disordered protein apolipoprotein E (ApoE), and a disordered amyloid protein (Aβ40). We find evidence for hidden states that are not apparent in smFRET experiments because of time averaging with other structures, akin to states in fast exchange in NMR, and evaluate different force fields. Finally, we show how remaining discrepancies between computations and experiments can be used to guide additional simulations and build structural models for states that were previously unaccounted for. We expect our approach will enable combining simulations and experiments to understand the link between sequence, structure, and function in many settings.
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Affiliation(s)
- Justin J. Miller
- Departments of Biochemistry & Biophysics and Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, United States
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Upasana L. Mallimadugula
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Maxwell I. Zimmerman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Melissa D. Stuchell-Brereton
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Gregory R. Bowman
- Departments of Biochemistry & Biophysics and Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, United States
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
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7
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Payne-Dwyer A, Kumar G, Barrett J, Gherman LK, Hodgkinson M, Plevin M, Mackinder L, Leake MC, Schaefer C. Predicting Rubisco-Linker Condensation from Titration in the Dilute Phase. PHYSICAL REVIEW LETTERS 2024; 132:218401. [PMID: 38856270 DOI: 10.1103/physrevlett.132.218401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 04/09/2024] [Indexed: 06/11/2024]
Abstract
The condensation of Rubisco holoenzymes and linker proteins into "pyrenoids," a crucial supercharger of photosynthesis in algae, is qualitatively understood in terms of "sticker-and-spacer" theory. We derive semianalytical partition sums for small Rubisco-linker aggregates, which enable the calculation of both dilute-phase titration curves and dimerization diagrams. By fitting the titration curves to surface plasmon resonance and single-molecule fluorescence microscopy data, we extract the molecular properties needed to predict dimerization diagrams. We use these to estimate typical concentrations for condensation, and successfully compare these to microscopy observations.
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Affiliation(s)
- Alex Payne-Dwyer
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, United Kingdom
| | - Gaurav Kumar
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - James Barrett
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Laura K Gherman
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
- York Structural Biology Laboratory, The University of York; York, YO10 5DD, United Kingdom
| | - Michael Hodgkinson
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Michael Plevin
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
- York Structural Biology Laboratory, The University of York; York, YO10 5DD, United Kingdom
| | - Luke Mackinder
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Mark C Leake
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, United Kingdom
- Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Charley Schaefer
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, United Kingdom
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8
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Sauer MA, Colburn T, Maiti S, Heyden M, Matyushov DV. Linear and Nonlinear Dielectric Response of Intrinsically Disordered Proteins. J Phys Chem Lett 2024; 15:5420-5427. [PMID: 38743557 DOI: 10.1021/acs.jpclett.4c00866] [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: 05/16/2024]
Abstract
Linear and nonlinear dielectric responses of solutions of intrinsically disordered proteins (IDPs) were analyzed by combining molecular dynamics simulations with formal theories. A large increment of the linear dielectric function over that of the solvent is found and related to large dipole moments of IDPs. The nonlinear dielectric effect (NDE) of the IDP far exceeds that of the bulk electrolyte, offering a route to interrogate protein conformational and rotational statistics and dynamics. Conformational flexibility of the IDP makes the dipole moment statistics consistent with the gamma/log-normal distributions and contributes to the NDE through the dipole moment's non-Gaussian parameter. The intrinsic non-Gaussian parameter of the dipole moment combines with the protein osmotic compressibility in the nonlinear dielectric susceptibility when dipolar correlations are screened by the electrolyte. The NDE is dominated by dipolar correlations when electrolyte screening is reduced.
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Affiliation(s)
- Michael A Sauer
- School of Molecular Sciences, Arizona State University, PO Box 871504, Tempe, Arizona 85287-1504, United States
| | - Taylor Colburn
- Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona 85287-1504, United States
| | - Sthitadhi Maiti
- School of Molecular Sciences, Arizona State University, PO Box 871504, Tempe, Arizona 85287-1504, United States
| | - Matthias Heyden
- School of Molecular Sciences, Arizona State University, PO Box 871504, Tempe, Arizona 85287-1504, United States
| | - Dmitry V Matyushov
- School of Molecular Sciences and Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona 85287-1504, United States
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9
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Waszkiewicz R, Michaś A, Białobrzewski MK, Klepka BP, Cieplak-Rotowska MK, Staszałek Z, Cichocki B, Lisicki M, Szymczak P, Niedzwiecka A. Hydrodynamic Radii of Intrinsically Disordered Proteins: Fast Prediction by Minimum Dissipation Approximation and Experimental Validation. J Phys Chem Lett 2024; 15:5024-5033. [PMID: 38696815 PMCID: PMC11103702 DOI: 10.1021/acs.jpclett.4c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/12/2024] [Accepted: 04/26/2024] [Indexed: 05/04/2024]
Abstract
The diffusion coefficients of globular and fully unfolded proteins can be predicted with high accuracy solely from their mass or chain length. However, this approach fails for intrinsically disordered proteins (IDPs) containing structural domains. We propose a rapid predictive methodology for estimating the diffusion coefficients of IDPs. The methodology uses accelerated conformational sampling based on self-avoiding random walks and includes hydrodynamic interactions between coarse-grained protein subunits, modeled using the generalized Rotne-Prager-Yamakawa approximation. To estimate the hydrodynamic radius, we rely on the minimum dissipation approximation recently introduced by Cichocki et al. Using a large set of experimentally measured hydrodynamic radii of IDPs over a wide range of chain lengths and domain contributions, we demonstrate that our predictions are more accurate than the Kirkwood approximation and phenomenological approaches. Our technique may prove to be valuable in predicting the hydrodynamic properties of both fully unstructured and multidomain disordered proteins.
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Affiliation(s)
- Radost Waszkiewicz
- Institute
of Theoretical Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland
| | - Agnieszka Michaś
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Michał K. Białobrzewski
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Barbara P. Klepka
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | | | - Zuzanna Staszałek
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Bogdan Cichocki
- Institute
of Theoretical Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland
| | - Maciej Lisicki
- Institute
of Theoretical Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland
| | - Piotr Szymczak
- Institute
of Theoretical Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland
| | - Anna Niedzwiecka
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
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10
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Badreldin M, Salas-Ambrosio P, Bourasseau S, Lecommandoux S, Harrisson S, Bonduelle C. Toward Synthetic Intrinsically Disordered Polypeptides (IDPs): Controlled Incorporation of Glycine in the Ring-Opening Polymerization of N-Carboxyanhydrides. Biomacromolecules 2024; 25:3033-3043. [PMID: 38652289 DOI: 10.1021/acs.biomac.4c00142] [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: 04/25/2024]
Abstract
Intrinsically disordered proteins (IDPs) do not have a well-defined folded structure but instead behave as extended polymer chains in solution. Many IDPs are rich in glycine residues, which create steric barriers to secondary structuring and protein folding. Inspired by this feature, we have studied how the introduction of glycine residues influences the secondary structure of a model polypeptide, poly(l-glutamic acid), a helical polymer. For this purpose, we carried out ring-opening copolymerization with γ-benzyl-l-glutamate and glycine N-carboxyanhydride (NCA) monomers. We aimed to control the glycine distribution within PBLG by adjusting the reactivity ratios of the two NCAs using different reaction conditions (temperature, solvent). The relationship between those conditions, the monomer distributions, and the secondary structure enabled the design of intrinsically disordered polypeptides when a highly gradient microstructure was achieved in DMSO.
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Affiliation(s)
- Mostafa Badreldin
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
| | - Pedro Salas-Ambrosio
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
- Department of Chemistry and Biochemistry, University of California Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Sylvain Bourasseau
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
| | | | - Simon Harrisson
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
| | - Colin Bonduelle
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600 Pessac, France
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11
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Baxa MC, Lin X, Mukinay CD, Chakravarthy S, Sachleben JR, Antilla S, Hartrampf N, Riback JA, Gagnon IA, Pentelute BL, Clark PL, Sosnick TR. How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins. Protein Sci 2024; 33:e4986. [PMID: 38607226 PMCID: PMC11010952 DOI: 10.1002/pro.4986] [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: 10/23/2023] [Revised: 03/13/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024]
Abstract
Despite the generally accepted role of the hydrophobic effect as the driving force for folding, many intrinsically disordered proteins (IDPs), including those with hydrophobic content typical of foldable proteins, behave nearly as self-avoiding random walks (SARWs) under physiological conditions. Here, we tested how temperature and ionic conditions influence the dimensions of the N-terminal domain of pertactin (PNt), an IDP with an amino acid composition typical of folded proteins. While PNt contracts somewhat with temperature, it nevertheless remains expanded over 10-58°C, with a Flory exponent, ν, >0.50. Both low and high ionic strength also produce contraction in PNt, but this contraction is mitigated by reducing charge segregation. With 46% glycine and low hydrophobicity, the reduced form of snow flea anti-freeze protein (red-sfAFP) is unaffected by temperature and ionic strength and persists as a near-SARW, ν ~ 0.54, arguing that the thermal contraction of PNt is due to stronger interactions between hydrophobic side chains. Additionally, red-sfAFP is a proxy for the polypeptide backbone, which has been thought to collapse in water. Increasing the glycine segregation in red-sfAFP had minimal effect on ν. Water remained a good solvent even with 21 consecutive glycine residues (ν > 0.5), and red-sfAFP variants lacked stable backbone hydrogen bonds according to hydrogen exchange. Similarly, changing glycine segregation has little impact on ν in other glycine-rich proteins. These findings underscore the generality that many disordered states can be expanded and unstructured, and that the hydrophobic effect alone is insufficient to drive significant chain collapse for typical protein sequences.
