1
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Grimes J, Koszegi Z, Lanoiselée Y, Miljus T, O'Brien SL, Stepniewski TM, Medel-Lacruz B, Baidya M, Makarova M, Mistry R, Goulding J, Drube J, Hoffmann C, Owen DM, Shukla AK, Selent J, Hill SJ, Calebiro D. Plasma membrane preassociation drives β-arrestin coupling to receptors and activation. Cell 2023; 186:2238-2255.e20. [PMID: 37146613 PMCID: PMC7614532 DOI: 10.1016/j.cell.2023.04.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 12/16/2022] [Accepted: 04/12/2023] [Indexed: 05/07/2023]
Abstract
β-arrestin plays a key role in G protein-coupled receptor (GPCR) signaling and desensitization. Despite recent structural advances, the mechanisms that govern receptor-β-arrestin interactions at the plasma membrane of living cells remain elusive. Here, we combine single-molecule microscopy with molecular dynamics simulations to dissect the complex sequence of events involved in β-arrestin interactions with both receptors and the lipid bilayer. Unexpectedly, our results reveal that β-arrestin spontaneously inserts into the lipid bilayer and transiently interacts with receptors via lateral diffusion on the plasma membrane. Moreover, they indicate that, following receptor interaction, the plasma membrane stabilizes β-arrestin in a longer-lived, membrane-bound state, allowing it to diffuse to clathrin-coated pits separately from the activating receptor. These results expand our current understanding of β-arrestin function at the plasma membrane, revealing a critical role for β-arrestin preassociation with the lipid bilayer in facilitating its interactions with receptors and subsequent activation.
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Affiliation(s)
- Jak Grimes
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham B15 2TT, UK
| | - Zsombor Koszegi
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham B15 2TT, UK
| | - Yann Lanoiselée
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham B15 2TT, UK
| | - Tamara Miljus
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham B15 2TT, UK
| | - Shannon L O'Brien
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham B15 2TT, UK
| | - Tomasz M Stepniewski
- Research Program on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, 08003, Spain
| | - Brian Medel-Lacruz
- Research Program on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, 08003, Spain
| | - Mithu Baidya
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Maria Makarova
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham B15 2TT, UK; School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ravi Mistry
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham B15 2TT, UK
| | - Joëlle Goulding
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham B15 2TT, UK; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Julia Drube
- Institut für Molekulare Zellbiologie, Center for Molecular Biomedicine, Universitätsklinikum Jena, Friedrich-Schiller-Universität, Jena 07745, Germany
| | - Carsten Hoffmann
- Institut für Molekulare Zellbiologie, Center for Molecular Biomedicine, Universitätsklinikum Jena, Friedrich-Schiller-Universität, Jena 07745, Germany
| | - Dylan M Owen
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham B15 2TT, UK; Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Arun K Shukla
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Jana Selent
- Research Program on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, 08003, Spain
| | - Stephen J Hill
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham B15 2TT, UK; Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Davide Calebiro
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham B15 2TT, UK.
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2
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Aptamer Affinity to P53 DBD: A Molecular Dynamics Study. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
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3
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Calebiro D, Koszegi Z, Lanoiselée Y, Miljus T, O'Brien S. G protein-coupled receptor-G protein interactions: a single-molecule perspective. Physiol Rev 2020; 101:857-906. [PMID: 33331229 DOI: 10.1152/physrev.00021.2020] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
G protein-coupled receptors (GPCRs) regulate many cellular and physiological processes, responding to a diverse range of extracellular stimuli including hormones, neurotransmitters, odorants, and light. Decades of biochemical and pharmacological studies have provided fundamental insights into the mechanisms of GPCR signaling. Thanks to recent advances in structural biology, we now possess an atomistic understanding of receptor activation and G protein coupling. However, how GPCRs and G proteins interact in living cells to confer signaling efficiency and specificity remains insufficiently understood. The development of advanced optical methods, including single-molecule microscopy, has provided the means to study receptors and G proteins in living cells with unprecedented spatio-temporal resolution. The results of these studies reveal an unexpected level of complexity, whereby GPCRs undergo transient interactions among themselves as well as with G proteins and structural elements of the plasma membrane to form short-lived signaling nanodomains that likely confer both rapidity and specificity to GPCR signaling. These findings may provide new strategies to pharmaceutically modulate GPCR function, which might eventually pave the way to innovative drugs for common diseases such as diabetes or heart failure.
