1
|
Jang H, Pawate AS, Bhargava R, Kenis PJA. Polymeric microfluidic continuous flow mixer combined with hyperspectral FT-IR imaging for studying rapid biomolecular events. LAB ON A CHIP 2019; 19:2598-2609. [PMID: 31259340 DOI: 10.1039/c9lc00182d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Early reaction intermediates in protein folding, such as those resulting in β-amyloid formation due to transient misfolding, emerge within a few hundred microseconds. Here, we report a method to obtain sub-millisecond temporal resolution and molecular structural information of protein (mis-)folding events by using a microfluidic continuous-flow mixer (MCFM) in combination with Fourier transform infrared (FT-IR) imaging. The MCFMs are made out of cyclic olefin copolymer (COC) films, because this approach allows for rapid prototyping of different mixer designs. Furthermore, COC offers high IR transparency between 1500 and 2500 cm-1, thus maximizing the signal to noise ratio of the IR data obtained from a sample of interest. By combining narrow and wide channel widths in MCFM design, the platform provides fast mixing (460 μs) to induce protein (mis-)folding, and it maximizes the residence time in the observing area, so a wide range of reaction timescales can be captured in a single image. We validated the platform for its ability to induce and observe sub-millisecond processes by studying two systems: (i) the mixing of H2O and D2O and (ii) the mixing induced deprotonation of carboxylic acid. First, we observed excellent agreement between simulated and experimental data of the on-chip mixing of H2O and D2O, which verifies the distance-reaction time relationships based on simulation. Second, deprotonation of carboxylic acid by on-chip mixing with sodium hydroxide solution validates the ability of the platform to induce rapid pH jump that is needed for some biomolecular reactions. Finally, we studied the methanol-induced partial-unfolding of ubiquitin to show that our platform can be used to study biomolecular events 'on-pathway' using FT-IR imaging. We successfully extracted kinetic and structural details of the conformational changes along the channel. Our results are in agreement with prior studies that required more elaborate stopped flow approaches to acquire data for different time points. In summary, the reported method uses an easy-to-fabricate microfluidic mixer platform integrated with hyperspectral FT-IR imaging for rapid acquisition of structural details and kinetic parameters of biomolecular reactions. This approach does not need stopped flow or molecular imaging probes, as required respectively for alternative FT-IR spectroscopy and fluorescence approaches.
Collapse
Affiliation(s)
- Hyukjin Jang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1406 W Green St, Urbana, IL, USA. and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Mathews Ave, Urbana, IL, USA
| | - Ashtamurthy S Pawate
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL, USA
| | - Rohit Bhargava
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1406 W Green St, Urbana, IL, USA. and Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL, USA and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Mathews Ave, Urbana, IL, USA
| | - Paul J A Kenis
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1406 W Green St, Urbana, IL, USA. and Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL, USA and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Mathews Ave, Urbana, IL, USA
| |
Collapse
|
2
|
Witkowska D, Rowińska-Żyrek M. Biophysical approaches for the study of metal-protein interactions. J Inorg Biochem 2019; 199:110783. [PMID: 31349072 DOI: 10.1016/j.jinorgbio.2019.110783] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions play important roles for a variety of cell functions, often involving metal ions; in fact, metal-ion binding mediates and regulates the activity of a wide range of biomolecules. Enlightening all of the specific features of metal-protein and metal-mediated protein-protein interactions can be a very challenging task; a detailed knowledge of the thermodynamic and spectroscopic parameters and the structural changes of the protein is normally required. For this purpose, many experimental techniques are employed, embracing all fields of Analytical and Bioinorganic Chemistry. In addition, the use of peptide models, reproducing the primary sequence of the metal-binding sites, is also proved to be useful. In this paper, a review of the most useful techniques for studying ligand-protein interactions with a special emphasis on metal-protein interactions is provided, with a critical summary of their strengths and limitations.
Collapse
Affiliation(s)
- Danuta Witkowska
- Public Higher Medical Professional School in Opole, Katowicka 68, 45060 Opole, Poland.
| | | |
Collapse
|
3
|
Abdizadeh H, Atilgan C. Predicting long term cooperativity and specific modulators of receptor interactions in human transferrin from dynamics within a single microstate. Phys Chem Chem Phys 2016; 18:7916-26. [DOI: 10.1039/c5cp05107j] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
PRS identifies regions contacting rapidly evolving residues that mechanically manipulate dissociation from the pathogen in the human transferrin–bacterial receptor complex.
Collapse
Affiliation(s)
- Haleh Abdizadeh
- Faculty of Engineering and Natural Sciences
- Sabanci University
- Tuzla
- Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences
- Sabanci University
- Tuzla
- Turkey
| |
Collapse
|
4
|
Sharabi O, Shirian J, Grossman M, Lebendiker M, Sagi I, Shifman J. Affinity- and specificity-enhancing mutations are frequent in multispecific interactions between TIMP2 and MMPs. PLoS One 2014; 9:e93712. [PMID: 24710006 PMCID: PMC3977929 DOI: 10.1371/journal.pone.0093712] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 03/05/2014] [Indexed: 12/04/2022] Open
Abstract
Multispecific proteins play a major role in controlling various functions such as signaling, regulation of transcription/translation, and immune response. Hence, a thorough understanding of the atomic-level principles governing multispecific interactions is important not only for the advancement of basic science but also for applied research such as drug design. Here, we study evolution of an exemplary multispecific protein, a Tissue Inhibitor of Matrix Metalloproteinases 2 (TIMP2) that binds with comparable affinities to more than twenty-six members of the Matrix Metalloproteinase (MMP) and the related ADAMs families. We postulate that due to its multispecific nature, TIMP2 is not optimized to bind to any individual MMP type, but rather embodies a compromise required for interactions with all MMPs. To explore this hypothesis, we perform computational saturation mutagenesis of the TIMP2 binding interface and predict changes in free energy of binding to eight MMP targets. Computational results reveal the non-optimality of the TIMP2 binding interface for all studied proteins, identifying many affinity-enhancing mutations at multiple positions. Several TIMP2 point mutants predicted to enhance binding affinity and/or binding specificity towards MMP14 were selected for experimental verification. Experimental results show high abundance of affinity-enhancing mutations in TIMP2, with some point mutations producing more than ten-fold improvement in affinity to MMP14. Our computational and experimental results collaboratively demonstrate that the TIMP2 sequence lies far from the fitness maximum when interacting with its target enzymes. This non-optimality of the binding interface and high potential for improvement might characterize all proteins evolved for binding to multiple targets.
Collapse
Affiliation(s)
- Oz Sharabi
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jason Shirian
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Moran Grossman
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Mario Lebendiker
- Wolfson Center for Structural Biology, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Irit Sagi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Julia Shifman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
| |
Collapse
|