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Affiliation(s)
- Michael C. Baxa
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
| | - Xiaoxuan Lin
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
| | - Cedrick D. Mukinay
- Department of Chemistry & BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team (BioCAT), Center for Synchrotron Radiation Research and Instrumentation and Department of Biological and Chemical SciencesIllinois Institute of TechnologyChicagoIllinoisUSA
- Present address:
Cytiva, Fast TrakMarlboroughMAUSA
| | | | - Sarah Antilla
- Department of Materials Science and EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Nina Hartrampf
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Present address:
Department of ChemistryUniversity of ZurichSwitzerland
| | - Joshua A. Riback
- Graduate Program in Biophysical ScienceUniversity of ChicagoChicagoIllinoisUSA
- Present address:
Department of Molecular and Cellular BiologyBaylor College of MedicineHoustonTXUSA
| | - Isabelle A. Gagnon
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
| | - Bradley L. Pentelute
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Patricia L. Clark
- Department of Chemistry & BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Tobin R. Sosnick
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
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12
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Firouzbakht A, Haider A, Gaalswyk K, Alaeen S, Ghosh K, Gruebele M. HYPK: A marginally disordered protein sensitive to charge decoration. Proc Natl Acad Sci U S A 2024; 121:e2316408121. [PMID: 38657047 PMCID: PMC11067017 DOI: 10.1073/pnas.2316408121] [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: 09/20/2023] [Accepted: 03/20/2024] [Indexed: 04/26/2024] Open
Abstract
Intrinsically disordered proteins (IDPs) that lie close to the empirical boundary separating IDPs and folded proteins in Uversky's charge-hydropathy plot may behave as "marginal IDPs" and sensitively switch conformation upon changes in environment (temperature, crowding, and charge screening), sequence, or both. In our search for such a marginal IDP, we selected Huntingtin-interacting protein K (HYPK) near that boundary as a candidate; PKIα, also near that boundary, has lower secondary structure propensity; and Crk1, just across the boundary on the folded side, has higher secondary structure propensity. We used a qualitative Förster resonance energy transfer-based assay together with circular dichroism to simultaneously probe global and local conformation. HYPK shows several unique features indicating marginality: a cooperative transition in end-to-end distance with temperature, like Crk1 and folded proteins, but unlike PKIα; enhanced secondary structure upon crowding, in contrast to Crk1 and PKIα; and a cross-over from salt-induced expansion to compaction at high temperature, likely due to a structure-to-disorder transition not seen in Crk1 and PKIα. We then tested HYPK's sensitivity to charge patterning by designing charge-flipped variants including two specific sequences with identical amino acid composition that markedly differ in their predicted size and response to salt. The experimentally observed trends, also including mutants of PKIα, verify the predictions from sequence charge decoration metrics. Marginal proteins like HYPK show features of both folded and disordered proteins that make them sensitive to physicochemical perturbations and structural control by charge patterning.
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Affiliation(s)
- Arash Firouzbakht
- Department of Chemistry, University of Illinois at Urbana Champaign, Urbana Champaign, IL61801
| | - Austin Haider
- Department of Molecular and Cellular Biophysics, University of Denver, Denver, CO80210
| | - Kari Gaalswyk
- Department of Physics and Astronomy, University of Denver, Denver, CO80210
| | - Sepehr Alaeen
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana Champaign, Urbana Champaign, IL61801
| | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, CO80210
| | - Martin Gruebele
- Department of Chemistry, University of Illinois at Urbana Champaign, Urbana Champaign, IL61801
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana Champaign, Urbana Champaign, IL61801
- Department of Physics, University of Illinois at Urbana Champaign, Urbana Champaign, IL61801
- Carle-Illinois College of Medicine, University of Illinois Urbana Champaign, Urbana Champaign, IL61801
- Center for Advanced Study, University of Illinois Urbana Champaign, Urbana Champaign, IL61801
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13
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Jaufer AM, Bouhadana A, Fanucci GE. Hydrophobic Clusters Regulate Surface Hydration Dynamics of Bacillus subtilis Lipase A. J Phys Chem B 2024; 128:3919-3928. [PMID: 38628066 DOI: 10.1021/acs.jpcb.4c00405] [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: 04/26/2024]
Abstract
The surface hydration diffusivity of Bacillus subtilis Lipase A (BSLA) has been characterized by low-field Overhauser dynamic nuclear polarization (ODNP) relaxometry using a series of spin-labeled constructs. Sites for spin-label incorporation were previously designed via an atomistic computational approach that screened for surface exposure, reflective of the surface hydration comparable to other proteins studied by this method, as well as minimal impact on protein function, dynamics, and structure of BSLA by excluding any surface site that participated in greater than 30% occupancy of a hydrogen bonding network within BSLA. Experimental ODNP relaxometry coupling factor results verify the overall surface hydration behavior for these BSLA spin-labeled sites similar to other globular proteins. Here, by plotting the ODNP parameters of relative diffusive water versus the relative bound water, we introduce an effective "phase-space" analysis, which provides a facile visual comparison of the ODNP parameters of various biomolecular systems studied to date. We find notable differences when comparing BSLA to other systems, as well as when comparing different clusters on the surface of BSLA. Specifically, we find a grouping of sites that correspond to the spin-label surface location within the two main hydrophobic core clusters of the branched aliphatic amino acids isoleucine, leucine, and valine cores observed in the BSLA crystal structure. The results imply that hydrophobic clustering may dictate local surface hydration properties, perhaps through modulation of protein conformations and samplings of the unfolded states, providing insights into how the dynamics of the hydration shell is coupled to protein motion and fluctuations.
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Affiliation(s)
- Afnan M Jaufer
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
- George and Josephine Butler Polymer Research Laboratory, University of Florida, Gainesville, Florida 32611, United States
| | - Adam Bouhadana
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
- George and Josephine Butler Polymer Research Laboratory, University of Florida, Gainesville, Florida 32611, United States
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14
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Lorton BM, Warren C, Ilyas H, Nandigrami P, Hegde S, Cahill S, Lehman SM, Shabanowitz J, Hunt DF, Fiser A, Cowburn D, Shechter D. Glutamylation of Npm2 and Nap1 acidic disordered regions increases DNA mimicry and histone chaperone efficiency. iScience 2024; 27:109458. [PMID: 38571760 PMCID: PMC10987829 DOI: 10.1016/j.isci.2024.109458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/08/2024] [Accepted: 03/07/2024] [Indexed: 04/05/2024] Open
Abstract
Histone chaperones-structurally diverse, non-catalytic proteins enriched with acidic intrinsically disordered regions (IDRs)-protect histones from spurious nucleic acid interactions and guide their deposition into and out of nucleosomes. Despite their conservation and ubiquity, the function of the chaperone acidic IDRs remains unclear. Here, we show that the Xenopus laevis Npm2 and Nap1 acidic IDRs are substrates for TTLL4 (Tubulin Tyrosine Ligase Like 4)-catalyzed post-translational glutamate-glutamylation. We demonstrate that to bind, stabilize, and deposit histones into nucleosomes, chaperone acidic IDRs function as DNA mimetics. Our biochemical, computational, and biophysical studies reveal that glutamylation of these chaperone polyelectrolyte acidic stretches functions to enhance DNA electrostatic mimicry, promoting the binding and stabilization of H2A/H2B heterodimers and facilitating nucleosome assembly. This discovery provides insights into both the previously unclear function of the acidic IDRs and the regulatory role of post-translational modifications in chromatin dynamics.
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Affiliation(s)
- Benjamin M. Lorton
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Christopher Warren
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Humaira Ilyas
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Prithviraj Nandigrami
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Systems & Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Subray Hegde
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Sean Cahill
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Stephanie M. Lehman
- Department of Chemistry, University of Virginia, Charlottesville, VA 22908, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, VA 22908, USA
| | - Donald F. Hunt
- Departments of Chemistry and Pathology, University of Virginia, Charlottesville, VA 22908, USA
| | - Andras Fiser
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Systems & Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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15
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Lotthammer JM, Ginell GM, Griffith D, Emenecker RJ, Holehouse AS. Direct prediction of intrinsically disordered protein conformational properties from sequence. Nat Methods 2024; 21:465-476. [PMID: 38297184 PMCID: PMC10927563 DOI: 10.1038/s41592-023-02159-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 12/20/2023] [Indexed: 02/02/2024]
Abstract
Intrinsically disordered regions (IDRs) are ubiquitous across all domains of life and play a range of functional roles. While folded domains are generally well described by a stable three-dimensional structure, IDRs exist in a collection of interconverting states known as an ensemble. This structural heterogeneity means that IDRs are largely absent from the Protein Data Bank, contributing to a lack of computational approaches to predict ensemble conformational properties from sequence. Here we combine rational sequence design, large-scale molecular simulations and deep learning to develop ALBATROSS, a deep-learning model for predicting ensemble dimensions of IDRs, including the radius of gyration, end-to-end distance, polymer-scaling exponent and ensemble asphericity, directly from sequences at a proteome-wide scale. ALBATROSS is lightweight, easy to use and accessible as both a locally installable software package and a point-and-click-style interface via Google Colab notebooks. We first demonstrate the applicability of our predictors by examining the generalizability of sequence-ensemble relationships in IDRs. Then, we leverage the high-throughput nature of ALBATROSS to characterize the sequence-specific biophysical behavior of IDRs within and between proteomes.
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Affiliation(s)
- Jeffrey M Lotthammer
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Garrett M Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Daniel Griffith
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Ryan J Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA.
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16
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Holehouse AS, Kragelund BB. The molecular basis for cellular function of intrinsically disordered protein regions. Nat Rev Mol Cell Biol 2024; 25:187-211. [PMID: 37957331 DOI: 10.1038/s41580-023-00673-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Intrinsically disordered protein regions exist in a collection of dynamic interconverting conformations that lack a stable 3D structure. These regions are structurally heterogeneous, ubiquitous and found across all kingdoms of life. Despite the absence of a defined 3D structure, disordered regions are essential for cellular processes ranging from transcriptional control and cell signalling to subcellular organization. Through their conformational malleability and adaptability, disordered regions extend the repertoire of macromolecular interactions and are readily tunable by their structural and chemical context, making them ideal responders to regulatory cues. Recent work has led to major advances in understanding the link between protein sequence and conformational behaviour in disordered regions, yet the link between sequence and molecular function is less well defined. Here we consider the biochemical and biophysical foundations that underlie how and why disordered regions can engage in productive cellular functions, provide examples of emerging concepts and discuss how protein disorder contributes to intracellular information processing and regulation of cellular function.
