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Mehta S, Bahadur J, Kumar A, Kumar S, Sen D. Unveiling the Electrostatically Driven Collapsing and Relaxation of Polyelectrolyte-Colloid Complexes: A Tunable Pathway to Colloidal Assembly. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024. [PMID: 39364558 DOI: 10.1021/acs.langmuir.4c01795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2024]
Abstract
Polyelectrolyte-colloid (PEC) complexes, ubiquitous across diverse fields, exhibit remarkable phase transitions, mimicking intricate biological assemblies. While the role of electrostatic forces in the PEC complex assembly is undeniable, achieving a holistic comprehension remains an elusive goal. This study unveils a fascinating phenomenon: the formation of highly collapsed coacervate structures in PEC complexes at elevated polyelectrolyte concentrations, followed by the swelling of complexes at even higher concentrations. Employing anionic silica colloids and cationic chitosan as a model system, small-angle X-ray/neutron (SAXS/SANS) elucidates the transition from a bead-on-a-necklace-like phase to a dense packed coacervate state (with volume fraction ∼0.62) until 3 wt % concentration of the polyelectrolyte. However, beyond 3 wt %, swelling of the dense collapsed assembly is observed. This structural evolution of PEC complexes as a function of chitosan concentration is attributed to the interplay of electrostatically driven interactions and the Donnan effect. Notably, the critical concentration for coacervation, Cs*, demonstrates a linear dependence on the initial colloid concentration. Interestingly, a complete expansion of the coacervate is observed at a high polyelectrolyte concentration, particularly for dilute colloid solutions (2 wt %). Furthermore, the addition of an electrolyte sheds light on the delicate interplay of forces. While a low electrolyte concentration partially screens charges, leading to a shift in phase diagram, higher concentrations trigger complete coacervate dissolution beyond the critical electrolyte concentration of 0.2 M, due to the complete screening of electrostatic charges.
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Affiliation(s)
- Swati Mehta
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Jitendra Bahadur
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Ashwani Kumar
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Sugam Kumar
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Debasis Sen
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
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2
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Zheng Y, Li Q, Freiberger MI, Song H, Hu G, Zhang M, Gu R, Li J. Predicting the Dynamic Interaction of Intrinsically Disordered Proteins. J Chem Inf Model 2024; 64:6768-6777. [PMID: 39163306 DOI: 10.1021/acs.jcim.4c00930] [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: 08/22/2024]
Abstract
Intrinsically disordered proteins (IDPs) participate in various biological processes. Interactions involving IDPs are usually dynamic and are affected by their inherent conformation fluctuations. Comprehensive characterization of these interactions based on current techniques is challenging. Here, we present GSALIDP, a GraphSAGE-embedded LSTM network, to capture the dynamic nature of IDP-involved interactions and predict their behaviors. This framework models multiple conformations of IDP as a dynamic graph, which can effectively describe the fluctuation of its flexible conformation. The dynamic interaction between IDPs is studied, and the data sets of IDP conformations and their interactions are obtained through atomistic molecular dynamic (MD) simulations. Residues of IDP are encoded through a series of features including their frustration. GSALIDP can effectively predict the interaction sites of IDP and the contact residue pairs between IDPs. Its performance in predicting IDP interactions is on par with or even better than the conventional models in predicting the interaction of structural proteins. To the best of our knowledge, this is the first model to extend the protein interaction prediction to IDP-involved interactions.
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Affiliation(s)
- Yuchuan Zheng
- School of Physics, Zhejiang University, Hangzhou 310058, PR China
| | - Qixiu Li
- School of Physics, Zhejiang University, Hangzhou 310058, PR China
| | - Maria I Freiberger
- Protein Physiology Lab, Departamento de Quimica Biologica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires-CONICET-IQUIBICEN, Buenos Aires C1428EGA, Argentina
| | - Haoyu Song
- School of Physics, Zhejiang University, Hangzhou 310058, PR China
| | - Guorong Hu
- School of Physics, Zhejiang University, Hangzhou 310058, PR China
| | - Moxin Zhang
- School of Physics, Zhejiang University, Hangzhou 310058, PR China
| | - Ruoxu Gu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Jingyuan Li
- School of Physics, Zhejiang University, Hangzhou 310058, PR China
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3
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Zhang G, Chu X. Balancing thermodynamic stability, dynamics, and kinetics in phase separation of intrinsically disordered proteins. J Chem Phys 2024; 161:095102. [PMID: 39225535 DOI: 10.1063/5.0220861] [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: 05/29/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024] Open
Abstract
Intrinsically disordered proteins (IDPs) are prevalent participants in liquid-liquid phase separation due to their inherent potential for promoting multivalent binding. Understanding the underlying mechanisms of phase separation is challenging, as phase separation is a complex process, involving numerous molecules and various types of interactions. Here, we used a simplified coarse-grained model of IDPs to investigate the thermodynamic stability of the dense phase, conformational properties of IDPs, chain dynamics, and kinetic rates of forming condensates. We focused on the IDP system, in which the oppositely charged IDPs are maximally segregated, inherently possessing a high propensity for phase separation. By varying interaction strengths, salt concentrations, and temperatures, we observed that IDPs in the dense phase exhibited highly conserved conformational characteristics, which are more extended than those in the dilute phase. Although the chain motions and global conformational dynamics of IDPs in the condensates are slow due to the high viscosity, local chain flexibility at the short timescales is largely preserved with respect to that at the free state. Strikingly, we observed a non-monotonic relationship between interaction strengths and kinetic rates for forming condensates. As strong interactions of IDPs result in high stable condensates, our results suggest that the thermodynamics and kinetics of phase separation are decoupled and optimized by the speed-stability balance through underlying molecular interactions. Our findings contribute to the molecular-level understanding of phase separation and offer valuable insights into the developments of engineering strategies for precise regulation of biomolecular condensates.
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Affiliation(s)
- Guoqing Zhang
- Advanced Materials Thrust, Function Hub, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, Guangdong 511400, China
| | - Xiakun Chu
- Advanced Materials Thrust, Function Hub, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, Guangdong 511400, China
- Guangzhou Municipal Key Laboratory of Materials Informatics, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, Guangdong 511400, China
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR 999077, China
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4
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Shi Y, Tang S, Yuan X, Li Z, Wen S, Li Z, Su B, Yan C, Chen L. In Situ 4D Printing of Polyelectrolyte/Magnetic Composites for Sutureless Gastric Perforation Sealing. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307601. [PMID: 38047896 DOI: 10.1002/adma.202307601] [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: 07/30/2023] [Revised: 10/18/2023] [Indexed: 12/05/2023]
Abstract
In situ bioprinting has emerged as one of the most promising techniques for the sutureless tissue sealing of internal organs. However, most existing in situ bioprinting methods are limited by the complex and confined printing space inside the organs, harsh curing conditions for printable bioinks, and poor ability to suturelessly seal injured parts. The combination of in situ bioprinting and 4D printing is a promising technique for tissue repair. Herein, the in situ 4D printing of polyelectrolyte/magnetic composites by gastroscopy for sutureless internal tissue sealing is reported. Using gastric perforation as an example, a gelatin/sodium alginate/magnetic bioink is developed, which can be precisely located by a gastroscope with the assistance of an external magnetic field, solidified in gastric fluid, and firmly adhered to tissue surfaces. The solidified bioink along the defect can be attracted by an external magnetic field, resulting in sutureless sealing. A demonstration using a porcine stomach with an artificial perforation confirms the feasibility of sutureless sealing using 4D printing. Moreover, an in vivo investigation on gastric perforation in a rat model identifies the biocompatibility by H&E and CD68+ staining. This study provides a new orientation and concept for functionality-modified in situ 4D bioprinting.
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Affiliation(s)
- Yunsong Shi
- School of Stomatology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan, 430022, China
| | - Sihan Tang
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xi Yuan
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Zhuofan Li
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Shifeng Wen
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Zhongwei Li
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Bin Su
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Chunze Yan
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
- Engineering Research Center of Ceramic Materials for Additive Manufacturing, Ministry of Education, Wuhan, 430074, China
| | - Lili Chen
- School of Stomatology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan, 430022, China
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5
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Gopich IV, Chung HS. Unraveling Burst Selection Bias in Single-Molecule FRET of Species with Unequal Brightness and Diffusivity. J Phys Chem B 2024; 128:5576-5589. [PMID: 38833567 DOI: 10.1021/acs.jpcb.4c01178] [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: 06/06/2024]
Abstract
Single-molecule free diffusion experiments enable accurate quantification of coexisting species or states. However, unequal brightness and diffusivity introduce a burst selection bias and affect the interpretation of experimental results. We address this issue with a photon-by-photon maximum likelihood method, burstML, which explicitly considers burst selection criteria. BurstML accurately estimates parameters, including photon count rates, diffusion times, Förster resonance energy transfer (FRET) efficiencies, and population, even in cases where species are poorly distinguished in FRET efficiency histograms. We develop a quantitative theory that determines the fraction of photon bursts corresponding to each species and thus obtain accurate species populations from the measured burst fractions. In addition, we provide a simple approximate formula for burst fractions and establish the range of parameters where unequal brightness and diffusivity can significantly affect the results obtained by conventional methods. The performance of the burstML method is compared with that of a maximum likelihood method that assumes equal species brightness and diffusivity, as well as standard Gaussian fitting of FRET efficiency histograms, using both simulated and real single-molecule data for cold-shock protein, protein L, and protein G. The burstML method enhances the accuracy of parameter estimation in single-molecule fluorescence studies.
