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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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2
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Phillips M, Muthukumar M, Ghosh K. Beyond monopole electrostatics in regulating conformations of intrinsically disordered proteins. PNAS NEXUS 2024; 3:pgae367. [PMID: 39253398 PMCID: PMC11382291 DOI: 10.1093/pnasnexus/pgae367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 08/13/2024] [Indexed: 09/11/2024]
Abstract
Conformations and dynamics of an intrinsically disordered protein (IDP) depend on its composition of charged and uncharged amino acids, and their specific placement in the protein sequence. In general, the charge (positive or negative) on an amino acid residue in the protein is not a fixed quantity. Each of the ionizable groups can exist in an equilibrated distribution of fully ionized state (monopole) and an ion-pair (dipole) state formed between the ionizing group and its counterion from the background electrolyte solution. The dipole formation (counterion condensation) depends on the protein conformation, which in turn depends on the distribution of charges and dipoles on the molecule. Consequently, effective charges of ionizable groups in the IDP backbone may differ from their chemical charges in isolation-a phenomenon termed charge-regulation. Accounting for the inevitable dipolar interactions, that have so far been ignored, and using a self-consistent procedure, we present a theory of charge-regulation as a function of sequence, temperature, and ionic strength. The theory quantitatively agrees with both charge reduction and salt-dependent conformation data of Prothymosin-alpha and makes several testable predictions. We predict charged groups are less ionized in sequences where opposite charges are well mixed compared to sequences where they are strongly segregated. Emergence of dipolar interactions from charge-regulation allows spontaneous coexistence of two phases having different conformations and charge states, sensitively depending on the charge patterning. These findings highlight sequence dependent charge-regulation and its potential exploitation by biological regulators such as phosphorylation and mutations in controlling protein conformation and function.
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Affiliation(s)
- Michael Phillips
- Department of Physics and Astronomy, University of Denver, Denver, CO 80208, USA
| | - Murugappan Muthukumar
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA
| | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, CO 80208, USA
- Molecular and Cellular Biophysics, University of Denver, Denver, CO 80208, USA
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3
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Lebedenko OO, Sekhar A, Skrynnikov NR. Order/Disorder Transitions Upon Protein Binding: A Unifying Perspective. Proteins 2024. [PMID: 39158131 DOI: 10.1002/prot.26737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 07/11/2024] [Accepted: 07/30/2024] [Indexed: 08/20/2024]
Abstract
When two proteins bind to each other, this process is often accompanied by a change in their structural states (from disordered to ordered or vice versa). As it turns out, there are 10 distinct possibilities for such binding-related order/disorder transitions. Out of this number, seven scenarios have been experimentally observed, while another three remain hitherto unreported. As an example, we discuss the so-called mutual synergistic folding, whereby two disordered proteins come together to form a fully structured complex. Our bioinformatics analysis of the Protein Databank found potential new examples of this remarkable binding mechanism.
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Affiliation(s)
- Olga O Lebedenko
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, Russia
| | - Ashok Sekhar
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, Bengaluru, India
| | - Nikolai R Skrynnikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, Russia
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
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4
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Paul T, Zhang P, Zhang Z, Fargason T, De Silva NIU, Powell E, Ekpenyong E, Jamal S, Yu Y, Prevelige P, Lu R, Zhang J. The U1-70K and SRSF1 interaction is modulated by phosphorylation during the early stages of spliceosome assembly. Protein Sci 2024; 33:e5117. [PMID: 39023093 PMCID: PMC11255866 DOI: 10.1002/pro.5117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/22/2024] [Accepted: 07/01/2024] [Indexed: 07/20/2024]
Abstract
In eukaryotes, pre-mRNA splicing is vital for RNA processing and orchestrated by the spliceosome, whose assembly starts with the interaction between U1-70K and SR proteins. Despite the significance of the U1-70K/SR interaction, the dynamic nature of the complex and the challenges in obtaining soluble U1-70K have impeded a comprehensive understanding of the interaction at the structural level for decades. We overcome the U1-70K solubility issues, enabling us to characterize the interaction between U1-70K and SRSF1, a representative SR protein. We unveil specific interactions: phosphorylated SRSF1 RS with U1-70K BAD1, and SRSF1 RRM1 with U1-70K RRM. The RS/BAD1 interaction plays a dominant role, whereas the interaction between the RRM domains further enhances the stability of the U1-70K/SRSF1 complex. The RRM interaction involves the C-terminal extension of U1-70K RRM and the conserved acid patches on SRSF1 RRM1 that is involved in SRSF1 phase separation. Our circular dichroism spectra reveal that BAD1 adapts an α-helical conformation and RS is intrinsically disordered. Intriguingly, BAD1 undergoes a conformation switch from α-helix to β-strand and random coil upon RS binding. In addition to the regulatory mechanism via SRSF1 phosphorylation, the U1-70K/SRSF1 interaction is also regulated by U1-70K BAD1 phosphorylation. We find that U1-70K phosphorylation inhibits the U1-70K and SRSF1 interaction. Our structural findings are validated through in vitro splicing assays and in-cell saturated domain scanning using the CRISPR method, providing new insights into the intricate regulatory mechanisms of pre-mRNA splicing.
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Affiliation(s)
- Trent Paul
- Department of ChemistryUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Pengcheng Zhang
- Department of Medicine, Division of Hematology/OncologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Zihan Zhang
- Department of ChemistryUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Talia Fargason
- Department of ChemistryUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | | | - Erin Powell
- Department of ChemistryUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Ethan Ekpenyong
- Department of ChemistryUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Shariq Jamal
- Department of ChemistryUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Yanbao Yu
- Department of Chemistry and BiochemistryUniversity of DelawareNewarkDelawareUSA
| | - Peter Prevelige
- Department of MicrobiologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Rui Lu
- Department of Medicine, Division of Hematology/OncologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Jun Zhang
- Department of ChemistryUniversity of Alabama at BirminghamBirminghamAlabamaUSA
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5
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Steffen FD, Cunha RA, Sigel RKO, Börner R. FRET-guided modeling of nucleic acids. Nucleic Acids Res 2024; 52:e59. [PMID: 38869063 PMCID: PMC11260485 DOI: 10.1093/nar/gkae496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 05/29/2024] [Indexed: 06/14/2024] Open
Abstract
The functional diversity of RNAs is encoded in their innate conformational heterogeneity. The combination of single-molecule spectroscopy and computational modeling offers new attractive opportunities to map structural transitions within nucleic acid ensembles. Here, we describe a framework to harmonize single-molecule Förster resonance energy transfer (FRET) measurements with molecular dynamics simulations and de novo structure prediction. Using either all-atom or implicit fluorophore modeling, we recreate FRET experiments in silico, visualize the underlying structural dynamics and quantify the reaction coordinates. Using multiple accessible-contact volumes as a post hoc scoring method for fragment assembly in Rosetta, we demonstrate that FRET can be used to filter a de novo RNA structure prediction ensemble by refuting models that are not compatible with in vitro FRET measurement. We benchmark our FRET-assisted modeling approach on double-labeled DNA strands and validate it against an intrinsically dynamic manganese(II)-binding riboswitch. We show that a FRET coordinate describing the assembly of a four-way junction allows our pipeline to recapitulate the global fold of the riboswitch displayed by the crystal structure. We conclude that computational fluorescence spectroscopy facilitates the interpretability of dynamic structural ensembles and improves the mechanistic understanding of nucleic acid interactions.
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Affiliation(s)
- Fabio D Steffen
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Richard A Cunha
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Richard Börner
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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6
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Mitra R, Usher ET, Dedeoğlu S, Crotteau MJ, Fraser OA, Yennawar NH, Gadkari VV, Ruotolo BT, Holehouse AS, Salmon L, Showalter SA, Bardwell JCA. Molecular insights into the interaction between a disordered protein and a folded RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598678. [PMID: 38915483 PMCID: PMC11195163 DOI: 10.1101/2024.06.12.598678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Intrinsically disordered protein regions (IDRs) are well-established as contributors to intermolecular interactions and the formation of biomolecular condensates. In particular, RNA-binding proteins (RBPs) often harbor IDRs in addition to folded RNA-binding domains that contribute to RBP function. To understand the dynamic interactions of an IDR-RNA complex, we characterized the RNA-binding features of a small (68 residues), positively charged IDR-containing protein, SERF. At high concentrations, SERF and RNA undergo charge-driven associative phase separation to form a protein- and RNA-rich dense phase. A key advantage of this model system is that this threshold for demixing is sufficiently high that we could use solution-state biophysical methods to interrogate the stoichiometric complexes of SERF with RNA in the one-phase regime. Herein, we describe our comprehensive characterization of SERF alone and in complex with a small fragment of the HIV-1 TAR RNA (TAR) with complementary biophysical methods and molecular simulations. We find that this binding event is not accompanied by the acquisition of structure by either molecule; however, we see evidence for a modest global compaction of the SERF ensemble when bound to RNA. This behavior likely reflects attenuated charge repulsion within SERF via binding to the polyanionic RNA and provides a rationale for the higher-order assembly of SERF in the context of RNA. We envision that the SERF-RNA system will lower the barrier to accessing the details that support IDR-RNA interactions and likewise deepen our understanding of the role of IDR-RNA contacts in complex formation and liquid-liquid phase separation.
