1
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Xu J, Brown NJS, Seol Y, Neuman KC. Heterogeneous distribution of kinesin-streptavidin complexes revealed by mass photometry. SOFT MATTER 2024. [PMID: 38832814 DOI: 10.1039/d3sm01702h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Kinesin-streptavidin complexes are widely used in microtubule-based active-matter studies. The stoichiometry of the complexes is empirically tuned but experimentally challenging to determine. Here, mass photometry measurements reveal heterogenous distributions of kinesin-streptavidin complexes. Our binding model indicates that heterogeneity arises from both the kinesin-streptavidin mixing ratio and the kinesin-biotinylation efficiency.
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Affiliation(s)
- Jing Xu
- Department of Physics, University of California, Merced, CA 95343, USA.
| | - Nathaniel J S Brown
- Department of Quantitative and Systems Biology, University of California, Merced, CA 95343, USA
| | - Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
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2
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Yao J, Hong H. Steric trapping strategy for studying the folding of helical membrane proteins. Methods 2024; 225:1-12. [PMID: 38428472 PMCID: PMC11107808 DOI: 10.1016/j.ymeth.2024.02.007] [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: 11/16/2023] [Revised: 02/11/2024] [Accepted: 02/18/2024] [Indexed: 03/03/2024] Open
Abstract
Elucidating the folding energy landscape of membrane proteins is essential to the understanding of the proteins' stabilizing forces, folding mechanisms, biogenesis, and quality control. This is not a trivial task because the reversible control of folding is inherently difficult in a lipid bilayer environment. Recently, novel methods have been developed, each of which has a unique strength in investigating specific aspects of membrane protein folding. Among such methods, steric trapping is a versatile strategy allowing a reversible control of membrane protein folding with minimal perturbation of native protein-water and protein-lipid interactions. In a nutshell, steric trapping exploits the coupling of spontaneous denaturation of a doubly biotinylated protein to the simultaneous binding of bulky monovalent streptavidin molecules. This strategy has been evolved to investigate key elements of membrane protein folding such as thermodynamic stability, spontaneous denaturation rates, conformational features of the denatured states, and cooperativity of stabilizing interactions. In this review, we describe the critical methodological advancement, limitation, and outlook of the steric trapping strategy.
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Affiliation(s)
- Jiaqi Yao
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Heedeok Hong
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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3
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Xu J, Brown NJS, Seol Y, Neuman KC. Heterogeneous distribution of kinesin-streptavidin complexes revealed by Mass Photometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.21.572878. [PMID: 38187562 PMCID: PMC10769409 DOI: 10.1101/2023.12.21.572878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Kinesin-streptavidin complexes are widely used in microtubule-based active-matter studies. The stoichiometry of the complexes is empirically tuned but experimentally challenging to determine. Here, mass photometry measurements reveal heterogenous distributions of kinesin-streptavidin complexes. Our binding model indicates that heterogeneity arises from both the kinesin-streptavidin mixing ratio and the kinesin-biotinylation efficiency.
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Affiliation(s)
- Jing Xu
- Department of Physics, University of California, Merced, CA 95343, USA
| | - Nathaniel J. S. Brown
- Department of Quantitative and Systems Biology, University of California, Merced, CA 95343, USA
| | - Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Keir C. Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
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4
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Lyu J, Zhang T, Marty MT, Clemmer D, Russell DH, Laganowsky A. Double and triple thermodynamic mutant cycles reveal the basis for specific MsbA-lipid interactions. eLife 2024; 12:RP91094. [PMID: 38252560 PMCID: PMC10945598 DOI: 10.7554/elife.91094] [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] [Indexed: 01/24/2024] Open
Abstract
Structural and functional studies of the ATP-binding cassette transporter MsbA have revealed two distinct lipopolysaccharide (LPS) binding sites: one located in the central cavity and the other at a membrane-facing, exterior site. Although these binding sites are known to be important for MsbA function, the thermodynamic basis for these specific MsbA-LPS interactions is not well understood. Here, we use native mass spectrometry to determine the thermodynamics of MsbA interacting with the LPS-precursor 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)2-lipid A (KDL). The binding of KDL is solely driven by entropy, despite the transporter adopting an inward-facing conformation or trapped in an outward-facing conformation with adenosine 5'-diphosphate and vanadate. An extension of the mutant cycle approach is employed to probe basic residues that interact with KDL. We find the molecular recognition of KDL is driven by a positive coupling entropy (as large as -100 kJ/mol at 298 K) that outweighs unfavorable coupling enthalpy. These findings indicate that alterations in solvent reorganization and conformational entropy can contribute significantly to the free energy of protein-lipid association. The results presented herein showcase the advantage of native MS to obtain thermodynamic insight into protein-lipid interactions that would otherwise be intractable using traditional approaches, and this enabling technology will be instrumental in the life sciences and drug discovery.
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Affiliation(s)
- Jixing Lyu
- Department of Chemistry, Texas A&M UniversityCollege StationUnited States
| | - Tianqi Zhang
- Department of Chemistry, Texas A&M UniversityCollege StationUnited States
| | - Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, The University of ArizonaTucsonUnited States
| | - David Clemmer
- Department of Chemistry, Indiana UniversityBloomingtonUnited States
| | - David H Russell
- Department of Chemistry, Texas A&M UniversityCollege StationUnited States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M UniversityCollege StationUnited States
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5
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Rashid SA, Dong Y, Ogasawara H, Vierengel M, Essien ME, Salaita K. All-Covalent Nuclease-Resistant and Hydrogel-Tethered DNA Hairpin Probes Map pN Cell Traction Forces. ACS APPLIED MATERIALS & INTERFACES 2023; 15:33362-33372. [PMID: 37409737 PMCID: PMC10360067 DOI: 10.1021/acsami.3c04826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/15/2023] [Indexed: 07/07/2023]
Abstract
Cells sense and respond to the physical properties of their environment through receptor-mediated signaling, a process known as mechanotransduction, which can modulate critical cellular functions such as proliferation, differentiation, and survival. At the molecular level, cell adhesion receptors, such as integrins, transmit piconewton (pN)-scale forces to the extracellular matrix, and the magnitude of the force plays a critical role in cell signaling. The most sensitive approach to measuring integrin forces involves DNA hairpin-based sensors, which are used to quantify and map forces in living cells. Despite the broad use of DNA hairpin sensors to study a variety of mechanotransduction processes, these sensors are typically anchored to rigid glass slides, which are orders of magnitude stiffer than the extracellular matrix and hence modulate native biological responses. Here, we have developed nuclease-resistant DNA hairpin probes that are all covalently tethered to PEG hydrogels to image cell traction forces on physiologically relevant substrate stiffness. Using HeLa cells as a model cell line, we show that the molecular forces transmitted by integrins are highly sensitive to the bulk modulus of the substrate, and cells cultured on the 6 and 13 kPa gels produced a greater number of hairpin unfolding events compared to the 2 kPa substrates. Tension signals are spatially colocalized with pY118-paxillin, confirming focal adhesion-mediated probe opening. Additionally, we found that integrin forces are greater than 5.8 pN but less than 19 pN on 13 kPa gels. This work provides a general strategy to integrate molecular tension probes into hydrogels, which can better mimic in vivo mechanotransduction.
