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Ramanathan A, Ma H, Parvatikar A, Chennubhotla SC. Artificial intelligence techniques for integrative structural biology of intrinsically disordered proteins. Curr Opin Struct Biol 2021; 66:216-224. [PMID: 33421906 DOI: 10.1016/j.sbi.2020.12.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 12/16/2022]
Abstract
We outline recent developments in artificial intelligence (AI) and machine learning (ML) techniques for integrative structural biology of intrinsically disordered proteins (IDP) ensembles. IDPs challenge the traditional protein structure-function paradigm by adapting their conformations in response to specific binding partners leading them to mediate diverse, and often complex cellular functions such as biological signaling, self-organization and compartmentalization. Obtaining mechanistic insights into their function can therefore be challenging for traditional structural determination techniques. Often, scientists have to rely on piecemeal evidence drawn from diverse experimental techniques to characterize their functional mechanisms. Multiscale simulations can help bridge critical knowledge gaps about IDP structure-function relationships-however, these techniques also face challenges in resolving emergent phenomena within IDP conformational ensembles. We posit that scalable statistical inference techniques can effectively integrate information gleaned from multiple experimental techniques as well as from simulations, thus providing access to atomistic details of these emergent phenomena.
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Affiliation(s)
- Arvind Ramanathan
- Data Science & Learning Division, Argonne National Laboratory, Lemont, IL 60439, United States; Consortium for Advanced Science and Engineering (CASE), University of Chicago, Hyde Park, IL, United States.
| | - Heng Ma
- Data Science & Learning Division, Argonne National Laboratory, Lemont, IL 60439, United States
| | - Akash Parvatikar
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - S Chakra Chennubhotla
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States
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52
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Casier R, Duhamel J. The Effect of Amino Acid Size on the Internal Dynamics and Conformational Freedom of Polypeptides. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c02153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Remi Casier
- Institute for Polymer Research, Waterloo Institute for Nanotechnology, Department of Chemistry, University of Waterloo, Waterloo, ON N2L3G1, Canada
| | - Jean Duhamel
- Institute for Polymer Research, Waterloo Institute for Nanotechnology, Department of Chemistry, University of Waterloo, Waterloo, ON N2L3G1, Canada
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53
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Sottini A, Borgia A, Borgia MB, Bugge K, Nettels D, Chowdhury A, Heidarsson PO, Zosel F, Best RB, Kragelund BB, Schuler B. Polyelectrolyte interactions enable rapid association and dissociation in high-affinity disordered protein complexes. Nat Commun 2020; 11:5736. [PMID: 33184256 PMCID: PMC7661507 DOI: 10.1038/s41467-020-18859-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/14/2020] [Indexed: 02/07/2023] Open
Abstract
Highly charged intrinsically disordered proteins can form complexes with very high affinity in which both binding partners fully retain their disorder and dynamics, exemplified by the positively charged linker histone H1.0 and its chaperone, the negatively charged prothymosin α. Their interaction exhibits another surprising feature: The association/dissociation kinetics switch from slow two-state-like exchange at low protein concentrations to fast exchange at higher, physiologically relevant concentrations. Here we show that this change in mechanism can be explained by the formation of transient ternary complexes favored at high protein concentrations that accelerate the exchange between bound and unbound populations by orders of magnitude. Molecular simulations show how the extreme disorder in such polyelectrolyte complexes facilitates (i) diffusion-limited binding, (ii) transient ternary complex formation, and (iii) fast exchange of monomers by competitive substitution, which together enable rapid kinetics. Biological polyelectrolytes thus have the potential to keep regulatory networks highly responsive even for interactions with extremely high affinities.
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Affiliation(s)
- Andrea Sottini
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Alessandro Borgia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Madeleine B Borgia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Katrine Bugge
- Structural Biology and NMR Laboratory (SBiNLab) and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Aritra Chowdhury
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Pétur O Heidarsson
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
- Department of Biochemistry, Science Institute, University of Iceland, Dunhagi 3, 107, Reykjavík, Iceland
| | - Franziska Zosel
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
- Novo Nordisk A/S, Novo Nordisk Park, 2760, Måløv, Denmark
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory (SBiNLab) and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200, Copenhagen, Denmark.
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
- Department of Physics, University of Zurich, Zurich, Switzerland.
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54
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Amin AN, Lin YH, Das S, Chan HS. Analytical Theory for Sequence-Specific Binary Fuzzy Complexes of Charged Intrinsically Disordered Proteins. J Phys Chem B 2020; 124:6709-6720. [PMID: 32639157 DOI: 10.1021/acs.jpcb.0c04575] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Intrinsically disordered proteins (IDPs) are important for biological functions. In contrast to folded proteins, molecular recognition among certain IDPs is "fuzzy" in that their binding and/or phase separation are stochastically governed by the interacting IDPs' amino acid sequences, while their assembled conformations remain largely disordered. To help elucidate a basic aspect of this fascinating yet poorly understood phenomenon, the binding of a homo or heterodimeric pair of polyampholytic IDPs is modeled statistical mechanically using cluster expansion. We find that the binding affinities of binary fuzzy complexes in the model correlate strongly with a newly derived simple "joint sequence charge decoration" parameter readily calculable from the pair of IDPs' sequence charge patterns. Predictions by our analytical theory are in essential agreement with coarse-grained explicit-chain simulations. This computationally efficient theoretical framework is expected to be broadly applicable to rationalizing and predicting sequence-specific IDP-IDP polyelectrostatic interactions.