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Affiliation(s)
- Rishav Mitra
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Emery T. Usher
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO, USA
| | - Selin Dedeoğlu
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs, (CRMN), UMR 5082, CNRS, ENS Lyon, UCBL, Université de Lyon, 69100 Villeurbanne, France
| | - Matthew J. Crotteau
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Olivia A. Fraser
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Neela H. Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Varun V. Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO, USA
| | - Loïc Salmon
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs, (CRMN), UMR 5082, CNRS, ENS Lyon, UCBL, Université de Lyon, 69100 Villeurbanne, France
| | - Scott A. Showalter
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - James C. A. Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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7
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Shukla S, Bhattacharya A, Sehrawat P, Agarwal P, Shobhawat R, Malik N, Duraisamy K, Rangan NS, Hosur RV, Kumar A. Disorder in CENP-A Cse4 tail-chaperone interaction facilitates binding with Ame1/Okp1 at the kinetochore. Structure 2024; 32:690-705.e6. [PMID: 38565139 DOI: 10.1016/j.str.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 11/16/2023] [Accepted: 03/06/2024] [Indexed: 04/04/2024]
Abstract
The centromere is epigenetically marked by a histone H3 variant-CENP-A. The budding yeast CENP-A called Cse4, consists of an unusually long N-terminus that is known to be involved in kinetochore assembly. Its disordered chaperone, Scm3 is responsible for the centromeric deposition of Cse4 as well as in the maintenance of a segregation-competent kinetochore. In this study, we show that the Cse4 N-terminus is intrinsically disordered and interacts with Scm3 at multiple sites, and the complex does not gain any substantial structure. Additionally, the complex forms a synergistic association with an essential inner kinetochore component (Ctf19-Mcm21-Okp1-Ame1), and a model has been suggested to this effect. Thus, our study provides mechanistic insights into the Cse4 N-terminus-chaperone interaction and also illustrates how intrinsically disordered proteins mediate assembly of complex multiprotein networks, in general.
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Affiliation(s)
- Shivangi Shukla
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | | | - Parveen Sehrawat
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Prakhar Agarwal
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Rahul Shobhawat
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Nikita Malik
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Kalaiyarasi Duraisamy
- Centre for Advanced Protein Studies, Syngene International Limited, Bangalore, India
| | | | - Ramakrishna V Hosur
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Ashutosh Kumar
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India.
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8
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Ginell GM, Emenecker RJ, Lotthammer JM, Usher ET, Holehouse AS. Direct prediction of intermolecular interactions driven by disordered regions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597104. [PMID: 38895487 PMCID: PMC11185574 DOI: 10.1101/2024.06.03.597104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Intrinsically disordered regions (IDRs) are critical for a wide variety of cellular functions, many of which involve interactions with partner proteins. Molecular recognition is typically considered through the lens of sequence-specific binding events. However, a growing body of work has shown that IDRs often interact with partners in a manner that does not depend on the precise order of the amino acid order, instead driven by complementary chemical interactions leading to disordered bound-state complexes. Despite this emerging paradigm, we lack tools to describe, quantify, predict, and interpret these types of structurally heterogeneous interactions from the underlying amino acid sequences. Here, we repurpose the chemical physics developed originally for molecular simulations to develop an approach for predicting intermolecular interactions between IDRs and partner proteins. Our approach enables the direct prediction of phase diagrams, the identification of chemically-specific interaction hotspots on IDRs, and a route to develop and test mechanistic hypotheses regarding IDR function in the context of molecular recognition. We use our approach to examine a range of systems and questions to highlight its versatility and applicability.
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Affiliation(s)
- Garrett M. Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Ryan. J Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Jeffrey M. Lotthammer
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Emery T. Usher
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
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9
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Alston JJ, Soranno A, Holehouse AS. Conserved molecular recognition by an intrinsically disordered region in the absence of sequence conservation. RESEARCH SQUARE 2024:rs.3.rs-4477977. [PMID: 38883712 PMCID: PMC11177979 DOI: 10.21203/rs.3.rs-4477977/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Intrinsically disordered regions (IDRs) are critical for cellular function yet often appear to lack sequence conservation when assessed by multiple sequence alignments. This raises the question of if and how function can be encoded and preserved in these regions despite massive sequence variation. To address this question, we have applied coarse-grained molecular dynamics simulations to investigate non-specific RNA binding of coronavirus nucleocapsid proteins. Coronavirus nucleocapsid proteins consist of multiple interspersed disordered and folded domains that bind RNA. Here, we focus on the first two domains of coronavirus nucleocapsid proteins: the disordered N-terminal domain (NTD) and the folded RNA binding domain (RBD). While the NTD is highly variable across evolution, the RBD is structurally conserved. This combination makes the NTD-RBD a convenient model system for exploring the interplay between an IDR adjacent to a folded domain and how changes in IDR sequence can influence molecular recognition of a partner. Our results reveal a surprising degree of sequence-specificity encoded by both the composition and the precise order of the amino acids in the NTD. The presence of an NTD can - depending on the sequence - either suppress or enhance RNA binding. Despite this sensitivity, large-scale variation in NTD sequences is possible while certain sequence features are retained. Consequently, a conformationally-conserved dynamic and disordered RNA:protein complex is found across nucleocapsid protein orthologs despite large-scale changes in both NTD sequence and RBD surface chemistry. Taken together, these insights shed light on the ability of disordered regions to preserve functional characteristics despite their sequence variability.
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Affiliation(s)
- Jhullian J. Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
- Present Address, Program In Cellular and Molecular Medicine (PCMM), Boston Children’s Hospital, Boston, MA, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
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10
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Waszkiewicz R, Michaś A, Białobrzewski MK, Klepka BP, Cieplak-Rotowska MK, Staszałek Z, Cichocki B, Lisicki M, Szymczak P, Niedzwiecka A. Hydrodynamic Radii of Intrinsically Disordered Proteins: Fast Prediction by Minimum Dissipation Approximation and Experimental Validation. J Phys Chem Lett 2024; 15:5024-5033. [PMID: 38696815 PMCID: PMC11103702 DOI: 10.1021/acs.jpclett.4c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/12/2024] [Accepted: 04/26/2024] [Indexed: 05/04/2024]
Abstract
The diffusion coefficients of globular and fully unfolded proteins can be predicted with high accuracy solely from their mass or chain length. However, this approach fails for intrinsically disordered proteins (IDPs) containing structural domains. We propose a rapid predictive methodology for estimating the diffusion coefficients of IDPs. The methodology uses accelerated conformational sampling based on self-avoiding random walks and includes hydrodynamic interactions between coarse-grained protein subunits, modeled using the generalized Rotne-Prager-Yamakawa approximation. To estimate the hydrodynamic radius, we rely on the minimum dissipation approximation recently introduced by Cichocki et al. Using a large set of experimentally measured hydrodynamic radii of IDPs over a wide range of chain lengths and domain contributions, we demonstrate that our predictions are more accurate than the Kirkwood approximation and phenomenological approaches. Our technique may prove to be valuable in predicting the hydrodynamic properties of both fully unstructured and multidomain disordered proteins.
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Affiliation(s)
- Radost Waszkiewicz
- Institute
of Theoretical Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland
| | - Agnieszka Michaś
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Michał K. Białobrzewski
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Barbara P. Klepka
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | | | - Zuzanna Staszałek
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Bogdan Cichocki
- Institute
of Theoretical Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland
| | - Maciej Lisicki
- Institute
of Theoretical Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland
| | - Piotr Szymczak
- Institute
of Theoretical Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland
| | - Anna Niedzwiecka
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
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11
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Sahoo BR, Kocman V, Clark N, Myers N, Deng X, Wong EL, Yang HJ, Kotar A, Guzman BB, Dominguez D, Plavec J, Bardwell JCA. Protein G-quadruplex interactions and their effects on phase transitions and protein aggregation. Nucleic Acids Res 2024; 52:4702-4722. [PMID: 38572746 PMCID: PMC11077067 DOI: 10.1093/nar/gkae229] [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: 12/06/2023] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024] Open
Abstract
The SERF family of proteins were originally discovered for their ability to accelerate amyloid formation. Znf706 is an uncharacterized protein whose N-terminus is homologous to SERF proteins. We show here that human Znf706 can promote protein aggregation and amyloid formation. Unexpectedly, Znf706 specifically interacts with stable, non-canonical nucleic acid structures known as G-quadruplexes. G-quadruplexes can affect gene regulation and suppress protein aggregation; however, it is unknown if and how these two activities are linked. We find Znf706 binds preferentially to parallel G-quadruplexes with low micromolar affinity, primarily using its N-terminus, and upon interaction, its dynamics are constrained. G-quadruplex binding suppresses Znf706's ability to promote protein aggregation. Znf706 in conjunction with G-quadruplexes therefore may play a role in regulating protein folding. RNAseq analysis shows that Znf706 depletion specifically impacts the mRNA abundance of genes that are predicted to contain high G-quadruplex density. Our studies give insight into how proteins and G-quadruplexes interact, and how these interactions affect both partners and lead to the modulation of protein aggregation and cellular mRNA levels. These observations suggest that the SERF family of proteins, in conjunction with G-quadruplexes, may have a broader role in regulating protein folding and gene expression than previously appreciated.
