1
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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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2
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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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3
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Zavrtanik U, Medved T, Purič S, Vranken W, Lah J, Hadži S. Leucine Motifs Stabilize Residual Helical Structure in Disordered Proteins. J Mol Biol 2024; 436:168444. [PMID: 38218366 DOI: 10.1016/j.jmb.2024.168444] [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: 12/03/2023] [Revised: 12/31/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
Many examples are known of regions of intrinsically disordered proteins that fold into α-helices upon binding to their targets. These helical binding motifs (HBMs) can be partially helical also in the unbound state, and this so-called residual structure can affect binding affinity and kinetics. To investigate the underlying mechanisms governing the formation of residual helical structure, we assembled a dataset of experimental helix contents of 65 peptides containing HBM that fold-upon-binding. The average residual helicity is 17% and increases to 60% upon target binding. The helix contents of residual and target-bound structures do not correlate, however the relative location of helix elements in both states shows a strong overlap. Compared to the general disordered regions, HBMs are enriched in amino acids with high helix preference and these residues are typically involved in target binding, explaining the overlap in helix positions. In particular, we find that leucine residues and leucine motifs in HBMs are the major contributors to helix stabilization and target-binding. For the two model peptides, we show that substitution of leucine motifs to other hydrophobic residues (valine or isoleucine) leads to reduction of residual helicity, supporting the role of leucine as helix stabilizer. From the three hydrophobic residues only leucine can efficiently stabilize residual helical structure. We suggest that the high occurrence of leucine motifs and a general preference for leucine at binding interfaces in HBMs can be explained by its unique ability to stabilize helical elements.
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Affiliation(s)
- Uroš Zavrtanik
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tadej Medved
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Samo Purič
- Graduate Study Program, Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Wim Vranken
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Interuniversity Institute of Bioinformatics in Brussels, ULB/VUB, Triomflaan, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium; VIB Structural Biology Research Centre, Brussels 1050, Belgium
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - San Hadži
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia.
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4
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Tesei G, Trolle AI, Jonsson N, Betz J, Knudsen FE, Pesce F, Johansson KE, Lindorff-Larsen K. Conformational ensembles of the human intrinsically disordered proteome. Nature 2024; 626:897-904. [PMID: 38297118 DOI: 10.1038/s41586-023-07004-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/19/2023] [Indexed: 02/02/2024]
Abstract
Intrinsically disordered proteins and regions (collectively, IDRs) are pervasive across proteomes in all kingdoms of life, help to shape biological functions and are involved in numerous diseases. IDRs populate a diverse set of transiently formed structures and defy conventional sequence-structure-function relationships1. Developments in protein science have made it possible to predict the three-dimensional structures of folded proteins at the proteome scale2. By contrast, there is a lack of knowledge about the conformational properties of IDRs, partly because the sequences of disordered proteins are poorly conserved and also because only a few of these proteins have been characterized experimentally. The inability to predict structural properties of IDRs across the proteome has limited our understanding of the functional roles of IDRs and how evolution shapes them. As a supplement to previous structural studies of individual IDRs3, we developed an efficient molecular model to generate conformational ensembles of IDRs and thereby to predict their conformational properties from sequences4,5. Here we use this model to simulate nearly all of the IDRs in the human proteome. Examining conformational ensembles of 28,058 IDRs, we show how chain compaction is correlated with cellular function and localization. We provide insights into how sequence features relate to chain compaction and, using a machine-learning model trained on our simulation data, show the conservation of conformational properties across orthologues. Our results recapitulate observations from previous studies of individual protein systems and exemplify how to link-at the proteome scale-conformational ensembles with cellular function and localization, amino acid sequence, evolutionary conservation and disease variants. Our freely available database of conformational properties will encourage further experimental investigation and enable the generation of hypotheses about the biological roles and evolution of IDRs.
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Affiliation(s)
- Giulio Tesei
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Anna Ida Trolle
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Nicolas Jonsson
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Johannes Betz
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Frederik E Knudsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Francesco Pesce
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer E Johansson
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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5
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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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6
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Madhurima K, Nandi B, Munshi S, Naganathan AN, Sekhar A. Functional regulation of an intrinsically disordered protein via a conformationally excited state. SCIENCE ADVANCES 2023; 9:eadh4591. [PMID: 37379390 PMCID: PMC10306299 DOI: 10.1126/sciadv.adh4591] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 05/23/2023] [Indexed: 06/30/2023]
Abstract
A longstanding goal in the field of intrinsically disordered proteins (IDPs) is to characterize their structural heterogeneity and pinpoint the role of this heterogeneity in IDP function. Here, we use multinuclear chemical exchange saturation (CEST) nuclear magnetic resonance to determine the structure of a thermally accessible globally folded excited state in equilibrium with the intrinsically disordered native ensemble of a bacterial transcriptional regulator CytR. We further provide evidence from double resonance CEST experiments that the excited state, which structurally resembles the DNA-bound form of cytidine repressor (CytR), recognizes DNA by means of a "folding-before-binding" conformational selection pathway. The disorder-to-order regulatory switch in DNA recognition by natively disordered CytR therefore operates through a dynamical variant of the lock-and-key mechanism where the structurally complementary conformation is transiently accessed via thermal fluctuations.
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Affiliation(s)
- Kulkarni Madhurima
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, Bengaluru 560 012, India
| | - Bodhisatwa Nandi
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, Bengaluru 560 012, India
| | - Sneha Munshi
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Athi N. Naganathan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Ashok Sekhar
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, Bengaluru 560 012, India
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7
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Williamson MP. Protein Binding: A Fuzzy Concept. Life (Basel) 2023; 13:life13040855. [PMID: 37109384 PMCID: PMC10145316 DOI: 10.3390/life13040855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/16/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Our understanding of protein binding interactions has matured significantly over the last few years, largely as a result of trying to make sense of the binding interactions of intrinsically disordered proteins. Here, we bring together some disparate ideas that have largely developed independently, and show that they can be linked into a coherent picture that provides insight into quantitative aspects of protein interactions, in particular that transient protein interactions are often optimised for speed, rather than tight binding.
