1
|
Zhang L, Brown MC, Mutter AC, Greenland KN, Cooley JW, Koder RL. Protein dynamics govern the oxyferrous state lifetime of an artificial oxygen transport protein. Biophys J 2023; 122:4440-4450. [PMID: 37865818 PMCID: PMC10698322 DOI: 10.1016/j.bpj.2023.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/26/2023] [Accepted: 10/19/2023] [Indexed: 10/23/2023] Open
Abstract
It has long been known that the alteration of protein side chains that occlude or expose the heme cofactor to water can greatly affect the stability of the oxyferrous heme state. Here, we demonstrate that the rate of dynamically driven water penetration into the core of an artificial oxygen transport protein also correlates with oxyferrous state lifetime by reducing global dynamics, without altering the structure of the active site, via the simple linking of the two monomers in a homodimeric artificial oxygen transport protein using a glycine-rich loop. The tethering of these two helices does not significantly affect the active site structure, pentacoordinate heme-binding affinity, reduction potential, or gaseous ligand affinity. It does, however, significantly reduce the hydration of the protein core, as demonstrated by resonance Raman spectroscopy, backbone amide hydrogen exchange, and pKa shifts in buried histidine side chains. This further destabilizes the charge-buried entatic state and nearly triples the oxyferrous state lifetime. These data are the first direct evidence that dynamically driven water penetration is a rate-limiting step in the oxidation of these complexes. It furthermore demonstrates that structural rigidity that limits water penetration is a critical design feature in metalloenzyme construction and provides an explanation for both the failures and successes of earlier attempts to create oxygen-binding proteins.
Collapse
Affiliation(s)
- Lei Zhang
- Department of Physics, The City College of New York, New York, New York
| | - Mia C Brown
- Department of Chemistry, University of Missouri, Columbia, Missouri
| | - Andrew C Mutter
- Department of Biochemistry, The City College of New York, New York, New York
| | - Kelly N Greenland
- Department of Physics, The City College of New York, New York, New York
| | - Jason W Cooley
- Department of Chemistry, University of Missouri, Columbia, Missouri
| | - Ronald L Koder
- Department of Physics, The City College of New York, New York, New York; Graduate Programs of Physics, Biology, Chemistry and Biochemistry, The Graduate Center of CUNY, New York, New York.
| |
Collapse
|
2
|
Visca H, DuPont M, Moshnikova A, Crawford T, Engelman DM, Andreev OA, Reshetnyak YK. pHLIP Peptides Target Acidity in Activated Macrophages. Mol Imaging Biol 2022; 24:874-885. [PMID: 35604527 PMCID: PMC9681937 DOI: 10.1007/s11307-022-01737-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/19/2022] [Accepted: 04/27/2022] [Indexed: 12/29/2022]
Abstract
PURPOSE Acidity can be a useful alternative biomarker for the targeting of metabolically active cells in certain diseased tissues, as in acute inflammation or aggressive tumors. We investigated the targeting of activated macrophages by pH low insertion peptides (pHLIPs), an established technology for targeting cell-surface acidity. PROCEDURES The uptake of fluorescent pHLIPs by activated macrophages was studied in cell cultures, in a mouse model of lung inflammation, and in a mouse tumor model. Fluorescence microscopy, whole-body and organ imaging, immunohistochemistry, and FACS analysis were employed. RESULTS We find that cultured, activated macrophages readily internalize pHLIPs. The uptake is higher in glycolytic macrophages activated by LPS and INF-γ compared to macrophages activated by IL-4/IL-13. Fluorescent pHLIPs target LPS-induced lung inflammation in mice. In addition to marking cancer cells within the tumor microenvironment, fluorescent pHLIPs target CD45+, CD11b+, F4/80+, and CD206+ tumor-associated macrophages with no significant targeting of other immune cells. Also, fluorescent pHLIPs target CD206-positive cells found in the inguinal lymph nodes of animals inoculated with breast cancer cells in mammary fat pads. CONCLUSIONS pHLIP peptides sense low cell surface pH, which triggers their insertion into the cell membrane. Unlike cancerous cells, activated macrophages do not retain inserted pHLIPs on their surfaces, instead their highly active membrane recycling moves the pHLIPs into endosomes. Targeting activated macrophages in diseased tissues may enable clinical visualization and therapeutic opportunities.