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Affiliation(s)
- Sk Aysha Rashid
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Yixiao Dong
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Hiroaki Ogasawara
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Maia Vierengel
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Mark Edoho Essien
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Khalid Salaita
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
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6
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Iida S, Kameda T. Dissociation Rate Calculation via Constant-Force Steered Molecular Dynamics Simulation. J Chem Inf Model 2023. [PMID: 37188657 DOI: 10.1021/acs.jcim.2c01529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Steered molecular dynamics (SMD) simulations are used to study molecular dissociation events by applying a harmonic force to the molecules and pulling them at a constant velocity. Instead of constant-velocity pulling, we use a constant force: the constant-force SMD (CF-SMD) simulation. The CF-SMD simulation employs a constant force to reduce the activation barrier of molecular dissociation, thereby enhancing the dissociation event. Here, we present the capability of the CF-SMD simulation to estimate the dissociation time at equilibrium. We performed all-atom CF-SMD simulations for NaCl and protein-ligand systems, producing dissociation time at various forces. We extrapolated these values to the dissociation rate without a constant force using Bell's model or the Dudko-Hummer-Szabo model. We demonstrate that the CF-SMD simulations with the models predicted the dissociation time in equilibrium. A CF-SMD simulation is a powerful tool for estimating the dissociation rate in a direct and computationally efficient manner.
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Affiliation(s)
- Shinji Iida
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
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7
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Bloomer BJ, Clark DS, Hartwig JF. Progress, Challenges, and Opportunities with Artificial Metalloenzymes in Biosynthesis. Biochemistry 2023; 62:221-228. [PMID: 35195998 DOI: 10.1021/acs.biochem.1c00829] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In this Perspective, we present progress, outstanding challenges, and opportunities for the incorporation of artificial metalloenzymes (ArMs) into biosynthetic pathways. We first explain discoveries within the field of ArMs that led to the potential inclusion of these enzymes in biosynthesis. We then describe the specific barriers that our laboratory, in collaboration with the laboratories of Keasling and Mukhopadhyay, addressed to establish a biosynthetic pathway containing an ArM. This biosynthesis produced an unnatural cyclopropyl terpenoid by combining heterologous production of the terpene with modification of its terminal alkene by an ArM built from a cytochrome P450. Finally, we describe the remaining challenges and opportunities related to the application of ArMs in synthetic biology.
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Affiliation(s)
- Brandon J Bloomer
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Douglas S Clark
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - John F Hartwig
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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8
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I.M.H. Abdulrahman Y, Zaki M, Alhaddad MR, Hairat S, Akhtar K. Structural elucidation of new ferrocene appended scaffold and their metal complexes: Comparative in vitroDNA/BSA Binding and antibacterial assay. Inorganica Chim Acta 2023. [DOI: 10.1016/j.ica.2023.121398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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9
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Kumar S, Zhu Y, Stover L, Laganowsky A. Step toward Probing the Nonannular Belt of Membrane Proteins. Anal Chem 2022; 94:13906-13912. [PMID: 36170465 DOI: 10.1021/acs.analchem.2c02811] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Integral membrane proteins are embedded in the biological membrane, where they carry out numerous biological processes. Although lipids present in the membrane are crucial for membrane protein function, it remains difficult to characterize many lipid binding events to membrane proteins, such as those that form the annular belt. Here, we use native mass spectrometry along with the charge-reducing properties of trimethylamine N-oxide (TMAO) to characterize a large number of lipid binding events to the bacterial ammonia channel (AmtB). In the absence of TMAO, significant peak overlap between neighboring charge states is observed, resulting in erroneous abundances for different molecular species. With the addition of TMAO, the weighted average charge state (Zavg) was decreased. In addition, the increased spacing between nearby charge states enabled a higher number of lipid binding species to be observed while minimizing mass spectral peak overlap. These conditions helped us to determine the equilibrium binding constants (Kd) for up to 16 lipid binding events. The binding constants for the first few lipid binding events display the highest affinity, whereas the binding constants for higher lipid binding events converge to a similar value. These findings suggest a transition from nonannular to annular lipid binding to AmtB.
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Affiliation(s)
- Smriti Kumar
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yun Zhu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lauren Stover
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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10
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Gavriilidou AFM, Sokratous K, Yen HY, De Colibus L. High-Throughput Native Mass Spectrometry Screening in Drug Discovery. Front Mol Biosci 2022; 9:837901. [PMID: 35495635 PMCID: PMC9047894 DOI: 10.3389/fmolb.2022.837901] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/15/2022] [Indexed: 12/15/2022] Open
Abstract
The design of new therapeutic molecules can be significantly informed by studying protein-ligand interactions using biophysical approaches directly after purification of the protein-ligand complex. Well-established techniques utilized in drug discovery include isothermal titration calorimetry, surface plasmon resonance, nuclear magnetic resonance spectroscopy, and structure-based drug discovery which mainly rely on protein crystallography and, more recently, cryo-electron microscopy. Protein-ligand complexes are dynamic, heterogeneous, and challenging systems that are best studied with several complementary techniques. Native mass spectrometry (MS) is a versatile method used to study proteins and their non-covalently driven assemblies in a native-like folded state, providing information on binding thermodynamics and stoichiometry as well as insights on ternary and quaternary protein structure. Here, we discuss the basic principles of native mass spectrometry, the field’s recent progress, how native MS is integrated into a drug discovery pipeline, and its future developments in drug discovery.