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Affiliation(s)
- Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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6
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Hernández‐Sánchez I, Rindfleisch T, Alpers J, Dulle M, Garvey CJ, Knox‐Brown P, Miettinen MS, Nagy G, Pusterla JM, Rekas A, Shou K, Stadler AM, Walther D, Wolff M, Zuther E, Thalhammer A. Functional in vitro diversity of an intrinsically disordered plant protein during freeze-thawing is encoded by its structural plasticity. Protein Sci 2024; 33:e4989. [PMID: 38659213 PMCID: PMC11043620 DOI: 10.1002/pro.4989] [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: 10/25/2023] [Revised: 03/09/2024] [Accepted: 03/31/2024] [Indexed: 04/26/2024]
Abstract
Intrinsically disordered late embryogenesis abundant (LEA) proteins play a central role in the tolerance of plants and other organisms to dehydration brought upon, for example, by freezing temperatures, high salt concentration, drought or desiccation, and many LEA proteins have been found to stabilize dehydration-sensitive cellular structures. Their conformational ensembles are highly sensitive to the environment, allowing them to undergo conformational changes and adopt ordered secondary and quaternary structures and to participate in formation of membraneless organelles. In an interdisciplinary approach, we discovered how the functional diversity of the Arabidopsis thaliana LEA protein COR15A found in vitro is encoded in its structural repertoire, with the stabilization of membranes being achieved at the level of secondary structure and the stabilization of enzymes accomplished by the formation of oligomeric complexes. We provide molecular details on intra- and inter-monomeric helix-helix interactions, demonstrate how oligomerization is driven by an α-helical molecular recognition feature (α-MoRF) and provide a rationale that the formation of noncanonical, loosely packed, right-handed coiled-coils might be a recurring theme for homo- and hetero-oligomerization of LEA proteins.
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Affiliation(s)
- Itzell Hernández‐Sánchez
- Max‐Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Present address:
Center for Desert Agriculture, Biological and Environmental Science and Engineering DivisionKing Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Tobias Rindfleisch
- Max‐Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Physical BiochemistryUniversity of PotsdamPotsdamGermany
- Department of ChemistryUniversity of BergenBergenNorway
- Computational Biology Unit, Department of InformaticsUniversity of BergenBergenNorway
| | - Jessica Alpers
- Max‐Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Martin Dulle
- Jülich Centre for Neutron Science (JCNS‐1) and Institute of Biological Information Processing (IBI‐8: Neutron Scattering and Biological Matter)Forschungszentrum Jülich GmbHJülichGermany
| | | | - Patrick Knox‐Brown
- Physical BiochemistryUniversity of PotsdamPotsdamGermany
- Present address:
Department of Discovery Pharmaceutical SciencesMerck & Co., Inc.South San FranciscoCaliforniaUSA
| | - Markus S. Miettinen
- Department of ChemistryUniversity of BergenBergenNorway
- Computational Biology Unit, Department of InformaticsUniversity of BergenBergenNorway
- Department of Theory and Bio‐SystemsMax Planck Institute of Colloids and InterfacesPotsdamGermany
| | - Gergely Nagy
- Neutron Scattering DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Julio M. Pusterla
- Jülich Centre for Neutron Science (JCNS‐1) and Institute of Biological Information Processing (IBI‐8: Neutron Scattering and Biological Matter)Forschungszentrum Jülich GmbHJülichGermany
| | - Agata Rekas
- Australian Nuclear Science and Technology Organization (ANSTO)KirraweeNew South WalesAustralia
| | - Keyun Shou
- Jülich Centre for Neutron Science (JCNS‐1) and Institute of Biological Information Processing (IBI‐8: Neutron Scattering and Biological Matter)Forschungszentrum Jülich GmbHJülichGermany
- Australian Nuclear Science and Technology Organization (ANSTO)KirraweeNew South WalesAustralia
- Institute of Physical Chemistry, RWTH Aachen UniversityAachenGermany
| | - Andreas M. Stadler
- Jülich Centre for Neutron Science (JCNS‐1) and Institute of Biological Information Processing (IBI‐8: Neutron Scattering and Biological Matter)Forschungszentrum Jülich GmbHJülichGermany
- Institute of Physical Chemistry, RWTH Aachen UniversityAachenGermany
| | - Dirk Walther
- Max‐Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Martin Wolff
- Physical BiochemistryUniversity of PotsdamPotsdamGermany
| | - Ellen Zuther
- Max‐Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Present address:
Center of Artificial Intelligence in Public Health Research (ZKI‐PH)Robert Koch InstituteBerlinGermany
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7
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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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8
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Cubuk J, Alston J, Incicco JJ, Holehouse A, Hall K, Stuchell-Brereton M, Soranno A. The disordered N-terminal tail of SARS-CoV-2 Nucleocapsid protein forms a dynamic complex with RNA. Nucleic Acids Res 2024; 52:2609-2624. [PMID: 38153183 PMCID: PMC10954482 DOI: 10.1093/nar/gkad1215] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 11/17/2023] [Accepted: 12/11/2023] [Indexed: 12/29/2023] Open
Abstract
The SARS-CoV-2 Nucleocapsid (N) protein is responsible for condensation of the viral genome. Characterizing the mechanisms controlling nucleic acid binding is a key step in understanding how condensation is realized. Here, we focus on the role of the RNA binding domain (RBD) and its flanking disordered N-terminal domain (NTD) tail, using single-molecule Förster Resonance Energy Transfer and coarse-grained simulations. We quantified contact site size and binding affinity for nucleic acids and concomitant conformational changes occurring in the disordered region. We found that the disordered NTD increases the affinity of the RBD for RNA by about 50-fold. Binding of both nonspecific and specific RNA results in a modulation of the tail configurations, which respond in an RNA length-dependent manner. Not only does the disordered NTD increase affinity for RNA, but mutations that occur in the Omicron variant modulate the interactions, indicating a functional role of the disordered tail. Finally, we found that the NTD-RBD preferentially interacts with single-stranded RNA and that the resulting protein:RNA complexes are flexible and dynamic. We speculate that this mechanism of interaction enables the Nucleocapsid protein to search the viral genome for and bind to high-affinity motifs.
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Affiliation(s)
- Jasmine Cubuk
- 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
| | - 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
| | - J Jeremías Incicco
- 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
| | - Alex S Holehouse
- 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
| | - Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA
| | - Melissa D Stuchell-Brereton
- 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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9
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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: 62] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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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10
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Lei M, Liao H, Wang S, Zhou H, Zhu J, Wan H, Payne GF, Liu C, Qu X. Electro-Sorting Create Heterogeneity: Constructing A Multifunctional Janus Film with Integrated Compositional and Microstructural Gradients for Guided Bone Regeneration. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307606. [PMID: 38225697 DOI: 10.1002/advs.202307606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/25/2023] [Indexed: 01/17/2024]
Abstract
Biology remains the envy of flexible soft matter fabrication because it can satisfy multiple functional needs by organizing a small set of proteins and polysaccharides into hierarchical systems with controlled heterogeneity in composition and microstructure. Here, it is reported that controlled, mild electronic inputs (<10 V; <20 min) induce a homogeneous gelatin-chitosan mixture to undergo sorting and bottom-up self-assembly into a Janus film with compositional gradient (i.e., from chitosan-enriched layer to chitosan/gelatin-contained layer) and tunable dense-porous gradient microstructures (e.g., porosity, pore size, and ratio of dense to porous layers). This Janus film performs is shown multiple functions for guided bone regeneration: the integration of compositional and microstructural features confers flexible mechanics, asymmetric properties for interfacial wettability, molecular transport (directional growth factor release), and cellular responses (prevents fibroblast infiltration but promotes osteoblast growth and differentiation). Overall, this work demonstrates the versatility of electrofabrication for the customized manufacturing of functional gradient soft matter.
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Affiliation(s)
- Miao Lei
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Haitao Liao
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Shijia Wang
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Hang Zhou
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jianwei Zhu
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Haoran Wan
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Gregory F Payne
- Institute for Bioscience and Biotechnology Research and Robert E. Fischell Biomedical Device Institute, 5118 A. James Clark Hall, College Park, Maryland, 20742, USA
| | - Changsheng Liu
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Xue Qu
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of materials science and engineering, East China University of Science and Technology, Shanghai, 200237, China
- Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China
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11
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Bjarnason S, McIvor JAP, Prestel A, Demény KS, Bullerjahn JT, Kragelund BB, Mercadante D, Heidarsson PO. DNA binding redistributes activation domain ensemble and accessibility in pioneer factor Sox2. Nat Commun 2024; 15:1445. [PMID: 38365983 PMCID: PMC10873366 DOI: 10.1038/s41467-024-45847-2] [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: 07/13/2023] [Accepted: 02/01/2024] [Indexed: 02/18/2024] Open
Abstract
More than 1600 human transcription factors orchestrate the transcriptional machinery to control gene expression and cell fate. Their function is conveyed through intrinsically disordered regions (IDRs) containing activation or repression domains but lacking quantitative structural ensemble models prevents their mechanistic decoding. Here we integrate single-molecule FRET and NMR spectroscopy with molecular simulations showing that DNA binding can lead to complex changes in the IDR ensemble and accessibility. The C-terminal IDR of pioneer factor Sox2 is highly disordered but its conformational dynamics are guided by weak and dynamic charge interactions with the folded DNA binding domain. Both DNA and nucleosome binding induce major rearrangements in the IDR ensemble without affecting DNA binding affinity. Remarkably, interdomain interactions are redistributed in complex with DNA leading to variable exposure of two activation domains critical for transcription. Charged intramolecular interactions allowing for dynamic redistributions may be common in transcription factors and necessary for sensitive tuning of structural ensembles.
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Affiliation(s)
- Sveinn Bjarnason
- Department of Biochemistry, Science Institute, University of Iceland, Sturlugata 7, 102, Reykjavík, Iceland
| | - Jordan A P McIvor
- School of Chemical Science, University of Auckland, Auckland, New Zealand
| | - Andreas Prestel
- Department of Biology, REPIN and Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Kinga S Demény
- Department of Biochemistry, Science Institute, University of Iceland, Sturlugata 7, 102, Reykjavík, Iceland
| | - Jakob T Bullerjahn
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt am Main, Germany
| | - Birthe B Kragelund
- Department of Biology, REPIN and Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Davide Mercadante
- School of Chemical Science, University of Auckland, Auckland, New Zealand.
| | - Pétur O Heidarsson
- Department of Biochemistry, Science Institute, University of Iceland, Sturlugata 7, 102, Reykjavík, Iceland.