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Affiliation(s)
- Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA.
- Center for Biomolecular Condensates, Washington University in St Louis, St Louis, MO, USA.
| | - Birthe B Kragelund
- REPIN, Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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17
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Kravikass M, Koren G, Saleh OA, Beck R. From isolated polyelectrolytes to star-like assemblies: the role of sequence heterogeneity on the statistical structure of the intrinsically disordered neurofilament-low tail domain. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2024; 47:13. [PMID: 38358563 PMCID: PMC10869404 DOI: 10.1140/epje/s10189-024-00409-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 02/02/2024] [Indexed: 02/16/2024]
Abstract
Intrinsically disordered proteins (IDPs) are a subset of proteins that lack stable secondary structure. Given their polymeric nature, previous mean-field approximations have been used to describe the statistical structure of IDPs. However, the amino-acid sequence heterogeneity and complex intermolecular interaction network have significantly impeded the ability to get proper approximations. One such case is the intrinsically disordered tail domain of neurofilament low (NFLt), which comprises a 50 residue-long uncharged domain followed by a 96 residue-long negatively charged domain. Here, we measure two NFLt variants to identify the impact of the NFLt two main subdomains on its complex interactions and statistical structure. Using synchrotron small-angle x-ray scattering, we find that the uncharged domain of the NFLt induces attractive interactions that cause it to self-assemble into star-like polymer brushes. On the other hand, when the uncharged domain is truncated, the remaining charged N-terminal domains remain isolated in solution with typical polyelectrolyte characteristics. We further discuss how competing long- and short-ranged interactions within the polymer brushes dominate their ensemble structure and, in turn, their implications on previously observed phenomena in NFL native and diseased states.
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Affiliation(s)
- Mathar Kravikass
- School of Physics and Astronomy, The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- The Center of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel
| | - Gil Koren
- School of Physics and Astronomy, The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- The Center of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel
| | - Omar A Saleh
- Materials Department, Biomolecular Sciences and Engineering Program, University of California, Santa Barbara, USA
- Physics Department, University of California, Santa Barbara, USA
| | - Roy Beck
- School of Physics and Astronomy, The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel.
- The Center of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel.
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18
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Garg A, González-Foutel NS, Gielnik MB, Kjaergaard M. Design of functional intrinsically disordered proteins. Protein Eng Des Sel 2024; 37:gzae004. [PMID: 38431892 DOI: 10.1093/protein/gzae004] [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: 10/02/2023] [Revised: 12/22/2023] [Indexed: 03/05/2024] Open
Abstract
Many proteins do not fold into a fixed three-dimensional structure, but rather function in a highly disordered state. These intrinsically disordered proteins pose a unique challenge to protein engineering and design: How can proteins be designed de novo if not by tailoring their structure? Here, we will review the nascent field of design of intrinsically disordered proteins with focus on applications in biotechnology and medicine. The design goals should not necessarily be the same as for de novo design of folded proteins as disordered proteins have unique functional strengths and limitations. We focus on functions where intrinsically disordered proteins are uniquely suited including disordered linkers, desiccation chaperones, sensors of the chemical environment, delivery of pharmaceuticals, and constituents of biomolecular condensates. Design of functional intrinsically disordered proteins relies on a combination of computational tools and heuristics gleaned from sequence-function studies. There are few cases where intrinsically disordered proteins have made it into industrial applications. However, we argue that disordered proteins can perform many roles currently performed by organic polymers, and that these proteins might be more designable due to their modularity.
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Affiliation(s)
- Ankush Garg
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | | | - Maciej B Gielnik
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Magnus Kjaergaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
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19
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Yuan J, Tanaka H. Hydrodynamic Effects on the Collapse Kinetics of Flexible Polyelectrolytes. PHYSICAL REVIEW LETTERS 2024; 132:038101. [PMID: 38307078 DOI: 10.1103/physrevlett.132.038101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/05/2023] [Accepted: 11/28/2023] [Indexed: 02/04/2024]
Abstract
Understanding the collapse kinetics of polyelectrolytes (PEs) is crucial for comprehending various biological and industrial phenomena. Despite occurring in an aqueous environment, previous computational studies have overlooked the influence of hydrodynamic interactions (HIs) facilitated by fluid motion. Here, we directly compute the Navier-Stokes equation to investigate the collapse kinetics of a highly charged flexible PE. Our findings reveal that HI accelerates PE collapse induced by hydrophobicity and multivalent salt. In the case of hydrophobicity, HI induces long-range collective motion of monomers, accelerating the coarsening of local clusters through either Brownian-coagulation-like or evaporation-condensation-like processes, depending on the strength of hydrophobicity with respect to electrostatic interaction. Regarding multivalent salt, HI does not affect the condensation dynamics of multivalent ions but facilitates quicker movement of local dipolar clusters along the PE, thereby expediting the collapse process. These results provide valuable insights into the underlying mechanisms of HI in PE collapse kinetics.
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Affiliation(s)
- Jiaxing Yuan
- Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hajime Tanaka
- Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Fundamental Engineering, Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
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20
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Wang J, Devarajan DS, Kim YC, Nikoubashman A, Mittal J. Sequence-Dependent Conformational Transitions of Disordered Proteins During Condensation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575294. [PMID: 38260590 PMCID: PMC10802556 DOI: 10.1101/2024.01.11.575294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Intrinsically disordered proteins (IDPs) can form biomolecular condensates through phase separation. It is recognized that the conformation of IDPs in the dense and dilute phases as well as at the interfaces of condensates can critically impact the resulting properties associated with their functionality. However, a comprehensive understanding of the conformational transitions of IDPs during condensation remains elusive. In this study, we employ a coarse-grained polyampholyte model, comprising an equal number of oppositely charged residues-glutamic acid and lysine-whereby conformations and phase behavior can be readily tuned by altering the protein sequence. By manipulating the sequence patterns from perfectly alternating to block-like, we obtain chains with ideal-like conformations to semi-compact structures in the dilute phase, while in the dense phase, the chain conformation is approximately that of an ideal chain, irrespective of the protein sequence. By performing simulations at different concentrations, we find that the chains assemble from the dilute phase through small oligomeric clusters to the dense phase, accompanied by a gradual swelling of the individual chains. We further demonstrate that these findings are applicable to several naturally occurring proteins involved in the formation of biological condensates. Concurrently, we delve deeper into the chain conformations within the condensate, revealing that chains at the interface show a strong sequence dependence, but remain more collapsed than those in the bulk-like dense phase. This study addresses critical gaps in our knowledge of IDP conformations within condensates as a function of protein sequence.
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Affiliation(s)
- Jiahui Wang
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States
| | | | - Young C. Kim
- Center for Materials Physics and Technology, Naval Research Laboratory, Washington, DC 20375, United States
| | - Arash Nikoubashman
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany
- Institut für Theoretische Physik, Technische Universität Dresden, 01069 Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01062 Dresden, Germany
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX 77843, United States
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21
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Seth S, Stine B, Bhattacharya A. Fine structures of intrinsically disordered proteins. J Chem Phys 2024; 160:014902. [PMID: 38165099 DOI: 10.1063/5.0176306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/05/2023] [Indexed: 01/03/2024] Open
Abstract
We report simulation studies of 33 single intrinsically disordered proteins (IDPs) using coarse-grained bead-spring models where interactions among different amino acids are introduced through a hydropathy matrix and additional screened Coulomb interaction for the charged amino acid beads. Our simulation studies of two different hydropathy scales (HPS1, HPS2) [Dignon et al., PLoS Comput. Biol. 14, e1005941 (2018); Tesei et al. Proc. Natl. Acad. Sci. U. S. A. 118, e2111696118 (2021)] and the comparison with the existing experimental data indicate an optimal interaction parameter ϵ = 0.1 and 0.2 kcal/mol for the HPS1 and HPS2 hydropathy scales. We use these best-fit parameters to investigate both the universal aspects as well as the fine structures of the individual IDPs by introducing additional characteristics. (i) First, we investigate the polymer-specific scaling relations of the IDPs in comparison to the universal scaling relations [Bair et al., J. Chem. Phys. 158, 204902 (2023)] for the homopolymers. By studying the scaled end-to-end distances ⟨RN2⟩/(2Lℓp) and the scaled transverse fluctuations l̃⊥2=⟨l⊥2⟩/L, we demonstrate that IDPs are broadly characterized with a Flory exponent of ν ≃ 0.56 with the conclusion that conformations of the IDPs interpolate between Gaussian and self-avoiding random walk chains. Then, we introduce (ii) Wilson charge index (W) that captures the essential features of charge interactions and distribution in the sequence space and (iii) a skewness index (S) that captures the finer shape variation of the gyration radii distributions as a function of the net charge per residue and charge asymmetry parameter. Finally, our study of the (iv) variation of ⟨Rg⟩ as a function of salt concentration provides another important metric to bring out finer characteristics of the IDPs, which may carry relevant information for the origin of life.