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11
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Kocheril PA, Lenz KD, Mascareñas DDL, Morales-Garcia JE, Anderson AS, Mukundan H. Portable Waveguide-Based Optical Biosensor. BIOSENSORS 2022; 12:bios12040195. [PMID: 35448255 PMCID: PMC9025188 DOI: 10.3390/bios12040195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 05/31/2023]
Abstract
Rapid, on-site diagnostics allow for timely intervention and response for warfighter support, environmental monitoring, and global health needs. Portable optical biosensors are being widely pursued as a means of achieving fieldable biosensing due to the potential speed and accuracy of optical detection. We recently developed the portable engineered analytic sensor with automated sampling (PEGASUS) with the goal of developing a fieldable, generalizable biosensing platform. Here, we detail the development of PEGASUS's sensing hardware and use a test-bed system of identical sensing hardware and software to demonstrate detection of a fluorescent conjugate at 1 nM through biotin-streptavidin chemistry.
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Affiliation(s)
- Philip A. Kocheril
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (P.A.K.); (K.D.L.); (A.S.A.)
| | - Kiersten D. Lenz
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (P.A.K.); (K.D.L.); (A.S.A.)
| | - David D. L. Mascareñas
- National Security Education Center, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (D.D.L.M.); (J.E.M.-G.)
| | - John E. Morales-Garcia
- National Security Education Center, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (D.D.L.M.); (J.E.M.-G.)
| | - Aaron S. Anderson
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (P.A.K.); (K.D.L.); (A.S.A.)
| | - Harshini Mukundan
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (P.A.K.); (K.D.L.); (A.S.A.)
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12
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Klaczko ME, Lucas K, Salminen AT, McCloskey MC, Ozgurun B, Ward BM, Flax J, McGrath JL. Rapid and specific detection of intact viral particles using functionalized microslit silicon membranes as a fouling-based sensor. Analyst 2021; 147:213-222. [PMID: 34933322 DOI: 10.1039/d1an01504d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The COVID-19 pandemic demonstrated the public health benefits of reliable and accessible point-of-care (POC) diagnostic tests for viral infections. Despite the rapid development of gold-standard reverse transcription polymerase chain reaction (RT-PCR) assays for SARS-CoV-2 only weeks into the pandemic, global demand created logistical challenges that delayed access to testing for months and helped fuel the spread of COVID-19. Additionally, the extreme sensitivity of RT-PCR had a costly downside as the tests could not differentiate between patients with active infection and those who were no longer infectious but still shedding viral genomes. To address these issues for the future, we propose a novel membrane-based sensor that only detects intact virions. The sensor combines affinity and size based detection on a membrane-based sensor and does not require external power to operate or read. Specifically, the presence of intact virions, but not viral debris, fouls the membrane and triggers a macroscopically visible hydraulic switch after injection of a 40 μL sample with a pipette. The device, which we call the μSiM-DX (microfluidic device featuring a silicon membrane for diagnostics), features a biotin-coated microslit membrane with pores ∼2-3× larger than the intact virus. Streptavidin-conjugated antibody recognizing viral surface proteins are incubated with the sample for ∼1 hour prior to injection into the device, and positive/negative results are obtained within ten seconds of sample injection. Proof-of-principle tests have been performed using preparations of vaccinia virus. After optimizing slit pore sizes and porous membrane area, the fouling-based sensor exhibits 100% specificity and 97% sensitivity for vaccinia virus (n = 62). Moreover, the dynamic range of the sensor extends at least from 105.9 virions per mL to 1010.4 virions per mL covering the range of mean viral loads in symptomatic COVID-19 patients (105.6-107 RNA copies per mL). Forthcoming work will test the ability of our sensor to perform similarly in biological fluids and with SARS-CoV-2, to fully test the potential of a membrane fouling-based sensor to serve as a PCR-free alternative for POC containment efforts in the spread of infectious disease.
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Affiliation(s)
- Michael E Klaczko
- Department of Chemistry, University of Rochester, Rochester, NY, 14627 USA
| | - Kilean Lucas
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, 14627 USA.
| | - Alec T Salminen
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, 14627 USA.
| | - Molly C McCloskey
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, 14627 USA.
| | - Baturay Ozgurun
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, 14627 USA.
| | - Brian M Ward
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642 USA
| | - Jonathan Flax
- Department of Urology, University of Rochester Medical Center, Rochester, NY, 14642 USA
| | - James L McGrath
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, 14627 USA.
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13
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Bennett JL, Nguyen GTH, Donald WA. Protein-Small Molecule Interactions in Native Mass Spectrometry. Chem Rev 2021; 122:7327-7385. [PMID: 34449207 DOI: 10.1021/acs.chemrev.1c00293] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Small molecule drug discovery has been propelled by the continual development of novel scientific methodologies to occasion therapeutic advances. Although established biophysical methods can be used to obtain information regarding the molecular mechanisms underlying drug action, these approaches are often inefficient, low throughput, and ineffective in the analysis of heterogeneous systems including dynamic oligomeric assemblies and proteins that have undergone extensive post-translational modification. Native mass spectrometry can be used to probe protein-small molecule interactions with unprecedented speed and sensitivity, providing unique insights into polydisperse biomolecular systems that are commonly encountered during the drug discovery process. In this review, we describe potential and proven applications of native MS in the study of interactions between small, drug-like molecules and proteins, including large multiprotein complexes and membrane proteins. Approaches to quantify the thermodynamic and kinetic properties of ligand binding are discussed, alongside a summary of gas-phase ion activation techniques that have been used to interrogate the structure of protein-small molecule complexes. We additionally highlight some of the key areas in modern drug design for which native mass spectrometry has elicited significant advances. Future developments and applications of native mass spectrometry in drug discovery workflows are identified, including potential pathways toward studying protein-small molecule interactions on a whole-proteome scale.