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12
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Sipko EL, Chappell GF, Berlow RB. Multivalency emerges as a common feature of intrinsically disordered protein interactions. Curr Opin Struct Biol 2024; 84:102742. [PMID: 38096754 DOI: 10.1016/j.sbi.2023.102742] [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: 09/18/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 02/09/2024]
Abstract
Intrinsically disordered proteins (IDPs) use their unique molecular properties and conformational plasticity to interact with cellular partners in a wide variety of biological contexts. Multivalency is an important feature of IDPs that allows for utilization of an expanded toolkit for interactions with other macromolecules and confers additional complexity to molecular recognition processes. Recent studies have offered insights into how multivalent interactions of IDPs enable responsive and sensitive regulation in the context of transcription and cellular signaling. Multivalency is also widely recognized as an important feature of IDP interactions that mediate formation of biomolecular condensates. We highlight recent examples of multivalent interactions of IDPs across diverse contexts to illustrate the breadth of biological processes that utilize multivalency in molecular interactions.
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Affiliation(s)
- Emily L Sipko
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Garrett F Chappell
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rebecca B Berlow
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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13
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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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14
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Papageorgiou AC, Pospisilova M, Cibulka J, Ashraf R, Waudby CA, Kadeřávek P, Maroz V, Kubicek K, Prokop Z, Krejci L, Tripsianes K. Recognition and coacervation of G-quadruplexes by a multifunctional disordered region in RECQ4 helicase. Nat Commun 2023; 14:6751. [PMID: 37875529 PMCID: PMC10598209 DOI: 10.1038/s41467-023-42503-z] [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: 02/09/2022] [Accepted: 10/12/2023] [Indexed: 10/26/2023] Open
Abstract
Biomolecular polyelectrolyte complexes can be formed between oppositely charged intrinsically disordered regions (IDRs) of proteins or between IDRs and nucleic acids. Highly charged IDRs are abundant in the nucleus, yet few have been functionally characterized. Here, we show that a positively charged IDR within the human ATP-dependent DNA helicase Q4 (RECQ4) forms coacervates with G-quadruplexes (G4s). We describe a three-step model of charge-driven coacervation by integrating equilibrium and kinetic binding data in a global numerical model. The oppositely charged IDR and G4 molecules form a complex in the solution that follows a rapid nucleation-growth mechanism leading to a dynamic equilibrium between dilute and condensed phases. We also discover a physical interaction with Replication Protein A (RPA) and demonstrate that the IDR can switch between the two extremes of the structural continuum of complexes. The structural, kinetic, and thermodynamic profile of its interactions revealed a dynamic disordered complex with nucleic acids and a static ordered complex with RPA protein. The two mutually exclusive binding modes suggest a regulatory role for the IDR in RECQ4 function by enabling molecular handoffs. Our study extends the functional repertoire of IDRs and demonstrates a role of polyelectrolyte complexes involved in G4 binding.
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Affiliation(s)
- Anna C Papageorgiou
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Michaela Pospisilova
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jakub Cibulka
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Raghib Ashraf
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Pavel Kadeřávek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Volha Maroz
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Karel Kubicek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St Anne's University Hospital, Brno, Czech Republic
| | - Lumir Krejci
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.
- International Clinical Research Center, St Anne's University Hospital, Brno, Czech Republic.
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15
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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: 10] [Impact Index Per Article: 10.0] [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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16
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Dyson HJ, Wright PE. From Immunogenic Peptides to Intrinsically Disordered Proteins. Isr J Chem 2023; 63:e202300051. [PMID: 38454968 PMCID: PMC10919381 DOI: 10.1002/ijch.202300051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Indexed: 03/09/2024]
Abstract
It is hard to evaluate the role of individual mentors in the genesis of important ideas. In the case of our realization that proteins do not have to be stably folded to be functional, the influence of Richard Lerner and our collaborative work in the 1980s on the conformations of immunogenic peptides provided a base level of thinking about the nature of polypeptides in water solutions that led us to formulate and develop our ideas on the importance of intrinsic disorder in proteins. This review describes how the insights gained into the behavior of peptides led directly to the realization that proteins were not only capable of being functional while disordered, but also that disorder provided a distinct functional advantage in many important cellular processes.
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Affiliation(s)
- H Jane Dyson
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037
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17
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Vedel IM, Papagiannoula A, Naudi-Fabra S, Milles S. Nuclear magnetic resonance/single molecule fluorescence combinations to study dynamic protein systems. Curr Opin Struct Biol 2023; 82:102659. [PMID: 37499445 PMCID: PMC10565672 DOI: 10.1016/j.sbi.2023.102659] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/04/2023] [Accepted: 06/28/2023] [Indexed: 07/29/2023]
Abstract
Many proteins require different structural states or conformations for function, and intrinsically disordered proteins, i.e. proteins without stable three-dimensional structure, are certainly an extreme. Single molecule fluorescence and nuclear magnetic resonance (NMR) spectroscopy are both exceptionally well suited to decipher and describe these states and their interconversion. Different time scales, from picoseconds to several milliseconds, can be addressed by both techniques. The length scales probed and the sample requirements (e.g. concentration, molecular weight, sample complexity) are, however, vastly different, making NMR and single molecule fluorescence an excellent combination for integrated studies. Here, we review recently undertaken approaches for the combined use of NMR and single molecule fluorescence to study protein dynamics.
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Affiliation(s)
- Ida Marie Vedel
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Andromachi Papagiannoula
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Samuel Naudi-Fabra
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Sigrid Milles
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany.
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18
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Das SK, Kumar A, Hao F, Cutter DiPiazza AR, Fang H, Lee TH, Hayes JJ. Histone H3 Tail Modifications Alter Structure and Dynamics of the H1 C-Terminal Domain Within Nucleosomes. J Mol Biol 2023; 435:168242. [PMID: 37619707 PMCID: PMC10530611 DOI: 10.1016/j.jmb.2023.168242] [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: 06/27/2023] [Revised: 08/10/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023]
Abstract
The highly positively charged and intrinsically disordered H1 C-terminal domain (CTD) undergoes extensive condensation upon binding to nucleosomes, and stabilizes nucleosomes and higher-order chromatin structures but its interactions in chromatin are not well defined. Using single-molecule FRET we found that about half of the H1 CTDs in H1-nucleosome complexes exhibit well-defined FRET values indicative of distinct, static conformations, while the remainder of the population exhibits exchange between multiple defined FRET structures. Moreover, crosslinking studies indicate that the first 30 residues of the H1 CTD participate in relatively localized contacts with the first ∼25 bp of linker DNA, and that two separate regions in the CTD contribute to H1-dependent organization of linker DNA. Finally, we show that acetylation mimetics within the histone H3 tail markedly reduce the overall extent of H1 CTD condensation and significantly increase the fraction of H1 CTDs undergoing dynamic exchange between FRET states. Our results indicate the nucleosome-bound H1 CTD adopts loosely defined structures that exhibit significantly enhanced dynamics and decondensation upon epigenetic acetylation within the H3 tail.
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Affiliation(s)
- Subhra Kanti Das
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Ashok Kumar
- Department of Biochemistry and Biophysics, Rochester University Medical Center, Rochester, NY 14625, United States
| | - Fanfan Hao
- Department of Biochemistry and Biophysics, Rochester University Medical Center, Rochester, NY 14625, United States
| | - Amber R Cutter DiPiazza
- Department of Biochemistry and Biophysics, Rochester University Medical Center, Rochester, NY 14625, United States
| | - He Fang
- Department of Biochemistry and Biophysics, Rochester University Medical Center, Rochester, NY 14625, United States
| | - Tae-Hee Lee
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States.
| | - Jeffrey J Hayes
- Department of Biochemistry and Biophysics, Rochester University Medical Center, Rochester, NY 14625, United States.
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19
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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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20
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Camacho-Zarco AR, Yu L, Krischuns T, Dedeoglu S, Maurin D, Bouvignies G, Crépin T, Ruigrok RWH, Cusack S, Naffakh N, Blackledge M. Multivalent Dynamic Colocalization of Avian Influenza Polymerase and Nucleoprotein by Intrinsically Disordered ANP32A Reveals the Molecular Basis of Human Adaptation. J Am Chem Soc 2023; 145:20985-21001. [PMID: 37707433 PMCID: PMC10540212 DOI: 10.1021/jacs.3c06965] [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: 07/01/2023] [Indexed: 09/15/2023]
Abstract
Adaptation of avian influenza RNA polymerase (FluPol) to human cells requires mutations on the 627-NLS domains of the PB2 subunit. The E627K adaptive mutation compensates a 33-amino-acid deletion in the acidic intrinsically disordered domain of the host transcription regulator ANP32A, a deletion that restricts FluPol activity in mammalian cells. The function of ANP32A in the replication transcription complex and in particular its role in host restriction remains poorly understood. Here we characterize ternary complexes formed between ANP32A, FluPol, and the viral nucleoprotein, NP, supporting the putative role of ANP32A in shuttling NP to the replicase complex. We demonstrate that while FluPol and NP can simultaneously bind distinct linear motifs on avian ANP32A, the deletion in the shorter human ANP32A blocks this mode of colocalization. NMR reveals that NP and human-adapted FluPol, containing the E627 K mutation, simultaneously bind the identical extended linear motif on human ANP32A in an electrostatically driven, highly dynamic and multivalent ternary complex. This study reveals a probable molecular mechanism underlying host adaptation, whereby E627K, which enhances the basic surface of the 627 domain, is selected to confer the necessary multivalent properties to allow ANP32A to colocalize NP and FluPol in human cells.