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Affiliation(s)
- Davide Calebiro
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Zsombor Koszegi
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Yann Lanoiselée
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Tamara Miljus
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Shannon O'Brien
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
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4
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Gallagher EE, Song JM, Menon A, Mishra LD, Chmiel AF, Garner AL. Consideration of Binding Kinetics in the Design of Stapled Peptide Mimics of the Disordered Proteins Eukaryotic Translation Initiation Factor 4E-Binding Protein 1 and Eukaryotic Translation Initiation Factor 4G. J Med Chem 2019; 62:4967-4978. [PMID: 31033289 PMCID: PMC6679956 DOI: 10.1021/acs.jmedchem.9b00068] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Protein disorder plays a crucial role in signal transduction and is key for many cellular processes including transcription, translation, and cell cycle. Within the intrinsically disordered protein interactome, the α-helix is commonly used for binding, which is induced via a disorder-to-order transition. Because the targeting of protein-protein interactions (PPIs) remains an important challenge in medicinal chemistry, efforts have been made to mimic this secondary structure for rational inhibitor design through the use of stapled peptides. Cap-dependent mRNA translation is regulated by two disordered proteins, 4E-BP1 and eIF4G, that inhibit or stimulate the activity of the m7G cap-binding translation initiation factor, eIF4E, respectively. Both use an α-helical motif for eIF4E binding, warranting the investigation of stapled peptide mimics for manipulating eIF4E PPIs. Herein, we describe our efforts toward this goal, resulting in the synthesis of a cell-active stapled peptide for further development in manipulating aberrant cap-dependent translation in human diseases.
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Affiliation(s)
- Erin E Gallagher
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 1600 Huron Parkway, NCRC B520 , Ann Arbor , Michigan 48109 , United States
| | - James M Song
- Program in Chemical Biology , University of Michigan , 210 Washtenaw Avenue , Ann Arbor , Michigan 48109 , United States
| | - Arya Menon
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 1600 Huron Parkway, NCRC B520 , Ann Arbor , Michigan 48109 , United States
| | - Lauren D Mishra
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 1600 Huron Parkway, NCRC B520 , Ann Arbor , Michigan 48109 , United States
| | - Alyah F Chmiel
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 1600 Huron Parkway, NCRC B520 , Ann Arbor , Michigan 48109 , United States
| | - Amanda L Garner
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 1600 Huron Parkway, NCRC B520 , Ann Arbor , Michigan 48109 , United States
- Program in Chemical Biology , University of Michigan , 210 Washtenaw Avenue , Ann Arbor , Michigan 48109 , United States
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5
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Menssen RJ, Tokmakoff A. Length-Dependent Melting Kinetics of Short DNA Oligonucleotides Using Temperature-Jump IR Spectroscopy. J Phys Chem B 2019; 123:756-767. [PMID: 30614693 DOI: 10.1021/acs.jpcb.8b09487] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In this work, we utilize Fourier transform infrared and temperature-jump (T-jump) infrared (IR) spectroscopy to investigate the melting thermodynamics and kinetics of a series of five DNA sequences ranging from 6 to 14 base pairs long. IR spectroscopy is well suited for the study of DNA because of its ability to distinguish base-specific information, and the nanosecond time resolution of the T-jump apparatus can access the relevant range of kinetics. Eyring analysis of a two-state model examines both the activation enthalpy and entropy, providing new insights into the energetic driving forces and physical processes behind the association and dissociation while also helping to clarify the commonly observed negative activation energy. Global analysis of the thermodynamic and kinetic data applying a linear dependence of activation barriers on oligo length provides a holistic result by producing reasonable agreement between our data and existing nearest-neighbor (NN) thermodynamic parameters blending the experimental results with established predictive models. By studying the trends in the thermodynamics and kinetics as a function of length, this work demonstrates a direct correlation between the effects additional dinucleotides have on the kinetics and the NN parameters for those dinucleotides. This result further supports the development of a kinetic analogue to the thermodynamic NN parameters.