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Affiliation(s)
- Mike P Williamson
- School of Biosciences, University of Sheffield, Firth Court, Sheffield S10 2TN, UK
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8
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Thole JF, Waudby CA, Pielak GJ. Disordered proteins mitigate the temperature dependence of site-specific binding free energies. J Biol Chem 2023; 299:102984. [PMID: 36739945 PMCID: PMC10027511 DOI: 10.1016/j.jbc.2023.102984] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/12/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Biophysical characterization of protein-protein interactions involving disordered proteins is challenging. A common simplification is to measure the thermodynamics and kinetics of disordered site binding using peptides containing only the minimum residues necessary. We should not assume, however, that these few residues tell the whole story. Son of sevenless, a multidomain signaling protein from Drosophila melanogaster, is critical to the mitogen-activated protein kinase pathway, passing an external signal to Ras, which leads to cellular responses. The disordered 55 kDa C-terminal domain of Son of sevenless is an autoinhibitor that blocks guanidine exchange factor activity. Activation requires another protein, Downstream of receptor kinase (Drk), which contains two Src homology 3 domains. Here, we utilized NMR spectroscopy and isothermal titration calorimetry to quantify the thermodynamics and kinetics of the N-terminal Src homology 3 domain binding to the strongest sites incorporated into the flanking disordered sequences. Comparing these results to those for isolated peptides provides information about how the larger domain affects binding. The affinities of sites on the disordered domain are like those of the peptides at low temperatures but less sensitive to temperature. Our results, combined with observations showing that intrinsically disordered proteins become more compact with increasing temperature, suggest a mechanism for this effect.
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Affiliation(s)
- Joseph F Thole
- Department of Chemistry, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Molecular and Cellular Biophysics Program, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Gary J Pielak
- Department of Chemistry, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Molecular and Cellular Biophysics Program, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Department of Biochemistry & Biophysics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Lineberger Cancer Center, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Integrative Program for Biological and Genome Sciences, UNC - Chapel Hill, Chapel Hill, North Carolina, USA.
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9
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Payliss BJ, Tse YWE, Reichheld SE, Lemak A, Yun HY, Houliston S, Patel A, Arrowsmith CH, Sharpe S, Wyatt HD. Phosphorylation of the DNA repair scaffold SLX4 drives folding of the SAP domain and activation of the MUS81-EME1 endonuclease. Cell Rep 2022; 41:111537. [DOI: 10.1016/j.celrep.2022.111537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/11/2022] [Accepted: 09/29/2022] [Indexed: 11/03/2022] Open
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10
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Villegas JA, Levy ED. A unified statistical potential reveals that amino acid stickiness governs nonspecific recruitment of client proteins into condensates. Protein Sci 2022; 31:e4361. [PMID: 35762716 PMCID: PMC9207749 DOI: 10.1002/pro.4361] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 11/07/2022]
Abstract
Membraneless organelles are cellular compartments that form by liquid-liquid phase separation of one or more components. Other molecules, such as proteins and nucleic acids, will distribute between the cytoplasm and the liquid compartment in accordance with the thermodynamic drive to lower the free energy of the system. The resulting distribution colocalizes molecular species to carry out a diversity of functions. Two factors could drive this partitioning: the difference in solvation between the dilute versus dense phase and intermolecular interactions between the client and scaffold proteins. Here, we develop a set of knowledge-based potentials that allow for the direct comparison between stickiness, which is dominated by desolvation energy, and pairwise residue contact propensity terms. We use these scales to examine experimental data from two systems: protein cargo dissolving within phase-separated droplets made from FG repeat proteins of the nuclear pore complex and client proteins dissolving within phase-separated FUS droplets. These analyses reveal a close agreement between the stickiness of the client proteins and the experimentally determined values of the partition coefficients (R > 0.9), while pairwise residue contact propensities between client and scaffold show weaker correlations. Hence, the stickiness of client proteins is sufficient to explain their differential partitioning within these two phase-separated systems without taking into account the composition of the condensate. This result implies that selective trafficking of client proteins to distinct membraneless organelles requires recognition elements beyond the client sequence composition. STATEMENT: Empirical potentials for amino acid stickiness and pairwise residue contact propensities are derived. These scales are unique in that they enable direct comparison of desolvation versus contact terms. We find that partitioning of a client protein to a condensate is best explained by amino acid stickiness.
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Affiliation(s)
- José A. Villegas
- Department of Chemical and Structural BiologyWeizmann Institute of ScienceRehovotIsrael
- Present address:
Department of Pharmaceutical SciencesCollege of Pharmacy, University of Illinois ChicagoChicagoIL60612
| | - Emmanuel D. Levy
- Department of Chemical and Structural BiologyWeizmann Institute of ScienceRehovotIsrael
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11
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Affinity of disordered protein complexes is modulated by entropy-energy reinforcement. Proc Natl Acad Sci U S A 2022; 119:e2120456119. [PMID: 35727975 PMCID: PMC9245678 DOI: 10.1073/pnas.2120456119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Intrinsically disordered proteins (IDPs), which are very common and essential to many biological activities, sometimes function via interaction with another IDP and form a fuzzy complex, which can be highly stable. It is unclear what the biophysical forces are that govern their thermodynamics and specificity, which are essential for de novo fuzzy complex design. Here, we explored the fuzzy complex formed between ProTα and H1, which are oppositely charged IDPs, by swapping the charges between them, generating variants that have either greater polyampholytic or polyelectrolytic nature as well as different charge patterns. Charge swapping and shuffling dramatically change the affinity of the fuzzy complex, which is contributed to by both enthalpy and entropy, where the latter is dominated by counterion release. The association between two intrinsically disordered proteins (IDPs) may produce a fuzzy complex characterized by a high binding affinity, similar to that found in the ultrastable complexes formed between two well-structured proteins. Here, using coarse-grained simulations, we quantified the biophysical forces driving the formation of such fuzzy complexes. We found that the high-affinity complex formed between the highly and oppositely charged H1 and ProTα proteins is sensitive to electrostatic interactions. We investigated 52 variants of the complex by swapping charges between the two oppositely charged proteins to produce sequences whose negatively or positively charged residue content was more homogeneous or heterogenous (i.e., polyelectrolytic or polyampholytic, having higher or lower absolute net charges, respectively) than the wild type. We also changed the distributions of oppositely charged residues within each participating sequence to produce variants in which the charges were segregated or well mixed. Both types of changes significantly affect binding affinity in fuzzy complexes, which is governed by both enthalpy and entropy. The formation of H1–ProTa is supported by an increase in configurational entropy and by entropy due to counterion release. The latter can be twice as large as the former, illustrating the dominance of counterion entropy in modulating the binding thermodynamics. Complexes formed between proteins with greater absolute net charges are more stable, both enthalpically and entropically, indicating that enthalpy and entropy have a mutually reinforcing effect. The sensitivity of the thermodynamics of the complex to net charge and the charge pattern within each of the binding constituents may provide a means to achieve binding specificity between IDPs.
