1
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Struts AV, Barmasov AV, Fried SDE, Hewage KSK, Perera SMDC, Brown MF. Osmotic stress studies of G-protein-coupled receptor rhodopsin activation. Biophys Chem 2024; 304:107112. [PMID: 37952496 DOI: 10.1016/j.bpc.2023.107112] [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: 05/06/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 11/14/2023]
Abstract
We summarize and critically review osmotic stress studies of the G-protein-coupled receptor rhodopsin. Although small amounts of structural water are present in these receptors, the effect of bulk water on their function remains uncertain. Studies of the influences of osmotic stress on the GPCR archetype rhodopsin have given insights into the functional role of water in receptor activation. Experimental work has discovered that osmolytes shift the metarhodopsin equilibrium after photoactivation, either to the active or inactive conformations according to their molar mass. At least 80 water molecules are found to enter rhodopsin in the transition to the photoreceptor active state. We infer that this movement of water is both necessary and sufficient for receptor activation. If the water influx is prevented, e.g., by large polymer osmolytes or by dehydration, then the receptor functional transition is back shifted. These findings imply a new paradigm in which rhodopsin becomes solvent swollen in the activation mechanism. Water thus acts as an allosteric modulator of function for rhodopsin-like receptors in lipid membranes.
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Affiliation(s)
- Andrey V Struts
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA; Laboratory of Biomolecular NMR, St.-Petersburg State University, 199034 St.-Petersburg, Russia
| | - Alexander V Barmasov
- Department of Biophysics, St.-Petersburg State Pediatric Medical University, 194100 St.-Petersburg, Russia; Department of Physics, St.-Petersburg State University, 199034 St.-Petersburg, Russia
| | - Steven D E Fried
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Kushani S K Hewage
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | | | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA; Department of Physics, University of Arizona, Tucson, AZ 85721, USA.
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2
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Pierro A, Tamburrini KC, Leguenno H, Gerbaud G, Etienne E, Guigliarelli B, Belle V, Zambelli B, Mileo E. In-cell investigation of the conformational landscape of the GTPase UreG by SDSL-EPR. iScience 2023; 26:107855. [PMID: 37766968 PMCID: PMC10520941 DOI: 10.1016/j.isci.2023.107855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/07/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
UreG is a cytosolic GTPase involved in the maturation network of urease, an Ni-containing bacterial enzyme. Previous investigations in vitro showed that UreG features a flexible tertiary organization, making this protein the first enzyme discovered to be intrinsically disordered. To determine whether this heterogeneous behavior is maintained in the protein natural environment, UreG structural dynamics was investigated directly in intact bacteria by in-cell EPR. This approach, based on site-directed spin labeling coupled to electron paramagnetic resonance (SDSL-EPR) spectroscopy, enables the study of proteins in their native environment. The results show that UreG maintains heterogeneous structural landscape in-cell, existing in a conformational ensemble of two major conformers, showing either random coil-like or compact properties. These data support the physiological relevance of the intrinsically disordered nature of UreG and indicates a role of protein flexibility for this specific enzyme, possibly related to the regulation of promiscuous protein interactions for metal ion delivery.
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Affiliation(s)
- Annalisa Pierro
- Aix Marseille Univ, CNRS, BIP, IMM, 13009 Marseille, France
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Ketty Concetta Tamburrini
- Aix Marseille Univ, CNRS, AFMB, 13009 Marseille, France
- INRAE, Aix Marseille Univ, BBF, 13009 Marseille, France
| | - Hugo Leguenno
- Aix Marseille Univ, CNRS, IMM, Microscopy Core Facility, 13009 Marseille, France
| | | | | | | | - Valérie Belle
- Aix Marseille Univ, CNRS, BIP, IMM, 13009 Marseille, France
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy
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3
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Chen M, Kálai T, Cascio D, Bridges MD, Whitelegge JP, Elgeti M, Hubbell WL. A Highly Ordered Nitroxide Side Chain for Distance Mapping and Monitoring Slow Structural Fluctuations in Proteins. APPLIED MAGNETIC RESONANCE 2023; 55:251-277. [PMID: 38357006 PMCID: PMC10861403 DOI: 10.1007/s00723-023-01618-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/06/2023] [Accepted: 09/09/2023] [Indexed: 02/16/2024]
Abstract
Site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) is an established tool for exploring protein structure and dynamics. Although nitroxide side chains attached to a single cysteine via a disulfide linkage are commonly employed in SDSL-EPR, their internal flexibility complicates applications to monitor slow internal motions in proteins and to structure determination by distance mapping. Moreover, the labile disulfide linkage prohibits the use of reducing agents often needed for protein stability. To enable the application of SDSL-EPR to the measurement of slow internal dynamics, new spin labels with hindered internal motion are desired. Here, we introduce a highly ordered nitroxide side chain, designated R9, attached at a single cysteine residue via a non-reducible thioether linkage. The reaction to introduce R9 is highly selective for solvent-exposed cysteine residues. Structures of R9 at two helical sites in T4 Lysozyme were determined by X-ray crystallography and the mobility in helical sequences was characterized by EPR spectral lineshape analysis, Saturation Transfer EPR, and Saturation Recovery EPR. In addition, interspin distance measurements between pairs of R9 residues are reported. Collectively, all data indicate that R9 will be useful for monitoring slow internal structural fluctuations, and applications to distance mapping via dipolar spectroscopy and relaxation enhancement methods are anticipated. Supplementary Information The online version contains supplementary material available at 10.1007/s00723-023-01618-8.
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Affiliation(s)
- Mengzhen Chen
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 USA
| | - Tamás Kálai
- Institute of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Pécs, Szigeti St. 12, Pecs, 7624 Hungary
| | - Duilio Cascio
- Department of Biological Chemistry, UCLA-DOE Institute, Howard Hughes Medical Institute, and Molecular Biology Institute, University of California, Los Angeles, CA 90095 USA
| | - Michael D. Bridges
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 USA
| | - Julian P. Whitelegge
- The Pasarow Mass Spectrometry Laboratory, David Geffen School of Medicine, The Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095 USA
| | - Matthias Elgeti
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 USA
- Present Address: Institute for Drug Discovery, Leipzig University Medical Center, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Wayne L. Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 USA
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4
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Bluma MS, Schultz KM, Kristich CJ, Klug CS. Conformational changes in the activation loop of a bacterial PASTA kinase. Protein Sci 2023; 32:e4697. [PMID: 37312631 PMCID: PMC10303680 DOI: 10.1002/pro.4697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/15/2023]
Abstract
Many bacterial genomes encode a transmembrane protein kinase belonging to the PASTA kinase family, which controls numerous processes in diverse bacterial pathogens, including antibiotic resistance, cell division, stress resistance, toxin production, and virulence. PASTA kinases share a conserved three-part domain architecture, consisting of an extracellular PASTA domain, proposed to sense the peptidoglycan layer status, a single transmembrane helix, and an intracellular Ser/Thr kinase domain. The crystal structures of the kinase domain from two homologous PASTA kinases reveal a characteristic two-lobed structure typical of eukaryotic protein kinases with a centrally located, but unresolved, activation loop that becomes phosphorylated and regulates downstream signaling pathways. We previously identified three sites of phosphorylation on the activation loop (T163, T166, and T168) of IreK, a PASTA kinase from the pathogen Enterococcus faecalis, as well as a distal phosphorylation site (T218) that each influence IreK activity in vivo. Still, the mechanism by which loop phosphorylation regulates PASTA kinase function is yet unknown. Therefore, we utilized site-directed spin labeling (SDSL) and continuous wave (CW) electron paramagnetic resonance (EPR) spectroscopy to assess the E. faecalis IreK kinase activation loop dynamics, including the effects of phosphorylation on activation loop motion, and the IreK-IreB interaction. Our results reveal that the IreK activation loop occupies a more immobile state when dephosphorylated, and that loop autophosphorylation shifts the loop to a more mobile state that can then enable interaction with IreB, a known substrate.
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Affiliation(s)
- Matthew S. Bluma
- Department of Microbiology & ImmunologyMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Kathryn M. Schultz
- Department of BiophysicsMedical College of WisconsinMilwaukeeWisconsinUSA
| | | | - Candice S. Klug
- Department of BiophysicsMedical College of WisconsinMilwaukeeWisconsinUSA
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5
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Pan Y, Li Q, Liu W, Armstrong Z, MacRae A, Feng L, McNeff C, Zhao P, Li H, Yang Z. Unveiling the orientation and dynamics of enzymes in unstructured artificial compartments of metal-organic frameworks (MOFs). NANOSCALE 2023; 15:2573-2577. [PMID: 36655708 DOI: 10.1039/d2nr06659a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Confining enzymes in well-shaped MOF compartments is a promising approach to mimic the cellular environment of enzymes and determine enzyme structure-function relationship therein. Under the cellular crowding, however, enzymes can also be confined in unstructured spaces that are close to the shapes/outlines of the enzyme. Therefore, for a better understanding of enzymes in their physiological environments, it is necessary to study enzymes in these unstructured spaces. However, practically it is challenging to create compartments that are close to the outline of an enzyme and probe enzyme structural information therein. Here, for proof-of-principle, we confined a model enzyme, lysozyme, in the crystal defects of a MOF via co-crystallization, where lysozyme served as the nuclei for MOF crystal scaffolds to grow on so that unstructured spaces close to the outline of lysozyme are created, and determined enzyme relative orientation and dynamics. This effort is important for understanding enzymes in near-native environments and guiding the rational design of biocatalysts that mimic how nature confines enzymes.
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Affiliation(s)
- Yanxiong Pan
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China.
| | - Qiaobin Li
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, USA
| | - Wei Liu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China.
| | - Zoe Armstrong
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, USA
| | - Austin MacRae
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, USA
| | - Li Feng
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, USA
| | - Charles McNeff
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, USA
| | - Pinjing Zhao
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, USA
| | - Hui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, USA
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6
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Guidelines for the Simulations of Nitroxide X-Band cw EPR Spectra from Site-Directed Spin Labeling Experiments Using S imLabel. Molecules 2023; 28:molecules28031348. [PMID: 36771013 PMCID: PMC9919594 DOI: 10.3390/molecules28031348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023] Open
Abstract
Site-directed spin labeling (SDSL) combined with continuous wave electron paramagnetic resonance (cw EPR) spectroscopy is a powerful technique to reveal, at the local level, the dynamics of structural transitions in proteins. Here, we consider SDSL-EPR based on the selective grafting of a nitroxide on the protein under study, followed by X-band cw EPR analysis. To extract valuable quantitative information from SDSL-EPR spectra and thus give a reliable interpretation on biological system dynamics, a numerical simulation of the spectra is required. However, regardless of the numerical tool chosen to perform such simulations, the number of parameters is often too high to provide unambiguous results. In this study, we have chosen SimLabel to perform such simulations. SimLabel is a graphical user interface (GUI) of Matlab, using some functions of Easyspin. An exhaustive review of the parameters used in this GUI has enabled to define the adjustable parameters during the simulation fitting and to fix the others prior to the simulation fitting. Among them, some are set once and for all (gy, gz) and others are determined (Az, gx) thanks to a supplementary X-band spectrum recorded on a frozen solution. Finally, we propose guidelines to perform the simulation of X-band cw-EPR spectra of nitroxide labeled proteins at room temperature, with no need of uncommon higher frequency spectrometry and with the minimal number of variable parameters.