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Affiliation(s)
- Ryan J Menssen
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics , The University of Chicago , 929 East 57th Street , Chicago , Illinois 60637 , United States
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics , The University of Chicago , 929 East 57th Street , Chicago , Illinois 60637 , United States
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6
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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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7
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Xie ZR, Chen J, Wu Y. Predicting Protein-protein Association Rates using Coarse-grained Simulation and Machine Learning. Sci Rep 2017; 7:46622. [PMID: 28418043 PMCID: PMC5394550 DOI: 10.1038/srep46622] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/21/2017] [Indexed: 12/20/2022] Open
Abstract
Protein–protein interactions dominate all major biological processes in living cells. We have developed a new Monte Carlo-based simulation algorithm to study the kinetic process of protein association. We tested our method on a previously used large benchmark set of 49 protein complexes. The predicted rate was overestimated in the benchmark test compared to the experimental results for a group of protein complexes. We hypothesized that this resulted from molecular flexibility at the interface regions of the interacting proteins. After applying a machine learning algorithm with input variables that accounted for both the conformational flexibility and the energetic factor of binding, we successfully identified most of the protein complexes with overestimated association rates and improved our final prediction by using a cross-validation test. This method was then applied to a new independent test set and resulted in a similar prediction accuracy to that obtained using the training set. It has been thought that diffusion-limited protein association is dominated by long-range interactions. Our results provide strong evidence that the conformational flexibility also plays an important role in regulating protein association. Our studies provide new insights into the mechanism of protein association and offer a computationally efficient tool for predicting its rate.
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Affiliation(s)
- Zhong-Ru Xie
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Yeshiva University, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Jiawen Chen
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Yeshiva University, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Yeshiva University, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
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8
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Mollica L, Bessa LM, Hanoulle X, Jensen MR, Blackledge M, Schneider R. Binding Mechanisms of Intrinsically Disordered Proteins: Theory, Simulation, and Experiment. Front Mol Biosci 2016; 3:52. [PMID: 27668217 PMCID: PMC5016563 DOI: 10.3389/fmolb.2016.00052] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 08/24/2016] [Indexed: 12/21/2022] Open
Abstract
In recent years, protein science has been revolutionized by the discovery of intrinsically disordered proteins (IDPs). In contrast to the classical paradigm that a given protein sequence corresponds to a defined structure and an associated function, we now know that proteins can be functional in the absence of a stable three-dimensional structure. In many cases, disordered proteins or protein regions become structured, at least locally, upon interacting with their physiological partners. Many, sometimes conflicting, hypotheses have been put forward regarding the interaction mechanisms of IDPs and the potential advantages of disorder for protein-protein interactions. Whether disorder may increase, as proposed, e.g., in the “fly-casting” hypothesis, or decrease binding rates, increase or decrease binding specificity, or what role pre-formed structure might play in interactions involving IDPs (conformational selection vs. induced fit), are subjects of intense debate. Experimentally, these questions remain difficult to address. Here, we review experimental studies of binding mechanisms of IDPs using NMR spectroscopy and transient kinetic techniques, as well as the underlying theoretical concepts and numerical methods that can be applied to describe these interactions at the atomic level. The available literature suggests that the kinetic and thermodynamic parameters characterizing interactions involving IDPs can vary widely and that there may be no single common mechanism that can explain the different binding modes observed experimentally. Rather, disordered proteins appear to make combined use of features such as pre-formed structure and flexibility, depending on the individual system and the functional context.
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Affiliation(s)
- Luca Mollica
- CompuNet, Drug Discovery and Development, Istituto Italiano di Tecnologia Genova, Italy
| | - Luiza M Bessa
- NMR & Molecular Interactions, Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle Lille, France
| | - Xavier Hanoulle
- NMR & Molecular Interactions, Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle Lille, France
| | | | - Martin Blackledge
- Institut de Biologie Structurale, CEA, CNRS, Université Grenoble Alpes Grenoble, France
| | - Robert Schneider
- NMR & Molecular Interactions, Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle Lille, France
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9
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Pantoja-Uceda D, Neira JL, Saelices L, Robles-Rengel R, Florencio FJ, Muro-Pastor MI, Santoro J. Dissecting the Binding between Glutamine Synthetase and Its Two Natively Unfolded Protein Inhibitors. Biochemistry 2016; 55:3370-82. [DOI: 10.1021/acs.biochem.6b00072] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - 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),
Unidad Asociada IQFR-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Lorena Saelices
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain
