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Mayse LA, Movileanu L. Gating of β-Barrel Protein Pores, Porins, and Channels: An Old Problem with New Facets. Int J Mol Sci 2023; 24:12095. [PMID: 37569469 PMCID: PMC10418385 DOI: 10.3390/ijms241512095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
β barrels are ubiquitous proteins in the outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria. These transmembrane proteins (TMPs) execute a wide variety of tasks. For example, they can serve as transporters, receptors, membrane-bound enzymes, as well as adhesion, structural, and signaling elements. In addition, multimeric β barrels are common structural scaffolds among many pore-forming toxins. Significant progress has been made in understanding the functional, structural, biochemical, and biophysical features of these robust and versatile proteins. One frequently encountered fundamental trait of all β barrels is their voltage-dependent gating. This process consists of reversible or permanent conformational transitions between a large-conductance, highly permeable open state and a low-conductance, solute-restrictive closed state. Several intrinsic molecular mechanisms and environmental factors modulate this universal property of β barrels. This review article outlines the typical signatures of voltage-dependent gating. Moreover, we discuss recent developments leading to a better qualitative understanding of the closure dynamics of these TMPs.
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Affiliation(s)
- Lauren A. Mayse
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244, USA;
- Department of Biomedical and Chemical Engineering, Syracuse University, 223 Link Hall, Syracuse, NY 13244, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244, USA;
- Department of Biomedical and Chemical Engineering, Syracuse University, 223 Link Hall, Syracuse, NY 13244, USA
- The BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
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2
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Benkerrou D, Ceccarelli M. Free energy calculations and molecular properties of substrate translocation through OccAB porins. Phys Chem Chem Phys 2018. [DOI: 10.1039/c7cp08299a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We investigated with molecular modeling the translocation of simple substrates through four similar specific bacterial porins from the Acinetobacter baumannii pathogen providing structure–function analysis at the molecular level.
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Thakur AK, Larimi MG, Gooden K, Movileanu L. Aberrantly Large Single-Channel Conductance of Polyhistidine Arm-Containing Protein Nanopores. Biochemistry 2017; 56:4895-4905. [PMID: 28812882 DOI: 10.1021/acs.biochem.7b00577] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There have been only a few studies reporting on the impact of polyhistidine affinity tags on the structure, function, and dynamics of proteins. Because of the relatively short size of the tags, they are often thought to have little or no effect on the conformation or activity of a protein. Here, using membrane protein design and single-molecule electrophysiology, we determined that the presence of a hexahistidine arm at the N-terminus of a truncated FhuA-based protein nanopore, leaving the C-terminus untagged, produces an unusual increase in the unitary conductance to ∼8 nS in 1 M KCl. To the best of our knowledge, this is the largest single-channel conductance ever recorded with a monomeric β-barrel outer membrane protein. The hexahistidine arm was captured by an anti-polyhistidine tag monoclonal antibody added to the side of the channel-forming protein addition, but not to the opposite side, documenting that this truncated FhuA-based protein nanopore inserts into a planar lipid bilayer with a preferred orientation. This finding is in agreement with the protein insertion in vivo, in which the large loops face the extracellular side of the membrane. The aberrantly large single-channel conductance, likely induced by a greater cross-sectional area of the pore lumen, along with the vectorial insertion into a lipid membrane, will have profound implications for further developments of engineered protein nanopores.