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7
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Belcher Dufrisne M, Swope N, Kieber M, Yang JY, Han J, Li J, Moremen KW, Prestegard JH, Columbus L. Human CEACAM1 N-domain dimerization is independent from glycan modifications. Structure 2022; 30:658-670.e5. [PMID: 35219398 PMCID: PMC9081242 DOI: 10.1016/j.str.2022.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/15/2021] [Accepted: 02/01/2022] [Indexed: 12/31/2022]
Abstract
Carcinoembryonic cellular adhesion molecules (CEACAMs) serve diverse roles in cell signaling, proliferation, and survival and are made up of one or several immunoglobulin (Ig)-like ectodomains glycosylated in vivo. The physiological oligomeric state and how it contributes to protein function are central to understanding CEACAMs. Two putative dimer conformations involving different CEACAM1 N-terminal Ig-like domain (CCM1) protein faces (ABED and GFCC'C″) were identified from crystal structures. GFCC'C″ was identified as the dominant CCM1 solution dimer, but ambiguity regarding the effect of glycosylation on dimer formation calls its physiological relevance into question. We present the first crystal structure of minimally glycosylated CCM1 in the GFCC'C″ dimer conformation and characterization in solution by continuous-wave and double electron-electron resonance electron paramagnetic resonance spectroscopy. Our results suggest the GFCC'C″ dimer is dominant in solution with different levels of glycosylation, and structural conservation and co-evolved residues support that the GFCC'C″ dimer is conserved across CEACAMs.
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Affiliation(s)
| | - Nicole Swope
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Marissa Kieber
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Ji Han
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Jason Li
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA.
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8
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Singewald K, Wilkinson JA, Saxena AS. Copper Based Site-directed Spin Labeling of Proteins for Use in Pulsed and Continuous Wave EPR Spectroscopy. Bio Protoc 2021; 11:e4258. [PMID: 35087917 DOI: 10.21769/bioprotoc.4258] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/08/2021] [Accepted: 10/13/2021] [Indexed: 11/02/2022] Open
Abstract
Site-directed spin labeling in conjunction with electron paramagnetic resonance (EPR) is an attractive approach to measure residue specific dynamics and point-to-point distance distributions in a biomolecule. Here, we focus on the labeling of proteins with a Cu(II)-nitrilotriacetic acid (NTA) complex, by exploiting two strategically placed histidine residues (called the dHis motif). This labeling strategy has emerged as a means to overcome key limitations of many spin labels. Through utilizing the dHis motif, Cu(II)NTA rigidly binds to a protein without depending on cysteine residues. This protocol outlines three major points: the synthesis of the Cu(II)NTA complex; the measurement of continuous wave and pulsed EPR spectra, to verify a successful synthesis, as well as successful protein labeling; and utilizing Cu(II)NTA labeled proteins, to measure distance constraints and backbone dynamics. In doing so, EPR measurements are less influenced by sidechain motion, which influences the breadth of the measured distance distributions between two spins, as well as the measured residue-specific dynamics. More broadly, such EPR-based distance measurements provide unique structural constraints for integrative structural biophysics and complement traditional biophysical techniques, such as NMR, cryo-EM, FRET, and crystallography. Graphic abstract: Monitoring the success of Cu(II)NTA labeling.
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Affiliation(s)
- Kevin Singewald
- Department of Chemistry, University of Pittsburgh, Pittsburgh, USA
| | | | - And Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, USA
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9
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Pan Y, Li H, Li Q, Lenertz M, Schuster I, Jordahl D, Zhu X, Chen B, Yang Z. Protocol for resolving enzyme orientation and dynamics in advanced porous materials via SDSL-EPR. STAR Protoc 2021; 2:100676. [PMID: 34308381 PMCID: PMC8287244 DOI: 10.1016/j.xpro.2021.100676] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Enzyme encapsulation in metal-organic frameworks (MOFs)/covalent-organic frameworks (COFs) provides advancement in biocatalysis, yet the structural basis underlying the catalytic performance is challenging to probe. Here, we present an effective protocol to determine the orientation and dynamics of enzymes in MOFs/COFs using site-directed spin labeling and electron paramagnetic resonance spectroscopy. The protocol is demonstrated using lysozyme and can be generalized to other enzymes. For complete information on the generation and use of this protocol, please refer to Pan et al. (2021a). A protocol to resolve protein orientation/dynamics in porous materials is provided Site-directed spin labeling is combined with electron paramagnetic resonance Principles of protein labeling and key data acquisition steps are summarized Spectral simulation details with troubleshooting procedures are detailed
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Affiliation(s)
- Yanxiong Pan
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58102, USA
| | - Hui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Qiaobin Li
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58102, USA
| | - Mary Lenertz
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58102, USA
| | - Isabelle Schuster
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58102, USA
| | - Drew Jordahl
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58102, USA
| | - Xiao Zhu
- Research Computing, Information Technology at Purdue (ITaP), Purdue University, West Lafayette, IN 47907, USA.,Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Bingcan Chen
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58102, USA
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10
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Bonucci A, Palomino-Schätzlein M, Malo de Molina P, Arbe A, Pierattelli R, Rizzuti B, Iovanna JL, Neira JL. Crowding Effects on the Structure and Dynamics of the Intrinsically Disordered Nuclear Chromatin Protein NUPR1. Front Mol Biosci 2021; 8:684622. [PMID: 34291085 PMCID: PMC8287036 DOI: 10.3389/fmolb.2021.684622] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/22/2021] [Indexed: 01/02/2023] Open
Abstract
The intracellular environment is crowded with macromolecules, including sugars, proteins and nucleic acids. In the cytoplasm, crowding effects are capable of excluding up to 40% of the volume available to any macromolecule when compared to dilute conditions. NUPR1 is an intrinsically disordered protein (IDP) involved in cell-cycle regulation, stress-cell response, apoptosis processes, DNA binding and repair, chromatin remodeling and transcription. Simulations of molecular crowding predict that IDPs can adopt compact states, as well as more extended conformations under crowding conditions. In this work, we analyzed the conformation and dynamics of NUPR1 in the presence of two synthetic polymers, Ficoll-70 and Dextran-40, which mimic crowding effects in the cells, at two different concentrations (50 and 150 mg/ml). The study was carried out by using a multi-spectroscopic approach, including: site-directed spin labelling electron paramagnetic resonance spectroscopy (SDSL-EPR), nuclear magnetic resonance spectroscopy (NMR), circular dichroism (CD), small angle X-ray scattering (SAXS) and dynamic light scattering (DLS). SDSL-EPR spectra of two spin-labelled mutants indicate that there was binding with the crowders and that the local dynamics of the C and N termini of NUPR1 were partially affected by the crowders. However, the overall disordered nature of NUPR1 did not change substantially in the presence of the crowders, as shown by circular dichroism CD and NMR, and further confirmed by EPR. The changes in the dynamics of the paramagnetic probes appear to be related to preferred local conformations and thus crowding agents partially affect some specific regions, further pinpointing that NUPR1 flexibility has a key physiological role in its activity.
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Affiliation(s)
- Alessio Bonucci
- CERM & Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino (Florence), Italy
| | | | - Paula Malo de Molina
- Centro de Física de Materiales (CFM), CSIC-UPV/EHU, San Sebastián, Spain.,IKERBASQUE-Basque Foundation for Science, Bilbao, Spain
| | - Arantxa Arbe
- Centro de Física de Materiales (CFM), CSIC-UPV/EHU, San Sebastián, Spain
| | - Roberta Pierattelli
- CERM & Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino (Florence), Italy
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, Rende, Italy.,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
| | - Juan L Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - José L Neira
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain.,IDIBE, Universidad Miguel Hernández, Elche (Alicante), Spain
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11
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Sharma GS, Krishna S, Khan S, Dar TA, Khan KA, Singh LR. Protecting thermodynamic stability of protein: The basic paradigm against stress and unfolded protein response by osmolytes. Int J Biol Macromol 2021; 177:229-240. [PMID: 33607142 DOI: 10.1016/j.ijbiomac.2021.02.102] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 01/10/2023]
Abstract
Organic osmolytes are known to play important role in stress protection by stabilizing macromolecules and suppressing harmful effects on functional activity. There is existence of several reports in the literature regarding their effects on structural, functional and thermodynamic aspects of many enzymes and the interaction parameters with proteins have been explored. Osmolytes are compatible with enzyme function and therefore, can be accumulated up to several millimolar concentrations. From the thermodynamic point of view, osmolyte raises mid-point of thermal denaturation (Tm) of proteins while having no significant effect on ΔGD° (free energy change at physiological condition). Unfavorable interaction with the peptide backbone due to preferential hydration is the major driving force for folding of unfolded polypeptide in presence of osmolyte. However, the thermodynamic basis of stress protection and origin of compatibility paradigm has been a debatable issue. In the present manuscript, we attempt to elaborate the origin of stress protection and compatibility paradigm of osmolytes based on the effect on thermodynamic stability of proteins. We also infer that protective effects of osmolytes on ΔGD° (of proteins) could also indicate its potential involvement in unfolded protein response and overall stress biology on macromolecular level.
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Affiliation(s)
- Gurumayum Suraj Sharma
- Department of Botany, Bhaskaracharya College of Applied Sciences, University of Delhi, Delhi, India
| | - Snigdha Krishna
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Sheeza Khan
- School of Life Sciences, B. S. Abdur Rahman Crescent Institute of Science and Technology, Chennai, India
| | - Tanveer A Dar
- Department of Clinical Biochemistry, University of Kashmir, Srinagar, J&K, India
| | - Khurshid A Khan
- School of Life Sciences, B. S. Abdur Rahman Crescent Institute of Science and Technology, Chennai, India
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12
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Chawla U, Perera SMDC, Fried SDE, Eitel AR, Mertz B, Weerasinghe N, Pitman MC, Struts AV, Brown MF. Activation of the G‐Protein‐Coupled Receptor Rhodopsin by Water. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202003342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Udeep Chawla
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
| | | | - Steven D. E. Fried
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
| | - Anna R. Eitel
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
| | - Blake Mertz
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
| | - Nipuna Weerasinghe
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
| | - Michael C. Pitman
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
| | - Andrey V. Struts
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
- Laboratory of Biomolecular NMR St. Petersburg State University St. Petersburg 199034 Russia
| | - Michael F. Brown
- Department of Chemistry and Biochemistry University of Arizona Tucson AZ 85721 USA
- Department of Physics University of Arizona Tucson AZ 85721 USA
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13
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Doni D, Passerini L, Audran G, Marque SRA, Schulz M, Santos J, Costantini P, Bortolus M, Carbonera D. Effects of Fe 2+/Fe 3+ Binding to Human Frataxin and Its D122Y Variant, as Revealed by Site-Directed Spin Labeling (SDSL) EPR Complemented by Fluorescence and Circular Dichroism Spectroscopies. Int J Mol Sci 2020; 21:E9619. [PMID: 33348670 PMCID: PMC7766144 DOI: 10.3390/ijms21249619] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 12/17/2022] Open
Abstract
Frataxin is a highly conserved protein whose deficiency results in the neurodegenerative disease Friederich's ataxia. Frataxin's actual physiological function has been debated for a long time without reaching a general agreement; however, it is commonly accepted that the protein is involved in the biosynthetic iron-sulphur cluster (ISC) machinery, and several authors have pointed out that it also participates in iron homeostasis. In this work, we use site-directed spin labeling coupled to electron paramagnetic resonance (SDSL EPR) to add new information on the effects of ferric and ferrous iron binding on the properties of human frataxin in vitro. Using SDSL EPR and relating the results to fluorescence experiments commonly performed to study iron binding to FXN, we produced evidence that ferric iron causes reversible aggregation without preferred interfaces in a concentration-dependent fashion, starting at relatively low concentrations (micromolar range), whereas ferrous iron binds without inducing aggregation. Moreover, our experiments show that the ferrous binding does not lead to changes of protein conformation. The data reported in this study reveal that the currently reported binding stoichiometries should be taken with caution. The use of a spin label resistant to reduction, as well as the comparison of the binding effect of Fe2+ in wild type and in the pathological D122Y variant of frataxin, allowed us to characterize the Fe2+ binding properties of different protein sites and highlight the effect of the D122Y substitution on the surrounding residues. We suggest that both Fe2+ and Fe3+ might play a relevant role in the context of the proposed FXN physiological functions.