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Affiliation(s)
- Bikash R Sahoo
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Vojč Kocman
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Nathan Clark
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Nikhil Myers
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Xiexiong Deng
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ee L Wong
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Harry J Yang
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Anita Kotar
- National Institute of Chemistry, Ljubljana, Slovenia
| | | | | | - Janez Plavec
- National Institute of Chemistry, Ljubljana, Slovenia
| | - James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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12
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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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13
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Firouzbakht A, Haider A, Gaalswyk K, Alaeen S, Ghosh K, Gruebele M. HYPK: A marginally disordered protein sensitive to charge decoration. Proc Natl Acad Sci U S A 2024; 121:e2316408121. [PMID: 38657047 PMCID: PMC11067017 DOI: 10.1073/pnas.2316408121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 03/20/2024] [Indexed: 04/26/2024] Open
Abstract
Intrinsically disordered proteins (IDPs) that lie close to the empirical boundary separating IDPs and folded proteins in Uversky's charge-hydropathy plot may behave as "marginal IDPs" and sensitively switch conformation upon changes in environment (temperature, crowding, and charge screening), sequence, or both. In our search for such a marginal IDP, we selected Huntingtin-interacting protein K (HYPK) near that boundary as a candidate; PKIα, also near that boundary, has lower secondary structure propensity; and Crk1, just across the boundary on the folded side, has higher secondary structure propensity. We used a qualitative Förster resonance energy transfer-based assay together with circular dichroism to simultaneously probe global and local conformation. HYPK shows several unique features indicating marginality: a cooperative transition in end-to-end distance with temperature, like Crk1 and folded proteins, but unlike PKIα; enhanced secondary structure upon crowding, in contrast to Crk1 and PKIα; and a cross-over from salt-induced expansion to compaction at high temperature, likely due to a structure-to-disorder transition not seen in Crk1 and PKIα. We then tested HYPK's sensitivity to charge patterning by designing charge-flipped variants including two specific sequences with identical amino acid composition that markedly differ in their predicted size and response to salt. The experimentally observed trends, also including mutants of PKIα, verify the predictions from sequence charge decoration metrics. Marginal proteins like HYPK show features of both folded and disordered proteins that make them sensitive to physicochemical perturbations and structural control by charge patterning.
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Affiliation(s)
- Arash Firouzbakht
- Department of Chemistry, University of Illinois at Urbana Champaign, Urbana Champaign, IL61801
| | - Austin Haider
- Department of Molecular and Cellular Biophysics, University of Denver, Denver, CO80210
| | - Kari Gaalswyk
- Department of Physics and Astronomy, University of Denver, Denver, CO80210
| | - Sepehr Alaeen
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana Champaign, Urbana Champaign, IL61801
| | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, CO80210
| | - Martin Gruebele
- Department of Chemistry, University of Illinois at Urbana Champaign, Urbana Champaign, IL61801
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana Champaign, Urbana Champaign, IL61801
- Department of Physics, University of Illinois at Urbana Champaign, Urbana Champaign, IL61801
- Carle-Illinois College of Medicine, University of Illinois Urbana Champaign, Urbana Champaign, IL61801
- Center for Advanced Study, University of Illinois Urbana Champaign, Urbana Champaign, IL61801
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14
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Jankowski MS, Griffith D, Shastry DG, Pelham JF, Ginell GM, Thomas J, Karande P, Holehouse AS, Hurley JM. Disordered clock protein interactions and charge blocks turn an hourglass into a persistent circadian oscillator. Nat Commun 2024; 15:3523. [PMID: 38664421 PMCID: PMC11045787 DOI: 10.1038/s41467-024-47761-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: 09/07/2023] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Organismal physiology is widely regulated by the molecular circadian clock, a feedback loop composed of protein complexes whose members are enriched in intrinsically disordered regions. These regions can mediate protein-protein interactions via SLiMs, but the contribution of these disordered regions to clock protein interactions had not been elucidated. To determine the functionality of these disordered regions, we applied a synthetic peptide microarray approach to the disordered clock protein FRQ in Neurospora crassa. We identified residues required for FRQ's interaction with its partner protein FRH, the mutation of which demonstrated FRH is necessary for persistent clock oscillations but not repression of transcriptional activity. Additionally, the microarray demonstrated an enrichment of FRH binding to FRQ peptides with a net positive charge. We found that positively charged residues occurred in significant "blocks" within the amino acid sequence of FRQ and that ablation of one of these blocks affected both core clock timing and physiological clock output. Finally, we found positive charge clusters were a commonly shared molecular feature in repressive circadian clock proteins. Overall, our study suggests a mechanistic purpose for positive charge blocks and yielded insights into repressive arm protein roles in clock function.
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Affiliation(s)
- Meaghan S Jankowski
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Daniel Griffith
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Divya G Shastry
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Jacqueline F Pelham
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Garrett M Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joshua Thomas
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Pankaj Karande
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Jennifer M Hurley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
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15
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Zarin T, Lehner B. A complete map of specificity encoding for a partially fuzzy protein interaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591103. [PMID: 38712134 PMCID: PMC11071492 DOI: 10.1101/2024.04.25.591103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Thousands of human proteins function by binding short linear motifs embedded in intrinsically disordered regions. How affinity and specificity are encoded in these binding domains and the motifs themselves is not well understood. The evolvability of binding specificity - how rapidly and extensively it can change upon mutation - is also largely unexplored, as is the contribution of 'fuzzy' dynamic residues to affinity and specificity in protein-protein interactions. Here we report the first complete map of specificity encoding for a globular protein domain. Quantifying >200,000 energetic interactions between a PDZ domain and its ligand identifies 20 major energetically coupled pairs of sites that control specificity. These are organized into six modules, with most mutations in each module reprogramming specificity for a single position in the ligand. Nine of the major energetic couplings controlling specificity are between structural contacts and 11 have an allosteric mechanism of action. The dynamic tail of the ligand is more robust to mutation than the structured residues but contributes additively to binding affinity and communicates with structured residues to enable changes in specificity. Our results quantify the binding specificities of >1,800 globular proteins to reveal how specificity is encoded and provide a direct comparison of the encoding of affinity and specificity in structured and dynamic molecular recognition.
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Affiliation(s)
- Taraneh Zarin
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Ben Lehner
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
- Wellcome Sanger Institute, Cambridge, UK
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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16
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Jung J, Tan C, Sugita Y. GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems. Nat Commun 2024; 15:3370. [PMID: 38643169 PMCID: PMC11032353 DOI: 10.1038/s41467-024-47654-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 04/08/2024] [Indexed: 04/22/2024] Open
Abstract
Residue-level coarse-grained (CG) molecular dynamics (MD) simulation is widely used to investigate slow biological processes that involve multiple proteins, nucleic acids, and their complexes. Biomolecules in a large simulation system are distributed non-uniformly, limiting computational efficiency with conventional methods. Here, we develop a hierarchical domain decomposition scheme with dynamic load balancing for heterogeneous biomolecular systems to keep computational efficiency even after drastic changes in particle distribution. These schemes are applied to the dynamics of intrinsically disordered protein (IDP) droplets. During the fusion of two droplets, we find that the changes in droplet shape correlate with the mixing of IDP chains. Additionally, we simulate large systems with multiple IDP droplets, achieving simulation sizes comparable to those observed in microscopy. In our MD simulations, we directly observe Ostwald ripening, a phenomenon where small droplets dissolve and their molecules redeposit into larger droplets. These methods have been implemented in CGDYN of the GENESIS software, offering a tool for investigating mesoscopic biological processes using the residue-level CG models.
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Affiliation(s)
- Jaewoon Jung
- 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
| | - Cheng Tan
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, 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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17
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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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18
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Hadži S, Živič Z, Kovačič M, Zavrtanik U, Haesaerts S, Charlier D, Plavec J, Volkov AN, Lah J, Loris R. Fuzzy recognition by the prokaryotic transcription factor HigA2 from Vibrio cholerae. Nat Commun 2024; 15:3105. [PMID: 38600130 PMCID: PMC11006873 DOI: 10.1038/s41467-024-47296-3] [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: 05/21/2023] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
Disordered protein sequences can exhibit different binding modes, ranging from well-ordered folding-upon-binding to highly dynamic fuzzy binding. The primary function of the intrinsically disordered region of the antitoxin HigA2 from Vibrio cholerae is to neutralize HigB2 toxin through ultra-high-affinity folding-upon-binding interaction. Here, we show that the same intrinsically disordered region can also mediate fuzzy interactions with its operator DNA and, through interplay with the folded helix-turn-helix domain, regulates transcription from the higBA2 operon. NMR, SAXS, ITC and in vivo experiments converge towards a consistent picture where a specific set of residues in the intrinsically disordered region mediate electrostatic and hydrophobic interactions while "hovering" over the DNA operator. Sensitivity of the intrinsically disordered region to scrambling the sequence, position-specific contacts and absence of redundant, multivalent interactions, point towards a more specific type of fuzzy binding. Our work demonstrates how a bacterial regulator achieves dual functionality by utilizing two distinct interaction modes within the same disordered sequence.