Collapse
Affiliation(s)
- Hannah Visca
- Physics Department, University of Rhode Island, Kingston, RI, USA
| | - Michael DuPont
- Physics Department, University of Rhode Island, Kingston, RI, USA
| | - Anna Moshnikova
- Physics Department, University of Rhode Island, Kingston, RI, USA
| | - Troy Crawford
- Physics Department, University of Rhode Island, Kingston, RI, USA
| | - Donald M Engelman
- Department of Molecular Biophysics and Biochemistry, Yale, New Haven, CT, USA
| | - Oleg A Andreev
- Physics Department, University of Rhode Island, Kingston, RI, USA
| | | |
Collapse
|
3
|
Ataka K, Drauschke J, Stulberg V, Koksch B, Heberle J. pH-induced insertion of pHLIP into a lipid bilayer: In-situ SEIRAS characterization of a folding intermediate at neutral pH. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183873. [PMID: 35104491 DOI: 10.1016/j.bbamem.2022.183873] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/22/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
The pH low insertion peptide (pHLIP) is a pH-sensitive cell penetrating peptide that transforms from an unstructured coil on the membrane surface at pH > 7, to a transmembrane (TM) α-helix at pH < 5. By exploiting this unique property, pHLIP attracts interest as a potential tool for drug delivery and visualisation of acidic tissues produced by various maladies such as cancer, inflammation, hypoxia etc. Even though the structures of initial and end states of pHLIP insertion have been widely accepted, the intermediate structures in between these two states are less clear. Here, we have applied in situ Surface-Enhanced Infrared Absorption spectroscopy to examine the pH-induced insertion and folding processes of pHLIP into a solid-supported lipid bilayer. We show that formation of partially helical structure already takes place at pH only slightly below 7.0, but with the helical axis parallel to the membrane surface. The peptide starts to reorientate its helix from horizontal to vertical direction, accompanied by the insertion into the TM region at pH < 6.2. Further insertion into the TM region of the peptide results in an increase of inherent α-helical structure and complete secondary structure formation at pH 5.3. Analysis of the changes of the carboxylate vibrational bands upon pH titration shows two distinctive groups of aspartates and glutamates with pKa values of 4.5 and 6.3, respectively. Comparison to the amide bands of the peptide backbone suggests that the latter Asp/Glu groups are directly involved in the conformational changes of pHLIP in the respective intermediate states.
Collapse
Affiliation(s)
- Kenichi Ataka
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
| | - Janina Drauschke
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Valentina Stulberg
- Institute for Chemistry and Biochemistry, Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Arnimallee 20, 14195, Berlin, Germany
| | - Beate Koksch
- Institute for Chemistry and Biochemistry, Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Arnimallee 20, 14195, Berlin, Germany
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
| |
Collapse
|
4
|
Reshetnyak YK, Moshnikova A, Andreev OA, Engelman DM. Targeting Acidic Diseased Tissues by pH-Triggered Membrane-Associated Peptide Folding. Front Bioeng Biotechnol 2020; 8:335. [PMID: 32411684 PMCID: PMC7198868 DOI: 10.3389/fbioe.2020.00335] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/26/2020] [Indexed: 12/19/2022] Open
Abstract
The advantages of targeted therapy have motivated many efforts to find distinguishing features between the molecular cell surface landscapes of diseased and normal cells. Typically, the features have been proteins, lipids or carbohydrates, but other approaches are emerging. In this discussion, we examine the use of cell surface acidity as a feature that can be exploited by using pH-sensitive peptide folding to target agents to diseased cell surfaces or cytoplasms.