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12
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Zavrtanik U, Hadži S, Lah J. Unraveling the Thermodynamics of Ultra-tight Binding of Intrinsically Disordered Proteins. Front Mol Biosci 2021; 8:726824. [PMID: 34532345 PMCID: PMC8438204 DOI: 10.3389/fmolb.2021.726824] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/20/2021] [Indexed: 01/08/2023] Open
Abstract
Protein interactions mediated by the intrinsically disordered proteins (IDPs) are generally associated with lower affinities compared to those between globular proteins. Here, we characterize the association between the intrinsically disordered HigA2 antitoxin and its globular target HigB2 toxin from Vibrio cholerae using competition ITC experiments. We demonstrate that this interaction reaches one of the highest affinities reported for IDP-target systems (KD = 3 pM) and can be entirely attributed to a short, 20-residue-long interaction motif that folds into α-helix upon binding. We perform an experimentally based decomposition of the IDP-target association parameters into folding and binding contributions, which allows a direct comparison of the binding contribution with those from globular ultra-high affinity binders. We find that the HigA2-HigB2 interface is energy optimized to a similar extent as the interfaces of globular ultra-high affinity complexes, such as barnase-barstar. Evaluation of other ultra-high affinity IDP-target systems shows that a strategy based on entropy optimization can also achieve comparably high, picomolar affinities. Taken together, these examples show how IDP-target interactions achieve picomolar affinities either through enthalpy optimization (HigA2-HigB2), resembling the ultra-high affinity binding of globular proteins, or via bound-state fuzziness and entropy optimization (CcdA-CcdB, histone H1-prothymosin α).
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Affiliation(s)
- Uroš Zavrtanik
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - San Hadži
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
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13
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Enthalpy-Entropy Compensation in the Promiscuous Interaction of an Intrinsically Disordered Protein with Homologous Protein Partners. Biomolecules 2021; 11:biom11081204. [PMID: 34439869 PMCID: PMC8391806 DOI: 10.3390/biom11081204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/01/2021] [Accepted: 08/09/2021] [Indexed: 01/07/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) can engage in promiscuous interactions with their protein targets; however, it is not clear how this feature is encoded in the primary sequence of the IDPs and to what extent the surface properties and the shape of the binding cavity dictate the binding mode and the final bound conformation. Here we show, using a combination of nuclear magnetic resonance (NMR) spectroscopy and isothermal titration calorimetry (ITC), that the promiscuous interaction of the intrinsically disordered regulatory domain of the mitogen-activated protein kinase kinase MKK4 with p38α and JNK1 is facilitated by folding-upon-binding into two different conformations, despite the high sequence conservation and structural homology between p38α and JNK1. Our results support a model whereby the specific surface properties of JNK1 and p38α dictate the bound conformation of MKK4 and that enthalpy–entropy compensation plays a major role in maintaining comparable binding affinities for MKK4 towards the two kinases.
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14
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Lindorff-Larsen K, Kragelund BB. On the potential of machine learning to examine the relationship between sequence, structure, dynamics and function of intrinsically disordered proteins. J Mol Biol 2021; 433:167196. [PMID: 34390736 DOI: 10.1016/j.jmb.2021.167196] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) constitute a broad set of proteins with few uniting and many diverging properties. IDPs-and intrinsically disordered regions (IDRs) interspersed between folded domains-are generally characterized as having no persistent tertiary structure; instead they interconvert between a large number of different and often expanded structures. IDPs and IDRs are involved in an enormously wide range of biological functions and reveal novel mechanisms of interactions, and while they defy the common structure-function paradigm of folded proteins, their structural preferences and dynamics are important for their function. We here discuss open questions in the field of IDPs and IDRs, focusing on areas where machine learning and other computational methods play a role. We discuss computational methods aimed to predict transiently formed local and long-range structure, including methods for integrative structural biology. We discuss the many different ways in which IDPs and IDRs can bind to other molecules, both via short linear motifs, as well as in the formation of larger dynamic complexes such as biomolecular condensates. We discuss how experiments are providing insight into such complexes and may enable more accurate predictions. Finally, we discuss the role of IDPs in disease and how new methods are needed to interpret the mechanistic effects of genomic variants in IDPs.
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Affiliation(s)
- Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen. Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen. Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
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15
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On the specificity of protein-protein interactions in the context of disorder. Biochem J 2021; 478:2035-2050. [PMID: 34101805 PMCID: PMC8203207 DOI: 10.1042/bcj20200828] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 02/07/2023]
Abstract
With the increased focus on intrinsically disordered proteins (IDPs) and their large interactomes, the question about their specificity — or more so on their multispecificity — arise. Here we recapitulate how specificity and multispecificity are quantified and address through examples if IDPs in this respect differ from globular proteins. The conclusion is that quantitatively, globular proteins and IDPs are similar when it comes to specificity. However, compared with globular proteins, IDPs have larger interactome sizes, a phenomenon that is further enabled by their flexibility, repetitive binding motifs and propensity to adapt to different binding partners. For IDPs, this adaptability, interactome size and a higher degree of multivalency opens for new interaction mechanisms such as facilitated exchange through trimer formation and ultra-sensitivity via threshold effects and ensemble redistribution. IDPs and their interactions, thus, do not compromise the definition of specificity. Instead, it is the sheer size of their interactomes that complicates its calculation. More importantly, it is this size that challenges how we conceptually envision, interpret and speak about their specificity.