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Affiliation(s)
- Davide Doni
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy; (D.D.); (P.C.)
| | - Leonardo Passerini
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy; (L.P.); (D.C.)
| | - Gérard Audran
- Institut de Chimie Radicalaire, Aix Marseille Universitè, CNRS, ICR, UMR 7273, Case 551, Ave Escadrille Normandie Niemen, CEDEX 20, 13397 Marseille, France; (G.A.); (S.R.A.M.); (M.S.)
| | - Sylvain R. A. Marque
- Institut de Chimie Radicalaire, Aix Marseille Universitè, CNRS, ICR, UMR 7273, Case 551, Ave Escadrille Normandie Niemen, CEDEX 20, 13397 Marseille, France; (G.A.); (S.R.A.M.); (M.S.)
| | - Marvin Schulz
- Institut de Chimie Radicalaire, Aix Marseille Universitè, CNRS, ICR, UMR 7273, Case 551, Ave Escadrille Normandie Niemen, CEDEX 20, 13397 Marseille, France; (G.A.); (S.R.A.M.); (M.S.)
| | - Javier Santos
- Departamento de Química Biológica, Instituto de Biociencias, Biotecnología y Biomedicina (iB3-UBA), Facultad de Ciencia Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160—Ciudad Universitaria, 1428EGA CONICET, Godoy Cruz 2290, Buenos Aires C1425FQB, Argentina;
- Instituto de Química y Fisicoquímica Biológicas Dr. Alejandro Paladini, Universidad de Buenos Aires, CONICET, Junín 956, Buenos Aires 1113AAD, Argentina
| | - Paola Costantini
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy; (D.D.); (P.C.)
| | - Marco Bortolus
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy; (L.P.); (D.C.)
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy; (L.P.); (D.C.)
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14
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Structure and regulation of the BsYetJ calcium channel in lipid nanodiscs. Proc Natl Acad Sci U S A 2020; 117:30126-30134. [PMID: 33208533 DOI: 10.1073/pnas.2014094117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
BsYetJ is a bacterial homolog of transmembrane BAX inhibitor-1 motif-containing 6 (TMBIM6) membrane protein that plays a key role in the control of calcium homeostasis. However, the BsYetJ (or TMBIM6) structure embedded in a lipid bilayer is uncharacterized, let alone the molecular mechanism of the calcium transport activity. Herein, we report structures of BsYetJ in lipid nanodiscs identified by double electron-electron resonance spectroscopy. Our results reveal that BsYetJ in lipid nanodiscs is structurally different from those crystallized in detergents. We show that BsYetJ conformation is pH-sensitive in apo state (lacking calcium), whereas in a calcium-containing solution it is stuck in an intermediate, inert to pH changes. Only when the transmembrane calcium gradient is established can the calcium-release activity of holo-BsYetJ occur and be mediated by pH-dependent conformational changes, suggesting a dual gating mechanism. Conformational substates involved in the process and a key residue D171 relevant to the gating of calcium are identified. Our study suggests that BsYetJ/TMBIM6 is a pH-dependent, voltage-gated calcium channel.
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15
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Viewing rare conformations of the β 2 adrenergic receptor with pressure-resolved DEER spectroscopy. Proc Natl Acad Sci U S A 2020; 117:31824-31831. [PMID: 33257561 DOI: 10.1073/pnas.2013904117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The β2 adrenergic receptor (β2AR) is an archetypal G protein coupled receptor (GPCR). One structural signature of GPCR activation is a large-scale movement (ca. 6 to 14 Å) of transmembrane helix 6 (TM6) to a conformation which binds and activates a cognate G protein. The β2AR exhibits a low level of agonist-independent G protein activation. The structural origin of this basal activity and its suppression by inverse agonists is unknown but could involve a unique receptor conformation that promotes G protein activation. Alternatively, a conformational selection model proposes that a minor population of the canonical active receptor conformation exists in equilibrium with inactive forms, thus giving rise to basal activity of the ligand-free receptor. Previous spin-labeling and fluorescence resonance energy transfer experiments designed to monitor the positional distribution of TM6 did not detect the presence of the active conformation of ligand-free β2AR. Here we employ spin-labeling and pressure-resolved double electron-electron resonance spectroscopy to reveal the presence of a minor population of unliganded receptor, with the signature outward TM6 displacement, in equilibrium with inactive conformations. Binding of inverse agonists suppresses this population. These results provide direct structural evidence in favor of a conformational selection model for basal activity in β2AR and provide a mechanism for inverse agonism. In addition, they emphasize 1) the importance of minor populations in GPCR catalytic function; 2) the use of spin-labeling and variable-pressure electron paramagnetic resonance to reveal them in a membrane protein; and 3) the quantitative evaluation of their thermodynamic properties relative to the inactive forms, including free energy, partial molar volume, and compressibility.
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16
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Chawla U, Perera SMDC, Fried SDE, Eitel AR, Mertz B, Weerasinghe N, Pitman MC, Struts AV, Brown MF. Activation of the G-Protein-Coupled Receptor Rhodopsin by Water. Angew Chem Int Ed Engl 2020; 60:2288-2295. [PMID: 32596956 DOI: 10.1002/anie.202003342] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/28/2020] [Indexed: 12/31/2022]
Abstract
Visual rhodopsin is an important archetype for G-protein-coupled receptors, which are membrane proteins implicated in cellular signal transduction. Herein, we show experimentally that approximately 80 water molecules flood rhodopsin upon light absorption to form a solvent-swollen active state. An influx of mobile water is necessary for activating the photoreceptor, and this finding is supported by molecular dynamics (MD) simulations. Combined force-based measurements involving osmotic and hydrostatic pressure indicate the expansion occurs by changes in cavity volumes, together with greater hydration in the active metarhodopsin-II state. Moreover, we discovered that binding and release of the C-terminal helix of transducin is coupled to hydration changes as may occur in visual signal amplification. Hydration-dehydration explains signaling by a dynamic allosteric mechanism, in which the soft membrane matter (lipids and water) has a pivotal role in the catalytic G-protein cycle.
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Affiliation(s)
- Udeep Chawla
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | | | - Steven D E Fried
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Anna R Eitel
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Blake Mertz
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Nipuna Weerasinghe
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Michael C Pitman
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Andrey V Struts
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA.,Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA.,Department of Physics, University of Arizona, Tucson, AZ, 85721, USA
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17
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Park J, Lee M, Lee B, Castaneda N, Tetard L, Kang EH. Crowding tunes the organization and mechanics of actin bundles formed by crosslinking proteins. FEBS Lett 2020; 595:26-40. [PMID: 33020904 DOI: 10.1002/1873-3468.13949] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 01/05/2023]
Abstract
Fascin and α-actinin form higher-ordered actin bundles that mediate numerous cellular processes including cell morphogenesis and movement. While it is understood crosslinked bundle formation occurs in crowded cytoplasm, how crowding affects the bundling activities of the two crosslinking proteins is not known. Here, we demonstrate how solution crowding modulates the organization and mechanical properties of fascin- and α-actinin-induced bundles, utilizing total internal reflection fluorescence and atomic force microscopy imaging. Molecular dynamics simulations support the inference that crowding reduces binding interaction between actin filaments and fascin or the calponin homology 1 domain of α-actinin evidenced by interaction energy and hydrogen bonding analysis. Based on our findings, we suggest a mechanism of crosslinked actin bundle assembly and mechanics in crowded intracellular environments.
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Affiliation(s)
- Jinho Park
- NanoScience Technology Center, University of Central Florida, Orlando, FL, USA.,Department of Materials Science and Engineering, University of Central Florida, Orlando, FL, USA
| | - Myeongsang Lee
- NanoScience Technology Center, University of Central Florida, Orlando, FL, USA
| | - Briana Lee
- NanoScience Technology Center, University of Central Florida, Orlando, FL, USA
| | - Nicholas Castaneda
- NanoScience Technology Center, University of Central Florida, Orlando, FL, USA.,Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Laurene Tetard
- NanoScience Technology Center, University of Central Florida, Orlando, FL, USA.,Department of Physics, University of Central Florida, Orlando, FL, USA
| | - Ellen Hyeran Kang
- NanoScience Technology Center, University of Central Florida, Orlando, FL, USA.,Department of Materials Science and Engineering, University of Central Florida, Orlando, FL, USA.,Department of Physics, University of Central Florida, Orlando, FL, USA
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18
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Tsai RF, Lin NC, Kao TY, Kuo YH, Lo FC, Liaw WF, Chiang YW. Nitrosylation of the Diiron Core Mediated by the N Domain of YtfE. J Phys Chem Lett 2020; 11:8538-8542. [PMID: 32940468 DOI: 10.1021/acs.jpclett.0c02200] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The YtfE protein catalyzes the reduction of NO to N2O, protecting iron-sulfur clusters from nitrosylation. The structure of YtfE has a two-domain architecture, with a diiron-containing C-terminal domain linked to an N-terminal domain, in which the function of the latter is enigmatic. Here, by using electron spin resonance (ESR) spectroscopy, we show that YtfE exists in two conformational states, one of which has not been reported. Under high osmotic stress, YtfE adopts a homogeneous conformation (C state) similar to the known crystal structure. In a regular buffer, the N-terminal domain switches between the C state and a previously unidentified conformation (C' state), the latter of which has more space at the domain interface to allow the trafficking of NO molecules and thus is proposed to be a functionally active state. The conformational switch between the C and C' states is pivotal for facilitating NO access to the diiron core.
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Affiliation(s)
- Ruei-Fong Tsai
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Nien-Chen Lin
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Te-Yu Kao
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Yun-Hsuan Kuo
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Feng-Chun Lo
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Wen-Feng Liaw
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
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19
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Pierro A, Etienne E, Gerbaud G, Guigliarelli B, Ciurli S, Belle V, Zambelli B, Mileo E. Nickel and GTP Modulate Helicobacter pylori UreG Structural Flexibility. Biomolecules 2020; 10:E1062. [PMID: 32708696 PMCID: PMC7408563 DOI: 10.3390/biom10071062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/25/2020] [Accepted: 07/10/2020] [Indexed: 12/14/2022] Open
Abstract
UreG is a P-loop GTP hydrolase involved in the maturation of nickel-containing urease, an essential enzyme found in plants, fungi, bacteria, and archaea. This protein couples the hydrolysis of GTP to the delivery of Ni(II) into the active site of apo-urease, interacting with other urease chaperones in a multi-protein complex necessary for enzyme activation. Whereas the conformation of Helicobacter pylori (Hp) UreG was solved by crystallography when it is in complex with two other chaperones, in solution the protein was found in a disordered and flexible form, defining it as an intrinsically disordered enzyme and indicating that the well-folded structure found in the crystal state does not fully reflect the behavior of the protein in solution. Here, isothermal titration calorimetry and site-directed spin labeling coupled to electron paramagnetic spectroscopy were successfully combined to investigate HpUreG structural dynamics in solution and the effect of Ni(II) and GTP on protein mobility. The results demonstrate that, although the protein maintains a flexible behavior in the metal and nucleotide bound forms, concomitant addition of Ni(II) and GTP exerts a structural change through the crosstalk of different protein regions.
