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Herling TW, Cassaignau AME, Wentink AS, Peter QAE, Kumar PC, Kartanas T, Schneider MM, Cabrita LD, Christodoulou J, Knowles TPJ. Thermodynamic profiles for cotranslational trigger factor substrate recognition. SCIENCE ADVANCES 2024; 10:eadn4824. [PMID: 38985872 PMCID: PMC11235164 DOI: 10.1126/sciadv.adn4824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 06/04/2024] [Indexed: 07/12/2024]
Abstract
Molecular chaperones are central to the maintenance of proteostasis in living cells. A key member of this protein family is trigger factor (TF), which acts throughout the protein life cycle and has a ubiquitous role as the first chaperone encountered by proteins during synthesis. However, our understanding of how TF achieves favorable interactions with such a diverse substrate base remains limited. Here, we use microfluidics to reveal the thermodynamic determinants of this process. We find that TF binding to empty 70S ribosomes is enthalpy-driven, with micromolar affinity, while nanomolar affinity is achieved through a favorable entropic contribution for both intrinsically disordered and folding-competent nascent chains. These findings suggest a general mechanism for cotranslational TF function, which relies on occupation of the exposed TF-substrate binding groove rather than specific complementarity between chaperone and nascent chain. These insights add to our wider understanding of how proteins can achieve broad substrate specificity.
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Affiliation(s)
- Therese W. Herling
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Anaïs M. E. Cassaignau
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1 6BT, UK
| | - Anne S. Wentink
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1 6BT, UK
| | - Quentin A. E. Peter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Pavan C. Kumar
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Tadas Kartanas
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Matthias M. Schneider
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Lisa D. Cabrita
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1 6BT, UK
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1 6BT, UK
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
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2
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Herling TW, Invernizzi G, Ausserwöger H, Bjelke JR, Egebjerg T, Lund S, Lorenzen N, Knowles TPJ. Nonspecificity fingerprints for clinical-stage antibodies in solution. Proc Natl Acad Sci U S A 2023; 120:e2306700120. [PMID: 38109540 PMCID: PMC10756282 DOI: 10.1073/pnas.2306700120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 11/06/2023] [Indexed: 12/20/2023] Open
Abstract
Monoclonal antibodies (mAbs) have successfully been developed for the treatment of a wide range of diseases. The clinical success of mAbs does not solely rely on optimal potency and safety but also require good biophysical properties to ensure a high developability potential. In particular, nonspecific interactions are a key developability parameter to monitor during discovery and development. Despite an increased focus on the detection of nonspecific interactions, their underlying physicochemical origins remain poorly understood. Here, we employ solution-based microfluidic technologies to characterize a set of clinical-stage mAbs and their interactions with commonly used nonspecificity ligands to generate nonspecificity fingerprints, providing quantitative data on the underlying physical chemistry. Furthermore, the solution-based analysis enables us to measure binding affinities directly, and we evaluate the contribution of avidity in nonspecific binding by mAbs. We find that avidity can increase the apparent affinity by two orders of magnitude. Notably, we find that a subset of these highly developed mAbs show nonspecific electrostatic interactions, even at physiological pH and ionic strength, and that they can form microscale particles with charge-complementary polymers. The group of mAb constructs flagged here for nonspecificity are among the worst performers in independent reports of surface and column-based screens. The solution measurements improve on the state-of-the-art by providing a stand-alone result for individual mAbs without the need to benchmark against cohort data. Based on our findings, we propose a quantitative solution-based nonspecificity score, which can be integrated in the development workflow for biological therapeutics and more widely in protein engineering.
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Affiliation(s)
- Therese W. Herling
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | | | - Hannes Ausserwöger
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Jais Rose Bjelke
- Global Research Technologies, Novo Nordisk A/S, Måløv2760, Denmark
| | - Thomas Egebjerg
- Global Research Technologies, Novo Nordisk A/S, Måløv2760, Denmark
| | - Søren Lund
- Global Research Technologies, Novo Nordisk A/S, Måløv2760, Denmark
| | - Nikolai Lorenzen
- Global Research Technologies, Novo Nordisk A/S, Måløv2760, Denmark
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
- Department of Physics, University of Cambridge, CambridgeCB3 0HE, United Kingdom
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3
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Ausserwöger H, Schneider MM, Herling TW, Arosio P, Invernizzi G, Knowles TPJ, Lorenzen N. Non-specificity as the sticky problem in therapeutic antibody development. Nat Rev Chem 2022; 6:844-861. [PMID: 37117703 DOI: 10.1038/s41570-022-00438-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2022] [Indexed: 11/16/2022]
Abstract
Antibodies are highly potent therapeutic scaffolds with more than a hundred different products approved on the market. Successful development of antibody-based drugs requires a trade-off between high target specificity and target binding affinity. In order to better understand this problem, we here review non-specific interactions and explore their fundamental physicochemical origins. We discuss the role of surface patches - clusters of surface-exposed amino acid residues with similar physicochemical properties - as inducers of non-specific interactions. These patches collectively drive interactions including dipole-dipole, π-stacking and hydrophobic interactions to complementary moieties. We elucidate links between these supramolecular assembly processes and macroscopic development issues, such as decreased physical stability and poor in vivo half-life. Finally, we highlight challenges and opportunities for optimizing protein binding specificity and minimizing non-specificity for future generations of therapeutics.