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Affiliation(s)
- Aldo R. Camacho-Zarco
- Institut
de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS
UMR5075, 71 Avenue des
Martyrs, 38000 Grenoble, France
| | - Lefan Yu
- Institut
de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS
UMR5075, 71 Avenue des
Martyrs, 38000 Grenoble, France
| | - Tim Krischuns
- Institut
Pasteur, Université Paris Cité,
CNRS UMR3569, Unité Biologie des ARN et Virus Influenza, 75015 Paris, France
| | - Selin Dedeoglu
- Institut
de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS
UMR5075, 71 Avenue des
Martyrs, 38000 Grenoble, France
| | - Damien Maurin
- Institut
de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS
UMR5075, 71 Avenue des
Martyrs, 38000 Grenoble, France
| | - Guillaume Bouvignies
- Laboratoire
des Biomolécules, Département de Chimie, École
Normale Supérieur, UPMC Université Paris 06, CNRS, PSL Research University, 24 rue Lhomond, 75005 Paris, France
| | - Thibaut Crépin
- Institut
de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS
UMR5075, 71 Avenue des
Martyrs, 38000 Grenoble, France
| | - Rob W. H. Ruigrok
- Institut
de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS
UMR5075, 71 Avenue des
Martyrs, 38000 Grenoble, France
| | - Stephan Cusack
- European
Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Nadia Naffakh
- Institut
Pasteur, Université Paris Cité,
CNRS UMR3569, Unité Biologie des ARN et Virus Influenza, 75015 Paris, France
| | - Martin Blackledge
- Institut
de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS
UMR5075, 71 Avenue des
Martyrs, 38000 Grenoble, France
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21
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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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22
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Xu (徐伟青) LW, Jazani S, Kilic Z, Pressé S. Single-Molecule Reaction-Diffusion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.05.556378. [PMID: 37732202 PMCID: PMC10508780 DOI: 10.1101/2023.09.05.556378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
We propose to capture reaction-diffusion on a molecule-by-molecule basis from the fastest acquirable timescale, namely individual photon arrivals. We illustrate our method on intrinsically disordered human proteins, the linker histone H1.0 as well as its chaperone prothymosin α , as these diffuse through an illuminated confocal spot and interact forming larger ternary complexes on millisecond timescales. Most importantly, single-molecule reaction-diffusion, smRD, reveals single molecule properties without trapping or otherwise confining molecules to surfaces. We achieve smRD within a Bayesian paradigm and term our method Bayes-smRD. Bayes-smRD is further free of the average, bulk, results inherent to the analysis of long photon arrival traces by fluorescence correlation spectroscopy. In learning from thousands of photon arrivals continuous spatial positions and discrete conformational and photophysical state changes, Bayes-smRD estimates kinetic parameters on a molecule-by-molecule basis with two to three orders of magnitude less data than tools such as fluorescence correlation spectroscopy thereby also dramatically reducing sample photodamage.
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Affiliation(s)
- Lance W.Q. Xu (徐伟青)
- Center for Biological Physics, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Sina Jazani
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins Medicine, Baltimore, MD 21205, USA
| | - Zeliha Kilic
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Steve Pressé
- Center for Biological Physics, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- School of Molecular Science, Arizona State University, Tempe, AZ 85287, USA
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23
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Schiavina M, Konrat R, Ceccolini I, Mateos B, Konrat R, Felli IC, Pierattelli R. Studies of proline conformational dynamics in IDPs by 13C-detected cross-correlated NMR relaxation. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 354:107539. [PMID: 37632987 DOI: 10.1016/j.jmr.2023.107539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/28/2023]
Abstract
Intrinsically disordered proteins (IDPs) are significantly enriched in proline residues, which can populate specific local secondary structural elements called PPII helices, characterized by small packing densities. Proline is often thought to promote disorder, but it can participate in specific π·CH interactions with aromatic side chains resulting in reduced conformational flexibilities of the polypeptide. Differential local motional dynamics are relevant for the stabilization of preformed structural elements and can serve as nucleation sites for the establishment of long-range interactions. NMR experiments to probe the dynamics of proline ring systems would thus be highly desirable. Here we present a pulse scheme based on 13C detection to quantify dipole-dipole cross-correlated relaxation (CCR) rates at methylene CH2 groups in proline residues. Applying 13C-CON detection strategy provides exquisite spectral resolution allowing applications also to high molecular weight IDPs even in conditions approaching the physiological ones. The pulse scheme is illustrated with an application to the 220 amino acids long protein Osteopontin, an extracellular cytokine involved in inflammation and cancer progression, and a construct in which three proline-aromatic sequence patches have been mutated.
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Affiliation(s)
- Marco Schiavina
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Ruth Konrat
- Department of Structural and Computational Biology, University of Vienna, Max F. Perutz Laboratories Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Irene Ceccolini
- Department of Structural and Computational Biology, University of Vienna, Max F. Perutz Laboratories Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Borja Mateos
- Department of Structural and Computational Biology, University of Vienna, Max F. Perutz Laboratories Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, University of Vienna, Max F. Perutz Laboratories Vienna Biocenter Campus 5, 1030 Vienna, Austria.
| | - Isabella C Felli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.
| | - Roberta Pierattelli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.
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24
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Meng F, Kim JY, Gopich IV, Chung HS. Single-molecule FRET and molecular diffusion analysis characterize stable oligomers of amyloid-β 42 of extremely low population. PNAS NEXUS 2023; 2:pgad253. [PMID: 37564361 PMCID: PMC10411938 DOI: 10.1093/pnasnexus/pgad253] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/12/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
Soluble oligomers produced during protein aggregation have been thought to be toxic species causing various diseases. Characterization of these oligomers is difficult because oligomers are a heterogeneous mixture, which is not readily separable, and may appear transiently during aggregation. Single-molecule spectroscopy can provide valuable information by detecting individual oligomers, but there have been various problems in determining the size and concentration of oligomers. In this work, we develop and use a method that analyzes single-molecule fluorescence burst data of freely diffusing molecules in solution based on molecular diffusion theory and maximum likelihood method. We demonstrate that the photon count rate, diffusion time, population, and Förster resonance energy transfer (FRET) efficiency can be accurately determined from simulated data and the experimental data of a known oligomerization system, the tetramerization domain of p53. We used this method to characterize the oligomers of the 42-residue amyloid-β (Aβ42) peptide. Combining peptide incubation in a plate reader and single-molecule free-diffusion experiments allows for the detection of stable oligomers appearing at various stages of aggregation. We find that the average size of these oligomers is 70-mer and their overall population is very low, less than 1 nM, in the early and middle stages of aggregation of 1 µM Aβ42 peptide. Based on their average size and long diffusion time, we predict the oligomers have a highly elongated rod-like shape.
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Affiliation(s)
- Fanjie Meng
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Jae-Yeol Kim
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
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25
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Galvanetto N, Ivanović MT, Chowdhury A, Sottini A, Nüesch MF, Nettels D, Best RB, Schuler B. Extreme dynamics in a biomolecular condensate. Nature 2023:10.1038/s41586-023-06329-5. [PMID: 37468629 DOI: 10.1038/s41586-023-06329-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/14/2023] [Indexed: 07/21/2023]
Abstract
Proteins and nucleic acids can phase-separate in the cell to form concentrated biomolecular condensates1-4. The functions of condensates span many length scales: they modulate interactions and chemical reactions at the molecular scale5, organize biochemical processes at the mesoscale6 and compartmentalize cells4. Understanding the underlying mechanisms of these processes will require detailed knowledge of the rich dynamics across these scales7. The mesoscopic dynamics of biomolecular condensates have been extensively characterized8, but their behaviour at the molecular scale has remained more elusive. Here, as an example of biomolecular phase separation, we study complex coacervates of two highly and oppositely charged disordered human proteins9. Their dense phase is 1,000 times more concentrated than the dilute phase, and the resulting percolated interaction network10 leads to a bulk viscosity 300 times greater than that of water. However, single-molecule spectroscopy optimized for measurements within individual droplets reveals that at the molecular scale, the disordered proteins remain exceedingly dynamic, with their chain configurations interconverting on submicrosecond timescales. Massive all-atom molecular dynamics simulations reproduce the experimental observations and explain this apparent discrepancy: the underlying interactions between individual charged side chains are short-lived and exchange on a pico- to nanosecond timescale. Our results indicate that, despite the high macroscopic viscosity of phase-separated systems, local biomolecular rearrangements required for efficient reactions at the molecular scale can remain rapid.
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Affiliation(s)
- Nicola Galvanetto
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
- Department of Physics, University of Zurich, Zurich, Switzerland.
| | - Miloš T Ivanović
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
| | - Aritra Chowdhury
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Andrea Sottini
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Mark F Nüesch
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
- Department of Physics, University of Zurich, Zurich, Switzerland.
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26
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Gopich IV, Kim JY, Chung HS. Analysis of photon trajectories from diffusing single molecules. J Chem Phys 2023; 159:024119. [PMID: 37431909 PMCID: PMC10474944 DOI: 10.1063/5.0153114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/19/2023] [Indexed: 07/12/2023] Open
Abstract
In single-molecule free diffusion experiments, molecules spend most of the time outside a laser spot and generate bursts of photons when they diffuse through the focal spot. Only these bursts contain meaningful information and, therefore, are selected using physically reasonable criteria. The analysis of the bursts must take into account the precise way they were chosen. We present new methods that allow one to accurately determine the brightness and diffusivity of individual molecule species from the photon arrival times of selected bursts. We derive analytical expressions for the distribution of inter-photon times (with and without burst selection), the distribution of the number of photons in a burst, and the distribution of photons in a burst with recorded arrival times. The theory accurately treats the bias introduced due to the burst selection criteria. We use a Maximum Likelihood (ML) method to find the molecule's photon count rate and diffusion coefficient from three kinds of data, i.e., the bursts of photons with recorded arrival times (burstML), inter-photon times in bursts (iptML), and the numbers of photon counts in a burst (pcML). The performance of these new methods is tested on simulated photon trajectories and on an experimental system, the fluorophore Atto 488.