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16
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Launay H, Shao H, Bornet O, Cantrelle FX, Lebrun R, Receveur-Brechot V, Gontero B. Flexibility of Oxidized and Reduced States of the Chloroplast Regulatory Protein CP12 in Isolation and in Cell Extracts. Biomolecules 2021; 11:biom11050701. [PMID: 34066751 PMCID: PMC8151241 DOI: 10.3390/biom11050701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 12/12/2022] Open
Abstract
In the chloroplast, Calvin–Benson–Bassham enzymes are active in the reducing environment created in the light by electrons from the photosystems. In the dark, these enzymes are inhibited, mainly caused by oxidation of key regulatory cysteine residues. CP12 is a small protein that plays a role in this regulation with four cysteine residues that undergo a redox transition. Using amide-proton exchange with solvent, measured by nuclear magnetic resonance (NMR) and mass-spectrometry, we confirmed that reduced CP12 is intrinsically disordered. Using real-time NMR, we showed that the oxidation of the two disulfide bridges is simultaneous. In oxidized CP12, the C23–C31 pair is in a region that undergoes a conformational exchange in the NMR-intermediate timescale. The C66–C75 pair is in the C-terminus that folds into a stable helical turn. We confirmed that these structural states exist in a physiologically relevant environment: a cell extract from Chlamydomonas reinhardtii. Consistent with these structural equilibria, the reduction is slower for the C66–C75 pair than for the C23–C31 pair. The redox mid-potentials for the two cysteine pairs differ and are similar to those found for glyceraldehyde 3-phosphate dehydrogenase and phosphoribulokinase, consistent with the regulatory role of CP12.
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Affiliation(s)
- Helene Launay
- Aix Marseille Univ, CNRS, BIP, UMR7281, F-13402 Marseille, France; (H.S.); (V.R.-B.)
- Correspondence: (H.L.); (B.G.)
| | - Hui Shao
- Aix Marseille Univ, CNRS, BIP, UMR7281, F-13402 Marseille, France; (H.S.); (V.R.-B.)
| | - Olivier Bornet
- NMR Platform, Institut de Microbiologie de la Méditerranée, Aix Marseille Univ, F-13009 Marseille, France;
| | - Francois-Xavier Cantrelle
- CNRS, ERL9002, Integrative Structural Biology, Univ. Lille, F-59658 Lille, France;
- U1167, INSERM, CHU Lille, Institut Pasteur de Lille, F-59019 Lille, France
| | - Regine Lebrun
- Plate-forme Protéomique, Marseille Protéomique (MaP), IMM FR 3479, 31 Chemin Joseph Aiguier, F-13009 Marseille, France;
| | | | - Brigitte Gontero
- Aix Marseille Univ, CNRS, BIP, UMR7281, F-13402 Marseille, France; (H.S.); (V.R.-B.)
- Correspondence: (H.L.); (B.G.)
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17
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Bugge K, Staby L, Salladini E, Falbe-Hansen RG, Kragelund BB, Skriver K. αα-Hub domains and intrinsically disordered proteins: A decisive combo. J Biol Chem 2021; 296:100226. [PMID: 33361159 PMCID: PMC7948954 DOI: 10.1074/jbc.rev120.012928] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/22/2020] [Accepted: 12/22/2020] [Indexed: 01/02/2023] Open
Abstract
Hub proteins are central nodes in protein-protein interaction networks with critical importance to all living organisms. Recently, a new group of folded hub domains, the αα-hubs, was defined based on a shared αα-hairpin supersecondary structural foundation. The members PAH, RST, TAFH, NCBD, and HHD are found in large proteins such as Sin3, RCD1, TAF4, CBP, and harmonin, which organize disordered transcriptional regulators and membrane scaffolds in interactomes of importance to human diseases and plant quality. In this review, studies of structures, functions, and complexes across the αα-hubs are described and compared to provide a unified description of the group. This analysis expands the associated molecular concepts of "one domain-one binding site", motif-based ligand binding, and coupled folding and binding of intrinsically disordered ligands to additional concepts of importance to signal fidelity. These include context, motif reversibility, multivalency, complex heterogeneity, synergistic αα-hub:ligand folding, accessory binding sites, and supramodules. We propose that these multifaceted protein-protein interaction properties are made possible by the characteristics of the αα-hub fold, including supersite properties, dynamics, variable topologies, accessory helices, and malleability and abetted by adaptability of the disordered ligands. Critically, these features provide additional filters for specificity. With the presentations of new concepts, this review opens for new research questions addressing properties across the group, which are driven from concepts discovered in studies of the individual members. Combined, the members of the αα-hubs are ideal models for deconvoluting signal fidelity maintained by folded hubs and their interactions with intrinsically disordered ligands.
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Affiliation(s)
- Katrine Bugge
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Staby
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Edoardo Salladini
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus G Falbe-Hansen
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Birthe B Kragelund
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Karen Skriver
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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18
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Zou J, Simmerling C, Raleigh DP. Dissecting the Energetics of Intrinsically Disordered Proteins via a Hybrid Experimental and Computational Approach. J Phys Chem B 2019; 123:10394-10402. [PMID: 31702919 PMCID: PMC7291390 DOI: 10.1021/acs.jpcb.9b08323] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Intrinsically disordered proteins (IDPs) play important roles in biology, but little is known about the energetics of their inter-residue interactions. Methods that have been successfully applied to analyze the energetics of globular proteins are not applicable to the fluctuating partially ordered ensembles populated by IDPs. A combined computational experimental strategy is introduced for analyzing the energetic role of individual residues in the free state of IDPs. The approach combines experimental measurements of the binding of wild-type and mutant IDPs to their partners with alchemical free energy calculations of the structured complexes. These data allow quantitative information to be deduced about the free state via a thermodynamic cycle. The approach is validated by the analysis of the effects of mutations upon the binding free energy of the ovomucoid inhibitor third binding domain to its partners and is applied to the C-terminal domain of the measles virus nucleoprotein, a 125-residue IDP involved in the RNA transcription and replication of measles virus. The analysis reveals significant inter-residue interactions in the unbound IDP and suggests a biological role for them. The work demonstrates that advances in force fields and computational hardware have now led to the point where it is possible to develop methods, which integrate experimental and computational techniques to reveal insights that cannot be studied using either technique alone.