Collapse
Affiliation(s)
- Yana K Reshetnyak
- Department of Physics, The University of Rhode Island, Kingston, RI, United States
| | - Anna Moshnikova
- Department of Physics, The University of Rhode Island, Kingston, RI, United States
| | - Oleg A Andreev
- Department of Physics, The University of Rhode Island, Kingston, RI, United States
| | - Donald M Engelman
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| |
Collapse
|
5
|
Gupta C, Ren Y, Mertz B. Cooperative Nonbonded Forces Control Membrane Binding of the pH-Low Insertion Peptide pHLIP. Biophys J 2018; 115:2403-2412. [PMID: 30503536 DOI: 10.1016/j.bpj.2018.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/10/2018] [Accepted: 11/01/2018] [Indexed: 02/06/2023] Open
Abstract
Peptides with the ability to bind and insert into the cell membrane have immense potential in biomedical applications. pH (low) insertion peptide (pHLIP), a water-soluble polypeptide derived from helix C of bacteriorhodopsin, can insert into a membrane at acidic pH to form a stable transmembrane α-helix. The insertion process takes place in three stages: pHLIP is unstructured and soluble in water at neutral pH (state I), unstructured and bound to the surface of a membrane at neutral pH (state II), and inserted into the membrane as an α-helix at low pH (state III). Using molecular dynamics simulations, we have modeled state II of pHLIP and a fast-folding variant of pHLIP, in which each peptide is bound to a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer surface. Our results provide strong support for recently published spectroscopic studies, namely that pHLIP preferentially binds to the bilayer surface as a function of location of anionic amino acids and that backbone dehydration occurs upon binding. Unexpectedly, we also observed several instances of segments of pHLIP folding into a stable helical turn. Our results provide a molecular level of detail that is essential to providing new insights into pHLIP function and to facilitate design of variants with improved membrane-active capabilities.
Collapse
Affiliation(s)
- Chitrak Gupta
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia
| | - Yue Ren
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia
| | - Blake Mertz
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia.
| |
Collapse
|
6
|
A New Method to Determine the Transmembrane Conformation of Substrates in Intramembrane Proteolysis by Deep-UV Resonance Raman Spectroscopy. Methods Enzymol 2016; 584:207-228. [PMID: 28065264 DOI: 10.1016/bs.mie.2016.10.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We present a new method based on deep-UV resonance Raman spectroscopy to determine the backbone conformation of intramembrane protease substrates. The classical amide vibrational modes reporting on the conformation of just the transmembrane region of the substrate can be resolved from solvent exchangeable regions outside the detergent micelle by partial deuteration of the solvent. In the presence of isotopically triple-labeled intramembrane protease, these amide modes can be accurately measured to monitor the transmembrane conformation of the substrate during intramembrane proteolysis.
Collapse
|
7
|
Xiong J, JiJi RD. Insights into the aggregation mechanism of Aβ(25-40). Biophys Chem 2016; 220:42-48. [PMID: 27856006 DOI: 10.1016/j.bpc.2016.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/06/2016] [Accepted: 11/08/2016] [Indexed: 12/01/2022]
Abstract
The hydrophobic fragment of the Alzheimer's related β-amyloid (Aβ) peptide, Aβ(25-40), aggregates and forms insoluble amyloid fibrils at a rate similar to the full-length peptide. In order to gain insight into the fibrillization of Aβ(25-40) and the ability of the flavonoid myricetin to inhibit its aggregation, the isoleucine at position 32 (I32A) and the glycine at position 37 (G37A) in the full-length peptide were replaced with alanine. Thioflavin T assays indicate that substitution of isoleucine for alanine significantly reduces the rate and extent of fibrillization compared to the Aβ(25-40) and G37A peptides. Although all three peptides are fully disordered initially, circular dichroism studies suggest the structure of the I32A and G37A peptides are different from the parent peptide Aβ(25-40). Introduction of myricetin to the peptide samples results in modest structural changes for the Aβ(25-40) and G37A peptides but not the I32A peptide. Aβ(25-40) oligomers were predominantly tetramers, whereas I32A and G37A oligomers were a mixture of trimers and dimers. After 48h of incubation at 37°C, the amount of tetramers and trimers in solution dropped for the Aβ(25-40) and G37A peptides but remained similar for the I32A peptide. Incubation of Aβ(25-40) with myricetin increased the relative proportion of trimers to tetramers. Ultraviolet resonance Raman studies suggests that the I32A peptide may be more hydrated than the Aβ(25-40) and G37A peptides. Taken together, these data indicate the structural changes observed for the Aβ(25-40) and G37A peptides upon introduction of myricetin are localized around residue 32 and could arise from hydrophobic interactions between the peptide and the flavonoid or interference with the self-association of the peptide in this region. Substitution of isoleucine at position 32 with alanine had little effect on the peptide's secondary structure but dramatically decreased the propensity of the peptide fibrillize.