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Affiliation(s)
- Irina V. Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jae-Yeol Kim
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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27
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Vendruscolo M. Thermodynamic and kinetic approaches for drug discovery to target protein misfolding and aggregation. Expert Opin Drug Discov 2023:1-11. [PMID: 37276120 DOI: 10.1080/17460441.2023.2221024] [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] [Received: 01/23/2023] [Accepted: 05/30/2023] [Indexed: 06/07/2023]
Abstract
INTRODUCTION Protein misfolding diseases, including Alzheimer's and Parkinson's diseases, are characterized by the aberrant aggregation of proteins. These conditions are still largely untreatable, despite having a major impact on our healthcare systems and societies. AREAS COVERED We describe drug discovery strategies to target protein misfolding and aggregation. We compare thermodynamic approaches, which are based on the stabilization of the native states of proteins, with kinetic approaches, which are based on the slowing down of the aggregation process. This comparison is carried out in terms of the current knowledge of the process of protein misfolding and aggregation, the mechanisms of disease and the therapeutic targets. EXPERT OPINION There is an unmet need for disease-modifying treatments that target protein misfolding and aggregation for the over 50 human disorders known to be associated with this phenomenon. With the approval of the first drugs that can prevent misfolding or inhibit aggregation, future efforts will be focused on the discovery of effective compounds with these mechanisms of action for a wide range of conditions.
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Affiliation(s)
- Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
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28
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Yu F, Sukenik S. Structural Preferences Shape the Entropic Force of Disordered Protein Ensembles. J Phys Chem B 2023; 127:4235-4244. [PMID: 37155239 PMCID: PMC10201532 DOI: 10.1021/acs.jpcb.3c00698] [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: 01/31/2023] [Revised: 04/24/2023] [Indexed: 05/10/2023]
Abstract
Intrinsically disordered protein regions (IDRs) make up over 30% of the human proteome and exist in a dynamic conformational ensemble instead of a native, well-folded structure. Tethering IDRs to a surface (for example, the surface of a well-folded region of the same protein) can reduce the number of accessible conformations in these ensembles. This reduces the ensemble's conformational entropy, generating an effective entropic force that pulls away from the point of tethering. Recent experimental work has shown that this entropic force causes measurable, physiologically relevant changes to protein function. But how the magnitude of this force depends on IDR sequence remains unexplored. Here, we use all-atom simulations to analyze how structural preferences in IDR ensembles contribute to the entropic force they exert upon tethering. We show that sequence-encoded structural preferences play an important role in determining the magnitude of this force: compact, spherical ensembles generate an entropic force that can be several times higher than more extended ensembles. We further show that changes in the surrounding solution's chemistry can modulate the IDR entropic force strength. We propose that the entropic force is a sequence-dependent, environmentally tunable property of terminal IDR sequences.
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Affiliation(s)
- Feng Yu
- Quantitative
Systems Biology Program, University of California, Merced, California 95343, United States
| | - Shahar Sukenik
- Quantitative
Systems Biology Program, University of California, Merced, California 95343, United States
- Department
of Chemistry and Biochemistry, University
of California, Merced, California 95343, United States
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29
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Das SK, Kumar A, Hao F, DiPiazza ARC, Lee TH, Hayes JJ. Histone H3 tail modifications regulate structure and dynamics of the H1 C-terminal domain within nucleosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540398. [PMID: 37214834 PMCID: PMC10197648 DOI: 10.1101/2023.05.11.540398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Despite their importance, how linker histone H1s interact in chromatin and especially how the highly positively charged and intrinsically disordered H1 C-terminal domain (CTD) binds and stabilizes nucleosomes and higher-order chromatin structures remains unclear. Using single-molecule FRET we found that about half of the H1 CTDs in H1-nucleosome complexes exhibit well-defined FRET values indicative of distinct, static conformations, while the remainder of the population exhibits dynamically changing values, similar to that observed for H1 in the absence of nucleosomes. We also find that the first 30 residues of the CTD participate in relatively localized interactions with the first ∼20 bp of linker DNA, and that two separate regions in the CTD contribute to H1-dependent organization of linker DNA, consistent with some non-random CTD-linker DNA interactions. Finally, our data show that acetylation mimetics within the histone H3 tail induce decondensation and enhanced dynamics of the nucleosome-bound H1 CTD. (148 words).
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30
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Chhabra Y, Seiffert P, Gormal RS, Vullings M, Lee CMM, Wallis TP, Dehkhoda F, Indrakumar S, Jacobsen NL, Lindorff-Larsen K, Durisic N, Waters MJ, Meunier FA, Kragelund BB, Brooks AJ. Tyrosine kinases compete for growth hormone receptor binding and regulate receptor mobility and degradation. Cell Rep 2023; 42:112490. [PMID: 37163374 DOI: 10.1016/j.celrep.2023.112490] [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] [Received: 10/17/2022] [Revised: 03/07/2023] [Accepted: 04/24/2023] [Indexed: 05/12/2023] Open
Abstract
Growth hormone (GH) acts via JAK2 and LYN to regulate growth, metabolism, and neural function. However, the relationship between these tyrosine kinases remains enigmatic. Through an interdisciplinary approach combining cell biology, structural biology, computation, and single-particle tracking on live cells, we find overlapping LYN and JAK2 Box1-Box2-binding regions in GH receptor (GHR). Our data implicate direct competition between JAK2 and LYN for GHR binding and imply divergent signaling profiles. We show that GHR exhibits distinct mobility states within the cell membrane and that activation of LYN by GH mediates GHR immobilization, thereby initiating its nanoclustering in the membrane. Importantly, we observe that LYN mediates cytokine receptor degradation, thereby controlling receptor turnover and activity, and this applies to related cytokine receptors. Our study offers insight into the molecular interactions of LYN with GHR and highlights important functions for LYN in regulating GHR nanoclustering, signaling, and degradation, traits broadly relevant to many cytokine receptors.
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Affiliation(s)
- Yash Chhabra
- Frazer Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia; The University of Queensland, Institute for Molecular Bioscience, St. Lucia, QLD 4072, Australia; Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21204, USA.
| | - Pernille Seiffert
- Structural Biology and NMR Laboratory (SBiNLab) and REPIN, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Rachel S Gormal
- The Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Manon Vullings
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, QLD 4072, Australia
| | | | - Tristan P Wallis
- The Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Farhad Dehkhoda
- Frazer Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Sowmya Indrakumar
- Structural Biology and NMR Laboratory (SBiNLab) and REPIN, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark; Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Nina L Jacobsen
- Structural Biology and NMR Laboratory (SBiNLab) and REPIN, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Nela Durisic
- The Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Michael J Waters
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, QLD 4072, Australia
| | - Frédéric A Meunier
- The Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory (SBiNLab) and REPIN, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Andrew J Brooks
- Frazer Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia; The University of Queensland, Institute for Molecular Bioscience, St. Lucia, QLD 4072, Australia.
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31
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Tan C, Niitsu A, Sugita Y. Highly Charged Proteins and Their Repulsive Interactions Antagonize Biomolecular Condensation. JACS AU 2023; 3:834-848. [PMID: 37006777 PMCID: PMC10052238 DOI: 10.1021/jacsau.2c00646] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 06/19/2023]
Abstract
Biomolecular condensation is involved in various cellular processes; therefore, regulation of condensation is crucial to prevent deleterious protein aggregation and maintain a stable cellular environment. Recently, a class of highly charged proteins, known as heat-resistant obscure (Hero) proteins, was shown to protect other client proteins from pathological aggregation. However, the molecular mechanisms by which Hero proteins protect other proteins from aggregation remain unknown. In this study, we performed multiscale molecular dynamics (MD) simulations of Hero11, a Hero protein, and the C-terminal low-complexity domain (LCD) of the transactive response DNA-binding protein 43 (TDP-43), a client protein of Hero11, under various conditions to examine their interactions with each other. We found that Hero11 permeates into the condensate formed by the LCD of TDP-43 (TDP-43-LCD) and induces changes in conformation, intermolecular interactions, and dynamics of TDP-43-LCD. We also examined possible Hero11 structures in atomistic and coarse-grained MD simulations and found that Hero11 with a higher fraction of disordered region tends to assemble on the surface of the condensates. Based on the simulation results, we have proposed three possible mechanisms for Hero11's regulatory function: (i) In the dense phase, TDP-43-LCD reduces contact with each other and shows faster diffusion and decondensation due to the repulsive Hero11-Hero11 interactions. (ii) In the dilute phase, the saturation concentration of TDP-43-LCD is increased, and its conformation is relatively more extended and variant, induced by the attractive Hero11-TDP-43-LCD interactions. (iii) Hero11 on the surface of small TDP-43-LCD condensates can contribute to avoiding their fusion due to repulsive interactions. The proposed mechanisms provide new insights into the regulation of biomolecular condensation in cells under various conditions.
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Affiliation(s)
- Cheng Tan
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Ai Niitsu
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Yuji Sugita
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
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32
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Williamson MP. Protein Binding: A Fuzzy Concept. Life (Basel) 2023; 13:life13040855. [PMID: 37109384 PMCID: PMC10145316 DOI: 10.3390/life13040855] [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: 02/28/2023] [Revised: 03/16/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Our understanding of protein binding interactions has matured significantly over the last few years, largely as a result of trying to make sense of the binding interactions of intrinsically disordered proteins. Here, we bring together some disparate ideas that have largely developed independently, and show that they can be linked into a coherent picture that provides insight into quantitative aspects of protein interactions, in particular that transient protein interactions are often optimised for speed, rather than tight binding.