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Affiliation(s)
- Junjie Zou
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-3400, United S tates
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-3400, United S tates
| | - Daniel P. Raleigh
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-3400, United S tates
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19
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Arbesú M, Pons M. Integrating disorder in globular multidomain proteins: Fuzzy sensors and the role of SH3 domains. Arch Biochem Biophys 2019; 677:108161. [PMID: 31678340 DOI: 10.1016/j.abb.2019.108161] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/20/2019] [Accepted: 10/24/2019] [Indexed: 12/25/2022]
Abstract
Intrinsically disordered proteins represent about one third of eukaryotic proteins. An additional third correspond to proteins containing folded domains as well as large intrinsically disordered regions (IDR). While IDRs may represent functionally autonomous domains, in some instances it has become clear that they provide a new layer of regulation for the activity displayed by the folded domains. The sensitivity of the conformational ensembles defining the properties of IDR to small changes in the cellular environment and the capacity to modulate this response through post-translational modifications makes IDR ideal sensors enabling continuous, integrative responses to complex cellular inputs. Folded domains (FD), on the other hand, are ideal effectors, e.g. by catalyzing enzymatic reactions or participating in binary on/off switches. In this perspective review we discuss the possible role of intramolecular fuzzy complexes to integrate the very different dynamic scales of IDR and FD, inspired on the recent observations of such dynamic complexes in Src family kinases, and we explore the possible general role of the SH3 domains connecting IDRs and FD.
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Affiliation(s)
- Miguel Arbesú
- Biomolecular NMR laboratory. Department of Inorganic and Organic Chemistry. University of Barcelona, Baldiri Reixac, 10-12, 08028, Barcelona, Spain
| | - Miquel Pons
- Biomolecular NMR laboratory. Department of Inorganic and Organic Chemistry. University of Barcelona, Baldiri Reixac, 10-12, 08028, Barcelona, Spain.
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20
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Sluchanko NN, Bustos DM. Intrinsic disorder associated with 14-3-3 proteins and their partners. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 166:19-61. [PMID: 31521232 DOI: 10.1016/bs.pmbts.2019.03.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein-protein interactions (PPIs) mediate a variety of cellular processes and form complex networks, where connectivity is achieved owing to the "hub" proteins whose interaction with multiple protein partners is facilitated by the intrinsically disordered protein regions (IDPRs) and posttranslational modifications (PTMs). Universal regulatory proteins of the eukaryotic 14-3-3 family nicely exemplify these concepts and are the focus of this chapter. The extremely wide interactome of 14-3-3 proteins is characterized by high levels of intrinsic disorder (ID) enabling protein phosphorylation and consequent specific binding to the well-structured 14-3-3 dimers, one of the first phosphoserine/phosphothreonine binding modules discovered. However, high ID enrichment also challenges structural studies, thereby limiting the progress in the development of small molecule modulators of the key 14-3-3 PPIs of increased medical importance. Besides the well-known structural flexibility of their variable C-terminal tails, recent studies revealed the strong and conserved ID propensity hidden in the N-terminal segment of 14-3-3 proteins (~40 residues), normally forming the α-helical dimerization region, that may have a potential role for the dimer/monomer dynamics and recently reported moonlighting chaperone-like activity of these proteins. We review the role of ID in the 14-3-3 structure, their interactome, and also in selected 14-3-3 complexes. In addition, we discuss approaches that, in the future, may help minimize the disproportion between the large amount of known 14-3-3 partners and the small number of 14-3-3 complexes characterized with atomic precision, to unleash the whole potential of 14-3-3 PPIs as drug targets.
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Affiliation(s)
- Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation; Department of Biophysics, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russian Federation.
| | - Diego M Bustos
- Instituto de Histología y Embriología (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CC56, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina; Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
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21
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Peng Y, Alexov E, Basu S. Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases. Int J Mol Sci 2019; 20:ijms20030548. [PMID: 30696058 PMCID: PMC6386852 DOI: 10.3390/ijms20030548] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 01/25/2019] [Accepted: 01/26/2019] [Indexed: 12/25/2022] Open
Abstract
Structural information of biological macromolecules is crucial and necessary to deliver predictions about the effects of mutations-whether polymorphic or deleterious (i.e., disease causing), wherein, thermodynamic parameters, namely, folding and binding free energies potentially serve as effective biomarkers. It may be emphasized that the effect of a mutation depends on various factors, including the type of protein (globular, membrane or intrinsically disordered protein) and the structural context in which it occurs. Such information may positively aid drug-design. Furthermore, due to the intrinsic plasticity of proteins, even mutations involving radical change of the structural and physico⁻chemical properties of the amino acids (native vs. mutant) can still have minimal effects on protein thermodynamics. However, if a mutation causes significant perturbation by either folding or binding free energies, it is quite likely to be deleterious. Mitigating such effects is a promising alternative to the traditional approaches of designing inhibitors. This can be done by structure-based in silico screening of small molecules for which binding to the dysfunctional protein restores its wild type thermodynamics. In this review we emphasize the effects of mutations on two important biophysical properties, stability and binding affinity, and how structures can be used for structure-based drug design to mitigate the effects of disease-causing variants on the above biophysical properties.