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Affiliation(s)
- Annalisa Pierro
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France; (A.P.); (E.E.); (G.G.); (B.G.); (V.B.)
| | - Emilien Etienne
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France; (A.P.); (E.E.); (G.G.); (B.G.); (V.B.)
| | - Guillaume Gerbaud
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France; (A.P.); (E.E.); (G.G.); (B.G.); (V.B.)
| | - Bruno Guigliarelli
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France; (A.P.); (E.E.); (G.G.); (B.G.); (V.B.)
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy;
| | - Valérie Belle
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France; (A.P.); (E.E.); (G.G.); (B.G.); (V.B.)
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy;
| | - Elisabetta Mileo
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France; (A.P.); (E.E.); (G.G.); (B.G.); (V.B.)
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20
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Farmakes J, Schuster I, Overby A, Alhalhooly L, Lenertz M, Li Q, Ugrinov A, Choi Y, Pan Y, Yang Z. Enzyme Immobilization on Graphite Oxide (GO) Surface via One-Pot Synthesis of GO/Metal-Organic Framework Composites for Large-Substrate Biocatalysis. ACS APPLIED MATERIALS & INTERFACES 2020; 12:23119-23126. [PMID: 32338863 DOI: 10.1021/acsami.0c04101] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Although enzyme immobilization has improved many areas, biocatalysis involving large-size substrates is still challenging for immobilization platform design because of the protein damage under the often "harsh" reaction conditions required for these reactions. Our recent efforts indicate the potential of using Metal-Organic Frameworks (MOFs) to partially confine enzymes on the surface of MOF-based composites while offering sufficient substrate contact. Still, improvements are required to expand the feasible pH range and the efficiency of contacting substrates. In this contribution, we discovered that Zeolitic Imidazolate Framework (ZIF) and a new calcium-carboxylate based MOF (CaBDC) can both be coprecipitated with a model large-substrate enzyme, lysozyme (lys), to anchor the enzyme on the surface of graphite oxide (GO). We observed lys activity against its native substrate, bacterial cell walls, indicating lys was confined on composite surface. Remarkably, lys@GO/CaBDC displayed a stronger catalytic efficiency at pH 6.2 as compared to pH 7.4, indicating CaBDC is a good candidate for biocatalysis under acidic conditions as compared to ZIFs which disassemble under pH < 7. Furthermore, to understand the regions of lys being exposed to the reaction medium, we carried out a site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy study. Our data showed a preferential orientation of lys in GO/ZIF composite, whereas a random orientation in GO/CaBDC. This is the first report on immobilizing solution-state large-substrate enzymes on GO surface using two different MOFs via one-pot synthesis. These platforms can be generalized to other large-substrate enzymes to carry out catalysis under the optimal buffer/pH conditions. The orientation of enzyme at the molecular level on composite surfaces is critical for guiding the rational design of new composites.
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Affiliation(s)
- Jasmin Farmakes
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Isabelle Schuster
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Amanda Overby
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Lina Alhalhooly
- Department of Physics, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Mary Lenertz
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Qiaobin Li
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Angel Ugrinov
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Yongki Choi
- Department of Physics, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Yanxiong Pan
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
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21
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Sun Q, Pan Y, Wang X, Li H, Farmakes J, Aguila B, Yang Z, Ma S. Mapping out the Degree of Freedom of Hosted Enzymes in Confined Spatial Environments. Chem 2019. [DOI: 10.1016/j.chempr.2019.10.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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22
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Li H, Pan Y, Farmakes J, Xiao F, Liu G, Chen B, Zhu X, Rao J, Yang Z. A sulfonated mesoporous silica nanoparticle for enzyme protection against denaturants and controlled release under reducing conditions. J Colloid Interface Sci 2019; 556:292-300. [DOI: 10.1016/j.jcis.2019.08.063] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 01/23/2023]
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23
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Hines JP, Dent MR, Stevens DJ, Burstyn JN. Site-directed spin label electron paramagnetic resonance spectroscopy as a probe of conformational dynamics in the Fe(III) "locked-off" state of the CO-sensing transcription factor CooA. Protein Sci 2018; 27:1670-1679. [PMID: 30168206 PMCID: PMC6194275 DOI: 10.1002/pro.3449] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/25/2018] [Accepted: 05/29/2018] [Indexed: 01/30/2023]
Abstract
The transcriptional activator CooA belongs to the CRP/FNR (cAMP receptor protein/fumarate and nitrate reductase) superfamily of transcriptional regulators and uses heme to sense carbon monoxide (CO). Effector-driven allosteric activation is well understood in CRP, a CooA homologue. A structural allosteric activation model for CooA exists which parallels that of CRP; however, the role of protein dynamics, which is crucial in CRP, is not well understood in CooA. We employed site-directed spin labeling electron paramagnetic resonance spectroscopy to probe CooA motions on the μs-ms timescale. We created a series of Cys substitution variants, each with a cysteine residue introduced into a key functional region of the protein: K26C, E60C, F132C, D134C, and S175C. The heme environment and DNA binding affinity of each variant were comparable to those of wild-type CooA, with the exception of F132C, which displayed reduced DNA binding affinity. This observation confirms a previously hypothesized role for Phe132 in transmitting the allosteric CO binding signal. Osmolyte perturbation studies of Fe(III) "locked-off" CooA variants labeled with either MTSL or MAL-6 nitroxide spin labels revealed that multicomponent EPR spectra report on conformational flexibility on the μs-ms timescale. Multiple dynamic populations exist at every site examined in the structurally uncharacterized Fe(III) "locked-off" CooA. This observation suggests that, in direct contrast to effector-free CRP, Fe(III) "locked-off" CooA undergoes conformational exchange on the μs-ms timescale. Importantly, we establish MAL-6 as a spin label with a redox-stable linkage that may be utilized to compare conformational dynamics between functional states of CooA.
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Affiliation(s)
- Judy P. Hines
- Department of ChemistryUniversity of Wisconsin–MadisonMadisonWisconsin
| | - Matthew R. Dent
- Department of ChemistryUniversity of Wisconsin–MadisonMadisonWisconsin
| | - Daniel J. Stevens
- Department of ChemistryUniversity of Wisconsin–MadisonMadisonWisconsin
| | - Judith N. Burstyn
- Department of ChemistryUniversity of Wisconsin–MadisonMadisonWisconsin
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24
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Sarver JL, Zhang M, Liu L, Nyenhuis D, Cafiso DS. A Dynamic Protein-Protein Coupling between the TonB-Dependent Transporter FhuA and TonB. Biochemistry 2018; 57:1045-1053. [PMID: 29338257 DOI: 10.1021/acs.biochem.7b01223] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial outer membrane TonB-dependent transporters function by executing cycles of binding and unbinding to the inner membrane protein TonB. In the vitamin B12 transporter BtuB and the ferric citrate transporter FecA, substrate binding increases the periplasmic exposure of the Ton box, an energy-coupling segment. This increased exposure appears to enhance the affinity of the transporter for TonB. Here, continuous wave and pulse EPR spectroscopy were used to examine the state of the Ton box in the Escherichia coli ferrichrome transporter FhuA. In its apo state, the Ton box of FhuA samples a broad range of positions and multiple conformational substates. When bound to ferrichrome, the Ton box does not extend further into the periplasm, although the structural states sampled by the FhuA Ton box are altered. When bound to a soluble fragment of TonB, the TonB-FhuA complex remains heterogeneous and dynamic, indicating that TonB does not make strong, specific contacts with either the FhuA barrel or the core region of the transporter. This result differs from that seen in the crystal structure of the TonB-FhuA complex. These data indicate that unlike BtuB and FecA, the periplasmic exposure of the Ton box in FhuA does not change significantly in the presence of substrate and that allosteric control of transporter-TonB interactions functions by a different mechanism than that seen in either BtuB or FecA. Moreover, the data indicate that models involving a rotation of TonB relative to the transporter are unlikely to underlie the mechanism that drives TonB-dependent transport.
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Affiliation(s)
- Jessica L Sarver
- Department of Chemistry and Center for Membrane Biology, University of Virginia , McCormick Road, Charlottesville, Virginia 22904, United States
| | - Michael Zhang
- Department of Chemistry and Center for Membrane Biology, University of Virginia , McCormick Road, Charlottesville, Virginia 22904, United States
| | - Lishan Liu
- Department of Chemistry and Center for Membrane Biology, University of Virginia , McCormick Road, Charlottesville, Virginia 22904, United States
| | - David Nyenhuis
- Department of Chemistry and Center for Membrane Biology, University of Virginia , McCormick Road, Charlottesville, Virginia 22904, United States
| | - David S Cafiso
- Department of Chemistry and Center for Membrane Biology, University of Virginia , McCormick Road, Charlottesville, Virginia 22904, United States
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25
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Budamagunta MS, Guo F, Sun N, Shibata B, FitzGerald PG, Voss JC, Hess JF. Production of recombinant human tektin 1, 2, and 4 and in vitro assembly of human tektin 1. Cytoskeleton (Hoboken) 2017; 75:3-11. [PMID: 29108134 DOI: 10.1002/cm.21418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 10/24/2017] [Accepted: 11/01/2017] [Indexed: 11/10/2022]
Abstract
Proteins predicted to be composed of large stretches of coiled-coil structure have often proven difficult to crystallize for structural determination. We have successfully applied EPR spectroscopic techniques to the study of the structure and assembly of full-length human vimentin assembled into native 11 nm filaments, in physiologic solution, circumventing the limitations of crystallizing shorter peptide sequences. Tektins are a small family of highly alpha helical filamentous proteins found in the doublet microtubules of cilia and related structures. Tektins exhibit several similarities to intermediate filaments (IFs): moderate molecular weight, highly alpha helical, hypothesized to be coiled-coil, and homo- and heteromeric assembly into long smooth filaments. In this report, we show the application of IF research methodologies to the study of tektin structure and assembly. To begin in vitro studies, expression constructs for human tektins 1, 2, and 4 were synthesized. Recombinant tektins were produced in E. coli and purified by chromatography. Preparations of tektin 1 successfully formed filaments. The recombinant human tektin 1 was used to produce antibodies which recognized an antigen in mouse testes, most likely present in sperm flagella. Finally, we report the creation of seven mutants to analyze predictions of coiled-coil structure in the rod 1A domain of tektin 1. Although this region is predicted to be coiled-coil, our EPR analysis does not reflect the parallel, in register, coiled-coil structure as demonstrated in vimentin and kinesin. These results document that tektin can be successfully expressed and assembled in vitro, and that SDSL EPR techniques can be used for structural analysis.