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Affiliation(s)
- Mike P Williamson
- School of Biosciences, University of Sheffield, Firth Court, Sheffield S10 2TN, UK
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33
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Madsen M, Prestel A, Madland E, Westh P, Tøndervik A, Sletta H, Peters GHJ, Aachmann FL, Kragelund BB, Svensson B. Molecular insights into alginate β-lactoglobulin A multivalencies-The foundation for their amorphous aggregates and coacervation. Protein Sci 2023; 32:e4556. [PMID: 36571497 PMCID: PMC9847093 DOI: 10.1002/pro.4556] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/06/2022] [Accepted: 12/22/2022] [Indexed: 12/27/2022]
Abstract
For improved control of biomaterial property design, a better understanding of complex coacervation involving anionic polysaccharides and proteins is needed. Here, we address the initial steps in condensate formation of β-lactoglobulin A (β-LgA) with nine defined alginate oligosaccharides (AOSs) and describe their multivalent interactions in structural detail. Binding of AOSs containing four, five, or six uronic acid residues (UARs), either all mannuronate (M), all guluronate (G), or alternating M and G embodying the block structural components of alginates, was characterized by isothermal titration calorimetry, nuclear magnetic resonance spectroscopy (NMR), and molecular docking. β-LgA was highly multivalent exhibiting binding stoichiometries decreasing from five to two AOSs with increasing degree of polymerization (DP) and similar affinities in the mid micromolar range. The different AOS binding sites on β-LgA were identified by NMR chemical shift perturbation analyses and showed diverse compositions of charged, polar and hydrophobic residues. Distinct sites for the shorter AOSs merged to accommodate longer AOSs. The AOSs bound dynamically to β-LgA, as concluded from saturation transfer difference and 1 H-ligand-targeted NMR analyses. Molecular docking using Glide within the Schrödinger suite 2016-1 revealed the orientation of AOSs to only vary slightly at the preferred β-LgA binding site resulting in similar XP glide scores. The multivalency coupled with highly dynamic AOS binding with lack of confined conformations in the β-LgA complexes may help explain the first steps toward disordered β-LgA alginate coacervate structures.
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Affiliation(s)
- Mikkel Madsen
- Enzyme and Protein Chemistry, Department of Biotechnology and BiomedicineTechnical University of DenmarkKgs. LyngbyDenmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| | - Eva Madland
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food ScienceNTNU Norwegian University of Science and TechnologyTrondheimNorway
| | - Peter Westh
- Interfacial Enzymology, Department of Biotechnology and BiomedicineTechnical University of DenmarkKgs. LyngbyDenmark
| | - Anne Tøndervik
- Department of Biotechnology and Nanomedicine, SINTEF IndustryTrondheimNorway
| | - Håvard Sletta
- Department of Biotechnology and Nanomedicine, SINTEF IndustryTrondheimNorway
| | - Günther H. J. Peters
- Biophysical and Biomedicinal Chemistry, Department of ChemistryTechnical University of DenmarkKgs. LyngbyDenmark
| | - Finn L. Aachmann
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food ScienceNTNU Norwegian University of Science and TechnologyTrondheimNorway
| | - Birthe B. Kragelund
- Structural Biology and NMR Laboratory, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and BiomedicineTechnical University of DenmarkKgs. LyngbyDenmark
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34
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Yu F, Sukenik S. Structural preferences shape the entropic force of disordered protein ensembles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.20.524980. [PMID: 36711874 PMCID: PMC9882287 DOI: 10.1101/2023.01.20.524980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Intrinsically disordered protein regions (IDRs) make up over 30% of the human proteome and instead of a native, well-folded structure exist in a dynamic conformational ensemble. Tethering IDRs to a surface (for example, the surface of a well-folded region of the same protein) can reduce the number of accessible conformations in IDR ensembles. This reduces the ensemble's conformational entropy, generating an effective entropic force that pulls away from the point of tethering. Recent experimental work has shown that this entropic force causes measurable, physiologically relevant changes to protein function, but how the magnitude of this force depends on the IDR sequence remains unexplored. Here we use all-atom simulations to analyze how structural preferences encoded in dozens of IDR ensembles contribute to the entropic force they exert upon tethering. We show that sequence-encoded structural preferences play an important role in determining the magnitude of this force and that compact, spherical ensembles generate an entropic force that can be several times higher than more extended ensembles. We further show that changes in the surrounding solution's chemistry can modulate IDR entropic force strength. We propose that the entropic force is a sequence-dependent, environmentally tunable property of terminal IDR sequences.
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Affiliation(s)
- Feng Yu
- Quantitative Systems Biology Program, University of California, Merced, California, United States
| | - Shahar Sukenik
- Quantitative Systems Biology Program, University of California, Merced, California, United States
- Department of Chemistry and Biochemistry, University of California, Merced, California, United States
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35
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Moses K, Van Tassel PR. Polyelectrolyte Influence on Beta-Hairpin Peptide Stability: A Simulation Study. J Phys Chem B 2023; 127:359-370. [PMID: 36574611 DOI: 10.1021/acs.jpcb.2c06641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Assemblies of proteins and charged macromolecules (polyelectrolytes) find important applications as pharmaceutical formulations, biocatalysts, and cell-contacting substrates. A key question is how the polymer component influences the structure and function of the protein. The present paper addresses the influence of charged polymers on the thermal stability of two model beta-hairpin-forming peptides through an all-atom, replica exchange molecular dynamics simulation. The (negatively charged) peptides consist of the terminal 16 amino acids of the B1 domain of Protein G (GB1) and a variant with three of the GB1 residues substituted with tryptophan (Tryptophan Zipper 4, or TZ4). A (cationic) lysine polymer is seen to thermally stabilize TZ4 and destabilize GB1, while a (also cationic) chitosan polymer slightly stabilizes GB1 but has essentially no effect on TZ4. Free energy profiles reveal folded and unfolded conformations to be separated by kinetic barriers generally acting in the direction of the thermodynamically favored state. Through application of an Ising-like statistical mechanical model, a mechanism is proposed based on competition between (indirect) entropic stabilization of folded versus unfolded states and (direct) competition for hydrogen-bonding and hydrophobic interactions. These findings have important implications to the design of polyelectrolyte-based materials for biomedical and biotechnological applications.
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Affiliation(s)
- Kevin Moses
- Dept. of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520-8286, United States
| | - Paul R Van Tassel
- Dept. of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520-8286, United States
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36
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Alemasova EE, Lavrik OI. Poly(ADP-ribose) in Condensates: The PARtnership of Phase Separation and Site-Specific Interactions. Int J Mol Sci 2022; 23:14075. [PMID: 36430551 PMCID: PMC9694962 DOI: 10.3390/ijms232214075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022] Open
Abstract
Biomolecular condensates are nonmembrane cellular compartments whose formation in many cases involves phase separation (PS). Despite much research interest in this mechanism of macromolecular self-organization, the concept of PS as applied to a live cell faces certain challenges. In this review, we discuss a basic model of PS and the role of site-specific interactions and percolation in cellular PS-related events. Using a multivalent poly(ADP-ribose) molecule as an example, which has high PS-driving potential due to its structural features, we consider how site-specific interactions and network formation are involved in the formation of phase-separated cellular condensates.
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Affiliation(s)
- Elizaveta E. Alemasova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia
| | - Olga I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
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37
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Richter WF, Nayak S, Iwasa J, Taatjes DJ. The Mediator complex as a master regulator of transcription by RNA polymerase II. Nat Rev Mol Cell Biol 2022; 23:732-749. [PMID: 35725906 PMCID: PMC9207880 DOI: 10.1038/s41580-022-00498-3] [Citation(s) in RCA: 95] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2022] [Indexed: 02/08/2023]
Abstract
The Mediator complex, which in humans is 1.4 MDa in size and includes 26 subunits, controls many aspects of RNA polymerase II (Pol II) function. Apart from its size, a defining feature of Mediator is its intrinsic disorder and conformational flexibility, which contributes to its ability to undergo phase separation and to interact with a myriad of regulatory factors. In this Review, we discuss Mediator structure and function, with emphasis on recent cryogenic electron microscopy data of the 4.0-MDa transcription preinitiation complex. We further discuss how Mediator and sequence-specific DNA-binding transcription factors enable enhancer-dependent regulation of Pol II function at distal gene promoters, through the formation of molecular condensates (or transcription hubs) and chromatin loops. Mediator regulation of Pol II reinitiation is also discussed, in the context of transcription bursting. We propose a working model for Mediator function that combines experimental results and theoretical considerations related to enhancer-promoter interactions, which reconciles contradictory data regarding whether enhancer-promoter communication is direct or indirect. We conclude with a discussion of Mediator's potential as a therapeutic target and of future research directions.
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Affiliation(s)
- William F Richter
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Shraddha Nayak
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Janet Iwasa
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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38
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Alemasova EE, Lavrik OI. A sePARate phase? Poly(ADP-ribose) versus RNA in the organization of biomolecular condensates. Nucleic Acids Res 2022; 50:10817-10838. [PMID: 36243979 PMCID: PMC9638928 DOI: 10.1093/nar/gkac866] [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: 03/24/2022] [Revised: 09/14/2022] [Accepted: 10/09/2022] [Indexed: 11/13/2022] Open
Abstract
Condensates are biomolecular assemblies that concentrate biomolecules without the help of membranes. They are morphologically highly versatile and may emerge via distinct mechanisms. Nucleic acids-DNA, RNA and poly(ADP-ribose) (PAR) play special roles in the process of condensate organization. These polymeric scaffolds provide multiple specific and nonspecific interactions during nucleation and 'development' of macromolecular assemblages. In this review, we focus on condensates formed with PAR. We discuss to what extent the literature supports the phase separation origin of these structures. Special attention is paid to similarities and differences between PAR and RNA in the process of dynamic restructuring of condensates during their functioning.