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Affiliation(s)
- Yunhui Peng
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
| | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
| | - Sankar Basu
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
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22
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Sticht J, Bertazzon M, Henning LM, Licha JR, Abualrous ET, Freund C. FBP21's C-Terminal Domain Remains Dynamic When Wrapped around the c-Sec63 Unit of Brr2 Helicase. Biophys J 2018; 116:406-418. [PMID: 30558886 DOI: 10.1016/j.bpj.2018.11.3123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 10/12/2018] [Accepted: 11/19/2018] [Indexed: 01/20/2023] Open
Abstract
Based on our recent finding that FBP21 regulates human Brr2 helicase activity involved in the activation of the spliceosomal B-complex, we investigated the structural and dynamic contribution of FBP21 to the interaction. By using NMR spectroscopy, we could show that the 50 C-terminal residues of FBP21 (FBP21326-376), which are sufficient to fully form the interaction with the C-terminal Sec63 unit of Brr2 (Brr2C-Sec63), adopt a random-coil conformation in their unbound state. Upon interaction with Brr2C-Sec63, 42 residues of FBP21326-376 cover the large binding site on Brr2C-Sec63 in an extended conformation. Short charged motifs are steering complex formation, still allowing the bound state to retain dynamics. Based on fragment docking in combination with experimental restraints, we present models of the complex structure. The FBP21326-376/Brr2C-Sec63 interaction thus presents an example of an intrinsically disordered protein/ordered-protein interaction in which a large binding site provides high specificity and, in combination with conformational disorder, displays a relatively high affinity.
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Affiliation(s)
- Jana Sticht
- Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany; Core Facility BioSupraMol, Freie Universität Berlin, Berlin, Germany.
| | - Miriam Bertazzon
- Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Lisa M Henning
- Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Jan R Licha
- Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Esam T Abualrous
- Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany; Computational Molecular Biology Group, Freie Universität Berlin, Berlin, Germany
| | - Christian Freund
- Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany.
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23
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Abstract
NMR spectroscopy has proven to be a key method for studying intrinsically disordered proteins (IDPs). Nonetheless, traditional NMR methods developed for solving structures of ordered protein complexes are insufficient for the full characterization of dynamic IDP complexes, where the energy landscape is broader and more rugged. Furthermore, due to their high sensitivity to environmental changes, NMR studies of IDP complexes must be conducted with extra care and the observed NMR parameters thoroughly evaluated to enable disentanglement of binding events from ensemble distribution changes. In this chapter, written for the non-NMR expert, we start out by outlining sample preparation for IDP complexes, guide through the recording and evaluation of diagnostic 1H,15N-HSQC spectra, and delineate more sophisticated NMR strategies to follow for the particular type of complex. The most relevant experiments are then described in terms of aims, needs, pitfalls, analysis, and expected outcomes, with references to recent examples.
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24
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Zhao B, Xue B. Decision-Tree Based Meta-Strategy Improved Accuracy of Disorder Prediction and Identified Novel Disordered Residues Inside Binding Motifs. Int J Mol Sci 2018; 19:E3052. [PMID: 30301243 PMCID: PMC6213717 DOI: 10.3390/ijms19103052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 09/24/2018] [Accepted: 10/04/2018] [Indexed: 02/06/2023] Open
Abstract
Using computational techniques to identify intrinsically disordered residues is practical and effective in biological studies. Therefore, designing novel high-accuracy strategies is always preferable when existing strategies have a lot of room for improvement. Among many possibilities, a meta-strategy that integrates the results of multiple individual predictors has been broadly used to improve the overall performance of predictors. Nonetheless, a simple and direct integration of individual predictors may not effectively improve the performance. In this project, dual-threshold two-step significance voting and neural networks were used to integrate the predictive results of four individual predictors, including: DisEMBL, IUPred, VSL2, and ESpritz. The new meta-strategy has improved the prediction performance of intrinsically disordered residues significantly, compared to all four individual predictors and another four recently-designed predictors. The improvement was validated using five-fold cross-validation and in independent test datasets.
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Affiliation(s)
- Bi Zhao
- Department of Cell Biology, Microbiology and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, Tampa, FL 33620, USA.
| | - Bin Xue
- Department of Cell Biology, Microbiology and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, Tampa, FL 33620, USA.
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25
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Arbesú M, Iruela G, Fuentes H, Teixeira JMC, Pons M. Intramolecular Fuzzy Interactions Involving Intrinsically Disordered Domains. Front Mol Biosci 2018; 5:39. [PMID: 29761107 PMCID: PMC5936776 DOI: 10.3389/fmolb.2018.00039] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/03/2018] [Indexed: 01/16/2023] Open
Abstract
Structural disorder is an essential ingredient for function in many proteins and protein complexes. Fuzzy complexes describe the many instances where disorder is maintained as a critical element of protein interactions. In this minireview we discuss how intramolecular fuzzy interactions function in signaling complexes. Focussing on the Src family of kinases, we argue that the intrinsically disordered domains that are unique for each of the family members and display a clear fingerprint of long range interactions in Src, might have critical roles as functional sensor or effectors and mediate allosteric communication via fuzzy interactions.
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Affiliation(s)
- Miguel Arbesú
- BioNMR Laboratory, Inorganic and Organic Chemistry Department, University of Barcelona, Barcelona, Spain
| | - Guillermo Iruela
- BioNMR Laboratory, Inorganic and Organic Chemistry Department, University of Barcelona, Barcelona, Spain
| | - Héctor Fuentes
- BioNMR Laboratory, Inorganic and Organic Chemistry Department, University of Barcelona, Barcelona, Spain
| | - João M C Teixeira
- BioNMR Laboratory, Inorganic and Organic Chemistry Department, University of Barcelona, Barcelona, Spain
| | - Miquel Pons
- BioNMR Laboratory, Inorganic and Organic Chemistry Department, University of Barcelona, Barcelona, Spain
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26
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Eukaryotic transcription factors: paradigms of protein intrinsic disorder. Biochem J 2017; 474:2509-2532. [DOI: 10.1042/bcj20160631] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/19/2017] [Accepted: 05/05/2017] [Indexed: 12/17/2022]
Abstract
Gene-specific transcription factors (TFs) are key regulatory components of signaling pathways, controlling, for example, cell growth, development, and stress responses. Their biological functions are determined by their molecular structures, as exemplified by their structured DNA-binding domains targeting specific cis-acting elements in genes, and by the significant lack of fixed tertiary structure in their extensive intrinsically disordered regions. Recent research in protein intrinsic disorder (ID) has changed our understanding of transcriptional activation domains from ‘negative noodles’ to ID regions with function-related, short sequence motifs and molecular recognition features with structural propensities. This review focuses on molecular aspects of TFs, which represent paradigms of ID-related features. Through specific examples, we review how the ID-associated flexibility of TFs enables them to participate in large interactomes, how they use only a few hydrophobic residues, short sequence motifs, prestructured motifs, and coupled folding and binding for their interactions with co-activators, and how their accessibility to post-translational modification affects their interactions. It is furthermore emphasized how classic biochemical concepts like allostery, conformational selection, induced fit, and feedback regulation are undergoing a revival with the appreciation of ID. The review also describes the most recent advances based on computational simulations of ID-based interaction mechanisms and structural analysis of ID in the context of full-length TFs and suggests future directions for research in TF ID.