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Affiliation(s)
- M S Budamagunta
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, California, 95616
| | - F Guo
- Department of Molecular and Cellular Biology, University of California, Davis, California, 95616
| | - N Sun
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California, Davis, California, 95616
| | - B Shibata
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California, Davis, California, 95616
| | - P G FitzGerald
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California, Davis, California, 95616
| | - J C Voss
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, California, 95616
| | - J F Hess
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California, Davis, California, 95616
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26
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Conformational Heterogeneity in the Activation Mechanism of Bax. Structure 2017; 25:1310-1316.e3. [PMID: 28712810 DOI: 10.1016/j.str.2017.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 06/05/2017] [Accepted: 06/16/2017] [Indexed: 01/02/2023]
Abstract
Bax is known for its pro-apoptotic role within the mitochondrial pathway of apoptosis. However, the mechanism for transitioning Bax from cytosolic to membrane-bound oligomer remains elusive. Previous nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) studies defined monomeric Bax as conformationally homogeneous. Yet it has recently been proposed that monomeric Bax exists in equilibrium with a minor state that is distinctly different from its NMR structure. Here, we revisited the structural analysis of Bax using methods uniquely suited for unveiling "invisible" states of proteins, namely, NMR paramagnetic relaxation enhancements and EPR double electron-electron resonance (DEER). Additionally we examined the effect of glycerol, the co-solvent of choice in DEER studies, on the structure of Bax using NMR chemical-shift perturbations and residual dipolar couplings. Based on our combined NMR and EPR results, Bax is a conformationally homogeneous protein prior to its activation.
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27
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Ge J, Bouriyaphone SD, Serebrennikova TA, Astashkin AV, Nesmelov YE. Macromolecular Crowding Modulates Actomyosin Kinetics. Biophys J 2017; 111:178-84. [PMID: 27410745 DOI: 10.1016/j.bpj.2016.05.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 05/18/2016] [Accepted: 05/19/2016] [Indexed: 11/17/2022] Open
Abstract
Actomyosin kinetics is usually studied in dilute solutions, which do not reflect conditions in the cytoplasm. In cells, myosin and actin work in a dense macromolecular environment. High concentrations of macromolecules dramatically reduce the amount of free space available for all solutes, which results in an effective increase of the solutes' chemical potential and protein stabilization. Moreover, in a crowded solution, the chemical potential depends on the size of the solute, with larger molecules experiencing a larger excluded volume than smaller ones. Therefore, since myosin interacts with two ligands of different sizes (actin and ATP), macromolecular crowding can modulate the kinetics of individual steps of the actomyosin ATPase cycle. To emulate the effect of crowding in cells, we studied actomyosin cycle reactions in the presence of a high-molecular-weight polymer, Ficoll70. We observed an increase in the maximum velocity of the actomyosin ATPase cycle, and our transient-kinetics experiments showed that virtually all individual steps of the actomyosin cycle were affected by the addition of Ficoll70. The observed effects of macromolecular crowding on the myosin-ligand interaction cannot be explained by the increase of a solute's chemical potential. A time-resolved Förster resonance energy transfer experiment confirmed that the myosin head assumes a more compact conformation in the presence of Ficoll70 than in a dilute solution. We conclude that the crowding-induced myosin conformational change plays a major role in the changed kinetics of actomyosin ATPase.
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Affiliation(s)
- Jinghua Ge
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina; Center for Biomedical Engineering and Science, University of North Carolina, Charlotte, North Carolina
| | - Sherry D Bouriyaphone
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina
| | | | - Andrei V Astashkin
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona
| | - Yuri E Nesmelov
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina; Center for Biomedical Engineering and Science, University of North Carolina, Charlotte, North Carolina.
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28
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Pan Y, Neupane S, Farmakes J, Bridges M, Froberg J, Rao J, Qian SY, Liu G, Choi Y, Yang Z. Probing the structural basis and adsorption mechanism of an enzyme on nano-sized protein carriers. NANOSCALE 2017; 9:3512-3523. [PMID: 28244542 DOI: 10.1039/c7nr00276a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Silica nanoparticles (SiNPs) are important nano-sized, solid-state carriers/hosts to load, store, and deliver biological or pharmaceutical cargoes. They are also good potential solid supports to immobilize proteins for fundamental protein structure and dynamics studies. However, precaution is necessary when using SiNPs in these areas because adsorption might alter the activity of the cargoes, especially when enzymes are loaded. Therefore, it becomes important to understand the structural basis of the cargo enzyme activity changes, if there is any. The high complexity and dynamics of the nano-bio interface present many challenges. Reported here is a comprehensive study of the structure, dynamics, and activity of a model enzyme, T4 lysozyme, upon adsorption to a few surface-modified SiNPs using several experimental techniques. Not surprisingly, a significant activity loss on each studied SiNP was found. The structural basis of the activity loss was identified based on results from a unique technique, the Electron Paramagnetic Resonance (EPR) spectroscopy, which probes structural information regardless of the complexity. Several docking models of the enzyme on SiNPs with different surfaces, at different enzyme-to-SiNP ratios are proposed. Interestingly, we found that the adsorbed enzyme can be desorbed via pH adjustment, which highlighted the potential to use SiNPs for enzyme/protein delivery or storage due to the high capacity. In order to use SiNPs as enzyme hosts, minimizing the enzymatic activity loss upon adsorption is needed. Lastly, the work outlined here demonstrate the use of EPR in probing structural information on the complex (inorganic)nano-bio interface.
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Affiliation(s)
- Yanxiong Pan
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA.
| | - Sunanda Neupane
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA.
| | - Jasmin Farmakes
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA.
| | - Michael Bridges
- Jules Stein Eye Institute, University of California, Los Angeles, CA 90025, USA
| | - James Froberg
- Department of Physics, North Dakota State University, Fargo, ND 58108, USA
| | - Jiajia Rao
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Steven Y Qian
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Guodong Liu
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA.
| | - Yongki Choi
- Department of Physics, North Dakota State University, Fargo, ND 58108, USA
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA.
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29
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Consentius P, Gohlke U, Loll B, Alings C, Heinemann U, Wahl MC, Risse T. Combining EPR spectroscopy and X-ray crystallography to elucidate the structure and dynamics of conformationally constrained spin labels in T4 lysozyme single crystals. Phys Chem Chem Phys 2017; 19:20723-20734. [DOI: 10.1039/c7cp03144k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Unraveling structural and dynamic details of spin labeled proteins using a combination of single crystal EPR spectroscopy and X-ray crystallography.
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Affiliation(s)
- Philipp Consentius
- Freie Universität Berlin
- Institute of Chemistry and Biochemistry
- 14195 Berlin
- Germany
| | - Ulrich Gohlke
- Medicine in the Helmholtz Association
- 13125 Berlin
- Germany
| | - Bernhard Loll
- Freie Universität Berlin
- Institute of Chemistry and Biochemistry
- Laboratory of Structural Biochemistry
- 14195 Berlin
- Germany
| | - Claudia Alings
- Freie Universität Berlin
- Institute of Chemistry and Biochemistry
- Laboratory of Structural Biochemistry
- 14195 Berlin
- Germany
| | - Udo Heinemann
- Freie Universität Berlin
- Institute of Chemistry and Biochemistry
- 14195 Berlin
- Germany
- Medicine in the Helmholtz Association
| | - Markus C. Wahl
- Freie Universität Berlin
- Institute of Chemistry and Biochemistry
- Laboratory of Structural Biochemistry
- 14195 Berlin
- Germany
| | - Thomas Risse
- Freie Universität Berlin
- Institute of Chemistry and Biochemistry
- 14195 Berlin
- Germany
- Berlin Joint EPR Laboratory, Freie Universität Berlin
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30
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Bartelli NL, Hazelbauer GL. Bacterial Chemoreceptor Dynamics: Helical Stability in the Cytoplasmic Domain Varies with Functional Segment and Adaptational Modification. J Mol Biol 2016; 428:3789-804. [PMID: 27318193 PMCID: PMC5193150 DOI: 10.1016/j.jmb.2016.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 12/28/2022]
Abstract
Dynamics are thought to be important features of structure and signaling in the cytoplasmic domain of bacterial chemoreceptors. However, little is known about which structural features are dynamic. For this largely helical domain, comprising a four-helix bundle and an extended four-helix coiled coil, functionally important structural dynamics likely involves helical mobility and stability. To investigate, we used continuous wave EPR spectroscopy and site-specific spin labels that directly probed, in essentially physiological conditions, the mobility of helical backbones in the cytoplasmic domain of intact chemoreceptor Tar homodimers inserted into lipid bilayers of Nanodiscs. We observed differences among functional regions, between companion helices in helical hairpins of the coiled coil and between receptor conformational states generated by adaptational modification. Increased adaptational modification decreased helical dynamics while preserving dynamics differences among functional regions and between companion helices. In contrast, receptor ligand occupancy did not have a discernable effect on dynamics to which our approach was sensitive, implying that the two sensory inputs alter different chemoreceptor features. Spectral fitting indicated that differences in helical dynamics we observed for ensemble spin-label mobility reflected differences in proportions of a minority receptor population in which the otherwise helical backbone was essentially disordered. We suggest that our measurements provided site-specific snapshots of equilibria between a majority state of well-ordered helix and a minority state of locally disordered polypeptide backbone. Thus, the proportion of polypeptide chain that is locally and presumably transiently disordered is a structural feature of cytoplasmic domain dynamics that varies with functional region and modification-induced signaling state.
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Affiliation(s)
- Nicholas L Bartelli
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, MO 65211, USA
| | - Gerald L Hazelbauer
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, MO 65211, USA.
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31
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Freeman AJ, Stevens M, Declais AC, Leahy A, Mackay K, El Mkami H, Lilley DMJ, Norman DG. Analysis of the Intrinsically Disordered N-Terminus of the DNA Junction-Resolving Enzyme T7 Endonuclease I: Identification of Structure Formed upon DNA Binding. Biochemistry 2016; 55:4166-72. [PMID: 27387136 PMCID: PMC4990344 DOI: 10.1021/acs.biochem.6b00242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/14/2016] [Indexed: 02/07/2023]
Abstract
The four-way (Holliday) DNA junction of homologous recombination is processed by the symmetrical cleavage of two strands by a nuclease. These junction-resolving enzymes bind to four-way junctions in dimeric form, distorting the structure of the junction in the process. Crystal structures of T7 endonuclease I have been determined as free protein, and the complex with a DNA junction. In neither crystal structure was the N-terminal 16-amino acid peptide visible, yet deletion of this peptide has a marked effect on the resolution process. Here we have investigated the N-terminal peptide by inclusion of spin-label probes at unique sites within this region, studied by electron paramagnetic resonance. Continuous wave experiments show that these labels are mobile in the free protein but become constrained on binding a DNA junction, with the main interaction occurring for residues 7-10 and 12. Distance measurements between equivalent positions within the two peptides of a dimer using PELDOR showed that the intermonomeric distances for residues 2-12 are long and broadly distributed in the free protein but are significantly shortened and become more defined on binding to DNA. These results suggest that the N-terminal peptides become more organized on binding to the DNA junction and nestle into the minor grooves at the branchpoint, consistent with the biochemical data indicating an important role in the resolution process. This study demonstrates the presence of structure within a protein region that cannot be viewed by crystallography.
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Affiliation(s)
- Alasdair
D. J. Freeman
- Nucleic
Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | - Michael Stevens
- Nucleic
Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | - Anne-Cecile Declais
- Nucleic
Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | - Adam Leahy
- Nucleic
Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | - Katherine Mackay
- Nucleic
Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | - Hassane El Mkami
- School
of Physics and Astronomy, University of
St Andrews, St Andrews FE2 4KM, U.K.
| | - David M. J. Lilley
- Nucleic
Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | - David G. Norman
- Nucleic
Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, U.K.