| | - Rocío Robles-Rengel
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain
| | - Francisco J. Florencio
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain
| | - M. Isabel Muro-Pastor
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain
| | - Jorge Santoro
- Instituto
de Química Física Rocasolano (IQFR), CSIC, 28006 Madrid, Spain
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10
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Umezawa K, Ohnuki J, Higo J, Takano M. Intrinsic disorder accelerates dissociation rather than association. Proteins 2016; 84:1124-33. [DOI: 10.1002/prot.25057] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 03/16/2016] [Accepted: 04/24/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Koji Umezawa
- Department of Pure and Applied Physics; Waseda University; Okubo 3-4-1, Shinjuku-Ku Tokyo 169-8555 Japan
| | - Jun Ohnuki
- Department of Pure and Applied Physics; Waseda University; Okubo 3-4-1, Shinjuku-Ku Tokyo 169-8555 Japan
| | - Junichi Higo
- Institute for Protein Research, Osaka University; Suita Osaka 565-0871 Japan
| | - Mitsunori Takano
- Department of Pure and Applied Physics; Waseda University; Okubo 3-4-1, Shinjuku-Ku Tokyo 169-8555 Japan
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11
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Cao H, Huang Y, Liu Z. Interplay between binding affinity and kinetics in protein-protein interactions. Proteins 2016; 84:920-33. [PMID: 27018856 DOI: 10.1002/prot.25041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/24/2016] [Accepted: 03/17/2016] [Indexed: 12/18/2022]
Abstract
To clarify the interplay between the binding affinity and kinetics of protein-protein interactions, and the possible role of intrinsically disordered proteins in such interactions, molecular simulations were carried out on 20 protein complexes. With bias potential and reweighting techniques, the free energy profiles were obtained under physiological affinities, which showed that the bound-state valley is deep with a barrier height of 12 - 33 RT. From the dependence of the affinity on interface interactions, the entropic contribution to the binding affinity is approximated to be proportional to the interface area. The extracted dissociation rates based on the Arrhenius law correlate reasonably well with the experimental values (Pearson correlation coefficient R = 0.79). For each protein complex, a linear free energy relationship between binding affinity and the dissociation rate was confirmed, but the distribution of the slopes for intrinsically disordered proteins showed no essential difference with that observed for ordered proteins. A comparison with protein folding was also performed. Proteins 2016; 84:920-933. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Huaiqing Cao
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.,Center for Quantitative Biology, and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing, 100871, China
| | - Yongqi Huang
- Institute of Theoretical Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, China
| | - Zhirong Liu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.,Center for Quantitative Biology, and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing, 100871, China
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12
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Fu Y, Guo Y, Wang Y, Luo J, Pu X, Li M, Zhang Z. Exploring the relationship between hub proteins and drug targets based on GO and intrinsic disorder. Comput Biol Chem 2015; 56:41-8. [PMID: 25854804 DOI: 10.1016/j.compbiolchem.2015.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 03/13/2015] [Accepted: 03/21/2015] [Indexed: 11/25/2022]
Abstract
Protein-protein interactions (PPIs) play essential roles in many biological processes. In protein-protein interaction networks, hubs involve in numbers of PPIs and may constitute an important source of drug targets. The intrinsic disorder proteins (IDPs) with unstable structures can promote the promiscuity of hubs and also involve in many disease pathways, so they also could serve as potential drug targets. Moreover, proteins with similar functions measured by semantic similarity of gene ontology (GO) terms tend to interact with each other. Here, the relationship between hub proteins and drug targets based on GO terms and intrinsic disorder was explored. The semantic similarities of GO terms and genes between two proteins, and the rate of intrinsic disorder residues of each protein were extracted as features to characterize the functional similarity between two interacting proteins. Only using 8 feature variables, prediction models by support vector machine (SVM) were constructed to predict PPIs. The accuracy of the model on the PPI data from human hub proteins is as high as 83.72%, which is very promising compared with other PPI prediction models with hundreds or even thousands of features. Then, 118 of 142 PPIs between hubs are correctly predicted that the two interacting proteins are targets of the same drugs. The results indicate that only 8 functional features are fully efficient for representing PPIs. In order to identify new targets from IDP dataset, the PPIs between hubs and IDPs are predicted by the SVM model and the model yields a prediction accuracy of 75.84%. Further research proves that 3 of 5 PPIs between hubs and IDPs are correctly predicted that the two interacting proteins are targets of the same drugs. All results demonstrate that the model with only 8-dimensional features from GO terms and intrinsic disorder still gives a good performance in predicting PPIs and further identifying drug targets.
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Affiliation(s)
- Yuanyuan Fu
- College of Chemistry, Sichuan University, Chengdu 610064, PR China
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu 610064, PR China.
| | - Yuelong Wang
- College of Chemistry, Sichuan University, Chengdu 610064, PR China
| | - Jiesi Luo
- College of Chemistry, Sichuan University, Chengdu 610064, PR China
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu 610064, PR China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu 610064, PR China.