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Affiliation(s)
- Swarnadeep Seth
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
| | - Brandon Stine
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
| | - Aniket Bhattacharya
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
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22
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Pacios LF, Sánchez F, Ponz F. Intrinsic disorder in the dynamic evolution of structure, stability, and flexibility of potyviral VLP assemblies: A computational study. Int J Biol Macromol 2024; 254:127798. [PMID: 37924902 DOI: 10.1016/j.ijbiomac.2023.127798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/18/2023] [Accepted: 10/29/2023] [Indexed: 11/06/2023]
Abstract
An all-atom Molecular Dynamics (MD) study was applied to three viral nanoparticles (VLPs) of Turnip mosaic virus (TuMV), a potyvirus: the particles genetically functionalized with two peptides, VIP (human vasoactive intestinal peptide) and VEGFR (peptide derived from the human receptor 3 of the vascular endothelial growth factor), and the non-functionalized VLP. Previous experimental results showed that VIP-VLP was the only construct of the three that was not viable. VLPs subjected to our MD study were modeled by four complete turns of the particle involving 35 subunits of the coat protein (CP). The MD simulations showed differences in structures and interaction energies associated to the crucial contribution of the disordered N-terminal arms of CP to the global stability of the particle. These differences suggested an overall stability greater in VEGFR-VLP and smaller in VIP-VLP as compared to the unfunctionalized VLP. Our novel MD study of potyviral VLPs revealed essential clues about structure and interactions of these assembled protein particles and suggests that the computational prediction of the viability of VLPs can be a valuable contribution in the field of viral nanobiotechnology.
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Affiliation(s)
- Luis F Pacios
- Departamento de Biotecnología-Biología Vegetal, ETSIAAB, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain; Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Flora Sánchez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Fernando Ponz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, 28223 Pozuelo de Alarcón, Madrid, Spain.
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23
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Vancraenenbroeck R, Hofmann H. Electrostatics and hydrophobicity in the dynamics of intrinsically disordered proteins. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:133. [PMID: 38127117 PMCID: PMC10739388 DOI: 10.1140/epje/s10189-023-00383-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023]
Abstract
Internal friction is a major contribution to the dynamics of intrinsically disordered proteins (IDPs). Yet, the molecular origin of internal friction has so far been elusive. Here, we investigate whether attractive electrostatic interactions in IDPs modulate internal friction differently than the hydrophobic effect. To this end, we used nanosecond fluorescence correlation spectroscopy (nsFCS) and single-molecule Förster resonance energy transfer (FRET) to quantify the conformation and dynamics of the disordered DNA-binding domains Myc, Max and Mad at different salt concentrations. We find that internal friction effects are stronger when the chain is compacted by electrostatic attractions compared to the hydrophobic effect. Although the effect is moderate, the results show that the heteropolymeric nature of IDPs is reflected in their dynamics.
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Affiliation(s)
- Renee Vancraenenbroeck
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Herzl St. 234, 76100, Rehovot, Israel
- Present Address: Department of Structural and Molecular Biology, University College London, Darwin Building, 107 Gower Street, London, WC1E 6BT, UK
| | - Hagen Hofmann
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Herzl St. 234, 76100, Rehovot, Israel.
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24
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Moses D, Ginell GM, Holehouse AS, Sukenik S. Intrinsically disordered regions are poised to act as sensors of cellular chemistry. Trends Biochem Sci 2023; 48:1019-1034. [PMID: 37657994 PMCID: PMC10840941 DOI: 10.1016/j.tibs.2023.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 09/03/2023]
Abstract
Intrinsically disordered proteins and protein regions (IDRs) are abundant in eukaryotic proteomes and play a wide variety of essential roles. Instead of folding into a stable structure, IDRs exist in an ensemble of interconverting conformations whose structure is biased by sequence-dependent interactions. The absence of a stable 3D structure, combined with high solvent accessibility, means that IDR conformational biases are inherently sensitive to changes in their environment. Here, we argue that IDRs are ideally poised to act as sensors and actuators of cellular physicochemistry. We review the physical principles that underlie IDR sensitivity, the molecular mechanisms that translate this sensitivity to function, and recent studies where environmental sensing by IDRs may play a key role in their downstream function.
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Affiliation(s)
- David Moses
- Department of Chemistry and Biochemistry, University of California, Merced, CA, USA
| | - Garrett M Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA; Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA; Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO, USA.
| | - Shahar Sukenik
- Department of Chemistry and Biochemistry, University of California, Merced, CA, USA; Quantitative Systems Biology Program, University of California, Merced, CA, USA.
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25
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Lee NK, Chae MK, Jung Y, Johner A, Joanny JF. Polyelectrolytes: From Seminal Works to the Influence of the Charge Sequence. Polymers (Basel) 2023; 15:4593. [PMID: 38232020 PMCID: PMC10708673 DOI: 10.3390/polym15234593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/19/2023] [Accepted: 11/27/2023] [Indexed: 01/19/2024] Open
Abstract
We propose a selected tour of the physics of polyelectrolytes (PE) following the line initiated by de Gennes and coworkers in their seminal 1976 paper. The early works which used uniform charge distributions along the PE backbone achieved tremendous progress and set most milestones in the field. Recently, the focus has shifted to the role of the charge sequence. Revisited topics include PE complexation and polyampholytes (PA). We develop the example of a random PE in poor solvent forming pearl-necklace structures. It is shown that the pearls typically adopt very asymmetric mass and charge distributions. Individual sequences do not necessarily reflect the ensemble statistics and a rich variety of behaviors emerges (specially for PA). Pearl necklaces are dynamic structures and switch between various types of pearl-necklace structures, as described for both PE and PA.
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Affiliation(s)
- Nam-Kyung Lee
- Department of Physics and Astronomy, Sejong University, Seoul 05006, Republic of Korea;
| | - Min-Kyung Chae
- National Institute for Mathematical Sciences, Daejeon 34047, Republic of Korea;
| | - Youngkyun Jung
- Supercomputing Center, Korea Institute of Science and Technology Information, Daejeon 34141, Republic of Korea;
| | - Albert Johner
- Institut Charles Sadron CNRS-Unistra, 6 rue Boussingault, 67083 Strasbourg, France
| | - Jean-Francois Joanny
- Institut Curie, Physique des cellules et Cancer, Collège de France Soft Matter and Biophysics Chair, 11, PSL University, Place Marcelin-Berthelot, 75231 Paris, France;
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26
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Dunleavy KM, Li T, Milshteyn E, Jaufer AM, Walker SA, Fanucci GE. Charge Distribution Patterns of IA 3 Impact Conformational Expansion and Hydration Diffusivity of the Disordered Ensemble. J Phys Chem B 2023; 127:9734-9746. [PMID: 37936402 DOI: 10.1021/acs.jpcb.3c06170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
IA3 is a 68 amino acid natural peptide/protein inhibitor of yeast aspartic proteinase A (YPRA) that is intrinsically disordered in solution with induced N-terminal helicity when in the protein complex with YPRA. Based on the intrinsically disordered protein (IDP) parameters of fractional net charge (FNC), net charge density per residue (NCPR), and charge patterning (κ), the two domains of IA3 are defined to occupy different domains within conformationally based subclasses of IDPs, thus making IA3 a bimodal domain IDP. Site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy and low-field Overhauser dynamic nuclear polarization (ODNP) spectroscopy results show that these two domains possess different degrees of compaction and hydration diffusivity behavior. This work suggests that SDSL EPR line shapes, analyzed in terms of their local tumbling volume (VL), provide insights into the compaction of the unstructured IDP ensemble in solution and that protein sequence and net charge distribution patterns within a conformational subclass can impact bound water hydration dynamics, thus possibly offering an alternative thermodynamic property that can encode conformational binding and behavior of IDPs and liquid-liquid phase separations.
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Affiliation(s)
- Katie M Dunleavy
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Tianyan Li
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Eugene Milshteyn
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Afnan M Jaufer
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Shamon A Walker
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
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27
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Emenecker RJ, Guadalupe K, Shamoon NM, Sukenik S, Holehouse AS. Sequence-ensemble-function relationships for disordered proteins in live cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.29.564547. [PMID: 37961106 PMCID: PMC10634935 DOI: 10.1101/2023.10.29.564547] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Intrinsically disordered protein regions (IDRs) are ubiquitous across all kingdoms of life and play a variety of essential cellular roles. IDRs exist in a collection of structurally distinct conformers known as an ensemble. An IDR's amino acid sequence determines its ensemble, which in turn can play an important role in dictating molecular function. Yet a clear link connecting IDR sequence, its ensemble properties, and its molecular function in living cells has not been directly established. Here, we set out to test this sequence-ensemble-function paradigm using a novel computational method (GOOSE) that enables the rational design of libraries of IDRs by systematically varying specific sequence properties. Using ensemble FRET, we measured the ensemble dimensions of a library of rationally designed IDRs in human-derived cell lines, revealing how IDR sequence influences ensemble dimensions in situ. Furthermore, we show that the interplay between sequence and ensemble can tune an IDR's ability to sense changes in cell volume - a de novo molecular function for these synthetic sequences. Our results establish biophysical rules for intracellular sequence-ensemble relationships, enable a new route for understanding how IDR sequences map to function in live cells, and set the ground for the design of synthetic IDRs with de novo function.
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Affiliation(s)
- Ryan J. Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Karina Guadalupe
- Department of Chemistry and Biochemistry, University of California, Merced, CA
- Center for Cellular and Biomolecular Machines, University of California, Merced, CA
| | - Nora M. Shamoon
- Center for Cellular and Biomolecular Machines, University of California, Merced, CA
- Quantitative Systems Biology Program, University of California, Merced, CA
| | - Shahar Sukenik
- Department of Chemistry and Biochemistry, University of California, Merced, CA
- Center for Cellular and Biomolecular Machines, University of California, Merced, CA
- Quantitative Systems Biology Program, University of California, Merced, CA
- Health Sciences Research Institute, University of California, Merced, CA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
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28
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Holehouse A, Emenecker R, Guadalupe K, Shamoon N, Sukenik S. Sequence-ensemble-function relationships for disordered proteins in live cells. RESEARCH SQUARE 2023:rs.3.rs-3501110. [PMID: 37986812 PMCID: PMC10659550 DOI: 10.21203/rs.3.rs-3501110/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Intrinsically disordered protein regions (IDRs) are ubiquitous across all kingdoms of life and play a variety of essential cellular roles. IDRs exist in a collection of structurally distinct conformers known as an ensemble. IDR amino acid sequence determines its ensemble, which in turn can play an important role in dictating molecular function. Yet a clear link connecting IDR sequence, its ensemble properties, and its molecular function in living cells has not been systematically established. Here, we set out to test this sequence-ensemble-function paradigm using a novel computational method (GOOSE) that enables the rational design of libraries of IDRs by systematically varying specific sequence properties. Using ensemble FRET, we measured the ensemble dimensions of a library of rationally designed IDRs in human-derived cell lines, revealing how IDR sequence influences ensemble dimensions in situ. Furthermore, we show that the interplay between sequence and ensemble can tune an IDR's ability to sense changes in cell volume - a de novomolecular function for these synthetic sequences. Our results establish biophysical rules for intracellular sequence-ensemble relationships, enable a new route for understanding how IDR sequences map to function in live cells, and set the ground for the design of synthetic IDRs with de novo function.