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Affiliation(s)
- San Hadži
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Zala Živič
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Matic Kovačič
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova, 19, 1000, Ljubljana, Slovenia
| | - Uroš Zavrtanik
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Sarah Haesaerts
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Daniel Charlier
- Research group of Microbiology, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova, 19, 1000, Ljubljana, Slovenia
| | - Alexander N Volkov
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Jean Jeener NMR Centre, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia.
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium.
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19
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Feld LG, Boehme SC, Morad V, Sahin Y, Kaul CJ, Dirin DN, Rainò G, Kovalenko MV. Quantifying Förster Resonance Energy Transfer from Single Perovskite Quantum Dots to Organic Dyes. ACS NANO 2024; 18:9997-10007. [PMID: 38547379 PMCID: PMC11008358 DOI: 10.1021/acsnano.3c11359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/07/2024] [Accepted: 03/20/2024] [Indexed: 04/10/2024]
Abstract
Colloidal quantum dots (QDs) are promising regenerable photoredox catalysts offering broadly tunable redox potentials along with high absorption coefficients. QDs have thus far been examined for various organic transformations, water splitting, and CO2 reduction. Vast opportunities emerge from coupling QDs with other homogeneous catalysts, such as transition metal complexes or organic dyes, into hybrid nanoassemblies exploiting energy transfer (ET), leveraging a large absorption cross-section of QDs and long-lived triplet states of cocatalysts. However, a thorough understanding and further engineering of the complex operational mechanisms of hybrid nanoassemblies require simultaneously controlling the surface chemistry of the QDs and probing dynamics at sufficient spatiotemporal resolution. Here, we probe the ET from single lead halide perovskite QDs, capped by alkylphospholipid ligands, to organic dye molecules employing single-particle photoluminescence spectroscopy with single-photon resolution. We identify a Förster-type ET by spatial, temporal, and photon-photon correlations in the QD and dye emission. Discrete quenching steps in the acceptor emission reveal stochastic photobleaching events of individual organic dyes, allowing a precise quantification of the transfer efficiency, which is >70% for QD-dye complexes with strong donor-acceptor spectral overlap. Our work explores the processes occurring at the QD/molecule interface and demonstrates the feasibility of sensitizing organic photocatalysts with QDs.
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Affiliation(s)
- Leon G. Feld
- Institute
of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
- Laboratory
for Thin Films and Photovoltaics, Empa −
Swiss Federal Laboratories for Materials Science and Technology, CH-8600 Dübendorf, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Simon C. Boehme
- Institute
of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
- Laboratory
for Thin Films and Photovoltaics, Empa −
Swiss Federal Laboratories for Materials Science and Technology, CH-8600 Dübendorf, Switzerland
| | - Viktoriia Morad
- Institute
of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
- Laboratory
for Thin Films and Photovoltaics, Empa −
Swiss Federal Laboratories for Materials Science and Technology, CH-8600 Dübendorf, Switzerland
| | - Yesim Sahin
- Institute
of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
- Laboratory
for Thin Films and Photovoltaics, Empa −
Swiss Federal Laboratories for Materials Science and Technology, CH-8600 Dübendorf, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Christoph J. Kaul
- Institute
of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
- Laboratory
for Thin Films and Photovoltaics, Empa −
Swiss Federal Laboratories for Materials Science and Technology, CH-8600 Dübendorf, Switzerland
| | - Dmitry N. Dirin
- Institute
of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
- Laboratory
for Thin Films and Photovoltaics, Empa −
Swiss Federal Laboratories for Materials Science and Technology, CH-8600 Dübendorf, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Gabriele Rainò
- Institute
of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
- Laboratory
for Thin Films and Photovoltaics, Empa −
Swiss Federal Laboratories for Materials Science and Technology, CH-8600 Dübendorf, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Maksym V. Kovalenko
- Institute
of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
- Laboratory
for Thin Films and Photovoltaics, Empa −
Swiss Federal Laboratories for Materials Science and Technology, CH-8600 Dübendorf, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, ETH Zürich, CH-8093 Zürich, Switzerland
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20
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Gupta MN, Uversky VN. Protein structure-function continuum model: Emerging nexuses between specificity, evolution, and structure. Protein Sci 2024; 33:e4968. [PMID: 38532700 DOI: 10.1002/pro.4968] [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: 12/02/2023] [Revised: 02/18/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
The rationale for replacing the old binary of structure-function with the trinity of structure, disorder, and function has gained considerable ground in recent years. A continuum model based on the expanded form of the existing paradigm can now subsume importance of both conformational flexibility and intrinsic disorder in protein function. The disorder is actually critical for understanding the protein-protein interactions in many regulatory processes, formation of membrane-less organelles, and our revised notions of specificity as amply illustrated by moonlighting proteins. While its importance in formation of amyloids and function of prions is often discussed, the roles of intrinsic disorder in infectious diseases and protein function under extreme conditions are also becoming clear. This review is an attempt to discuss how our current understanding of protein function, specificity, and evolution fit better with the continuum model. This integration of structure and disorder under a single model may bring greater clarity in our continuing quest for understanding proteins and molecular mechanisms of their functionality.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
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21
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Mindel V, Brodsky S, Cohen A, Manadre W, Jonas F, Carmi M, Barkai N. Intrinsically disordered regions of the Msn2 transcription factor encode multiple functions using interwoven sequence grammars. Nucleic Acids Res 2024; 52:2260-2272. [PMID: 38109289 PMCID: PMC10954448 DOI: 10.1093/nar/gkad1191] [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: 09/18/2023] [Revised: 11/04/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023] Open
Abstract
Intrinsically disordered regions (IDRs) are abundant in eukaryotic proteins, but their sequence-function relationship remains poorly understood. IDRs of transcription factors (TFs) can direct promoter selection and recruit coactivators, as shown for the budding yeast TF Msn2. To examine how IDRs encode both these functions, we compared genomic binding specificity, coactivator recruitment, and gene induction amongst a large set of designed Msn2-IDR mutants. We find that both functions depend on multiple regions across the > 600AA IDR. Yet, transcription activity was readily disrupted by mutations that showed no effect on the Msn2 binding specificity. Our data attribute this differential sensitivity to the integration of a relaxed, composition-based code directing binding specificity with a more stringent, motif-based code controlling the recruitment of coactivators and transcription activity. Therefore, Msn2 utilizes interwoven sequence grammars for encoding multiple functions, suggesting a new IDR design paradigm of potentially general use.
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Affiliation(s)
- Vladimir Mindel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sagie Brodsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Aileen Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Wajd Manadre
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Felix Jonas
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Miri Carmi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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22
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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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23
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Sahoo BR, Kocman V, Clark N, Myers N, Deng X, Wong EL, Yang HJ, Kotar A, Guzman BB, Dominguez D, Plavec J, Bardwell JC. Protein G-quadruplex interactions and their effects on phase transitions and protein aggregation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.21.558871. [PMID: 37790366 PMCID: PMC10542165 DOI: 10.1101/2023.09.21.558871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The SERF family of proteins were originally discovered for their ability to accelerate amyloid formation. Znf706 is an uncharacterized protein whose N-terminus is homologous to SERF proteins. We show here that human Znf706 can promote protein aggregation and amyloid formation. Unexpectedly, Znf706 specifically interacts with stable, non-canonical nucleic acid structures known as G-quadruplexes. G-quadruplexes can affect gene regulation and suppress protein aggregation; however, it is unknown if and how these two activities are linked. We find Znf706 binds preferentially to parallel G-quadruplexes with low micromolar affinity, primarily using its N-terminus, and upon interaction, its dynamics are constrained. G-quadruplex binding suppresses Znf706's ability to promote protein aggregation. Znf706 in conjunction with G-quadruplexes therefore may play a role in regulating protein folding. RNAseq analysis shows that Znf706 depletion specifically impacts the mRNA abundance of genes that are predicted to contain high G-quadruplex density. Our studies give insight into how proteins and G-quadruplexes interact, and how these interactions affect both partners and lead to the modulation of protein aggregation and cellular mRNA levels. These observations suggest that the SERF family of proteins, in conjunction with G-quadruplexes, may have a broader role in regulating protein folding and gene expression than previously appreciated.
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Affiliation(s)
- Bikash R. Sahoo
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Vojč Kocman
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Nathan Clark
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Nikhil Myers
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Xiexiong Deng
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ee L. Wong
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Harry J. Yang
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Anita Kotar
- National Institute of Chemistry, Ljubljana, Slovenia
| | | | | | - Janez Plavec
- National Institute of Chemistry, Ljubljana, Slovenia
| | - James C.A. Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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24
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Heckmeier PJ, Ruf J, Rochereau C, Hamm P. A billion years of evolution manifest in nanosecond protein dynamics. Proc Natl Acad Sci U S A 2024; 121:e2318743121. [PMID: 38412135 DOI: 10.1073/pnas.2318743121] [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: 10/27/2023] [Accepted: 01/24/2024] [Indexed: 02/29/2024] Open
Abstract
Protein dynamics form a critical bridge between protein structure and function, yet the impact of evolution on ultrafast processes inside proteins remains enigmatic. This study delves deep into nanosecond-scale protein dynamics of a structurally and functionally conserved protein across species separated by almost a billion years, investigating ten homologs in complex with their ligand. By inducing a photo-triggered destabilization of the ligand inside the binding pocket, we resolved distinct kinetic footprints for each homolog via transient infrared spectroscopy. Strikingly, we found a cascade of rearrangements within the protein complex which manifest in time points of increased dynamic activity conserved over hundreds of millions of years within a narrow window. Among these processes, one displays a subtle temporal shift correlating with evolutionary divergence, suggesting reduced selective pressure in the past. Our study not only uncovers the impact of evolution on molecular processes in a specific case, but has also the potential to initiate a field of scientific inquiry within molecular paleontology, where species are compared and classified based on the rapid pace of protein dynamic processes; a field which connects the shortest conceivable time scale in living matter (10[Formula: see text] s) with the largest ones (10[Formula: see text] s).