| | - Zhihang Zhang
- College of Chemistry, Sichuan University, Chengdu 610064, PR China
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13
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Rogers J, Wong CT, Clarke J. Coupled folding and binding of the disordered protein PUMA does not require particular residual structure. J Am Chem Soc 2014; 136:5197-200. [PMID: 24654952 PMCID: PMC4017604 DOI: 10.1021/ja4125065] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Indexed: 11/29/2022]
Abstract
Many cellular proteins are 'disordered' in isolation. A subset of these intrinsically disordered proteins (IDPs) can, upon binding another molecule, fold to a well-defined three-dimensional structure. In the structurally heterogeneous, unbound ensemble of these IDPs, conformations are likely to exist that, in part, resemble the final bound form. It has been suggested that these conformations, displaying 'residual structure', could be important for the mechanism of such coupled folding and binding reactions. PUMA, of the BCL-2 family, is an IDP in isolation but will form a single, contiguous α-helix upon binding the folded protein MCL-1. Using the helix-breaking residue proline, we systematically target each potential turn of helix of unbound PUMA and assess the binding to MCL-1 using time-resolved stopped-flow techniques. All proline-containing mutants bound, and although binding was weaker than the wild-type protein, association rate constants were largely unaffected. We conclude that population of particular residual structure, containing a specific helical turn, is neither required for the binding nor for fast association of PUMA and MCL-1.
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Affiliation(s)
- Joseph
M. Rogers
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Chi T. Wong
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
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14
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Nakamoto M, Hoshino Y, Miura Y. Effect of Physical Properties of Nanogel Particles on the Kinetic Constants of Multipoint Protein Recognition Process. Biomacromolecules 2014; 15:541-7. [DOI: 10.1021/bm401536v] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Masahiko Nakamoto
- Department of Chemical Engineering, Kyushu University, 744
Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yu Hoshino
- Department of Chemical Engineering, Kyushu University, 744
Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshiko Miura
- Department of Chemical Engineering, Kyushu University, 744
Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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15
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Kastritis PL, Bonvin AMJJ. Molecular origins of binding affinity: seeking the Archimedean point. Curr Opin Struct Biol 2013; 23:868-77. [PMID: 23876790 DOI: 10.1016/j.sbi.2013.07.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/01/2013] [Accepted: 07/02/2013] [Indexed: 11/29/2022]
Abstract
Connecting three dimensional structure and affinity is analogous to seeking the 'Archimedean point', a vantage point from where any observer can quantitatively perceive the subject of inquiry. Here we review current knowledge and challenges that lie ahead of us in the quest for this Archimedean point. We argue that current models are limited in reproducing measured data because molecular description of binding affinity must expand beyond the interfacial contribution and also incorporate effects stemming from conformational changes/dynamics and long-range interactions. Fortunately, explicit modeling of various kinetic schemes underlying biomolecular recognition and confined systems that reflect in vivo interactions are coming within reach. This quest will hopefully lead to an accurate biophysical interpretation of binding affinity that would allow unprecedented understanding of the molecular basis of life through unraveling the why's of interaction networks.
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Affiliation(s)
- Panagiotis L Kastritis
- Bijvoet Center for Biomolecular Research, Science Faculty - Chemistry, Utrecht University, 3584CH Utrecht, The Netherlands
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16
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Sikora JR, Rauzan B, Stegemann R, Deckert A. Modeling stopped-flow data for nucleic acid duplex formation reactions: the importance of off-path intermediates. J Phys Chem B 2013; 117:8966-76. [PMID: 23902467 DOI: 10.1021/jp404550a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Evidence for unexpected off-path intermediates to DNA duplex formation is presented. These off-path intermediates are shown to involve unimolecular and, in one case, bimolecular structure in one of the single strands of complementary DNA. Three models are developed to account for the observed single-stranded structures that are formed in parallel with duplex formation. These models are applied to the analysis of stopped-flow data for eight different nonself-complementary duplex formation reactions in order to extract the elementary rate constant for formation of the duplex from the complementary random coil single-stranded DNA. The free energy of activation (at 25 °C) for the denaturation of each duplex is calculated from these data and is shown to have a linear correlation to the overall standard free energy for duplex formation (also at 25 °C). Duplexes that contain mismatches obey a parallel linear free-energy (LFE) relationship with a y-intercept that is greater than that of duplexes without mismatches. Slopes near unity for the LFE relationships indicate that all duplexes go through an early, unstructured transition state.