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29
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Nepal S, Holmstrom ED. Single-molecule-binding studies of antivirals targeting the hepatitis C virus core protein. J Virol 2023; 97:e0089223. [PMID: 37772835 PMCID: PMC10617558 DOI: 10.1128/jvi.00892-23] [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: 06/14/2023] [Accepted: 08/10/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE The hepatitis C virus is associated with nearly 300,000 deaths annually. At the core of the virus is an RNA-protein complex called the nucleocapsid, which consists of the viral genome and many copies of the core protein. Because the assembly of the nucleocapsid is a critical step in viral replication, a considerable amount of effort has been devoted to identifying antiviral therapeutics that can bind to the core protein and disrupt assembly. Although several candidates have been identified, little is known about how they interact with the core protein or how those interactions alter the structure and thus the function of this viral protein. Our work biochemically characterizes several of these binding interactions, highlighting both similarities and differences as well as strengths and weaknesses. These insights bolster the notion that this viral protein is a viable target for novel therapeutics and will help to guide future developments of these candidate antivirals.
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Affiliation(s)
- Sudip Nepal
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Erik D. Holmstrom
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
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30
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Pesce F, Bremer A, Tesei G, Hopkins JB, Grace CR, Mittag T, Lindorff-Larsen K. Design of intrinsically disordered protein variants with diverse structural properties. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.22.563461. [PMID: 37961110 PMCID: PMC10634714 DOI: 10.1101/2023.10.22.563461] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Intrinsically disordered proteins (IDPs) perform a wide range of functions in biology, suggesting that the ability to design IDPs could help expand the repertoire of proteins with novel functions. Designing IDPs with specific structural or functional properties has, however, been difficult, in part because determining accurate conformational ensembles of IDPs generally requires a combination of computational modelling and experiments. Motivated by recent advancements in efficient physics-based models for simulations of IDPs, we have developed a general algorithm for designing IDPs with specific structural properties. We demonstrate the power of the algorithm by generating variants of naturally occurring IDPs with different levels of compaction and that vary more than 100 fold in their propensity to undergo phase separation, even while keeping a fixed amino acid composition. We experimentally tested designs of variants of the low-complexity domain of hnRNPA1 and find high accuracy in our computational predictions, both in terms of single-chain compaction and propensity to undergo phase separation. We analyze the sequence features that determine changes in compaction and propensity to phase separate and find an overall good agreement with previous findings for naturally occurring sequences. Our general, physics-based method enables the design of disordered sequences with specified conformational properties. Our algorithm thus expands the toolbox for protein design to include also the most flexible proteins and will enable the design of proteins whose functions exploit the many properties afforded by protein disorder.
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Affiliation(s)
- Francesco Pesce
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anne Bremer
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Giulio Tesei
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jesse B. Hopkins
- BioCAT, Department of Physics, Illinois Institute of Technology, Chicago, IL, USA
| | - Christy R. Grace
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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31
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Truong HP, Koren G, Avinery R, Beck R, Saleh OA. Pincus blob elasticity in an intrinsically disordered protein. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:100. [PMID: 37847354 DOI: 10.1140/epje/s10189-023-00360-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/29/2023] [Indexed: 10/18/2023]
Abstract
Understanding the dynamic structure of intrinsically disordered proteins (IDPs) is important to deciphering their biological functions. Here, we exploit precision entropic elasticity measurements to infer the conformational behavior of a model IDP construct formed from the disordered tail of the neurofilament low molecular weight protein. The IDP construct notably displays a low-force power-law elastic regime, consistent with the Pincus blob model, which allows direct extraction of the Flory exponent, [Formula: see text], from the force-extension relationship. We find [Formula: see text] increases with added denaturant, transitioning from a nearly ideal chain to a swollen chain in a manner quantitatively consistent with measurements of IDP dimensions from other experimental techniques. We suggest that measurements of entropic elasticity could be broadly useful in the study of IDP structure.
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Affiliation(s)
- Hoang P Truong
- Materials Department, University of California, Santa Barbara, USA
| | - Gil Koren
- The Raymond and Beverly Sackler School of Physics and Astronomy and The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- The Center of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel
| | - Ram Avinery
- The Raymond and Beverly Sackler School of Physics and Astronomy and The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- The Center of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel
| | - Roy Beck
- The Raymond and Beverly Sackler School of Physics and Astronomy and The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- The Center of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel
| | - Omar A Saleh
- Materials Department, University of California, Santa Barbara, USA.
- Biomolecular Sciences and Engineering Department, University of California, Santa Barbara, USA.
- Physics Department, University of California, Santa Barbara, USA.
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32
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Chowdhury A, Borgia A, Ghosh S, Sottini A, Mitra S, Eapen RS, Borgia MB, Yang T, Galvanetto N, Ivanović MT, Łukijańczuk P, Zhu R, Nettels D, Kundagrami A, Schuler B. Driving forces of the complex formation between highly charged disordered proteins. Proc Natl Acad Sci U S A 2023; 120:e2304036120. [PMID: 37796987 PMCID: PMC10576128 DOI: 10.1073/pnas.2304036120] [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: 03/14/2023] [Accepted: 08/22/2023] [Indexed: 10/07/2023] Open
Abstract
Highly disordered complexes between oppositely charged intrinsically disordered proteins present a new paradigm of biomolecular interactions. Here, we investigate the driving forces of such interactions for the example of the highly positively charged linker histone H1 and its highly negatively charged chaperone, prothymosin α (ProTα). Temperature-dependent single-molecule Förster resonance energy transfer (FRET) experiments and isothermal titration calorimetry reveal ProTα-H1 binding to be enthalpically unfavorable, and salt-dependent affinity measurements suggest counterion release entropy to be an important thermodynamic driving force. Using single-molecule FRET, we also identify ternary complexes between ProTα and H1 in addition to the heterodimer at equilibrium and show how they contribute to the thermodynamics observed in ensemble experiments. Finally, we explain the observed thermodynamics quantitatively with a mean-field polyelectrolyte theory that treats counterion release explicitly. ProTα-H1 complex formation resembles the interactions between synthetic polyelectrolytes, and the underlying principles are likely to be of broad relevance for interactions between charged biomolecules in general.
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Affiliation(s)
- Aritra Chowdhury
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Alessandro Borgia
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Souradeep Ghosh
- Department of Physical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur741246, India
| | - Andrea Sottini
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Soumik Mitra
- Department of Physical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur741246, India
| | - Rohan S. Eapen
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | | | - Tianjin Yang
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Nicola Galvanetto
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
- Department of Physics, University of Zurich, Zurich8057, Switzerland
| | - Miloš T. Ivanović
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Paweł Łukijańczuk
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Ruijing Zhu
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Arindam Kundagrami
- Department of Physical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur741246, India
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
- Department of Physics, University of Zurich, Zurich8057, Switzerland
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33
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Białobrzewski MK, Klepka BP, Michaś A, Cieplak-Rotowska MK, Staszałek Z, Niedźwiecka A. Diversity of hydrodynamic radii of intrinsically disordered proteins. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:607-618. [PMID: 37831084 PMCID: PMC10618399 DOI: 10.1007/s00249-023-01683-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/08/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023]
Abstract
Intrinsically disordered proteins (IDPs) form an important class of biomolecules regulating biological processes in higher organisms. The lack of a fixed spatial structure facilitates them to perform their regulatory functions and allows the efficiency of biochemical reactions to be controlled by temperature and the cellular environment. From the biophysical point of view, IDPs are biopolymers with a broad configuration state space and their actual conformation depends on non-covalent interactions of its amino acid side chain groups at given temperature and chemical conditions. Thus, the hydrodynamic radius (Rh) of an IDP of a given polymer length (N) is a sequence- and environment-dependent variable. We have reviewed the literature values of hydrodynamic radii of IDPs determined experimentally by SEC, AUC, PFG NMR, DLS, and FCS, and complement them with our FCS results obtained for a series of protein fragments involved in the regulation of human gene expression. The data collected herein show that the values of hydrodynamic radii of IDPs can span the full space between the folded globular and denatured proteins in the Rh(N) diagram.
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Affiliation(s)
- Michał K Białobrzewski
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland
| | - Barbara P Klepka
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland
| | - Agnieszka Michaś
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland
| | - Maja K Cieplak-Rotowska
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, PL-02093, Warsaw, Poland
- The International Institute of Molecular Mechanisms and Machines, Polish Academy of Sciences, Flisa 6, PL-02247, Warsaw, Poland
| | - Zuzanna Staszałek
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland
| | - Anna Niedźwiecka
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland.
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34
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Yang T, Buholzer KJ, Sottini A, Cao X, deMello A, Nettels D, Schuler B. Rapid droplet-based mixing for single-molecule spectroscopy. Nat Methods 2023; 20:1479-1482. [PMID: 37749213 DOI: 10.1038/s41592-023-01995-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/02/2023] [Indexed: 09/27/2023]
Abstract
Probing non-equilibrium dynamics with single-molecule spectroscopy is important for dissecting biomolecular mechanisms. However, existing microfluidic rapid-mixing systems for this purpose are incompatible with surface-adhesive biomolecules, exhibit undesirable flow dispersion and are often demanding to fabricate. Here we introduce droplet-based microfluidic mixing for single-molecule spectroscopy to overcome these limitations in a wide range of applications. We demonstrate its robust functionality with binding kinetics of even very surface-adhesive proteins on the millisecond timescale.