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4
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Diffusional microfluidics for protein analysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2021.116508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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5
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Arter WE, Saar KL, Herling TW, Knowles TPJ. Microchip Free-Flow Electrophoresis for Bioanalysis, Sensing, and Purification. Methods Mol Biol 2022; 2394:249-266. [PMID: 35094333 DOI: 10.1007/978-1-0716-1811-0_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The separation of complex mixtures is ubiquitous throughout molecular biology, and techniques such as gel-based electrophoresis are common laboratory practice. Such methods are not without their drawbacks, however, which include non-specific interactions between analyte and the separation matrix, poor yields in purification and non-continuous analyte throughput. Microfluidic techniques, which exploit physical phenomena unique to the microscale, promise to improve many aspects of traditional laboratory procedures. These methods offer a quantitative, solution-based alternative to traditional gel electrophoresis, with rapid measurement times enabling the analysis of transient or weak biomolecular interactions that would be challenging to observe with traditional methods. Here, we present a protocol for the lithographic fabrication and operation of microfluidic chips capable of free-flow electrophoretic (FFE) fractionation and analysis of biological analytes. We demonstrate the efficacy of our approach through a protein-sensing methodology based on FFE fractionation of DNA-protein mixtures. In addition, the FFE technique described here can be readily adapted to suit a variety of preparative and analytical applications, providing information on the charge, zeta-potential, and interactions of analytes.
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Affiliation(s)
- William E Arter
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Kadi L Saar
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Cambridge, UK.
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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6
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Grant J, Kimmel BR, Szymczak LC, Roll J, Mrksich M. Characterizing Enzyme Cooperativity with Imaging SAMDI-MS. Chemistry 2021; 28:e202103807. [PMID: 34890480 DOI: 10.1002/chem.202103807] [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: 10/22/2021] [Indexed: 11/11/2022]
Abstract
This paper describes a method that combines a microfluidic device and self-assembled monolayers for matrix-assisted laser desorption/ionization mass spectrometry (SAMDI) mass spectrometry to calculate the cooperativity in binding of calcium ions to peptidylarginine deiminase type 2 (PAD2). This example uses only 120 µL of enzyme solution and three fluidic inputs. This microfluidic device incorporates a self-assembled monolayer that is functionalized with a peptide substrate for PAD2. The enzyme and different concentrations of calcium ions are flowed through each of eight channels, where the position along the channel corresponds to reaction time and position across the channel corresponds to the concentration of Ca2+. Imaging SAMDI (iSAMDI) is then used to determine the yield for the enzyme reaction at each 200 µm pixel on the monolayer, providing a time course for the reactions. Analysis of the peptide conversion as a function of position and time gives the degree of cooperativity (n) and the concentration of ligand required for half maximal activity (K0.5) for the Ca2+ - dependent activation of PAD2. This work establishes a high-throughput and label-free method for studying enzyme-ligand binding interactions and widens the applicability of microfluidics and matrix-assisted laser desorption/ionization mass spectrometry (MALDI) imaging mass spectrometry.
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Affiliation(s)
| | - Blaise R Kimmel
- Northwestern University, Chemical and Biological Engineering, UNITED STATES
| | | | - Juliet Roll
- Northwestern University, Biomedical Engineering, UNITED STATES
| | - Milan Mrksich
- Northwestern University, Department of Chemistry, 2145 Sheridan Road, 60208, Evanston, UNITED STATES
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7
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Schneider MM, Gautam S, Herling TW, Andrzejewska E, Krainer G, Miller AM, Trinkaus VA, Peter QAE, Ruggeri FS, Vendruscolo M, Bracher A, Dobson CM, Hartl FU, Knowles TPJ. The Hsc70 disaggregation machinery removes monomer units directly from α-synuclein fibril ends. Nat Commun 2021; 12:5999. [PMID: 34650037 PMCID: PMC8516981 DOI: 10.1038/s41467-021-25966-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 08/25/2021] [Indexed: 02/02/2023] Open
Abstract
Molecular chaperones contribute to the maintenance of cellular protein homoeostasis through assisting de novo protein folding and preventing amyloid formation. Chaperones of the Hsp70 family can further disaggregate otherwise irreversible aggregate species such as α-synuclein fibrils, which accumulate in Parkinson's disease. However, the mechanisms and kinetics of this key functionality are only partially understood. Here, we combine microfluidic measurements with chemical kinetics to study α-synuclein disaggregation. We show that Hsc70 together with its co-chaperones DnaJB1 and Apg2 can completely reverse α-synuclein aggregation back to its soluble monomeric state. This reaction proceeds through first-order kinetics where monomer units are removed directly from the fibril ends with little contribution from intermediate fibril fragmentation steps. These findings extend our mechanistic understanding of the role of chaperones in the suppression of amyloid proliferation and in aggregate clearance, and inform on possibilities and limitations of this strategy in the development of therapeutics against synucleinopathies.