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27
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Olsen JG, Teilum K, Kragelund BB. Behaviour of intrinsically disordered proteins in protein-protein complexes with an emphasis on fuzziness. Cell Mol Life Sci 2017; 74:3175-3183. [PMID: 28597296 PMCID: PMC5533869 DOI: 10.1007/s00018-017-2560-7] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/01/2017] [Indexed: 12/24/2022]
Abstract
Intrinsically disordered proteins (IDPs) do not, by themselves, fold into a compact globular structure. They are extremely dynamic and flexible, and are typically involved in signalling and transduction of information through binding to other macromolecules. The reason for their existence may lie in their malleability, which enables them to bind several different partners with high specificity. In addition, their interactions with other macromolecules can be regulated by a variable amount of chemically diverse post-translational modifications. Four kinetically and energetically different types of complexes between an IDP and another macromolecule are reviewed: (1) simple two-state binding involving a single binding site, (2) avidity, (3) allovalency and (4) fuzzy binding; the last three involving more than one site. Finally, a qualitative definition of fuzzy binding is suggested, examples are provided, and its distinction to allovalency and avidity is highlighted and discussed.
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Affiliation(s)
- Johan G Olsen
- Structural Biology and NMR Laboratory (SBiNLab) and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory (SBiNLab) and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory (SBiNLab) and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.
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28
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Shammas SL. Mechanistic roles of protein disorder within transcription. Curr Opin Struct Biol 2017; 42:155-161. [PMID: 28262589 DOI: 10.1016/j.sbi.2017.02.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/26/2017] [Accepted: 02/13/2017] [Indexed: 12/28/2022]
Abstract
Understanding the interactions of proteins involved in transcriptional regulation is critical to describing biological systems because they control the expression profile of the cell. Yet sadly they belong to a less well biophysically characterized subset of proteins; they frequently contain long disordered regions that are highly dynamic. A key question therefore is, why? What functional roles does protein disorder play in transcriptional regulation? Experimental data exemplifying these roles are starting to emerge, with common themes being enabling complexity within networks and quick responses. Most recently a role for disorder in mediating phase transitions of membrane-less organelles has been proposed.
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Affiliation(s)
- Sarah L Shammas
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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29
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Teilum K, Kunze MBA, Erlendsson S, Kragelund BB. (S)Pinning down protein interactions by NMR. Protein Sci 2017; 26:436-451. [PMID: 28019676 PMCID: PMC5326574 DOI: 10.1002/pro.3105] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 12/14/2016] [Accepted: 12/14/2016] [Indexed: 11/29/2022]
Abstract
Protein molecules are highly diverse communication platforms and their interaction repertoire stretches from atoms over small molecules such as sugars and lipids to macromolecules. An important route to understanding molecular communication is to quantitatively describe their interactions. These types of analyses determine the amounts and proportions of individual constituents that participate in a reaction as well as their rates of reactions and their thermodynamics. Although many different methods are available, there is currently no single method able to quantitatively capture and describe all types of protein reactions, which can span orders of magnitudes in affinities, reaction rates, and lifetimes of states. As the more versatile technique, solution NMR spectroscopy offers a remarkable catalogue of methods that can be successfully applied to the quantitative as well as qualitative descriptions of protein interactions. In this review we provide an easy-access approach to NMR for the non-NMR specialist and describe how and when solution state NMR spectroscopy is the method of choice for addressing protein ligand interaction. We describe very briefly the theoretical background and illustrate simple protein-ligand interactions as well as typical strategies for measuring binding constants using NMR spectroscopy. Finally, this review provides examples of caveats of the method as well as the options to improve the outcome of an NMR analysis of a protein interaction reaction.
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Affiliation(s)
- Kaare Teilum
- Structural Biology and NMR LaboratoryThe Linderstrøm‐Lang Centre for Protein Science, Department of Biology, University of CopenhagenOle Maaløes Vej 5, DK‐2200Copenhagen NDenmark
| | - Micha Ben Achim Kunze
- Structural Biology and NMR LaboratoryThe Linderstrøm‐Lang Centre for Protein Science, Department of Biology, University of CopenhagenOle Maaløes Vej 5, DK‐2200Copenhagen NDenmark
| | - Simon Erlendsson
- Structural Biology and NMR LaboratoryThe Linderstrøm‐Lang Centre for Protein Science, Department of Biology, University of CopenhagenOle Maaløes Vej 5, DK‐2200Copenhagen NDenmark
| | - Birthe B. Kragelund
- Structural Biology and NMR LaboratoryThe Linderstrøm‐Lang Centre for Protein Science, Department of Biology, University of CopenhagenOle Maaløes Vej 5, DK‐2200Copenhagen NDenmark
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Rozentur-Shkop E, Goobes G, Chill JH. A J-modulated protonless NMR experiment characterizes the conformational ensemble of the intrinsically disordered protein WIP. JOURNAL OF BIOMOLECULAR NMR 2016; 66:243-257. [PMID: 27844185 DOI: 10.1007/s10858-016-0073-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 11/01/2016] [Indexed: 06/06/2023]
Abstract
Intrinsically disordered proteins (IDPs) are multi-conformational polypeptides that lack a single stable three-dimensional structure. It has become increasingly clear that the versatile IDPs play key roles in a multitude of biological processes, and, given their flexible nature, NMR is a leading method to investigate IDP behavior on the molecular level. Here we present an IDP-tailored J-modulated experiment designed to monitor changes in the conformational ensemble characteristic of IDPs by accurately measuring backbone one- and two-bond J(15N,13Cα) couplings. This concept was realized using a unidirectional (H)NCO 13C-detected experiment suitable for poor spectral dispersion and optimized for maximum coverage of amino acid types. To demonstrate the utility of this approach we applied it to the disordered actin-binding N-terminal domain of WASp interacting protein (WIP), a ubiquitous key modulator of cytoskeletal changes in a range of biological systems. One- and two-bond J(15N,13Cα) couplings were acquired for WIP residues 2-65 at various temperatures, and in denaturing and crowding environments. Under native conditions fitted J-couplings identified in the WIP conformational ensemble a propensity for extended conformation at residues 16-23 and 45-60, and a helical tendency at residues 28-42. These findings are consistent with a previous study of the based upon chemical shift and RDC data and confirm that the WIP2-65 conformational ensemble is biased towards the structure assumed by this fragment in its actin-bound form. The effects of environmental changes upon this ensemble were readily apparent in the J-coupling data, which reflected a significant decrease in structural propensity at higher temperatures, in the presence of 8 M urea, and under the influence of a bacterial cell lysate. The latter suggests that crowding can cause protein unfolding through protein-protein interactions that stabilize the unfolded state. We conclude that J-couplings are a useful measureable in characterizing structural ensembles in IDPs, and that the proposed experiment provides a practical method for accurately performing such measurements, once again emphasizing the power of NMR in studying IDP behavior.