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Affiliation(s)
- Avinash Kumar Thakur
- Department of Physics, Syracuse University , 201 Physics Building, Syracuse, New York 13244-1130, United States.,Structural Biology, Biochemistry, and Biophysics Program, Syracuse University , 111 College Place, Syracuse, New York 13244-4100, United States
| | - Motahareh Ghahari Larimi
- Department of Physics, Syracuse University , 201 Physics Building, Syracuse, New York 13244-1130, United States
| | - Kristin Gooden
- Department of Physics and Astronomy, University of Missouri , 223 Physics Building, Columbia, Missouri 65211-7010, United States
| | - Liviu Movileanu
- Department of Physics, Syracuse University , 201 Physics Building, Syracuse, New York 13244-1130, United States.,Structural Biology, Biochemistry, and Biophysics Program, Syracuse University , 111 College Place, Syracuse, New York 13244-4100, United States.,Department of Biomedical and Chemical Engineering, Syracuse University , 329 Link Hall, Syracuse, New York 13244, United States
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Wolfe AJ, Hsueh YC, Blanden AR, Mohammad MM, Pham B, Thakur AK, Loh SN, Chen M, Movileanu L. Interrogating Detergent Desolvation of Nanopore-Forming Proteins by Fluorescence Polarization Spectroscopy. Anal Chem 2017; 89:8013-8020. [PMID: 28650154 PMCID: PMC5558884 DOI: 10.1021/acs.analchem.7b01339] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Understanding how membrane proteins interact with detergents is of fundamental and practical significance in structural and chemical biology as well as in nanobiotechnology. Current methods for inspecting protein-detergent complex (PDC) interfaces require high concentrations of protein and are of low throughput. Here, we describe a scalable, spectroscopic approach that uses nanomolar protein concentrations in native solutions. This approach, which is based on steady-state fluorescence polarization (FP) spectroscopy, kinetically resolves the dissociation of detergents from membrane proteins and protein unfolding. For satisfactorily solubilizing detergents, at concentrations much greater than the critical micelle concentration (CMC), the fluorescence anisotropy was independent of detergent concentration. In contrast, at detergent concentrations comparable with or below the CMC, the anisotropy readout underwent a time-dependent decrease, showing a specific and sensitive protein unfolding signature. Functionally reconstituted membrane proteins into a bilayer membrane confirmed predictions made by these FP-based determinations with respect to varying refolding conditions. From a practical point of view, this 96-well analytical approach will facilitate a massively parallel assessment of the PDC interfacial interactions under a fairly broad range of micellar and environmental conditions. We expect that these studies will potentially accelerate research in membrane proteins pertaining to their extraction, solubilization, stabilization, and crystallization, as well as reconstitution into bilayer membranes.
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Affiliation(s)
- Aaron J. Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, USA
| | - Yi-Ching Hsueh
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Adam R. Blanden
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Av., Syracuse, New York 13210, USA
| | - Mohammad M. Mohammad
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Bach Pham
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003-9336, USA
| | - Avinash K. Thakur
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, USA
| | - Stewart N. Loh
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Av., Syracuse, New York 13210, USA
| | - Min Chen
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003-9336, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, USA
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Couoh-Cardel S, Hsueh YC, Wilkens S, Movileanu L. Yeast V-ATPase Proteolipid Ring Acts as a Large-conductance Transmembrane Protein Pore. Sci Rep 2016; 6:24774. [PMID: 27098228 PMCID: PMC4838861 DOI: 10.1038/srep24774] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/04/2016] [Indexed: 12/12/2022] Open
Abstract
The vacuolar H+ -ATPase (V-ATPase) is a rotary motor enzyme that acidifies intracellular organelles and the extracellular milieu in some tissues. Besides its canonical proton-pumping function, V-ATPase’s membrane sector, Vo, has been implicated in non-canonical functions including membrane fusion and neurotransmitter release. Here, we report purification and biophysical characterization of yeast V-ATPase c subunit ring (c-ring) using electron microscopy and single-molecule electrophysiology. We find that yeast c-ring forms dimers mediated by the c subunits’ cytoplasmic loops. Electrophysiology measurements of the c-ring reconstituted into a planar lipid bilayer revealed a large unitary conductance of ~8.3 nS. Thus, the data support a role of V-ATPase c-ring in membrane fusion and neuronal communication.