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Affiliation(s)
- Matthias M. Schneider
- grid.5335.00000000121885934Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Saurabh Gautam
- grid.418615.f0000 0004 0491 845XDepartment of Cellular Biochemistry, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany ,Present Address: ViraTherapeutics GmbH, 6063 Rum, Austria
| | - Therese W. Herling
- grid.5335.00000000121885934Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Ewa Andrzejewska
- grid.5335.00000000121885934Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Georg Krainer
- grid.5335.00000000121885934Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Alyssa M. Miller
- grid.5335.00000000121885934Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Victoria A. Trinkaus
- grid.418615.f0000 0004 0491 845XDepartment of Cellular Biochemistry, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany ,grid.452617.3Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Quentin A. E. Peter
- grid.5335.00000000121885934Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Francesco Simone Ruggeri
- grid.5335.00000000121885934Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Michele Vendruscolo
- grid.5335.00000000121885934Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Andreas Bracher
- grid.418615.f0000 0004 0491 845XDepartment of Cellular Biochemistry, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Christopher M. Dobson
- grid.5335.00000000121885934Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - F. Ulrich Hartl
- grid.418615.f0000 0004 0491 845XDepartment of Cellular Biochemistry, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany ,grid.452617.3Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Tuomas P. J. Knowles
- grid.5335.00000000121885934Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK ,grid.5335.00000000121885934Department of Physics, Cavendish Laboratory, University of Cambridge, JJ Thomson Road, Cambridge, CB3 0HE UK
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8
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Zhang Y, Wright MA, Saar KL, Challa P, Morgunov AS, Peter QAE, Devenish S, Dobson CM, Knowles TPJ. Machine learning-aided protein identification from multidimensional signatures. LAB ON A CHIP 2021; 21:2922-2931. [PMID: 34109955 PMCID: PMC8314522 DOI: 10.1039/d0lc01148g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
The ability to determine the identity of specific proteins is a critical challenge in many areas of cellular and molecular biology, and in medical diagnostics. Here, we present a macine learning aided microfluidic protein characterisation strategy that within a few minutes generates a three-dimensional fingerprint of a protein sample indicative of its amino acid composition and size and, thereby, creates a unique signature for the protein. By acquiring such multidimensional fingerprints for a set of ten proteins and using machine learning approaches to classify the fingerprints, we demonstrate that this strategy allows proteins to be classified at a high accuracy, even though classification using a single dimension is not possible. Moreover, we show that the acquired fingerprints correlate with the amino acid content of the samples, which makes it is possible to identify proteins directly from their sequence without requiring any prior knowledge about the fingerprints. These findings suggest that such a multidimensional profiling strategy can lead to the development of a novel method for protein identification in a microfluidic format.
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Affiliation(s)
- Yuewen Zhang
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Maya A Wright
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Kadi L Saar
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. and Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge CB3 0HE, UK
| | - Pavankumar Challa
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Alexey S Morgunov
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. and Fluidic Analytics Ltd., Cambridge, UK
| | - Quentin A E Peter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | | | - Christopher M Dobson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. and Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge CB3 0HE, UK
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9
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Sprenger J, Trifan A, Patel N, Vanderbeck A, Bredfelt J, Tajkhorshid E, Rowlett R, Lo Leggio L, Åkerfeldt KS, Linse S. Calmodulin complexes with brain and muscle creatine kinase peptides. Curr Res Struct Biol 2021; 3:121-132. [PMID: 34235492 PMCID: PMC8244255 DOI: 10.1016/j.crstbi.2021.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/27/2021] [Accepted: 05/03/2021] [Indexed: 01/18/2023] Open
Abstract
Calmodulin (CaM) is a ubiquitous Ca2+ sensing protein that binds to and modulates numerous target proteins and enzymes during cellular signaling processes. A large number of CaM-target complexes have been identified and structurally characterized, revealing a wide diversity of CaM-binding modes. A newly identified target is creatine kinase (CK), a central enzyme in cellular energy homeostasis. This study reports two high-resolution X-ray structures, determined to 1.24 Å and 1.43 Å resolution, of calmodulin in complex with peptides from human brain and muscle CK, respectively. Both complexes adopt a rare extended binding mode with an observed stoichiometry of 1:2 CaM:peptide, confirmed by isothermal titration calorimetry, suggesting that each CaM domain independently binds one CK peptide in a Ca2+-depended manner. While the overall binding mode is similar between the structures with muscle or brain-type CK peptides, the most significant difference is the opposite binding orientation of the peptides in the N-terminal domain. This may extrapolate into distinct binding modes and regulation of the full-length CK isoforms. The structural insights gained in this study strengthen the link between cellular energy homeostasis and Ca2+-mediated cell signaling and may shed light on ways by which cells can 'fine tune' their energy levels to match the spatial and temporal demands.
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Key Words
- ADP, Adenosine diphosphate
- ATP, Adenosine triphosphate
- CK, Creatine kinase
- CKB, Creatine kinase, brain-type
- CKM, Creatine kinase, muscle-type
- Ca2+, Calcium ion (divalent)
- CaM, Calmodulin
- Calcium signaling
- Calmodulin X-ray structure
- Cellular energy metabolism
- Cr, Creatine
- CrP, Creatine phosphate
- Enzyme regulation
- Fmoc, Fluorenylmethoxycarbonyl
- ITC, Isothermal titration calorimetry
- Isothermal titration calorimetry
- MR, Molecular replacement
- PDB, Protein data bank
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Affiliation(s)
- Janina Sprenger
- Department of Biochemistry and Structural Biology, Chemical Center, PO Box 124, SE-221 00, Lund, Sweden
- Chemistry Department, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
| | - Anda Trifan
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 405 N Matthews, Urbana, IL, 61801, USA
| | - Neal Patel
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, PA, 19041, USA
| | - Ashley Vanderbeck
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, PA, 19041, USA
| | - Jenny Bredfelt
- Department of Biochemistry and Structural Biology, Chemical Center, PO Box 124, SE-221 00, Lund, Sweden
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 405 N Matthews, Urbana, IL, 61801, USA
| | - Roger Rowlett
- Department of Chemistry, Colgate University, 13 Oak Drive, Hamilton, NY, 13346, USA
| | - Leila Lo Leggio
- Chemistry Department, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
| | - Karin S. Åkerfeldt
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, PA, 19041, USA
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Chemical Center, PO Box 124, SE-221 00, Lund, Sweden
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10
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Plata M, Hale W, Sharma M, Werner JM, Utz M. Microfluidic platform for serial mixing experiments with in operando nuclear magnetic resonance spectroscopy. LAB ON A CHIP 2021; 21:1598-1603. [PMID: 33662071 DOI: 10.1039/d0lc01100b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We present a microfluidic platform that allows in operando nuclear magnetic resonance (NMR) observation of serial mixing experiments. Gradually adding one reagent to another is a fundamental experimental modality, widely used to quantify equilibrium constants, for titrations, and in chemical kinetics studies. NMR provides a non-invasive means to quantify concentrations and to follow structural changes at the molecular level as a function of exchanged volume. Using active pneumatic valving on the microfluidic device directly inside an NMR spectrometer equipped with a transmission-line NMR microprobe, the system allows injection of aliquots and in situ mixing in a sample volume of less than 10 μL.