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32
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Yang Z, Bridges MD, López CJ, Rogozhnikova OY, Trukhin DV, Brooks EK, Tormyshev V, Halpern HJ, Hubbell WL. A triarylmethyl spin label for long-range distance measurement at physiological temperatures using T1 relaxation enhancement. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 269:50-54. [PMID: 27214582 PMCID: PMC4958593 DOI: 10.1016/j.jmr.2016.05.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/09/2016] [Accepted: 05/10/2016] [Indexed: 05/19/2023]
Abstract
Site-directed spin labeling (SDSL) in combination with electron paramagnetic resonance (EPR) spectroscopy has become an important tool for measuring distances in proteins on the order of a few nm. For this purpose pairs of spin labels, most commonly nitroxides, are site-selectively introduced into the protein. Recent efforts to develop new spin labels are focused on tailoring the intrinsic properties of the label to either extend the upper limit of measurable distances at physiological temperature, or to provide a unique spectral lineshape so that selective pairwise distances can be measured in a protein or complex containing multiple spin label species. Triarylmethyl (TAM) radicals are the foundation for a new class of spin labels that promise to provide both capabilities. Here we report a new methanethiosulfonate derivative of a TAM radical that reacts rapidly and selectively with an engineered cysteine residue to generate a TAM containing side chain (TAM1) in high yield. With a TAM1 residue and Cu(2+) bound to an engineered Cu(2+) binding site, enhanced T1 relaxation of TAM should enable measurement of interspin distances up to 50Å at physiological temperature. To achieve favorable TAM1-labeled protein concentrations without aggregation, proteins are tethered to a solid support either site-selectively using an unnatural amino acid or via native lysine residues. The methodology is general and readily extendable to complex systems, including membrane proteins.
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Affiliation(s)
- Zhongyu Yang
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael D Bridges
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Carlos J López
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Olga Yu Rogozhnikova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitry V Trukhin
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Evan K Brooks
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Victor Tormyshev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Howard J Halpern
- The Center for EPR Imaging in vivo Physiology, Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637, USA.
| | - Wayne L Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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33
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Mikles DC, Bhat V, Schuchardt BJ, McDonald CB, Farooq A. Effect of osmolytes on the binding of EGR1 transcription factor to DNA. Biopolymers 2016; 103:74-87. [PMID: 25269753 DOI: 10.1002/bip.22556] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 08/16/2014] [Accepted: 08/19/2014] [Indexed: 11/11/2022]
Abstract
Osmolytes play a key role in maintaining protein stability and mediating macromolecular interactions within the intracellular environment of the cell. Herein, we show that osmolytes such as glycerol, sucrose, and polyethylene glycol 400 (PEG400) mitigate the binding of early growth response (protein) 1 (EGR1) transcription factor to DNA in a differential manner. Thus, while physiological concentrations of glycerol only moderately reduce the binding affinity, addition of sucrose and PEG400 is concomitant with a loss in the binding affinity by an order of magnitude. This salient observation suggests that EGR1 is most likely subject to conformational equilibrium and that the osmolytes exert their effect via favorable interactions with the unliganded conformation. Consistent with this notion, our analysis reveals that while EGR1 displays rather high structural stability in complex with DNA, the unliganded conformation becomes significantly destabilized in solution. In particular, while liganded EGR1 adopts a well-defined arc-like architecture, the unliganded protein samples a comparatively large conformational space between two distinct states that periodically interconvert between an elongated rod-like shape and an arc-like conformation on a submicrosecond time scale. Consequently, the ability of osmolytes to favorably interact with the unliganded conformation so as to stabilize it could account for the negative effect of osmotic stress on EGR1-DNA interaction observed here. Taken together, our study sheds new light on the role of osmolytes in modulating a key protein-DNA interaction.
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Affiliation(s)
- David C Mikles
- Department of Biochemistry and Molecular Biology, Leonard Miller School of Medicine, University of Miami, Miami, FL, 33136
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34
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Petrlova J, Hilt S, Budamagunta M, Domingo-Espín J, Voss JC, Lagerstedt JO. Molecular crowding impacts the structure of apolipoprotein A-I with potential implications on in vivo metabolism and function. Biopolymers 2016; 105:683-92. [PMID: 27122373 DOI: 10.1002/bip.22865] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 03/14/2016] [Accepted: 04/25/2016] [Indexed: 11/08/2022]
Abstract
The effect molecular crowding, defined as the volume exclusion exerted by one soluble inert molecule upon another soluble molecule, has on the structure and self-interaction of lipid-free apoA-I were explored. The influence of molecular crowding on lipid-free apoA-I oligomerization and internal dynamics has been analyzed using electron paramagnetic resonance (EPR) spectroscopy measurements of nitroxide spin label at selected positions throughout the protein sequence and at varying concentrations of the crowding agent Ficoll-70. The targeted positions include sites previously shown to be sensitive for detecting intermolecular interaction via spin-spin coupling. Circular dichroism was used to study secondary structural changes in lipid-free apoA-I imposed by increasing concentrations of the crowding agent. Crosslinking and SDS-PAGE gel analysis was employed to further characterize the role molecular crowding plays in inducing apoA-I oligomerization. It was concluded that the dynamic apoA-I structure and oligomeric state was altered in the presence of the crowding agent. It was also found that the C-terminal was slightly more sensitive to molecular crowding. Finally, the data described the region around residue 217 in the C-terminal domain of apoA-I as the most sensitive reporter of the crowding-induced self-association of apoA-I. The implications of this behavior to in vivo functionality are discussed. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 683-692, 2016.
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Affiliation(s)
- Jitka Petrlova
- Department of Experimental Medical Science, Lund University, Lund, S-221 84, Sweden
| | - Silvia Hilt
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA, 95616
| | - Madhu Budamagunta
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA, 95616
| | - Joan Domingo-Espín
- Department of Experimental Medical Science, Lund University, Lund, S-221 84, Sweden
| | - John C Voss
- Department of Experimental Medical Science, Lund University, Lund, S-221 84, Sweden.,Department of Biochemistry and Molecular Medicine, University of California, Davis, CA, 95616
| | - Jens O Lagerstedt
- Department of Experimental Medical Science, Lund University, Lund, S-221 84, Sweden
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35
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Dawidowski D, Cafiso DS. Munc18-1 and the Syntaxin-1 N Terminus Regulate Open-Closed States in a t-SNARE Complex. Structure 2016; 24:392-400. [PMID: 26876096 DOI: 10.1016/j.str.2016.01.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/29/2015] [Accepted: 01/08/2016] [Indexed: 10/22/2022]
Abstract
Neuronal exocytosis is mediated by SNARE proteins, which assemble into a highly stable four-helical bundle in a process that is not well understood. Here, electron paramagnetic resonance spectroscopy was used to examine how the t-SNAREs syntaxin and SNAP25 assemble in the presence and absence of the regulatory protein Munc18-1. Syntaxin and SNAP25 form a 2:1 complex, which is structurally heterogeneous and persists in the presence of excess SNAP25. Munc18-1 dissociates this 2:1 complex, but a 1:1 complex is retained where syntaxin is in a closed state. In the absence of an N-terminal fragment of syntaxin, Munc18-1 also stabilizes a 1:1 complex of sytaxin/SNAP25; however, syntaxin now samples an open state. These data demonstrate that the open-closed syntaxin equilibrium is shifted toward the open state when syntaxin and Munc18-1 are associated with SNAP25, and the results indicate that a syntaxin/SNAP25:Munc18-1 complex is a likely starting point for SNARE assembly.
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Affiliation(s)
- Damian Dawidowski
- Department of Chemistry, Center for Membrane Biology at the University of Virginia, McCormick Road, Charlottesville, VA 22904-4319, USA
| | - David S Cafiso
- Department of Chemistry, Center for Membrane Biology at the University of Virginia, McCormick Road, Charlottesville, VA 22904-4319, USA.
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36
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Sahu ID, Craig AF, Dunagan MM, Troxel KR, Zhang R, Meiberg AG, Harmon CN, McCarrick RM, Kroncke BM, Sanders CR, Lorigan GA. Probing Structural Dynamics and Topology of the KCNE1 Membrane Protein in Lipid Bilayers via Site-Directed Spin Labeling and Electron Paramagnetic Resonance Spectroscopy. Biochemistry 2015; 54:6402-12. [PMID: 26418890 DOI: 10.1021/acs.biochem.5b00505] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
KCNE1 is a single transmembrane protein that modulates the function of voltage-gated potassium channels, including KCNQ1. Hereditary mutations in the genes encoding either protein can result in diseases such as congenital deafness, long QT syndrome, ventricular tachyarrhythmia, syncope, and sudden cardiac death. Despite the biological significance of KCNE1, the structure and dynamic properties of its physiologically relevant native membrane-bound state are not fully understood. In this study, the structural dynamics and topology of KCNE1 in bilayered lipid vesicles was investigated using site-directed spin labeling (SDSL) and electron paramagnetic resonance (EPR) spectroscopy. A 53-residue nitroxide EPR scan of the KCNE1 protein sequence including all 27 residues of the transmembrane domain (45-71) and 26 residues of the N- and C-termini of KCNE1 in lipid bilayered vesicles was analyzed in terms of nitroxide side-chain motion. Continuous wave-EPR spectral line shape analysis indicated the nitroxide spin label side-chains located in the KCNE1 TMD are less mobile when compared to the extracellular region of KCNE1. The EPR data also revealed that the C-terminus of KCNE1 is more mobile when compared to the N-terminus. EPR power saturation experiments were performed on 41 sites including 18 residues previously proposed to reside in the transmembrane domain (TMD) and 23 residues of the N- and C-termini to determine the topology of KCNE1 with respect to the 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG) lipid bilayers. The results indicated that the transmembrane domain is indeed buried within the membrane, spanning the width of the lipid bilayer. Power saturation data also revealed that the extracellular region of KCNE1 is solvent-exposed with some of the portions partially or weakly interacting with the membrane surface. These results are consistent with the previously published solution NMR structure of KCNE1 in micelles.
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Affiliation(s)
- Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Andrew F Craig
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Megan M Dunagan
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Kaylee R Troxel
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Rongfu Zhang
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Andrew G Meiberg
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Corrinne N Harmon
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Brett M Kroncke
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37232, United States
| | - Charles R Sanders
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37232, United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
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37
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Franck JM, Ding Y, Stone K, Qin PZ, Han S. Anomalously Rapid Hydration Water Diffusion Dynamics Near DNA Surfaces. J Am Chem Soc 2015; 137:12013-23. [PMID: 26256693 PMCID: PMC4656248 DOI: 10.1021/jacs.5b05813] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The emerging Overhauser effect dynamic nuclear polarization (ODNP) technique measures the translational mobility of water within the vicinity (5-15 Å) of preselected sites. The work presented here expands the capabilities of the ODNP technique and illuminates an important, previously unseen, property of the translational diffusion dynamics of water at the surface of DNA duplexes. We attach nitroxide radicals (i.e., spin labels) to multiple phosphate backbone positions of DNA duplexes, allowing ODNP to measure the hydration dynamics at select positions along the DNA surface. With a novel approach to ODNP analysis, we isolate the contributions of water molecules at these sites that undergo free translational diffusion from water molecules that either loosely bind to or exchange protons with the DNA. The results reveal that a significant population of water in a localized volume adjacent to the DNA surface exhibits fast, bulk-like characteristics and moves unusually rapidly compared to water found in similar probe volumes near protein and membrane surfaces. Control studies show that the observation of these characteristics are upheld even when the DNA duplex is tethered to streptavidin or the mobility of the nitroxides is altered. This implies that, as compared to protein or lipid surfaces, it is an intrinsic feature of the DNA duplex surface that it interacts only weakly with a significant fraction of the surface hydration water network. The displacement of this translationally mobile water is energetically less costly than that of more strongly bound water by up to several kBT and thus can lower the activation barrier for interactions involving the DNA surface.