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Affiliation(s)
| | - Jeannette Ruf
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | | | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
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25
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Stief T, Vormann K, Lakomek NA. Sensitivity-enhanced NMR 15N R 1 and R 1ρ relaxation experiments for the investigation of intrinsically disordered proteins at high magnetic fields. Methods 2024; 223:1-15. [PMID: 38242384 DOI: 10.1016/j.ymeth.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/21/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024] Open
Abstract
NMR relaxation experiments provide residue-specific insights into the structural dynamics of proteins. Here, we present an optimized set of sensitivity-enhanced 15N R1 and R1ρ relaxation experiments applicable to fully protonated proteins. The NMR pulse sequences are conceptually similar to the set of TROSY-based sequences and their HSQC counterpart (Lakomek et al., J. Biomol. NMR 2012). Instead of the TROSY read-out scheme, a sensitivity-enhanced HSQC read-out scheme is used, with improved and easier optimized water suppression. The presented pulse sequences are applied on the cytoplasmic domain of the SNARE protein Synpatobrevin-2 (Syb-2), which is intrinsically disordered in its monomeric pre-fusion state. A two-fold increase in the obtained signal-to-noise ratio is observed for this intrinsically disordered protein, therefore offering a four-fold reduction of measurement time compared to the TROSY-detected version. The inter-scan recovery delay can be shortened to two seconds. Pulse sequences were tested at 600 MHz and 1200 MHz 1H Larmor frequency, thus applicable over a wide magnetic field range. A comparison between protonated and deuterated protein samples reveals high agreement, indicating that reliable 15N R1 and R1ρ rate constants can be extracted for fully protonated and deuterated samples. The presented pulse sequences will benefit not only for IDPs but also for an entire range of low and medium-sized proteins.
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Affiliation(s)
- Tobias Stief
- Institute of Biological Information Processing (IBI-7), Forschungszentrum Jülich, Jülich, Germany; Institute of Physical Biology, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Katharina Vormann
- Institute of Biological Information Processing (IBI-7), Forschungszentrum Jülich, Jülich, Germany; Institute of Physical Biology, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nils-Alexander Lakomek
- Institute of Biological Information Processing (IBI-7), Forschungszentrum Jülich, Jülich, Germany; Institute of Physical Biology, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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26
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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: 55] [Impact Index Per Article: 55.0] [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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27
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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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28
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Mantonico MV, De Leo F, Quilici G, Colley LS, De Marchis F, Crippa M, Mezzapelle R, Schulte T, Zucchelli C, Pastorello C, Carmeno C, Caprioglio F, Ricagno S, Giachin G, Ghitti M, Bianchi ME, Musco G. The acidic intrinsically disordered region of the inflammatory mediator HMGB1 mediates fuzzy interactions with CXCL12. Nat Commun 2024; 15:1201. [PMID: 38331917 PMCID: PMC10853541 DOI: 10.1038/s41467-024-45505-7] [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: 05/17/2023] [Accepted: 01/26/2024] [Indexed: 02/10/2024] Open
Abstract
Chemokine heterodimers activate or dampen their cognate receptors during inflammation. The CXCL12 chemokine forms with the fully reduced (fr) alarmin HMGB1 a physiologically relevant heterocomplex (frHMGB1•CXCL12) that synergically promotes the inflammatory response elicited by the G-protein coupled receptor CXCR4. The molecular details of complex formation were still elusive. Here we show by an integrated structural approach that frHMGB1•CXCL12 is a fuzzy heterocomplex. Unlike previous assumptions, frHMGB1 and CXCL12 form a dynamic equimolar assembly, with structured and unstructured frHMGB1 regions recognizing the CXCL12 dimerization surface. We uncover an unexpected role of the acidic intrinsically disordered region (IDR) of HMGB1 in heterocomplex formation and its binding to CXCR4 on the cell surface. Our work shows that the interaction of frHMGB1 with CXCL12 diverges from the classical rigid heterophilic chemokines dimerization. Simultaneous interference with multiple interactions within frHMGB1•CXCL12 might offer pharmacological strategies against inflammatory conditions.
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Affiliation(s)
- Malisa Vittoria Mantonico
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
- School of Medicine, Università Vita e Salute-San Raffaele, Milan, Italy
| | - Federica De Leo
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
- Experimental Therapeutics Program, IFOM ETS - The AIRC Institute of Molecular Oncology and AIRC, Fondazione AIRC per la Ricerca sul Cancro ETS, Milan, Italy
| | - Giacomo Quilici
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Liam Sean Colley
- HMGBiotech S.r.l., 20133, Milan, Italy
- School of Medicine and Surgery, Università Milano-Bicocca, 20126, Milan, Italy
| | - Francesco De Marchis
- School of Medicine, Università Vita e Salute-San Raffaele, Milan, Italy
- Chromatin Dynamics Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Massimo Crippa
- Chromatin Dynamics Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Rosanna Mezzapelle
- School of Medicine, Università Vita e Salute-San Raffaele, Milan, Italy
- Chromatin Dynamics Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Tim Schulte
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Milan, Italy
| | - Chiara Zucchelli
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Chiara Pastorello
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Camilla Carmeno
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Francesca Caprioglio
- School of Medicine, Università Vita e Salute-San Raffaele, Milan, Italy
- Chromatin Dynamics Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Stefano Ricagno
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Milan, Italy
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Gabriele Giachin
- Department of Chemical Sciences (DiSC), University of Padua, 35131, Padova, Italy
| | - Michela Ghitti
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy.
| | - Marco Emilio Bianchi
- School of Medicine, Università Vita e Salute-San Raffaele, Milan, Italy
- Chromatin Dynamics Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Giovanna Musco
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy.
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29
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Arai M, Suetaka S, Ooka K. Dynamics and interactions of intrinsically disordered proteins. Curr Opin Struct Biol 2024; 84:102734. [PMID: 38039868 DOI: 10.1016/j.sbi.2023.102734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 12/03/2023]
Abstract
Intrinsically disordered proteins (IDPs) are widespread in eukaryotes and participate in a variety of important cellular processes. Numerous studies using state-of-the-art experimental and theoretical methods have advanced our understanding of IDPs and revealed that disordered regions engage in a large repertoire of intra- and intermolecular interactions through their conformational dynamics, thereby regulating many intracellular functions in concert with folded domains. The mechanisms by which IDPs interact with their partners are diverse, depending on their conformational propensities, and include induced fit, conformational selection, and their mixtures. In addition, IDPs are implicated in many diseases, and progress has been made in designing inhibitors of IDP-mediated interactions. Here we review these recent advances with a focus on the dynamics and interactions of IDPs.
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Affiliation(s)
- Munehito Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan; Komaba Organization for Educational Excellence, College of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan; Department of Physics, Graduate School of Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan.
| | - Shunji Suetaka
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Koji Ooka
- Komaba Organization for Educational Excellence, College of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
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30
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Ghosh C, Nagpal S, Muñoz V. Molecular simulations integrated with experiments for probing the interaction dynamics and binding mechanisms of intrinsically disordered proteins. Curr Opin Struct Biol 2024; 84:102756. [PMID: 38118365 PMCID: PMC11242915 DOI: 10.1016/j.sbi.2023.102756] [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: 10/08/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/22/2023]
Abstract
Intrinsically disordered proteins (IDPs) exploit their plasticity to deploy a rich panoply of soft interactions and binding phenomena. Advances in tailoring molecular simulations for IDPs combined with experimental cross-validation offer an atomistic view of the mechanisms that control IDP binding, function, and dysfunction. The emerging theme is that unbound IDPs autonomously form transient local structures and self-interactions that determine their binding behavior. Recent results have shed light on whether and how IDPs fold, stay disordered or drive condensation upon binding; how they achieve binding specificity and select among competing partners. The disorder-binding paradigm is now being proactively used by researchers to target IDPs for rational drug design and engineer molecular responsive elements for biosensing applications.
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Affiliation(s)
- Catherine Ghosh
- NSF-CREST Center for Cellular and Biomolecular Machines (CCBM), University of California at Merced, Merced, 95343 CA, USA; Department of Bioengineering, University of California at Merced, Merced, 95343 CA, USA. https://twitter.com/cat_ghosh
| | - Suhani Nagpal
- NSF-CREST Center for Cellular and Biomolecular Machines (CCBM), University of California at Merced, Merced, 95343 CA, USA; Department of Bioengineering, University of California at Merced, Merced, 95343 CA, USA; OpenEye, Cadence Molecular Sciences, Boston, 02114 MA, USA
| | - Victor Muñoz
- NSF-CREST Center for Cellular and Biomolecular Machines (CCBM), University of California at Merced, Merced, 95343 CA, USA; Department of Bioengineering, University of California at Merced, Merced, 95343 CA, USA.