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Affiliation(s)
- Alan N Amin
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Yi-Hsuan Lin
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Suman Das
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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Rogers JM. Peptide Folding and Binding Probed by Systematic Non-canonical Mutagenesis. Front Mol Biosci 2020; 7:100. [PMID: 32671094 PMCID: PMC7326784 DOI: 10.3389/fmolb.2020.00100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/04/2020] [Indexed: 12/20/2022] Open
Abstract
Many proteins and peptides fold upon binding another protein. Mutagenesis has proved an essential tool in the study of these multi-step molecular recognition processes. By comparing the biophysical behavior of carefully selected mutants, the concert of interactions and conformational changes that occur during folding and binding can be separated and assessed. Recently, this mutagenesis approach has been radically expanded by deep mutational scanning methods, which allow for many thousands of mutations to be examined in parallel. Furthermore, these high-throughput mutagenesis methods have been expanded to include mutations to non-canonical amino acids, returning peptide structure-activity relationships with unprecedented depth and detail. These developments are timely, as the insights they provide can guide the optimization of de novo cyclic peptides, a promising new modality for chemical probes and therapeutic agents.
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Affiliation(s)
- Joseph M Rogers
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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56
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Yruela I, Neira JL. Intrinsically disordered proteins in biology: One for all, all for one. Arch Biochem Biophys 2020; 684:108328. [PMID: 32145248 DOI: 10.1016/j.abb.2020.108328] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Inmaculada Yruela
- Group of Computational and Structural Biology, Estación Experimental de Aula Dei (EEAD-CSIC), Avda. Montañana 1005, 50059, Zaragoza, Spain; Group of Biochemistry, Biophysics and Computational Biology (BIFI-Unizar) Joint Unit to CSIC, Spain.
| | - José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202, Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018, Zaragoza, Spain.
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57
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Toto A, Malagrinò F, Visconti L, Troilo F, Pagano L, Brunori M, Jemth P, Gianni S. Templated folding of intrinsically disordered proteins. J Biol Chem 2020; 295:6586-6593. [PMID: 32253236 DOI: 10.1074/jbc.rev120.012413] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Much of our current knowledge of biological chemistry is founded in the structure-function relationship, whereby sequence determines structure that determines function. Thus, the discovery that a large fraction of the proteome is intrinsically disordered, while being functional, has revolutionized our understanding of proteins and raised new and interesting questions. Many intrinsically disordered proteins (IDPs) have been determined to undergo a disorder-to-order transition when recognizing their physiological partners, suggesting that their mechanisms of folding are intrinsically different from those observed in globular proteins. However, IDPs also follow some of the classic paradigms established for globular proteins, pointing to important similarities in their behavior. In this review, we compare and contrast the folding mechanisms of globular proteins with the emerging features of binding-induced folding of intrinsically disordered proteins. Specifically, whereas disorder-to-order transitions of intrinsically disordered proteins appear to follow rules of globular protein folding, such as the cooperative nature of the reaction, their folding pathways are remarkably more malleable, due to the heterogeneous nature of their folding nuclei, as probed by analysis of linear free-energy relationship plots. These insights have led to a new model for the disorder-to-order transition in IDPs termed "templated folding," whereby the binding partner dictates distinct structural transitions en route to product, while ensuring a cooperative folding.
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Affiliation(s)
- Angelo Toto
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Francesca Malagrinò
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Lorenzo Visconti
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Francesca Troilo
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Livia Pagano
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Maurizio Brunori
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Stefano Gianni
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
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Investigating the ferric ion binding site of magnetite biomineralisation protein Mms6. PLoS One 2020; 15:e0228708. [PMID: 32097412 PMCID: PMC7041794 DOI: 10.1371/journal.pone.0228708] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/21/2020] [Indexed: 11/19/2022] Open
Abstract
The biomineralization protein Mms6 has been shown to be a major player in the formation of magnetic nanoparticles both within the magnetosomes of magnetotactic bacteria and as an additive in synthetic magnetite precipitation assays. Previous studies have highlighted the ferric iron binding capability of the protein and this activity is thought to be crucial to its mineralizing properties. To understand how this protein binds ferric ions we have prepared a series of single amino acid substitutions within the C-terminal binding region of Mms6 and have used a ferric binding assay to probe the binding site at the level of individual residues which has pinpointed the key residues of E44, E50 and R55 involved in Mms6 ferric binding. No aspartic residues bound ferric ions. A nanoplasmonic sensing experiment was used to investigate the unstable EER44, 50,55AAA triple mutant in comparison to native Mms6. This suggests a difference in interaction with iron ions between the two and potential changes to the surface precipitation of iron oxide when the pH is increased. All-atom simulations suggest that disruptive mutations do not fundamentally alter the conformational preferences of the ferric binding region. Instead, disruption of these residues appears to impede a sequence-specific motif in the C-terminus critical to ferric ion binding.
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59
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Sigalov AB. Letter to the Editor: No folding upon binding of intrinsically disordered proteins: Still interesting but not unique and novel. A commentary on “A novel mode of interaction between intrinsically disordered proteins. by Hibino, E. and Hoshino, M., Biophysics and Physicobiology 17, 86–93 (2020). DOI: 10.2142/biophysico.BSJ-2020012”. Biophys Physicobiol 2020; 17:156-158. [PMID: 33447498 PMCID: PMC7781792 DOI: 10.2142/biophysico.bsj-2020025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/27/2020] [Indexed: 12/01/2022] Open
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