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Affiliation(s)
- Marek Plata
- School of Chemistry, University of Southampton, SO17 1BJ, UK. and Institute for Life Sciences, University of Southampton, SO17 1BJ, UK and School of Biological Sciences, University of Southampton, SO17 1BJ, UK
| | - William Hale
- School of Chemistry, University of Southampton, SO17 1BJ, UK.
| | | | - Jörn M Werner
- Institute for Life Sciences, University of Southampton, SO17 1BJ, UK and School of Biological Sciences, University of Southampton, SO17 1BJ, UK
| | - Marcel Utz
- School of Chemistry, University of Southampton, SO17 1BJ, UK. and Institute for Life Sciences, University of Southampton, SO17 1BJ, UK
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11
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Zhang Y, Herling TW, Kreida S, Peter QAE, Kartanas T, Törnroth-Horsefield S, Linse S, Knowles TPJ. A microfluidic strategy for the detection of membrane protein interactions. LAB ON A CHIP 2020; 20:3230-3238. [PMID: 32744557 DOI: 10.1039/d0lc00205d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Membrane proteins perform a vast range of vital biological functions and are the gatekeepers for exchange of information and matter between the intracellular and extracellular environment. However, membrane protein interactions can be challenging to characterise in a quantitative manner due to the low solubility and large size of the membrane protein complex with associated lipid or detergent molecules. Here, we show that measurements of the changes in charge and diffusivity on the micron scale allow for non-disruptive studies of membrane protein interactions in solution. The approach presented here uses measurements of key physical properties of membrane proteins and their ligands to characterise the binding equilibrium parameters. We demonstrate this approach for human aquaporins (AQPs), key membrane proteins in the regulation of water homeostasis in cells. We perform quantitative measurements to characterise the interactions between two full-length AQP isoforms and the regulatory protein, calmodulin (CaM), and show that CaM selectively binds AQP0. Through direct measurements of the diffusivity and mobility in an external electric field, the diffusion coefficients and electrophoretic mobilities are determined for the individual components and the resulting AQP0-CaM complex. Furthermore, we obtain directly the binding equilibrium parameters and effective charge of each component. These results open up a route towards the use of microfluidics as a general platform in protein science and open up new possibilities for the characterisation of membrane protein interactions in solution.
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Affiliation(s)
- Yuewen Zhang
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Therese W Herling
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Stefan Kreida
- Department of Biochemistry and Structural Biology, Lund University, Lund, 221 00, Sweden.
| | - Quentin A E Peter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Tadas Kartanas
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | | | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, Lund, 221 00, Sweden.
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. and Cavendish Laboratory, University of Cambridge, J J Thomson Avenue, Cambridge, CB3 0HE, UK
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12
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Arter WE, Levin A, Krainer G, Knowles TPJ. Microfluidic approaches for the analysis of protein-protein interactions in solution. Biophys Rev 2020; 12:575-585. [PMID: 32266673 PMCID: PMC7242286 DOI: 10.1007/s12551-020-00679-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/02/2020] [Indexed: 12/15/2022] Open
Abstract
Exploration and characterisation of the human proteome is a key objective enabling a heightened understanding of biological function, malfunction and pharmaceutical design. Since proteins typically exhibit their behaviour by binding to other proteins, the challenge of probing protein-protein interactions has been the focus of new and improved experimental approaches. Here, we review recently developed microfluidic techniques for the study and quantification of protein-protein interactions. We focus on methodologies that utilise the inherent strength of microfluidics for the control of mass transport on the micron scale, to facilitate surface and membrane-free interrogation and quantification of interacting proteins. Thus, the microfluidic tools described here provide the capability to yield insights on protein-protein interactions under physiological conditions. We first discuss the defining principles of microfluidics, and methods for the analysis of protein-protein interactions that utilise the diffusion-controlled mixing characteristic of fluids at the microscale. We then describe techniques that employ electrophoretic forces to manipulate and fractionate interacting protein systems for their biophysical characterisation, before discussing strategies that use microdroplet compartmentalisation for the analysis of protein interactions. We conclude by highlighting future directions for the field, such as the integration of microfluidic experiments into high-throughput workflows for the investigation of protein interaction networks.
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Affiliation(s)
- William E Arter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Aviad Levin
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Georg Krainer
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK.