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Affiliation(s)
- Jack L Bennett
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Giang T H Nguyen
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
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14
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Protein Secondary Structure Affects Glycan Clustering in Native Mass Spectrometry. Life (Basel) 2021; 11:life11060554. [PMID: 34208397 PMCID: PMC8231113 DOI: 10.3390/life11060554] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 01/01/2023] Open
Abstract
Infection by the humannoroviruses (hNoV), for the vast majority of strains, requires attachment of the viral capsid to histo blood group antigens (HBGAs). The HBGA-binding pocket is formed by dimers of the protruding domain (P dimers) of the capsid protein VP1. Several studies have focused on HBGA binding to P dimers, reporting binding affinities and stoichiometries. However, nuclear magnetic resonance spectroscopy (NMR) and native mass spectrometry (MS) analyses yielded incongruent dissociation constants (KD) for the binding of HBGAs to P dimers and, in some cases, disagreed on whether glycans bind at all. We hypothesized that glycan clustering during electrospray ionization in native MS critically depends on the physicochemical properties of the protein studied. It follows that the choice of a reference protein is crucial. We analysed carbohydrate clustering using various P dimers and eight non-glycan binding proteins serving as possible references. Data from native and ion mobility MS indicate that the mass fraction of β-sheets has a strong influence on the degree of glycan clustering. Therefore, the determination of specific glycan binding affinities from native MS must be interpreted cautiously.
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15
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Metal Nanoparticle and Quantum Dot Tags for Signal Amplification in Electrochemical Immunosensors for Biomarker Detection. CHEMOSENSORS 2021. [DOI: 10.3390/chemosensors9040085] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
With the increasing importance of healthcare and clinical diagnosis, as well as the growing demand for highly sensitive analytical instruments, immunosensors have received considerable attention. In this review, electrochemical immunosensor signal amplification strategies using metal nanoparticles (MNPs) and quantum dots (Qdots) as tags are overviewed, focusing on recent developments in the ultrasensitive detection of biomarkers. MNPs and Qdots can be used separately or in combination with other nanostructures, while performing the function of nanocarriers, electroactive labels, or catalysts. Thus, different functions of MNPs and Qdots as well as recent advances in electrochemical signal amplification are discussed. Additionally, the methods most often used for antibody immobilization on nanoparticles, immunoassay formats, and electrochemical methods for indirect biomarker detection are overviewed.
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16
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Riesenberg C, Iriarte-Valdez CA, Becker A, Dienerowitz M, Heisterkamp A, Ngezahayo A, Torres-Mapa ML. Probing Ligand-Receptor Interaction in Living Cells Using Force Measurements With Optical Tweezers. Front Bioeng Biotechnol 2020; 8:598459. [PMID: 33282853 PMCID: PMC7705203 DOI: 10.3389/fbioe.2020.598459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/01/2020] [Indexed: 01/08/2023] Open
Abstract
This work probes the binding kinetics of COOH-terminus of Clostridium perfringens enterotoxin (c-CPE) and claudin expressing MCF-7 cells using force spectroscopy with optical tweezers. c-CPE is of high biomedical interest due to its ability to specifically bind to claudin with high affinity as well as reversibly disrupt tight junctions whilst maintaining cell viability. We observed single-step rupture events between silica particles functionalized with c-CPE and MCF-7 cells. Extensive calibration of the optical tweezers' trap stiffness and displacement of the particle from trap center extracted a probable bond rupture force of ≈ 18 pN. The probability of rupture events with c-CPE functionalized silica particles increased by 50% compared to unfunctionalized particles. Additionally, rupture events were not observed when probing cells not expressing claudin with c-CPE coated particles. Overall, this work demonstrates that optical tweezers are invaluable tools to probe ligand-receptor interactions and their potential to study dynamic molecular events in drug-binding scenarios.
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Affiliation(s)
- Carolin Riesenberg
- Institute of Quantum Optics, Leibniz University Hannover, Hannover, Germany.,Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Hannover, Germany
| | - Christian Alejandro Iriarte-Valdez
- Institute of Quantum Optics, Leibniz University Hannover, Hannover, Germany.,Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Hannover, Germany
| | - Annegret Becker
- Institute of Cell Biology and Biophysics, Leibniz University Hannover, Hannover, Germany
| | - Maria Dienerowitz
- Single-Molecule Microscopy Group, Jena University Hospital, Jena, Germany
| | - Alexander Heisterkamp
- Institute of Quantum Optics, Leibniz University Hannover, Hannover, Germany.,Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Hannover, Germany
| | - Anaclet Ngezahayo
- Institute of Cell Biology and Biophysics, Leibniz University Hannover, Hannover, Germany
| | - Maria Leilani Torres-Mapa
- Institute of Quantum Optics, Leibniz University Hannover, Hannover, Germany.,Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Hannover, Germany
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17
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Yaman S, Tekin HC. Magnetic Susceptibility-Based Protein Detection Using Magnetic Levitation. Anal Chem 2020; 92:12556-12563. [DOI: 10.1021/acs.analchem.0c02479] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sena Yaman
- Department of Bioengineering, Izmir Institute of Technology, Izmir 35430, Turkey
| | - H. Cumhur Tekin
- Department of Bioengineering, Izmir Institute of Technology, Izmir 35430, Turkey
- METU MEMS Center, Ankara 06520, Turkey
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18
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Abstract
Accurate detection of target molecules at low concentrations in the presence of undesired molecules in abundance is a major challenge for biosensors. Nonspecific binding of undesired molecules to receptors limits the minimum detectable concentration of the target significantly. Dynamic tracking (DT) of binding and unbinding events allows us to overcome this challenge and provides a remarkable improvement in the minimum detectable target concentration. Through a combination of theoretical analysis and detailed statistical simulations, here we show that, with aggressive scaling, DT sensors are capable of fM detection limits even if the undesired molecules are present at nM concentrations, which is several orders of magnitude better than traditional endpoint (EP) biosensors. In addition, we propose a novel unconstrained detection scheme that does not rely on a priori knowledge of the dissociation constants and also allows facile back-extraction of critical parameters. Indeed, this work provides a theoretical basis for DT sensors and demonstrates its suitability to usher in a new paradigm on biosensing in hostile environments.