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Affiliation(s)
- Tianjin Yang
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
| | - Karin J Buholzer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Andrea Sottini
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Xiaobao Cao
- Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Andrew deMello
- Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
- Department of Physics, University of Zurich, Zurich, Switzerland.
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35
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Lorton BM, Warren C, Ilyas H, Nandigrami P, Hegde S, Cahill S, Lehman SM, Shabanowitz J, Hunt DF, Fiser A, Cowburn D, Shechter D. Glutamylation of Npm2 and Nap1 acidic disordered regions increases DNA charge mimicry to enhance chaperone efficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558337. [PMID: 37790377 PMCID: PMC10542154 DOI: 10.1101/2023.09.18.558337] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Histone chaperones-structurally diverse, non-catalytic proteins enriched with acidic intrinsically disordered regions (IDRs)-protect histones from spurious nucleic acid interactions and guide their deposition into and out of nucleosomes. Despite their conservation and ubiquity, the function of the chaperone acidic IDRs remains unclear. Here, we show that the Xenopus laevis Npm2 and Nap1 acidic IDRs are substrates for TTLL4 (Tubulin Tyrosine Ligase Like 4)-catalyzed post-translational glutamate-glutamylation. We demonstrate that, to bind, stabilize, and deposit histones into nucleosomes, chaperone acidic IDRs function as DNA mimetics. Our biochemical, computational, and biophysical studies reveal that glutamylation of these chaperone polyelectrolyte acidic stretches functions to enhance DNA electrostatic mimicry, promoting the binding and stabilization of H2A/H2B heterodimers and facilitating nucleosome assembly. This discovery provides insights into both the previously unclear function of the acidic IDRs and the regulatory role of post-translational modifications in chromatin dynamics.
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Affiliation(s)
- Benjamin M. Lorton
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Christopher Warren
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
- Current address: Merck & Co., Inc., 2025 E Scott Ave., Rahway, NJ 07065
| | - Humaira Ilyas
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Prithviraj Nandigrami
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
- Department of Systems & Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Subray Hegde
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Sean Cahill
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Stephanie M Lehman
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904
- GSK, Collegeville, Pennsylvania 19426
| | | | - Donald F. Hunt
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904
- Departments of Chemistry and Pathology, University of Virginia, Charlottesville, VA 22904
| | - Andras Fiser
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
- Department of Systems & Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
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36
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Schweitzer-Stenner R, Kurbaj R, O'Neill N, Andrews B, Shah R, Urbanc B. Conformational Manifold Sampled by Two Short Linear Motif Segments Probed by Circular Dichroism, Vibrational, and Nuclear Magnetic Resonance Spectroscopy. Biochemistry 2023; 62:2571-2586. [PMID: 37595285 DOI: 10.1021/acs.biochem.3c00212] [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: 08/20/2023]
Abstract
Disordered protein segments called short linear motifs (SLiM) serve as recognition sites for a variety of biological processes and act as targeting signals, modification, and ligand binding sites. While SLiMs do not adopt one of the known regular secondary structures, the conformational distribution might still reflect the structural propensities of their amino acid residues and possible interactions between them. In the past, conformational analyses of short peptides provided compelling evidence for the notion that individual residues are less conformationally flexible than locally expected for a random coil. Here, we combined various spectroscopies (NMR, IR, vibrational, and UV circular dichroism) to determine the Ramachandran plots of two SLiM motifs, i.e., GRRDSG and GRRTSG. They are two representatives of RxxS motifs that are capable of being phosphorylated by protein kinase A, an enzyme that plays a fundamental role in a variety of biological processes. Our results reveal that the nearest and non-nearest interactions between residues cause redistributions between polyproline II and β-strand basins while concomitantly stabilizing extended relative to turn-forming and helical structures. They also cause shifts in basin positions. With increasing temperature, β-strand populations become more populated at the expense of polyproline II. While molecular dynamics simulations with Amber ff14SB and CHARMM 36m force fields indicate residue-residue interactions, they do not account for the observed structural changes.
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Affiliation(s)
| | - Raghed Kurbaj
- Department of Chemistry, Drexel University, Philadelphia, PA19104Pennsylvania,United States
| | - Nichole O'Neill
- Department of Chemistry, Drexel University, Philadelphia, PA19104Pennsylvania,United States
| | - Brian Andrews
- Department of Physics, Drexel University, Philadelphia,PA19104Pennsylvania,United States
| | - Riya Shah
- Department of Physics, Drexel University, Philadelphia,PA19104Pennsylvania,United States
| | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia,PA19104Pennsylvania,United States
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Wilson C, Lewis KA, Fitzkee NC, Hough LE, Whitten ST. ParSe 2.0: A web tool to identify drivers of protein phase separation at the proteome level. Protein Sci 2023; 32:e4756. [PMID: 37574757 PMCID: PMC10464302 DOI: 10.1002/pro.4756] [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: 06/23/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
We have developed an algorithm, ParSe, which accurately identifies from the primary sequence those protein regions likely to exhibit physiological phase separation behavior. Originally, ParSe was designed to test the hypothesis that, for flexible proteins, phase separation potential is correlated to hydrodynamic size. While our results were consistent with that idea, we also found that many different descriptors could successfully differentiate between three classes of protein regions: folded, intrinsically disordered, and phase-separating intrinsically disordered. Consequently, numerous combinations of amino acid property scales can be used to make robust predictions of protein phase separation. Built from that finding, ParSe 2.0 uses an optimal set of property scales to predict domain-level organization and compute a sequence-based prediction of phase separation potential. The algorithm is fast enough to scan the whole of the human proteome in minutes on a single computer and is equally or more accurate than other published predictors in identifying proteins and regions within proteins that drive phase separation. Here, we describe a web application for ParSe 2.0 that may be accessed through a browser by visiting https://stevewhitten.github.io/Parse_v2_FASTA to quickly identify phase-separating proteins within large sequence sets, or by visiting https://stevewhitten.github.io/Parse_v2_web to evaluate individual protein sequences.
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Affiliation(s)
- Colorado Wilson
- Department of Chemistry and BiochemistryTexas State UniversitySan MarcosTexasUSA
- Present address:
Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular BiophysicsUniversity of Texas Medical BranchGalvestonTexasUSA
| | - Karen A. Lewis
- Department of Chemistry and BiochemistryTexas State UniversitySan MarcosTexasUSA
| | - Nicholas C. Fitzkee
- Department of ChemistryMississippi State UniversityMississippi StateMississippiUSA
| | - Loren E. Hough
- Department of PhysicsUniversity of Colorado BoulderBoulderColoradoUSA
- BioFrontiers InstituteUniversity of Colorado BoulderBoulderColoradoUSA
| | - Steven T. Whitten
- Department of Chemistry and BiochemistryTexas State UniversitySan MarcosTexasUSA
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38
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Bhopatkar AA, Kayed R. Flanking regions, amyloid cores, and polymorphism: the potential interplay underlying structural diversity. J Biol Chem 2023; 299:105122. [PMID: 37536631 PMCID: PMC10482755 DOI: 10.1016/j.jbc.2023.105122] [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: 04/26/2023] [Revised: 07/10/2023] [Accepted: 07/28/2023] [Indexed: 08/05/2023] Open
Abstract
The β-sheet-rich amyloid core is the defining feature of protein aggregates associated with neurodegenerative disorders. Recent investigations have revealed that there exist multiple examples of the same protein, with the same sequence, forming a variety of amyloid cores with distinct structural characteristics. These structural variants, termed as polymorphs, are hypothesized to influence the pathological profile and the progression of different neurodegenerative diseases, giving rise to unique phenotypic differences. Thus, identifying the origin and properties of these structural variants remain a focus of studies, as a preliminary step in the development of therapeutic strategies. Here, we review the potential role of the flanking regions of amyloid cores in inducing polymorphism. These regions, adjacent to the amyloid cores, show a preponderance for being structurally disordered, imbuing them with functional promiscuity. The dynamic nature of the flanking regions can then manifest in the form of conformational polymorphism of the aggregates. We take a closer look at the sequences flanking the amyloid cores, followed by a review of the polymorphic aggregates of the well-characterized proteins amyloid-β, α-synuclein, Tau, and TDP-43. We also consider different factors that can potentially influence aggregate structure and how these regions can be viewed as novel targets for therapeutic strategies by utilizing their unique structural properties.
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Affiliation(s)
- Anukool A Bhopatkar
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, Texas, USA; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, Texas, USA; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, USA.
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39
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Lalmansingh JM, Keeley AT, Ruff KM, Pappu RV, Holehouse AS. SOURSOP: A Python Package for the Analysis of Simulations of Intrinsically Disordered Proteins. J Chem Theory Comput 2023; 19:5609-5620. [PMID: 37463458 PMCID: PMC11188088 DOI: 10.1021/acs.jctc.3c00190] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Conformational heterogeneity is a defining hallmark of intrinsically disordered proteins and protein regions (IDRs). The functions of IDRs and the emergent cellular phenotypes they control are associated with sequence-specific conformational ensembles. Simulations of conformational ensembles that are based on atomistic and coarse-grained models are routinely used to uncover the sequence-specific interactions that may contribute to IDR functions. These simulations are performed either independently or in conjunction with data from experiments. Functionally relevant features of IDRs can span a range of length scales. Extracting these features requires analysis routines that quantify a range of properties. Here, we describe a new analysis suite simulation analysis of unfolded regions of proteins (SOURSOP), an object-oriented and open-source toolkit designed for the analysis of simulated conformational ensembles of IDRs. SOURSOP implements several analysis routines motivated by principles in polymer physics, offering a unique collection of simple-to-use functions to characterize IDR ensembles. As an extendable framework, SOURSOP supports the development and implementation of new analysis routines that can be easily packaged and shared.