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13
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Rho HS, Veltkamp HW, Hanke AT, Ottens M, Breukers C, Habibović P, Gardeniers H. Systematic Investigation of Insulin Fibrillation on a Chip. Molecules 2020; 25:molecules25061380. [PMID: 32197443 PMCID: PMC7144930 DOI: 10.3390/molecules25061380] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/13/2020] [Accepted: 03/17/2020] [Indexed: 12/29/2022] Open
Abstract
A microfluidic protein aggregation device (microPAD) that allows the user to perform a series of protein incubations with various concentrations of two reagents is demonstrated. The microfluidic device consists of 64 incubation chambers to perform individual incubations of the protein at 64 specific conditions. Parallel processes of metering reagents, stepwise concentration gradient generation, and mixing are achieved simultaneously by pneumatic valves. Fibrillation of bovine insulin was selected to test the device. The effect of insulin and sodium chloride (NaCl) concentration on the formation of fibrillar structures was studied by observing the growth rate of partially folded protein, using the fluorescent marker Thioflavin-T. Moreover, dual gradients of different NaCl and hydrochloric acid (HCl) concentrations were formed, to investigate their interactive roles in the formation of insulin fibrils and spherulites. The chip-system provides a bird’s eye view on protein aggregation, including an overview of the factors that affect the process and their interactions. This microfluidic platform is potentially useful for rapid analysis of the fibrillation of proteins associated with many misfolding-based diseases, such as quantitative and qualitative studies on amyloid growth.
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Affiliation(s)
- Hoon Suk Rho
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, 6200 MD Maastricht, The Netherlands; (H.S.R.); (P.H.)
- Mesoscale Chemical Systems Group, MESA+ Institute for Nanotechnology, University of Twente, 7522 NB Enschede, The Netherlands
| | - Henk-Willem Veltkamp
- Integrated Devices and Systems Group, MESA+ Institute for Nanotechnology, University of Twente, 7522 NB Enschede, The Netherlands;
| | - Alexander Thomas Hanke
- BioProcess Engineering Group, Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, 2628 CD Delft, The Netherlands; (A.T.H.); (M.O.)
| | - Marcel Ottens
- BioProcess Engineering Group, Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, 2628 CD Delft, The Netherlands; (A.T.H.); (M.O.)
| | - Christian Breukers
- Medical Cell BioPhysics Group, Technical Medical Centre, University of Twente, 7522 NB Enschede, The Netherlands;
| | - Pamela Habibović
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, 6200 MD Maastricht, The Netherlands; (H.S.R.); (P.H.)
| | - Han Gardeniers
- Mesoscale Chemical Systems Group, MESA+ Institute for Nanotechnology, University of Twente, 7522 NB Enschede, The Netherlands
- Correspondence: ; Tel.: +31-(0)53-489-4356
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14
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Azouz M, Gonin M, Fiedler S, Faherty J, Decossas M, Cullin C, Villette S, Lafleur M, D Alves I, Lecomte S, Ciaccafava A. Microfluidic diffusional sizing probes lipid nanodiscs formation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183215. [PMID: 32061645 DOI: 10.1016/j.bbamem.2020.183215] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 12/29/2022]
Abstract
The biophysical characterisation of membrane proteins and their interactions with lipids in native membrane habitat remains a major challenge. Indeed, traditional solubilisation procedures with detergents often causes the loss of native lipids surrounding membrane proteins, which ultimately impacts structural and functional properties. Recently, copolymer-based nanodiscs have emerged as a highly promising tool, thanks to their unique ability of solubilising membrane proteins directly from native membranes, in the shape of discoidal patches of lipid bilayers. While this methodology finally set us free from the use of detergents, some limitations are however associated with the use of such copolymers. Among them, one can cite the tedious control of the nanodiscs size, their instability in basic pH and in the presence of divalent cations. In this respect, many variants of the widely used Styrene Maleic Acid (SMA) copolymer have been developed to specifically address those limitations. With the multiplication of new SMA copolymer variants and the growing interest in copolymer-based nanodiscs for the characterisation of membrane proteins, there is a need to better understand and control their formation. Among the techniques used to characterise the solubilisation of lipid bilayer by amphipathic molecules, cryo-TEM, 31P NMR, DLS, ITC and fluorescence spectroscopy are the most widely used, with a consensus made in the sense that a combination of these techniques is required. In this work, we propose to evaluate the capacity of Microfluidic Diffusional Sizing (MDS) as a new method to follow copolymer nanodiscs formation. Originally designed to determine protein size through laminar flow diffusion, we present a novel application along with a protocol development to observe nanodiscs formation by MDS. We show that MDS allows to precisely measure the size of nanodiscs, and to determine the copolymer/lipid ratio at the onset of solubilisation. Finally, we use MDS to characterise peptide/nanodisc interaction. The technique shows a promising ability to highlight the pivotal role of lipids in promoting interactions through a case study with an aggregating peptide. This confirmed the relevance of using the MDS and nanodiscs as biomimetic models for such investigations.
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Affiliation(s)
- Mehdi Azouz
- Univ Bordeaux, CNRS, CBMN UMR 5248, Bat B14 Allée Geoffroy St Hilaire, F-33600 Pessac, France
| | - Mathilde Gonin
- Univ Bordeaux, CNRS, CBMN UMR 5248, Bat B14 Allée Geoffroy St Hilaire, F-33600 Pessac, France
| | - Sebastian Fiedler
- Fluidic Analytics Ltd, Unit A, The Paddocks Business Centre, Cherry Hinton Rd, Cambridge CB1 8DH, United Kingdom
| | - Jonathan Faherty
- Fluidic Analytics Ltd, Unit A, The Paddocks Business Centre, Cherry Hinton Rd, Cambridge CB1 8DH, United Kingdom
| | - Marion Decossas
- Univ Bordeaux, CNRS, CBMN UMR 5248, Bat B14 Allée Geoffroy St Hilaire, F-33600 Pessac, France
| | - Christophe Cullin
- Univ Bordeaux, CNRS, CBMN UMR 5248, Bat B14 Allée Geoffroy St Hilaire, F-33600 Pessac, France
| | - Sandrine Villette
- Univ Bordeaux, CNRS, CBMN UMR 5248, Bat B14 Allée Geoffroy St Hilaire, F-33600 Pessac, France
| | - Michel Lafleur
- Department of chemistry, Université de Montréal, 2900, Édouard-Montpetit blvd., Montréal, Québec, Canada
| | - Isabel D Alves
- Univ Bordeaux, CNRS, CBMN UMR 5248, Bat B14 Allée Geoffroy St Hilaire, F-33600 Pessac, France
| | - Sophie Lecomte
- Univ Bordeaux, CNRS, CBMN UMR 5248, Bat B14 Allée Geoffroy St Hilaire, F-33600 Pessac, France.
| | - Alexandre Ciaccafava
- Univ Bordeaux, CNRS, CBMN UMR 5248, Bat B14 Allée Geoffroy St Hilaire, F-33600 Pessac, France.