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Affiliation(s)
- Deepak Gopalan
- Department of Electrical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Pradeep R. Nair
- Department of Electrical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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19
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Poltash ML, McCabe JW, Shirzadeh M, Laganowsky A, Clowers BH, Russell DH. Fourier Transform-Ion Mobility-Orbitrap Mass Spectrometer: A Next-Generation Instrument for Native Mass Spectrometry. Anal Chem 2018; 90:10472-10478. [PMID: 30091588 DOI: 10.1021/acs.analchem.8b02463] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A new instrument configuration for native ion mobility-mass spectrometry (IM-MS) is described. Macromolecule ions are generated by using a static ESI source coupled to an RF ion funnel, and these ions are then mobility and mass analyzed using a periodic focusing drift tube IM analyzer and an Orbitrap mass spectrometer. The instrument design retains the capabilities for first-principles determination of rotationally averaged ion-neutral collision cross sections and high-resolution measurements in both mobility and mass analysis modes for intact protein complexes. Operation in the IM mode utilizes FT-IMS modes (originally described by Knorr ( Knorr , F. J. Anal. Chem . 1985 , 57 ( 2 ), 402 - 406 )), which provides a means to overcome the inherent duty cycle mismatch for drift tube (DT)-IM and Orbitrap mass analysis. The performance of the native ESI-FT-DT-IM-Orbitrap MS instrument was evaluated using the protein complexes Gln K (MW 44 kDa) and streptavidin (MW 53 kDa) bound to small molecules (ADP and biotin, respectively) and transthyretin (MW 56 kDa) bound to thyroxine and zinc.
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Affiliation(s)
- Michael L Poltash
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Jacob W McCabe
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Mehdi Shirzadeh
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Arthur Laganowsky
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Brian H Clowers
- Department of Chemistry , Washington State University , Pullman , Washington 99164 , United States
| | - David H Russell
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
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20
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Taylor SK, Tran TH, Liu MZ, Harris PE, Sun Y, Jambawalikar SR, Tong L, Stojanovic MN. Insulin Hexamer-Caged Gadolinium Ion as MRI Contrast-o-phore. Chemistry 2018; 24:10646-10652. [PMID: 29873848 DOI: 10.1002/chem.201801388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Indexed: 12/30/2022]
Abstract
High-relaxivity protein-complexes of GdIII are being pursued as MRI contrast agents in hope that they can be used at much lower doses that would minimize toxic-side effects of GdIII release from traditional contrast agents. We construct here a new type of protein-based MRI contrast agent, a proteinaceous cage based on a stable insulin hexamer in which GdIII is captured inside a water filled cavity. The macromolecular structure and the large number of "free" GdIII coordination sites available for water binding lead to exceptionally high relaxivities per one GdIII ion. The GdIII slowly diffuses out of this cage, but this diffusion can be prevented by addition of ligands that bind to the hexamer. The ligands that trigger structural changes in the hexamer, SCN- , Cl- and phenols, modulate relaxivities through an outside-in signaling that is allosterically transduced through the protein cage. Contrast-o-phores based on protein-caged metal ions have potential to become clinical contrast agents with environmentally-sensitive properties.
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Affiliation(s)
- Steven K Taylor
- Department of Medicine, Columbia University, 630 W. 168th St., Box 84, New York, NY, 10032, USA
| | - Timothy H Tran
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Michael Z Liu
- Department of Radiology, Columbia University, 177 Ft Washington Ave, New York, NY, 10032, USA
| | - Paul E Harris
- Department of Medicine, Columbia University, 630 W. 168th St., Box 84, New York, NY, 10032, USA
| | - Yanping Sun
- Irving Comprehensive Cancer Center, Columbia University, 622 W. 168th St., New York, NY, 10032, USA
| | - Sachin R Jambawalikar
- Department of Radiology, Columbia University, 177 Ft Washington Ave, New York, NY, 10032, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Milan N Stojanovic
- Departments of Medicine, Biomedical Engineering and Systems Biology, Columbia University, 630 W. 168th St., Box 84, New York, NY, 10032, USA
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21
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Abstract
Membrane proteins interact with a myriad of lipid species in the biological membrane, leading to a bewildering number of possible protein-lipid assemblies. Despite this inherent complexity, the identification of specific protein-lipid interactions and the crucial role of lipids in the folding, structure, and function of membrane proteins is emerging from an increasing number of reports. Fundamental questions remain, however, regarding the ability of specific lipid binding events to membrane proteins to alter remote binding sites for lipids of a different type, a property referred to as allostery [Monod J, Wyman J, Changeux JP (1965) J Mol Biol 12:88-118]. Here, we use native mass spectrometry to determine the allosteric nature of heterogeneous lipid binding events to membrane proteins. We monitored individual lipid binding events to the ammonia channel (AmtB) from Escherichia coli, enabling determination of their equilibrium binding constants. We found that different lipid pairs display a range of allosteric modulation. In particular, the binding of phosphatidylethanolamine and cardiolipin-like molecules to AmtB exhibited the largest degree of allosteric modulation, inspiring us to determine the cocrystal structure of AmtB in this lipid environment. The 2.45-Å resolution structure reveals a cardiolipin-like molecule bound to each subunit of the trimeric complex. Mutation of a single residue in AmtB abolishes the positive allosteric modulation observed for binding phosphatidylethanolamine and cardiolipin-like molecules. Our results demonstrate that specific lipid-protein interactions can act as allosteric modulators for the binding of different lipid types to integral membrane proteins.
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22
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Allosteric modulation of protein-protein interactions by individual lipid binding events. Nat Commun 2017; 8:2203. [PMID: 29259178 PMCID: PMC5736629 DOI: 10.1038/s41467-017-02397-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/22/2017] [Indexed: 11/29/2022] Open
Abstract
The diverse lipid environment of the biological membrane can modulate the structure and function of membrane proteins. However, little is known about the role that lipids play in modulating protein–protein interactions. Here we employed native mass spectrometry (MS) to determine how individual lipid-binding events to the ammonia channel (AmtB) modulate its interaction with the regulatory protein, GlnK. The thermodynamic signature of AmtB–GlnK in the absence of lipids indicates conformational dynamics. A small number of lipids bound to AmtB is sufficient to modulate the interaction with GlnK, and lipids with different headgroups display a range of allosteric modulation. We also find that lipid chain length and stereochemistry can affect the degree of allosteric modulation, indicating an unforeseen selectivity of membrane proteins toward the chemistry of lipid tails. These results demonstrate that individual lipid-binding events can allosterically modulate the interactions of integral membrane and soluble proteins. Native mass spectrometry (MS) is a technique that preserves non-covalent interactions in the mass spectrometer. Here the authors use native MS to study integral membrane proteins, and find that lipids with different headgroups and tails can allosterically modulate protein-protein interactions in different fashions.