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Affiliation(s)
- Jared M. Lalmansingh
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Alex T. Keeley
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana-Champaign, IL 61801, USA
| | - Kiersten M. Ruff
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Rohit V. Pappu
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Alex S. Holehouse
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
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40
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Alston JJ, Soranno A. Condensation Goes Viral: A Polymer Physics Perspective. J Mol Biol 2023; 435:167988. [PMID: 36709795 PMCID: PMC10368797 DOI: 10.1016/j.jmb.2023.167988] [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: 10/18/2022] [Revised: 01/18/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023]
Abstract
The past decade has seen a revolution in our understanding of how the cellular environment is organized, where an incredible body of work has provided new insights into the role played by membraneless organelles. These rapid advancements have been made possible by an increasing awareness of the peculiar physical properties that give rise to such bodies and the complex biology that enables their function. Viral infections are not extraneous to this. Indeed, in host cells, viruses can harness existing membraneless compartments or, even, induce the formation of new ones. By hijacking the cellular machinery, these intracellular bodies can assist in the replication, assembly, and packaging of the viral genome as well as in the escape of the cellular immune response. Here, we provide a perspective on the fundamental polymer physics concepts that may help connect and interpret the different observed phenomena, ranging from the condensation of viral genomes to the phase separation of multicomponent solutions. We complement the discussion of the physical basis with a description of biophysical methods that can provide quantitative insights for testing and developing theoretical and computational models.
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Affiliation(s)
- Jhullian J Alston
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA.
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41
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Abstract
Multivalent proteins and nucleic acids, collectively referred to as multivalent associative biomacromolecules, provide the driving forces for the formation and compositional regulation of biomolecular condensates. Here, we review the key concepts of phase transitions of aqueous solutions of associative biomacromolecules, specifically proteins that include folded domains and intrinsically disordered regions. The phase transitions of these systems come under the rubric of coupled associative and segregative transitions. The concepts underlying these processes are presented, and their relevance to biomolecular condensates is discussed.
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Affiliation(s)
- Rohit V Pappu
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Samuel R Cohen
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Furqan Dar
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mina Farag
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mrityunjoy Kar
- Max Planck Institute of Cell Biology and Genetics, 01307 Dresden, Germany
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42
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Koren G, Meir S, Holschuh L, Mertens HDT, Ehm T, Yahalom N, Golombek A, Schwartz T, Svergun DI, Saleh OA, Dzubiella J, Beck R. Intramolecular structural heterogeneity altered by long-range contacts in an intrinsically disordered protein. Proc Natl Acad Sci U S A 2023; 120:e2220180120. [PMID: 37459524 PMCID: PMC10372579 DOI: 10.1073/pnas.2220180120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 06/02/2023] [Indexed: 07/20/2023] Open
Abstract
Short-range interactions and long-range contacts drive the 3D folding of structured proteins. The proteins' structure has a direct impact on their biological function. However, nearly 40% of the eukaryotes proteome is composed of intrinsically disordered proteins (IDPs) and protein regions that fluctuate between ensembles of numerous conformations. Therefore, to understand their biological function, it is critical to depict how the structural ensemble statistics correlate to the IDPs' amino acid sequence. Here, using small-angle X-ray scattering and time-resolved Förster resonance energy transfer (trFRET), we study the intramolecular structural heterogeneity of the neurofilament low intrinsically disordered tail domain (NFLt). Using theoretical results of polymer physics, we find that the Flory scaling exponent of NFLt subsegments correlates linearly with their net charge, ranging from statistics of ideal to self-avoiding chains. Surprisingly, measuring the same segments in the context of the whole NFLt protein, we find that regardless of the peptide sequence, the segments' structural statistics are more expanded than when measured independently. Our findings show that while polymer physics can, to some level, relate the IDP's sequence to its ensemble conformations, long-range contacts between distant amino acids play a crucial role in determining intramolecular structures. This emphasizes the necessity of advanced polymer theories to fully describe IDPs ensembles with the hope that it will allow us to model their biological function.
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Affiliation(s)
- Gil Koren
- The School of Physics and Astronomy, Department of Condensed Matter, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
| | - Sagi Meir
- The School of Physics and Astronomy, Department of Condensed Matter, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
| | - Lennard Holschuh
- Applied Theoretical Physics-Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universit Freiburg, FreiburgD-79104, Germany
| | | | - Tamara Ehm
- The School of Physics and Astronomy, Department of Condensed Matter, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, MünchenD-80539, Germany
| | - Nadav Yahalom
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences and Tel Aviv University Center for Light–Matter Interaction, Tel Aviv University, Tel Aviv6997801, Israel
| | - Adina Golombek
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences and Tel Aviv University Center for Light–Matter Interaction, Tel Aviv University, Tel Aviv6997801, Israel
| | - Tal Schwartz
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences and Tel Aviv University Center for Light–Matter Interaction, Tel Aviv University, Tel Aviv6997801, Israel
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg22607, Germany
| | - Omar A. Saleh
- BMSE Program, University of California, Santa Barbara, CA93110
- Materials Department, University of California, Santa Barbara, CA93110
| | - Joachim Dzubiella
- Applied Theoretical Physics-Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universit Freiburg, FreiburgD-79104, Germany
- Cluster of Excellence livMatS @ FIT–Freiburg Center for Interactive Materials and Bioinspired Technologies, Albert-Ludwigs-Universit Freiburg, FreiburgD-79104, Germany
| | - Roy Beck
- The School of Physics and Astronomy, Department of Condensed Matter, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv69978, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv69978, Israel
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43
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Jonas F, Carmi M, Krupkin B, Steinberger J, Brodsky S, Jana T, Barkai N. The molecular grammar of protein disorder guiding genome-binding locations. Nucleic Acids Res 2023; 51:4831-4844. [PMID: 36938874 PMCID: PMC10250222 DOI: 10.1093/nar/gkad184] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/25/2023] [Accepted: 03/15/2023] [Indexed: 03/21/2023] Open
Abstract
Intrinsically disordered regions (IDRs) direct transcription factors (TFs) towards selected genomic occurrences of their binding motif, as exemplified by budding yeast's Msn2. However, the sequence basis of IDR-directed TF binding selectivity remains unknown. To reveal this sequence grammar, we analyze the genomic localizations of >100 designed IDR mutants, each carrying up to 122 mutations within this 567-AA region. Our data points at multivalent interactions, carried by hydrophobic-mostly aliphatic-residues dispersed within a disordered environment and independent of linear sequence motifs, as the key determinants of Msn2 genomic localization. The implications of our results for the mechanistic basis of IDR-based TF binding preferences are discussed.
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Affiliation(s)
- Felix Jonas
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Miri Carmi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Beniamin Krupkin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Joseph Steinberger
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sagie Brodsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tamar Jana
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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44
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Alston JJ, Ginell GM, Soranno A, Holehouse AS. The Analytical Flory Random Coil Is a Simple-to-Use Reference Model for Unfolded and Disordered Proteins. J Phys Chem B 2023; 127:4746-4760. [PMID: 37200094 PMCID: PMC10875986 DOI: 10.1021/acs.jpcb.3c01619] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Denatured, unfolded, and intrinsically disordered proteins (collectively referred to here as unfolded proteins) can be described using analytical polymer models. These models capture various polymeric properties and can be fit to simulation results or experimental data. However, the model parameters commonly require users' decisions, making them useful for data interpretation but less clearly applicable as stand-alone reference models. Here we use all-atom simulations of polypeptides in conjunction with polymer scaling theory to parameterize an analytical model of unfolded polypeptides that behave as ideal chains (ν = 0.50). The model, which we call the analytical Flory random coil (AFRC), requires only the amino acid sequence as input and provides direct access to probability distributions of global and local conformational order parameters. The model defines a specific reference state to which experimental and computational results can be compared and normalized. As a proof-of-concept, we use the AFRC to identify sequence-specific intramolecular interactions in simulations of disordered proteins. We also use the AFRC to contextualize a curated set of 145 different radii of gyration obtained from previously published small-angle X-ray scattering experiments of disordered proteins. The AFRC is implemented as a stand-alone software package and is also available via a Google Colab notebook. In summary, the AFRC provides a simple-to-use reference polymer model that can guide intuition and aid in interpreting experimental or simulation results.
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Affiliation(s)
- Jhullian J. Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Garrett M. Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
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45
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Gaalswyk K, Haider A, Ghosh K. Critical Assessment of Self-Consistency Checks in the All-Atom Molecular Dynamics Simulation of Intrinsically Disordered Proteins. J Chem Theory Comput 2023; 19:2973-2984. [PMID: 37133846 DOI: 10.1021/acs.jctc.2c01140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
All atom simulations can be used to quantify conformational properties of Intrinsically Disordered Proteins (IDP). However, simulations must satisfy convergence checks to ensure observables computed from simulation are reliable and reproducible. While absolute convergence is purely a theoretical concept requiring infinitely long simulation, a more practical, yet rigorous, approach is to impose Self Consistency Checks (SCCs) to gain confidence in the simulated data. Currently there is no study of SCCs in IDPs, unlike their folded counterparts. In this paper, we introduce different criteria for self-consistency checks for IDPs. Next, we impose these SCCs to critically assess the performance of different simulation protocols using the N terminal domain of HIV Integrase and the linker region of SARS-CoV-2 Nucleoprotein as two model IDPs. All simulation protocols begin with all-atom implicit solvent Monte Carlo (MC) simulation and subsequent clustering of MC generated conformations to create the representative structures of the IDPs. These representative structures serve as the initial structure for subsequent molecular dynamics (MD) runs with explicit solvent. We conclude that generating multiple short (∼3 μs) MD simulation trajectories─all starting from the most representative MC generated conformation─and merging them is the protocol of choice due to (i) its ability to satisfy multiple SCCs, (ii) consistently reproducing experimental data, and (iii) the efficiency of running independent trajectories in parallel by harnessing multiple cores available in modern GPU clusters. Running one long trajectory (greater than 20 μs) can also satisfy the first two criteria but is less desirable due to prohibitive computation time. These findings help resolve the challenge of identifying a usable starting configuration, provide an objective measure of SCC, and establish rigorous criteria to determine the minimum length (for one long simulation) or number of trajectories needed in all-atom simulation of IDPs.