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31
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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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32
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Kota D, Prasad R, Zhou HX. Adenosine Triphosphate Mediates Phase Separation of Disordered Basic Proteins by Bridging Intermolecular Interaction Networks. J Am Chem Soc 2024; 146:1326-1336. [PMID: 38174879 PMCID: PMC10843746 DOI: 10.1021/jacs.3c09134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Adenosine triphosphate (ATP) is an abundant molecule with crucial cellular roles as the energy currency and a building block of nucleic acids and for protein phosphorylation. Here we show that ATP mediates the phase separation of basic intrinsically disordered proteins (bIDPs). In the resulting condensates, ATP is highly concentrated (apparent partition coefficients up to 7700) and serves as bridges between bIDP chains. These liquid-like droplets have some of the lowest interfacial tension (∼25 pN/μm) but high zero-shear viscosities (1-15 Pa s) due to the bridged protein networks, and yet their fusion has some of the highest speeds (∼1 μm/ms). The rapid fusion manifests extreme shear thinning, where the apparent viscosity is lower than zero-shear viscosity by over 100-fold, made possible by fast reformation of the ATP bridges. At still higher concentrations, ATP does not dissolve bIDP droplets but results in aggregates and fibrils.
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Affiliation(s)
- Divya Kota
- Department of Chemistry, University of Illinois Chicago, Chicago IL 60607, USA
| | - Ramesh Prasad
- Department of Chemistry, University of Illinois Chicago, Chicago IL 60607, USA
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago IL 60607, USA
- Department of Physics, University of Illinois Chicago, Chicago IL 60607, USA
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33
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Chou HY, Aksimentiev A. RNA regulates cohesiveness and porosity of a biological condensate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574811. [PMID: 38260307 PMCID: PMC10802450 DOI: 10.1101/2024.01.09.574811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Biological condensates have emerged as key elements of a biological cell function, concentrating disparate biomolecules to accomplish specific biological tasks. RNA was identified as a key ingredient of such condensates, however, its effect on the physical properties of the condensate was found to depend on the condensate's composition while its effect on the microstructure has remained elusive. Here, we characterize the physical properties and the microstructure of a protein-RNA condensate by means of large-scale coarse-grained (CG) molecular dynamics simulations. By developing a custom CG model of RNA compatible with a popular CG model of proteins, we systematically investigate the structural, thermodynamic, and kinetic properties of condensate droplets containing thousands of individual protein and RNA molecules over a range of temperatures. While we find RNA to increase the condensate's cohesiveness, its effect on the condensate's fluidity is more nuanced with longer molecules compacting the condensate and making it less fluid. We show that a biological condensate has a sponge-like morphology of interconnected channels of size that increases with temperature and decreases in the presence of RNA. Our results suggest that longer RNA form a dynamic scaffold within a condensate, regulating not only its fluidity but also permeability to intruder molecules.
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34
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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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35
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Lebedenko OO, Salikov VA, Izmailov SA, Podkorytov IS, Skrynnikov NR. Using NMR diffusion data to validate MD models of disordered proteins: Test case of N-terminal tail of histone H4. Biophys J 2024; 123:80-100. [PMID: 37990496 PMCID: PMC10808029 DOI: 10.1016/j.bpj.2023.11.020] [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: 08/07/2023] [Revised: 10/28/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023] Open
Abstract
MD simulations can provide uniquely detailed models of intrinsically disordered proteins (IDPs). However, these models need careful experimental validation. The coefficient of translational diffusion Dtr, measurable by pulsed field gradient NMR, offers a potentially useful piece of experimental information related to the compactness of the IDP's conformational ensemble. Here, we investigate, both experimentally and via the MD modeling, the translational diffusion of a 25-residue N-terminal fragment from histone H4 (N-H4). We found that the predicted values of Dtr, as obtained from mean-square displacement of the peptide in the MD simulations, are largely determined by the viscosity of the MD water (which has been reinvestigated as a part of our study). Beyond that, our analysis of the diffusion data indicates that MD simulations of N-H4 in the TIP4P-Ew water give rise to an overly compact conformational ensemble for this peptide. In contrast, TIP4P-D and OPC simulations produce the ensembles that are consistent with the experimental Dtr result. These observations are supported by the analyses of the 15N spin relaxation rates. We also tested a number of empirical methods to predict Dtr based on IDP's coordinates extracted from the MD snapshots. In particular, we show that the popular approach involving the program HYDROPRO can produce misleading results. This happens because HYDROPRO is not intended to predict the diffusion properties of highly flexible biopolymers such as IDPs. Likewise, recent empirical schemes that exploit the relationship between the small-angle x-ray scattering-informed conformational ensembles of IDPs and the respective experimental Dtr values also prove to be problematic. In this sense, the first-principle calculations of Dtr from the MD simulations, such as demonstrated in this work, should provide a useful benchmark for future efforts in this area.
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Affiliation(s)
- Olga O Lebedenko
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, Russia
| | - Vladislav A Salikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, Russia
| | - Sergei A Izmailov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, Russia
| | - Ivan S Podkorytov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, Russia
| | - Nikolai R Skrynnikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, Russia; Department of Chemistry, Purdue University, West Lafayette, Indiana.
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Vancraenenbroeck R, Hofmann H. Electrostatics and hydrophobicity in the dynamics of intrinsically disordered proteins. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:133. [PMID: 38127117 PMCID: PMC10739388 DOI: 10.1140/epje/s10189-023-00383-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023]
Abstract
Internal friction is a major contribution to the dynamics of intrinsically disordered proteins (IDPs). Yet, the molecular origin of internal friction has so far been elusive. Here, we investigate whether attractive electrostatic interactions in IDPs modulate internal friction differently than the hydrophobic effect. To this end, we used nanosecond fluorescence correlation spectroscopy (nsFCS) and single-molecule Förster resonance energy transfer (FRET) to quantify the conformation and dynamics of the disordered DNA-binding domains Myc, Max and Mad at different salt concentrations. We find that internal friction effects are stronger when the chain is compacted by electrostatic attractions compared to the hydrophobic effect. Although the effect is moderate, the results show that the heteropolymeric nature of IDPs is reflected in their dynamics.
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Affiliation(s)
- Renee Vancraenenbroeck
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Herzl St. 234, 76100, Rehovot, Israel
- Present Address: Department of Structural and Molecular Biology, University College London, Darwin Building, 107 Gower Street, London, WC1E 6BT, UK
| | - Hagen Hofmann
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Herzl St. 234, 76100, Rehovot, Israel.
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37
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Mooren OL, Stuchell-Brereton MD, McConnell P, Yan C, Wilkerson EM, Goldfarb D, Cooper JA, Sept D, Soranno A. Biophysical Mechanism of Allosteric Regulation of Actin Capping Protein. J Mol Biol 2023; 435:168342. [PMID: 37924863 PMCID: PMC10872493 DOI: 10.1016/j.jmb.2023.168342] [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: 08/13/2023] [Revised: 10/28/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023]
Abstract
Actin capping protein (CP) can be regulated by steric and allosteric mechanisms. The molecular mechanism of the allosteric regulation at a biophysical level includes linkage between the binding sites for three ligands: F-actin, Capping-Protein-Interacting (CPI) motifs, and V-1/myotrophin, based on biochemical functional studies and solvent accessibility experiments. Here, we investigated the mechanism of allosteric regulation at the atomic level using single-molecule Förster resonance energy transfer (FRET) and molecular dynamics (MD) to assess the conformational and structural dynamics of CP in response to linked-binding site ligands. In the absence of ligand, both single-molecule FRET and MD revealed two distinct conformations of CP in solution; previous crystallographic studies revealed only one. Interaction with CPI-motif peptides induced conformations within CP that bring the cap and stalk closer, while interaction with V-1 moves them away from one another. Comparing CPI-motif peptides from different proteins, we identified variations in CP conformations and dynamics that are specific to each CPI motif. MD simulations for CP alone and in complex with a CPI motif and V-1 reveal atomistic details of the conformational changes. Analysis of the interaction of CP with wild-type (wt) and chimeric CPI-motif peptides using single-molecule FRET, isothermal calorimetry (ITC) and MD simulation indicated that conformational and affinity differences are intrinsic to the C-terminal portion of the CPI motif. We conclude that allosteric regulation of CP involves changes in conformation that disseminate across the protein to link distinct binding-site functions. Our results provide novel insights into the biophysical mechanism of the allosteric regulation of CP.
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Affiliation(s)
- Olivia L Mooren
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, United States
| | - Melissa D Stuchell-Brereton
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, United States; Center for Biomolecular Condensates, Washington University in St Louis, St. Louis, MO, United States
| | - Patrick McConnell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, United States
| | - Chenbo Yan
- Department of Biophysics, University of Michigan, Ann Arbor, MI, United States
| | - Emily M Wilkerson
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States; Institute for Informatics, Washington University School of Medicine, St. Louis, MO, United States
| | - Dennis Goldfarb
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States; Institute for Informatics, Washington University School of Medicine, St. Louis, MO, United States
| | - John A Cooper
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, United States.
| | - David Sept
- Department of Biophysics, University of Michigan, Ann Arbor, MI, United States; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States.