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Affiliation(s)
- Elizaveta E Alemasova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
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39
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Feng H, Zhou BR, Schwieters CD, Bai Y. Structural Mechanism of TAF-Iβ Chaperone Function on Linker Histone H1.10. J Mol Biol 2022; 434:167755. [PMID: 35870650 PMCID: PMC9489631 DOI: 10.1016/j.jmb.2022.167755] [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: 05/10/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 11/21/2022]
Abstract
Linker histone H1, facilitated by its chaperones, plays an essential role in regulating gene expression by maintaining chromatin's higher-order structure and epigenetic state. However, we know little about the structural mechanism of how the chaperones recognize linker histones and conduct their function. Here, we used biophysical and biochemical methods to investigate the recognition of human linker histone isoform H1.10 by the TAF-Iβ chaperone. Both H1.10 and TAF-Iβ proteins consist of folded cores and disordered tails. We found that H1.10 formed a complex with TAF-Iβ in a 2:2 stoichiometry. Using distance restraints obtained from methyl-TROSY NMR and spin labels, we built a structural model for the core region of the complex. In the model, the TAF-Iβ core interacts with the globular domain of H1.10 mainly through electrostatic interactions. We confirmed the interactions by measuring the effects of mutations on the binding affinity. A comparison of our structural model with the chromatosome structure shows that TAF-Iβ blocks the DNA binding sites of H1.10. Our study provides insights into the structural mechanism whereby TAF-Iβ functions as a chaperone by preventing H1.10 from interacting with DNA directly.
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Affiliation(s)
- Haniqao Feng
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Charles D Schwieters
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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40
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Schiavina M, Pontoriero L, Tagliaferro G, Pierattelli R, Felli IC. The Role of Disordered Regions in Orchestrating the Properties of Multidomain Proteins: The SARS-CoV-2 Nucleocapsid Protein and Its Interaction with Enoxaparin. Biomolecules 2022; 12:1302. [PMID: 36139141 PMCID: PMC9496478 DOI: 10.3390/biom12091302] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/09/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022] Open
Abstract
Novel and efficient strategies need to be developed to interfere with the SARS-CoV-2 virus. One of the most promising pharmaceutical targets is the nucleocapsid protein (N), responsible for genomic RNA packaging. N is composed of two folded domains and three intrinsically disordered regions (IDRs). The globular RNA binding domain (NTD) and the tethered IDRs are rich in positively charged residues. The study of the interaction of N with polyanions can thus help to elucidate one of the key driving forces responsible for its function, i.e., electrostatics. Heparin, one of the most negatively charged natural polyanions, has been used to contrast serious cases of COVID-19 infection, and we decided to study its interaction with N at the molecular level. We focused on the NTR construct, which comprises the NTD and two flanking IDRs, and on the NTD construct in isolation. We characterized this interaction using different nuclear magnetic resonance approaches and isothermal titration calorimetry. With these tools, we were able to identify an extended surface of NTD involved in the interaction. Moreover, we assessed the importance of the IDRs in increasing the affinity for heparin, highlighting how different tracts of these flexible regions modulate the interaction.
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Affiliation(s)
| | | | | | - Roberta Pierattelli
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Isabella C. Felli
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
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41
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Liu W, Jiang J, Lin Y, You Q, Wang L. Insight into Thermodynamic and Kinetic Profiles in Small-Molecule Optimization. J Med Chem 2022; 65:10809-10847. [PMID: 35969687 DOI: 10.1021/acs.jmedchem.2c00682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-activity relationships (SARs) and structure-property relationships (SPRs) have been considered the most important factors during the drug optimization process. For medicinal chemists, improvements in the potencies and druglike properties of small molecules are regarded as their major goals. Among them, the binding affinity and selectivity of small molecules on their targets are the most important indicators. In recent years, there has been growing interest in using thermodynamic and kinetic profiles to analyze ligand-receptor interactions, which could provide not only binding affinities but also detailed binding parameters for small-molecule optimization. In this perspective, we are trying to provide an insight into thermodynamic and kinetic profiles in small-molecule optimization. Through a highlight of strategies on the small-molecule optimization with specific cases, we aim to put forward the importance of structure-thermodynamic relationships (STRs) and structure-kinetic relationships (SKRs), which could provide more guidance to find safe and effective small-molecule drugs.
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jingsheng Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yating Lin
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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42
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Pontoriero L, Schiavina M, Korn SM, Schlundt A, Pierattelli R, Felli IC. NMR Reveals Specific Tracts within the Intrinsically Disordered Regions of the SARS-CoV-2 Nucleocapsid Protein Involved in RNA Encountering. Biomolecules 2022; 12:biom12070929. [PMID: 35883485 PMCID: PMC9312987 DOI: 10.3390/biom12070929] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 12/23/2022] Open
Abstract
The SARS-CoV-2 nucleocapsid (N) protein is crucial for the highly organized packaging and transcription of the genomic RNA. Studying atomic details of the role of its intrinsically disordered regions (IDRs) in RNA recognition is challenging due to the absence of structure and to the repetitive nature of their primary sequence. IDRs are known to act in concert with the folded domains of N and here we use NMR spectroscopy to identify the priming events of N interacting with a regulatory SARS-CoV-2 RNA element. 13C-detected NMR experiments, acquired simultaneously to 1H detected ones, provide information on the two IDRs flanking the N-terminal RNA binding domain (NTD) within the N-terminal region of the protein (NTR, 1–248). We identify specific tracts of the IDRs that most rapidly sense and engage with RNA, and thus provide an atom-resolved picture of the interplay between the folded and disordered regions of N during RNA interaction.
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Affiliation(s)
- Letizia Pontoriero
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Via L. Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; (L.P.); (M.S.)
| | - Marco Schiavina
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Via L. Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; (L.P.); (M.S.)
| | - Sophie M. Korn
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Molecular Biosciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany;
| | - Andreas Schlundt
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Molecular Biosciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany;
- Correspondence: (A.S.); (R.P.); (I.C.F.)
| | - Roberta Pierattelli
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Via L. Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; (L.P.); (M.S.)
- Correspondence: (A.S.); (R.P.); (I.C.F.)
| | - Isabella C. Felli
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Via L. Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; (L.P.); (M.S.)
- Correspondence: (A.S.); (R.P.); (I.C.F.)
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43
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Affinity of disordered protein complexes is modulated by entropy-energy reinforcement. Proc Natl Acad Sci U S A 2022; 119:e2120456119. [PMID: 35727975 PMCID: PMC9245678 DOI: 10.1073/pnas.2120456119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Intrinsically disordered proteins (IDPs), which are very common and essential to many biological activities, sometimes function via interaction with another IDP and form a fuzzy complex, which can be highly stable. It is unclear what the biophysical forces are that govern their thermodynamics and specificity, which are essential for de novo fuzzy complex design. Here, we explored the fuzzy complex formed between ProTα and H1, which are oppositely charged IDPs, by swapping the charges between them, generating variants that have either greater polyampholytic or polyelectrolytic nature as well as different charge patterns. Charge swapping and shuffling dramatically change the affinity of the fuzzy complex, which is contributed to by both enthalpy and entropy, where the latter is dominated by counterion release. The association between two intrinsically disordered proteins (IDPs) may produce a fuzzy complex characterized by a high binding affinity, similar to that found in the ultrastable complexes formed between two well-structured proteins. Here, using coarse-grained simulations, we quantified the biophysical forces driving the formation of such fuzzy complexes. We found that the high-affinity complex formed between the highly and oppositely charged H1 and ProTα proteins is sensitive to electrostatic interactions. We investigated 52 variants of the complex by swapping charges between the two oppositely charged proteins to produce sequences whose negatively or positively charged residue content was more homogeneous or heterogenous (i.e., polyelectrolytic or polyampholytic, having higher or lower absolute net charges, respectively) than the wild type. We also changed the distributions of oppositely charged residues within each participating sequence to produce variants in which the charges were segregated or well mixed. Both types of changes significantly affect binding affinity in fuzzy complexes, which is governed by both enthalpy and entropy. The formation of H1–ProTa is supported by an increase in configurational entropy and by entropy due to counterion release. The latter can be twice as large as the former, illustrating the dominance of counterion entropy in modulating the binding thermodynamics. Complexes formed between proteins with greater absolute net charges are more stable, both enthalpically and entropically, indicating that enthalpy and entropy have a mutually reinforcing effect. The sensitivity of the thermodynamics of the complex to net charge and the charge pattern within each of the binding constituents may provide a means to achieve binding specificity between IDPs.
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44
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Tang S, Gong J, Shi Y, Wen S, Zhao Q. Spontaneous water-on-water spreading of polyelectrolyte membranes inspired by skin formation. Nat Commun 2022; 13:3227. [PMID: 35680913 PMCID: PMC9184545 DOI: 10.1038/s41467-022-30973-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 05/26/2022] [Indexed: 11/17/2022] Open
Abstract
Stable interfaces between immiscible solvents are crucial for chemical synthesis and assembly, but interfaces between miscible solvents have been less explored. Here the authors report the spontaneous water-on-water spreading and self-assembly of polyelectrolyte membranes. An aqueous mixture solution containing poly(ethyleneimine) and poly(sodium 4-styrenesulfonate) spreads efficiently on acidic water, leading to the formation of hierarchically porous membranes. The reduced surface tension of the polyelectrolyte mixture solution drives the surface spreading, while the interfacial polyelectrolytes complexation triggered by the low pH of water mitigates water-in-water mixing. The synergy of surface tension and pH-dependent complexation represents a generic mechanism governing interfaces between miscible solvents for materials engineering, without the need for surfactants or sophisticated equipment. As a proof-of-concept, porous polyelectrolyte hybrid membranes are prepared by surface spreading, exhibiting exceptional solar thermal evaporation performance (2.8 kg/m2h) under 1-sun irradiation.