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Affiliation(s)
| | - Gil Goobes
- Department of Chemistry, Bar Ilan University, 52900, Ramat Gan, Israel
| | - Jordan H Chill
- Department of Chemistry, Bar Ilan University, 52900, Ramat Gan, Israel.
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31
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Bugge K, Lindorff-Larsen K, Kragelund BB. Understanding single-pass transmembrane receptor signaling from a structural viewpoint-what are we missing? FEBS J 2016; 283:4424-4451. [PMID: 27350538 DOI: 10.1111/febs.13793] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 06/10/2016] [Accepted: 06/27/2016] [Indexed: 11/30/2022]
Abstract
Single-pass transmembrane receptors are involved in essential processes of both physiological and pathological nature and represent more than 1300 proteins in the human genome. Despite the high biological relevance of these receptors, the mechanisms of the signal transductions they facilitate are incompletely understood. One major obstacle is the lack of structures of the transmembrane domains that connect the extracellular ligand-binding domains to the intracellular signaling platforms. Over a period of almost 20 years since the first structure was reported, only 21 of these receptors have become represented by a transmembrane domain structure. This scarceness stands in strong contrast to the significance of these transmembrane α-helices for receptor functionality. In this review, we explore the properties and qualities of the current set of structures, as well as the methodological difficulties associated with their characterization and the challenges left to be overcome. Without an increased and focused effort to bring this class of proteins on par with the remaining membrane protein field, a serious lag in their biological understanding looms. Design of pharmaceutical agents, prediction of mutational affects in relation to disease, and deciphering of functional mechanisms require high-resolution structural information, especially when dealing with a domain carrying so much functionality in so few residues.
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Affiliation(s)
- Katrine Bugge
- Department of Biology, Structural Biology and NMR Laboratory, University of Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, Structural Biology and NMR Laboratory, University of Copenhagen, Denmark
| | - Birthe B Kragelund
- Department of Biology, Structural Biology and NMR Laboratory, University of Copenhagen, Denmark
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32
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Order-Disorder Transitions in the Cardiac Troponin Complex. J Mol Biol 2016; 428:2965-77. [PMID: 27395017 DOI: 10.1016/j.jmb.2016.06.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/21/2016] [Accepted: 06/29/2016] [Indexed: 12/26/2022]
Abstract
The troponin complex is a molecular switch that ties shifting intracellular calcium concentration to association and dissociation of actin and myosin, effectively allowing excitation-contraction coupling in striated muscle. Although there is a long history of muscle biophysics and structural biology, many of the mechanistic details that enable troponin's function remain incompletely understood. This review summarizes the current structural understanding of the troponin complex on the muscle thin filament, focusing on conformational changes in flexible regions of the troponin I subunit. In particular, we focus on order-disorder transitions in the C-terminal domain of troponin I, which have important implications in cardiac disease and could also have potential as a model system for the study of coupled binding and folding.
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33
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Kannan S, Lane DP, Verma CS. Long range recognition and selection in IDPs: the interactions of the C-terminus of p53. Sci Rep 2016; 6:23750. [PMID: 27030593 PMCID: PMC4814905 DOI: 10.1038/srep23750] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/15/2016] [Indexed: 11/09/2022] Open
Abstract
The C-terminal domain of p53 is an extensively studied IDP, interacting with different partners through multiple distinct conformations. To explore the interplay between preformed structural elements and intrinsic fluctuations in its folding and binding we combine extensive atomistic equilibrium and non-equilibrium simulations. We find that the free peptide segment rapidly interconverts between ordered and disordered states with significant populations of the conformations that are seen in the complexed states. The underlying global folding-binding landscape points to a synergistic mechanism in which recognition is dictated via long range electrostatic recognition which results in the formation of reactive structures as far away as 10 Å, and binding proceeds with the steering of selected conformations followed by induced folding at the target surface or within a close range.
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Affiliation(s)
| | - David P Lane
- p53 Laboratory (A*STAR), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648
| | - Chandra S Verma
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
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Shammas SL, Crabtree MD, Dahal L, Wicky BIM, Clarke J. Insights into Coupled Folding and Binding Mechanisms from Kinetic Studies. J Biol Chem 2016; 291:6689-95. [PMID: 26851275 PMCID: PMC4807256 DOI: 10.1074/jbc.r115.692715] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) are characterized by a lack of persistent structure. Since their identification more than a decade ago, many questions regarding their functional relevance and interaction mechanisms remain unanswered. Although most experiments have taken equilibrium and structural perspectives, fewer studies have investigated the kinetics of their interactions. Here we review and highlight the type of information that can be gained from kinetic studies. In particular, we show how kinetic studies of coupled folding and binding reactions, an important class of signaling event, are needed to determine mechanisms.
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Affiliation(s)
- Sarah L Shammas
- From the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Michael D Crabtree
- From the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Liza Dahal
- From the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Basile I M Wicky
- From the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Jane Clarke
- From the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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