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, United States; Center for Biomolecular Condensates, Washington University in St Louis, St. Louis, MO, United States.
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38
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Fenton M, Gregory E, Daughdrill G. Protein disorder and autoinhibition: The role of multivalency and effective concentration. Curr Opin Struct Biol 2023; 83:102705. [PMID: 37778184 PMCID: PMC10841074 DOI: 10.1016/j.sbi.2023.102705] [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: 07/15/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023]
Abstract
Regulation of protein binding through autoinhibition commonly occurs via interactions involving intrinsically disordered regions (IDRs). These intramolecular interactions can directly or allosterically inhibit intermolecular protein or DNA binding, regulate enzymatic activity, and control the assembly of large macromolecular complexes. Autoinhibitory interactions mediated by protein disorder are inherently transient, making their identification and characterization challenging. In this review, we explore the structural and functional diversity of disorder-mediated autoinhibition for a variety of biological mechanisms, with a focus on the role of multivalency and effective concentration. We also discuss the evolution of disordered motifs that participate in autoinhibition using examples where sequence conservation varies from high to low. In some cases, identifiable motifs that are essential for autoinhibition remain intact within a rapidly evolving sequence, over long evolutionary distances. Finally, we examine the potential of AlphaFold2 to predict autoinhibitory intramolecular interactions involving IDRs.
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Affiliation(s)
- Malissa Fenton
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Emily Gregory
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Gary Daughdrill
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
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39
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Skriver K, Theisen FF, Kragelund BB. Conformational entropy in molecular recognition of intrinsically disordered proteins. Curr Opin Struct Biol 2023; 83:102697. [PMID: 37716093 DOI: 10.1016/j.sbi.2023.102697] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 09/18/2023]
Abstract
Broad conformational ensembles make intrinsically disordered proteins or regions entropically intriguing. Although methodologically challenging and understudied, emerging studies into their changes in conformational entropy (ΔS°conf) upon complex formation have provided both quantitative and qualitative insight. Recent work based on thermodynamics from isothermal titration calorimetry and NMR spectroscopy uncovers an expanded repertoire of regulatory mechanisms, where ΔS°conf plays roles in partner selection, state behavior, functional buffering, allosteric regulation, and drug design. We highlight these mechanisms to display the large entropic reservoir of IDPs for the regulation of molecular communication. We call upon the field to make efforts to contribute to this insight as more studies are needed for forwarding mechanistic decoding of intrinsically disordered proteins and their complexes.
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Affiliation(s)
- Karen Skriver
- The Linderstrøm Lang Centre for Protein Science, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark; REPIN, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Frederik Friis Theisen
- The Linderstrøm Lang Centre for Protein Science, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark; REPIN, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark. https://twitter.com/@FrederikTheisen
| | - Birthe B Kragelund
- The Linderstrøm Lang Centre for Protein Science, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark; REPIN, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark.
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40
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Hofmann H. All over or overall - Do we understand allostery? Curr Opin Struct Biol 2023; 83:102724. [PMID: 37898005 DOI: 10.1016/j.sbi.2023.102724] [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: 07/20/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/30/2023]
Abstract
Allostery is probably the most important concept in the regulation of cellular processes. Models to explain allostery are plenty. Each sheds light on different aspects but their entirety conveys an ambiguous feeling of comprehension and disappointment. Here, I discuss the most popular allostery models, their roots, similarities, and limitations. All of them are thermodynamic models. Naturally this bears a certain degree of redundancy, which forms the center of this review. After sixty years, many questions remain unanswered, mainly because our human longing for causality as base for understanding is not satisfied by thermodynamics alone. A description of allostery in terms of pathways, i.e., as a temporal chain of events, has been-, and still is-, a missing piece of the puzzle.
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Affiliation(s)
- Hagen Hofmann
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Herzl St. 234, 76100 Rehovot, Israel.
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41
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Uversky VN. Functional unfoldomics: Roles of intrinsic disorder in protein (multi)functionality. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:179-210. [PMID: 38220424 DOI: 10.1016/bs.apcsb.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Intrinsically disordered proteins (IDPs), which are functional proteins without stable tertiary structure, and hybrid proteins containing ordered domains and intrinsically disordered regions (IDRs) constitute prominent parts of all proteomes collectively known as unfoldomes. IDPs/IDRs exist as highly dynamic structural ensembles of rapidly interconverting conformations and are characterized by the exceptional structural heterogeneity, where their different parts are (dis)ordered to different degree, and their overall structure represents a complex mosaic of foldons, inducible foldons, inducible morphing foldons, non-foldons, semifoldons, and even unfoldons. Despite their lack of unique 3D structures, IDPs/IDRs play crucial roles in the control of various biological processes and the regulation of different cellular pathways and are commonly involved in recognition and signaling, indicating that the disorder-based functional repertoire is complementary to the functions of ordered proteins. Furthermore, IDPs/IDRs are frequently multifunctional, and this multifunctionality is defined by their structural flexibility and heterogeneity. Intrinsic disorder phenomenon is at the roots of the structure-function continuum model, where the structure continuum is defined by the presence of differently (dis)ordered regions, and the function continuum arises from the ability of all these differently (dis)ordered parts to have different functions. In their everyday life, IDPs/IDRs utilize a broad spectrum of interaction mechanisms thereby acting as interaction specialists. They are crucial for the biogenesis of numerous proteinaceous membrane-less organelles driven by the liquid-liquid phase separation. This review introduces functional unfoldomics by representing some aspects of the intrinsic disorder-based functionality.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
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42
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Yang J, Cheng WX, Wu G, Sheng S, Zhang P. Prediction of folding patterns for intrinsic disordered protein. Sci Rep 2023; 13:20343. [PMID: 37990040 PMCID: PMC10663623 DOI: 10.1038/s41598-023-45969-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/26/2023] [Indexed: 11/23/2023] Open
Abstract
The conformation flexibility of natural protein causes both complexity and difficulty to understand the relationship between structure and function. The prediction of intrinsically disordered protein primarily is focusing on to disclose the regions with structural flexibility involving relevant biological functions and various diseases. The order of amino acids in protein sequence determines possible conformations, folding flexibility and biological function. Although many methods provided the information of intrinsically disordered protein (IDP), but the results are mainly limited to determine the locations of regions without knowledge of possible folding conformations. Here, the developed protein folding fingerprint adopted the protein folding variation matrix (PFVM) to reveal all possible folding patterns for the intrinsically disordered protein along its sequence. The PFVM integrally exhibited the intrinsically disordered protein with disordering regions, degree of disorder as well as folding pattern. The advantage of PFVM will not only provide rich information for IDP, but also may promote the study of protein folding problem.
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Affiliation(s)
- Jiaan Yang
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, Guangdong, China.
- Micro Biotech, Ltd., Shanghai, 200123, China.
| | - Wen-Xiang Cheng
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, Guangdong, China
| | - Gang Wu
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Sitong Sheng
- HYK High-throughput Biotechnology Institute, Shenzhen, 518057, Guangdong, China
| | - Peng Zhang
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, Guangdong, China
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43
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Schedler B, Yukhnovets O, Lindner L, Meyer A, Fitter J. The Thermodynamic Fingerprints of Ultra-Tight Nanobody-Antigen Binding Probed via Two-Color Single-Molecule Coincidence Detection. Int J Mol Sci 2023; 24:16379. [PMID: 38003569 PMCID: PMC10671529 DOI: 10.3390/ijms242216379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Life on the molecular scale is based on a versatile interplay of biomolecules, a feature that is relevant for the formation of macromolecular complexes. Fluorescence-based two-color coincidence detection is widely used to characterize molecular binding and was recently improved by a brightness-gated version which gives more accurate results. We developed and established protocols which make use of coincidence detection to quantify binding fractions between interaction partners labeled with fluorescence dyes of different colors. Since the applied technique is intrinsically related to single-molecule detection, the concentration of diffusing molecules for confocal detection is typically in the low picomolar regime. This makes the approach a powerful tool for determining bi-molecular binding affinities, in terms of KD values, in this regime. We demonstrated the reliability of our approach by analyzing very strong nanobody-EGFP binding. By measuring the affinity at different temperatures, we were able to determine the thermodynamic parameters of the binding interaction. The results show that the ultra-tight binding is dominated by entropic contributions.