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Affiliation(s)
- Kari Gaalswyk
- Department of Physics and Astronomy, University of Denver, Denver, Colorado 80208, United States
| | - Austin Haider
- Department of Molecular and Cellular Biophysics, University of Denver, Denver, Colorado 80208, United States
| | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, Colorado 80208, United States
- Department of Molecular and Cellular Biophysics, University of Denver, Denver, Colorado 80208, United States
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46
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Martins GF, Nascimento C, Galamba N. Mechanistic Insights into Polyphenols' Aggregation Inhibition of α-Synuclein and Related Peptides. ACS Chem Neurosci 2023; 14:1905-1920. [PMID: 37125909 DOI: 10.1021/acschemneuro.3c00162] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
While several polyphenols were found to either inhibit or modulate the aggregation of proteins implicated in neurodegenerative diseases, such as Parkinson's disease (PD), discrepant action mechanisms have been reported. This, in addition to some polyphenols' pan-assay interference compounds' reputation, casts some doubts concerning their therapeutic relevance. Here, we studied, through molecular dynamics and enhanced sampling methods, the aggregation of 11-mer peptides from the non-amyloid-β component, an aggregation-prone domain of α-synuclein (α-syn) implicated in PD and other synucleinopathies, in neat water and aqueous solutions of resveratrol (RSV) and gallic acid (GA). Further, simulations of the complete protein were carried out in aqueous urea, RSV, and GA solutions. Our results show that peptide aggregation is not disrupted by either phenolic compound. Thus, instead, intrusion of RSV and GA in the inter-peptide region induces a peptide-peptide re-orientation, favoring terminal interactions that manifest in the formation of barrierless solvent-separated configurations. Moreover, although the (poly)phenols induce a pronounced peptide dewetting at high concentrations, β-sheet-rich regions, a hallmark of α-syn aggregation, are not disrupted. Thus, our results indicate that, if anything, RSV and GA delay or modulate peptide aggregation at high concentrations via the stabilization of solvent-separated conformations as opposed to aggregation inhibition. Structural analysis of the full protein, however, shows that the (poly)phenols induce more extended conformations of α-syn, similar to urea, possibly also influencing its aggregation propensity. However, opposite to urea, the (poly)phenols reduce α-syn's conformational space, likely due to steric effects and a slowdown of the solvent dynamics. These effects are concentration-dependent and possibly unattainable at therapeutic-relevant concentrations. These results suggest that the aggregation inhibition activity of RSV and GA in vitro should involve, instead, either the non-covalent binding to oligomeric intermediates or the stabilization of the monomer and/or oligomers through the formation of covalent bonds of the respective quinones with α-syn. In addition, the enhanced aggregation tendency of the peptides observed here could be associated with the formation of non-toxic oligomers, reported for some polyphenols.
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Affiliation(s)
- G F Martins
- BioISI─Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, Lisbon 1749-016, Portugal
| | - C Nascimento
- BioISI─Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, Lisbon 1749-016, Portugal
| | - N Galamba
- BioISI─Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, Lisbon 1749-016, Portugal
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47
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Schweitzer-Stenner R. The relevance of short peptides for an understanding of unfolded and intrinsically disordered proteins. Phys Chem Chem Phys 2023; 25:11908-11933. [PMID: 37096579 DOI: 10.1039/d3cp00483j] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Over the last thirty years the unfolded state of proteins has attracted considerable interest owing to the discovery of intrinsically disordered proteins which perform a plethora of functions despite resembling unfolded proteins to a significant extent. Research on both, unfolded and disordered proteins has revealed that their conformational properties can deviate locally from random coil behavior. In this context results from work on short oligopeptides suggest that individual amino acid residues sample the sterically allowed fraction of the Ramachandran plot to a different extent. Alanine has been found to exhibit a peculiarity in that it has a very high propensity for adopting polyproline II like conformations. This Perspectives article reviews work on short peptides aimed at exploring the Ramachandran distributions of amino acid residues in different contexts with experimental and computational means. Based on the thus provided overview the article discussed to what extent short peptides can serve as tools for exploring unfolded and disordered proteins and as benchmarks for the development of a molecular dynamics force field.
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Surguchov A, Emamzadeh FN, Titova M, Surguchev AA. Controversial Properties of Amyloidogenic Proteins and Peptides: New Data in the COVID Era. Biomedicines 2023; 11:1215. [PMID: 37189833 PMCID: PMC10136278 DOI: 10.3390/biomedicines11041215] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
For a long time, studies of amyloidogenic proteins and peptides (amyloidogenic PPs) have been focused basically on their harmful properties and association with diseases. A vast amount of research has investigated the structure of pathogenic amyloids forming fibrous deposits within or around cells and the mechanisms of their detrimental actions. Much less has been known about the physiologic functions and beneficial properties of amyloidogenic PPs. At the same time, amyloidogenic PPs have various useful properties. For example, they may render neurons resistant to viral infection and propagation and stimulate autophagy. We discuss here some of amyloidogenic PPs' detrimental and beneficial properties using as examples beta-amyloid (β-amyloid), implicated in the pathogenesis of Alzheimer's disease (AD), and α-synuclein-one of the hallmarks of Parkinson's disease (PD). Recently amyloidogenic PPs' antiviral and antimicrobial properties have attracted attention because of the COVID-19 pandemic and the growing threat of other viral and bacterial-induced diseases. Importantly, several COVID-19 viral proteins, e.g., spike, nucleocapsid, and envelope proteins, may become amyloidogenic after infection and combine their harmful action with the effect of endogenous APPs. A central area of current investigations is the study of the structural properties of amyloidogenic PPs, defining their beneficial and harmful properties, and identifying triggers that transform physiologically important amyloidogenic PPs into vicious substances. These directions are of paramount importance during the current SARS-CoV-2 global health crisis.
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Affiliation(s)
- Andrei Surguchov
- Department of Neurology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Fatemeh N. Emamzadeh
- Analytical Development Department, Iovance Biotherapeutics, Inc., Tampa, FL 33612, USA
| | - Mariya Titova
- The College of Liberal Arts & Sciences, Kansas University, Lawrence, KS 66045, USA
| | - Alexei A. Surguchev
- Department of Surgery, Section of Otolaryngology, Yale School of Medicine, Yale University, New Haven, CT 06520, USA
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de Bruyn E, Dorn AE, Zimmermann O, Rossetti G. SPEADI: Accelerated Analysis of IDP-Ion Interactions from MD-Trajectories. BIOLOGY 2023; 12:biology12040581. [PMID: 37106781 PMCID: PMC10135740 DOI: 10.3390/biology12040581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023]
Abstract
The disordered nature of Intrinsically Disordered Proteins (IDPs) makes their structural ensembles particularly susceptible to changes in chemical environmental conditions, often leading to an alteration of their normal functions. A Radial Distribution Function (RDF) is considered a standard method for characterizing the chemical environment surrounding particles during atomistic simulations, commonly averaged over an entire or part of a trajectory. Given their high structural variability, such averaged information might not be reliable for IDPs. We introduce the Time-Resolved Radial Distribution Function (TRRDF), implemented in our open-source Python package SPEADI, which is able to characterize dynamic environments around IDPs. We use SPEADI to characterize the dynamic distribution of ions around the IDPs Alpha-Synuclein (AS) and Humanin (HN) from Molecular Dynamics (MD) simulations, and some of their selected mutants, showing that local ion-residue interactions play an important role in the structures and behaviors of IDPs.
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Affiliation(s)
- Emile de Bruyn
- Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425 Jülich, Germany
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062 Aachen, Germany
| | - Anton Emil Dorn
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062 Aachen, Germany
| | - Olav Zimmermann
- Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Giulia Rossetti
- Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425 Jülich, Germany
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany
- Department of Neurology, RWTH Aachen University, 52062 Aachen, Germany
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Xue C, Pei Z, Wen P, Chin Y, Hu Y. Effects of pH and NaCl on the Spatial Structure and Conformation of Myofibrillar Proteins and the Emulsion Gel System—Insights from Computational Molecular Dynamics on Myosin of Golden Pompano. Gels 2023; 9:gels9040270. [PMID: 37102882 PMCID: PMC10137719 DOI: 10.3390/gels9040270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
In this study, the effects of pH and NaCl concentrations on the structure of golden pompano myosin and emulsion gel were analyzed using SEM in combination with molecular dynamics simulations (MDS). The microscopic morphology and spatial structure of myosin were investigated at different pH (3.0, 7.0, and 11.0) and NaCl concentrations (0.0, 0.2, 0.6, and 1.0 M), and their effects on the stability of emulsion gels were discussed. Our results show that pH had a greater effect on the microscopic morphology of myosin than NaCl. The MDS results show that under the condition of pH 7.0 and 0.6 M NaCl, the myosin expanded and experienced significant fluctuations in its amino acid residues. However, NaCl showed a greater effect on the number of hydrogen bonds than pH. Although changes in pH and NaCl concentrations only slightly altered the secondary structures in myosin, they, nevertheless, significantly influenced the protein spatial conformation. The stability of the emulsion gel was affected by pH changes but not NaCl concentrations, which only affect the rheology. The best elastic modulus G″ of the emulsion gel was obtained at pH 7.0 and 0.6 M NaCl. Based on the results, we conclude that pH changes have a greater influence than NaCl concentrations on the spatial structure and conformation of myosin, contributing to the instability of its emulsion gel state. The data from this study would serve as a valuable reference for emulsion gel rheology modification in future research.
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