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Affiliation(s)
- Sihan Tang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage (Ministry of Education), School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- State Key Laboratory of Materials Processing and Die & Mould Technology, Huazhong University of Science and Technology, Luoyu Road No. 1037, 430074, Wuhan, China
| | - Jiang Gong
- Key Laboratory of Material Chemistry for Energy Conversion and Storage (Ministry of Education), School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Yunsong Shi
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Shifeng Wen
- State Key Laboratory of Materials Processing and Die & Mould Technology, Huazhong University of Science and Technology, Luoyu Road No. 1037, 430074, Wuhan, China
| | - Qiang Zhao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage (Ministry of Education), School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China.
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45
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Zeng X, Ruff KM, Pappu RV. Competing interactions give rise to two-state behavior and switch-like transitions in charge-rich intrinsically disordered proteins. Proc Natl Acad Sci U S A 2022; 119:e2200559119. [PMID: 35512095 PMCID: PMC9171777 DOI: 10.1073/pnas.2200559119] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/12/2022] [Indexed: 11/18/2022] Open
Abstract
The most commonly occurring intrinsically disordered proteins (IDPs) are polyampholytes, which are defined by the duality of low net charge per residue and high fractions of charged residues. Recent experiments have uncovered nuances regarding sequence–ensemble relationships of model polyampholytic IDPs. These include differences in conformational preferences for sequences with lysine vs. arginine and the suggestion that well-mixed sequences form a range of conformations, including globules, conformations with ensemble averages that are reminiscent of ideal chains, or self-avoiding walks. Here, we explain these observations by analyzing results from atomistic simulations. We find that polyampholytic IDPs generally sample two distinct stable states, namely, globules and self-avoiding walks. Globules are favored by electrostatic attractions between oppositely charged residues, whereas self-avoiding walks are favored by favorable free energies of hydration of charged residues. We find sequence-specific temperatures of bistability at which globules and self-avoiding walks can coexist. At these temperatures, ensemble averages over coexisting states give rise to statistics that resemble ideal chains without there being an actual counterbalancing of intrachain and chain-solvent interactions. At equivalent temperatures, arginine-rich sequences tilt the preference toward globular conformations whereas lysine-rich sequences tilt the preference toward self-avoiding walks. We also identify differences between aspartate- and glutamate-containing sequences, whereby the shorter aspartate side chain engenders preferences for metastable, necklace-like conformations. Finally, although segregation of oppositely charged residues within the linear sequence maintains the overall two-state behavior, compact states are highly favored by such systems.
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Affiliation(s)
- Xiangze Zeng
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130
- Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130
| | - Kiersten M. Ruff
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130
- Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130
| | - Rohit V. Pappu
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130
- Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130
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46
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Camacho-Zarco AR, Schnapka V, Guseva S, Abyzov A, Adamski W, Milles S, Jensen MR, Zidek L, Salvi N, Blackledge M. NMR Provides Unique Insight into the Functional Dynamics and Interactions of Intrinsically Disordered Proteins. Chem Rev 2022; 122:9331-9356. [PMID: 35446534 PMCID: PMC9136928 DOI: 10.1021/acs.chemrev.1c01023] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Intrinsically disordered
proteins are ubiquitous throughout all
known proteomes, playing essential roles in all aspects of cellular
and extracellular biochemistry. To understand their function, it is
necessary to determine their structural and dynamic behavior and to
describe the physical chemistry of their interaction trajectories.
Nuclear magnetic resonance is perfectly adapted to this task, providing
ensemble averaged structural and dynamic parameters that report on
each assigned resonance in the molecule, unveiling otherwise inaccessible
insight into the reaction kinetics and thermodynamics that are essential
for function. In this review, we describe recent applications of NMR-based
approaches to understanding the conformational energy landscape, the
nature and time scales of local and long-range dynamics and how they
depend on the environment, even in the cell. Finally, we illustrate
the ability of NMR to uncover the mechanistic basis of functional
disordered molecular assemblies that are important for human health.
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Affiliation(s)
| | - Vincent Schnapka
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Serafima Guseva
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Anton Abyzov
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Wiktor Adamski
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Sigrid Milles
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | | | - Lukas Zidek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 82500 Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Kamenice 5, 82500 Brno, Czech Republic
| | - Nicola Salvi
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
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47
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Kulkarni P, Leite VBP, Roy S, Bhattacharyya S, Mohanty A, Achuthan S, Singh D, Appadurai R, Rangarajan G, Weninger K, Orban J, Srivastava A, Jolly MK, Onuchic JN, Uversky VN, Salgia R. Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma. BIOPHYSICS REVIEWS 2022; 3:011306. [PMID: 38505224 PMCID: PMC10903413 DOI: 10.1063/5.0080512] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/17/2022] [Indexed: 03/21/2024]
Abstract
Intrinsically disordered proteins (IDPs) are proteins that lack rigid 3D structure. Hence, they are often misconceived to present a challenge to Anfinsen's dogma. However, IDPs exist as ensembles that sample a quasi-continuum of rapidly interconverting conformations and, as such, may represent proteins at the extreme limit of the Anfinsen postulate. IDPs play important biological roles and are key components of the cellular protein interaction network (PIN). Many IDPs can interconvert between disordered and ordered states as they bind to appropriate partners. Conformational dynamics of IDPs contribute to conformational noise in the cell. Thus, the dysregulation of IDPs contributes to increased noise and "promiscuous" interactions. This leads to PIN rewiring to output an appropriate response underscoring the critical role of IDPs in cellular decision making. Nonetheless, IDPs are not easily tractable experimentally. Furthermore, in the absence of a reference conformation, discerning the energy landscape representation of the weakly funneled IDPs in terms of reaction coordinates is challenging. To understand conformational dynamics in real time and decipher how IDPs recognize multiple binding partners with high specificity, several sophisticated knowledge-based and physics-based in silico sampling techniques have been developed. Here, using specific examples, we highlight recent advances in energy landscape visualization and molecular dynamics simulations to discern conformational dynamics and discuss how the conformational preferences of IDPs modulate their function, especially in phenotypic switching. Finally, we discuss recent progress in identifying small molecules targeting IDPs underscoring the potential therapeutic value of IDPs. Understanding structure and function of IDPs can not only provide new insight on cellular decision making but may also help to refine and extend Anfinsen's structure/function paradigm.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Vitor B. P. Leite
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP), São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Supriyo Bhattacharyya
- Translational Bioinformatics, Center for Informatics, Department of Computational and Quantitative Medicine, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Srisairam Achuthan
- Center for Informatics, Division of Research Informatics, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Divyoj Singh
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Rajeswari Appadurai
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore 560012, India
| | - Keith Weninger
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Jose N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005-1892, USA
| | | | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
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48
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Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins. Biochem Soc Trans 2022; 50:541-554. [PMID: 35129612 DOI: 10.1042/bst20210499] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 12/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) and multidomain proteins with flexible linkers show a high level of structural heterogeneity and are best described by ensembles consisting of multiple conformations with associated thermodynamic weights. Determining conformational ensembles usually involves the integration of biophysical experiments and computational models. In this review, we discuss current approaches to determine conformational ensembles of IDPs and multidomain proteins, including the choice of biophysical experiments, computational models used to sample protein conformations, models to calculate experimental observables from protein structure, and methods to refine ensembles against experimental data. We also provide examples of recent applications of integrative conformational ensemble determination to study IDPs and multidomain proteins and suggest future directions for research in the field.
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49
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Release of linker histone from the nucleosome driven by polyelectrolyte competition with a disordered protein. Nat Chem 2022; 14:224-231. [PMID: 34992286 DOI: 10.1038/s41557-021-00839-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 10/19/2021] [Indexed: 12/13/2022]
Abstract
Highly charged intrinsically disordered proteins are essential regulators of chromatin structure and transcriptional activity. Here we identify a surprising mechanism of molecular competition that relies on the pronounced dynamical disorder present in these polyelectrolytes and their complexes. The highly positively charged human linker histone H1.0 (H1) binds to nucleosomes with ultrahigh affinity, implying residence times incompatible with efficient biological regulation. However, we show that the disordered regions of H1 retain their large-amplitude dynamics when bound to the nucleosome, which enables the highly negatively charged and disordered histone chaperone prothymosin α to efficiently invade the H1-nucleosome complex and displace H1 via a competitive substitution mechanism, vastly accelerating H1 dissociation. By integrating experiments and simulations, we establish a molecular model that rationalizes the remarkable kinetics of this process structurally and dynamically. Given the abundance of polyelectrolyte sequences in the nuclear proteome, this mechanism is likely to be widespread in cellular regulation.
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50
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Naudi-Fabra S, Blackledge M, Milles S. Synergies of Single Molecule Fluorescence and NMR for the Study of Intrinsically Disordered Proteins. Biomolecules 2021; 12:biom12010027. [PMID: 35053175 PMCID: PMC8773649 DOI: 10.3390/biom12010027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 11/16/2022] Open
Abstract
Single molecule fluorescence and nuclear magnetic resonance spectroscopy (NMR) are two very powerful techniques for the analysis of intrinsically disordered proteins (IDPs). Both techniques have individually made major contributions to deciphering the complex properties of IDPs and their interactions, and it has become evident that they can provide very complementary views on the distance-dynamics relationships of IDP systems. We now review the first approaches using both NMR and single molecule fluorescence to decipher the molecular properties of IDPs and their interactions. We shed light on how these two techniques were employed synergistically for multidomain proteins harboring intrinsically disordered linkers, for veritable IDPs, but also for liquid–liquid phase separated systems. Additionally, we provide insights into the first approaches to use single molecule Förster resonance energy transfer (FRET) and NMR for the description of multiconformational models of IDPs.
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