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15
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Hajipour MJ, Mehrani M, Abbasi SH, Amin A, Kassaian SE, Garbern JC, Caracciolo G, Zanganeh S, Chitsazan M, Aghaverdi H, Shahri SMK, Ashkarran A, Raoufi M, Bauser-Heaton H, Zhang J, Muehlschlegel JD, Moore A, Lee RT, Wu JC, Serpooshan V, Mahmoudi M. Nanoscale Technologies for Prevention and Treatment of Heart Failure: Challenges and Opportunities. Chem Rev 2019; 119:11352-11390. [PMID: 31490059 PMCID: PMC7003249 DOI: 10.1021/acs.chemrev.8b00323] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The adult myocardium has a limited regenerative capacity following heart injury, and the lost cells are primarily replaced by fibrotic scar tissue. Suboptimal efficiency of current clinical therapies to resurrect the infarcted heart results in injured heart enlargement and remodeling to maintain its physiological functions. These remodeling processes ultimately leads to ischemic cardiomyopathy and heart failure (HF). Recent therapeutic approaches (e.g., regenerative and nanomedicine) have shown promise to prevent HF postmyocardial infarction in animal models. However, these preclinical, clinical, and technological advancements have yet to yield substantial enhancements in the survival rate and quality of life of patients with severe ischemic injuries. This could be attributed largely to the considerable gap in knowledge between clinicians and nanobioengineers. Development of highly effective cardiac regenerative therapies requires connecting and coordinating multiple fields, including cardiology, cellular and molecular biology, biochemistry and chemistry, and mechanical and materials sciences, among others. This review is particularly intended to bridge the knowledge gap between cardiologists and regenerative nanomedicine experts. Establishing this multidisciplinary knowledge base may help pave the way for developing novel, safer, and more effective approaches that will enable the medical community to reduce morbidity and mortality in HF patients.
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Affiliation(s)
| | - Mehdi Mehrani
- Tehran Heart Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Ahmad Amin
- Rajaie Cardiovascular, Medical and Research Center, Iran University of Medical Science Tehran, Iran
| | | | - Jessica C. Garbern
- Department of Stem Cell and Regenerative Biology, Harvard University, Harvard Stem Cell Institute, Cambridge, Massachusetts, United States
- Department of Cardiology, Boston Children’s Hospital, Boston, Massachusetts, United States
| | - Giulio Caracciolo
- Department of Molecular Medicine, Sapienza University of Rome, V.le Regina Elena 291, 00161, Rome, Italy
| | - Steven Zanganeh
- Department of Radiology, Memorial Sloan Kettering, New York, NY 10065, United States
| | - Mitra Chitsazan
- Rajaie Cardiovascular, Medical and Research Center, Iran University of Medical Science Tehran, Iran
| | - Haniyeh Aghaverdi
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham & Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Seyed Mehdi Kamali Shahri
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham & Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Aliakbar Ashkarran
- Precision Health Program, Michigan State University, East Lansing, MI, United States
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham & Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Mohammad Raoufi
- Physical Chemistry I, Department of Chemistry and Biology & Research Center of Micro and Nanochemistry and Engineering, University of Siegen, Siegen, Germany
| | - Holly Bauser-Heaton
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Jianyi Zhang
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Jochen D. Muehlschlegel
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham & Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Anna Moore
- Precision Health Program, Michigan State University, East Lansing, MI, United States
| | - Richard T. Lee
- Department of Stem Cell and Regenerative Biology, Harvard University, Harvard Stem Cell Institute, Cambridge, Massachusetts, United States
- Department of Medicine, Division of Cardiology, Brigham and Women’s Hospital and Harvard Medical School, Cambridge, Massachusetts, United States
| | - Joseph C. Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California, United States
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, United States
| | - Vahid Serpooshan
- Department of Biomedical Engineering, Georgia Institute of Technology & Emory University School of Medicine, Atlanta, Georgia, United States
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Morteza Mahmoudi
- Precision Health Program, Michigan State University, East Lansing, MI, United States
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham & Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Connors Center for Women’s Health & Gender Biology, Brigham & Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States
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16
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Vanderpoorten O, Peter Q, Challa PK, Keyser UF, Baumberg J, Kaminski CF, Knowles TPJ. Scalable integration of nano-, and microfluidics with hybrid two-photon lithography. MICROSYSTEMS & NANOENGINEERING 2019; 5:40. [PMID: 31636930 PMCID: PMC6799807 DOI: 10.1038/s41378-019-0080-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/26/2019] [Accepted: 06/25/2019] [Indexed: 05/19/2023]
Abstract
Nanofluidic devices have great potential for applications in areas ranging from renewable energy to human health. A crucial requirement for the successful operation of nanofluidic devices is the ability to interface them in a scalable manner with the outside world. Here, we demonstrate a hybrid two photon nanolithography approach interfaced with conventional mask whole-wafer UV-photolithography to generate master wafers for the fabrication of integrated micro and nanofluidic devices. Using this approach we demonstrate the fabrication of molds from SU-8 photoresist with nanofluidic features down to 230 nm lateral width and channel heights from micron to sub-100 nm. Scanning electron microscopy and atomic force microscopy were used to characterize the printing capabilities of the system and show the integration of nanofluidic channels into an existing microfluidic chip design. The functionality of the devices was demonstrated through super-resolution microscopy, allowing the observation of features below the diffraction limit of light produced using our approach. Single molecule localization of diffusing dye molecules verified the successful imprint of nanochannels and the spatial confinement of molecules to 200 nm across the nanochannel molded from the master wafer. This approach integrates readily with current microfluidic fabrication methods and allows the combination of microfluidic devices with locally two-photon-written nano-sized functionalities, enabling rapid nanofluidic device fabrication and enhancement of existing microfluidic device architectures with nanofluidic features.