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23
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Xu F, Dang Q, Dai X, Fang X, Wang Y, Ding L, Ding CF. Characteristics of Ion Activation and Collision Induced Dissociation Using Digital Ion Trap Technology. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1351-1356. [PMID: 27150507 DOI: 10.1007/s13361-016-1407-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 04/05/2016] [Accepted: 04/06/2016] [Indexed: 06/05/2023]
Abstract
Collision induced dissociation (CID) is one of the most established techniques for tandem mass spectrometry analysis. The CID of mass selected ion could be realized by ion resonance excitation with a digital rectangular waveform. The method is simple, and highly efficient CID result could be obtained by optimizing the experimental parameters, such as digital waveform voltage, frequency, and q value. In this work, the relationship between ion trapping waveform voltage and frequency at preselected q value, the relationship between waveform frequency and the q value at certain ion trapping voltage for optimum CID efficiency were investigated. Experiment results showed that the max CID efficiency of precursor reserpine ions can be obtained at different trapping waveform voltage and frequency when q and β are different. Based on systematic experimental analysis, the optimum experimental conditions for high CID efficiency can be calculated at any selected β or q. By using digital ion trap technology, the CID process and efficient fragmentation of parent ions can be realized by simply changing the trapping waveform amplitude, frequency, and the β values in the digital ion trap mass spectrometry. The technology and method are simple. It has potential use in ion trap mass spectrometry. Graphical Abstract ᅟ.
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Affiliation(s)
- Fuxing Xu
- Department of Electric Engineering, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Molecular Catalysis and Functional Material, Department of Chemistry and Laser Chemistry Institute, Fudan University, Shanghai, China
| | - Qiankun Dang
- Shanghai Key Laboratory of Molecular Catalysis and Functional Material, Department of Chemistry and Laser Chemistry Institute, Fudan University, Shanghai, China
| | - Xinhua Dai
- National Institute of Metrology, Beijing, China
| | - Xiang Fang
- National Institute of Metrology, Beijing, China.
| | - Yuanyuan Wang
- Department of Electric Engineering, Fudan University, Shanghai, China
| | - Li Ding
- Shanghai Key Laboratory of Molecular Catalysis and Functional Material, Department of Chemistry and Laser Chemistry Institute, Fudan University, Shanghai, China
| | - Chuan-Fan Ding
- Shanghai Key Laboratory of Molecular Catalysis and Functional Material, Department of Chemistry and Laser Chemistry Institute, Fudan University, Shanghai, China.
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24
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Cong Y, Katipamula S, Trader CD, Orton DJ, Geng T, Baker ES, Kelly RT. Mass spectrometry-based monitoring of millisecond protein-ligand binding dynamics using an automated microfluidic platform. LAB ON A CHIP 2016; 16:1544-8. [PMID: 27009517 PMCID: PMC4846533 DOI: 10.1039/c6lc00183a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Characterizing protein-ligand binding dynamics is crucial for understanding protein function and for developing new therapeutic agents. We present a novel microfluidic platform that features rapid mixing of protein and ligand solutions, variable incubation times, and an integrated electrospray ionization source for mass spectrometry-based monitoring of protein-ligand binding dynamics. This platform offers many advantages, including solution-based binding, label-free detection, automated operation, rapid mixing, and low sample consumption.
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Affiliation(s)
- Yongzheng Cong
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA.
| | - Shanta Katipamula
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA.
| | - Cameron D Trader
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA.
| | - Daniel J Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Tao Geng
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA.
| | - Erin S Baker
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA.
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25
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Cong X, Liu Y, Liu W, Liang X, Russell DH, Laganowsky A. Determining Membrane Protein-Lipid Binding Thermodynamics Using Native Mass Spectrometry. J Am Chem Soc 2016; 138:4346-9. [PMID: 27015007 DOI: 10.1021/jacs.6b01771] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Membrane proteins are embedded in the biological membrane where the chemically diverse lipid environment can modulate their structure and function. However, the thermodynamics governing the molecular recognition and interaction of lipids with membrane proteins is poorly understood. Here, we report a method using native mass spectrometry (MS), to determine thermodynamics of individual ligand binding events to proteins. Unlike conventional methods, native MS can resolve individual ligand binding events and, coupled with an apparatus to control the temperature, determine binding thermodynamic parameters, such as for protein-lipid interactions. We validated our approach using three soluble protein-ligand systems (maltose binding protein, lysozyme, and nitrogen regulatory protein) and obtained similar results to those using isothermal titration calorimetry and surface plasmon resonance. We also determined for the first time the thermodynamics of individual lipid binding to the ammonia channel (AmtB), an integral membrane protein from Escherichia coli. Remarkably, we observed distinct thermodynamic signatures for the binding of different lipids and entropy-enthalpy compensation for binding lipids of variable chain length. Additionally, using a mutant form of AmtB that abolishes a specific phosphatidylglycerol (PG) binding site, we observed distinct changes in the thermodynamic signatures for binding PG, implying these signatures can identify key residues involved in specific lipid binding and potentially differentiate between specific lipid binding sites.