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Affiliation(s)
- Sergio Couoh-Cardel
- Department of Biochemistry &Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210, USA
| | - Yi-Ching Hsueh
- Department of Physics, Syracuse University, 201 Physics Bldg., Syracuse, New York 13244-1130, USA
| | - Stephan Wilkens
- Department of Biochemistry &Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Bldg., Syracuse, New York 13244-1130, USA.,Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, USA.,The Syracuse Biomaterials Institute, Syracuse University, 318 Bowne Hall, Syracuse, New York 13244-1200, USA
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Angevine CE, Seashols-Williams SJ, Reiner JE. Infrared Laser Heating Applied to Nanopore Sensing for DNA Duplex Analysis. Anal Chem 2016; 88:2645-51. [DOI: 10.1021/acs.analchem.5b03631] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Christopher E. Angevine
- Department of Physics, and ‡Department of
Forensic Science, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Sarah J. Seashols-Williams
- Department of Physics, and ‡Department of
Forensic Science, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Joseph E. Reiner
- Department of Physics, and ‡Department of
Forensic Science, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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Wang Y, Gu LQ. Biomedical diagnosis perspective of epigenetic detections using alpha-hemolysin nanopore. AIMS MATERIALS SCIENCE 2015; 2:448-472. [PMID: 30931380 PMCID: PMC6436813 DOI: 10.3934/matersci.2015.4.448] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The α-hemolysin nanopore has been studied for applications in DNA sequencing, various single-molecule detections, biomolecular interactions, and biochips. The detection of single molecules in a clinical setting could dramatically improve cancer detection and diagnosis as well as develop personalized medicine practices for patients. This brief review shortly presents the current solid state and protein nanopore platforms and their applications like biosensing and sequencing. We then elaborate on various epigenetic detections (like microRNA, G-quadruplex, DNA damages, DNA modifications) with the most widely used alpha-hemolysin pore from a biomedical diagnosis perspective. In these detections, a nanopore electrical current signature was generated by the interaction of a target with the pore. The signature often was evidenced by the difference in the event duration, current level, or both of them. An ideal signature would provide obvious differences in the nanopore signals between the target and the background molecules. The development of cancer biomarker detection techniques and nanopore devices have the potential to advance clinical research and resolve health problems. However, several challenges arise in applying nanopore devices to clinical studies, including super low physiological concentrations of biomarkers resulting in low sensitivity, complex biological sample contents resulting in false signals, and fast translocating speed through the pore resulting in poor detections. These issues and possible solutions are discussed.
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Affiliation(s)
- Yong Wang
- Department of Biological Engineering, Dalton Cardiovascular Research Center, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Li-qun Gu
- Department of Biological Engineering, Dalton Cardiovascular Research Center, University of Missouri-Columbia, Columbia, MO 65211, USA
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Wolfe AJ, Mohammad MM, Thakur AK, Movileanu L. Global redesign of a native β-barrel scaffold. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:19-29. [PMID: 26456555 DOI: 10.1016/j.bbamem.2015.10.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 10/03/2015] [Accepted: 10/07/2015] [Indexed: 11/30/2022]
Abstract
One persistent challenge in membrane protein design is accomplishing extensive modifications of proteins without impairing their functionality. A truncation derivative of the ferric hydroxamate uptake component A (FhuA), which featured the deletion of the 160-residue cork domain and five large extracellular loops, produced the conversion of a non-conductive, monomeric, 22-stranded β-barrel protein into a large-conductance protein pore. Here, we show that this redesigned β-barrel protein tolerates an extensive alteration in the internal surface charge, encompassing 25 negative charge neutralizations. By using single-molecule electrophysiology, we noted that a commonality of various truncation FhuA protein pores was the occurrence of 33% blockades of the unitary current at very high transmembrane potentials. We determined that these current transitions were stimulated by their interaction with an external cationic polypeptide, which occurred in a fashion dependent on the surface charge of the pore interior as well as the polypeptide characteristics. This study shows promise for extensive engineering of a large monomeric β-barrel protein pore in molecular biomedical diagnosis, therapeutics, and biosensor technology.
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Affiliation(s)
- Aaron J Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA; Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, NY 13244-4100, USA
| | - Mohammad M Mohammad
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA
| | - Avinash K Thakur
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA; Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, NY 13244-4100, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA; Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, NY 13244-4100, USA; The Syracuse Biomaterials Institute, Syracuse University, 121 Link Hall, Syracuse, NY 13244, USA.
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Pothula KR, Kleinekathöfer U. Theoretical analysis of ion conductance and gating transitions in the OpdK (OccK1) channel. Analyst 2015; 140:4855-64. [DOI: 10.1039/c5an00036j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Molecular simulations have been performed on the pore OpdK elucidating molecular details of ion conductance and a possible gating mechanism.
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