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Affiliation(s)
- Oliver Vanderpoorten
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS UK
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
- Cavendish Laboratory, Department of Physics, University of Cambridge, J. J. Thomson Avenue, Cambridge, CB30HE UK
| | - Quentin Peter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Pavan K. Challa
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Ulrich F. Keyser
- Cavendish Laboratory, Department of Physics, University of Cambridge, J. J. Thomson Avenue, Cambridge, CB30HE UK
| | - Jeremy Baumberg
- Cavendish Laboratory, Department of Physics, University of Cambridge, J. J. Thomson Avenue, Cambridge, CB30HE UK
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS UK
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
- Cavendish Laboratory, Department of Physics, University of Cambridge, J. J. Thomson Avenue, Cambridge, CB30HE UK
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17
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Sormanni P, Aprile FA, Vendruscolo M. Third generation antibody discovery methods: in silico rational design. Chem Soc Rev 2018; 47:9137-9157. [PMID: 30298157 DOI: 10.1039/c8cs00523k] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Owing to their outstanding performances in molecular recognition, antibodies are extensively used in research and applications in molecular biology, biotechnology and medicine. Recent advances in experimental and computational methods are making it possible to complement well-established in vivo (first generation) and in vitro (second generation) methods of antibody discovery with novel in silico (third generation) approaches. Here we describe the principles of computational antibody design and review the state of the art in this field. We then present Modular, a method that implements the rational design of antibodies in a modular manner, and describe the opportunities offered by this approach.
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Affiliation(s)
- Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
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18
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Hassan SA. Self-adaptive multiscaling algorithm for efficient simulations of many-protein systems in crowded conditions. Phys Chem Chem Phys 2018; 20:28544-28557. [PMID: 30421760 PMCID: PMC6752035 DOI: 10.1039/c8cp05517c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A method is described for the efficient simulation of multiprotein systems in crowded environments. It is based on an adaptive, reversible structural coarsening algorithm that preserves relevant physical features of the proteins across scales. Water is treated implicitly whereas all the other components of the aqueous solution, such as ions, cosolutes, or osmolytes, are treated in atomic detail. The focus is on the analytical adaptation of the solvent model to different levels of molecular resolutions, which allows continuous, on-the-fly transitions between scales. This permits the analytical calculation of forces during dynamics and preserves detailed balance in Monte Carlo simulations. A major computational speedup can be achieved in systems containing hundreds of proteins without cutting off the long-range interactions. The method can be combined with a self-adaptive configurational-bias sampling technique described previously, designed to detect strong, weak, or ultra-weak protein associations and shown to improve sampling efficiency and convergence. The implementation aims to simulate early stages of multimeric complexation, aggregation, or self-assembly. The method can be adopted as the basis for a more general algorithm to identify vertices, edges, and hubs in protein interaction networks or to predict critical steps in signal transduction pathways.
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Affiliation(s)
- Sergio A Hassan
- Center for Molecular Modeling, OIR/CIT, National Institutes of Health, U.S. DHHS, USA.
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19
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Shinde P, Mohan L, Kumar A, Dey K, Maddi A, Patananan AN, Tseng FG, Chang HY, Nagai M, Santra TS. Current Trends of Microfluidic Single-Cell Technologies. Int J Mol Sci 2018; 19:E3143. [PMID: 30322072 PMCID: PMC6213733 DOI: 10.3390/ijms19103143] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/27/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023] Open
Abstract
The investigation of human disease mechanisms is difficult due to the heterogeneity in gene expression and the physiological state of cells in a given population. In comparison to bulk cell measurements, single-cell measurement technologies can provide a better understanding of the interactions among molecules, organelles, cells, and the microenvironment, which can aid in the development of therapeutics and diagnostic tools. In recent years, single-cell technologies have become increasingly robust and accessible, although limitations exist. In this review, we describe the recent advances in single-cell technologies and their applications in single-cell manipulation, diagnosis, and therapeutics development.
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Affiliation(s)
- Pallavi Shinde
- Department of Engineering Design, Indian Institute of Technology Madras, Tamil Nadu 600036, India.
| | - Loganathan Mohan
- Department of Engineering Design, Indian Institute of Technology Madras, Tamil Nadu 600036, India.
| | - Amogh Kumar
- Department of Engineering Design, Indian Institute of Technology Madras, Tamil Nadu 600036, India.
| | - Koyel Dey
- Department of Engineering Design, Indian Institute of Technology Madras, Tamil Nadu 600036, India.
| | - Anjali Maddi
- Department of Engineering Design, Indian Institute of Technology Madras, Tamil Nadu 600036, India.
| | - Alexander N Patananan
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA 90095, USA.
| | - Fan-Gang Tseng
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu City 30071, Taiwan.
| | - Hwan-You Chang
- Department of Medical Science, National Tsing Hua University, Hsinchu City 30071, Taiwan.
| | - Moeto Nagai
- Department of Mechanical Engineering, Toyohashi University of Technology, Toyohashi 441-8580, Japan.
| | - Tuhin Subhra Santra
- Department of Engineering Design, Indian Institute of Technology Madras, Tamil Nadu 600036, India.