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Affiliation(s)
- Jacqueline R Sikora
- Department of Chemistry, Allegheny College, 520 North Main Street, Meadville, Pennsylvania 16335, USA
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17
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Uversky VN. The alphabet of intrinsic disorder: II. Various roles of glutamic acid in ordered and intrinsically disordered proteins. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e24684. [PMID: 28516010 PMCID: PMC5424795 DOI: 10.4161/idp.24684] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 03/27/2013] [Accepted: 04/12/2013] [Indexed: 11/19/2022]
Abstract
The ability of a protein to fold into unique functional state or to stay intrinsically disordered is encoded in its amino acid sequence. Both ordered and intrinsically disordered proteins (IDPs) are natural polypeptides that use the same arsenal of 20 proteinogenic amino acid residues as their major building blocks. The exceptional structural plasticity of IDPs, their capability to exist as heterogeneous structural ensembles and their wide array of important disorder-based biological functions that complements functional repertoire of ordered proteins are all rooted within the peculiar differential usage of these building blocks by ordered proteins and IDPs. In fact, some residues (so-called disorder-promoting residues) are noticeably more common in IDPs than in sequences of ordered proteins, which, in their turn, are enriched in several order-promoting residues. Furthermore, residues can be arranged according to their “disorder promoting potencies,” which are evaluated based on the relative abundances of various amino acids in ordered and disordered proteins. This review continues a series of publications on the roles of different amino acids in defining the phenomenon of protein intrinsic disorder and concerns glutamic acid, which is the second most disorder-promoting residue.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Moscow, Russia
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18
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Rauzan B, McMichael E, Cave R, Sevcik LR, Ostrosky K, Whitman E, Stegemann R, Sinclair AL, Serra MJ, Deckert AA. Kinetics and thermodynamics of DNA, RNA, and hybrid duplex formation. Biochemistry 2013; 52:765-72. [PMID: 23356429 DOI: 10.1021/bi3013005] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The rates of duplex formation for two octamers of DNA (5' d-CACGGCTC/5' d-GAGCCGTG and 5' d-CACAGCAC/5' d-GTGCTGTG), the homologous RNA, and both sets of hybrids in 1 M NaCl buffer have been measured using stopped-flow spectroscopy. In addition, the thermodynamic parameters, ΔH° and ΔS°, have been determined for the same sequences under the same buffer conditions using optical melting techniques. These data reveal a linear free energy relationship between the free energy of activation for denaturation and the change in free energy for formation of the duplexes. This relationship indicates that these duplex formation reactions occur through a common unstructured transition state that is more similar to the single strands in solution than to the ensuing duplex. In addition, these data confirm that the greater stability of RNA duplexes relative to that of homologous DNA and hybrid duplexes is controlled by the denaturation rate and not the duplex formation rate.
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Affiliation(s)
- Brittany Rauzan
- Department of Chemistry, Allegheny College , 520 North Main Street, Meadville, Pennsylvania 16335, United States
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19
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Uversky VN, Dunker AK. The case for intrinsically disordered proteins playing contributory roles in molecular recognition without a stable 3D structure. F1000 BIOLOGY REPORTS 2013; 5:1. [PMID: 23361308 PMCID: PMC3542772 DOI: 10.3410/b5-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The classical 'lock-and-key' and 'induced-fit' mechanisms for binding both originated in attempts to explain features of enzyme catalysis. For both of these mechanisms and for their recent refinements, enzyme catalysis requires exquisite spatial and electronic complementarity between the substrate and the catalyst. Thus, binding models derived from models originally based on catalysis will be highly biased towards mechanisms that utilize structural complementarity. If mere binding without catalysis is the endpoint, then the structural requirements for the interaction become much more relaxed. Recent observations on specific examples suggest that this relaxation can reach an extreme lack of specific 3D structure, leading to molecular recognition with biological consequences that depend not only upon structural and electrostatic complementarity between the binding partners but also upon kinetic, entropic, and generalized electrostatic effects. In addition to this discussion of binding without fixed structure, examples in which unstructured regions carry out important biological functions not involving molecular recognition will also be discussed. Finally, we discuss whether 'intrinsically disordered protein' (IDP) represents a useful new concept.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, University of South Florida Tampa, FL 33612, USA ; Institute for Biological Instrumentation, Russian Academy of Sciences 142290 Pushchino, Moscow Region, Russia
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20
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Kastritis PL, Bonvin AMJJ. On the binding affinity of macromolecular interactions: daring to ask why proteins interact. J R Soc Interface 2012; 10:20120835. [PMID: 23235262 PMCID: PMC3565702 DOI: 10.1098/rsif.2012.0835] [Citation(s) in RCA: 276] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Interactions between proteins are orchestrated in a precise and time-dependent manner, underlying cellular function. The binding affinity, defined as the strength of these interactions, is translated into physico-chemical terms in the dissociation constant (Kd), the latter being an experimental measure that determines whether an interaction will be formed in solution or not. Predicting binding affinity from structural models has been a matter of active research for more than 40 years because of its fundamental role in drug development. However, all available approaches are incapable of predicting the binding affinity of protein–protein complexes from coordinates alone. Here, we examine both theoretical and experimental limitations that complicate the derivation of structure–affinity relationships. Most work so far has concentrated on binary interactions. Systems of increased complexity are far from being understood. The main physico-chemical measure that relates to binding affinity is the buried surface area, but it does not hold for flexible complexes. For the latter, there must be a significant entropic contribution that will have to be approximated in the future. We foresee that any theoretical modelling of these interactions will have to follow an integrative approach considering the biology, chemistry and physics that underlie protein–protein recognition.