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Affiliation(s)
- John M. Franck
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA
- National Biomedical Center for Advanced ESR Technology, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY
| | - Yuan Ding
- Department of Chemistry, University of Southern California, Los Angeles, CA
| | - Katherine Stone
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA
- Pacira Pharmaceuticals, Inc, San Diego, CA
| | - Peter Z. Qin
- Department of Chemistry, University of Southern California, Los Angeles, CA
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA
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38
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Alvarez FJD, Orelle C, Huang Y, Bajaj R, Everly RM, Klug CS, Davidson AL. Full engagement of liganded maltose-binding protein stabilizes a semi-open ATP-binding cassette dimer in the maltose transporter. Mol Microbiol 2015; 98:878-94. [PMID: 26268698 DOI: 10.1111/mmi.13165] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2015] [Indexed: 01/31/2023]
Abstract
MalFGK2 is an ATP-binding cassette (ABC) transporter that mediates the uptake of maltose/maltodextrins into Escherichia coli. A periplasmic maltose-binding protein (MBP) delivers maltose to the transmembrane subunits (MalFG) and stimulates the ATPase activity of the cytoplasmic nucleotide-binding subunits (MalK dimer). This MBP-stimulated ATPase activity is independent of maltose for purified transporter in detergent micelles. However, when the transporter is reconstituted in membrane bilayers, only the liganded form of MBP efficiently stimulates its activity. To investigate the mechanism of maltose stimulation, electron paramagnetic resonance spectroscopy was used to study the interactions between the transporter and MBP in nanodiscs and in detergent. We found that full engagement of both lobes of maltose-bound MBP unto MalFGK2 is facilitated by nucleotides and stabilizes a semi-open MalK dimer. Maltose-bound MBP promotes the transition to the semi-open state of MalK when the transporter is in the membrane, whereas such regulation does not require maltose in detergent. We suggest that stabilization of the semi-open MalK2 conformation by maltose-bound MBP is key to the coupling of maltose transport to ATP hydrolysis in vivo, because it facilitates the progression of the MalK dimer from the open to the semi-open conformation, from which it can proceed to hydrolyze ATP.
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Affiliation(s)
| | - Cédric Orelle
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Yan Huang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Ruchika Bajaj
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - R Michael Everly
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Candice S Klug
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Amy L Davidson
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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39
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Altenbach C, López CJ, Hideg K, Hubbell WL. Exploring Structure, Dynamics, and Topology of Nitroxide Spin-Labeled Proteins Using Continuous-Wave Electron Paramagnetic Resonance Spectroscopy. Methods Enzymol 2015; 564:59-100. [PMID: 26477248 DOI: 10.1016/bs.mie.2015.08.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Structural and dynamical characterization of proteins is of central importance in understanding the mechanisms underlying their biological functions. Site-directed spin labeling (SDSL) combined with continuous-wave electron paramagnetic resonance (CW EPR) spectroscopy has shown the capability of providing this information with site-specific resolution under physiological conditions for proteins of any degree of complexity, including those associated with membranes. This chapter introduces methods commonly employed for SDSL and describes selected CW EPR-based methods that can be applied to (1) map secondary and tertiary protein structure, (2) determine membrane protein topology, (3) measure protein backbone flexibility, and (4) reveal the existence of conformational exchange at equilibrium.
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Affiliation(s)
- Christian Altenbach
- Department of Chemistry and Biochemistry, Jules Stein Eye Institute, University of California, Los Angeles, California, USA
| | - Carlos J López
- Department of Chemistry and Biochemistry, Jules Stein Eye Institute, University of California, Los Angeles, California, USA
| | - Kálmán Hideg
- Institute of Organic and Medicinal Chemistry, University of Pécs, Pécs, Hungary
| | - Wayne L Hubbell
- Department of Chemistry and Biochemistry, Jules Stein Eye Institute, University of California, Los Angeles, California, USA.
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40
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Bartelli NL, Hazelbauer GL. Differential backbone dynamics of companion helices in the extended helical coiled-coil domain of a bacterial chemoreceptor. Protein Sci 2015; 24:1764-76. [PMID: 26257396 DOI: 10.1002/pro.2767] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/31/2015] [Accepted: 08/03/2015] [Indexed: 12/25/2022]
Abstract
Cytoplasmic domains of transmembrane bacterial chemoreceptors are largely extended four-helix coiled coils. Previous observations suggested the domain was structurally dynamic. We probed directly backbone dynamics of this domain of the transmembrane chemoreceptor Tar from Escherichia coli using site-directed spin labeling and electron paramagnetic resonance (EPR) spectroscopy. Spin labels were positioned on solvent-exposed helical faces because EPR spectra for such positions reflect primarily polypeptide backbone movements. We acquired spectra for spin-labeled, intact receptor homodimers solubilized in detergent or inserted into native E. coli lipid bilayers in Nanodiscs, characterizing 16 positions distributed throughout the cytoplasmic domain and on both helices of its helical hairpins, one amino terminal to the membrane-distal tight turn (N-helix), and the other carboxyl terminal (C-helix). Detergent solubilization increased backbone dynamics for much of the domain, suggesting that loss of receptor activities upon solubilization reflects wide-spread destabilization. For receptors in either condition, we observed an unanticipated difference between the N- and C-helices. For bilayer-inserted receptors, EPR spectra from sites in the membrane-distal protein-interaction region and throughout the C-helix were typical of well-structured helices. In contrast, for approximately two-thirds of the N-helix, from its origin as the AS-2 helix of the membrane-proximal HAMP domain to the beginning of the membrane-distal protein-interaction region, spectra had a significantly mobile component, estimated by spectral deconvolution to average approximately 15%. Differential helical dynamics suggests a four-helix bundle organization with a pair of core scaffold helices and two more dynamic partner helices. This newly observed feature of chemoreceptor structure could be involved in receptor function.
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Affiliation(s)
- Nicholas L Bartelli
- Department of Biochemistry, University of Missouri Columbia, 117 Schweitzer Hall, Missouri, 65211
| | - Gerald L Hazelbauer
- Department of Biochemistry, University of Missouri Columbia, 117 Schweitzer Hall, Missouri, 65211
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41
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Structure-relaxation mechanism for the response of T4 lysozyme cavity mutants to hydrostatic pressure. Proc Natl Acad Sci U S A 2015; 112:E2437-46. [PMID: 25918400 DOI: 10.1073/pnas.1506505112] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Application of hydrostatic pressure shifts protein conformational equilibria in a direction to reduce the volume of the system. A current view is that the volume reduction is dominated by elimination of voids or cavities in the protein interior via cavity hydration, although an alternative mechanism wherein cavities are filled with protein side chains resulting from a structure relaxation has been suggested [López CJ, Yang Z, Altenbach C, Hubbell WL (2013) Proc Natl Acad Sci USA 110(46):E4306-E4315]. In the present study, mechanisms for elimination of cavities under high pressure are investigated in the L99A cavity mutant of T4 lysozyme and derivatives thereof using site-directed spin labeling, pressure-resolved double electron-electron resonance, and high-pressure circular dichroism spectroscopy. In the L99A mutant, the ground state is in equilibrium with an excited state of only ∼ 3% of the population in which the cavity is filled by a protein side chain [Bouvignies et al. (2011) Nature 477(7362):111-114]. The results of the present study show that in L99A the native ground state is the dominant conformation to pressures of 3 kbar, with cavity hydration apparently taking place in the range of 2-3 kbar. However, in the presence of additional mutations that lower the free energy of the excited state, pressure strongly populates the excited state, thereby eliminating the cavity with a native side chain rather than solvent. Thus, both cavity hydration and structure relaxation are mechanisms for cavity elimination under pressure, and which is dominant is determined by details of the energy landscape.
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42
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Chui AJ, López CJ, Brooks EK, Chua KC, Doupey TG, Foltz GN, Kamel JG, Larrosa E, Sadiki A, Bridges MD. Multiple structural states exist throughout the helical nucleation sequence of the intrinsically disordered protein stathmin, as reported by electron paramagnetic resonance spectroscopy. Biochemistry 2015; 54:1717-28. [PMID: 25715079 DOI: 10.1021/bi500894q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The intrinsically disordered protein (IDP) stathmin plays an important regulatory role in cytoskeletal maintenance through its helical binding to tubulin and microtubules. However, it lacks a stable fold in the absence of its binding partner. Although stathmin has been a focus of research over the past two decades, the solution-phase conformational dynamics of this IDP are poorly understood. It has been reported that stathmin is purely monomeric in solution and that it bears a short helical region of persistent foldedness, which may act to nucleate helical folding in the C-terminal direction. Here we report a comprehensive study of the structural equilibria local to this region in stathmin that contradicts these two claims. Using the technique of electron paramagnetic resonance (EPR) spectroscopy on spin-labeled stathmin mutants in the solution-phase and when immobilized on Sepharose solid support, we show that all sites in the helical nucleation region of stathmin exhibit multiple spectral components that correspond to dynamic states of differing mobilities and stabilities. Importantly, a state with relatively low mobility dominates each spectrum with an average population greater than 50%, which we suggest corresponds to an oligomerized state of the protein. This is in contrast to a less populated, more mobile state, which likely represents a helically folded monomeric state of stathmin, and a highly mobile state, which we propose is the random coil conformer of the protein. Our interpretation of the EPR data is confirmed by further characterization of the protein using the techniques of native and SDS PAGE, gel filtration chromatography, and multiangle and dynamic light scattering, all of which show the presence of oligomeric stathmin in solution. Collectively, these data suggest that stathmin exists in a diverse equilibrium of states throughout the purported helical nucleation region and that this IDP exhibits a propensity toward oligomerization.
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Affiliation(s)
- Ashley J Chui
- Department of Chemistry and Biochemistry, California State University Fullerton , Fullerton, California 92831-6866, United States
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43
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Yang Z, Bridges M, Lerch MT, Altenbach C, Hubbell WL. Saturation Recovery EPR and Nitroxide Spin Labeling for Exploring Structure and Dynamics in Proteins. Methods Enzymol 2015; 564:3-27. [DOI: 10.1016/bs.mie.2015.07.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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44
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Klare JP, Steinhoff HJ. Spin Labeling Studies of Transmembrane Signaling and Transport. Methods Enzymol 2015; 564:315-47. [DOI: 10.1016/bs.mie.2015.05.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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45
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López CJ, Fleissner MR, Brooks EK, Hubbell WL. Stationary-phase EPR for exploring protein structure, conformation, and dynamics in spin-labeled proteins. Biochemistry 2014; 53:7067-75. [PMID: 25333901 PMCID: PMC4238802 DOI: 10.1021/bi5011128] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
![]()
Proteins tethered to solid supports
are of increasing interest
in bioanalytical chemistry and protein science in general. However,
the extent to which tethering modifies the energy landscape and dynamics
of the protein is most often unknown because there are few biophysical
methods that can determine secondary and tertiary structures and explore
conformational equilibria and dynamics of a tethered protein with
site-specific resolution. Site-directed spin labeling (SDSL) combined
with electron paramagnetic resonance (EPR) offers a unique opportunity
for this purpose. Here, we employ a general strategy using unnatural
amino acids that enables efficient and site-specific tethering of
a spin-labeled protein to a Sepharose solid support. Remarkably, EPR
spectra of spin-labeled T4 lysozyme (T4L) reveal that a single site-specific
attachment suppresses rotational motion of the protein sufficiently
to allow interpretation of the spectral line shape in terms of protein
internal dynamics. Importantly, line shape analysis and distance mapping
using double electron–electron resonance reveal that internal
dynamics, the tertiary fold, conformational equilibria, and ligand
binding of the tethered proteins were similar to those in solution,
in contrast to random attachment via native lysine residues. The results
of this study set the stage for the development of an EPR-based flow
system that will house soluble and membrane proteins immobilized site-specifically,
thereby enabling facile screening of structural and dynamical effects
of binding partners.