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Affiliation(s)
- Xiao Cong
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center , Houston, Texas 77030, United States
| | - Yang Liu
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center , Houston, Texas 77030, United States
| | - Wen Liu
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center , Houston, Texas 77030, United States
| | - Xiaowen Liang
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center , Houston, Texas 77030, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University , College Station, Texas 77842, United States
| | - Arthur Laganowsky
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center , Houston, Texas 77030, United States.,Department of Chemistry, Texas A&M University , College Station, Texas 77842, United States.,Department of Microbial Pathogenesis & Immunology, College of Medicine, Texas A&M Health Science Center , Bryan, Texas 77807, United States
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26
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Khanal N, Pejaver V, Li Z, Radivojac P, Clemmer DE, Mukhopadhyay S. Position of Proline Mediates the Reactivity of S-Palmitoylation. ACS Chem Biol 2015; 10:2529-36. [PMID: 26255674 DOI: 10.1021/acschembio.5b00429] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Palmitoylation, a post-translational modification in which a saturated 16-carbon chain is added predominantly to a cysteine residue, participates in various biological functions. The position of proline relative to other residues being post-translationally modified has been previously reported as being important. We determined that proline is statistically enriched around cysteines known to be S-palmitoylated. The goal of this work was to determine how the position of proline influences the palmitoylation of the cysteine residue. We established a mass spectrometry-based approach to investigate time- and temperature-dependent kinetics of autopalmitoylation in vitro and to derive the thermodynamic parameters of the transition state associated with palmitoylation; to the best of our knowledge, our work is the first to study the kinetics and activation properties of the palmitoylation process. We then used these thermochemical parameters to determine if the position of proline relative to the modified cysteine is important for palmitoylation. Our results show that peptides with proline at the -1 position of cysteine in their sequence (PC) have lower enthalpic barriers and higher entropic barriers in comparison to the same peptides with proline at the +1 position of cysteine (CP); interestingly, the free-energy barriers for both pairs are almost identical. Molecular dynamics studies demonstrate that the flexibility of the cysteine backbone in the PC-containing peptide when compared to the CP-containing peptide explains the increased entropic barrier and decreased enthalpic barrier observed experimentally.
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Affiliation(s)
- Neelam Khanal
- Departments of †Chemistry, ‡Computer Science and Informatics, and §Biology, Indiana University, Bloomington, Indiana 47405, United States
| | - Vikas Pejaver
- Departments of †Chemistry, ‡Computer Science and Informatics, and §Biology, Indiana University, Bloomington, Indiana 47405, United States
| | - Zhiyu Li
- Departments of †Chemistry, ‡Computer Science and Informatics, and §Biology, Indiana University, Bloomington, Indiana 47405, United States
| | - Predrag Radivojac
- Departments of †Chemistry, ‡Computer Science and Informatics, and §Biology, Indiana University, Bloomington, Indiana 47405, United States
| | - David E. Clemmer
- Departments of †Chemistry, ‡Computer Science and Informatics, and §Biology, Indiana University, Bloomington, Indiana 47405, United States
| | - Suchetana Mukhopadhyay
- Departments of †Chemistry, ‡Computer Science and Informatics, and §Biology, Indiana University, Bloomington, Indiana 47405, United States
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27
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Jurchenko C, Salaita KS. Lighting Up the Force: Investigating Mechanisms of Mechanotransduction Using Fluorescent Tension Probes. Mol Cell Biol 2015; 35:2570-82. [PMID: 26031334 PMCID: PMC4524122 DOI: 10.1128/mcb.00195-15] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The ability of cells to sense the physical nature of their surroundings is critical to the survival of multicellular organisms. Cellular response to physical cues from adjacent cells and the extracellular matrix leads to a dynamic cycle in which cells respond by remodeling their local microenvironment, fine-tuning cell stiffness, polarity, and shape. Mechanical regulation is important in cellular development, normal morphogenesis, and wound healing. The mechanisms by which these finely balanced mechanotransduction events occur, however, are not well understood. In large part, this is due to the limited availability of tools to study molecular mechanotransduction events in live cells. Several classes of molecular tension probes have been recently developed which are rapidly transforming the study of mechanotransduction. Molecular tension probes are primarily based on fluorescence resonance energy transfer (FRET) and report on piconewton scale tension events in live cells. In this minireview, we describe the two main classes of tension probes, genetically encoded tension sensors and immobilized tension sensors, and discuss the advantages and limitations of each type. We discuss future opportunities to address major biological questions and outline the challenges facing the next generation of molecular tension probes.
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Affiliation(s)
- Carol Jurchenko
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
| | - Khalid S Salaita
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
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28
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Müller JM, Risse JM, Friehs K, Flaschel E. Model-based development of an assay for the rapid detection of biotin-blocked binding sites of streptavidin. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Jakob M. Müller
- Chair of Fermentation Engineering; Faculty of Technology; Bielefeld University; Bielefeld Germany
| | - Joe M. Risse
- Chair of Fermentation Engineering; Faculty of Technology; Bielefeld University; Bielefeld Germany
| | - Karl Friehs
- Chair of Fermentation Engineering; Faculty of Technology; Bielefeld University; Bielefeld Germany
| | - Erwin Flaschel
- Chair of Fermentation Engineering; Faculty of Technology; Bielefeld University; Bielefeld Germany
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29
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Quintyn R, Yan J, Wysocki V. Surface-Induced Dissociation of Homotetramers with D2 Symmetry Yields their Assembly Pathways and Characterizes the Effect of Ligand Binding. ACTA ACUST UNITED AC 2015; 22:583-92. [DOI: 10.1016/j.chembiol.2015.03.019] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 03/23/2015] [Accepted: 03/26/2015] [Indexed: 12/11/2022]
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30
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Jurchenko C, Chang Y, Narui Y, Zhang Y, Salaita KS. Integrin-generated forces lead to streptavidin-biotin unbinding in cellular adhesions. Biophys J 2014; 106:1436-46. [PMID: 24703305 DOI: 10.1016/j.bpj.2014.01.049] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 12/20/2013] [Accepted: 01/29/2014] [Indexed: 11/18/2022] Open
Abstract
The interplay between chemical and mechanical signals plays an important role in cell biology, and integrin receptors are the primary molecules involved in sensing and transducing external mechanical cues. We used integrin-specific probes in molecular tension fluorescence microscopy to investigate the pN forces exerted by integrin receptors in living cells. The molecular tension fluorescence microscopy probe consisted of a cyclic Arg-Gly-Asp-D-Phe-Lys(Cys) (cRGDfK(C)) peptide tethered to the terminus of a polyethylene glycol polymer that was attached to a surface through streptavidin-biotin linkage. A fluorescence resonance energy transfer mechanism was used to visualize tension-driven extension of the polymer. Surprisingly, we found that integrin receptors dissociate streptavidin-biotin tethered ligands in focal adhesions within 60 min of cell seeding. Although streptavidin-biotin binding affinity is described as the strongest noncovalent bond in nature, and is ~10(6) - 10(8) times larger than that of integrin-RGD affinity, our results suggest that individual integrin-ligand complexes undergo a marked enhancement in stability when the receptor assembles in the cell membrane. Based on the observation of streptavidin-biotin unbinding, we also conclude that the magnitude of integrin-ligand tension in focal adhesions can reach values that are at least 10 fold larger than was previously estimated using traction force microscopy-based methods.