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Affiliation(s)
- Panagiotis L Kastritis
- Bijvoet Center for Biomolecular Research, Faculty of Science, Chemistry, Utrecht University, , Padualaan 8, Utrecht, The Netherlands
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21
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Hoshino Y, Nakamoto M, Miura Y. Control of Protein-Binding Kinetics on Synthetic Polymer Nanoparticles by Tuning Flexibility and Inducing Conformation Changes of Polymer Chains. J Am Chem Soc 2012; 134:15209-12. [DOI: 10.1021/ja306053s] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yu Hoshino
- Department
of Chemical Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395,
Japan
| | - Masahiko Nakamoto
- Department
of Chemical Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395,
Japan
| | - Yoshiko Miura
- Department
of Chemical Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395,
Japan
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22
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Liu S, Fu R, Zhou LH, Chen SP. Application of consensus scoring and principal component analysis for virtual screening against β-secretase (BACE-1). PLoS One 2012; 7:e38086. [PMID: 22701601 PMCID: PMC3372491 DOI: 10.1371/journal.pone.0038086] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2011] [Accepted: 05/03/2012] [Indexed: 01/19/2023] Open
Abstract
Background In order to identify novel chemical classes of β-secretase (BACE-1) inhibitors, an alternative scoring protocol, Principal Component Analysis (PCA), was proposed to summarize most of the information from the original scoring functions and re-rank the results from the virtual screening against BACE-1. Method Given a training set (50 BACE-1 inhibitors and 9950 inactive diverse compounds), three rank-based virtual screening methods, individual scoring, conventional consensus scoring and PCA, were judged by the hit number in the top 1% of the ranked list. The docking poses were generated by Surflex, five scoring functions (Surflex_Score, D_Score, G_Score, ChemScore, and PMF_Score) were used for pose extraction. For each pose group, twelve scoring functions (Surflex_Score, D_Score, G_Score, ChemScore, PMF_Score, LigScore1, LigScore2, PLP1, PLP2, jain, Ludi_1, and Ludi_2) were used for the pose rank. For a test set, 113,228 chemical compounds (Sigma-Aldrich® corporate chemical directory) were docked by Surflex, then ranked by the same three ranking methods motioned above to select the potential active compounds for experimental test. Results For the training set, the PCA approach yielded consistently superior rankings compared to conventional consensus scoring and single scoring. For the test set, the top 20 compounds according to conventional consensus scoring were experimentally tested, no inhibitor was found. Then, we relied on PCA scoring protocol to test another different top 20 compounds and two low micromolar inhibitors (S450588 and 276065) were emerged through the BACE-1 fluorescence resonance energy transfer (FRET) assay. Conclusion The PCA method extends the conventional consensus scoring in a quantitative statistical manner and would appear to have considerable potential for chemical screening applications.
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Affiliation(s)
- Shu Liu
- Department of Anatomy, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, People’s Republic of China
- * E-mail: (S-PC); (SL)
| | - Rao Fu
- Department of Anatomy, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Li-Hua Zhou
- Department of Anatomy, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Sheng-Ping Chen
- Guangdong Province Key Laboratory of Functional Molecules in Oceanic Microorganism, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, People’s Republic of China
- * E-mail: (S-PC); (SL)
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23
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Cukier RI. Simulations of temperature and salt concentration effects on bZIP, a basic region leucine zipper. J Phys Chem B 2012; 116:6071-86. [PMID: 22559083 DOI: 10.1021/jp300836t] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Basic region leucine zipper (bZIP) transcription factors are dimeric proteins that recognize DNA. The monomers consist of a leucine zipper subdomain responsible for dimerization and a highly basic DNA recognition subdomain. Twelve explicit solvent molecular dynamics (MD) trajectories were run on the GCN4 bZIP transcriptional factor in the absence of DNA at three temperatures and two ion concentrations (0 mM with Cl(-) ions to neutralize the bZIP and 200 mM with additional Na(+) and Cl(-) ions) to probe the conformational ensemble that the basic region samples. In most trajectories, the basic region exhibits an alligator-jaw-like opening and closing (only one monomer moves), versus scissor-like motion, by a mainly rigid body, hinge motion centered on three "fork" residues that span the basic region to the coiled coil. In this motion, the α-helical character of the basic region monomers is mostly maintained. A broad range of distances is accessed, consistent with the absence of particular interactions for the basic region monomers. In two of the trajectories, the basic region monomers "collapse" to form a stable state. The coiled coil, leucine zipper subdomain is very stable for all of the trajectories. Ion solvation of the charged residue side chains is transient, on the scale of a few picoseconds. There is no evidence for persistent specific ion salt bridges to charged residues. For 0 mM, only certain basic region positively charged residues are substantially Cl(-) ion salt bridged. For 200 mM, in addition, some basic region negatively (positively) charged residues are salt bridged to Na(+) (Cl(-)) ions. The different ion solvation patterns at the two ion concentrations are not greatly temperature sensitive, and the conformational sampling found in the MD is remarkably unperturbed by ion concentration and/or temperature.