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20
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Nys G, Fillet M. Microfluidics contribution to pharmaceutical sciences: From drug discovery to post marketing product management. J Pharm Biomed Anal 2018; 159:348-362. [DOI: 10.1016/j.jpba.2018.07.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/08/2018] [Accepted: 07/10/2018] [Indexed: 12/18/2022]
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21
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Choudhary D, Kumar A, Magliery TJ, Sotomayor M. Using thermal scanning assays to test protein-protein interactions of inner-ear cadherins. PLoS One 2017; 12:e0189546. [PMID: 29261728 PMCID: PMC5736220 DOI: 10.1371/journal.pone.0189546] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/27/2017] [Indexed: 12/15/2022] Open
Abstract
Protein-protein interactions play a crucial role in biological processes such as cell-cell adhesion, immune system-pathogen interactions, and sensory perception. Understanding the structural determinants of protein-protein complex formation and obtaining quantitative estimates of their dissociation constant (KD) are essential for the study of these interactions and for the discovery of new therapeutics. At the same time, it is equally important to characterize protein-protein interactions in a high-throughput fashion. Here, we use a modified thermal scanning assay to test interactions of wild type (WT) and mutant variants of N-terminal fragments (EC1+2) of cadherin-23 and protocadherin-15, two proteins essential for inner-ear mechanotransduction. An environmentally sensitive fluorescent dye (SYPRO orange) is used to monitor melting temperature (Tm) shifts of protocadherin-15 EC1+2 (pcdh15) in the presence of increasing concentrations of cadherin-23 EC1+2 (cdh23). These Tm shifts are absent when we use proteins containing deafness-related missense mutations known to disrupt cdh23 binding to pcdh15, and are increased for some rationally designed mutants expected to enhance binding. In addition, surface plasmon resonance binding experiments were used to test if the Tm shifts correlated with changes in binding affinity. We used this approach to find a double mutation (cdh23(T15E)- pcdh15(G16D)) that enhances binding affinity of the cadherin complex by 1.98 kJ/mol, roughly two-fold that of the WT complex. We suggest that the thermal scanning methodology can be used in high-throughput format to quickly compare binding affinities (KD from nM up to 100 μM) for some heterodimeric protein complexes and to screen small molecule libraries to find protein-protein interaction inhibitors and enhancers.
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Affiliation(s)
- Deepanshu Choudhary
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Anusha Kumar
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Thomas J. Magliery
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
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22
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Pedde RD, Li H, Borchers CH, Akbari M. Microfluidic-Mass Spectrometry Interfaces for Translational Proteomics. Trends Biotechnol 2017; 35:954-970. [PMID: 28755975 DOI: 10.1016/j.tibtech.2017.06.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/05/2017] [Accepted: 06/09/2017] [Indexed: 12/29/2022]
Abstract
Interfacing mass spectrometry (MS) with microfluidic chips (μchip-MS) holds considerable potential to transform a clinician's toolbox, providing translatable methods for the early detection, diagnosis, monitoring, and treatment of noncommunicable diseases by streamlining and integrating laborious sample preparation workflows on high-throughput, user-friendly platforms. Overcoming the limitations of competitive immunoassays - currently the gold standard in clinical proteomics - μchip-MS can provide unprecedented access to complex proteomic assays having high sensitivity and specificity, but without the labor, costs, and complexities associated with conventional MS sample processing. This review surveys recent μchip-MS systems for clinical applications and examines their emerging role in streamlining the development and translation of MS-based proteomic assays by alleviating many of the challenges that currently inhibit widespread clinical adoption.
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Affiliation(s)
- R Daniel Pedde
- Laboratory for Innovations in Microengineering (LiME), Department of Mechanical Engineering, University of Victoria, 3800 Finnerty Rd., Victoria, BC, V8P 5C2, Canada; University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, 3101-4464 Markham St., Victoria, BC, V8Z 7X8, Canada
| | - Huiyan Li
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, 3101-4464 Markham St., Victoria, BC, V8Z 7X8, Canada
| | - Christoph H Borchers
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, 3101-4464 Markham St., Victoria, BC, V8Z 7X8, Canada; Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Rd., Victoria, BC, V8P 5C2, Canada; Gerald Bronfman Department of Oncology, McGill University, 5100 de Maisonneuve Blvd. West, Suite 720, Montreal, QC, H4A 3T2, Canada; Proteomics Centre, Jewish General Hospital, McGill University, 3755 Cote-Ste-Catherine Road, Montreal, QC, H3T 1E2, Canada.
| | - Mohsen Akbari
- Laboratory for Innovations in Microengineering (LiME), Department of Mechanical Engineering, University of Victoria, 3800 Finnerty Rd., Victoria, BC, V8P 5C2, Canada; Centre for Biomedical Research (CBR), University of Victoria, 3800 Finnerty Rd., Victoria, BC, V8P 5C2, Canada; Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd., Victoria, BC, V8P 5C2, Canada.
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23
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Crevillén AG, de Frutos M, Diez-Masa JC. On-chip single column transient isotachophoresis with free zone electrophoresis for preconcentration and separation of α-lactalbumin and β-lactoglobulin. Microchem J 2017. [DOI: 10.1016/j.microc.2017.04.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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