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Affiliation(s)
- Carlos J López
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California , Los Angeles, California 90095, United States
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46
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Yang Z, Jiménez-Osés G, López CJ, Bridges MD, Houk KN, Hubbell WL. Long-range distance measurements in proteins at physiological temperatures using saturation recovery EPR spectroscopy. J Am Chem Soc 2014; 136:15356-65. [PMID: 25290172 PMCID: PMC4227719 DOI: 10.1021/ja5083206] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Indexed: 11/28/2022]
Abstract
Site-directed spin labeling in combination with EPR is a powerful method for providing distances on the nm scale in biological systems. The most popular strategy, double electron-electron resonance (DEER), is carried out at cryogenic temperatures (50-80 K) to increase the short spin-spin relaxation time (T2) upon which the technique relies. A challenge is to measure long-range distances (20-60 Å) in proteins near physiological temperatures. Toward this goal we are investigating an alternative approach based on the distance-dependent enhancement of spin-lattice relaxation rate (T1(-1)) of a nitroxide spin label by a paramagnetic metal. With a commonly used nitroxide side chain (R1) and Cu(2+), it has been found that interspin distances ≤25 Å can be determined in this way (Jun et al. Biochemistry 2006, 45, 11666). Here, the upper limit of the accessible distance is extended to ≈40 Å using spin labels with long T1, a high-affinity 5-residue Cu(2+) binding loop inserted into the protein sequence, and pulsed saturation recovery to measure relaxation enhancement. Time-domain Cu(2+) electron paramagnetic resonance, quantum mechanical calculations, and molecular dynamics simulations provide information on the structure and geometry of the Cu(2+) loop and indicate that the metal ion is well-localized in the protein. An important aspect of these studies is that both Cu(2+)/nitroxide DEER at cryogenic temperatures and T1 relaxation measurements at room temperature can be carried out on the same sample, allowing both validation of the relaxation method and assessment of the effect of freezing on protein structure.
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Affiliation(s)
- Zhongyu Yang
- Jules Stein Eye Institute and Department of
Chemistry and Biochemistry, University of
California, Los Angeles, California 90095, United States
| | - Gonzalo Jiménez-Osés
- Jules Stein Eye Institute and Department of
Chemistry and Biochemistry, University of
California, Los Angeles, California 90095, United States
| | - Carlos J. López
- Jules Stein Eye Institute and Department of
Chemistry and Biochemistry, University of
California, Los Angeles, California 90095, United States
| | | | - K. N. Houk
- Jules Stein Eye Institute and Department of
Chemistry and Biochemistry, University of
California, Los Angeles, California 90095, United States
| | - Wayne L. Hubbell
- Jules Stein Eye Institute and Department of
Chemistry and Biochemistry, University of
California, Los Angeles, California 90095, United States
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47
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Cafiso DS. Identifying and quantitating conformational exchange in membrane proteins using site-directed spin labeling. Acc Chem Res 2014; 47:3102-9. [PMID: 25152957 PMCID: PMC4204925 DOI: 10.1021/ar500228s] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Protein structures are not static but sample different conformations
over a range of amplitudes and time scales. These fluctuations may
involve relatively small changes in bond angles or quite large rearrangements
in secondary structure and tertiary fold. The equilibrium between
discrete structural substates on the microsecond to millisecond time
scale is sometimes termed conformational exchange. Protein dynamics
and conformational exchange are believed to provide the basis for
many important activities, such as protein–protein and protein–ligand
interactions, enzymatic activity and protein allostery; however, for
many proteins, the dynamics and conformational exchange that lead
to function are poorly defined. Spectroscopic methods, such
as NMR, are among the most important
methods to explore protein dynamics and conformational exchange; however,
they are difficult to implement in some systems and with some types
of exchange events. Site-directed spin labeling (SDSL) is an EPR based
approach that is particularly well-suited to high molecular-weight
systems such as membrane proteins. Because of the relatively fast
time scale for EPR spectroscopy, it is an excellent method to examine
exchange. Conformations that are in exchange are captured as distinct
populations in the EPR spectrum, and this feature when combined with
the use of methods that can shift the free energy of conformational
substates allows one to identify regions of proteins that are in dynamic
exchange. In addition, modern pulse EPR methods have the ability to
examine conformational heterogeneity, resolve discrete protein states,
and identify the substates in exchange. Protein crystallography
has provided high-resolution models for
a number of membrane proteins; but because of conformational exchange,
these models do not always reflect the structures that are present
when the protein is in a native bilayer environment. In the case of
the Escherichia coli vitamin B12 transporter,
BtuB, the energy coupling segment of this protein undergoes a substrate-dependent
unfolding, which acts to couple this outer-membrane protein to the
inner-membrane protein TonB. EPR spectroscopy demonstrates that the
energy coupling segment is in equilibrium between ordered and disordered
states, and that substrate binding shifts this equilibrium to favor
an unfolded state. However, in crystal structures of BtuB, this segment
is resolved and folded within the protein, and neither the presence
of this equilibrium nor the substrate-induced change is revealed.
This is a result of the solute environment and the crystal lattice,
both of which act to stabilize one conformational substate of the
transporter. Using SDSL, it can be shown that conformational
exchange is present
in other regions of BtuB and in other members of this transporter
family. Conformational exchange has also been examined in systems
such as the plasma membrane SNARE protein, syntaxin 1A, where dynamics
are controlled by regulatory proteins such as munc18. Regulating the
microsecond to millisecond time scale dynamics in the neuronal SNAREs
is likely to be a key feature that regulates assembly of the SNAREs
and neurotransmitter release.
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Affiliation(s)
- David S. Cafiso
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia 22904-4319, United States
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48
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Shevelev GY, Krumkacheva OA, Lomzov AA, Kuzhelev AA, Rogozhnikova OY, Trukhin DV, Troitskaya TI, Tormyshev VM, Fedin MV, Pyshnyi DV, Bagryanskaya EG. Physiological-temperature distance measurement in nucleic acid using triarylmethyl-based spin labels and pulsed dipolar EPR spectroscopy. J Am Chem Soc 2014; 136:9874-7. [PMID: 24963806 DOI: 10.1021/ja505122n] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Resolving the nanometer-scale structure of biomolecules in natural conditions still remains a challenging task. We report the first distance measurement in nucleic acid at physiological temperature using electron paramagnetic resonance (EPR). The model 10-mer DNA duplex has been labeled with reactive forms of triarylmethyl radicals and then immobilized on a sorbent in water solution and investigated by double quantum coherence EPR. We succeeded in development of optimal triarylmethyl-based labels, approach for site-directed spin labeling and efficient immobilization procedure that, working together, allowed us to measure as long distances as ~4.6 nm with high accuracy at 310 K (37 °C).
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Affiliation(s)
- Georgiy Yu Shevelev
- Institute of Chemical Biology and Fundamental Medicine, §International Tomography Center, and #N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of the Sciences (SB RAS) , Novosibirsk 630090, Russia
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49
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Lu B, Kiessling V, Tamm LK, Cafiso DS. The juxtamembrane linker of full-length synaptotagmin 1 controls oligomerization and calcium-dependent membrane binding. J Biol Chem 2014; 289:22161-71. [PMID: 24973220 DOI: 10.1074/jbc.m114.569327] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Synaptotagmin 1 (Syt1) is the calcium sensor for synchronous neurotransmitter release. The two C2 domains of Syt1, which may mediate fusion by bridging the vesicle and plasma membranes, are connected to the vesicle membrane by a 60-residue linker. Here, we use site-directed spin labeling and a novel total internal reflection fluorescence vesicle binding assay to characterize the juxtamembrane linker and to test the ability of reconstituted full-length Syt1 to interact with opposing membrane surfaces. EPR spectroscopy demonstrates that the majority of the linker interacts with the membrane interface, thereby limiting the extension of the C2A and C2B domains into the cytoplasm. Pulse dipolar EPR spectroscopy provides evidence that purified full-length Syt1 is oligomerized in the membrane, and mutagenesis indicates that a glycine zipper/GXXXG motif within the linker helps mediate oligomerization. The total internal reflection fluorescence-based vesicle binding assay demonstrates that full-length Syt1 that is reconstituted into supported lipid bilayers will capture vesicles containing negatively charged lipid in a Ca(2+)-dependent manner. Moreover, the rate of vesicle capture increases with Syt1 density, and mutations in the GXXXG motif that inhibit oligomerization of Syt1 reduce the rate of vesicle capture. This work demonstrates that modifications within the 60-residue linker modulate both the oligomerization of Syt1 and its ability to interact with opposing bilayers. In addition to controlling its activity, the oligomerization of Syt1 may play a role in organizing proteins within the active zone of membrane fusion.
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Affiliation(s)
- Bin Lu
- From the Departments of Chemistry and the Center for Membrane Biology, University of Virginia, Charlottesville, Virginia 22904
| | - Volker Kiessling
- the Center for Membrane Biology, University of Virginia, Charlottesville, Virginia 22904 Molecular Physiology and Biological Physics and
| | - Lukas K Tamm
- the Center for Membrane Biology, University of Virginia, Charlottesville, Virginia 22904 Molecular Physiology and Biological Physics and
| | - David S Cafiso
- From the Departments of Chemistry and the Center for Membrane Biology, University of Virginia, Charlottesville, Virginia 22904
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50
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Mapping protein conformational heterogeneity under pressure with site-directed spin labeling and double electron-electron resonance. Proc Natl Acad Sci U S A 2014; 111:E1201-10. [PMID: 24707053 DOI: 10.1073/pnas.1403179111] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The dominance of a single native state for most proteins under ambient conditions belies the functional importance of higher-energy conformational states (excited states), which often are too sparsely populated to allow spectroscopic investigation. Application of high hydrostatic pressure increases the population of excited states for study, but structural characterization is not trivial because of the multiplicity of states in the ensemble and rapid (microsecond to millisecond) exchange between them. Site-directed spin labeling in combination with double electron-electron resonance (DEER) provides long-range (20-80 Å) distance distributions with angstrom-level resolution and thus is ideally suited to resolve conformational heterogeneity in an excited state populated under high pressure. DEER currently is performed at cryogenic temperatures. Therefore, a method was developed for rapidly freezing spin-labeled proteins under pressure to kinetically trap the high-pressure conformational ensemble for subsequent DEER data collection at atmospheric pressure. The methodology was evaluated using seven doubly-labeled mutants of myoglobin designed to monitor selected interhelical distances. For holomyoglobin, the distance distributions are narrow and relatively insensitive to pressure. In apomyoglobin, on the other hand, the distributions reveal a striking conformational heterogeneity involving specific helices in the pressure range of 0-3 kbar, where a molten globule state is formed. The data directly reveal the amplitude of helical fluctuations, information unique to the DEER method that complements previous rate determinations. Comparison of the distance distributions for pressure- and pH-populated molten globules shows them to be remarkably similar despite a lower helical content in the latter.
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