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Affiliation(s)
| | - Yuan Chang
- Department of Chemistry, Emory University, Atlanta, Georgia
| | - Yoshie Narui
- Department of Chemistry, Emory University, Atlanta, Georgia
| | - Yun Zhang
- Department of Chemistry, Emory University, Atlanta, Georgia
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31
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Liu L, Baergen A, Michelsen K, Kitova EN, Schnier PD, Klassen JS. Energetics of intermolecular hydrogen bonds in a hydrophobic protein cavity. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:742-750. [PMID: 24658798 DOI: 10.1007/s13361-014-0833-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 12/30/2013] [Accepted: 01/02/2014] [Indexed: 06/03/2023]
Abstract
This work explores the energetics of intermolecular H-bonds inside a hydrophobic protein cavity. Kinetic measurements were performed on the gaseous deprotonated ions (at the -7 charge state) of complexes of bovine β-lactoglobulin (Lg) and three monohydroxylated analogs of palmitic acid (PA): 3-hydroxypalmitic acid (3-OHPA), 7-hydroxypalmitic acid (7-OHPA), and 16-hydroxypalmitic acid (16-OHPA). From the increase in the activation energy for the dissociation of the (Lg + X-OHPA)⁷⁻ ions, compared with that of the (Lg + PA)⁷⁻ ion, it is concluded that the –OH groups of the X-OHPA ligands participate in strong (5-11 kcal mol⁻¹) intermolecular H-bonds in the hydrophobic cavity of Lg. The results of molecular dynamics (MD) simulations suggest that the –OH groups of 3-OHPA and 16-OHPA act as H-bond donors and interact with backbone carbonyl oxygens, whereas the –OH group of 7-OHPA acts as both H-bond donor and acceptor with nearby side chains. The capacity for intermolecular H-bonds within the Lg cavity, as suggested by the gas-phase measurements, does not necessarily lead to enhanced binding in aqueous solution. The association constant (Ka) measured for 7-OHPA [(2.3 ± 0.2) × 10⁵ M⁻¹] is similar to the value for the PA [(3.8 ± 0.1) × 10⁵ M⁻¹]; Ka for 3-OHPA [(1.1 ± 0.3) × 10⁶ M⁻¹] is approximately three-times larger, whereas Ka for 16-OHPA [(2.3 ± 0.2) × 10⁴ M⁻¹] is an order of magnitude smaller. Taken together, the results of this study suggest that the energetic penalty to desolvating the ligand –OH groups, which is necessary for complex formation, is similar in magnitude to the energetic contribution of the intermolecular H-bonds.
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32
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Lin H, Kitova EN, Klassen JS. Measuring positive cooperativity using the direct ESI-MS assay. Cholera toxin B subunit homopentamer binding to GM1 pentasaccharide. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:104-110. [PMID: 24122305 DOI: 10.1007/s13361-013-0751-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 08/12/2013] [Accepted: 08/12/2013] [Indexed: 06/02/2023]
Abstract
Direct electrospray ionization mass spectrometry (ESI-MS) assay was used to investigate the stepwise binding of the GM1 pentasaccharide β-D-Galp-(1→3)-β-D-GalpNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Galp-(1→4)-β-D-Glcp (GM1os) to the cholera toxin B subunit homopentamer (CTB5) and to establish conclusively whether GM1os binding is cooperative. Apparent association constants were measured for the stepwise addition of one to five GM1os to CTB5 at pH 6.9 and 22 °C. The intrinsic association constant, which was established from the apparent association constant for the addition of a single GM1os to CTB5, was found to be (3.2 ± 0.2) × 106 M(–1). This is in reasonable agreement with the reported value of (6.4 ± 0.3) × 106 M(–1), which was measured at pH 7.4 and 25 °C using isothermal titration calorimetry (ITC). Analysis of the apparent association constants provides direct and unambiguous evidence that GM1os binding exhibits small positive cooperativity. Binding was found to be sensitive to the number of ligand-bound nearest neighbor subunits, with the affinities enhanced by a factor of 1.7 and 2.9 when binding occurs next to one or two ligand-bound subunits, respectively. These findings, which provide quantitative support for the binding model proposed by Homans and coworkers [14], highlight the unique strengths of the direct ESI-MS assay for measuring cooperative ligand binding.
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Yao C, Na N, Huang L, He D, Ouyang J. High-throughput detection of drugs binding to proteins using desorption electrospray ionization mass spectrometry. Anal Chim Acta 2013; 794:60-6. [DOI: 10.1016/j.aca.2013.07.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 05/31/2013] [Accepted: 07/05/2013] [Indexed: 01/24/2023]
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Testa L, Brocca S, Santambrogio C, D'Urzo A, Habchi J, Longhi S, Uversky VN, Grandori R. Extracting structural information from charge-state distributions of intrinsically disordered proteins by non-denaturing electrospray-ionization mass spectrometry. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e25068. [PMID: 28516012 PMCID: PMC5424789 DOI: 10.4161/idp.25068] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/02/2013] [Accepted: 05/16/2013] [Indexed: 11/23/2022]
Abstract
Intrinsically disordered proteins (IDPs) exert key biological functions but tend to escape identification and characterization due to their high structural dynamics and heterogeneity. The possibility to dissect conformational ensembles by electrospray-ionization mass spectrometry (ESI-MS) offers an attracting possibility to develop a signature for this class of proteins based on their peculiar ionization behavior. This review summarizes available data on charge-state distributions (CSDs) obtained for IDPs by non-denaturing ESI-MS, with reference to globular or chemically denatured proteins. The results illustrate the contributions that direct ESI-MS analysis can give to the identification of new putative IDPs and to their conformational investigation.
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Affiliation(s)
- Lorenzo Testa
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Annalisa D'Urzo
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Johnny Habchi
- Aix-Marseille Université; CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB); Marseille, France
| | - Sonia Longhi
- Aix-Marseille Université; CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB); Marseille, France
| | - Vladimir N Uversky
- Department of Molecular Medicine; College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region, Russia
| | - Rita Grandori
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
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