Collapse
Affiliation(s)
- Jian Xiong
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO, USA
| | - Renee D JiJi
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO, USA.
| |
Collapse
|
8
|
López-Peña I, Leigh BS, Schlamadinger DE, Kim JE. Insights into Protein Structure and Dynamics by Ultraviolet and Visible Resonance Raman Spectroscopy. Biochemistry 2015. [PMID: 26219819 DOI: 10.1021/acs.biochem.5b00514] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Raman spectroscopy is a form of vibrational spectroscopy based on inelastic scattering of light. In resonance Raman spectroscopy, the wavelength of the incident light falls within an absorption band of a chromophore, and this overlap of excitation and absorption energy greatly enhances the Raman scattering efficiency of the absorbing species. The ability to probe vibrational spectra of select chromophores within a complex mixture of molecules makes resonance Raman spectroscopy an excellent tool for studies of biomolecules. In this Current Topic, we discuss the type of molecular insights obtained from steady-state and time-resolved resonance Raman studies of a prototypical photoactive protein, rhodopsin. We also review recent efforts in ultraviolet resonance Raman investigations of soluble and membrane-associated biomolecules, including integral membrane proteins and antimicrobial peptides. These examples illustrate that resonance Raman is a sensitive, selective, and practical method for studying the structures of biological molecules, and the molecular bonding, geometry, and environments of protein cofactors, the backbone, and side chains.
Collapse
Affiliation(s)
- Ignacio López-Peña
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Brian S Leigh
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Diana E Schlamadinger
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Judy E Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| |
Collapse
|
9
|
Deacon JC, Engelman DM, Barrera FN. Targeting acidity in diseased tissues: mechanism and applications of the membrane-inserting peptide, pHLIP. Arch Biochem Biophys 2014; 565:40-8. [PMID: 25444855 DOI: 10.1016/j.abb.2014.11.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 10/30/2014] [Accepted: 11/04/2014] [Indexed: 12/24/2022]
Abstract
pHLIPs are a family of soluble ∼36 amino acid peptides, which bind to membrane surfaces. If the environment is acidic, a pHLIP folds and inserts across the membrane to form a stable transmembrane helix, thus preferentially locating itself in acidic tissues. Since tumors and other disease tissues are acidic, pHLIPs' low-pH targeting behavior leads to applications as carriers for diagnostic and surgical imaging agents. The energy of membrane insertion can also be used to promote the insertion of modestly polar, normally cell-impermeable cargos across the cell membrane into the cytosol of targeted cells, leading to applications in tumor-targeted delivery of therapeutic molecules. We review the biochemical and biophysical basis of pHLIPs' unique properties, diagnostic and therapeutic applications, and the principles upon which translational applications are being developed.
Collapse
Affiliation(s)
- John C Deacon
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Donald M Engelman
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Francisco N Barrera
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA.
| |
Collapse
|
10
|
Xiong J, Roach CA, Oshokoya OO, Schroell RP, Yakubu RA, Eagleburger MK, Cooley JW, Jiji RD. Role of bilayer characteristics on the structural fate of aβ(1-40) and aβ(25-40). Biochemistry 2014; 53:3004-11. [PMID: 24702518 DOI: 10.1021/bi4016296] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The β-amyloid (Aβ) peptide is derived from the transmembrane (TM) helix of the amyloid precursor protein (APP) and has been shown to interact with membrane surfaces. To understand better the role of peptide-membrane interactions in cell death and ultimately in Alzheimer's disease, a better understanding of how membrane characteristics affect the binding, solvation, and secondary structure of Aβ is needed. Employing a combination of circular dichroism and deep-UV resonance Raman spectroscopies, Aβ(25-40) was found to fold spontaneously upon association with anionic lipid bilayers. The hydrophobic portion of the disease-related Aβ(1-40) peptide, Aβ(25-40), has often been used as a model for how its legacy TM region may behave structurally in aqueous solvents and during membrane encounters. The structure of the membrane-associated Aβ(25-40) peptide was found to depend on both the hydrophobic thickness of the bilayer and the duration of incubation. Similarly, the disease-related Aβ(1-40) peptide also spontaneously associates with anionic liposomes, where it initially adopts mixtures of disordered and helical structures. The partially disordered helical structures then convert to β-sheet structures over longer time frames. β-Sheet structure is formed prior to helical unwinding, implying a model in which β-sheet structure, formed initially from disordered regions, prompts the unwinding and destabilization of membrane-stabilized helical structure. A model is proposed to describe the mechanism of escape of Aβ(1-40) from the membrane surfaces following its formation by cleavage of APP within the membrane.
Collapse
Affiliation(s)
- Jian Xiong
- Department of Chemistry, University of Missouri , Columbia, Missouri 65211, United States
| | | | | | | | | | | | | | | |
Collapse
|