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Affiliation(s)
- Benno Schedler
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
| | - Olessya Yukhnovets
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
| | - Lennart Lindner
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
| | - Alida Meyer
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
| | - Jörg Fitter
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
- ER-C-3 Structural Biology & IBI-6 Cellular Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
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44
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Shukla VK, Heller GT, Hansen DF. Biomolecular NMR spectroscopy in the era of artificial intelligence. Structure 2023; 31:1360-1374. [PMID: 37848030 DOI: 10.1016/j.str.2023.09.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/19/2023]
Abstract
Biomolecular nuclear magnetic resonance (NMR) spectroscopy and artificial intelligence (AI) have a burgeoning synergy. Deep learning-based structural predictors have forever changed structural biology, yet these tools currently face limitations in accurately characterizing protein dynamics, allostery, and conformational heterogeneity. We begin by highlighting the unique abilities of biomolecular NMR spectroscopy to complement AI-based structural predictions toward addressing these knowledge gaps. We then highlight the direct integration of deep learning approaches into biomolecular NMR methods. AI-based tools can dramatically improve the acquisition and analysis of NMR spectra, enhancing the accuracy and reliability of NMR measurements, thus streamlining experimental processes. Additionally, deep learning enables the development of novel types of NMR experiments that were previously unattainable, expanding the scope and potential of biomolecular NMR spectroscopy. Ultimately, a combination of AI and NMR promises to further revolutionize structural biology on several levels, advance our understanding of complex biomolecular systems, and accelerate drug discovery efforts.
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Affiliation(s)
- Vaibhav Kumar Shukla
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Gabriella T Heller
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK.
| | - D Flemming Hansen
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK.
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45
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Alderson TR, Pritišanac I, Kolarić Đ, Moses AM, Forman-Kay JD. Systematic identification of conditionally folded intrinsically disordered regions by AlphaFold2. Proc Natl Acad Sci U S A 2023; 120:e2304302120. [PMID: 37878721 PMCID: PMC10622901 DOI: 10.1073/pnas.2304302120] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 08/30/2023] [Indexed: 10/27/2023] Open
Abstract
The AlphaFold Protein Structure Database contains predicted structures for millions of proteins. For the majority of human proteins that contain intrinsically disordered regions (IDRs), which do not adopt a stable structure, it is generally assumed that these regions have low AlphaFold2 confidence scores that reflect low-confidence structural predictions. Here, we show that AlphaFold2 assigns confident structures to nearly 15% of human IDRs. By comparison to experimental NMR data for a subset of IDRs that are known to conditionally fold (i.e., upon binding or under other specific conditions), we find that AlphaFold2 often predicts the structure of the conditionally folded state. Based on databases of IDRs that are known to conditionally fold, we estimate that AlphaFold2 can identify conditionally folding IDRs at a precision as high as 88% at a 10% false positive rate, which is remarkable considering that conditionally folded IDR structures were minimally represented in its training data. We find that human disease mutations are nearly fivefold enriched in conditionally folded IDRs over IDRs in general and that up to 80% of IDRs in prokaryotes are predicted to conditionally fold, compared to less than 20% of eukaryotic IDRs. These results indicate that a large majority of IDRs in the proteomes of human and other eukaryotes function in the absence of conditional folding, but the regions that do acquire folds are more sensitive to mutations. We emphasize that the AlphaFold2 predictions do not reveal functionally relevant structural plasticity within IDRs and cannot offer realistic ensemble representations of conditionally folded IDRs.
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Affiliation(s)
- T. Reid Alderson
- Department of Biochemistry, University of Toronto, Toronto, ONM5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ONM5S 1A8, Canada
| | - Iva Pritišanac
- Department of Cell and Systems Biology, University of Toronto, Toronto, ONM5S 35G, Canada
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ONM5G 0A4, Canada
- Department of Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz8010, Austria
| | - Đesika Kolarić
- Department of Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz8010, Austria
| | - Alan M. Moses
- Department of Cell and Systems Biology, University of Toronto, Toronto, ONM5S 35G, Canada
| | - Julie D. Forman-Kay
- Department of Biochemistry, University of Toronto, Toronto, ONM5S 1A8, Canada
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ONM5G 0A4, Canada
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46
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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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47
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Chowdhury A, Borgia A, Ghosh S, Sottini A, Mitra S, Eapen RS, Borgia MB, Yang T, Galvanetto N, Ivanović MT, Łukijańczuk P, Zhu R, Nettels D, Kundagrami A, Schuler B. Driving forces of the complex formation between highly charged disordered proteins. Proc Natl Acad Sci U S A 2023; 120:e2304036120. [PMID: 37796987 PMCID: PMC10576128 DOI: 10.1073/pnas.2304036120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/22/2023] [Indexed: 10/07/2023] Open
Abstract
Highly disordered complexes between oppositely charged intrinsically disordered proteins present a new paradigm of biomolecular interactions. Here, we investigate the driving forces of such interactions for the example of the highly positively charged linker histone H1 and its highly negatively charged chaperone, prothymosin α (ProTα). Temperature-dependent single-molecule Förster resonance energy transfer (FRET) experiments and isothermal titration calorimetry reveal ProTα-H1 binding to be enthalpically unfavorable, and salt-dependent affinity measurements suggest counterion release entropy to be an important thermodynamic driving force. Using single-molecule FRET, we also identify ternary complexes between ProTα and H1 in addition to the heterodimer at equilibrium and show how they contribute to the thermodynamics observed in ensemble experiments. Finally, we explain the observed thermodynamics quantitatively with a mean-field polyelectrolyte theory that treats counterion release explicitly. ProTα-H1 complex formation resembles the interactions between synthetic polyelectrolytes, and the underlying principles are likely to be of broad relevance for interactions between charged biomolecules in general.
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Affiliation(s)
- Aritra Chowdhury
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Alessandro Borgia
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Souradeep Ghosh
- Department of Physical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur741246, India
| | - Andrea Sottini
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Soumik Mitra
- Department of Physical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur741246, India
| | - Rohan S. Eapen
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | | | - Tianjin Yang
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Nicola Galvanetto
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
- Department of Physics, University of Zurich, Zurich8057, Switzerland
| | - Miloš T. Ivanović
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Paweł Łukijańczuk
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Ruijing Zhu
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
| | - Arindam Kundagrami
- Department of Physical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur741246, India
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich8057, Switzerland
- Department of Physics, University of Zurich, Zurich8057, Switzerland
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48
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Białobrzewski MK, Klepka BP, Michaś A, Cieplak-Rotowska MK, Staszałek Z, Niedźwiecka A. Diversity of hydrodynamic radii of intrinsically disordered proteins. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:607-618. [PMID: 37831084 PMCID: PMC10618399 DOI: 10.1007/s00249-023-01683-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/08/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023]
Abstract
Intrinsically disordered proteins (IDPs) form an important class of biomolecules regulating biological processes in higher organisms. The lack of a fixed spatial structure facilitates them to perform their regulatory functions and allows the efficiency of biochemical reactions to be controlled by temperature and the cellular environment. From the biophysical point of view, IDPs are biopolymers with a broad configuration state space and their actual conformation depends on non-covalent interactions of its amino acid side chain groups at given temperature and chemical conditions. Thus, the hydrodynamic radius (Rh) of an IDP of a given polymer length (N) is a sequence- and environment-dependent variable. We have reviewed the literature values of hydrodynamic radii of IDPs determined experimentally by SEC, AUC, PFG NMR, DLS, and FCS, and complement them with our FCS results obtained for a series of protein fragments involved in the regulation of human gene expression. The data collected herein show that the values of hydrodynamic radii of IDPs can span the full space between the folded globular and denatured proteins in the Rh(N) diagram.
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Affiliation(s)
- Michał K Białobrzewski
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland
| | - Barbara P Klepka
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland
| | - Agnieszka Michaś
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland
| | - Maja K Cieplak-Rotowska
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, PL-02093, Warsaw, Poland
- The International Institute of Molecular Mechanisms and Machines, Polish Academy of Sciences, Flisa 6, PL-02247, Warsaw, Poland
| | - Zuzanna Staszałek
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland
| | - Anna Niedźwiecka
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland.
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49
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Negri ML, D'Annunzio S, Vitali G, Zippo A. May the force be with you: Nuclear condensates function beyond transcription control: Potential nongenetic functions of nuclear condensates in physiological and pathological conditions. Bioessays 2023; 45:e2300075. [PMID: 37530178 DOI: 10.1002/bies.202300075] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/03/2023] [Accepted: 07/13/2023] [Indexed: 08/03/2023]
Abstract
Over the past decade, research has revealed biomolecular condensates' relevance in diverse cellular functions. Through a phase separation process, they concentrate macromolecules in subcompartments shaping the cellular organization and physiology. In the nucleus, biomolecular condensates assemble relevant biomolecules that orchestrate gene expression. We here hypothesize that chromatin condensates can also modulate the nongenetic functions of the genome, including the nuclear mechanical properties. The importance of chromatin condensates is supported by the genetic evidence indicating that mutations in their members are causative of a group of rare Mendelian diseases named chromatinopathies (CPs). Despite a broad spectrum of clinical features and the perturbations of the epigenetic machinery characterizing the CPs, recent findings highlighted negligible changes in gene expression. These data argue in favor of possible noncanonical functions of chromatin condensates in regulating the genome's spatial organization and, consequently, the nuclear mechanics. In this review, we discuss how condensates may impact nuclear mechanical properties, thus affecting the cellular response to mechanical cues and, eventually, cell fate and identity. Chromatin condensates organize macromolecules in the nucleus orchestrating the transcription regulation and mutations in their members are responsible for rare diseases named chromatinopathies. We argue that chromatin condensates, in concert with the nuclear lamina, may also govern the nuclear mechanical properties affecting the cellular response to external cues.
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Affiliation(s)
- Maria Luce Negri
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Sarah D'Annunzio
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Giulia Vitali
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessio Zippo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
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50
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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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