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Affiliation(s)
- Robert I Cukier
- Department of Chemistry Michigan State University, East Lansing, 48824-1322, United States.
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24
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Chen J. Towards the physical basis of how intrinsic disorder mediates protein function. Arch Biochem Biophys 2012; 524:123-31. [PMID: 22579883 DOI: 10.1016/j.abb.2012.04.024] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 04/28/2012] [Accepted: 04/30/2012] [Indexed: 02/06/2023]
Abstract
Intrinsically disordered proteins (IDPs) are an important class of functional proteins that is highly prevalent in biology and has broad association with human diseases. In contrast to structured proteins, free IDPs exist as heterogeneous and dynamical conformational ensembles under physiological conditions. Many concepts have been discussed on how such intrinsic disorder may provide crucial functional advantages, particularly in cellular signaling and regulation. Establishing the physical basis of these proposed phenomena requires not only detailed characterization of the disordered conformational ensembles, but also mechanistic understanding of the roles of various ensemble properties in IDP interaction and regulation. Here, we review the experimental and computational approaches that may be integrated to address many important challenges of establishing a "structural" basis of IDP function, and discuss some of the key emerging ideas on how the conformational ensembles of IDPs may mediate function, especially in coupled binding and folding interactions.
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Affiliation(s)
- Jianhan Chen
- Department of Biochemistry, Kansas State University, Manhattan, KS 66506, USA.
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25
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Haq SR, Chi CN, Bach A, Dogan J, Engström Å, Hultqvist G, Karlsson OA, Lundström P, Montemiglio LC, Strømgaard K, Gianni S, Jemth P. Side-chain interactions form late and cooperatively in the binding reaction between disordered peptides and PDZ domains. J Am Chem Soc 2011; 134:599-605. [PMID: 22129097 DOI: 10.1021/ja209341w] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Intrinsically disordered proteins are very common and mediate numerous protein-protein and protein-DNA interactions. While it is clear that these interactions are instrumental for the life of the mammalian cell, there is a paucity of data regarding their molecular binding mechanisms. Here we have used short peptides as a model system for intrinsically disordered proteins. Linear free energy relationships based on rate and equilibrium constants for the binding of these peptides to ordered target proteins, PDZ domains, demonstrate that native side-chain interactions form mainly after the rate-limiting barrier for binding and in a cooperative fashion. This finding suggests that these disordered peptides first form a weak encounter complex with non-native interactions. The data do not support the recent notion that the affinities of intrinsically disordered proteins toward their targets are generally governed by their association rate constants. Instead, we observed the opposite for peptide-PDZ interactions, namely, that changes in K(d) correlate with changes in k(off).
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Affiliation(s)
- S Raza Haq
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
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26
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Bao J, Krylova SM, Reinstein O, Johnson PE, Krylov SN. Label-free solution-based kinetic study of aptamer-small molecule interactions by kinetic capillary electrophoresis with UV detection revealing how kinetics control equilibrium. Anal Chem 2011; 83:8387-90. [PMID: 21995945 DOI: 10.1021/ac2026699] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here we demonstrate a label-free solution-based approach for studying the kinetics of biopolymer-small molecule interactions. The approach utilizes kinetic capillary electrophoresis (KCE) separation and UV light absorption detection of the unlabeled small molecule. In this proof-of-concept work, we applied KCE-UV to study kinetics of interaction between a small molecule and a DNA aptamer. From the kinetic analysis of a series of aptamers, we found that dissociation rather than binding controls the stability of the complex. Because of its label-free features and generic nature, KCE-UV promises to become a practical tool for challenging kinetic studies of biopolymer-small molecule interactions.
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